NIH Director's Transformative Research Award
NIH Director's Transformative Research Award
Get Program Updates
Program Publications
Publications Search by Program
Search Result
The search results on this publication page are automated on a monthly schedule based on acknowledgement of NIH Common Fund award numbers and intramural awards. Therefore, this list is not an exhaustive or error-free account of the program’s publications.
| Title | Author | Journal Name | PubMedID | Journal Abbreviation | Publication Date |
|---|---|---|---|---|---|
| NMR: an essential structural tool for integrative studies of T cell development, pMHC ligand recognition and TCR mechanobiology. | Mallis RJ, Brazin KN, Duke-Cohan JS, Hwang W, Wang JH, Wagner G, Arthanari H, Lang MJ, Reinherz EL | Journal of biomolecular NMR | 30815789 | J Biomol NMR | 2019 Jul |
| αβ T Cell Receptor Mechanosensing Forces out Serial Engagement. | Feng Y, Reinherz EL, Lang MJ | Trends in immunology | 30060805 | Trends Immunol | 2018 Aug |
| TCR-pMHC encounter differentially regulates transcriptomes of tissue-resident CD8 T cells. | Yoshizawa A, Bi K, Keskin DB, Zhang G, Reinhold B, Reinherz EL | European journal of immunology | 28872670 | Eur J Immunol | 2018 Jan |
| The T Cell Antigen Receptor α Transmembrane Domain Coordinates Triggering through Regulation of Bilayer Immersion and CD3 Subunit Associations. | Brazin KN, Mallis RJ, Boeszoermenyi A, Feng Y, Yoshizawa A, Reche PA, Kaur P, Bi K, Hussey RE, Duke-Cohan JS, Song L, Wagner G, Arthanari H, Lang MJ, Reinherz EL | Immunity | 30389415 | Immunity | 2018 Nov 20 |
| Mosaic Somatic Gene Recombination as a Potentially Unifying Hypothesis for Alzheimer's Disease. | Kaeser GE, Chun J | Frontiers in genetics | 32457796 | Front Genet | 2020 |
| The Gene Conundrum in Alzheimer's Disease. | Chun J | Cerebrum : the Dana forum on brain science | 32206173 | Cerebrum | 2019 Nov-Dec |
| Reply to: APP gene copy number changes reflect exogenous contamination. | Lee MH, Liu CS, Zhu Y, Kaeser GE, Rivera R, Romanow WJ, Kihara Y, Chun J | Nature | 32814882 | Nature | 2020 Aug |
| Brain cell somatic gene recombination and its phylogenetic foundations. | Kaeser G, Chun J | The Journal of biological chemistry | 32699111 | J Biol Chem | 2020 Sep 4 |
| The African Turquoise Killifish: A Scalable Vertebrate Model for Aging and Other Complex Phenotypes. | Boos F, Chen J, Brunet A | Cold Spring Harbor protocols | 37100468 | Cold Spring Harb Protoc | 2024 Mar 1 |
| Tutorial: practical considerations for tissue clearing and imaging. | Weiss KR, Voigt FF, Shepherd DP, Huisken J | Nature protocols | 34021294 | Nat Protoc | 2021 Jun |
| Dermomyotome-derived endothelial cells migrate to the dorsal aorta to support hematopoietic stem cell emergence. | Sahai-Hernandez P, Pouget C, Eyal S, Svoboda O, Chacon J, Grimm L, Gjøen T, Traver D | eLife | 37695317 | Elife | 2023 Sep 11 |
| Cardiac function modulates endocardial cell dynamics to shape the cardiac outflow tract. | Sidhwani P, Leerberg DM, Boezio GLM, Capasso TL, Yang H, Chi NC, Roman BL, Stainier DYR, Yelon D | Development (Cambridge, England) | 32439760 | Development | 2020 Jun 17 |
| Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases. | Zhang S, Shu H, Zhou J, Rubin-Sigler J, Yang X, Liu Y, Cooper-Knock J, Monte E, Zhu C, Tu S, Li H, Tong M, Ecker JR, Ichida JK, Shen Y, Zeng J, Tsao PS, Snyder MP | bioRxiv : the preprint server for biology | 38798507 | bioRxiv | 2024 May 14 |
| CLIP-Seq analysis enables the design of protective ribosomal RNA bait oligonucleotides against C9ORF72 ALS/FTD poly-GR pathophysiology. | Ortega JA, Sasselli IR, Boccitto M, Fleming AC, Fortuna TR, Li Y, Sato K, Clemons TD, Mckenna ED, Nguyen TP, Anderson EN, Asin J, Ichida JK, Pandey UB, Wolin SL, Stupp SI, Kiskinis E | Science advances | 37948524 | Sci Adv | 2023 Nov 10 |
| PIKFYVE inhibition mitigates disease in models of diverse forms of ALS. | Hung ST, Linares GR, Chang WH, Eoh Y, Krishnan G, Mendonca S, Hong S, Shi Y, Santana M, Kueth C, Macklin-Isquierdo S, Perry S, Duhaime S, Maios C, Chang J, Perez J, Couto A, Lai J, Li Y, Alworth SV, Hendricks E, Wang Y, Zlokovic BV, Dickman DK, Parker JA, Zarnescu DC, Gao FB, Ichida JK | Cell | 36754049 | Cell | 2023 Feb 16 |
| Deep learning modeling of rare noncoding genetic variants in human motor neurons defines CCDC146 as a therapeutic target for ALS. | Zhang S, Moll T, Rubin-Sigler J, Tu S, Li S, Yuan E, Liu M, Butt A, Harvey C, Gornall S, Alhalthli E, Shaw A, Souza CDS, Ferraiuolo L, Hornstein E, Shelkovnikova T, van Dijk CH, Timpanaro IS, Kenna KP, Zeng J, Tsao PS, Shaw PJ, Ichida JK, Cooper-Knock J, Snyder MP | medRxiv : the preprint server for health sciences | 38633814 | medRxiv | 2024 Apr 1 |
| SYF2 suppression mitigates neurodegeneration in models of diverse forms of ALS. | Linares GR, Li Y, Chang WH, Rubin-Sigler J, Mendonca S, Hong S, Eoh Y, Guo W, Huang YH, Chang J, Tu S, Dorjsuren N, Santana M, Hung ST, Yu J, Perez J, Chickering M, Cheng TY, Huang CC, Lee SJ, Deng HJ, Bach KT, Gray K, Subramanyam V, Rosenfeld J, Alworth SV, Goodarzi H, Ichida JK | Cell stem cell | 36736291 | Cell Stem Cell | 2023 Feb 2 |
| Environmental risk scores of persistent organic pollutants associate with higher ALS risk and shorter survival in a new Michigan case/control cohort. | Goutman SA, Boss J, Jang DG, Mukherjee B, Richardson RJ, Batterman S, Feldman EL | Journal of neurology, neurosurgery, and psychiatry | 37758454 | J Neurol Neurosurg Psychiatry | 2024 Feb 14 |
| Nanoplastics and Neurodegeneration in ALS. | Eisen A, Pioro EP, Goutman SA, Kiernan MC | Brain sciences | 38790450 | Brain Sci | 2024 May 7 |
| Occupational history associates with ALS survival and onset segment. | Goutman SA, Boss J, Godwin C, Mukherjee B, Feldman EL, Batterman SA | Amyotrophic lateral sclerosis & frontotemporal degeneration | 36193557 | Amyotroph Lateral Scler Frontotemporal Degener | 2023 May |
| Amyotrophic lateral sclerosis. | Feldman EL, Goutman SA, Petri S, Mazzini L, Savelieff MG, Shaw PJ, Sobue G | Lancet (London, England) | 36116464 | Lancet | 2022 Oct 15 |
| Priorities and Recommendations to Make ALS a Livable Disease Emanating from the 2024 National Academies of Sciences, Engineering, and Medicine Report Living with ALS. | Howard IM, Babu S, Carter C, Sakowski SA, Kurent JE, Cudkowicz ME, Feldman EL | Annals of neurology | 39390661 | Ann Neurol | 2024 Dec |
| Impact of the Adverse Social Exposome on Survival in Individuals With Amyotrophic Lateral Sclerosis. | Jang DG, Kind AJ, Patterson A, Pedde M, Powell WR, Feldman EL, Goutman SA | Neurology | 39879575 | Neurology | 2025 Feb 25 |
| Recent advances in the diagnosis and prognosis of amyotrophic lateral sclerosis. | Goutman SA, Hardiman O, Al-Chalabi A, Chió A, Savelieff MG, Kiernan MC, Feldman EL | The Lancet. Neurology | 35334233 | Lancet Neurol | 2022 May |
| Emerging insights into the complex genetics and pathophysiology of amyotrophic lateral sclerosis. | Goutman SA, Hardiman O, Al-Chalabi A, Chió A, Savelieff MG, Kiernan MC, Feldman EL | The Lancet. Neurology | 35334234 | Lancet Neurol | 2022 May |
| Role of the Exposome in Neurodegenerative Disease: Recent Insights and Future Directions. | Sakowski SA, Koubek EJ, Chen KS, Goutman SA, Feldman EL | Annals of neurology | 38411261 | Ann Neurol | 2024 Apr |
| Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank. | Jin W, Boss J, Bakulski KM, Goutman SA, Feldman EL, Fritsche LG, Mukherjee B | medRxiv : the preprint server for health sciences | 38585910 | medRxiv | 2024 Mar 30 |
| Metal mixtures associate with higher amyotrophic lateral sclerosis risk and mortality independent of genetic risk and correlate to self-reported exposures: a case-control study. | Jang DG, Dou J, Koubek EJ, Teener S, Zhao L, Bakulski KM, Mukherjee B, Batterman SA, Feldman EL, Goutman SA | medRxiv : the preprint server for health sciences | 38464233 | medRxiv | 2024 Feb 28 |
| Epigenetic age acceleration is associated with occupational exposures, sex, and survival in amyotrophic lateral sclerosis. | Zhao Y, Li X, Wang K, Iyer G, Sakowski SA, Zhao L, Teener S, Bakulski KM, Dou JF, Traynor BJ, Karnovsky A, Batterman SA, Feldman EL, Sartor MA, Goutman SA | EBioMedicine | 39369616 | EBioMedicine | 2024 Nov |
| Longitudinal Metabolomics in Amyotrophic Lateral Sclerosis Implicates Impaired Lipid Metabolism. | Guo K, Savelieff MG, Jang DG, Teener SJ, Zhao L, Hur J, Goutman SA, Feldman EL | Annals of neurology | 39976286 | Ann Neurol | 2025 Feb 20 |
| Awareness and care practices for rare neurologic diseases among senior neurologists: A global survey. | Jang DG, Federico A, Savelieff MG, Grisold W, Mancuso M, Molnar MJ, Feldman EL, Reynolds EL, World Federation of Neurology Subspecialist Group on Rare Neurologic Diseases | Journal of the neurological sciences | 39855013 | J Neurol Sci | 2025 Mar 15 |
| Stem cell therapy for central nervous system disorders: Metabolic interactions between transplanted cells and local microenvironments. | Sakowski SA, Chen KS | Neurobiology of disease | 35988874 | Neurobiol Dis | 2022 Oct 15 |
| Gut microbiome correlates with plasma lipids in amyotrophic lateral sclerosis. | Guo K, Figueroa-Romero C, Noureldein MH, Murdock BJ, Savelieff MG, Hur J, Goutman SA, Feldman EL | Brain : a journal of neurology | 37721161 | Brain | 2024 Feb 1 |
| Peripheral Immune Profiles Predict ALS Progression in an Age- and Sex-Dependent Manner. | Murdock BJ, Zhao B, Pawlowski KD, Famie JP, Piecuch CE, Webber-Davis IF, Teener SJ, Feldman EL, Zhao L, Goutman SA | Neurology(R) neuroimmunology & neuroinflammation | 38626361 | Neurol Neuroimmunol Neuroinflamm | 2024 May |
| Improving prediction models of amyotrophic lateral sclerosis (ALS) using polygenic, pre-existing conditions, and survey-based risk scores in the UK Biobank. | Jin W, Boss J, Bakulski KM, Goutman SA, Feldman EL, Fritsche LG, Mukherjee B | Journal of neurology | 39249108 | J Neurol | 2024 Oct |
| miRNA analysis reveals novel dysregulated pathways in amyotrophic lateral sclerosis. | Hur J, Paez-Colasante X, Figueroa-Romero C, Lo TW, Barmada SJ, Paulsen MT, Ljungman M, Alakwaa FM, Savelieff MG, Goutman SA, Feldman EL | Human molecular genetics | 36219176 | Hum Mol Genet | 2023 Mar 6 |
| Avocational exposure associations with ALS risk, survival, and phenotype: A Michigan-based case-control study. | Goutman SA, Boss J, Jang DG, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman EL, Batterman SA | Journal of the neurological sciences | 38278093 | J Neurol Sci | 2024 Feb 15 |
| The amyotrophic lateral sclerosis exposome: recent advances and future directions. | Goutman SA, Savelieff MG, Jang DG, Hur J, Feldman EL | Nature reviews. Neurology | 37709948 | Nat Rev Neurol | 2023 Oct |
| Residential exposure associations with ALS risk, survival, and phenotype: a Michigan-based case-control study. | Goutman SA, Boss J, Jang DG, Piecuch C, Farid H, Batra M, Mukherjee B, Feldman EL, Batterman SA | Amyotrophic lateral sclerosis & frontotemporal degeneration | 38557405 | Amyotroph Lateral Scler Frontotemporal Degener | 2024 Aug |
| Variable selection with multiply-imputed datasets: choosing between stacked and grouped methods. | Du J, Boss J, Han P, Beesley LJ, Kleinsasser M, Goutman SA, Batterman S, Feldman EL, Mukherjee B | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 36644406 | J Comput Graph Stat | 2022 |
| Cumulative Genetic Score and C9orf72 Repeat Status Independently Contribute to Amyotrophic Lateral Sclerosis Risk in 2 Case-Control Studies. | Dou J, Bakulski K, Guo K, Hur J, Zhao L, Saez-Atienzar S, Stark A, Chia R, García-Redondo A, Rojas-Garcia R, Vázquez Costa JF, Fernandez Santiago R, Bandres-Ciga S, Gómez-Garre P, Periñán MT, Mir P, Pérez-Tur J, Cardona F, Menendez-Gonzalez M, Riancho J, Borrego-Hernández D, Galán-Dávila L, Infante Ceberio J, Pastor P, Paradas C, Dols-Icardo O, Traynor BJ, Feldman EL, Goutman SA, Spanish Neurological Consortium | Neurology. Genetics | 37293291 | Neurol Genet | 2023 Aug |
| Multiple metal exposures associate with higher amyotrophic lateral sclerosis risk and mortality independent of genetic risk and correlate to self-reported exposures: a case-control study. | Jang DG, Dou JF, Koubek EJ, Teener S, Zhou L, Bakulski KM, Mukherjee B, Batterman SA, Feldman EL, Goutman SA | Journal of neurology, neurosurgery, and psychiatry | 39107037 | J Neurol Neurosurg Psychiatry | 2025 Mar 24 |
| Body mass index associates with amyotrophic lateral sclerosis survival and metabolomic profiles. | Goutman SA, Boss J, Iyer G, Habra H, Savelieff MG, Karnovsky A, Mukherjee B, Feldman EL | Muscle & nerve | 36321729 | Muscle Nerve | 2023 Mar |
| Single-cell atlas reveals correlates of high cognitive function, dementia, and resilience to Alzheimer's disease pathology. | Mathys H, Peng Z, Boix CA, Victor MB, Leary N, Babu S, Abdelhady G, Jiang X, Ng AP, Ghafari K, Kunisky AK, Mantero J, Galani K, Lohia VN, Fortier GE, Lotfi Y, Ivey J, Brown HP, Patel PR, Chakraborty N, Beaudway JI, Imhoff EJ, Keeler CF, McChesney MM, Patel HH, Patel SP, Thai MT, Bennett DA, Kellis M, Tsai LH | Cell | 37774677 | Cell | 2023 Sep 28 |
| A polygenic score method boosted by non-additive models. | Ohta R, Tanigawa Y, Suzuki Y, Kellis M, Morishita S | Nature communications | 38811555 | Nat Commun | 2024 May 29 |
| Multifaceted impact of specialized neuropeptide-intensive neurons on the selective vulnerability in Alzheimer's disease. | Li M, Flack N, Larsen PA | bioRxiv : the preprint server for biology | 38014130 | bioRxiv | 2024 Apr 22 |
| Power of inclusion: Enhancing polygenic prediction with admixed individuals. | Tanigawa Y, Kellis M | American journal of human genetics | 37890495 | Am J Hum Genet | 2023 Nov 2 |
| Integrated multimodal cell atlas of Alzheimer's disease. | Gabitto MI, Travaglini KJ, Rachleff VM, Kaplan ES, Long B, Ariza J, Ding Y, Mahoney JT, Dee N, Goldy J, Melief EJ, Agrawal A, Kana O, Zhen X, Barlow ST, Brouner K, Campos J, Campos J, Carr AJ, Casper T, Chakrabarty R, Clark M, Cool J, Dalley R, Darvas M, Ding SL, Dolbeare T, Egdorf T, Esposito L, Ferrer R, Fleckenstein LE, Gala R, Gary A, Gelfand E, Gloe J, Guilford N, Guzman J, Hirschstein D, Ho W, Hupp M, Jarsky T, Johansen N, Kalmbach BE, Keene LM, Khawand S, Kilgore MD, Kirkland A, Kunst M, Lee BR, Leytze M, Mac Donald CL, Malone J, Maltzer Z, Martin N, McCue R, McMillen D, Mena G, Meyerdierks E, Meyers KP, Mollenkopf T, Montine M, Nolan AL, Nyhus JK, Olsen PA, Pacleb M, Pagan CM, Peña N, Pham T, Pom CA, Postupna N, Rimorin C, Ruiz A, Saldi GA, Schantz AM, Shapovalova NV, Sorensen SA, Staats B, Sullivan M, Sunkin SM, Thompson C, Tieu M, Ting JT, Torkelson A, Tran T, Valera Cuevas NJ, Walling-Bell S, Wang MQ, Waters J, Wilson AM, Xiao M, Haynor D, Gatto NM, Jayadev S, Mufti S, Ng L, Mukherjee S, Crane PK, Latimer CS, Levi BP, Smith KA, Close JL, Miller JA, Hodge RD, Larson EB, Grabowski TJ, Hawrylycz M, Keene CD, Lein ES | Nature neuroscience | 39402379 | Nat Neurosci | 2024 Dec |
| Multifaceted Role of Specialized Neuropeptide-Intensive Neurons on the Selective Vulnerability to Alzheimer's Disease in the Human Brain. | Li M, Flack N, Larsen PA | Biomolecules | 39766225 | Biomolecules | 2024 Nov 27 |
| Opposing roles of p38α-mediated phosphorylation and PRMT1-mediated arginine methylation in driving TDP-43 proteinopathy. | Aikio M, Odeh HM, Wobst HJ, Lee BL, Chan Ú, Mauna JC, Mack KL, Class B, Ollerhead TA, Ford AF, Barbieri EM, Cupo RR, Drake LE, Smalley JL, Lin YT, Lam S, Thomas R, Castello N, Baral A, Beyer JN, Najar MA, Dunlop J, Gitler AD, Javaherian A, Kaye JA, Burslem GM, Brown DG, Donnelly CJ, Finkbeiner S, Moss SJ, Brandon NJ, Shorter J | Cell reports | 39817908 | Cell Rep | 2025 Jan 28 |
| Epigenomic dissection of Alzheimer's disease pinpoints causal variants and reveals epigenome erosion. | Xiong X, James BT, Boix CA, Park YP, Galani K, Victor MB, Sun N, Hou L, Ho LL, Mantero J, Scannail AN, Dileep V, Dong W, Mathys H, Bennett DA, Tsai LH, Kellis M | Cell | 37774680 | Cell | 2023 Sep 28 |
| Local translation in primary afferents and its contribution to pain. | Gale JR, Gedeon JY, Donnelly CJ, Gold MS | Pain | 35438669 | Pain | 2022 Dec 1 |
| Integrating single-cell RNA-seq datasets with substantial batch effects. | Hrovatin K, Moinfar AA, Zappia L, Lapuerta AT, Lengerich B, Kellis M, Theis FJ | bioRxiv : the preprint server for biology | 37961672 | bioRxiv | 2024 Feb 10 |
| Single-nucleus multiregion transcriptomic analysis of brain vasculature in Alzheimer's disease. | Sun N, Akay LA, Murdock MH, Park Y, Galiana-Melendez F, Bubnys A, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M | Nature neuroscience | 37264161 | Nat Neurosci | 2023 Jun |
| CUTS RNA Biosensor for the Real-Time Detection of TDP-43 Loss-of-Function. | Xie L, Merjane J, Bergmann CA, Xu J, Hurtle B, Donnelly CJ | bioRxiv : the preprint server for biology | 39026766 | bioRxiv | 2024 Jul 12 |
| Disrupting pathologic phase transitions in neurodegeneration. | Hurtle BT, Xie L, Donnelly CJ | The Journal of clinical investigation | 37395272 | J Clin Invest | 2023 Jul 3 |
| Single-cell dissection of the human motor and prefrontal cortices in ALS and FTLD. | Pineda SS, Lee H, Ulloa-Navas MJ, Linville RM, Garcia FJ, Galani K, Engelberg-Cook E, Castanedes MC, Fitzwalter BE, Pregent LJ, Gardashli ME, DeTure M, Vera-Garcia DV, Hucke ATS, Oskarsson BE, Murray ME, Dickson DW, Heiman M, Belzil VV, Kellis M | Cell | 38521060 | Cell | 2024 Apr 11 |
| Human microglial state dynamics in Alzheimer's disease progression. | Sun N, Victor MB, Park YP, Xiong X, Scannail AN, Leary N, Prosper S, Viswanathan S, Luna X, Boix CA, James BT, Tanigawa Y, Galani K, Mathys H, Jiang X, Ng AP, Bennett DA, Tsai LH, Kellis M | Cell | 37774678 | Cell | 2023 Sep 28 |
| Single-cell multiregion dissection of Alzheimer's disease. | Mathys H, Boix CA, Akay LA, Xia Z, Davila-Velderrain J, Ng AP, Jiang X, Abdelhady G, Galani K, Mantero J, Band N, James BT, Babu S, Galiana-Melendez F, Louderback K, Prokopenko D, Tanzi RE, Bennett DA, Tsai LH, Kellis M | Nature | 39048816 | Nature | 2024 Aug |
| Assays to measure small molecule Hsp70 agonist activity in vitro and in vivo. | Shapiro O, Woods C, Gleixner AM, Sannino S, Ngo M, McDaniels MD, Wipf P, Hukriede NA, Donnelly CJ, Brodsky JL | Analytical biochemistry | 39522672 | Anal Biochem | 2025 Feb |
| RNA aptamer reveals nuclear TDP-43 pathology is an early aggregation event that coincides with STMN-2 cryptic splicing and precedes clinical manifestation in ALS. | Spence H, Waldron FM, Saleeb RS, Brown AL, Rifai OM, Gilodi M, Read F, Roberts K, Milne G, Wilkinson D, O'Shaughnessy J, Pastore A, Fratta P, Shneider N, Tartaglia GG, Zacco E, Horrocks MH, Gregory JM | Acta neuropathologica | 38443601 | Acta Neuropathol | 2024 Mar 5 |
| Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. | Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN | bioRxiv : the preprint server for biology | 38585850 | bioRxiv | 2024 Mar 28 |
| Polysome collapse and RNA condensation fluidize the cytoplasm. | Xie Y, Shu T, Liu T, Spindler MC, Mahamid J, Hocky GM, Gresham D, Holt LJ | Molecular cell | 39059370 | Mol Cell | 2024 Jul 25 |
| Amygdala TDP-43 pathology is associated with behavioural dysfunction and ferritin accumulation in amyotrophic lateral sclerosis. | Rifai OM, Waldron FM, O'Shaughnessy J, Read FL, Gilodi M, Pastore A, Shneider N, Tartaglia GG, Zacco E, Spence H, Gregory JM | bioRxiv : the preprint server for biology | 38854008 | bioRxiv | 2024 Jun 1 |
| Condensation of LINE-1 is critical for retrotransposition. | Sil S, Keegan S, Ettefa F, Denes LT, Boeke JD, Holt LJ | eLife | 37114770 | Elife | 2023 Apr 28 |
| The environmental stress response regulates ribosome content in cell cycle-arrested S. cerevisiae. | Terhorst A, Sandikci A, Whittaker CA, Szórádi T, Holt LJ, Neurohr GE, Amon A | Frontiers in cell and developmental biology | 37123399 | Front Cell Dev Biol | 2023 |
| Macromolecular crowding: Sensing without a sensor. | Holt LJ, Delarue M | Current opinion in cell biology | 37897928 | Curr Opin Cell Biol | 2023 Dec |
| Phase Separation in Biology and Disease; Current Perspectives and Open Questions. | Boeynaems S, Chong S, Gsponer J, Holt L, Milovanovic D, Mitrea DM, Mueller-Cajar O, Portz B, Reilly JF, Reinkemeier CD, Sabari BR, Sanulli S, Shorter J, Sontag E, Strader L, Stachowiak J, Weber SC, White M, Zhang H, Zweckstetter M, Elbaum-Garfinkle S, Kriwacki R | Journal of molecular biology | 36690068 | J Mol Biol | 2023 Mar 1 |
| Development and Characterization of 50 nanometer diameter Genetically Encoded Multimeric Nanoparticles. | Hernandez CM, Duran-Chaparro DC, van Eeuwen T, Rout MP, Holt LJ | bioRxiv : the preprint server for biology | 39005449 | bioRxiv | 2024 Jul 7 |
| Condensed-phase signaling can expand kinase specificity and respond to macromolecular crowding. | Sang D, Shu T, Pantoja CF, Ibáñez de Opakua A, Zweckstetter M, Holt LJ | Molecular cell | 36108633 | Mol Cell | 2022 Oct 6 |
| Increased mesoscale diffusivity in response to acute glucose starvation. | Xie Y, Gresham D, Holt LJ | microPublication biology | 36908311 | MicroPubl Biol | 2023 |
| A genome-wide CRISPR screen identifies WDFY3 as a regulator of macrophage efferocytosis. | Shi J, Wu X, Wang Z, Li F, Meng Y, Moore RM, Cui J, Xue C, Croce KR, Yurdagul A Jr, Doench JG, Li W, Zarbalis KS, Tabas I, Yamamoto A, Zhang H | Nature communications | 36566259 | Nat Commun | 2022 Dec 24 |
| The broken Alzheimer's disease genome. | Gouveia Roque C, Phatnani H, Hengst U | Cell genomics | 38697121 | Cell Genom | 2024 May 8 |
| Clinicopathological analysis of NEK1 variants in amyotrophic lateral sclerosis. | Rifai OM, Waldron FM, Sleibi D, O'Shaughnessy J, Leighton DJ, Gregory JM | Brain pathology (Zurich, Switzerland) | 38986433 | Brain Pathol | 2025 Jan |
| Macromolecular interactions and geometrical confinement determine the 3D diffusion of ribosome-sized particles in live Escherichia coli cells. | Valverde-Mendez D, Sunol AM, Bratton BP, Delarue M, Hofmann JL, Sheehan JP, Gitai Z, Holt LJ, Shaevitz JW, Zia RN | Proceedings of the National Academy of Sciences of the United States of America | 39854229 | Proc Natl Acad Sci U S A | 2025 Jan 28 |
| Controlling the crowd with a WNK. | Holt LJ, Denes LT | Cell | 36423576 | Cell | 2022 Nov 23 |
| Increased mesoscale diffusivity in response to acute glucose starvation. | Xie Y, Gresham D, Holt L | bioRxiv : the preprint server for biology | 36711511 | bioRxiv | 2023 Jan 12 |
| Macromolecular crowding limits growth under pressure. | Alric B, Formosa-Dague C, Dague E, Holt LJ, Delarue M | Nature physics | 37152719 | Nat Phys | 2022 Apr |
| Epithelial tissue confinement inhibits cell growth and leads to volume-reducing divisions. | Devany J, Falk MJ, Holt LJ, Murugan A, Gardel ML | Developmental cell | 37339629 | Dev Cell | 2023 Aug 21 |
| Distinct neuroinflammatory signatures exist across genetic and sporadic amyotrophic lateral sclerosis cohorts. | Rifai OM, O'Shaughnessy J, Dando OR, Munro AF, Sewell MDE, Abrahams S, Waldron FM, Sibley CR, Gregory JM | Brain : a journal of neurology | 37450566 | Brain | 2023 Dec 1 |
| How it feels in a cell. | Bonucci M, Shu T, Holt LJ | Trends in cell biology | 37286396 | Trends Cell Biol | 2023 Nov |
| Mesoscale molecular assembly is favored by the active, crowded cytoplasm. | Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ | bioRxiv : the preprint server for biology | 37781612 | bioRxiv | 2023 Sep 21 |
| Oligodendroglial macroautophagy is essential for myelin sheath turnover to prevent neurodegeneration and death. | Aber ER, Griffey CJ, Davies T, Li AM, Yang YJ, Croce KR, Goldman JE, Grutzendler J, Canman JC, Yamamoto A | Cell reports | 36261002 | Cell Rep | 2022 Oct 18 |
| mRNA condensation fluidizes the cytoplasm. | Xie Y, Liu T, Gresham D, Holt LJ | bioRxiv : the preprint server for biology | 37398029 | bioRxiv | 2023 Jul 15 |
| Adult-onset deactivation of autophagy leads to loss of synapse homeostasis and cognitive impairment, with implications for alzheimer disease. | Grosso Jasutkar H, Wasserlein EM, Ishola A, Litt N, Staniszewski A, Arancio O, Yamamoto A | Autophagy | 38949671 | Autophagy | 2024 Nov |
| Two-color coincidence single-molecule pulldown for the specific detection of disease-associated protein aggregates. | Saleeb RS, Leighton C, Lee JE, O'Shaughnessy J, Jeacock K, Chappard A, Cumberland R, Zhao T, Ball SR, Sunde M, Clarke DJ, Piché K, McPhail JA, Louwrier A, Angers R, Gandhi S, Downey P, Kunath T, Horrocks MH | Science advances | 37967183 | Sci Adv | 2023 Nov 17 |
| Autophagy at the synapse, an early site of dysfunction in neurodegeneration. | Jasutkar HG, Yamamoto A | Current opinion in physiology | 36968133 | Curr Opin Physiol | 2023 Apr |
| Mesoscale molecular assembly is favored by the active, crowded cytoplasm. | Shu T, Mitra G, Alberts J, Viana MP, Levy ED, Hocky GM, Holt LJ | PRX life | 40162127 | PRX Life | 2024 Sep |
| Machine learning identifies routine blood tests as accurate predictive measures of pollution-dependent poor cognitive function. | Johnson H, Longden J, Cameron G, Waiter GD, Waldron FM, Gregory JM, Spence H | bioRxiv : the preprint server for biology | 39868217 | bioRxiv | 2025 Jan 13 |
| Stem cell transcriptional profiles from mouse subspecies reveal cis-regulatory evolution at translation genes. | Simon NM, Kim Y, Gribnau J, Bautista DM, Dutton JR, Brem RB | Heredity | 39164520 | Heredity (Edinb) | 2024 Nov |
| Basophils add fuel to the flame of eczema itch. | Mali SS, Bautista DM | Cell | 33482094 | Cell | 2021 Jan 21 |
| SARS-CoV-2 papain-like protease activates nociceptors to drive sneeze and pain. | Mali SS, Silva R, Gong Z, Cronce M, Vo U, Vuong C, Moayedi Y, Cox JS, Bautista DM | bioRxiv : the preprint server for biology | 38260476 | bioRxiv | 2024 Jan 11 |
| Avid lysosomal acidification in fibroblasts of the Mediterranean mouse Mus spretus. | Sui M, Teh J, Fort K, Shaw D, Sudmant P, Koide T, Good JM, Vazquez JM, Brem RB | bioRxiv : the preprint server for biology | 39974907 | bioRxiv | 2025 Feb 7 |
| Stem cell transcriptional profiles from mouse subspecies reveal cis -regulatory evolution at translation genes. | Simon NM, Kim Y, Bautista DM, Dutton JR, Brem RB | bioRxiv : the preprint server for biology | 37503246 | bioRxiv | 2024 Jul 20 |
| Expanding the AtLAS of non-coding RNA functions in the brain. | Regier MJ, Shepherd JD | Cell research | 32111970 | Cell Res | 2020 Apr |
| Intercellular Communication in the Nervous System Goes Viral. | Hantak MP, Einstein J, Kearns RB, Shepherd JD | Trends in neurosciences | 33485691 | Trends Neurosci | 2021 Apr |
| PNMA2 forms immunogenic non-enveloped virus-like capsids associated with paraneoplastic neurological syndrome. | Xu J, Erlendsson S, Singh M, Holling GA, Regier M, Ibiricu I, Einstein J, Hantak MP, Day GS, Piquet AL, Smith TL, Clardy SL, Whiteley AM, Feschotte C, Briggs JAG, Shepherd JD | Cell | 38301645 | Cell | 2024 Feb 15 |
| Arc mediates intercellular tau transmission via extracellular vesicles. | Tyagi M, Chadha R, de Hoog E, Sullivan KR, Walker AC, Northrop A, Fabian B, Fuxreiter M, Hyman BT, Shepherd JD | bioRxiv : the preprint server for biology | 39484489 | bioRxiv | 2024 Oct 22 |
| "Arc - A viral vector of memory and synaptic plasticity". | Sullivan KR, Ravens A, Walker AC, Shepherd JD | Current opinion in neurobiology | 39956025 | Curr Opin Neurobiol | 2025 Apr |
| Intercellular Arc Signaling Regulates Vasodilation. | de la Peña JB, Barragan-Iglesias P, Lou TF, Kunder N, Loerch S, Shukla T, Basavarajappa L, Song J, James DN, Megat S, Moy JK, Wanghzou A, Ray PR, Hoyt K, Steward O, Price TJ, Shepherd J, Campbell ZT | The Journal of neuroscience : the official journal of the Society for Neuroscience | 34326146 | J Neurosci | 2021 Sep 15 |
| The mammalian midbody and midbody remnant are assembly sites for RNA and localized translation. | Park S, Dahn R, Kurt E, Presle A, VanDenHeuvel K, Moravec C, Jambhekar A, Olukoga O, Shepherd J, Echard A, Blower M, Skop AR | Developmental cell | 37552987 | Dev Cell | 2023 Oct 9 |
| PNMA2 forms non-enveloped virus-like capsids that trigger paraneoplastic neurological syndrome. | Xu J, Erlendsson S, Singh M, Regier M, Ibiricu I, Day GS, Piquet AL, Clardy SL, Feschotte C, Briggs JAG, Shepherd JD | bioRxiv : the preprint server for biology | 36798413 | bioRxiv | 2023 Feb 9 |
| Origins, Biology, and Diseases of Tissue Macrophages. | Cox N, Pokrovskii M, Vicario R, Geissmann F | Annual review of immunology | 33902313 | Annu Rev Immunol | 2021 Apr 26 |
| Physiology and diseases of tissue-resident macrophages. | Lazarov T, Juarez-Carreño S, Cox N, Geissmann F | Nature | 37344646 | Nature | 2023 Jun |
| Mechanism of neurodegeneration mediated by clonal inflammatory microglia. | Vicario R, Fragkogianni S, Pokrovskii M, Mayer C, Lopez-Rodrigo E, Hu Y, Ogishi M, Alberdi A, Baako A, Ay O, Plu I, Sazdovitch V, Heritier S, Cohen-Aubart F, Shor N, Miyara M, Nguyen-Khac F, Viale A, Idbaih A, Amoura Z, Rosenblum MK, Zhang H, Karnoub ER, Sashittal P, Jakatdar A, Iacobuzio-Donahue CA, Abdel-Wahab O, Tabar V, Socci ND, Elemento O, Diamond EL, Boisson B, Casanova JL, Seilhean D, Haroche J, Donadieu J, Geissmann F | bioRxiv : the preprint server for biology | 39131366 | bioRxiv | 2024 Jul 31 |
| A microglia clonal inflammatory disorder in Alzheimer's Disease. | Vicario R, Fragkogianni S, Weber L, Lazarov T, Hu Y, Hayashi SY, Craddock BP, Socci ND, Alberdi A, Baako A, Ay O, Ogishi M, Lopez-Rodrigo E, Kappagantula R, Viale A, Iacobuzio-Donahue CA, Zhou T, Ransohoff RM, Chesworth R, Netherlands Brain Bank, Abdel-Wahab O, Boisson B, Elemento O, Casanova JL, Miller WT, Geissmann F | bioRxiv : the preprint server for biology | 38328106 | bioRxiv | 2024 Aug 3 |
| Clonal Hematopoiesis Is Associated With Long-Term Adverse Outcomes Following Cardiac Surgery. | Ninni S, Vicario R, Coisne A, Woitrain E, Tazibet A, Stewart CM, Diaz LA Jr, White JR, Koussa M, Dubrulle H, Juthier F, Jungling M, Vincentelli A, Edme JL, Nattel S, de Winther M, Geissmann F, Dombrowicz D, Staels B, Montaigne D | Journal of the American Heart Association | 39206728 | J Am Heart Assoc | 2024 Sep 3 |
| Hematopoietic Somatic Mosaicism Is Associated With an Increased Risk of Postoperative Atrial Fibrillation. | Ninni S, Dombrowicz D, Kuznetsova T, Vicario R, Gao V, Molendi-Coste O, Haas J, Woitrain E, Coisne A, Neele AE, Prange K, Willemsen L, Aghezzaf S, Fragkogianni S, Tazibet A, Pineau L, White JR, Eeckhoute J, Koussa M, Dubrulle H, Juthier F, Soquet J, Vincentelli A, Edme JL, de Winther M, Geissmann F, Staels B, Montaigne D | Journal of the American College of Cardiology | 36990546 | J Am Coll Cardiol | 2023 Apr 4 |
| Plasma membrane abundance dictates phagocytic capacity and functional cross-talk in myeloid cells. | Winer BY, Settle AH, Yakimov AM, Jeronimo C, Lazarov T, Tipping M, Saoi M, Sawh A, Sepp AL, Galiano M, Perry JSA, Wong YY, Geissmann F, Cross J, Zhou T, Kam LC, Pasolli HA, Hohl T, Cyster JG, Weiner OD, Huse M | Science immunology | 38848343 | Sci Immunol | 2024 Jun 7 |
| Nuclear envelope rupture is induced by actin-based nucleus confinement. | Hatch EM, Hetzer MW | The Journal of cell biology | 27697922 | J Cell Biol | 2016 Oct 10 |
| Caspase-mediated nuclear pore complex trimming in cell differentiation and endoplasmic reticulum stress. | Cho UH, Hetzer MW | eLife | 37665327 | Elife | 2023 Sep 4 |
| p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. | van de Ven RA, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer MW, Sahai E, Derksen PW | Nature communications | 28004812 | Nat Commun | 2016 Dec 22 |
| Tpr regulates the total number of nuclear pore complexes per cell nucleus. | McCloskey A, Ibarra A, Hetzer MW | Genes & development | 30228202 | Genes Dev | 2018 Oct 1 |
| Predicting age from the transcriptome of human dermal fibroblasts. | Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer MW, Navlakha S | Genome biology | 30567591 | Genome Biol | 2018 Dec 20 |
| Nucleoporin-mediated regulation of cell identity genes. | Ibarra A, Benner C, Tyagi S, Cool J, Hetzer MW | Genes & development | 27807035 | Genes Dev | 2016 Oct 15 |
| Age Mosaicism across Multiple Scales in Adult Tissues. | Arrojo E Drigo R, Lev-Ram V, Tyagi S, Ramachandra R, Deerinck T, Bushong E, Phan S, Orphan V, Lechene C, Ellisman MH, Hetzer MW | Cell metabolism | 31178361 | Cell Metab | 2019 Aug 6 |
| Selective clearance of the inner nuclear membrane protein emerin by vesicular transport during ER stress. | Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M | eLife | 31599721 | Elife | 2019 Oct 10 |
| Dynamic regulation of histone modifications and long-range chromosomal interactions during postmitotic transcriptional reactivation. | Kang H, Shokhirev MN, Xu Z, Chandran S, Dixon JR, Hetzer MW | Genes & development | 32499403 | Genes Dev | 2020 Jul 1 |
| Nuclear Periphery Takes Center Stage: The Role of Nuclear Pore Complexes in Cell Identity and Aging. | Cho UH, Hetzer MW | Neuron | 32553207 | Neuron | 2020 Jun 17 |
| Visualization of long-lived proteins reveals age mosaicism within nuclei of postmitotic cells. | Toyama BH, Arrojo E Drigo R, Lev-Ram V, Ramachandra R, Deerinck TJ, Lechene C, Ellisman MH, Hetzer MW | The Journal of cell biology | 30552100 | J Cell Biol | 2019 Feb 4 |
| Nup98 recruits the Wdr82-Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation in hematopoietic progenitor cells. | Franks TM, McCloskey A, Shokirev MN, Benner C, Rathore A, Hetzer MW | Genes & development | 29269482 | Genes Dev | 2017 Nov 15 |
| Direct reprogramming of human smooth muscle and vascular endothelial cells reveals defects associated with aging and Hutchinson-Gilford progeria syndrome. | Bersini S, Schulte R, Huang L, Tsai H, Hetzer MW | eLife | 32896271 | Elife | 2020 Sep 8 |
| Transcriptional and Functional Changes of the Human Microvasculature during Physiological Aging and Alzheimer Disease. | Bersini S, Arrojo E Drigo R, Huang L, Shokhirev MN, Hetzer MW | Advanced biosystems | 32402127 | Adv Biosyst | 2020 May |
| Coaching from the sidelines: the nuclear periphery in genome regulation. | Buchwalter A, Kaneshiro JM, Hetzer MW | Nature reviews. Genetics | 30356165 | Nat Rev Genet | 2019 Jan |
| Nucleolar expansion and elevated protein translation in premature aging. | Buchwalter A, Hetzer MW | Nature communications | 28855503 | Nat Commun | 2017 Aug 30 |
| Evolution of a transcriptional regulator from a transmembrane nucleoporin. | Franks TM, Benner C, Narvaiza I, Marchetto MC, Young JM, Malik HS, Gage FH, Hetzer MW | Genes & development | 27198230 | Genes Dev | 2016 May 15 |
| Nup93 regulates breast tumor growth by modulating cell proliferation and actin cytoskeleton remodeling. | Bersini S, Lytle NK, Schulte R, Huang L, Wahl GM, Hetzer MW | Life science alliance | 31959624 | Life Sci Alliance | 2020 Jan |
| Identification of long-lived proteins in the mitochondria reveals increased stability of the electron transport chain. | Krishna S, Arrojo E Drigo R, Capitanio JS, Ramachandra R, Ellisman M, Hetzer MW | Developmental cell | 34715012 | Dev Cell | 2021 Nov 8 |
| Disulfide bond in SUN2 regulates dynamic remodeling of LINC complexes at the nuclear envelope. | Sharma R, Hetzer MW | Life science alliance | 37188462 | Life Sci Alliance | 2023 Aug |
| Multifaceted Changes in Synaptic Composition and Astrocytic Involvement in a Mouse Model of Fragile X Syndrome. | Simhal AK, Zuo Y, Perez MM, Madison DV, Sapiro G, Micheva KD | Scientific reports | 31554841 | Sci Rep | 2019 Sep 25 |
| Knowing a synapse when you see one. | Burette A, Collman F, Micheva KD, Smith SJ, Weinberg RJ | Frontiers in neuroanatomy | 26283929 | Front Neuroanat | 2015 |
| Array tomography of physiologically-characterized CNS synapses. | Valenzuela RA, Micheva KD, Kiraly M, Li D, Madison DV | Journal of neuroscience methods | 27141856 | J Neurosci Methods | 2016 Aug 1 |
| A large fraction of neocortical myelin ensheathes axons of local inhibitory neurons. | Micheva KD, Wolman D, Mensh BD, Pax E, Buchanan J, Smith SJ, Bock DD | eLife | 27383052 | Elife | 2016 Jul 6 |
| A community-developed open-source computational ecosystem for big neuro data. | Vogelstein JT, Perlman E, Falk B, Baden A, Gray Roncal W, Chandrashekhar V, Collman F, Seshamani S, Patsolic JL, Lillaney K, Kazhdan M, Hider R Jr, Pryor D, Matelsky J, Gion T, Manavalan P, Wester B, Chevillet M, Trautman ET, Khairy K, Bridgeford E, Kleissas DM, Tward DJ, Crow AK, Hsueh B, Wright MA, Miller MI, Smith SJ, Vogelstein RJ, Deisseroth K, Burns R | Nature methods | 30377345 | Nat Methods | 2018 Nov |
| Frontotemporal dementia with the V337M MAPT mutation: Tau-PET and pathology correlations. | Spina S, Schonhaut DR, Boeve BF, Seeley WW, Ossenkoppele R, O'Neil JP, Lazaris A, Rosen HJ, Boxer AL, Perry DC, Miller BL, Dickson DW, Parisi JE, Jagust WJ, Murray ME, Rabinovici GD | Neurology | 28130473 | Neurology | 2017 Feb 21 |
| A Computational Synaptic Antibody Characterization Tool for Array Tomography. | Simhal AK, Gong B, Trimmer JS, Weinberg RJ, Smith SJ, Sapiro G, Micheva KD | Frontiers in neuroanatomy | 30065633 | Front Neuroanat | 2018 |
| Functional cortical neurons and astrocytes from human pluripotent stem cells in 3D culture. | Paşca AM, Sloan SA, Clarke LE, Tian Y, Makinson CD, Huber N, Kim CH, Park JY, O'Rourke NA, Nguyen KD, Smith SJ, Huguenard JR, Geschwind DH, Barres BA, Paşca SP | Nature methods | 26005811 | Nat Methods | 2015 Jul |
| Data-driven synapse classification reveals a logic of glutamate receptor diversity. | Micheva KD, Simhal AK, Schardt J, Smith SJ, Weinberg RJ, Owen SF | bioRxiv : the preprint server for biology | 39713368 | bioRxiv | 2025 Jan 14 |
| From cosmos to connectomes: the evolution of data-intensive science. | Burns R, Vogelstein JT, Szalay AS | Neuron | 25233306 | Neuron | 2014 Sep 17 |
| Single-cell transcriptomic evidence for dense intracortical neuropeptide networks. | Smith SJ, Sümbül U, Graybuck LT, Collman F, Seshamani S, Gala R, Gliko O, Elabbady L, Miller JA, Bakken TE, Rossier J, Yao Z, Lein E, Zeng H, Tasic B, Hawrylycz M | eLife | 31710287 | Elife | 2019 Nov 11 |
| Antibody validation: a view from the mountains. | Taussig MJ, Fonseca C, Trimmer JS | New biotechnology | 30086383 | N Biotechnol | 2018 Oct 25 |
| Sub-synaptic, multiplexed analysis of proteins reveals Fragile X related protein 2 is mislocalized in Fmr1 KO synapses. | Wang GX, Smith SJ, Mourrain P | eLife | 27770568 | Elife | 2016 Oct 22 |
| Subcellular organization of UBE3A in human cerebral cortex. | Burette AC, Judson MC, Li AN, Chang EF, Seeley WW, Philpot BD, Weinberg RJ | Molecular autism | 30364390 | Mol Autism | 2018 |
| Developing a Toolbox of Antibodies Validated for Array Tomography-Based Imaging of Brain Synapses. | Micheva KD, Gong B, Collman F, Weinberg RJ, Smith SJ, Trimmer JS, Murray KD | bioRxiv : the preprint server for biology | 37425759 | bioRxiv | 2023 Nov 8 |
| Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy. | Ounkomol C, Seshamani S, Maleckar MM, Collman F, Johnson GR | Nature methods | 30224672 | Nat Methods | 2018 Nov |
| Q&A: Array tomography. | Smith SJ | BMC biology | 30189863 | BMC Biol | 2018 Sep 6 |
| Distinctive Structural and Molecular Features of Myelinated Inhibitory Axons in Human Neocortex. | Micheva KD, Chang EF, Nana AL, Seeley WW, Ting JT, Cobbs C, Lein E, Smith SJ, Weinberg RJ, Madison DV | eNeuro | 30406183 | eNeuro | 2018 Sep-Oct |
| Kernel k-Groups via Hartigan's Method. | Franca G, Rizzo ML, Vogelstein JT | IEEE transactions on pattern analysis and machine intelligence | 32750776 | IEEE Trans Pattern Anal Mach Intell | 2021 Dec |
| A resource from 3D electron microscopy of hippocampal neuropil for user training and tool development. | Harris KM, Spacek J, Bell ME, Parker PH, Lindsey LF, Baden AD, Vogelstein JT, Burns R | Scientific data | 26347348 | Sci Data | 2015 |
| Mapping synapses by conjugate light-electron array tomography. | Collman F, Buchanan J, Phend KD, Micheva KD, Weinberg RJ, Smith SJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 25855189 | J Neurosci | 2015 Apr 8 |
| Mutations underlying Episodic Ataxia type-1 antagonize Kv1.1 RNA editing. | Ferrick-Kiddie EA, Rosenthal JJ, Ayers GD, Emeson RB | Scientific reports | 28216637 | Sci Rep | 2017 Feb 20 |
| Current strategies for Site-Directed RNA Editing using ADARs. | Montiel-Gonzalez MF, Diaz Quiroz JF, Rosenthal JJC | Methods (San Diego, Calif.) | 30502398 | Methods | 2019 Mar 1 |
| Comparative neurobiology of feeding in the opisthobranch sea slug, Aplysia, and the pulmonate snail, Helisoma: evolutionary considerations. | Wentzell MM, Martínez-Rubio C, Miller MW, Murphy AD | Brain, behavior and evolution | 20029185 | Brain Behav Evol | 2009 |
| An efficient system for selectively altering genetic information within mRNAs. | Montiel-González MF, Vallecillo-Viejo IC, Rosenthal JJ | Nucleic acids research | 27557710 | Nucleic Acids Res | 2016 Dec 1 |
| Feedback from peripheral musculature to central pattern generator in the neurogenic heart of the crab Callinectes sapidus: role of mechanosensitive dendrites. | García-Crescioni K, Fort TJ, Stern E, Brezina V, Miller MW | Journal of neurophysiology | 19828726 | J Neurophysiol | 2010 Jan |
| In Vivo Repair of a Protein Underlying a Neurological Disorder by Programmable RNA Editing. | Sinnamon JR, Kim SY, Fisk JR, Song Z, Nakai H, Jeng S, McWeeney SK, Mandel G | Cell reports | 32668243 | Cell Rep | 2020 Jul 14 |
| The emerging role of RNA editing in plasticity. | Rosenthal JJ | The Journal of experimental biology | 26085659 | J Exp Biol | 2015 Jun |
| Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme. | Vallecillo-Viejo IC, Liscovitch-Brauer N, Montiel-Gonzalez MF, Eisenberg E, Rosenthal JJC | RNA biology | 29099293 | RNA Biol | 2018 Jan 2 |
| In vitro and in cellula site-directed RNA editing using the λNDD-BoxB system. | Ojha N, Diaz Quiroz JF, Rosenthal JJC | Methods in enzymology | 34517953 | Methods Enzymol | 2021 |
| Trade-off between Transcriptome Plasticity and Genome Evolution in Cephalopods. | Liscovitch-Brauer N, Alon S, Porath HT, Elstein B, Unger R, Ziv T, Admon A, Levanon EY, Rosenthal JJC, Eisenberg E | Cell | 28388405 | Cell | 2017 Apr 6 |
| Site-directed RNA repair of endogenous Mecp2 RNA in neurons. | Sinnamon JR, Kim SY, Corson GM, Song Z, Nakai H, Adelman JP, Mandel G | Proceedings of the National Academy of Sciences of the United States of America | 29078406 | Proc Natl Acad Sci U S A | 2017 Oct 31 |
| Characterization of interfacial socket pressure in transhumeral prostheses: A case series. | Schofield JS, Schoepp KR, Williams HE, Carey JP, Marasco PD, Hebert JS | PloS one | 28575012 | PLoS One | 2017 |
| Characterization of the Sense of Agency over the Actions of Neural-machine Interface-operated Prostheses. | Schofield JS, Shell CE, Thumser ZC, Beckler DT, Nataraj R, Marasco PD | Journal of visualized experiments : JoVE | 30663709 | J Vis Exp | 2019 Jan 7 |
| The effect of biomechanical variables on force sensitive resistor error: Implications for calibration and improved accuracy. | Schofield JS, Evans KR, Hebert JS, Marasco PD, Carey JP | Journal of biomechanics | 26903413 | J Biomech | 2016 Mar 21 |
| Illusory movement perception improves motor control for prosthetic hands. | Marasco PD, Hebert JS, Sensinger JW, Shell CE, Schofield JS, Thumser ZC, Nataraj R, Beckler DT, Dawson MR, Blustein DH, Gill S, Mensh BD, Granja-Vazquez R, Newcomb MD, Carey JP, Orzell BM | Science translational medicine | 29540617 | Sci Transl Med | 2018 Mar 14 |
| Using proprioception to get a better grasp on embodiment. | Marasco PD | The Journal of physiology | 29194626 | J Physiol | 2018 Jan 15 |
| Advances in the measurement of prosthetic socket interface mechanics: a review of technology, techniques, and a 20-year update. | Young PR, Hebert JS, Marasco PD, Carey JP, Schofield JS | Expert review of medical devices | 37537898 | Expert Rev Med Devices | 2023 Jul-Dec |
| Characterizing the effects of amplitude, frequency and limb position on vibration induced movement illusions: Implications in sensory-motor rehabilitation. | Schofield JS, Dawson MR, Carey JP, Hebert JS | Technology and health care : official journal of the European Society for Engineering and Medicine | 25425585 | Technol Health Care | 2015 |
| The neural response properties and cortical organization of a rapidly adapting muscle sensory group response that overlaps with the frequencies that elicit the kinesthetic illusion. | Marasco PD, Bourbeau DJ, Shell CE, Granja-Vazquez R, Ina JG | PloS one | 29182648 | PLoS One | 2017 |
| Crossmodal congruency effect scores decrease with repeat test exposure. | Blustein D, Gill S, Wilson A, Sensinger J | PeerJ | 31179180 | PeerJ | 2019 |
| Intraoperative monitoring of neuromuscular function with soft, skin-mounted wireless devices. | Liu Y, Tian L, Raj MS, Cotton M, Ma Y, Ma S, McGrane B, Pendharkar AV, Dahaleh N, Olson L, Luan H, Block O, Suleski B, Zhou Y, Jayaraman C, Koski T, Aranyosi AJ, Wright JA, Jayaraman A, Huang Y, Ghaffari R, Kliot M, Rogers JA | NPJ digital medicine | 30882044 | NPJ Digit Med | 2018 |
| Battery-free, fully implantable optofluidic cuff system for wireless optogenetic and pharmacological neuromodulation of peripheral nerves. | Zhang Y, Mickle AD, Gutruf P, McIlvried LA, Guo H, Wu Y, Golden JP, Xue Y, Grajales-Reyes JG, Wang X, Krishnan S, Xie Y, Peng D, Su CJ, Zhang F, Reeder JT, Vogt SK, Huang Y, Rogers JA, Gereau RW 4th | Science advances | 31281895 | Sci Adv | 2019 Jul |
| Optogenetic Induction of Colonic Motility in Mice. | Hibberd TJ, Feng J, Luo J, Yang P, Samineni VK, Gereau RW 4th, Kelley N, Hu H, Spencer NJ | Gastroenterology | 29782847 | Gastroenterology | 2018 Aug |
| Optodynamic simulation of β-adrenergic receptor signalling. | Siuda ER, McCall JG, Al-Hasani R, Shin G, Il Park S, Schmidt MJ, Anderson SL, Planer WJ, Rogers JA, Bruchas MR | Nature communications | 26412387 | Nat Commun | 2015 Sep 28 |
| Wireless Optofluidic Systems for Programmable In Vivo Pharmacology and Optogenetics. | Jeong JW, McCall JG, Shin G, Zhang Y, Al-Hasani R, Kim M, Li S, Sim JY, Jang KI, Shi Y, Hong DY, Liu Y, Schmitz GP, Xia L, He Z, Gamble P, Ray WZ, Huang Y, Bruchas MR, Rogers JA | Cell | 26189679 | Cell | 2015 Jul 30 |
| Spotlight on pain: optogenetic approaches for interrogating somatosensory circuits. | Copits BA, Pullen MY, Gereau RW 4th | Pain | 27340912 | Pain | 2016 Nov |
| Soft, stretchable, fully implantable miniaturized optoelectronic systems for wireless optogenetics. | Park SI, Brenner DS, Shin G, Morgan CD, Copits BA, Chung HU, Pullen MY, Noh KN, Davidson S, Oh SJ, Yoon J, Jang KI, Samineni VK, Norman M, Grajales-Reyes JG, Vogt SK, Sundaram SS, Wilson KM, Ha JS, Xu R, Pan T, Kim TI, Huang Y, Montana MC, Golden JP, Bruchas MR, Gereau RW 4th, Rogers JA | Nature biotechnology | 26551059 | Nat Biotechnol | 2015 Dec |
| Distinct Subpopulations of Nucleus Accumbens Dynorphin Neurons Drive Aversion and Reward. | Al-Hasani R, McCall JG, Shin G, Gomez AM, Schmitz GP, Bernardi JM, Pyo CO, Park SI, Marcinkiewcz CM, Crowley NA, Krashes MJ, Lowell BB, Kash TL, Rogers JA, Bruchas MR | Neuron | 26335648 | Neuron | 2015 Sep 2 |
| Ultraminiaturized photovoltaic and radio frequency powered optoelectronic systems for wireless optogenetics. | Park SI, Shin G, Banks A, McCall JG, Siuda ER, Schmidt MJ, Chung HU, Noh KN, Mun JG, Rhodes J, Bruchas MR, Rogers JA | Journal of neural engineering | 26193450 | J Neural Eng | 2015 Oct |
| Stretchable multichannel antennas in soft wireless optoelectronic implants for optogenetics. | Park SI, Shin G, McCall JG, Al-Hasani R, Norris A, Xia L, Brenner DS, Noh KN, Bang SY, Bhatti DL, Jang KI, Kang SK, Mickle AD, Dussor G, Price TJ, Gereau RW 4th, Bruchas MR, Rogers JA | Proceedings of the National Academy of Sciences of the United States of America | 27911798 | Proc Natl Acad Sci U S A | 2016 Dec 13 |
| A dynamic set point for thermal adaptation requires phospholipase C-mediated regulation of TRPM8 in vivo. | Brenner DS, Golden JP, Vogt SK, Dhaka A, Story GM, Gereau RW IV | Pain | 25109670 | Pain | 2014 Oct |
| A technique to measure cold adaptation in freely behaving mice. | Brenner DS, Vogt SK, Gereau RW 4th | Journal of neuroscience methods | 25128723 | J Neurosci Methods | 2014 Oct 30 |
| Spatiotemporal control of opioid signaling and behavior. | Siuda ER, Copits BA, Schmidt MJ, Baird MA, Al-Hasani R, Planer WJ, Funderburk SC, McCall JG, Gereau RW 4th, Bruchas MR | Neuron | 25937173 | Neuron | 2015 May 20 |
| A wireless closed-loop system for optogenetic peripheral neuromodulation. | Mickle AD, Won SM, Noh KN, Yoon J, Meacham KW, Xue Y, McIlvried LA, Copits BA, Samineni VK, Crawford KE, Kim DH, Srivastava P, Kim BH, Min S, Shiuan Y, Yun Y, Payne MA, Zhang J, Jang H, Li Y, Lai HH, Huang Y, Park SI, Gereau RW 4th, Rogers JA | Nature | 30602791 | Nature | 2019 Jan |
| Optogenetic silencing of nociceptive primary afferents reduces evoked and ongoing bladder pain. | Samineni VK, Mickle AD, Yoon J, Grajales-Reyes JG, Pullen MY, Crawford KE, Noh KN, Gereau GB, Vogt SK, Lai HH, Rogers JA, Gereau RW 4th | Scientific reports | 29158567 | Sci Rep | 2017 Nov 20 |
| A bright future? Optogenetics in the periphery for pain research and therapy. | Mickle AD, Gereau RW 4th | Pain | 30113949 | Pain | 2018 Sep |
| Fabrication and application of flexible, multimodal light-emitting devices for wireless optogenetics. | McCall JG, Kim TI, Shin G, Huang X, Jung YH, Al-Hasani R, Omenetto FG, Bruchas MR, Rogers JA | Nature protocols | 24202555 | Nat Protoc | 2013 Dec |
| Fully implantable, battery-free wireless optoelectronic devices for spinal optogenetics. | Samineni VK, Yoon J, Crawford KE, Jeong YR, McKenzie KC, Shin G, Xie Z, Sundaram SS, Li Y, Yang MY, Kim J, Wu D, Xue Y, Feng X, Huang Y, Mickle AD, Banks A, Ha JS, Golden JP, Rogers JA, Gereau RW 4th | Pain | 28700536 | Pain | 2017 Nov |
| Miniaturized, Battery-Free Optofluidic Systems with Potential for Wireless Pharmacology and Optogenetics. | Noh KN, Park SI, Qazi R, Zou Z, Mickle AD, Grajales-Reyes JG, Jang KI, Gereau RW 4th, Xiao J, Rogers JA, Jeong JW | Small (Weinheim an der Bergstrasse, Germany) | 29215787 | Small | 2018 Jan |
| Differential Regulation of Bladder Pain and Voiding Function by Sensory Afferent Populations Revealed by Selective Optogenetic Activation. | DeBerry JJ, Samineni VK, Copits BA, Sullivan CJ, Vogt SK, Albers KM, Davis BM, Gereau RW IV | Frontiers in integrative neuroscience | 29483864 | Front Integr Neurosci | 2018 |
| Injectable, cellular-scale optoelectronics with applications for wireless optogenetics. | Kim TI, McCall JG, Jung YH, Huang X, Siuda ER, Li Y, Song J, Song YM, Pao HA, Kim RH, Lu C, Lee SD, Song IS, Shin G, Al-Hasani R, Kim S, Tan MP, Huang Y, Omenetto FG, Rogers JA, Bruchas MR | Science (New York, N.Y.) | 23580530 | Science | 2013 Apr 12 |
| Erratum: Thermal analysis of injectable, cellular-scale optoelectronics with pulsed power. | Li Y, Shi X, Song J, Lü C, Kim TI, McCall JG, Bruchas MR, Rogers JA, Huang Y | Proceedings. Mathematical, physical, and engineering sciences | 24062627 | Proc Math Phys Eng Sci | 2013 Sep 8 |
| Flexible Near-Field Wireless Optoelectronics as Subdermal Implants for Broad Applications in Optogenetics. | Shin G, Gomez AM, Al-Hasani R, Jeong YR, Kim J, Xie Z, Banks A, Lee SM, Han SY, Yoo CJ, Lee JL, Lee SH, Kurniawan J, Tureb J, Guo Z, Yoon J, Park SI, Bang SY, Nam Y, Walicki MC, Samineni VK, Mickle AD, Lee K, Heo SY, McCall JG, Pan T, Wang L, Feng X, Kim TI, Kim JK, Li Y, Huang Y, Gereau RW 4th, Ha JS, Bruchas MR, Rogers JA | Neuron | 28132830 | Neuron | 2017 Feb 8 |
| Divergent Modulation of Nociception by Glutamatergic and GABAergic Neuronal Subpopulations in the Periaqueductal Gray. | Samineni VK, Grajales-Reyes JG, Copits BA, O'Brien DE, Trigg SL, Gomez AM, Bruchas MR, Gereau RW 4th | eNeuro | 28374016 | eNeuro | 2017 Mar-Apr |
| RNA protein interaction in neurons. | Darnell RB | Annual review of neuroscience | 23701460 | Annu Rev Neurosci | 2013 Jul 8 |
| A Broad RNA Virus Survey Reveals Both miRNA Dependence and Functional Sequestration. | Scheel TK, Luna JM, Liniger M, Nishiuchi E, Rozen-Gagnon K, Shlomai A, Auray G, Gerber M, Fak J, Keller I, Bruggmann R, Darnell RB, Ruggli N, Rice CM | Cell host & microbe | 26962949 | Cell Host Microbe | 2016 Mar 9 |
| Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk. | Zhou J, Park CY, Theesfeld CL, Wong AK, Yuan Y, Scheckel C, Fak JJ, Funk J, Yao K, Tajima Y, Packer A, Darnell RB, Troyanskaya OG | Nature genetics | 31133750 | Nat Genet | 2019 Jun |
| HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism. | Weyn-Vanhentenryck SM, Mele A, Yan Q, Sun S, Farny N, Zhang Z, Xue C, Herre M, Silver PA, Zhang MQ, Krainer AR, Darnell RB, Zhang C | Cell reports | 24613350 | Cell Rep | 2014 Mar 27 |
| Progressive impairment of muscle regeneration in muscleblind-like 3 isoform knockout mice. | Poulos MG, Batra R, Li M, Yuan Y, Zhang C, Darnell RB, Swanson MS | Human molecular genetics | 23660517 | Hum Mol Genet | 2013 Sep 1 |
| Prediction of clustered RNA-binding protein motif sites in the mammalian genome. | Zhang C, Lee KY, Swanson MS, Darnell RB | Nucleic acids research | 23685613 | Nucleic Acids Res | 2013 Aug |
| cTag-PAPERCLIP Reveals Alternative Polyadenylation Promotes Cell-Type Specific Protein Diversity and Shifts Araf Isoforms with Microglia Activation. | Hwang HW, Saito Y, Park CY, Blachère NE, Tajima Y, Fak JJ, Zucker-Scharff I, Darnell RB | Neuron | 28910620 | Neuron | 2017 Sep 13 |
| PAPERCLIP Identifies MicroRNA Targets and a Role of CstF64/64tau in Promoting Non-canonical poly(A) Site Usage. | Hwang HW, Park CY, Goodarzi H, Fak JJ, Mele A, Moore MJ, Saito Y, Darnell RB | Cell reports | 27050522 | Cell Rep | 2016 Apr 12 |
| A majority of m6A residues are in the last exons, allowing the potential for 3' UTR regulation. | Ke S, Alemu EA, Mertens C, Gantman EC, Fak JJ, Mele A, Haripal B, Zucker-Scharff I, Moore MJ, Park CY, Vågbø CB, Kusśnierczyk A, Klungland A, Darnell JE Jr, Darnell RB | Genes & development | 26404942 | Genes Dev | 2015 Oct 1 |
| Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability. | Ince-Dunn G, Okano HJ, Jensen KB, Park WY, Zhong R, Ule J, Mele A, Fak JJ, Yang C, Zhang C, Yoo J, Herre M, Okano H, Noebels JL, Darnell RB | Neuron | 22998874 | Neuron | 2012 Sep 20 |
| BET protein Brd4 activates transcription in neurons and BET inhibitor Jq1 blocks memory in mice. | Korb E, Herre M, Zucker-Scharff I, Darnell RB, Allis CD | Nature neuroscience | 26301327 | Nat Neurosci | 2015 Oct |
| Blood transcriptomic signatures associated with molecular changes in the brain and clinical outcomes in Parkinson's disease. | Irmady K, Hale CR, Qadri R, Fak J, Simelane S, Carroll T, Przedborski S, Darnell RB | Nature communications | 37407548 | Nat Commun | 2023 Jul 5 |
| NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure. | Eom T, Zhang C, Wang H, Lay K, Fak J, Noebels JL, Darnell RB | eLife | 23359859 | Elife | 2013 Jan 22 |
| Transcriptome-wide miR-155 binding map reveals widespread noncanonical microRNA targeting. | Loeb GB, Khan AA, Canner D, Hiatt JB, Shendure J, Darnell RB, Leslie CS, Rudensky AY | Molecular cell | 23142080 | Mol Cell | 2012 Dec 14 |
| Loss of the multifunctional RNA-binding protein RBM47 as a source of selectable metastatic traits in breast cancer. | Vanharanta S, Marney CB, Shu W, Valiente M, Zou Y, Mele A, Darnell RB, Massagué J | eLife | 24898756 | Elife | 2014 Jun 4 |
| Differential NOVA2-Mediated Splicing in Excitatory and Inhibitory Neurons Regulates Cortical Development and Cerebellar Function. | Saito Y, Yuan Y, Zucker-Scharff I, Fak JJ, Jereb S, Tajima Y, Licatalosi DD, Darnell RB | Neuron | 30638744 | Neuron | 2019 Feb 20 |
| The Genetic Control of Stoichiometry Underlying Autism. | Darnell RB | Annual review of neuroscience | 32640929 | Annu Rev Neurosci | 2020 Jul 8 |
| RNA Identification of PRIME Cells Predicting Rheumatoid Arthritis Flares. | Orange DE, Yao V, Sawicka K, Fak J, Frank MO, Parveen S, Blachere NE, Hale C, Zhang F, Raychaudhuri S, Troyanskaya OG, Darnell RB | The New England journal of medicine | 32668112 | N Engl J Med | 2020 Jul 16 |
| PRIME Cells Predicting Rheumatoid Arthritis Flares. Reply. | Orange DE, Darnell RB | The New England journal of medicine | 33053295 | N Engl J Med | 2020 Oct 15 |
| AGO CLIP Reveals an Activated Network for Acute Regulation of Brain Glutamate Homeostasis in Ischemic Stroke. | Kobayashi M, Benakis C, Anderson C, Moore MJ, Poon C, Uekawa K, Dyke JP, Fak JJ, Mele A, Park CY, Zhou P, Anrather J, Iadecola C, Darnell RB | Cell reports | 31340158 | Cell Rep | 2019 Jul 23 |
| NOVA1 acts on Impact to regulate hypothalamic function and translation in inhibitory neurons. | Tajima Y, Ito K, Yuan Y, Frank MO, Saito Y, Darnell RB | Cell reports | 36716149 | Cell Rep | 2023 Feb 28 |
| Microexons--tiny but mighty. | Scheckel C, Darnell RB | The EMBO journal | 25535247 | EMBO J | 2015 Feb 3 |
| Hepatitis C virus RNA functionally sequesters miR-122. | Luna JM, Scheel TK, Danino T, Shaw KS, Mele A, Fak JJ, Nishiuchi E, Takacs CN, Catanese MT, de Jong YP, Jacobson IM, Rice CM, Darnell RB | Cell | 25768906 | Cell | 2015 Mar 12 |
| Mapping Argonaute and conventional RNA-binding protein interactions with RNA at single-nucleotide resolution using HITS-CLIP and CIMS analysis. | Moore MJ, Zhang C, Gantman EC, Mele A, Darnell JC, Darnell RB | Nature protocols | 24407355 | Nat Protoc | 2014 Feb |
| NOVA2-mediated RNA regulation is required for axonal pathfinding during development. | Saito Y, Miranda-Rottmann S, Ruggiu M, Park CY, Fak JJ, Zhong R, Duncan JS, Fabella BA, Junge HJ, Chen Z, Araya R, Fritzsch B, Hudspeth AJ, Darnell RB | eLife | 27223325 | Elife | 2016 May 25 |
| NOVA regulates Dcc alternative splicing during neuronal migration and axon guidance in the spinal cord. | Leggere JC, Saito Y, Darnell RB, Tessier-Lavigne M, Junge HJ, Chen Z | eLife | 27223328 | Elife | 2016 May 25 |
| Regulatory consequences of neuronal ELAV-like protein binding to coding and non-coding RNAs in human brain. | Scheckel C, Drapeau E, Frias MA, Park CY, Fak J, Zucker-Scharff I, Kou Y, Haroutunian V, Ma'ayan A, Buxbaum JD, Darnell RB | eLife | 26894958 | Elife | 2016 Feb 19 |
| FMRP regulates mRNAs encoding distinct functions in the cell body and dendrites of CA1 pyramidal neurons. | Hale CR, Sawicka K, Mora K, Fak JJ, Kang JJ, Cutrim P, Cialowicz K, Carroll TS, Darnell RB | eLife | 34939924 | Elife | 2021 Dec 23 |
| Immune Escape via a Transient Gene Expression Program Enables Productive Replication of a Latent Pathogen. | Linderman JA, Kobayashi M, Rayannavar V, Fak JJ, Darnell RB, Chao MV, Wilson AC, Mohr I | Cell reports | 28147283 | Cell Rep | 2017 Jan 31 |
| NOVA1 acts as an oncogenic RNA-binding protein to regulate cholesterol homeostasis in human glioblastoma cells. | Saito Y, Yang Y, Saito M, Park CY, Funato K, Tabar V, Darnell RB | Proceedings of the National Academy of Sciences of the United States of America | 38416679 | Proc Natl Acad Sci U S A | 2024 Mar 5 |
| Neuronal activity rapidly reprograms dendritic translation via eIF4G2:uORF binding. | Hacisuleyman E, Hale CR, Noble N, Luo JD, Fak JJ, Saito M, Chen J, Weissman JS, Darnell RB | Nature neuroscience | 38589584 | Nat Neurosci | 2024 May |
| T cells targeting a neuronal paraneoplastic antigen mediate tumor rejection and trigger CNS autoimmunity with humoral activation. | Blachère NE, Orange DE, Santomasso BD, Doerner J, Foo PK, Herre M, Fak J, Monette S, Gantman EC, Frank MO, Darnell RB | European journal of immunology | 25103845 | Eur J Immunol | 2014 Nov |
| Differential 3' Processing of Specific Transcripts Expands Regulatory and Protein Diversity Across Neuronal Cell Types. | Jereb S, Hwang HW, Van Otterloo E, Govek EE, Fak JJ, Yuan Y, Hatten ME, Darnell RB | eLife | 29578408 | Elife | 2018 Mar 26 |
| Excess Translation of Epigenetic Regulators Contributes to Fragile X Syndrome and Is Alleviated by Brd4 Inhibition. | Korb E, Herre M, Zucker-Scharff I, Gresack J, Allis CD, Darnell RB | Cell | 28823556 | Cell | 2017 Sep 7 |
| Comprehensive Identification of mRNA Polyadenylation Sites by PAPERCLIP. | Hwang HW, Darnell RB | Methods in molecular biology (Clifton, N.J.) | 28766291 | Methods Mol Biol | 2017 |
| Argonaute CLIP Defines a Deregulated miR-122-Bound Transcriptome that Correlates with Patient Survival in Human Liver Cancer. | Luna JM, Barajas JM, Teng KY, Sun HL, Moore MJ, Rice CM, Darnell RB, Ghoshal K | Molecular cell | 28735896 | Mol Cell | 2017 Aug 3 |
| m(6)A mRNA modifications are deposited in nascent pre-mRNA and are not required for splicing but do specify cytoplasmic turnover. | Ke S, Pandya-Jones A, Saito Y, Fak JJ, Vågbø CB, Geula S, Hanna JH, Black DL, Darnell JE Jr, Darnell RB | Genes & development | 28637692 | Genes Dev | 2017 May 15 |
| ZFP36 RNA-binding proteins restrain T cell activation and anti-viral immunity. | Moore MJ, Blachere NE, Fak JJ, Park CY, Sawicka K, Parveen S, Zucker-Scharff I, Moltedo B, Rudensky AY, Darnell RB | eLife | 29848443 | Elife | 2018 May 31 |
| miRNA-target chimeras reveal miRNA 3'-end pairing as a major determinant of Argonaute target specificity. | Moore MJ, Scheel TK, Luna JM, Park CY, Fak JJ, Nishiuchi E, Rice CM, Darnell RB | Nature communications | 26602609 | Nat Commun | 2015 Nov 25 |
| FMRP has a cell-type-specific role in CA1 pyramidal neurons to regulate autism-related transcripts and circadian memory. | Sawicka K, Hale CR, Park CY, Fak JJ, Gresack JE, Van Driesche SJ, Kang JJ, Darnell JC, Darnell RB | eLife | 31860442 | Elife | 2019 Dec 20 |
| Human Astrocyte Maturation Captured in 3D Cerebral Cortical Spheroids Derived from Pluripotent Stem Cells. | Sloan SA, Darmanis S, Huber N, Khan TA, Birey F, Caneda C, Reimer R, Quake SR, Barres BA, Paşca SP | Neuron | 28817799 | Neuron | 2017 Aug 16 |
| Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse. | Zhang Y, Sloan SA, Clarke LE, Caneda C, Plaza CA, Blumenthal PD, Vogel H, Steinberg GK, Edwards MS, Li G, Duncan JA 3rd, Cheshier SH, Shuer LM, Chang EF, Grant GA, Gephart MG, Barres BA | Neuron | 26687838 | Neuron | 2016 Jan 6 |
| Single-Cell RNA-Seq Analysis of Infiltrating Neoplastic Cells at the Migrating Front of Human Glioblastoma. | Darmanis S, Sloan SA, Croote D, Mignardi M, Chernikova S, Samghababi P, Zhang Y, Neff N, Kowarsky M, Caneda C, Li G, Chang SD, Connolly ID, Li Y, Barres BA, Gephart MH, Quake SR | Cell reports | 29091775 | Cell Rep | 2017 Oct 31 |
| A survey of human brain transcriptome diversity at the single cell level. | Darmanis S, Sloan SA, Zhang Y, Enge M, Caneda C, Shuer LM, Hayden Gephart MG, Barres BA, Quake SR | Proceedings of the National Academy of Sciences of the United States of America | 26060301 | Proc Natl Acad Sci U S A | 2015 Jun 9 |
| An RNA-sequencing transcriptome and splicing database of glia, neurons, and vascular cells of the cerebral cortex. | Zhang Y, Chen K, Sloan SA, Bennett ML, Scholze AR, O'Keeffe S, Phatnani HP, Guarnieri P, Caneda C, Ruderisch N, Deng S, Liddelow SA, Zhang C, Daneman R, Maniatis T, Barres BA, Wu JQ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 25186741 | J Neurosci | 2014 Sep 3 |
| Comprehensive Identification of Long Non-coding RNAs in Purified Cell Types from the Brain Reveals Functional LncRNA in OPC Fate Determination. | Dong X, Chen K, Cuevas-Diaz Duran R, You Y, Sloan SA, Zhang Y, Zong S, Cao Q, Barres BA, Wu JQ | PLoS genetics | 26683846 | PLoS Genet | 2015 Dec |
| Saturated Reconstruction of a Volume of Neocortex. | Kasthuri N, Hayworth KJ, Berger DR, Schalek RL, Conchello JA, Knowles-Barley S, Lee D, Vázquez-Reina A, Kaynig V, Jones TR, Roberts M, Morgan JL, Tapia JC, Seung HS, Roncal WG, Vogelstein JT, Burns R, Sussman DL, Priebe CE, Pfister H, Lichtman JW | Cell | 26232230 | Cell | 2015 Jul 30 |
| Reconstruction of genetically identified neurons imaged by serial-section electron microscopy. | Joesch M, Mankus D, Yamagata M, Shahbazi A, Schalek R, Suissa-Peleg A, Meister M, Lichtman JW, Scheirer WJ, Sanes JR | eLife | 27383271 | Elife | 2016 Jul 7 |
| An Individual Interneuron Participates in Many Kinds of Inhibition and Innervates Much of the Mouse Visual Thalamus. | Morgan JL, Lichtman JW | Neuron | 32142646 | Neuron | 2020 May 6 |
| The Fuzzy Logic of Network Connectivity in Mouse Visual Thalamus. | Morgan JL, Berger DR, Wetzel AW, Lichtman JW | Cell | 27015312 | Cell | 2016 Mar 24 |
| Neural Circuit Inference from Function to Structure. | Real E, Asari H, Gollisch T, Meister M | Current biology : CB | 28065610 | Curr Biol | 2017 Jan 23 |
| Digital Museum of Retinal Ganglion Cells with Dense Anatomy and Physiology. | Bae JA, Mu S, Kim JS, Turner NL, Tartavull I, Kemnitz N, Jordan CS, Norton AD, Silversmith WM, Prentki R, Sorek M, David C, Jones DL, Bland D, Sterling ALR, Park J, Briggman KL, Seung HS, Eyewirers | Cell | 29775596 | Cell | 2018 May 17 |
| Imaging ATUM ultrathin section libraries with WaferMapper: a multi-scale approach to EM reconstruction of neural circuits. | Hayworth KJ, Morgan JL, Schalek R, Berger DR, Hildebrand DG, Lichtman JW | Frontiers in neural circuits | 25018701 | Front Neural Circuits | 2014 |
| NeuroLines: A Subway Map Metaphor for Visualizing Nanoscale Neuronal Connectivity. | Al-Awami AK, Beyer J, Strobelt H, Kasthuri N, Lichtman JW, Pfister H, Hadwiger M | IEEE transactions on visualization and computer graphics | 26356951 | IEEE Trans Vis Comput Graph | 2014 Dec |
| Design and Evaluation of Interactive Proofreading Tools for Connectomics. | Haehn D, Knowles-Barley S, Roberts M, Beyer J, Kasthuri N, Lichtman JW, Pfister H | IEEE transactions on visualization and computer graphics | 26356960 | IEEE Trans Vis Comput Graph | 2014 Dec |
| Electron Microscopic Reconstruction of Functionally Identified Cells in a Neural Integrator. | Vishwanathan A, Daie K, Ramirez AD, Lichtman JW, Aksay ERF, Seung HS | Current biology : CB | 28712570 | Curr Biol | 2017 Jul 24 |
| Methods for Mapping Neuronal Activity to Synaptic Connectivity: Lessons From Larval Zebrafish. | Wanner AA, Vishwanathan A | Frontiers in neural circuits | 30410437 | Front Neural Circuits | 2018 |
| Multispectral tracing in densely labeled mouse brain with nTracer. | Roossien DH, Sadis BV, Yan Y, Webb JM, Min LY, Dizaji AS, Bogart LJ, Mazuski C, Huth RS, Stecher JS, Akula S, Shen F, Li Y, Xiao T, Vandenbrink M, Lichtman JW, Hensch TK, Herzog ED, Cai D | Bioinformatics (Oxford, England) | 30715234 | Bioinformatics | 2019 Sep 15 |
| Why not connectomics? | Morgan JL, Lichtman JW | Nature methods | 23722208 | Nat Methods | 2013 Jun |
| Space-time wiring specificity supports direction selectivity in the retina. | Kim JS, Greene MJ, Zlateski A, Lee K, Richardson M, Turaga SC, Purcaro M, Balkam M, Robinson A, Behabadi BF, Campos M, Denk W, Seung HS, EyeWirers | Nature | 24805243 | Nature | 2014 May 15 |
| Neuronal cell types and connectivity: lessons from the retina. | Seung HS, Sümbül U | Neuron | 25233310 | Neuron | 2014 Sep 17 |
| The big data challenges of connectomics. | Lichtman JW, Pfister H, Shavit N | Nature neuroscience | 25349911 | Nat Neurosci | 2014 Nov |
| Digital tissue and what it may reveal about the brain. | Morgan JL, Lichtman JW | BMC biology | 29084528 | BMC Biol | 2017 Oct 30 |
| Developmental Rewiring between Cerebellar Climbing Fibers and Purkinje Cells Begins with Positive Feedback Synapse Addition. | Wilson AM, Schalek R, Suissa-Peleg A, Jones TR, Knowles-Barley S, Pfister H, Lichtman JW | Cell reports | 31775050 | Cell Rep | 2019 Nov 26 |
| Clarifying Tissue Clearing. | Richardson DS, Lichtman JW | Cell | 26186186 | Cell | 2015 Jul 16 |
| Analogous Convergence of Sustained and Transient Inputs in Parallel On and Off Pathways for Retinal Motion Computation. | Greene MJ, Kim JS, Seung HS, EyeWirers | Cell reports | 26904938 | Cell Rep | 2016 Mar 1 |
| Large-scale automatic reconstruction of neuronal processes from electron microscopy images. | Kaynig V, Vazquez-Reina A, Knowles-Barley S, Roberts M, Jones TR, Kasthuri N, Miller E, Lichtman J, Pfister H | Medical image analysis | 25791436 | Med Image Anal | 2015 May |
| Fuz mutant mice reveal shared mechanisms between ciliopathies and FGF-related syndromes. | Tabler JM, Barrell WB, Szabo-Rogers HL, Healy C, Yeung Y, Perdiguero EG, Schulz C, Yannakoudakis BZ, Mesbahi A, Wlodarczyk B, Geissmann F, Finnell RH, Wallingford JB, Liu KJ | Developmental cell | 23806618 | Dev Cell | 2013 Jun 24 |
| New Techniques for the Study of Neural Tube Defects. | Lei Y, Finnell RH | Advanced techniques in biology & medicine | 27066597 | Adv Tech Biol Med | 2016 Feb |
| Roles for small noncoding RNAs in silencing of retrotransposons in the mammalian brain. | Nandi S, Chandramohan D, Fioriti L, Melnick AM, Hébert JM, Mason CE, Rajasethupathy P, Kandel ER | Proceedings of the National Academy of Sciences of the United States of America | 27791114 | Proc Natl Acad Sci U S A | 2016 Nov 8 |
| Enabling large-scale next-generation sequence assembly with Blacklight. | Couger MB, Pipes L, Squina F, Prade R, Siepel A, Palermo R, Katze MG, Mason CE, Blood PD | Concurrency and computation : practice & experience | 25294974 | Concurr Comput | 2014 Sep 10 |
| The Impact of Heterogeneity on Single-Cell Sequencing. | Goldman SL, MacKay M, Afshinnekoo E, Melnick AM, Wu S, Mason CE | Frontiers in genetics | 30881372 | Front Genet | 2019 |
| Epigenetic Modifications in Acute Myeloid Leukemia: Prognosis, Treatment, and Heterogeneity. | Goldman SL, Hassan C, Khunte M, Soldatenko A, Jong Y, Afshinnekoo E, Mason CE | Frontiers in genetics | 30881380 | Front Genet | 2019 |
| Identification of novel CELSR1 mutations in spina bifida. | Lei Y, Zhu H, Yang W, Ross ME, Shaw GM, Finnell RH | PloS one | 24632739 | PLoS One | 2014 |
| The birth of the Epitranscriptome: deciphering the function of RNA modifications. | Saletore Y, Meyer K, Korlach J, Vilfan ID, Jaffrey S, Mason CE | Genome biology | 23113984 | Genome Biol | 2012 Oct 31 |
| methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. | Akalin A, Kormaksson M, Li S, Garrett-Bakelman FE, Figueroa ME, Melnick A, Mason CE | Genome biology | 23034086 | Genome Biol | 2012 Oct 3 |
| High-throughput RNA sequencing reveals structural differences of orthologous brain-expressed genes between western lowland gorillas and humans. | Lipovich L, Hou ZC, Jia H, Sinkler C, McGowen M, Sterner KN, Weckle A, Sugalski AB, Pipes L, Gatti DL, Mason CE, Sherwood CC, Hof PR, Kuzawa CW, Grossman LI, Goodman M, Wildman DE | The Journal of comparative neurology | 26132897 | J Comp Neurol | 2016 Feb 1 |
| Rfx2 is required for spermatogenesis in the mouse. | Shawlot W, Vazquez-Chantada M, Wallingford JB, Finnell RH | Genesis (New York, N.Y. : 2000) | 26248850 | Genesis | 2015 Sep |
| The impact of read length on quantification of differentially expressed genes and splice junction detection. | Chhangawala S, Rudy G, Mason CE, Rosenfeld JA | Genome biology | 26100517 | Genome Biol | 2015 Jun 23 |
| Identification of kinase fusion oncogenes in post-Chernobyl radiation-induced thyroid cancers. | Ricarte-Filho JC, Li S, Garcia-Rendueles ME, Montero-Conde C, Voza F, Knauf JA, Heguy A, Viale A, Bogdanova T, Thomas GA, Mason CE, Fagin JA | The Journal of clinical investigation | 24135138 | J Clin Invest | 2013 Nov |
| Single-nucleotide-resolution mapping of m6A and m6Am throughout the transcriptome. | Linder B, Grozhik AV, Olarerin-George AO, Meydan C, Mason CE, Jaffrey SR | Nature methods | 26121403 | Nat Methods | 2015 Aug |
| Analysis of archived residual newborn screening blood spots after whole genome amplification. | Cantarel BL, Lei Y, Weaver D, Zhu H, Farrell A, Benstead-Hume G, Reese J, Finnell RH | BMC genomics | 26268606 | BMC Genomics | 2015 Aug 13 |
| Extensive sequencing of seven human genomes to characterize benchmark reference materials. | Zook JM, Catoe D, McDaniel J, Vang L, Spies N, Sidow A, Weng Z, Liu Y, Mason CE, Alexander N, Henaff E, McIntyre AB, Chandramohan D, Chen F, Jaeger E, Moshrefi A, Pham K, Stedman W, Liang T, Saghbini M, Dzakula Z, Hastie A, Cao H, Deikus G, Schadt E, Sebra R, Bashir A, Truty RM, Chang CC, Gulbahce N, Zhao K, Ghosh S, Hyland F, Fu Y, Chaisson M, Xiao C, Trow J, Sherry ST, Zaranek AW, Ball M, Bobe J, Estep P, Church GM, Marks P, Kyriazopoulou-Panagiotopoulou S, Zheng GX, Schnall-Levin M, Ordonez HS, Mudivarti PA, Giorda K, Sheng Y, Rypdal KB, Salit M | Scientific data | 27271295 | Sci Data | 2016 Jun 7 |
| Performance assessment of DNA sequencing platforms in the ABRF Next-Generation Sequencing Study. | Foox J, Tighe SW, Nicolet CM, Zook JM, Byrska-Bishop M, Clarke WE, Khayat MM, Mahmoud M, Laaguiby PK, Herbert ZT, Warner D, Grills GS, Jen J, Levy S, Xiang J, Alonso A, Zhao X, Zhang W, Teng F, Zhao Y, Lu H, Schroth GP, Narzisi G, Farmerie W, Sedlazeck FJ, Baldwin DA, Mason CE | Nature biotechnology | 34504351 | Nat Biotechnol | 2021 Sep |
| Genome-wide investigation identifies a rare copy-number variant burden associated with human spina bifida. | Wolujewicz P, Aguiar-Pulido V, AbdelAleem A, Nair V, Thareja G, Suhre K, Shaw GM, Finnell RH, Elemento O, Ross ME | Genetics in medicine : official journal of the American College of Medical Genetics | 33686259 | Genet Med | 2021 Jul |
| CIC missense variants contribute to susceptibility for spina bifida. | Han X, Cao X, Aguiar-Pulido V, Yang W, Karki M, Ramirez PAP, Cabrera RM, Lin YL, Wlodarczyk BJ, Shaw GM, Ross ME, Zhang C, Finnell RH, Lei Y | Human mutation | 36054333 | Hum Mutat | 2022 Dec |
| Distinct evolution and dynamics of epigenetic and genetic heterogeneity in acute myeloid leukemia. | Li S, Garrett-Bakelman FE, Chung SS, Sanders MA, Hricik T, Rapaport F, Patel J, Dillon R, Vijay P, Brown AL, Perl AE, Cannon J, Bullinger L, Luger S, Becker M, Lewis ID, To LB, Delwel R, Löwenberg B, Döhner H, Döhner K, Guzman ML, Hassane DC, Roboz GJ, Grimwade D, Valk PJ, D'Andrea RJ, Carroll M, Park CY, Neuberg D, Levine R, Melnick AM, Mason CE | Nature medicine | 27322744 | Nat Med | 2016 Jul |
| The Microbe Directory: An annotated, searchable inventory of microbes' characteristics. | Shaaban H, Westfall DA, Mohammad R, Danko D, Bezdan D, Afshinnekoo E, Segata N, Mason CE | Gates open research | 29630066 | Gates Open Res | 2018 Jan 5 |
| Folate-dependent methylation of septins governs ciliogenesis during neural tube closure. | Toriyama M, Toriyama M, Wallingford JB, Finnell RH | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 28432198 | FASEB J | 2017 Aug |
| Assessment of REPLI-g Multiple Displacement Whole Genome Amplification (WGA) Techniques for Metagenomic Applications. | Ahsanuddin S, Afshinnekoo E, Gandara J, Hakyemezoğlu M, Bezdan D, Minot S, Greenfield N, Mason CE | Journal of biomolecular techniques : JBT | 28344519 | J Biomol Tech | 2017 Apr |
| The pivotal regulatory landscape of RNA modifications. | Li S, Mason CE | Annual review of genomics and human genetics | 24898039 | Annu Rev Genomics Hum Genet | 2014 |
| Multi-platform assessment of transcriptome profiling using RNA-seq in the ABRF next-generation sequencing study. | Li S, Tighe SW, Nicolet CM, Grove D, Levy S, Farmerie W, Viale A, Wright C, Schweitzer PA, Gao Y, Kim D, Boland J, Hicks B, Kim R, Chhangawala S, Jafari N, Raghavachari N, Gandara J, Garcia-Reyero N, Hendrickson C, Roberson D, Rosenfeld J, Smith T, Underwood JG, Wang M, Zumbo P, Baldwin DA, Grills GS, Mason CE | Nature biotechnology | 25150835 | Nat Biotechnol | 2014 Sep |
| DNA hydroxymethylation profiling reveals that WT1 mutations result in loss of TET2 function in acute myeloid leukemia. | Rampal R, Alkalin A, Madzo J, Vasanthakumar A, Pronier E, Patel J, Li Y, Ahn J, Abdel-Wahab O, Shih A, Lu C, Ward PS, Tsai JJ, Hricik T, Tosello V, Tallman JE, Zhao X, Daniels D, Dai Q, Ciminio L, Aifantis I, He C, Fuks F, Tallman MS, Ferrando A, Nimer S, Paietta E, Thompson CB, Licht JD, Mason CE, Godley LA, Melnick A, Figueroa ME, Levine RL | Cell reports | 25482556 | Cell Rep | 2014 Dec 11 |
| Single-molecule sequencing detection of N6-methyladenine in microbial reference materials. | McIntyre ABR, Alexander N, Grigorev K, Bezdan D, Sichtig H, Chiu CY, Mason CE | Nature communications | 30718479 | Nat Commun | 2019 Feb 4 |
| Genome assembly and geospatial phylogenomics of the bed bug Cimex lectularius. | Rosenfeld JA, Reeves D, Brugler MR, Narechania A, Simon S, Durrett R, Foox J, Shianna K, Schatz MC, Gandara J, Afshinnekoo E, Lam ET, Hastie AR, Chan S, Cao H, Saghbini M, Kentsis A, Planet PJ, Kholodovych V, Tessler M, Baker R, DeSalle R, Sorkin LN, Kolokotronis SO, Siddall ME, Amato G, Mason CE | Nature communications | 26836631 | Nat Commun | 2016 Feb 2 |
| Performance evaluation of high-volume electret filter air samplers in aerosol microbiome research. | Bøifot KO, Gohli J, Skogan G, Dybwad M | Environmental microbiome | 33902714 | Environ Microbiome | 2020 Jul 28 |
| Dynamic evolution of clonal epialleles revealed by methclone. | Li S, Garrett-Bakelman F, Perl AE, Luger SM, Zhang C, To BL, Lewis ID, Brown AL, D'Andrea RJ, Ross ME, Levine R, Carroll M, Melnick A, Mason CE | Genome biology | 25260792 | Genome Biol | 2014 Sep 27 |
| An integrative computational approach for prioritization of genomic variants. | Dubchak I, Balasubramanian S, Wang S, Cem M, Sulakhe D, Poliakov A, Börnigen D, Xie B, Taylor A, Ma J, Paciorkowski AR, Mirzaa GM, Dave P, Agam G, Xu J, Al-Gazali L, Mason CE, Ross ME, Maltsev N, Gilliam TC | PloS one | 25506935 | PLoS One | 2014 |
| Assessment and improvement of Indian-origin rhesus macaque and Mauritian-origin cynomolgus macaque genome annotations using deep transcriptome sequencing data. | Peng X, Pipes L, Xiong H, Green RR, Jones DC, Ruzzo WL, Schroth GP, Mason CE, Palermo RE, Katze MG | Journal of medical primatology | 24810475 | J Med Primatol | 2014 Oct |
| Detecting and correcting systematic variation in large-scale RNA sequencing data. | Li S, Łabaj PP, Zumbo P, Sykacek P, Shi W, Shi L, Phan J, Wu PY, Wang M, Wang C, Thierry-Mieg D, Thierry-Mieg J, Kreil DP, Mason CE | Nature biotechnology | 25150837 | Nat Biotechnol | 2014 Sep |
| Autism-Like Behavior and Epigenetic Changes Associated with Autism as Consequences of In Utero Exposure to Environmental Pollutants in a Mouse Model. | Hill DS, Cabrera R, Wallis Schultz D, Zhu H, Lu W, Finnell RH, Wlodarczyk BJ | Behavioural neurology | 26586927 | Behav Neurol | 2015 |
| Complex translocation disrupting TCF4 and altering TCF4 isoform expression segregates as mild autosomal dominant intellectual disability. | Maduro V, Pusey BN, Cherukuri PF, Atkins P, du Souich C, Rupps R, Limbos M, Adams DR, Bhatt SS, Eydoux P, Links AE, Lehman A, Malicdan MC, Mason CE, Morimoto M, Mullikin JC, Sear A, Van Karnebeek C, Stankiewicz P, Gahl WA, Toro C, Boerkoel CF | Orphanet journal of rare diseases | 27179618 | Orphanet J Rare Dis | 2016 May 14 |
| The Power of Engaging Citizen Scientists for Scientific Progress. | Garbarino J, Mason CE | Journal of microbiology & biology education | 27047581 | J Microbiol Biol Educ | 2016 Mar |
| Autoantibodies against homocysteinylated protein in a mouse model of folate deficiency-induced neural tube defects. | Denny KJ, Kelly CF, Kumar V, Witham KL, Cabrera RM, Finnell RH, Taylor SM, Jeanes A, Woodruff TM | Birth defects research. Part A, Clinical and molecular teratology | 26900104 | Birth Defects Res A Clin Mol Teratol | 2016 Mar |
| Genomic Methods and Microbiological Technologies for Profiling Novel and Extreme Environments for the Extreme Microbiome Project (XMP). | Tighe S, Afshinnekoo E, Rock TM, McGrath K, Alexander N, McIntyre A, Ahsanuddin S, Bezdan D, Green SJ, Joye S, Stewart Johnson S, Baldwin DA, Bivens N, Ajami N, Carmical JR, Herriott IC, Colwell R, Donia M, Foox J, Greenfield N, Hunter T, Hoffman J, Hyman J, Jorgensen E, Krawczyk D, Lee J, Levy S, Garcia-Reyero N, Settles M, Thomas K, Gómez F, Schriml L, Kyrpides N, Zaikova E, Penterman J, Mason CE | Journal of biomolecular techniques : JBT | 28337070 | J Biomol Tech | 2017 Apr |
| Comprehensive analysis of mRNA methylation reveals enrichment in 3' UTRs and near stop codons. | Meyer KD, Saletore Y, Zumbo P, Elemento O, Mason CE, Jaffrey SR | Cell | 22608085 | Cell | 2012 Jun 22 |
| Neural tube defects, folate, and immune modulation. | Denny KJ, Jeanes A, Fathe K, Finnell RH, Taylor SM, Woodruff TM | Birth defects research. Part A, Clinical and molecular teratology | 24078477 | Birth Defects Res A Clin Mol Teratol | 2013 Sep |
| Characterizing multi-omic data in systems biology. | Mason CE, Porter SG, Smith TM | Advances in experimental medicine and biology | 24292960 | Adv Exp Med Biol | 2014 |
| Comprehensive evaluation of differential gene expression analysis methods for RNA-seq data. | Rapaport F, Khanin R, Liang Y, Pirun M, Krek A, Zumbo P, Mason CE, Socci ND, Betel D | Genome biology | 24020486 | Genome Biol | 2013 |
| An optimized algorithm for detecting and annotating regional differential methylation. | Li S, Garrett-Bakelman FE, Akalin A, Zumbo P, Levine R, To BL, Lewis ID, Brown AL, D'Andrea RJ, Melnick A, Mason CE | BMC bioinformatics | 23735126 | BMC Bioinformatics | 2013 |
| Characterization of the public transit air microbiome and resistome reveals geographical specificity. | Leung MHY, Tong X, Bøifot KO, Bezdan D, Butler DJ, Danko DC, Gohli J, Green DC, Hernandez MT, Kelly FJ, Levy S, Mason-Buck G, Nieto-Caballero M, Syndercombe-Court D, Udekwu K, Young BG, Mason CE, Dybwad M, Lee PKH | Microbiome | 34039416 | Microbiome | 2021 May 26 |
| The Metagenomics and Metadesign of the Subways and Urban Biomes (MetaSUB) International Consortium inaugural meeting report. | MetaSUB International Consortium | Microbiome | 27255532 | Microbiome | 2016 Jun 3 |
| Clinical Genomics: Challenges and Opportunities. | Vijay P, McIntyre AB, Mason CE, Greenfield JP, Li S | Critical reviews in eukaryotic gene expression | 27480773 | Crit Rev Eukaryot Gene Expr | 2016 |
| Combination Targeted Therapy to Disrupt Aberrant Oncogenic Signaling and Reverse Epigenetic Dysfunction in IDH2- and TET2-Mutant Acute Myeloid Leukemia. | Shih AH, Meydan C, Shank K, Garrett-Bakelman FE, Ward PS, Intlekofer AM, Nazir A, Stein EM, Knapp K, Glass J, Travins J, Straley K, Gliser C, Mason CE, Yen K, Thompson CB, Melnick A, Levine RL | Cancer discovery | 28193779 | Cancer Discov | 2017 May |
| Epigenetic therapy in a new era of medicine: creating and integrating molecular profiles of patients. | Afshinnekoo E, Mason CE | Annals of translational medicine | 27942527 | Ann Transl Med | 2016 Nov |
| N6-Methyladenosine in Flaviviridae Viral RNA Genomes Regulates Infection. | Gokhale NS, McIntyre ABR, McFadden MJ, Roder AE, Kennedy EM, Gandara JA, Hopcraft SE, Quicke KM, Vazquez C, Willer J, Ilkayeva OR, Law BA, Holley CL, Garcia-Blanco MA, Evans MJ, Suthar MS, Bradrick SS, Mason CE, Horner SM | Cell host & microbe | 27773535 | Cell Host Microbe | 2016 Nov 9 |
| A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. | Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CS, Federman S, Foox J, Gopez A, Li T, Chan R, Chu CS, Wabl CA, Gliwa AS, Reyes K, Pan CY, Guevara H, Wadford D, Miller S, Mason CE, Chiu CY | Science advances | 33536218 | Sci Adv | 2021 Feb |
| Cell-free DNA (cfDNA) and Exosome Profiling from a Year-Long Human Spaceflight Reveals Circulating Biomarkers. | Bezdan D, Grigorev K, Meydan C, Pelissier Vatter FA, Cioffi M, Rao V, MacKay M, Nakahira K, Burnham P, Afshinnekoo E, Westover C, Butler D, Mozsary C, Donahoe T, Foox J, Mishra T, Lucotti S, Rana BK, Melnick AM, Zhang H, Matei I, Kelsen D, Yu K, Lyden DC, Taylor L, Bailey SM, Snyder MP, Garrett-Bakelman FE, Ossowski S, De Vlaminck I, Mason CE | iScience | 33376973 | iScience | 2020 Dec 18 |
| Genetic and epigenetic heterogeneity and the impact on cancer relapse. | Hassan C, Afshinnekoo E, Li S, Wu S, Mason CE | Experimental hematology | 28705639 | Exp Hematol | 2017 Oct |
| Nanopore sequencing in microgravity. | McIntyre ABR, Rizzardi L, Yu AM, Alexander N, Rosen GL, Botkin DJ, Stahl SE, John KK, Castro-Wallace SL, McGrath K, Burton AS, Feinberg AP, Mason CE | NPJ microgravity | 28725742 | NPJ Microgravity | 2016 |
| Assessment of pharmacogenomic agreement. | Safikhani Z, El-Hachem N, Quevedo R, Smirnov P, Goldenberg A, Juul Birkbak N, Mason C, Hatzis C, Shi L, Aerts HJ, Quackenbush J, Haibe-Kains B | F1000Research | 27408686 | F1000Res | 2016 |
| Mutations in planar cell polarity gene SCRIB are associated with spina bifida. | Lei Y, Zhu H, Duhon C, Yang W, Ross ME, Shaw GM, Finnell RH | PloS one | 23922697 | PLoS One | 2013 |
| The non-human primate reference transcriptome resource (NHPRTR) for comparative functional genomics. | Pipes L, Li S, Bozinoski M, Palermo R, Peng X, Blood P, Kelly S, Weiss JM, Thierry-Mieg J, Thierry-Mieg D, Zumbo P, Chen R, Schroth GP, Mason CE, Katze MG | Nucleic acids research | 23203872 | Nucleic Acids Res | 2013 Jan |
| Two methods for full-length RNA sequencing for low quantities of cells and single cells. | Pan X, Durrett RE, Zhu H, Tanaka Y, Li Y, Zi X, Marjani SL, Euskirchen G, Ma C, Lamotte RH, Park IH, Snyder MP, Mason CE, Weissman SM | Proceedings of the National Academy of Sciences of the United States of America | 23267071 | Proc Natl Acad Sci U S A | 2013 Jan 8 |
| The continuing challenge of understanding, preventing, and treating neural tube defects. | Wallingford JB, Niswander LA, Shaw GM, Finnell RH | Science (New York, N.Y.) | 23449594 | Science | 2013 Mar 1 |
| Antiepileptic drugs and pregnancy outcomes. | Wlodarczyk BJ, Palacios AM, George TM, Finnell RH | American journal of medical genetics. Part A | 22711424 | Am J Med Genet A | 2012 Aug |
| A GCH1 haplotype and risk of neural tube defects in the National Birth Defects Prevention Study. | Lupo PJ, Chapa C, Nousome D, Duhon C, Canfield MA, Shaw GM, Finnell RH, Zhu H, National Birth Defects Prevention Study | Molecular genetics and metabolism | 23059057 | Mol Genet Metab | 2012 Nov |
| Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. | Akalin A, Garrett-Bakelman FE, Kormaksson M, Busuttil J, Zhang L, Khrebtukova I, Milne TA, Huang Y, Biswas D, Hess JL, Allis CD, Roeder RG, Valk PJ, Löwenberg B, Delwel R, Fernandez HF, Paietta E, Tallman MS, Schroth GP, Mason CE, Melnick A, Figueroa ME | PLoS genetics | 22737091 | PLoS Genet | 2012 |
| A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium. | SEQC/MAQC-III Consortium | Nature biotechnology | 25150838 | Nat Biotechnol | 2014 Sep |
| Tissue-specific transcriptome sequencing analysis expands the non-human primate reference transcriptome resource (NHPRTR). | Peng X, Thierry-Mieg J, Thierry-Mieg D, Nishida A, Pipes L, Bozinoski M, Thomas MJ, Kelly S, Weiss JM, Raveendran M, Muzny D, Gibbs RA, Rogers J, Schroth GP, Katze MG, Mason CE | Nucleic acids research | 25392405 | Nucleic Acids Res | 2015 Jan |
| Precision Metagenomics: Rapid Metagenomic Analyses for Infectious Disease Diagnostics and Public Health Surveillance. | Afshinnekoo E, Chou C, Alexander N, Ahsanuddin S, Schuetz AN, Mason CE | Journal of biomolecular techniques : JBT | 28337072 | J Biomol Tech | 2017 Apr |
| Multi-omic, Single-Cell, and Biochemical Profiles of Astronauts Guide Pharmacological Strategies for Returning to Gravity. | Gertz ML, Chin CR, Tomoiaga D, MacKay M, Chang C, Butler D, Afshinnekoo E, Bezdan D, Schmidt MA, Mozsary C, Melnick A, Garrett-Bakelman F, Crucian B, Lee SMC, Zwart SR, Smith SM, Meydan C, Mason CE | Cell reports | 33242408 | Cell Rep | 2020 Dec 8 |
| Rare LRP6 variants identified in spina bifida patients. | Lei Y, Fathe K, McCartney D, Zhu H, Yang W, Ross ME, Shaw GM, Finnell RH | Human mutation | 25546815 | Hum Mutat | 2015 Mar |
| Genetic and epigenetic heterogeneity in acute myeloid leukemia. | Li S, Mason CE, Melnick A | Current opinion in genetics & development | 27162099 | Curr Opin Genet Dev | 2016 Feb |
| Genomic approaches to the assessment of human spina bifida risk. | Ross ME, Mason CE, Finnell RH | Birth defects research | 27883265 | Birth Defects Res | 2017 Jan 30 |
| Enhanced reduced representation bisulfite sequencing for assessment of DNA methylation at base pair resolution. | Garrett-Bakelman FE, Sheridan CK, Kacmarczyk TJ, Ishii J, Betel D, Alonso A, Mason CE, Figueroa ME, Melnick AM | Journal of visualized experiments : JoVE | 25742437 | J Vis Exp | 2015 Feb 24 |
| Mutational cooperativity linked to combinatorial epigenetic gain of function in acute myeloid leukemia. | Shih AH, Jiang Y, Meydan C, Shank K, Pandey S, Barreyro L, Antony-Debre I, Viale A, Socci N, Sun Y, Robertson A, Cavatore M, de Stanchina E, Hricik T, Rapaport F, Woods B, Wei C, Hatlen M, Baljevic M, Nimer SD, Tallman M, Paietta E, Cimmino L, Aifantis I, Steidl U, Mason C, Melnick A, Levine RL | Cancer cell | 25873173 | Cancer Cell | 2015 Apr 13 |
| Translating current biomedical therapies for long duration, deep space missions. | Iosim S, MacKay M, Westover C, Mason CE | Precision clinical medicine | 31886035 | Precis Clin Med | 2019 Dec |
| Systems biology analysis of human genomes points to key pathways conferring spina bifida risk. | Aguiar-Pulido V, Wolujewicz P, Martinez-Fundichely A, Elhaik E, Thareja G, Abdel Aleem A, Chalhoub N, Cuykendall T, Al-Zamer J, Lei Y, El-Bashir H, Musser JM, Al-Kaabi A, Shaw GM, Khurana E, Suhre K, Mason CE, Elemento O, Finnell RH, Ross ME | Proceedings of the National Academy of Sciences of the United States of America | 34916285 | Proc Natl Acad Sci U S A | 2021 Dec 21 |
| Haplotype diversity and sequence heterogeneity of human telomeres. | Grigorev K, Foox J, Bezdan D, Butler D, Luxton JJ, Reed J, McKenna MJ, Taylor L, George KA, Meydan C, Bailey SM, Mason CE | Genome research | 34162698 | Genome Res | 2021 Jul |
| Ozone Disinfection for Elimination of Bacteria and Degradation of SARS-CoV2 RNA for Medical Environments. | Westover C, Rahmatulloev S, Danko D, Afshin EE, O'Hara NB, Ounit R, Bezdan D, Mason CE | Genes | 36672826 | Genes (Basel) | 2022 Dec 28 |
| Metalloprotein-based MRI probes. | Matsumoto Y, Jasanoff A | FEBS letters | 23376346 | FEBS Lett | 2013 Apr 17 |
| Screen-based analysis of magnetic nanoparticle libraries formed using peptidic iron oxide ligands. | Barch M, Okada S, Bartelle BB, Jasanoff A | Journal of the American Chemical Society | 25158100 | J Am Chem Soc | 2014 Sep 10 |
| Magnetic Detection of Neural Activity by Nanocoil Transducers. | Bok I, Phillips J, Zhu T, Lu J, Detienne E, Lima EA, Weiss BP, Jasanoff A, Hai A | Nano letters | 39319575 | Nano Lett | 2024 Oct 23 |
| Adventures in neurobioengineering. | Jasanoff A | ACS chemical neuroscience | 22896800 | ACS Chem Neurosci | 2012 Aug 15 |
| Magneto-fluorescent core-shell supernanoparticles. | Chen O, Riedemann L, Etoc F, Herrmann H, Coppey M, Barch M, Farrar CT, Zhao J, Bruns OT, Wei H, Guo P, Cui J, Jensen R, Chen Y, Harris DK, Cordero JM, Wang Z, Jasanoff A, Fukumura D, Reimer R, Dahan M, Jain RK, Bawendi MG | Nature communications | 25298155 | Nat Commun | 2014 Oct 9 |
| Engineering intracellular biomineralization and biosensing by a magnetic protein. | Matsumoto Y, Chen R, Anikeeva P, Jasanoff A | Nature communications | 26522873 | Nat Commun | 2015 Nov 2 |
| Molecular imaging with engineered physiology. | Desai M, Slusarczyk AL, Chapin A, Barch M, Jasanoff A | Nature communications | 27910951 | Nat Commun | 2016 Dec 2 |
| Magnetic nanosensors optimized for rapid and reversible self-assembly. | Rodriguez E, Lelyveld VS, Atanasijevic T, Okada S, Jasanoff A | Chemical communications (Cambridge, England) | 24566735 | Chem Commun (Camb) | 2014 Apr 7 |
| Molecular-level functional magnetic resonance imaging of dopaminergic signaling. | Lee T, Cai LX, Lelyveld VS, Hai A, Jasanoff A | Science (New York, N.Y.) | 24786083 | Science | 2014 May 2 |
| Wireless resonant circuits for the minimally invasive sensing of biophysical processes in magnetic resonance imaging. | Hai A, Spanoudaki VC, Bartelle BB, Jasanoff A | Nature biomedical engineering | 30932065 | Nat Biomed Eng | 2019 Jan |
| Molecular fMRI of Serotonin Transport. | Hai A, Cai LX, Lee T, Lelyveld VS, Jasanoff A | Neuron | 27773583 | Neuron | 2016 Nov 23 |
| Hybrid decoding of both spikes and low-frequency local field potentials for brain-machine interfaces. | Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 25570632 | Annu Int Conf IEEE Eng Med Biol Soc | 2014 |
| A freely-moving monkey treadmill model. | Foster JD, Nuyujukian P, Freifeld O, Gao H, Walker R, I Ryu S, H Meng T, Murmann B, J Black M, Shenoy KV | Journal of neural engineering | 24995476 | J Neural Eng | 2014 Aug |
| A Brain-Machine Interface Operating with a Real-Time Spiking Neural Network Control Algorithm. | Dethier J, Nuyujukian P, Eliasmith C, Stewart T, Elassaad SA, Shenoy KV, Boahen K | Advances in neural information processing systems | 25309106 | Adv Neural Inf Process Syst | 2011 |
| Simultaneous motor preparation and execution in a last-moment reach correction task. | Ames KC, Ryu SI, Shenoy KV | Nature communications | 31221968 | Nat Commun | 2019 Jun 20 |
| Unsupervised Discovery of Demixed, Low-Dimensional Neural Dynamics across Multiple Timescales through Tensor Component Analysis. | Williams AH, Kim TH, Wang F, Vyas S, Ryu SI, Shenoy KV, Schnitzer M, Kolda TG, Ganguli S | Neuron | 29887338 | Neuron | 2018 Jun 27 |
| Self-recalibrating classifiers for intracortical brain-computer interfaces. | Bishop W, Chestek CC, Gilja V, Nuyujukian P, Foster JD, Ryu SI, Shenoy KV, Yu BM | Journal of neural engineering | 24503597 | J Neural Eng | 2014 Apr |
| Combining Wireless Neural Recording and Video Capture for the Analysis of Natural Gait. | Foster JD, Freifeld O, Nuyujukian P, Ryu SI, Black MJ, Shenoy KV | International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering | 26019730 | Int IEEE EMBS Conf Neural Eng | 2011 Apr-May |
| A High-Performance Neural Prosthesis Incorporating Discrete State Selection With Hidden Markov Models. | Kao JC, Nuyujukian P, Ryu SI, Shenoy KV | IEEE transactions on bio-medical engineering | 27337709 | IEEE Trans Biomed Eng | 2017 Apr |
| A high performing brain-machine interface driven by low-frequency local field potentials alone and together with spikes. | Stavisky SD, Kao JC, Nuyujukian P, Ryu SI, Shenoy KV | Journal of neural engineering | 25946198 | J Neural Eng | 2015 Jun |
| Neural Population Dynamics Underlying Motor Learning Transfer. | Vyas S, Even-Chen N, Stavisky SD, Ryu SI, Nuyujukian P, Shenoy KV | Neuron | 29456026 | Neuron | 2018 Mar 7 |
| Structure in Neural Activity during Observed and Executed Movements Is Shared at the Neural Population Level, Not in Single Neurons. | Jiang X, Saggar H, Ryu SI, Shenoy KV, Kao JC | Cell reports | 32783934 | Cell Rep | 2020 Aug 11 |
| Leveraging historical knowledge of neural dynamics to rescue decoder performance as neural channels are lost: "Decoder hysteresis". | Kao JC, Ryu SI, Shenoy KV | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736448 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 Aug |
| Motor Cortical Visuomotor Feedback Activity Is Initially Isolated from Downstream Targets in Output-Null Neural State Space Dimensions. | Stavisky SD, Kao JC, Ryu SI, Shenoy KV | Neuron | 28625485 | Neuron | 2017 Jul 5 |
| Trial-by-Trial Motor Cortical Correlates of a Rapidly Adapting Visuomotor Internal Model. | Stavisky SD, Kao JC, Ryu SI, Shenoy KV | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28087767 | J Neurosci | 2017 Feb 15 |
| Design and validation of a real-time spiking-neural-network decoder for brain-machine interfaces. | Dethier J, Nuyujukian P, Ryu SI, Shenoy KV, Boahen K | Journal of neural engineering | 23574919 | J Neural Eng | 2013 Jun |
| Studying brain organization via spontaneous fMRI signal. | Power JD, Schlaggar BL, Petersen SE | Neuron | 25459408 | Neuron | 2014 Nov 19 |
| A neural network that finds a naturalistic solution for the production of muscle activity. | Sussillo D, Churchland MM, Kaufman MT, Shenoy KV | Nature neuroscience | 26075643 | Nat Neurosci | 2015 Jul |
| Tensor Analysis Reveals Distinct Population Structure that Parallels the Different Computational Roles of Areas M1 and V1. | Seely JS, Kaufman MT, Ryu SI, Shenoy KV, Cunningham JP, Churchland MM | PLoS computational biology | 27814353 | PLoS Comput Biol | 2016 Nov |
| Discovering Precise Temporal Patterns in Large-Scale Neural Recordings through Robust and Interpretable Time Warping. | Williams AH, Poole B, Maheswaranathan N, Dhawale AK, Fisher T, Wilson CD, Brann DH, Trautmann EM, Ryu S, Shusterman R, Rinberg D, Ölveczky BP, Shenoy KV, Ganguli S | Neuron | 31786013 | Neuron | 2020 Jan 22 |
| High-fidelity musculoskeletal modeling reveals that motor planning variability contributes to the speed-accuracy tradeoff. | Al Borno M, Vyas S, Shenoy KV, Delp SL | eLife | 33325369 | Elife | 2020 Dec 16 |
| A recurrent neural network for closed-loop intracortical brain-machine interface decoders. | Sussillo D, Nuyujukian P, Fan JM, Kao JC, Stavisky SD, Ryu S, Shenoy K | Journal of neural engineering | 22427488 | J Neural Eng | 2012 Apr |
| Selective modulation of cortical state during spatial attention. | Engel TA, Steinmetz NA, Gieselmann MA, Thiele A, Moore T, Boahen K | Science (New York, N.Y.) | 27934763 | Science | 2016 Dec 2 |
| Brain-machine interface cursor position only weakly affects monkey and human motor cortical activity in the absence of arm movements. | Stavisky SD, Kao JC, Nuyujukian P, Pandarinath C, Blabe C, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV | Scientific reports | 30397281 | Sci Rep | 2018 Nov 5 |
| Accurate Estimation of Neural Population Dynamics without Spike Sorting. | Trautmann EM, Stavisky SD, Lahiri S, Ames KC, Kaufman MT, O'Shea DJ, Vyas S, Sun X, Ryu SI, Ganguli S, Shenoy KV | Neuron | 31171448 | Neuron | 2019 Jul 17 |
| Intention estimation in brain-machine interfaces. | Fan JM, Nuyujukian P, Kao JC, Chestek CA, Ryu SI, Shenoy KV | Journal of neural engineering | 24654266 | J Neural Eng | 2014 Feb |
| A high-performance keyboard neural prosthesis enabled by task optimization. | Nuyujukian P, Fan JM, Kao JC, Ryu SI, Shenoy KV | IEEE transactions on bio-medical engineering | 25203982 | IEEE Trans Biomed Eng | 2015 Jan |
| Performance sustaining intracortical neural prostheses. | Nuyujukian P, Kao JC, Fan JM, Stavisky SD, Ryu SI, Shenoy KV | Journal of neural engineering | 25307561 | J Neural Eng | 2014 Dec |
| Spiking Neural Network Decoder for Brain-Machine Interfaces. | Dethier J, Gilja V, Nuyujukian P, Elassaad SA, Shenoy KV, Boahen K | International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering | 24352611 | Int IEEE EMBS Conf Neural Eng | 2011 |
| Structure and variability of delay activity in premotor cortex. | Even-Chen N, Sheffer B, Vyas S, Ryu SI, Shenoy KV | PLoS computational biology | 30794541 | PLoS Comput Biol | 2019 Feb |
| Inferring single-trial neural population dynamics using sequential auto-encoders. | Pandarinath C, O'Shea DJ, Collins J, Jozefowicz R, Stavisky SD, Kao JC, Trautmann EM, Kaufman MT, Ryu SI, Hochberg LR, Henderson JM, Shenoy KV, Abbott LF, Sussillo D | Nature methods | 30224673 | Nat Methods | 2018 Oct |
| Leveraging neural dynamics to extend functional lifetime of brain-machine interfaces. | Kao JC, Ryu SI, Shenoy KV | Scientific reports | 28784984 | Sci Rep | 2017 Aug 7 |
| Augmenting intracortical brain-machine interface with neurally driven error detectors. | Even-Chen N, Stavisky SD, Kao JC, Ryu SI, Shenoy KV | Journal of neural engineering | 29130452 | J Neural Eng | 2017 Dec |
| A low-power band of neuronal spiking activity dominated by local single units improves the performance of brain-machine interfaces. | Nason SR, Vaskov AK, Willsey MS, Welle EJ, An H, Vu PP, Bullard AJ, Nu CS, Kao JC, Shenoy KV, Jang T, Kim HS, Blaauw D, Patil PG, Chestek CA | Nature biomedical engineering | 32719512 | Nat Biomed Eng | 2020 Oct |
| Speech-related dorsal motor cortex activity does not interfere with iBCI cursor control. | Stavisky SD, Willett FR, Avansino DT, Hochberg LR, Shenoy KV, Henderson JM | Journal of neural engineering | 32023225 | J Neural Eng | 2020 Feb 5 |
| Single-trial dynamics of motor cortex and their applications to brain-machine interfaces. | Kao JC, Nuyujukian P, Ryu SI, Churchland MM, Cunningham JP, Shenoy KV | Nature communications | 26220660 | Nat Commun | 2015 Jul 29 |
| Combining decoder design and neural adaptation in brain-machine interfaces. | Shenoy KV, Carmena JM | Neuron | 25459407 | Neuron | 2014 Nov 19 |
| Auto-deleting brain machine interface: Error detection using spiking neural activity in the motor cortex. | Even-Chen N, Stavisky SD, Kao JC, Ryu SI, Shenoy KV | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736203 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 |
| ERAASR: an algorithm for removing electrical stimulation artifacts from multielectrode array recordings. | O'Shea DJ, Shenoy KV | Journal of neural engineering | 29265009 | J Neural Eng | 2018 Apr |
| High-Throughput Mapping of Long-Range Neuronal Projection Using In Situ Sequencing. | Chen X, Sun YC, Zhan H, Kebschull JM, Fischer S, Matho K, Huang ZJ, Gillis J, Zador AM | Cell | 31626774 | Cell | 2019 Oct 17 |
| Sequencing the connectome. | Zador AM, Dubnau J, Oyibo HK, Zhan H, Cao G, Peikon ID | PLoS biology | 23109909 | PLoS Biol | 2012 |
| A New Defective Helper RNA to Produce Recombinant Sindbis Virus that Infects Neurons but does not Propagate. | Kebschull JM, Garcia da Silva P, Zador AM | Frontiers in neuroanatomy | 27252627 | Front Neuroanat | 2016 |
| Assessing the replicability of spatial gene expression using atlas data from the adult mouse brain. | Lu S, Ortiz C, Fürth D, Fischer S, Meletis K, Zador A, Gillis J | PLoS biology | 34280183 | PLoS Biol | 2021 Jul |
| Integrating barcoded neuroanatomy with spatial transcriptional profiling enables identification of gene correlates of projections. | Sun YC, Chen X, Fischer S, Lu S, Zhan H, Gillis J, Zador AM | Nature neuroscience | 33972801 | Nat Neurosci | 2021 Jun |
| BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. | Huang L, Kebschull JM, Fürth D, Musall S, Kaufman MT, Churchland AK, Zador AM | Cell | 32619423 | Cell | 2020 Jul 9 |
| BRICseq Bridges Brain-wide Interregional Connectivity to Neural Activity and Gene Expression in Single Animals. | Huang L, Kebschull JM, Fürth D, Musall S, Kaufman MT, Churchland AK, Zador AM | Cell | 33357401 | Cell | 2020 Dec 23 |
| BARcode DEmixing through Non-negative Spatial Regression (BarDensr). | Chen S, Loper J, Chen X, Vaughan A, Zador AM, Paninski L | PLoS computational biology | 33684106 | PLoS Comput Biol | 2021 Mar |
| Cellular anatomy of the mouse primary motor cortex. | Muñoz-Castañeda R, Zingg B, Matho KS, Chen X, Wang Q, Foster NN, Li A, Narasimhan A, Hirokawa KE, Huo B, Bannerjee S, Korobkova L, Park CS, Park YG, Bienkowski MS, Chon U, Wheeler DW, Li X, Wang Y, Naeemi M, Xie P, Liu L, Kelly K, An X, Attili SM, Bowman I, Bludova A, Cetin A, Ding L, Drewes R, D'Orazi F, Elowsky C, Fischer S, Galbavy W, Gao L, Gillis J, Groblewski PA, Gou L, Hahn JD, Hatfield JT, Hintiryan H, Huang JJ, Kondo H, Kuang X, Lesnar P, Li X, Li Y, Lin M, Lo D, Mizrachi J, Mok S, Nicovich PR, Palaniswamy R, Palmer J, Qi X, Shen E, Sun YC, Tao HW, Wakemen W, Wang Y, Yao S, Yuan J, Zhan H, Zhu M, Ng L, Zhang LI, Lim BK, Hawrylycz M, Gong H, Gee JC, Kim Y, Chung K, Yang XW, Peng H, Luo Q, Mitra PP, Zador AM, Zeng H, Ascoli GA, Josh Huang Z, Osten P, Harris JA, Dong HW | Nature | 34616071 | Nature | 2021 Oct |
| Long-term Cre-mediated retrograde tagging of neurons using a novel recombinant pseudorabies virus. | Oyibo HK, Znamenskiy P, Oviedo HV, Enquist LW, Zador AM | Frontiers in neuroanatomy | 25232307 | Front Neuroanat | 2014 |
| Sources of PCR-induced distortions in high-throughput sequencing data sets. | Kebschull JM, Zador AM | Nucleic acids research | 26187991 | Nucleic Acids Res | 2015 Dec 2 |
| The logic of single-cell projections from visual cortex. | Han Y, Kebschull JM, Campbell RAA, Cowan D, Imhof F, Zador AM, Mrsic-Flogel TD | Nature | 29590093 | Nature | 2018 Apr 5 |
| In vivo generation of DNA sequence diversity for cellular barcoding. | Peikon ID, Gizatullina DI, Zador AM | Nucleic acids research | 25013177 | Nucleic Acids Res | 2014 |
| High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA. | Kebschull JM, Garcia da Silva P, Reid AP, Peikon ID, Albeanu DF, Zador AM | Neuron | 27545715 | Neuron | 2016 Sep 7 |
| SYNPLA, a method to identify synapses displaying plasticity after learning. | Dore K, Pao Y, Soria Lopez J, Aronson S, Zhan H, Ghosh S, Merrill S, Zador AM, Malinow R, Kebschull JM | Proceedings of the National Academy of Sciences of the United States of America | 31974314 | Proc Natl Acad Sci U S A | 2020 Feb 11 |
| High-throughput in vivo vertebrate screening. | Pardo-Martin C, Chang TY, Koo BK, Gilleland CL, Wasserman SC, Yanik MF | Nature methods | 20639868 | Nat Methods | 2010 Aug |
| Fully automated cellular-resolution vertebrate screening platform with parallel animal processing. | Chang TY, Pardo-Martin C, Allalou A, Wählby C, Yanik MF | Lab on a chip | 22159032 | Lab Chip | 2012 Feb 21 |
| Organ-targeted high-throughput in vivo biologics screen identifies materials for RNA delivery. | Chang TY, Shi P, Steinmeyer JD, Chatnuntawech I, Tillberg P, Love KT, Eimon PM, Anderson DG, Yanik MF | Integrative biology : quantitative biosciences from nano to macro | 25184623 | Integr Biol (Camb) | 2014 Oct |
| Computer-Assisted Transgenesis of Caenorhabditis elegans for Deep Phenotyping. | Gilleland CL, Falls AT, Noraky J, Heiman MG, Yanik MF | Genetics | 26163188 | Genetics | 2015 Sep |
| Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects. | Eimon PM, Ghannad-Rezaie M, De Rienzo G, Allalou A, Wu Y, Gao M, Roy A, Skolnick J, Yanik MF | Nature communications | 29335539 | Nat Commun | 2018 Jan 15 |
| High-throughput hyperdimensional vertebrate phenotyping. | Pardo-Martin C, Allalou A, Medina J, Eimon PM, Wählby C, Fatih Yanik M | Nature communications | 23403568 | Nat Commun | 2013 |
| Studying apoptosis in the Zebrafish. | Eimon PM | Methods in enzymology | 24974299 | Methods Enzymol | 2014 |
| Simultaneous top-down modulation of the primary somatosensory cortex and thalamic nuclei during active tactile discrimination. | Pais-Vieira M, Lebedev MA, Wiest MC, Nicolelis MA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23447616 | J Neurosci | 2013 Feb 27 |
| Reprogramming movements: extraction of motor intentions from cortical ensemble activity when movement goals change. | Ifft PJ, Lebedev MA, Nicolelis MA | Frontiers in neuroengineering | 22826698 | Front Neuroeng | 2012 |
| Subcortical neuronal ensembles: an analysis of motor task association, tremor, oscillations, and synchrony in human patients. | Hanson TL, Fuller AM, Lebedev MA, Turner DA, Nicolelis MA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22723703 | J Neurosci | 2012 Jun 20 |
| Building an organic computing device with multiple interconnected brains. | Pais-Vieira M, Chiuffa G, Lebedev M, Yadav A, Nicolelis MA | Scientific reports | 26158615 | Sci Rep | 2015 Jul 9 |
| A Brain to Spine Interface for Transferring Artificial Sensory Information. | Yadav AP, Li D, Nicolelis MAL | Scientific reports | 31964948 | Sci Rep | 2020 Jan 21 |
| Spinal cord stimulation alleviates motor deficits in a primate model of Parkinson disease. | Santana MB, Halje P, Simplício H, Richter U, Freire MAM, Petersson P, Fuentes R, Nicolelis MAL | Neuron | 25447740 | Neuron | 2014 Nov 19 |
| Active tactile exploration using a brain-machine-brain interface. | O'Doherty JE, Lebedev MA, Ifft PJ, Zhuang KZ, Shokur S, Bleuler H, Nicolelis MA | Nature | 21976021 | Nature | 2011 Oct 5 |
| Chronic spinal cord electrical stimulation protects against 6-hydroxydopamine lesions. | Yadav AP, Fuentes R, Zhang H, Vinholo T, Wang CH, Freire MA, Nicolelis MA | Scientific reports | 24452435 | Sci Rep | 2014 Jan 23 |
| Cortical correlates of fitts' law. | Ifft PJ, Lebedev MA, Nicolelis MA | Frontiers in integrative neuroscience | 22275888 | Front Integr Neurosci | 2011 |
| A Closed Loop Brain-machine Interface for Epilepsy Control Using Dorsal Column Electrical Stimulation. | Pais-Vieira M, Yadav AP, Moreira D, Guggenmos D, Santos A, Lebedev M, Nicolelis MAL | Scientific reports | 27605389 | Sci Rep | 2016 Sep 8 |
| Cortical and thalamic contributions to response dynamics across layers of the primary somatosensory cortex during tactile discrimination. | Pais-Vieira M, Kunicki C, Tseng PH, Martin J, Lebedev M, Nicolelis MA | Journal of neurophysiology | 26180115 | J Neurophysiol | 2015 Sep |
| Neural integration of reward, arousal, and feeding: recruitment of VTA, lateral hypothalamus, and ventral striatal neurons. | Gutierrez R, Lobo MK, Zhang F, de Lecea L | IUBMB life | 21901814 | IUBMB Life | 2011 Oct |
| Cell diversity and network dynamics in photosensitive human brain organoids. | Quadrato G, Nguyen T, Macosko EZ, Sherwood JL, Min Yang S, Berger DR, Maria N, Scholvin J, Goldman M, Kinney JP, Boyden ES, Lichtman JW, Williams ZM, McCarroll SA, Arlotta P | Nature | 28445462 | Nature | 2017 May 4 |
| DeCoN: genome-wide analysis of in vivo transcriptional dynamics during pyramidal neuron fate selection in neocortex. | Molyneaux BJ, Goff LA, Brettler AC, Chen HH, Hrvatin S, Rinn JL, Arlotta P | Neuron | 25556833 | Neuron | 2015 Jan 21 |
| Multiple knockout mouse models reveal lincRNAs are required for life and brain development. | Sauvageau M, Goff LA, Lodato S, Bonev B, Groff AF, Gerhardinger C, Sanchez-Gomez DB, Hacisuleyman E, Li E, Spence M, Liapis SC, Mallard W, Morse M, Swerdel MR, D'Ecclessis MF, Moore JC, Lai V, Gong G, Yancopoulos GD, Frendewey D, Kellis M, Hart RP, Valenzuela DM, Arlotta P, Rinn JL | eLife | 24381249 | Elife | 2013 Dec 31 |
| Robust, synergistic regulation of human gene expression using TALE activators. | Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK | Nature methods | 23396285 | Nat Methods | 2013 Mar |
| Dissecting neural function using targeted genome engineering technologies. | Hsu PD, Zhang F | ACS chemical neuroscience | 22896804 | ACS Chem Neurosci | 2012 Aug 15 |
| RNA-guided genome editing of mammalian cells. | Pyzocha NK, Ran FA, Hsu PD, Zhang F | Methods in molecular biology (Clifton, N.J.) | 24557909 | Methods Mol Biol | 2014 |
| Therapeutic genome editing: prospects and challenges. | Cox DB, Platt RJ, Zhang F | Nature medicine | 25654603 | Nat Med | 2015 Feb |
| Direct lineage reprogramming of post-mitotic callosal neurons into corticofugal neurons in vivo. | Rouaux C, Arlotta P | Nature cell biology | 23334497 | Nat Cell Biol | 2013 Feb |
| Development and applications of CRISPR-Cas9 for genome engineering. | Hsu PD, Lander ES, Zhang F | Cell | 24906146 | Cell | 2014 Jun 5 |
| A transcription activator-like effector toolbox for genome engineering. | Sanjana NE, Cong L, Zhou Y, Cunniff MM, Feng G, Zhang F | Nature protocols | 22222791 | Nat Protoc | 2012 Jan 5 |
| Multiplex genome engineering using CRISPR/Cas systems. | Cong L, Ran FA, Cox D, Lin S, Barretto R, Habib N, Hsu PD, Wu X, Jiang W, Marraffini LA, Zhang F | Science (New York, N.Y.) | 23287718 | Science | 2013 Feb 15 |
| Efficient construction of sequence-specific TAL effectors for modulating mammalian transcription. | Zhang F, Cong L, Lodato S, Kosuri S, Church GM, Arlotta P | Nature biotechnology | 21248753 | Nat Biotechnol | 2011 Feb |
| CRISPR RNA-guided activation of endogenous human genes. | Maeder ML, Linder SJ, Cascio VM, Fu Y, Ho QH, Joung JK | Nature methods | 23892898 | Nat Methods | 2013 Oct |
| Optical control of mammalian endogenous transcription and epigenetic states. | Konermann S, Brigham MD, Trevino A, Hsu PD, Heidenreich M, Cong L, Platt RJ, Scott DA, Church GM, Zhang F | Nature | 23877069 | Nature | 2013 Aug 22 |
| Comprehensive interrogation of natural TALE DNA-binding modules and transcriptional repressor domains. | Cong L, Zhou R, Kuo YC, Cunniff M, Zhang F | Nature communications | 22828628 | Nat Commun | 2012 Jul 24 |
| In vivo interrogation of gene function in the mammalian brain using CRISPR-Cas9. | Swiech L, Heidenreich M, Banerjee A, Habib N, Li Y, Trombetta J, Sur M, Zhang F | Nature biotechnology | 25326897 | Nat Biotechnol | 2015 Jan |
| CRISPR/Cas9 cleavage of viral DNA efficiently suppresses hepatitis B virus. | Ramanan V, Shlomai A, Cox DB, Schwartz RE, Michailidis E, Bhatta A, Scott DA, Zhang F, Rice CM, Bhatia SN | Scientific reports | 26035283 | Sci Rep | 2015 Jun 2 |
| Stress. | Procko C, Shaham S | Current biology : CB | 22115453 | Curr Biol | 2011 Nov 22 |
| Some, but not all, retromer components promote morphogenesis of C. elegans sensory compartments. | Oikonomou G, Perens EA, Lu Y, Shaham S | Developmental biology | 22138055 | Dev Biol | 2012 Feb 1 |
| Two novel DEG/ENaC channel subunits expressed in glia are needed for nose-touch sensitivity in Caenorhabditis elegans. | Han L, Wang Y, Sangaletti R, D'Urso G, Lu Y, Shaham S, Bianchi L | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23325233 | J Neurosci | 2013 Jan 16 |
| PROS-1/Prospero Is a Major Regulator of the Glia-Specific Secretome Controlling Sensory-Neuron Shape and Function in C. elegans. | Wallace SW, Singhvi A, Liang Y, Lu Y, Shaham S | Cell reports | 27068465 | Cell Rep | 2016 Apr 19 |
| Sensory organ remodeling in Caenorhabditis elegans requires the zinc-finger protein ZTF-16. | Procko C, Lu Y, Shaham S | Genetics | 22298710 | Genetics | 2012 Apr |
| The microRNA miR-124 controls gene expression in the sensory nervous system of Caenorhabditis elegans. | Clark AM, Goldstein LD, Tevlin M, Tavaré S, Shaham S, Miska EA | Nucleic acids research | 20176573 | Nucleic Acids Res | 2010 Jun |
| The glia of Caenorhabditis elegans. | Oikonomou G, Shaham S | Glia | 21732423 | Glia | 2011 Sep |
| A spatial and temporal map of C. elegans gene expression. | Spencer WC, Zeller G, Watson JD, Henz SR, Watkins KL, McWhirter RD, Petersen S, Sreedharan VT, Widmer C, Jo J, Reinke V, Petrella L, Strome S, Von Stetina SE, Katz M, Shaham S, Rätsch G, Miller DM 3rd | Genome research | 21177967 | Genome Res | 2011 Feb |
| Opposing activities of LIT-1/NLK and DAF-6/patched-related direct sensory compartment morphogenesis in C. elegans. | Oikonomou G, Perens EA, Lu Y, Watanabe S, Jorgensen EM, Shaham S | PLoS biology | 21857800 | PLoS Biol | 2011 Aug |
| Glia initiate brain assembly through noncanonical Chimaerin-Furin axon guidance in C. elegans. | Rapti G, Li C, Shan A, Lu Y, Shaham S | Nature neuroscience | 28846083 | Nat Neurosci | 2017 Oct |
| FBN-1, a fibrillin-related protein, is required for resistance of the epidermis to mechanical deformation during C. elegans embryogenesis. | Kelley M, Yochem J, Krieg M, Calixto A, Heiman MG, Kuzmanov A, Meli V, Chalfie M, Goodman MB, Shaham S, Frand A, Fay DS | eLife | 25798732 | Elife | 2015 Mar 23 |
| Development of neurons and glia. | Pfaff S, Shaham S | Current opinion in neurobiology | 24358527 | Curr Opin Neurobiol | 2013 Dec |
| Assisted morphogenesis: glial control of dendrite shapes. | Procko C, Shaham S | Current opinion in cell biology | 20678911 | Curr Opin Cell Biol | 2010 Oct |
| Chemosensory organs as models of neuronal synapses. | Shaham S | Nature reviews. Neuroscience | 20029439 | Nat Rev Neurosci | 2010 Mar |
| A Glial K/Cl Transporter Controls Neuronal Receptive Ending Shape by Chloride Inhibition of an rGC. | Singhvi A, Liu B, Friedman CJ, Fong J, Lu Y, Huang XY, Shaham S | Cell | 27062922 | Cell | 2016 May 5 |
| Directional locomotion of C. elegans in the absence of external stimuli. | Peliti M, Chuang JS, Shaham S | PloS one | 24223821 | PLoS One | 2013 |
| Glia delimit shape changes of sensory neuron receptive endings in C. elegans. | Procko C, Lu Y, Shaham S | Development (Cambridge, England) | 21350017 | Development | 2011 Apr |
| On the morphogenesis of glial compartments in the sensory organs of Caenorhabditis elegans. | Oikonomou G, Shaham S | Worm | 24058823 | Worm | 2012 Jan 1 |
| Forward and reverse mutagenesis in C. elegans. | Kutscher LM, Shaham S | WormBook : the online review of C. elegans biology | 24449699 | WormBook | 2014 Jan 17 |
| Intraflagellar transport delivers tubulin isotypes to sensory cilium middle and distal segments. | Hao L, Thein M, Brust-Mascher I, Civelekoglu-Scholey G, Lu Y, Acar S, Prevo B, Shaham S, Scholey JM | Nature cell biology | 21642982 | Nat Cell Biol | 2011 Jun 5 |
| Glutamate spillover in C. elegans triggers repetitive behavior through presynaptic activation of MGL-2/mGluR5. | Katz M, Corson F, Keil W, Singhal A, Bae A, Lu Y, Liang Y, Shaham S | Nature communications | 31015396 | Nat Commun | 2019 Apr 23 |
| Glial development and function in the nervous system of Caenorhabditis elegans. | Shaham S | Cold Spring Harbor perspectives in biology | 25573712 | Cold Spring Harb Perspect Biol | 2015 Jan 8 |
| MicroRNA-276a functions in ellipsoid body and mushroom body neurons for naive and conditioned olfactory avoidance in Drosophila. | Li W, Cressy M, Qin H, Fulga T, Van Vactor D, Dubnau J | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23536094 | J Neurosci | 2013 Mar 27 |
| Mobile genetic elements and genome evolution 2014. | Singh PK, Bourque G, Craig NL, Dubnau JT, Feschotte C, Flasch DA, Gunderson KL, Malik HS, Moran JV, Peters JE, Slotkin RK, Levin HL | Mobile DNA | 30117500 | Mob DNA | 2014 |
| A prion-mediated mechanism for memory proposed in Drosophila. | Li W, Dubnau J | Neuron | 23083729 | Neuron | 2012 Oct 18 |
| Activation of transposable elements during aging and neuronal decline in Drosophila. | Li W, Prazak L, Chatterjee N, Grüninger S, Krug L, Theodorou D, Dubnau J | Nature neuroscience | 23563579 | Nat Neurosci | 2013 May |
| The role of transposable elements in health and diseases of the central nervous system. | Reilly MT, Faulkner GJ, Dubnau J, Ponomarev I, Gage FH | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24198348 | J Neurosci | 2013 Nov 6 |
| Transposable elements in TDP-43-mediated neurodegenerative disorders. | Li W, Jin Y, Prazak L, Hammell M, Dubnau J | PloS one | 22957047 | PLoS One | 2012 |
| Systems memory consolidation in Drosophila. | Dubnau J, Chiang AS | Current opinion in neurobiology | 23084099 | Curr Opin Neurobiol | 2013 Feb |
| Emerging roles for ectonucleotidases in pain-sensing neurons. | Street SE, Zylka MJ | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 21116251 | Neuropsychopharmacology | 2011 Jan |
| Optimizing promoters for recombinant adeno-associated virus-mediated gene expression in the peripheral and central nervous system using self-complementary vectors. | Gray SJ, Foti SB, Schwartz JW, Bachaboina L, Taylor-Blake B, Coleman J, Ehlers MD, Zylka MJ, McCown TJ, Samulski RJ | Human gene therapy | 21476867 | Hum Gene Ther | 2011 Sep |
| The lipid kinase PIP5K1C regulates pain signaling and sensitization. | Wright BD, Loo L, Street SE, Ma A, Taylor-Blake B, Stashko MA, Jin J, Janzen WP, Frye SV, Zylka MJ | Neuron | 24853942 | Neuron | 2014 May 21 |
| Enhanced behavioral responses to cold stimuli following CGRPα sensory neuron ablation are dependent on TRPM8. | McCoy ES, Zylka MJ | Molecular pain | 25406633 | Mol Pain | 2014 Nov 19 |
| Recombinant ecto-5'-nucleotidase (CD73) has long lasting antinociceptive effects that are dependent on adenosine A1 receptor activation. | Sowa NA, Voss MK, Zylka MJ | Molecular pain | 20398264 | Mol Pain | 2010 Apr 14 |
| Topoisomerase inhibitors unsilence the dormant allele of Ube3a in neurons. | Huang HS, Allen JA, Mabb AM, King IF, Miriyala J, Taylor-Blake B, Sciaky N, Dutton JW Jr, Lee HM, Chen X, Jin J, Bridges AS, Zylka MJ, Roth BL, Philpot BD | Nature | 22190039 | Nature | 2011 Dec 21 |
| PAPupuncture has localized and long-lasting antinociceptive effects in mouse models of acute and chronic pain. | Hurt JK, Zylka MJ | Molecular pain | 22524543 | Mol Pain | 2012 Apr 23 |
| Peptidergic CGRPα primary sensory neurons encode heat and itch and tonically suppress sensitivity to cold. | McCoy ES, Taylor-Blake B, Street SE, Pribisko AL, Zheng J, Zylka MJ | Neuron | 23523592 | Neuron | 2013 Apr 10 |
| Photochemical activation of TRPA1 channels in neurons and animals. | Kokel D, Cheung CY, Mills R, Coutinho-Budd J, Huang L, Setola V, Sprague J, Jin S, Jin YN, Huang XP, Bruni G, Woolf CJ, Roth BL, Hamblin MR, Zylka MJ, Milan DJ, Peterson RT | Nature chemical biology | 23396078 | Nat Chem Biol | 2013 Apr |
| Development of a High-Throughput Screening Assay to Identify Inhibitors of the Lipid Kinase PIP5K1C. | Wright BD, Simpson C, Stashko M, Kireev D, Hull-Ryde EA, Zylka MJ, Janzen WP | Journal of biomolecular screening | 25534829 | J Biomol Screen | 2015 Jun |
| Biological constraints limit the use of rapamycin-inducible FKBP12-Inp54p for depleting PIP2 in dorsal root ganglia neurons. | Coutinho-Budd JC, Snider SB, Fitzpatrick BJ, Rittiner JE, Zylka MJ | Journal of negative results in biomedicine | 24010830 | J Negat Results Biomed | 2013 Sep 8 |
| Overexpression of diacylglycerol kinase η enhances Gαq-coupled G protein-coupled receptor signaling. | Rittiner JE, Brings VE, Zylka MJ | Molecular pharmacology | 24608858 | Mol Pharmacol | 2014 May |
| Lipid kinases as therapeutic targets for chronic pain. | Loo L, Wright BD, Zylka MJ | Pain | 25789432 | Pain | 2015 Apr |
| Prostatic acid phosphatase reduces thermal sensitivity and chronic pain sensitization by depleting phosphatidylinositol 4,5-bisphosphate. | Sowa NA, Street SE, Vihko P, Zylka MJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 20685973 | J Neurosci | 2010 Aug 4 |
| Angelman syndrome: insights into genomic imprinting and neurodevelopmental phenotypes. | Mabb AM, Judson MC, Zylka MJ, Philpot BD | Trends in neurosciences | 21592595 | Trends Neurosci | 2011 Jun |
| Ecto-5'-nucleotidase (CD73) inhibits nociception by hydrolyzing AMP to adenosine in nociceptive circuits. | Sowa NA, Taylor-Blake B, Zylka MJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 20147550 | J Neurosci | 2010 Feb 10 |
| Deletion of ENTPD3 does not impair nucleotide hydrolysis in primary somatosensory neurons or spinal cord. | McCoy E, Street S, Taylor-Blake B, Yi J, Edwards M, Wightman M, Zylka M | F1000Research | 25717362 | F1000Res | 2014 |
| High-throughput screen identifies cyclic nucleotide analogs that inhibit prostatic acid phosphatase. | McCoy ES, Lea WA, Mott BT, Maloney DJ, Jadhav A, Simeonov A, Zylka MJ | Journal of biomolecular screening | 23190738 | J Biomol Screen | 2013 Apr |
| Orally active adenosine A(1) receptor agonists with antinociceptive effects in mice. | Korboukh I, Hull-Ryde EA, Rittiner JE, Randhawa AS, Coleman J, Fitzpatrick BJ, Setola V, Janzen WP, Frye SV, Zylka MJ, Jin J | Journal of medicinal chemistry | 22738238 | J Med Chem | 2012 Jul 26 |
| Needling adenosine receptors for pain relief. | Zylka MJ | Nature neuroscience | 20581811 | Nat Neurosci | 2010 Jul |
| Secretion and N-linked glycosylation are required for prostatic acid phosphatase catalytic and antinociceptive activity. | Hurt JK, Fitzpatrick BJ, Norris-Drouin J, Zylka MJ | PloS one | 22389722 | PLoS One | 2012 |
| Tissue-nonspecific alkaline phosphatase acts redundantly with PAP and NT5E to generate adenosine in the dorsal spinal cord. | Street SE, Kramer NJ, Walsh PL, Taylor-Blake B, Yadav MC, King IF, Vihko P, Wightman RM, Millán JL, Zylka MJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23825434 | J Neurosci | 2013 Jul 3 |
| CGRPα-expressing sensory neurons respond to stimuli that evoke sensations of pain and itch. | McCoy ES, Taylor-Blake B, Zylka MJ | PloS one | 22563493 | PLoS One | 2012 |
| Prostatic acid phosphatase is required for the antinociceptive effects of thiamine and benfotiamine. | Hurt JK, Coleman JL, Fitzpatrick BJ, Taylor-Blake B, Bridges AS, Vihko P, Zylka MJ | PloS one | 23119057 | PLoS One | 2012 |
| PAP and NT5E inhibit nociceptive neurotransmission by rapidly hydrolyzing nucleotides to adenosine. | Street SE, Walsh PL, Sowa NA, Taylor-Blake B, Guillot TS, Vihko P, Wightman RM, Zylka MJ | Molecular pain | 22011440 | Mol Pain | 2011 Oct 19 |
| AMP is an adenosine A1 receptor agonist. | Rittiner JE, Korboukh I, Hull-Ryde EA, Jin J, Janzen WP, Frye SV, Zylka MJ | The Journal of biological chemistry | 22215671 | J Biol Chem | 2012 Feb 17 |
| Pain-relieving prospects for adenosine receptors and ectonucleotidases. | Zylka MJ | Trends in molecular medicine | 21236731 | Trends Mol Med | 2011 Apr |
| Targeting astrocyte signaling for chronic pain. | Gao YJ, Ji RR | Neurotherapeutics : the journal of the American Society for Experimental NeuroTherapeutics | 20880510 | Neurotherapeutics | 2010 Oct |
| Acute morphine activates satellite glial cells and up-regulates IL-1β in dorsal root ganglia in mice via matrix metalloprotease-9. | Berta T, Liu T, Liu YC, Xu ZZ, Ji RR | Molecular pain | 22439811 | Mol Pain | 2012 Mar 22 |
| Glia and pain: is chronic pain a gliopathy? | Ji RR, Berta T, Nedergaard M | Pain | 23792284 | Pain | 2013 Dec |
| Tissue plasminogen activator contributes to morphine tolerance and induces mechanical allodynia via astrocytic IL-1β and ERK signaling in the spinal cord of mice. | Berta T, Liu YC, Xu ZZ, Ji RR | Neuroscience | 23707980 | Neuroscience | 2013 Sep 5 |
| The c-Jun N-terminal kinase 1 (JNK1) in spinal astrocytes is required for the maintenance of bilateral mechanical allodynia under a persistent inflammatory pain condition. | Gao YJ, Xu ZZ, Liu YC, Wen YR, Decosterd I, Ji RR | Pain | 20022176 | Pain | 2010 Feb |
| Interferon alpha inhibits spinal cord synaptic and nociceptive transmission via neuronal-glial interactions. | Liu CC, Gao YJ, Luo H, Berta T, Xu ZZ, Ji RR, Tan PH | Scientific reports | 27670299 | Sci Rep | 2016 Sep 27 |
| Connexin-43 induces chemokine release from spinal cord astrocytes to maintain late-phase neuropathic pain in mice. | Chen G, Park CK, Xie RG, Berta T, Nedergaard M, Ji RR | Brain : a journal of neurology | 24919967 | Brain | 2014 Aug |
| A feed-forward spinal cord glycinergic neural circuit gates mechanical allodynia. | Lu Y, Dong H, Gao Y, Gong Y, Ren Y, Gu N, Zhou S, Xia N, Sun YY, Ji RR, Xiong L | The Journal of clinical investigation | 23979158 | J Clin Invest | 2013 Sep |
| Microglia and spinal cord synaptic plasticity in persistent pain. | Taves S, Berta T, Chen G, Ji RR | Neural plasticity | 24024042 | Neural Plast | 2013 |
| Extracellular caspase-6 drives murine inflammatory pain via microglial TNF-α secretion. | Berta T, Park CK, Xu ZZ, Xie RG, Liu T, Lü N, Liu YC, Ji RR | The Journal of clinical investigation | 24531553 | J Clin Invest | 2014 Mar |
| β-arrestin-2 regulates NMDA receptor function in spinal lamina II neurons and duration of persistent pain. | Chen G, Xie RG, Gao YJ, Xu ZZ, Zhao LX, Bang S, Berta T, Park CK, Lay M, Chen W, Ji RR | Nature communications | 27538456 | Nat Commun | 2016 Aug 19 |
| Identification and signature profiles for pro-resolving and inflammatory lipid mediators in human tissue. | Colas RA, Shinohara M, Dalli J, Chiang N, Serhan CN | American journal of physiology. Cell physiology | 24696140 | Am J Physiol Cell Physiol | 2014 Jul 1 |
| Light touch induces ERK activation in superficial dorsal horn neurons after inflammation: involvement of spinal astrocytes and JNK signaling in touch-evoked central sensitization and mechanical allodynia. | Gao YJ, Ji RR | Journal of neurochemistry | 20722971 | J Neurochem | 2010 Oct |
| Spinal injection of TNF-α-activated astrocytes produces persistent pain symptom mechanical allodynia by releasing monocyte chemoattractant protein-1. | Gao YJ, Zhang L, Ji RR | Glia | 20737477 | Glia | 2010 Nov 15 |
| Targeting microglial purinergic signaling to improve morphine analgesia. | Ji RR | Pain | 20584568 | Pain | 2010 Sep |
| Large A-fiber activity is required for microglial proliferation and p38 MAPK activation in the spinal cord: different effects of resiniferatoxin and bupivacaine on spinal microglial changes after spared nerve injury. | Suter MR, Berta T, Gao YJ, Decosterd I, Ji RR | Molecular pain | 19772627 | Mol Pain | 2009 Sep 22 |
| Glial cells and chronic pain. | Gosselin RD, Suter MR, Ji RR, Decosterd I | The Neuroscientist : a review journal bringing neurobiology, neurology and psychiatry | 20581331 | Neuroscientist | 2010 Oct |
| Oxidative stress induces itch via activation of transient receptor potential subtype ankyrin 1 in mice. | Liu T, Ji RR | Neuroscience bulletin | 22466125 | Neurosci Bull | 2012 Apr |
| Resolving TRPV1- and TNF-α-mediated spinal cord synaptic plasticity and inflammatory pain with neuroprotectin D1. | Park CK, Lü N, Xu ZZ, Liu T, Serhan CN, Ji RR | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22016541 | J Neurosci | 2011 Oct 19 |
| Toll-like receptor 7 mediates pruritus. | Liu T, Xu ZZ, Park CK, Berta T, Ji RR | Nature neuroscience | 21037581 | Nat Neurosci | 2010 Dec |
| TNF-α contributes to spinal cord synaptic plasticity and inflammatory pain: distinct role of TNF receptor subtypes 1 and 2. | Zhang L, Berta T, Xu ZZ, Liu T, Park JY, Ji RR | Pain | 21159431 | Pain | 2011 Feb |
| Resolvins are potent analgesics for arthritic pain. | Xu ZZ, Ji RR | British journal of pharmacology | 21418190 | Br J Pharmacol | 2011 Sep |
| A monoclonal antibody that targets a NaV1.7 channel voltage sensor for pain and itch relief. | Lee JH, Park CK, Chen G, Han Q, Xie RG, Liu T, Ji RR, Lee SY | Cell | 24856969 | Cell | 2014 Jun 5 |
| Vagus nerve controls resolution and pro-resolving mediators of inflammation. | Mirakaj V, Dalli J, Granja T, Rosenberger P, Serhan CN | The Journal of experimental medicine | 24863066 | J Exp Med | 2014 Jun 2 |
| Resolvin E1 inhibits neuropathic pain and spinal cord microglial activation following peripheral nerve injury. | Xu ZZ, Berta T, Ji RR | Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology | 22878925 | J Neuroimmune Pharmacol | 2013 Mar |
| New insights into the mechanisms of itch: are pain and itch controlled by distinct mechanisms? | Liu T, Ji RR | Pflugers Archiv : European journal of physiology | 23636773 | Pflugers Arch | 2013 Dec |
| Chemokine contribution to neuropathic pain: respective induction of CXCL1 and CXCR2 in spinal cord astrocytes and neurons. | Zhang ZJ, Cao DL, Zhang X, Ji RR, Gao YJ | Pain | 23831863 | Pain | 2013 Oct |
| Emerging roles of resolvins in the resolution of inflammation and pain. | Ji RR, Xu ZZ, Strichartz G, Serhan CN | Trends in neurosciences | 21963090 | Trends Neurosci | 2011 Nov |
| Nociceptive neurons regulate innate and adaptive immunity and neuropathic pain through MyD88 adapter. | Liu XJ, Zhang Y, Liu T, Xu ZZ, Park CK, Berta T, Jiang D, Ji RR | Cell research | 25112711 | Cell Res | 2014 Nov |
| Extracellular microRNAs activate nociceptor neurons to elicit pain via TLR7 and TRPA1. | Park CK, Xu ZZ, Berta T, Han Q, Chen G, Liu XJ, Ji RR | Neuron | 24698267 | Neuron | 2014 Apr 2 |
| Development of a membrane-anchored chemerin receptor agonist as a novel modulator of allergic airway inflammation and neuropathic pain. | Doyle JR, Krishnaji ST, Zhu G, Xu ZZ, Heller D, Ji RR, Levy BD, Kumar K, Kopin AS | The Journal of biological chemistry | 24659779 | J Biol Chem | 2014 May 9 |
| Emerging role of Toll-like receptors in the control of pain and itch. | Liu T, Gao YJ, Ji RR | Neuroscience bulletin | 22466124 | Neurosci Bull | 2012 Apr |
| Chemokines, neuronal-glial interactions, and central processing of neuropathic pain. | Gao YJ, Ji RR | Pharmacology & therapeutics | 20117131 | Pharmacol Ther | 2010 Apr |
| Acute morphine induces matrix metalloproteinase-9 up-regulation in primary sensory neurons to mask opioid-induced analgesia in mice. | Liu YC, Berta T, Liu T, Tan PH, Ji RR | Molecular pain | 22444868 | Mol Pain | 2012 Mar 25 |
| Emerging targets in neuroinflammation-driven chronic pain. | Ji RR, Xu ZZ, Gao YJ | Nature reviews. Drug discovery | 24948120 | Nat Rev Drug Discov | 2014 Jul |
| Lipoxin A4 inhibits microglial activation and reduces neuroinflammation and neuropathic pain after spinal cord hemisection. | Martini AC, Berta T, Forner S, Chen G, Bento AF, Ji RR, Rae GA | Journal of neuroinflammation | 27059991 | J Neuroinflammation | 2016 Apr 8 |
| Microglial Signaling in Chronic Pain with a Special Focus on Caspase 6, p38 MAP Kinase, and Sex Dependence. | Berta T, Qadri YJ, Chen G, Ji RR | Journal of dental research | 27307048 | J Dent Res | 2016 Sep |
| Intrathecal bone marrow stromal cells inhibit neuropathic pain via TGF-β secretion. | Chen G, Park CK, Xie RG, Ji RR | The Journal of clinical investigation | 26168219 | J Clin Invest | 2015 Aug 3 |
| Neuroprotectin/protectin D1 protects against neuropathic pain in mice after nerve trauma. | Xu ZZ, Liu XJ, Berta T, Park CK, Lü N, Serhan CN, Ji RR | Annals of neurology | 23686636 | Ann Neurol | 2013 Sep |
| Loss of NR1 subunit of NMDARs in primary sensory neurons leads to hyperexcitability and pain hypersensitivity: involvement of Ca(2+)-activated small conductance potassium channels. | Pagadala P, Park CK, Bang S, Xu ZZ, Xie RG, Liu T, Han BX, Tracey WD Jr, Wang F, Ji RR | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23946399 | J Neurosci | 2013 Aug 14 |
| Resolvin D2 is a potent endogenous inhibitor for transient receptor potential subtype V1/A1, inflammatory pain, and spinal cord synaptic plasticity in mice: distinct roles of resolvin D1, D2, and E1. | Park CK, Xu ZZ, Liu T, Lü N, Serhan CN, Ji RR | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22171045 | J Neurosci | 2011 Dec 14 |
| Decoding functional metabolomics with docosahexaenoyl ethanolamide (DHEA) identifies novel bioactive signals. | Yang R, Fredman G, Krishnamoorthy S, Agrawal N, Irimia D, Piomelli D, Serhan CN | The Journal of biological chemistry | 21757729 | J Biol Chem | 2011 Sep 9 |
| Enduring prevention and transient reduction of postoperative pain by intrathecal resolvin D1. | Huang L, Wang CF, Serhan CN, Strichartz G | Pain | 21255928 | Pain | 2011 Mar |
| Targeting CYP2J to reduce paclitaxel-induced peripheral neuropathic pain. | Sisignano M, Angioni C, Park CK, Meyer Dos Santos S, Jordan H, Kuzikov M, Liu D, Zinn S, Hohman SW, Schreiber Y, Zimmer B, Schmidt M, Lu R, Suo J, Zhang DD, Schäfer SM, Hofmann M, Yekkirala AS, de Bruin N, Parnham MJ, Woolf CJ, Ji RR, Scholich K, Geisslinger G | Proceedings of the National Academy of Sciences of the United States of America | 27791151 | Proc Natl Acad Sci U S A | 2016 Nov 1 |
| Resolvins RvE1 and RvD1 attenuate inflammatory pain via central and peripheral actions. | Xu ZZ, Zhang L, Liu T, Park JY, Berta T, Yang R, Serhan CN, Ji RR | Nature medicine | 20383154 | Nat Med | 2010 May |
| Short small-interfering RNAs produce interferon-α-mediated analgesia. | Tan PH, Gao YJ, Berta T, Xu ZZ, Ji RR | British journal of anaesthesia | 22307241 | Br J Anaesth | 2012 Apr |
| Moving beyond "good fat, bad fat": the complex roles of dietary lipids in cellular function and health: session abstracts. | Abumrad NA, Piomelli D, Yurko-Mauro K, Merrill A, Clandinin MT, Serhan CN | Advances in nutrition (Bethesda, Md.) | 22332103 | Adv Nutr | 2012 Jan |
| Macrophage proresolving mediator maresin 1 stimulates tissue regeneration and controls pain. | Serhan CN, Dalli J, Karamnov S, Choi A, Park CK, Xu ZZ, Ji RR, Zhu M, Petasis NA | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 22253477 | FASEB J | 2012 Apr |
| Specialized Pro-Resolving Mediators as Resolution Pharmacology for the Control of Pain and Itch. | Ji RR | Annual review of pharmacology and toxicology | 36100219 | Annu Rev Pharmacol Toxicol | 2023 Jan 20 |
| Molecularly-guided spatial proteomics captures single-cell identity and heterogeneity of the nervous system. | Dutta S, Pang M, Coughlin GM, Gudavalli S, Roukes ML, Chou TF, Gradinaru V | bioRxiv : the preprint server for biology | 39990460 | bioRxiv | 2025 Feb 10 |
| Entrapment and social problem-solving in suicidal behavior across the adult lifespan. | Wang C, Keilp JG, Galfalvy H, Bridge JA, Sheftall AH, Szanto K | Journal of affective disorders | 36842650 | J Affect Disord | 2023 May 15 |
| Assessing the Validity of the Ask Suicide-Screening Questions in Black Youth. | Horowitz LM, Mournet AM, Sheftall A, He JP, Lowry NJ, Aguinaldo LD, Sullivant SA, Wharff EA, Merikangas KR, Pao M, Bridge JA | Journal of the Academy of Consultation-Liaison Psychiatry | 36273745 | J Acad Consult Liaison Psychiatry | 2023 Jul-Aug |
| Severity and Transition of Suicidal Behaviors in Childhood: Sex, Racial, and Ethnic Differences in the Adolescent Brain Cognitive Development (ABCD) Study. | Ortin-Peralta A, Sheftall AH, Osborn A, Miranda R | The Journal of adolescent health : official publication of the Society for Adolescent Medicine | 37389520 | J Adolesc Health | 2023 Oct |
| Neurocognitive and clinical characteristics of elementary school-aged children with a history of suicidal thoughts and behaviors. | Chen Q, Armstrong SE, Vakil F, Bridge JA, Keilp JG, Sheftall AH | Journal of affective disorders | 37442443 | J Affect Disord | 2023 Oct 15 |
| Alterations in performance and discriminating power of the death/suicide implicit association test across the lifespan. | Ruch DA, Bridge JA, Tissue J, Madden SP, Galfavy H, Gorlyn M, Sheftall AH, Szanto K, Keilp JG | Psychiatry research | 38492262 | Psychiatry Res | 2024 May |
| Longitudinal trajectories of suicidal ideation among child welfare-involved 7- to 12-year-old children. | Ayer L, Hassler G, Ohana E, Sheftall AH, Anderson NW, Griffin BA | Journal of child psychology and psychiatry, and allied disciplines | 38659338 | J Child Psychol Psychiatry | 2024 Nov |
| National Trends in Suicide Among Asian American or Pacific Islander Youth. | Keum BT, Oh S, Sheftall AH | JAMA network open | 39052296 | JAMA Netw Open | 2024 Jul 1 |
| Preteen Suicide Risk Screening in the Pediatric Outpatient Setting: A Clinical Pathway. | Hennefield L, Denton EG, Chen PG, Sheftall AH, Ayer L | Journal of the Academy of Consultation-Liaison Psychiatry | 38908827 | J Acad Consult Liaison Psychiatry | 2024 Nov-Dec |
| The valine-arginine dipeptide repeat protein encoded by mammalian telomeric RNA appears highly expressed in mitosis and may repress global translation. | Al-Turki TM, Mantri V, Willcox S, Mills CA, Herring LE, Cho SJ, Lee H, Meyer C, Anton ES, Griffith JD | bioRxiv : the preprint server for biology | 39211251 | bioRxiv | 2024 Jul 29 |
| Radial glia promote microglial development through integrin α(V)β(8) -TGFβ1 signaling. | McKinsey GL, Santander N, Zhang X, Kleemann K, Tran L, Katewa A, Conant K, Barraza M, Waddell K, Lizama C, La Russa M, Koo HJ, Lee H, Mukherjee D, Paidassi H, Anton ES, Atabai K, Sheppard D, Butovsky O, Arnold TD | bioRxiv : the preprint server for biology | 37790363 | bioRxiv | 2023 Sep 21 |
| Mapping of neuronal and glial primary cilia contactome and connectome in the human cerebral cortex. | Wu JY, Cho SJ, Descant K, Li PH, Shapson-Coe A, Januszewski M, Berger DR, Meyer C, Casingal C, Huda A, Liu J, Ghashghaei T, Brenman M, Jiang M, Scarborough J, Pope A, Jain V, Stein JL, Guo J, Yasuda R, Lichtman JW, Anton ES | Neuron | 37898123 | Neuron | 2024 Jan 3 |
| Embryo model completes gastrulation to neurulation and organogenesis. | Amadei G, Handford CE, Qiu C, De Jonghe J, Greenfeld H, Tran M, Martin BK, Chen DY, Aguilera-Castrejon A, Hanna JH, Elowitz MB, Hollfelder F, Shendure J, Glover DM, Zernicka-Goetz M | Nature | 36007540 | Nature | 2022 Oct |
| Synthetic mammalian signaling circuits for robust cell population control. | Ma Y, Budde MW, Mayalu MN, Zhu J, Lu AC, Murray RM, Elowitz MB | Cell | 35235768 | Cell | 2022 Mar 17 |
| EasyFlow: An open source, user friendly cytometry analyzer with graphic user interface (GUI). | Ma Y, Antebi Y | bioRxiv : the preprint server for biology | 37609189 | bioRxiv | 2023 Aug 9 |
| Principles of Computation by Competitive Protein Dimerization Networks. | Parres-Gold J, Levine M, Emert B, Stuart A, Elowitz MB | bioRxiv : the preprint server for biology | 37961250 | bioRxiv | 2024 Sep 15 |
| EasyFlow: An open-source, user-friendly cytometry analyzer with graphic user interface (GUI). | Ma Y, Eizenberg-Magar I, Antebi Y | PloS one | 39536028 | PLoS One | 2024 |
| Simultaneous Protein and RNA Analysis in Single Extracellular Vesicles, Including Viruses. | Troyer Z, Gololobova O, Koppula A, Liao Z, Horns F, Elowitz MB, Tosar JP, Batish M, Witwer KW | ACS nano | 39306763 | ACS Nano | 2024 Oct 1 |
| A synthetic protein-level neural network in mammalian cells. | Chen Z, Linton JM, Xia S, Fan X, Yu D, Wang J, Zhu R, Elowitz MB | Science (New York, N.Y.) | 39666795 | Science | 2024 Dec 13 |
| Engineering RNA export for measurement and manipulation of living cells. | Horns F, Martinez JA, Fan C, Haque M, Linton JM, Tobin V, Santat L, Maggiolo AO, Bjorkman PJ, Lois C, Elowitz MB | Cell | 37437570 | Cell | 2023 Aug 17 |
| Imaging cell lineage with a synthetic digital recording system. | Chow KK, Budde MW, Granados AA, Cabrera M, Yoon S, Cho S, Huang TH, Koulena N, Frieda KL, Cai L, Lois C, Elowitz MB | Science (New York, N.Y.) | 33833095 | Science | 2021 Apr 9 |
| Ligand-receptor promiscuity enables cellular addressing. | Su CJ, Murugan A, Linton JM, Yeluri A, Bois J, Klumpe H, Langley MA, Antebi YE, Elowitz MB | Cell systems | 35421362 | Cell Syst | 2022 May 18 |
| The computational capabilities of many-to-many protein interaction networks. | Klumpe HE, Garcia-Ojalvo J, Elowitz MB, Antebi YE | Cell systems | 37348461 | Cell Syst | 2023 Jun 21 |
| Integrated spatial genomics reveals global architecture of single nuclei. | Takei Y, Yun J, Zheng S, Ollikainen N, Pierson N, White J, Shah S, Thomassie J, Suo S, Eng CL, Guttman M, Yuan GC, Cai L | Nature | 33505024 | Nature | 2021 Feb |
| Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH. | Eng CL, Lawson M, Zhu Q, Dries R, Koulena N, Takei Y, Yun J, Cronin C, Karp C, Yuan GC, Cai L | Nature | 30911168 | Nature | 2019 Apr |
| Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH. | Shah S, Takei Y, Zhou W, Lubeck E, Yun J, Eng CL, Koulena N, Cronin C, Karp C, Liaw EJ, Amin M, Cai L | Cell | 29887381 | Cell | 2018 Jul 12 |
| The context-dependent, combinatorial logic of BMP signaling. | Klumpe HE, Langley MA, Linton JM, Su CJ, Antebi YE, Elowitz MB | Cell systems | 35421361 | Cell Syst | 2022 May 18 |
| Lineage motifs: developmental modules for control of cell type proportions. | Tran M, Askary A, Elowitz MB | bioRxiv : the preprint server for biology | 37333085 | bioRxiv | 2023 Jun 7 |
| In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription. | Askary A, Sanchez-Guardado L, Linton JM, Chadly DM, Budde MW, Cai L, Lois C, Elowitz MB | Nature biotechnology | 31740838 | Nat Biotechnol | 2020 Jan |
| Programmable protein circuit design. | Chen Z, Elowitz MB | Cell | 33848464 | Cell | 2021 Apr 29 |
| Giotto: a toolbox for integrative analysis and visualization of spatial expression data. | Dries R, Zhu Q, Dong R, Eng CL, Li H, Liu K, Fu Y, Zhao T, Sarkar A, Bao F, George RE, Pierson N, Cai L, Yuan GC | Genome biology | 33685491 | Genome Biol | 2021 Mar 8 |
| Constitutive splicing and economies of scale in gene expression. | Ding F, Elowitz MB | Nature structural & molecular biology | 31133700 | Nat Struct Mol Biol | 2019 Jun |
| Projection neurons are necessary for the maintenance of the mouse olfactory circuit. | Sánchez-Guardado L, Razavi P, Wang B, Callejas-Marín A, Lois C | eLife | 39671236 | Elife | 2024 Dec 13 |
| A conserved morphogenetic mechanism for epidermal ensheathment of nociceptive sensory neurites. | Jiang N, Rasmussen JP, Clanton JA, Rosenberg MF, Luedke KP, Cronan MR, Parker ED, Kim HJ, Vaughan JC, Sagasti A, Parrish JZ | eLife | 30855229 | Elife | 2019 Mar 11 |
| A BODIPY-Based Donor/Donor-Acceptor System: Towards Highly Efficient Long-Wavelength-Excitable Near-IR Polymer Dots with Narrow and Strong Absorption Features. | Chen L, Chen D, Jiang Y, Zhang J, Yu J, DuFort CC, Hingorani SR, Zhang X, Wu C, Chiu DT | Angewandte Chemie (International ed. in English) | 30912228 | Angew Chem Int Ed Engl | 2019 May 20 |
| Microtubule Acetylation Is Required for Mechanosensation in Drosophila. | Yan C, Wang F, Peng Y, Williams CR, Jenkins B, Wildonger J, Kim HJ, Perr JB, Vaughan JC, Kern ME, Falvo MR, O'Brien ET 3rd, Superfine R, Tuthill JC, Xiang Y, Rogers SL, Parrish JZ | Cell reports | 30355484 | Cell Rep | 2018 Oct 23 |
| Dual lineage tracing shows that glomerular parietal epithelial cells can transdifferentiate toward the adult podocyte fate. | Kaverina NV, Eng DG, Freedman BS, Kutz JN, Chozinski TJ, Vaughan JC, Miner JH, Pippin JW, Shankland SJ | Kidney international | 31200942 | Kidney Int | 2019 Sep |
| Multi-immersion open-top light-sheet microscope for high-throughput imaging of cleared tissues. | Glaser AK, Reder NP, Chen Y, Yin C, Wei L, Kang S, Barner LA, Xie W, McCarty EF, Mao C, Halpern AR, Stoltzfus CR, Daniels JS, Gerner MY, Nicovich PR, Vaughan JC, True LD, Liu JTC | Nature communications | 31273194 | Nat Commun | 2019 Jul 4 |
| Superresolution imaging of Drosophila tissues using expansion microscopy. | Jiang N, Kim HJ, Chozinski TJ, Azpurua JE, Eaton BA, Vaughan JC, Parrish JZ | Molecular biology of the cell | 29688792 | Mol Biol Cell | 2018 Jun 15 |
| Versatile, do-it-yourself, low-cost spinning disk confocal microscope. | Halpern AR, Lee MY, Howard MD, Woodworth MA, Nicovich PR, Vaughan JC | Biomedical optics express | 35284165 | Biomed Opt Express | 2022 Feb 1 |
| BODIPY-based near-infrared semiconducting polymer dot for selective yellow laser-excited cell imaging. | Chen L, Jiang Y, Xu S, Zhang J, Jung SR, Yu J, Zhang X, Chiu DT | RSC advances | 37223645 | RSC Adv | 2023 May 15 |
| Highly multiplexed fluorescence microscopy with spectrally tunable semiconducting polymer dots. | Guo Z, Poudel C, Sarfatis MC, Yu J, Wong M, Chiu DT, Vaughan JC | Science advances | 39661691 | Sci Adv | 2024 Dec 13 |
| Switchable Fluorophores for Single-Molecule Localization Microscopy. | Li H, Vaughan JC | Chemical reviews | 30221931 | Chem Rev | 2018 Sep 26 |
| The Giardia ventrolateral flange is a lamellar membrane protrusion that supports attachment. | Hardin WR, Alas GCM, Taparia N, Thomas EB, Steele-Ogus MC, Hvorecny KL, Halpern AR, Tůmová P, Kollman JM, Vaughan JC, Sniadecki NJ, Paredez AR | PLoS pathogens | 35482847 | PLoS Pathog | 2022 Apr |
| Error-Correction Method for High-Throughput Sizing of Nanoscale Vesicles with Single-Molecule Localization Microscopy. | Jung SR, Kim J, Vojtech L, Vaughan JC, Chiu DT | The journal of physical chemistry. B | 36944080 | J Phys Chem B | 2023 Mar 30 |
| Hybrid Structured Illumination Expansion Microscopy Reveals Microbial Cytoskeleton Organization. | Halpern AR, Alas GCM, Chozinski TJ, Paredez AR, Vaughan JC | ACS nano | 29165993 | ACS Nano | 2017 Dec 26 |
| Extended-Depth 3D Super-Resolution Imaging Using Probe-Refresh STORM. | Lin D, Gagnon LA, Howard MD, Halpern AR, Vaughan JC | Biophysical journal | 29694874 | Biophys J | 2018 Apr 24 |
| Prostate Cancer Risk Stratification via Nondestructive 3D Pathology with Deep Learning-Assisted Gland Analysis. | Xie W, Reder NP, Koyuncu C, Leo P, Hawley S, Huang H, Mao C, Postupna N, Kang S, Serafin R, Gao G, Han Q, Bishop KW, Barner LA, Fu P, Wright JL, Keene CD, Vaughan JC, Janowczyk A, Glaser AK, Madabhushi A, True LD, Liu JTC | Cancer research | 34853071 | Cancer Res | 2022 Jan 15 |
| Fluorescent labeling of abundant reactive entities (FLARE) for cleared-tissue and super-resolution microscopy. | Lee MY, Mao C, Glaser AK, Woodworth MA, Halpern AR, Ali A, Liu JTC, Vaughan JC | Nature protocols | 35110740 | Nat Protoc | 2022 Mar |
| Volumetric, Nanoscale Optical Imaging of Mouse and Human Kidney via Expansion Microscopy. | Chozinski TJ, Mao C, Halpern AR, Pippin JW, Shankland SJ, Alpers CE, Najafian B, Vaughan JC | Scientific reports | 29991751 | Sci Rep | 2018 Jul 10 |
| Ratiometric Barcoding for Mass Cytometry. | Wu X, DeGottardi Q, Wu IC, Wu L, Yu J, Kwok WW, Chiu DT | Analytical chemistry | 30139253 | Anal Chem | 2018 Sep 18 |
| Feature-rich covalent stains for super-resolution and cleared tissue fluorescence microscopy. | Mao C, Lee MY, Jhan JR, Halpern AR, Woodworth MA, Glaser AK, Chozinski TJ, Shin L, Pippin JW, Shankland SJ, Liu JTC, Vaughan JC | Science advances | 32518827 | Sci Adv | 2020 May |
| Ultrabright Pdots with a Large Absorbance Cross Section and High Quantum Yield. | Zhang J, Yu J, Jiang Y, Chiu DT | ACS applied materials & interfaces | 35258939 | ACS Appl Mater Interfaces | 2022 Mar 23 |
| Nondestructive 3D Pathology with Light-Sheet Fluorescence Microscopy for Translational Research and Clinical Assays. | Liu JTC, Glaser AK, Poudel C, Vaughan JC | Annual review of analytical chemistry (Palo Alto, Calif.) | 36854208 | Annu Rev Anal Chem (Palo Alto Calif) | 2023 Jun 14 |
| Immuno-SABER enables highly multiplexed and amplified protein imaging in tissues. | Saka SK, Wang Y, Kishi JY, Zhu A, Zeng Y, Xie W, Kirli K, Yapp C, Cicconet M, Beliveau BJ, Lapan SW, Yin S, Lin M, Boyden ES, Kaeser PS, Pihan G, Church GM, Yin P | Nature biotechnology | 31427819 | Nat Biotechnol | 2019 Sep |
| APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer's Disease Phenotypes in Human iPSC-Derived Brain Cell Types. | Lin YT, Seo J, Gao F, Feldman HM, Wen HL, Penney J, Cam HP, Gjoneska E, Raja WK, Cheng J, Rueda R, Kritskiy O, Abdurrob F, Peng Z, Milo B, Yu CJ, Elmsaouri S, Dey D, Ko T, Yankner BA, Tsai LH | Neuron | 29861287 | Neuron | 2018 Jun 27 |
| APOE4 Causes Widespread Molecular and Cellular Alterations Associated with Alzheimer's Disease Phenotypes in Human iPSC-Derived Brain Cell Types. | Lin YT, Seo J, Gao F, Feldman HM, Wen HL, Penney J, Cam HP, Gjoneska E, Raja WK, Cheng J, Rueda R, Kritskiy O, Abdurrob F, Peng Z, Milo B, Yu CJ, Elmsaouri S, Dey D, Ko T, Yankner BA, Tsai LH | Neuron | 29953873 | Neuron | 2018 Jun 27 |
| The adaptive aging brain. | Aron L, Zullo J, Yankner BA | Current opinion in neurobiology | 34689041 | Curr Opin Neurobiol | 2022 Feb |
| A neurodegeneration checkpoint mediated by REST protects against the onset of Alzheimer's disease. | Aron L, Qiu C, Ngian ZK, Liang M, Drake D, Choi J, Fernandez MA, Roche P, Bunting EL, Lacey EK, Hamplova SE, Yuan M, Wolfe MS, Bennett DA, Lee EA, Yankner BA | Nature communications | 37919281 | Nat Commun | 2023 Nov 2 |
| REST and Neural Gene Network Dysregulation in iPSC Models of Alzheimer's Disease. | Meyer K, Feldman HM, Lu T, Drake D, Lim ET, Ling KH, Bishop NA, Pan Y, Seo J, Lin YT, Su SC, Church GM, Tsai LH, Yankner BA | Cell reports | 30699343 | Cell Rep | 2019 Jan 29 |
| Barcoded oligonucleotides ligated on RNA amplified for multiplexed and parallel in situ analyses. | Liu S, Punthambaker S, Iyer EPR, Ferrante T, Goodwin D, Fürth D, Pawlowski AC, Jindal K, Tam JM, Mifflin L, Alon S, Sinha A, Wassie AT, Chen F, Cheng A, Willocq V, Meyer K, Ling KH, Camplisson CK, Kohman RE, Aach J, Lee JH, Yankner BA, Boyden ES, Church GM | Nucleic acids research | 33693773 | Nucleic Acids Res | 2021 Jun 4 |
| Orgo-Seq integrates single-cell and bulk transcriptomic data to identify cell type specific-driver genes associated with autism spectrum disorder. | Lim ET, Chan Y, Dawes P, Guo X, Erdin S, Tai DJC, Liu S, Reichert JM, Burns MJ, Chan YK, Chiang JJ, Meyer K, Zhang X, Walsh CA, Yankner BA, Raychaudhuri S, Hirschhorn JN, Gusella JF, Talkowski ME, Church GM | Nature communications | 35688811 | Nat Commun | 2022 Jun 10 |
| oFlowSeq: a quantitative approach to identify protein coding mutations affecting cell type enrichment using mosaic CRISPR-Cas9 edited cerebral organoids. | Dawes P, Murray LF, Olson MN, Barton NJ, Smullen M, Suresh M, Yan G, Zhang Y, Fernandez-Fontaine A, English J, Uddin M, Pak C, Church GM, Chan Y, Lim ET | Human genetics | 36877372 | Hum Genet | 2023 Aug |
| Impaired neural stress resistance and loss of REST in bipolar disorder. | Meyer K, Ling KH, Yeo PL, Spathopoulou A, Drake D, Choi J, Aron L, Garcia-Corral M, Ko T, Lee EA, Tam JM, Perlis RH, Church GM, Tsai LH, Yankner BA | Molecular psychiatry | 37938767 | Mol Psychiatry | 2024 Jan |
| Slowing Down Aging. | Meyer K, Yankner BA | Cell metabolism | 28978424 | Cell Metab | 2017 Oct 3 |
| Regulation of lifespan by neural excitation and REST. | Zullo JM, Drake D, Aron L, O'Hern P, Dhamne SC, Davidsohn N, Mao CA, Klein WH, Rotenberg A, Bennett DA, Church GM, Colaiácovo MP, Yankner BA | Nature | 31619788 | Nature | 2019 Oct |
| TBK1 Suppresses RIPK1-Driven Apoptosis and Inflammation during Development and in Aging. | Xu D, Jin T, Zhu H, Chen H, Ofengeim D, Zou C, Mifflin L, Pan L, Amin P, Li W, Shan B, Naito MG, Meng H, Li Y, Pan H, Aron L, Adiconis X, Levin JZ, Yankner BA, Yuan J | Cell | 30146158 | Cell | 2018 Sep 6 |
| FACS-Based Sequencing Approach to Evaluate Cell Type to Genotype Associations Using Cerebral Organoids. | Murray L, Olson MN, Barton N, Dawes P, Chan Y, Lim ET | Methods in molecular biology (Clifton, N.J.) | 37300776 | Methods Mol Biol | 2023 |
| Latent Sex Differences in Molecular Signaling That Underlies Excitatory Synaptic Potentiation in the Hippocampus. | Jain A, Huang GZ, Woolley CS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30578341 | J Neurosci | 2019 Feb 27 |
| Mechanisms That Underlie Expression of Estradiol-Induced Excitatory Synaptic Potentiation in the Hippocampus Differ between Males and Females. | Jain A, Woolley CS | The Journal of neuroscience : the official journal of the Society for Neuroscience | 36650060 | J Neurosci | 2023 Feb 22 |
| Multiplexed detection of RNA using MERFISH and branched DNA amplification. | Xia C, Babcock HP, Moffitt JR, Zhuang X | Scientific reports | 31118500 | Sci Rep | 2019 May 22 |
| Multiplexed imaging of high-density libraries of RNAs with MERFISH and expansion microscopy. | Wang G, Moffitt JR, Zhuang X | Scientific reports | 29555914 | Sci Rep | 2018 Mar 19 |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T, Ang CE, Zhuang X | Cell | 37172568 | Cell | 2023 May 11 |
| Imaging-based pooled CRISPR screening reveals regulators of lncRNA localization. | Wang C, Lu T, Emanuel G, Babcock HP, Zhuang X | Proceedings of the National Academy of Sciences of the United States of America | 31085639 | Proc Natl Acad Sci U S A | 2019 May 28 |
| Genome-Scale Imaging of the 3D Organization and Transcriptional Activity of Chromatin. | Su JH, Zheng P, Kinrot SS, Bintu B, Zhuang X | Cell | 32822575 | Cell | 2020 Sep 17 |
| High-performance multiplexed fluorescence in situ hybridization in culture and tissue with matrix imprinting and clearing. | Moffitt JR, Hao J, Bambah-Mukku D, Lu T, Dulac C, Zhuang X | Proceedings of the National Academy of Sciences of the United States of America | 27911841 | Proc Natl Acad Sci U S A | 2016 Dec 13 |
| Conservation and divergence of cortical cell organization in human and mouse revealed by MERFISH. | Fang R, Xia C, Close JL, Zhang M, He J, Huang Z, Halpern AR, Long B, Miller JA, Lein ES, Zhuang X | Science (New York, N.Y.) | 35771910 | Science | 2022 Jul |
| High-throughput single-cell gene-expression profiling with multiplexed error-robust fluorescence in situ hybridization. | Moffitt JR, Hao J, Wang G, Chen KH, Babcock HP, Zhuang X | Proceedings of the National Academy of Sciences of the United States of America | 27625426 | Proc Natl Acad Sci U S A | 2016 Sep 27 |
| Spatial transcriptome profiling by MERFISH reveals subcellular RNA compartmentalization and cell cycle-dependent gene expression. | Xia C, Fan J, Emanuel G, Hao J, Zhuang X | Proceedings of the National Academy of Sciences of the United States of America | 31501331 | Proc Natl Acad Sci U S A | 2019 Sep 24 |
| m(6)A-binding YTHDF proteins promote stress granule formation. | Fu Y, Zhuang X | Nature chemical biology | 32451507 | Nat Chem Biol | 2020 Sep |
| Spatially resolved epigenomic profiling of single cells in complex tissues. | Lu T, Ang CE, Zhuang X | Cell | 36272405 | Cell | 2022 Nov 10 |
| COVID-19 and the HIV continuum in people living with HIV enrolled in Collaborating Consortium of Cohorts Producing NIDA Opportunities (C3PNO) cohorts. | Lesko CR, Keruly JC, Moore RD, Shen NM, Pytell JD, Lau B, Fojo AT, Mehta SH, Kipke M, Baum MK, Shoptaw S, Gorbach PM, Mustanski B, Javanbakht M, Siminski S, Chander G | Drug and alcohol dependence | 35331581 | Drug Alcohol Depend | 2022 Dec 1 |
| Telemedicine and visit completion among people with HIV during the coronavirus disease 2019 pandemic compared with prepandemic. | El-Nahal WG, Shen NM, Keruly JC, Jones JL, Fojo AT, Lau B, Manabe YC, Moore RD, Gebo KA, Lesko CR, Chander G | AIDS (London, England) | 34711737 | AIDS | 2022 Mar 1 |
| Molecular, spatial, and functional single-cell profiling of the hypothalamic preoptic region. | Moffitt JR, Bambah-Mukku D, Eichhorn SW, Vaughn E, Shekhar K, Perez JD, Rubinstein ND, Hao J, Regev A, Dulac C, Zhuang X | Science (New York, N.Y.) | 30385464 | Science | 2018 Nov 16 |
| High-throughput, image-based screening of pooled genetic-variant libraries. | Emanuel G, Moffitt JR, Zhuang X | Nature methods | 29083401 | Nat Methods | 2017 Dec |
| Sequence determinants of improved CRISPR sgRNA design. | Xu H, Xiao T, Chen CH, Li W, Meyer CA, Wu Q, Wu D, Cong L, Zhang F, Liu JS, Brown M, Liu XS | Genome research | 26063738 | Genome Res | 2015 Aug |
| Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. | Shmakov S, Abudayyeh OO, Makarova KS, Wolf YI, Gootenberg JS, Semenova E, Minakhin L, Joung J, Konermann S, Severinov K, Zhang F, Koonin EV | Molecular cell | 26593719 | Mol Cell | 2015 Nov 5 |
| Brains, genes, and primates. | Izpisua Belmonte JC, Callaway EM, Caddick SJ, Churchland P, Feng G, Homanics GE, Lee KF, Leopold DA, Miller CT, Mitchell JF, Mitalipov S, Moutri AR, Movshon JA, Okano H, Reynolds JH, Ringach D, Sejnowski TJ, Silva AC, Strick PL, Wu J, Zhang F | Neuron | 25950631 | Neuron | 2015 May 6 |
| Nucleic acid detection with CRISPR-Cas13a/C2c2. | Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F | Science (New York, N.Y.) | 28408723 | Science | 2017 Apr 28 |
| Structural Basis for the Altered PAM Recognition by Engineered CRISPR-Cpf1. | Nishimasu H, Yamano T, Gao L, Zhang F, Ishitani R, Nureki O | Molecular cell | 28595896 | Mol Cell | 2017 Jul 6 |
| Massively parallel single-nucleus RNA-seq with DroNc-seq. | Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A | Nature methods | 28846088 | Nat Methods | 2017 Oct |
| Engineering of CRISPR-Cas12b for human genome editing. | Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F | Nature communications | 30670702 | Nat Commun | 2019 Jan 22 |
| Effects of 3D culturing conditions on the transcriptomic profile of stem-cell-derived neurons. | Tekin H, Simmons S, Cummings B, Gao L, Adiconis X, Hession CC, Ghoshal A, Dionne D, Choudhury SR, Yesilyurt V, Sanjana NE, Shi X, Lu C, Heidenreich M, Pan JQ, Levin JZ, Zhang F | Nature biomedical engineering | 30271673 | Nat Biomed Eng | 2018 Jul |
| Unexpected connections between type VI-B CRISPR-Cas systems, bacterial natural competence, ubiquitin signaling network and DNA modification through a distinct family of membrane proteins. | Makarova KS, Gao L, Zhang F, Koonin EV | FEMS microbiology letters | 31089700 | FEMS Microbiol Lett | 2019 Apr 1 |
| A Survey of Genome Editing Activity for 16 Cas12a Orthologs. | Zetsche B, Abudayyeh OO, Gootenberg JS, Scott DA, Zhang F | The Keio journal of medicine | 31723075 | Keio J Med | 2020 Sep 25 |
| In vivo genome editing improves muscle function in a mouse model of Duchenne muscular dystrophy. | Nelson CE, Hakim CH, Ousterout DG, Thakore PI, Moreb EA, Castellanos Rivera RM, Madhavan S, Pan X, Ran FA, Yan WX, Asokan A, Zhang F, Duan D, Gersbach CA | Science (New York, N.Y.) | 26721684 | Science | 2016 Jan 22 |
| Structure and Engineering of Francisella novicida Cas9. | Hirano H, Gootenberg JS, Horii T, Abudayyeh OO, Kimura M, Hsu PD, Nakane T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O | Cell | 26875867 | Cell | 2016 Feb 25 |
| Diverse evolutionary roots and mechanistic variations of the CRISPR-Cas systems. | Mohanraju P, Makarova KS, Zetsche B, Zhang F, Koonin EV, van der Oost J | Science (New York, N.Y.) | 27493190 | Science | 2016 Aug 5 |
| RNA targeting with CRISPR-Cas13. | Abudayyeh OO, Gootenberg JS, Essletzbichler P, Han S, Joung J, Belanto JJ, Verdine V, Cox DBT, Kellner MJ, Regev A, Lander ES, Voytas DF, Ting AY, Zhang F | Nature | 28976959 | Nature | 2017 Oct 12 |
| Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA. | Yamano T, Nishimasu H, Zetsche B, Hirano H, Slaymaker IM, Li Y, Fedorova I, Nakane T, Makarova KS, Koonin EV, Ishitani R, Zhang F, Nureki O | Cell | 27114038 | Cell | 2016 May 5 |
| Diverse enzymatic activities mediate antiviral immunity in prokaryotes. | Gao L, Altae-Tran H, Böhning F, Makarova KS, Segel M, Schmid-Burgk JL, Koob J, Wolf YI, Koonin EV, Zhang F | Science (New York, N.Y.) | 32855333 | Science | 2020 Aug 28 |
| LAMP-Seq enables sensitive, multiplexed COVID-19 diagnostics using molecular barcoding. | Ludwig KU, Schmithausen RM, Li D, Jacobs ML, Hollstein R, Blumenstock K, Liebing J, Słabicki M, Ben-Shmuel A, Israeli O, Weiss S, Ebert TS, Paran N, Rüdiger W, Wilbring G, Feldman D, Lippke B, Ishorst N, Hochfeld LM, Beins EC, Kaltheuner IH, Schmitz M, Wöhler A, Döhla M, Sib E, Jentzsch M, Moench EC, Borrajo JD, Strecker J, Reinhardt J, Cleary B, Geyer M, Hölzel M, Macrae R, Nöthen MM, Hoffmann P, Exner M, Regev A, Zhang F, Schmid-Burgk JL | Nature biotechnology | 34188222 | Nat Biotechnol | 2021 Dec |
| Genomic determinants of pathogenicity in SARS-CoV-2 and other human coronaviruses. | Gussow AB, Auslander N, Faure G, Wolf YI, Zhang F, Koonin EV | Proceedings of the National Academy of Sciences of the United States of America | 32522874 | Proc Natl Acad Sci U S A | 2020 Jun 30 |
| In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes. | Jin X, Simmons SK, Guo A, Shetty AS, Ko M, Nguyen L, Jokhi V, Robinson E, Oyler P, Curry N, Deangeli G, Lodato S, Levin JZ, Regev A, Zhang F, Arlotta P | Science (New York, N.Y.) | 33243861 | Science | 2020 Nov 27 |
| Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing. | Joung J, Ladha A, Saito M, Kim NG, Woolley AE, Segel M, Barretto RPJ, Ranu A, Macrae RK, Faure G, Ioannidi EI, Krajeski RN, Bruneau R, Huang MW, Yu XG, Li JZ, Walker BD, Hung DT, Greninger AL, Jerome KR, Gootenberg JS, Abudayyeh OO, Zhang F | The New England journal of medicine | 32937062 | N Engl J Med | 2020 Oct 8 |
| Crystal Structure of Staphylococcus aureus Cas9. | Nishimasu H, Cong L, Yan WX, Ran FA, Zetsche B, Li Y, Kurabayashi A, Ishitani R, Zhang F, Nureki O | Cell | 26317473 | Cell | 2015 Aug 27 |
| BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis. | Canver MC, Smith EC, Sher F, Pinello L, Sanjana NE, Shalem O, Chen DD, Schupp PG, Vinjamur DS, Garcia SP, Luc S, Kurita R, Nakamura Y, Fujiwara Y, Maeda T, Yuan GC, Zhang F, Orkin SH, Bauer DE | Nature | 26375006 | Nature | 2015 Nov 12 |
| Applications of CRISPR-Cas systems in neuroscience. | Heidenreich M, Zhang F | Nature reviews. Neuroscience | 26656253 | Nat Rev Neurosci | 2016 Jan |
| Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR-mediated direct in vivo screening. | Wang G, Chow RD, Ye L, Guzman CD, Dai X, Dong MB, Zhang F, Sharp PA, Platt RJ, Chen S | Science advances | 29503867 | Sci Adv | 2018 Feb |
| Structural Basis for the Canonical and Non-canonical PAM Recognition by CRISPR-Cpf1. | Yamano T, Zetsche B, Ishitani R, Zhang F, Nishimasu H, Nureki O | Molecular cell | 28781234 | Mol Cell | 2017 Aug 17 |
| Field-deployable viral diagnostics using CRISPR-Cas13. | Myhrvold C, Freije CA, Gootenberg JS, Abudayyeh OO, Metsky HC, Durbin AF, Kellner MJ, Tan AL, Paul LM, Parham LA, Garcia KF, Barnes KG, Chak B, Mondini A, Nogueira ML, Isern S, Michael SF, Lorenzana I, Yozwiak NL, MacInnis BL, Bosch I, Gehrke L, Zhang F, Sabeti PC | Science (New York, N.Y.) | 29700266 | Science | 2018 Apr 27 |
| SHERLOCK: nucleic acid detection with CRISPR nucleases. | Kellner MJ, Koob JG, Gootenberg JS, Abudayyeh OO, Zhang F | Nature protocols | 31548639 | Nat Protoc | 2019 Oct |
| CRISPR-Based Therapeutic Genome Editing: Strategies and In Vivo Delivery by AAV Vectors. | Wang D, Zhang F, Gao G | Cell | 32243786 | Cell | 2020 Apr 2 |
| CRISPR-Cas9: Prospects and Challenges. | Zhang F | Human gene therapy | 26176430 | Hum Gene Ther | 2015 Jul |
| A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks. | Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A | Cell | 26189680 | Cell | 2015 Jul 30 |
| Div-Seq: Single-nucleus RNA-Seq reveals dynamics of rare adult newborn neurons. | Habib N, Li Y, Heidenreich M, Swiech L, Avraham-Davidi I, Trombetta JJ, Hession C, Zhang F, Regev A | Science (New York, N.Y.) | 27471252 | Science | 2016 Aug 26 |
| C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. | Abudayyeh OO, Gootenberg JS, Konermann S, Joung J, Slaymaker IM, Cox DB, Shmakov S, Makarova KS, Semenova E, Minakhin L, Severinov K, Regev A, Lander ES, Koonin EV, Zhang F | Science (New York, N.Y.) | 27256883 | Science | 2016 Aug 5 |
| Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6. | Gootenberg JS, Abudayyeh OO, Kellner MJ, Joung J, Collins JJ, Zhang F | Science (New York, N.Y.) | 29449508 | Science | 2018 Apr 27 |
| High-resolution interrogation of functional elements in the noncoding genome. | Sanjana NE, Wright J, Zheng K, Shalem O, Fontanillas P, Joung J, Cheng C, Regev A, Zhang F | Science (New York, N.Y.) | 27708104 | Science | 2016 Sep 30 |
| GUIDES: sgRNA design for loss-of-function screens. | Meier JA, Zhang F, Sanjana NE | Nature methods | 28858339 | Nat Methods | 2017 Aug 31 |
| Chd8 Mutation Leads to Autistic-like Behaviors and Impaired Striatal Circuits. | Platt RJ, Zhou Y, Slaymaker IM, Shetty AS, Weisbach NR, Kim JA, Sharma J, Desai M, Sood S, Kempton HR, Crabtree GR, Feng G, Zhang F | Cell reports | 28402856 | Cell Rep | 2017 Apr 11 |
| Diversity and evolution of class 2 CRISPR-Cas systems. | Shmakov S, Smargon A, Scott D, Cox D, Pyzocha N, Yan W, Abudayyeh OO, Gootenberg JS, Makarova KS, Wolf YI, Severinov K, Zhang F, Koonin EV | Nature reviews. Microbiology | 28111461 | Nat Rev Microbiol | 2017 Mar |
| AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma. | Chow RD, Guzman CD, Wang G, Schmidt F, Youngblood MW, Ye L, Errami Y, Dong MB, Martinez MA, Zhang S, Renauer P, Bilguvar K, Gunel M, Sharp PA, Zhang F, Platt RJ, Chen S | Nature neuroscience | 28805815 | Nat Neurosci | 2017 Oct |
| An RNA-aptamer-based two-color CRISPR labeling system. | Wang S, Su JH, Zhang F, Zhuang X | Scientific reports | 27229896 | Sci Rep | 2016 May 27 |
| Rationally engineered Cas9 nucleases with improved specificity. | Slaymaker IM, Gao L, Zetsche B, Scott DA, Yan WX, Zhang F | Science (New York, N.Y.) | 26628643 | Science | 2016 Jan 1 |
| Hypoxia as a therapy for mitochondrial disease. | Jain IH, Zazzeron L, Goli R, Alexa K, Schatzman-Bone S, Dhillon H, Goldberger O, Peng J, Shalem O, Sanjana NE, Zhang F, Goessling W, Zapol WM, Mootha VK | Science (New York, N.Y.) | 26917594 | Science | 2016 Apr 1 |
| In vivo gene editing in dystrophic mouse muscle and muscle stem cells. | Tabebordbar M, Zhu K, Cheng JKW, Chew WL, Widrick JJ, Yan WX, Maesner C, Wu EY, Xiao R, Ran FA, Cong L, Zhang F, Vandenberghe LH, Church GM, Wagers AJ | Science (New York, N.Y.) | 26721686 | Science | 2016 Jan 22 |
| High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage. | Slaymaker IM, Mesa P, Kellner MJ, Kannan S, Brignole E, Koob J, Feliciano PR, Stella S, Abudayyeh OO, Gootenberg JS, Strecker J, Montoya G, Zhang F | Cell reports | 30917325 | Cell Rep | 2019 Mar 26 |
| Optical Pooled Screens in Human Cells. | Feldman D, Singh A, Schmid-Burgk JL, Carlson RJ, Mezger A, Garrity AJ, Zhang F, Blainey PC | Cell | 31626775 | Cell | 2019 Oct 17 |
| Highly Parallel Profiling of Cas9 Variant Specificity. | Schmid-Burgk JL, Gao L, Li D, Gardner Z, Strecker J, Lash B, Zhang F | Molecular cell | 32187529 | Mol Cell | 2020 May 21 |
| Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening. | Joung J, Konermann S, Gootenberg JS, Abudayyeh OO, Platt RJ, Brigham MD, Sanjana NE, Zhang F | Nature protocols | 28333914 | Nat Protoc | 2017 Apr |
| Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. | Zetsche B, Gootenberg JS, Abudayyeh OO, Slaymaker IM, Makarova KS, Essletzbichler P, Volz SE, Joung J, van der Oost J, Regev A, Koonin EV, Zhang F | Cell | 26422227 | Cell | 2015 Oct 22 |
| Engineered CRISPR-Cas9 nuclease with expanded targeting space. | Nishimasu H, Shi X, Ishiguro S, Gao L, Hirano S, Okazaki S, Noda T, Abudayyeh OO, Gootenberg JS, Mori H, Oura S, Holmes B, Tanaka M, Seki M, Hirano H, Aburatani H, Ishitani R, Ikawa M, Yachie N, Zhang F, Nureki O | Science (New York, N.Y.) | 30166441 | Science | 2018 Sep 21 |
| A cytosine deaminase for programmable single-base RNA editing. | Abudayyeh OO, Gootenberg JS, Franklin B, Koob J, Kellner MJ, Ladha A, Joung J, Kirchgatterer P, Cox DBT, Zhang F | Science (New York, N.Y.) | 31296651 | Science | 2019 Jul 26 |
| Compact RNA editors with small Cas13 proteins. | Kannan S, Altae-Tran H, Jin X, Madigan VJ, Oshiro R, Makarova KS, Koonin EV, Zhang F | Nature biotechnology | 34462587 | Nat Biotechnol | 2022 Feb |
| Structure and engineering of the minimal type VI CRISPR-Cas13bt3. | Nakagawa R, Kannan S, Altae-Tran H, Takeda SN, Tomita A, Hirano H, Kusakizako T, Nishizawa T, Yamashita K, Zhang F, Nishimasu H, Nureki O | Molecular cell | 36027912 | Mol Cell | 2022 Sep 1 |
| Engineered Cpf1 variants with altered PAM specificities. | Gao L, Cox DBT, Yan WX, Manteiga JC, Schneider MW, Yamano T, Nishimasu H, Nureki O, Crosetto N, Zhang F | Nature biotechnology | 28581492 | Nat Biotechnol | 2017 Aug |
| Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array. | Zetsche B, Heidenreich M, Mohanraju P, Fedorova I, Kneppers J, DeGennaro EM, Winblad N, Choudhury SR, Abudayyeh OO, Gootenberg JS, Wu WY, Scott DA, Severinov K, van der Oost J, Zhang F | Nature biotechnology | 27918548 | Nat Biotechnol | 2017 Jan |
| RNA editing with CRISPR-Cas13. | Cox DBT, Gootenberg JS, Abudayyeh OO, Franklin B, Kellner MJ, Joung J, Zhang F | Science (New York, N.Y.) | 29070703 | Science | 2017 Nov 24 |
| Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13. | Abudayyeh OO, Gootenberg JS, Kellner MJ, Zhang F | The CRISPR journal | 31225754 | CRISPR J | 2019 Jun |
| DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction. | Weinstein JA, Regev A, Zhang F | Cell | 31230717 | Cell | 2019 Jun 27 |
| Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9. | Hirano S, Abudayyeh OO, Gootenberg JS, Horii T, Ishitani R, Hatada I, Zhang F, Nishimasu H, Nureki O | Nature communications | 31036811 | Nat Commun | 2019 Apr 29 |
| Implications of human genetic variation in CRISPR-based therapeutic genome editing. | Scott DA, Zhang F | Nature medicine | 28759051 | Nat Med | 2017 Sep |
| Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood. | Joung J, Engreitz JM, Konermann S, Abudayyeh OO, Verdine VK, Aguet F, Gootenberg JS, Sanjana NE, Wright JB, Fulco CP, Tseng YY, Yoon CH, Boehm JS, Lander ES, Zhang F | Nature | 28792927 | Nature | 2017 Aug 17 |
| Programmable Inhibition and Detection of RNA Viruses Using Cas13. | Freije CA, Myhrvold C, Boehm CK, Lin AE, Welch NL, Carter A, Metsky HC, Luo CY, Abudayyeh OO, Gootenberg JS, Yozwiak NL, Zhang F, Sabeti PC | Molecular cell | 31607545 | Mol Cell | 2019 Dec 5 |
| Mice with Shank3 Mutations Associated with ASD and Schizophrenia Display Both Shared and Distinct Defects. | Zhou Y, Kaiser T, Monteiro P, Zhang X, Van der Goes MS, Wang D, Barak B, Zeng M, Li C, Lu C, Wells M, Amaya A, Nguyen S, Lewis M, Sanjana N, Zhou Y, Zhang M, Zhang F, Fu Z, Feng G | Neuron | 26687841 | Neuron | 2016 Jan 6 |
| Discovery of proteins associated with a predefined genomic locus via dCas9-APEX-mediated proximity labeling. | Myers SA, Wright J, Peckner R, Kalish BT, Zhang F, Carr SA | Nature methods | 29735997 | Nat Methods | 2018 Jun |
| Pluripotent stem cell-derived models of neurological diseases reveal early transcriptional heterogeneity. | Sorek M, Oweis W, Nissim-Rafinia M, Maman M, Simon S, Hession CC, Adiconis X, Simmons SK, Sanjana NE, Shi X, Lu C, Pan JQ, Xu X, Pouladi MA, Ellerby LM, Zhang F, Levin JZ, Meshorer E | Genome biology | 33663567 | Genome Biol | 2021 Mar 4 |
| The evolution of red color vision is linked to coordinated rhodopsin tuning in lycaenid butterflies. | Liénard MA, Bernard GD, Allen A, Lassance JM, Song S, Childers RR, Yu N, Ye D, Stephenson A, Valencia-Montoya WA, Salzman S, Whitaker MRL, Calonje M, Zhang F, Pierce NE | Proceedings of the National Academy of Sciences of the United States of America | 33547236 | Proc Natl Acad Sci U S A | 2021 Feb 9 |
| RNA-guided DNA insertion with CRISPR-associated transposases. | Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F | Science (New York, N.Y.) | 31171706 | Science | 2019 Jul 5 |
| BLISS is a versatile and quantitative method for genome-wide profiling of DNA double-strand breaks. | Yan WX, Mirzazadeh R, Garnerone S, Scott D, Schneider MW, Kallas T, Custodio J, Wernersson E, Li Y, Gao L, Federova Y, Zetsche B, Zhang F, Bienko M, Crosetto N | Nature communications | 28497783 | Nat Commun | 2017 May 12 |
| Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28. | Smargon AA, Cox DBT, Pyzocha NK, Zheng K, Slaymaker IM, Gootenberg JS, Abudayyeh OA, Essletzbichler P, Shmakov S, Makarova KS, Koonin EV, Zhang F | Molecular cell | 28065598 | Mol Cell | 2017 Feb 16 |
| Extended depth-of-field light-sheet microscopy improves imaging of large volumes at high numerical aperture. | Keomanee-Dizon K, Jones M, Luu P, Fraser SE, Truong TV | Applied physics letters | 36276589 | Appl Phys Lett | 2022 Oct 17 |
| Adaptive optics improves multiphoton super-resolution imaging. | Zheng W, Wu Y, Winter P, Fischer R, Nogare DD, Hong A, McCormick C, Christensen R, Dempsey WP, Arnold DB, Zimmerberg J, Chitnis A, Sellers J, Waterman C, Shroff H | Nature methods | 28628128 | Nat Methods | 2017 Sep |
| Using enhanced number and brightness to measure protein oligomerization dynamics in live cells. | Cutrale F, Rodriguez D, Hortigüela V, Chiu CL, Otterstrom J, Mieruszynski S, Seriola A, Larrañaga E, Raya A, Lakadamyali M, Fraser SE, Martinez E, Ojosnegros S | Nature protocols | 30675035 | Nat Protoc | 2019 Feb |
| ERMrest: A Collaborative Data Catalog with Fine Grain Access Control. | Czajkowski K, Kesselman C, Schuler R | Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience | 29756002 | Proc IEEE Int Conf Escience | 2017 Oct |
| High-contrast, synchronous volumetric imaging with selective volume illumination microscopy. | Truong TV, Holland DB, Madaan S, Andreev A, Keomanee-Dizon K, Troll JV, Koo DES, McFall-Ngai MJ, Fraser SE | Communications biology | 32060411 | Commun Biol | 2020 Feb 14 |
| Sharing Begins at Home: How Continuous and Ubiquitous FAIRness Can Enhance Research Productivity and Data Reuse. | Dempsey W, Foster I, Fraser S, Kesselman C | Harvard data science review | 36035065 | Harv Data Sci Rev | 2022 Summer |
| Genetic and neuronal regulation of sleep by neuropeptide VF. | Lee DA, Andreev A, Truong TV, Chen A, Hill AJ, Oikonomou G, Pham U, Hong YK, Tran S, Glass L, Sapin V, Engle J, Fraser SE, Prober DA | eLife | 29106375 | Elife | 2017 Nov 6 |
| Regional synapse gain and loss accompany memory formation in larval zebrafish. | Dempsey WP, Du Z, Nadtochiy A, Smith CD, Czajkowski K, Andreev A, Robson DN, Li JM, Applebaum S, Truong TV, Kesselman C, Fraser SE, Arnold DB | Proceedings of the National Academy of Sciences of the United States of America | 35031564 | Proc Natl Acad Sci U S A | 2022 Jan 18 |
| Experiences with Deriva: An Asset Management Platform for Accelerating eScience. | Bugacov A, Czajkowski K, Kesselman C, Kumar A, Schuler RE, Tangmunarunkit H | Proceedings ... IEEE International Conference on eScience. IEEE International Conference on eScience | 29756001 | Proc IEEE Int Conf Escience | 2017 Oct |
| Puzzle Imaging: Using Large-Scale Dimensionality Reduction Algorithms for Localization. | Glaser JI, Zamft BM, Church GM, Kording KP | PloS one | 26192446 | PLoS One | 2015 |
| Chemically Inducible Chromosomal Evolution (CIChE) for Multicopy Metabolic Pathway Engineering. | Love AM, Biggs BW, Tyo KEJ, Ajikumar PK | Methods in molecular biology (Clifton, N.J.) | 30788784 | Methods Mol Biol | 2019 |
| Single-Cell CRISPR-Based Lineage Tracing in Mice. | Kalhor K, Church GM | Biochemistry | 31730337 | Biochemistry | 2019 Dec 3 |
| Model-guided mechanism discovery and parameter selection for directed evolution. | Stainbrook SC, Tyo KEJ | Applied microbiology and biotechnology | 31686141 | Appl Microbiol Biotechnol | 2019 Dec |
| Wide-field three-photon excitation in biological samples. | Rowlands CJ, Park D, Bruns OT, Piatkevich KD, Fukumura D, Jain RK, Bawendi MG, Boyden ES, So PT | Light, science & applications | 29152380 | Light Sci Appl | 2017 May 5 |
| Expansion microscopy: enabling single cell analysis in intact biological systems. | Alon S, Huynh GH, Boyden ES | The FEBS journal | 29938896 | FEBS J | 2019 Apr |
| Spontaneous CRISPR loci generation in vivo by non-canonical spacer integration. | Nivala J, Shipman SL, Church GM | Nature microbiology | 29379209 | Nat Microbiol | 2018 Mar |
| Development of novel metabolite-responsive transcription factors via transposon-mediated protein fusion. | Younger AKD, Su PY, Shepard AJ, Udani SV, Cybulski TR, Tyo KEJ, Leonard JN | Protein engineering, design & selection : PEDS | 29385546 | Protein Eng Des Sel | 2018 Feb 1 |
| Expansion microscopy of C. elegans. | Yu CJ, Barry NC, Wassie AT, Sinha A, Bhattacharya A, Asano S, Zhang C, Chen F, Hobert O, Goodman MB, Haspel G, Boyden ES | eLife | 32356725 | Elife | 2020 May 1 |
| RNA timestamps identify the age of single molecules in RNA sequencing. | Rodriques SG, Chen LM, Liu S, Zhong ED, Scherrer JR, Boyden ES, Chen F | Nature biotechnology | 33077959 | Nat Biotechnol | 2021 Mar |
| ExCel: Super-Resolution Imaging of C. elegans with Expansion Microscopy. | Yu CJ, Orozco Cosio DM, Boyden ES | Methods in molecular biology (Clifton, N.J.) | 35320565 | Methods Mol Biol | 2022 |
| A robotic multidimensional directed evolution approach applied to fluorescent voltage reporters. | Piatkevich KD, Jung EE, Straub C, Linghu C, Park D, Suk HJ, Hochbaum DR, Goodwin D, Pnevmatikakis E, Pak N, Kawashima T, Yang CT, Rhoades JL, Shemesh O, Asano S, Yoon YG, Freifeld L, Saulnier JL, Riegler C, Engert F, Hughes T, Drobizhev M, Szabo B, Ahrens MB, Flavell SW, Sabatini BL, Boyden ES | Nature chemical biology | 29483642 | Nat Chem Biol | 2018 Apr |
| Closed-Loop Real-Time Imaging Enables Fully Automated Cell-Targeted Patch-Clamp Neural Recording In Vivo. | Suk HJ, van Welie I, Kodandaramaiah SB, Allen B, Forest CR, Boyden ES | Neuron | 28858614 | Neuron | 2017 Aug 30 |
| Microchip amplifier for in vitro, in vivo, and automated whole cell patch-clamp recording. | Harrison RR, Kolb I, Kodandaramaiah SB, Chubykin AA, Yang A, Bear MF, Boyden ES, Forest CR | Journal of neurophysiology | 25429119 | J Neurophysiol | 2015 Feb 15 |
| Spatial information in large-scale neural recordings. | Cybulski TR, Glaser JI, Marblestone AH, Zamft BM, Boyden ES, Church GM, Kording KP | Frontiers in computational neuroscience | 25653613 | Front Comput Neurosci | 2014 |
| Nanoscale imaging of RNA with expansion microscopy. | Chen F, Wassie AT, Cote AJ, Sinha A, Alon S, Asano S, Daugharthy ER, Chang JB, Marblestone A, Church GM, Raj A, Boyden ES | Nature methods | 27376770 | Nat Methods | 2016 Aug |
| Nucleotide-time alignment for molecular recorders. | Cybulski TR, Boyden ES, Church GM, Tyo KEJ, Kording KP | PLoS computational biology | 28459860 | PLoS Comput Biol | 2017 May |
| Advances in the automation of whole-cell patch clamp technology. | Suk HJ, Boyden ES, van Welie I | Journal of neuroscience methods | 31336060 | J Neurosci Methods | 2019 Oct 1 |
| A cryptography-based approach for movement decoding. | Dyer EL, Gheshlaghi Azar M, Perich MG, Fernandes HL, Naufel S, Miller LE, Körding KP | Nature biomedical engineering | 31015712 | Nat Biomed Eng | 2017 Dec |
| Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. | Alon S, Goodwin DR, Sinha A, Wassie AT, Chen F, Daugharthy ER, Bando Y, Kajita A, Xue AG, Marrett K, Prior R, Cui Y, Payne AC, Yao CC, Suk HJ, Wang R, Yu CJ, Tillberg P, Reginato P, Pak N, Liu S, Punthambaker S, Iyer EPR, Kohman RE, Miller JA, Lein ES, Lako A, Cullen N, Rodig S, Helvie K, Abravanel DL, Wagle N, Johnson BE, Klughammer J, Slyper M, Waldman J, Jané-Valbuena J, Rozenblatt-Rosen O, Regev A, IMAXT Consortium, Church GM, Marblestone AH, Boyden ES | Science (New York, N.Y.) | 33509999 | Science | 2021 Jan 29 |
| Molecular recordings by directed CRISPR spacer acquisition. | Shipman SL, Nivala J, Macklis JD, Church GM | Science (New York, N.Y.) | 27284167 | Science | 2016 Jul 29 |
| Hybrid Microscopy: Enabling Inexpensive High-Performance Imaging through Combined Physical and Optical Magnifications. | Zhang YS, Chang JB, Alvarez MM, Trujillo-de Santiago G, Aleman J, Batzaya B, Krishnadoss V, Ramanujam AA, Kazemzadeh-Narbat M, Chen F, Tillberg PW, Dokmeci MR, Boyden ES, Khademhosseini A | Scientific reports | 26975883 | Sci Rep | 2016 Mar 15 |
| Evidence for Long-Timescale Patterns of Synaptic Inputs in CA1 of Awake Behaving Mice. | Kolb I, Talei Franzesi G, Wang M, Kodandaramaiah SB, Forest CR, Boyden ES, Singer AC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 29279309 | J Neurosci | 2018 Feb 14 |
| DNA binding strength increases the processivity and activity of a Y-Family DNA polymerase. | Wu J, de Paz A, Zamft BM, Marblestone AH, Boyden ES, Kording KP, Tyo KEJ | Scientific reports | 28684739 | Sci Rep | 2017 Jul 6 |
| Post-translational digital data encoding into the genomes of mammalian cell populations. | Callisto A, Strutz J, Leeper K, Kalhor R, Church G, Tyo KEJ, Bhan N | bioRxiv : the preprint server for biology | 38765976 | bioRxiv | 2024 Dec 9 |
| Lineage barcoding in mice with homing CRISPR. | Leeper K, Kalhor K, Vernet A, Graveline A, Church GM, Mali P, Kalhor R | Nature protocols | 33692551 | Nat Protoc | 2021 Apr |
| Rapidly evolving homing CRISPR barcodes. | Kalhor R, Mali P, Church GM | Nature methods | 27918539 | Nat Methods | 2017 Feb |
| Expansion Mini-Microscopy: An Enabling Alternative in Point-of-Care Diagnostics. | Zhang YS, Santiago GT, Alvarez MM, Schiff SJ, Boyden ES, Khademhosseini A | Current opinion in biomedical engineering | 29062977 | Curr Opin Biomed Eng | 2017 Mar |
| Iterative expansion microscopy. | Chang JB, Chen F, Yoon YG, Jung EE, Babcock H, Kang JS, Asano S, Suk HJ, Pak N, Tillberg PW, Wassie AT, Cai D, Boyden ES | Nature methods | 28417997 | Nat Methods | 2017 Jun |
| High-resolution mapping of DNA polymerase fidelity using nucleotide imbalances and next-generation sequencing. | de Paz AM, Cybulski TR, Marblestone AH, Zamft BM, Church GM, Boyden ES, Kording KP, Tyo KEJ | Nucleic acids research | 29718339 | Nucleic Acids Res | 2018 Jul 27 |
| 3D nanofabrication by volumetric deposition and controlled shrinkage of patterned scaffolds. | Oran D, Rodriques SG, Gao R, Asano S, Skylar-Scott MA, Chen F, Tillberg PW, Marblestone AH, Boyden ES | Science (New York, N.Y.) | 30545883 | Science | 2018 Dec 14 |
| Relationship Between Sleep Quality and Mood: Ecological Momentary Assessment Study. | Triantafillou S, Saeb S, Lattie EG, Mohr DC, Kording KP | JMIR mental health | 30916663 | JMIR Ment Health | 2019 Mar 27 |
| Developmental barcoding of whole mouse via homing CRISPR. | Kalhor R, Kalhor K, Mejia L, Leeper K, Graveline A, Mali P, Church GM | Science (New York, N.Y.) | 30093604 | Science | 2018 Aug 31 |
| On Functions Computed on Trees. | Farhoodi R, Filom K, Jones IS, Kording KP | Neural computation | 31525312 | Neural Comput | 2019 Nov |
| CRISPR-Cas encoding of a digital movie into the genomes of a population of living bacteria. | Shipman SL, Nivala J, Macklis JD, Church GM | Nature | 28700573 | Nature | 2017 Jul 20 |
| Noninvasive Deep Brain Stimulation via Temporally Interfering Electric Fields. | Grossman N, Bono D, Dedic N, Kodandaramaiah SB, Rudenko A, Suk HJ, Cassara AM, Neufeld E, Kuster N, Tsai LH, Pascual-Leone A, Boyden ES | Cell | 28575667 | Cell | 2017 Jun 1 |
| A novel flexible cuff-like microelectrode for dual purpose, acute and chronic electrical interfacing with the mouse cervical vagus nerve. | Caravaca AS, Tsaava T, Goldman L, Silverman H, Riggott G, Chavan SS, Bouton C, Tracey KJ, Desimone R, Boyden ES, Sohal HS, Olofsson PS | Journal of neural engineering | 28628030 | J Neural Eng | 2017 Dec |
| Recording Temporal Signals with Minutes Resolution Using Enzymatic DNA Synthesis. | Bhan N, Callisto A, Strutz J, Glaser J, Kalhor R, Boyden ES, Church G, Kording K, Tyo KEJ | Journal of the American Chemical Society | 34591459 | J Am Chem Soc | 2021 Oct 13 |
| Engineering Ca(2+)-Dependent DNA Polymerase Activity. | Biggs BW, de Paz AM, Bhan NJ, Cybulski TR, Church GM, Tyo KEJ | ACS synthetic biology | 37856140 | ACS Synth Biol | 2023 Nov 17 |
| Inferring causal connectivity from pairwise recordings and optogenetics. | Lepperød ME, Stöber T, Hafting T, Fyhn M, Kording KP | PLoS computational biology | 37934793 | PLoS Comput Biol | 2023 Nov |
| The Development and Analysis of Integrated Neuroscience Data. | Glaser JI, Kording KP | Frontiers in computational neuroscience | 26903852 | Front Comput Neurosci | 2016 |
| Optical imaging. Expansion microscopy. | Chen F, Tillberg PW, Boyden ES | Science (New York, N.Y.) | 25592419 | Science | 2015 Jan 30 |
| Toward an Integration of Deep Learning and Neuroscience. | Marblestone AH, Wayne G, Kording KP | Frontiers in computational neuroscience | 27683554 | Front Comput Neurosci | 2016 |
| Assembly and operation of the autopatcher for automated intracellular neural recording in vivo. | Kodandaramaiah SB, Holst GL, Wickersham IR, Singer AC, Franzesi GT, McKinnon ML, Forest CR, Boyden ES | Nature protocols | 26938115 | Nat Protoc | 2016 Apr |
| Programmable RNA-binding protein composed of repeats of a single modular unit. | Adamala KP, Martin-Alarcon DA, Boyden ES | Proceedings of the National Academy of Sciences of the United States of America | 27118836 | Proc Natl Acad Sci U S A | 2016 May 10 |
| Rapid Sequential in Situ Multiplexing with DNA Exchange Imaging in Neuronal Cells and Tissues. | Wang Y, Woehrstein JB, Donoghue N, Dai M, Avendaño MS, Schackmann RCJ, Zoeller JJ, Wang SSH, Tillberg PW, Park D, Lapan SW, Boyden ES, Brugge JS, Kaeser PS, Church GM, Agasti SS, Jungmann R, Yin P | Nano letters | 28933153 | Nano Lett | 2017 Oct 11 |
| Expansion microscopy: development and neuroscience applications. | Karagiannis ED, Boyden ES | Current opinion in neurobiology | 29316506 | Curr Opin Neurobiol | 2018 Jun |
| Modern Machine Learning as a Benchmark for Fitting Neural Responses. | Benjamin AS, Fernandes HL, Tomlinson T, Ramkumar P, VerSteeg C, Chowdhury RH, Miller LE, Kording KP | Frontiers in computational neuroscience | 30072887 | Front Comput Neurosci | 2018 |
| Engineering genetic circuit interactions within and between synthetic minimal cells. | Adamala KP, Martin-Alarcon DA, Guthrie-Honea KR, Boyden ES | Nature chemistry | 28430194 | Nat Chem | 2017 May |
| Could a Neuroscientist Understand a Microprocessor? | Jonas E, Kording KP | PLoS computational biology | 28081141 | PLoS Comput Biol | 2017 Jan |
| Diversity of transgenic mouse models for selective targeting of midbrain dopamine neurons. | Lammel S, Steinberg EE, Földy C, Wall NR, Beier K, Luo L, Malenka RC | Neuron | 25611513 | Neuron | 2015 Jan 21 |
| The BRAIN Initiative: developing technology to catalyse neuroscience discovery. | Jorgenson LA, Newsome WT, Anderson DJ, Bargmann CI, Brown EN, Deisseroth K, Donoghue JP, Hudson KL, Ling GS, MacLeish PR, Marder E, Normann RA, Sanes JR, Schnitzer MJ, Sejnowski TJ, Tank DW, Tsien RY, Ugurbil K, Wingfield JC | Philosophical transactions of the Royal Society of London. Series B, Biological sciences | 25823863 | Philos Trans R Soc Lond B Biol Sci | 2015 May 19 |
| Integration of optogenetics with complementary methodologies in systems neuroscience. | Kim CK, Adhikari A, Deisseroth K | Nature reviews. Neuroscience | 28303019 | Nat Rev Neurosci | 2017 Mar 17 |
| Two eARCHT3.0 Lines for Optogenetic Silencing of Dopaminergic and Serotonergic Neurons. | Krol A, Lopez-Huerta VG, Corey TEC, Deisseroth K, Ting JT, Feng G | Frontiers in neural circuits | 30774584 | Front Neural Circuits | 2019 |
| Circuit dynamics of adaptive and maladaptive behaviour. | Deisseroth K | Nature | 24429629 | Nature | 2014 Jan 16 |
| Structural and molecular interrogation of intact biological systems. | Chung K, Wallace J, Kim SY, Kalyanasundaram S, Andalman AS, Davidson TJ, Mirzabekov JJ, Zalocusky KA, Mattis J, Denisin AK, Pak S, Bernstein H, Ramakrishnan C, Grosenick L, Gradinaru V, Deisseroth K | Nature | 23575631 | Nature | 2013 May 16 |
| Imaging zebrafish neural circuitry from whole brain to synapse. | Leung LC, Wang GX, Mourrain P | Frontiers in neural circuits | 23630470 | Front Neural Circuits | 2013 |
| A Neural Basis for Control of Cichlid Female Reproductive Behavior by Prostaglandin F2α. | Juntti SA, Hilliard AT, Kent KR, Kumar A, Nguyen A, Jimenez MA, Loveland JL, Mourrain P, Fernald RD | Current biology : CB | 26996507 | Curr Biol | 2016 Apr 4 |
| Genetically targeted chemical assembly of functional materials in living cells, tissues, and animals. | Liu J, Kim YS, Richardson CE, Tom A, Ramakrishnan C, Birey F, Katsumata T, Chen S, Wang C, Wang X, Joubert LM, Jiang Y, Wang H, Fenno LE, Tok JB, Pașca SP, Shen K, Bao Z, Deisseroth K | Science (New York, N.Y.) | 32193327 | Science | 2020 Mar 20 |
| Rabies screen reveals GPe control of cocaine-triggered plasticity. | Beier KT, Kim CK, Hoerbelt P, Hung LW, Heifets BD, DeLoach KE, Mosca TJ, Neuner S, Deisseroth K, Luo L, Malenka RC | Nature | 28902833 | Nature | 2017 Sep 21 |
| Three-dimensional intact-tissue sequencing of single-cell transcriptional states. | Wang X, Allen WE, Wright MA, Sylwestrak EL, Samusik N, Vesuna S, Evans K, Liu C, Ramakrishnan C, Liu J, Nolan GP, Bava FA, Deisseroth K | Science (New York, N.Y.) | 29930089 | Science | 2018 Jul 27 |
| Basolateral amygdala bidirectionally modulates stress-induced hippocampal learning and memory deficits through a p25/Cdk5-dependent pathway. | Rei D, Mason X, Seo J, Gräff J, Rudenko A, Wang J, Rueda R, Siegert S, Cho S, Canter RG, Mungenast AE, Deisseroth K, Tsai LH | Proceedings of the National Academy of Sciences of the United States of America | 25995364 | Proc Natl Acad Sci U S A | 2015 Jun 9 |
| Simultaneous cellular-resolution optical perturbation and imaging of place cell firing fields. | Rickgauer JP, Deisseroth K, Tank DW | Nature neuroscience | 25402854 | Nat Neurosci | 2014 Dec |
| Permanent genetic access to transiently active neurons via TRAP: targeted recombination in active populations. | Guenthner CJ, Miyamichi K, Yang HH, Heller HC, Luo L | Neuron | 23764283 | Neuron | 2013 Jun 5 |
| Circuit Architecture of VTA Dopamine Neurons Revealed by Systematic Input-Output Mapping. | Beier KT, Steinberg EE, DeLoach KE, Xie S, Miyamichi K, Schwarz L, Gao XJ, Kremer EJ, Malenka RC, Luo L | Cell | 26232228 | Cell | 2015 Jul 30 |
| Targeting cells with single vectors using multiple-feature Boolean logic. | Fenno LE, Mattis J, Ramakrishnan C, Hyun M, Lee SY, He M, Tucciarone J, Selimbeyoglu A, Berndt A, Grosenick L, Zalocusky KA, Bernstein H, Swanson H, Perry C, Diester I, Boyce FM, Bass CE, Neve R, Huang ZJ, Deisseroth K | Nature methods | 24908100 | Nat Methods | 2014 Jul |
| Enhancing the performance of the light field microscope using wavefront coding. | Cohen N, Yang S, Andalman A, Broxton M, Grosenick L, Deisseroth K, Horowitz M, Levoy M | Optics express | 25322056 | Opt Express | 2014 Oct 6 |
| Optical neural interfaces. | Warden MR, Cardin JA, Deisseroth K | Annual review of biomedical engineering | 25014785 | Annu Rev Biomed Eng | 2014 Jul 11 |
| Natural neural projection dynamics underlying social behavior. | Gunaydin LA, Grosenick L, Finkelstein JC, Kauvar IV, Fenno LE, Adhikari A, Lammel S, Mirzabekov JJ, Airan RD, Zalocusky KA, Tye KM, Anikeeva P, Malenka RC, Deisseroth K | Cell | 24949967 | Cell | 2014 Jun 19 |
| Prolonged, brain-wide expression of nuclear-localized GCaMP3 for functional circuit mapping. | Kim CK, Miri A, Leung LC, Berndt A, Mourrain P, Tank DW, Burdine RD | Frontiers in neural circuits | 25505384 | Front Neural Circuits | 2014 |
| Visualizing hypothalamic network dynamics for appetitive and consummatory behaviors. | Jennings JH, Ung RL, Resendez SL, Stamatakis AM, Taylor JG, Huang J, Veleta K, Kantak PA, Aita M, Shilling-Scrivo K, Ramakrishnan C, Deisseroth K, Otte S, Stuber GD | Cell | 25635459 | Cell | 2015 Jan 29 |
| Closed-loop and activity-guided optogenetic control. | Grosenick L, Marshel JH, Deisseroth K | Neuron | 25856490 | Neuron | 2015 Apr 8 |
| Ventral hippocampal afferents to the nucleus accumbens regulate susceptibility to depression. | Bagot RC, Parise EM, Peña CJ, Zhang HX, Maze I, Chaudhury D, Persaud B, Cachope R, Bolaños-Guzmán CA, Cheer JF, Deisseroth K, Han MH, Nestler EJ | Nature communications | 25952660 | Nat Commun | 2015 May 8 |
| Ancestral Circuits for the Coordinated Modulation of Brain State. | Lovett-Barron M, Andalman AS, Allen WE, Vesuna S, Kauvar I, Burns VM, Deisseroth K | Cell | 29103613 | Cell | 2017 Nov 30 |
| BLIMP1 Induces Transient Metastatic Heterogeneity in Pancreatic Cancer. | Chiou SH, Risca VI, Wang GX, Yang D, Grüner BM, Kathiria AS, Ma RK, Vaka D, Chu P, Kozak M, Castellini L, Graves EE, Kim GE, Mourrain P, Koong AC, Giaccia AJ, Winslow MM | Cancer discovery | 28790031 | Cancer Discov | 2017 Oct |
| MicroRNA-9 Couples Brain Neurogenesis and Angiogenesis. | Madelaine R, Sloan SA, Huber N, Notwell JH, Leung LC, Skariah G, Halluin C, Paşca SP, Bejerano G, Krasnow MA, Barres BA, Mourrain P | Cell reports | 28813666 | Cell Rep | 2017 Aug 15 |
| CloudReg: automatic terabyte-scale cross-modal brain volume registration. | Chandrashekhar V, Tward DJ, Crowley D, Crow AK, Wright MA, Hsueh BY, Gore F, Machado TA, Branch A, Rosenblum JS, Deisseroth K, Vogelstein JT | Nature methods | 34253927 | Nat Methods | 2021 Aug |
| Wiring and Molecular Features of Prefrontal Ensembles Representing Distinct Experiences. | Ye L, Allen WE, Thompson KR, Tian Q, Hsueh B, Ramakrishnan C, Wang AC, Jennings JH, Adhikari A, Halpern CH, Witten IB, Barth AL, Luo L, McNab JA, Deisseroth K | Cell | 27238022 | Cell | 2016 Jun 16 |
| Fmr1 KO and fenobam treatment differentially impact distinct synapse populations of mouse neocortex. | Wang GX, Smith SJ, Mourrain P | Neuron | 25521380 | Neuron | 2014 Dec 17 |
| Enhancer divergence and cis-regulatory evolution in the human and chimp neural crest. | Prescott SL, Srinivasan R, Marchetto MC, Grishina I, Narvaiza I, Selleri L, Gage FH, Swigut T, Wysocka J | Cell | 26365491 | Cell | 2015 Sep 24 |
| L1-associated genomic regions are deleted in somatic cells of the healthy human brain. | Erwin JA, Paquola AC, Singer T, Gallina I, Novotny M, Quayle C, Bedrosian TA, Alves FI, Butcher CR, Herdy JR, Sarkar A, Lasken RS, Muotri AR, Gage FH | Nature neuroscience | 27618310 | Nat Neurosci | 2016 Dec |
| Patch-Seq Protocol to Analyze the Electrophysiology, Morphology and Transcriptome of Whole Single Neurons Derived From Human Pluripotent Stem Cells. | van den Hurk M, Erwin JA, Yeo GW, Gage FH, Bardy C | Frontiers in molecular neuroscience | 30147644 | Front Mol Neurosci | 2018 |
| The role of adult hippocampal neurogenesis in brain health and disease. | Toda T, Parylak SL, Linker SB, Gage FH | Molecular psychiatry | 29679070 | Mol Psychiatry | 2019 Jan |
| Insights into the role of somatic mosaicism in the brain. | Paquola ACM, Erwin JA, Gage FH | Current opinion in systems biology | 29226270 | Curr Opin Syst Biol | 2017 Feb |
| Nuclear RNA-seq of single neurons reveals molecular signatures of activation. | Lacar B, Linker SB, Jaeger BN, Krishnaswami SR, Barron JJ, Kelder MJE, Parylak SL, Paquola ACM, Venepally P, Novotny M, O'Connor C, Fitzpatrick C, Erwin JA, Hsu JY, Husband D, McConnell MJ, Lasken R, Gage FH | Nature communications | 27090946 | Nat Commun | 2016 Apr 19 |
| To eat, or not to eat, that is the question: Neural stem cells escape phagocytosis in autism with macrocephaly. | Schafer ST, Gage FH | Proceedings of the National Academy of Sciences of the United States of America | 33883269 | Proc Natl Acad Sci U S A | 2021 May 11 |
| Increasing the resolution of the adult neurogenesis picture. | Lacar B, Parylak SL, Vadodaria KC, Sarkar A, Gage FH | F1000prime reports | 24592320 | F1000Prime Rep | 2014 |
| Paradox of pattern separation and adult neurogenesis: A dual role for new neurons balancing memory resolution and robustness. | Johnston ST, Shtrahman M, Parylak S, Gonçalves JT, Gage FH | Neurobiology of learning and memory | 26549627 | Neurobiol Learn Mem | 2016 Mar |
| Early life experience drives structural variation of neural genomes in mice. | Bedrosian TA, Quayle C, Novaresi N, Gage FH | Science (New York, N.Y.) | 29567711 | Science | 2018 Mar 23 |
| An in vitro model of lissencephaly: expanding the role of DCX during neurogenesis. | Shahsavani M, Pronk RJ, Falk R, Lam M, Moslem M, Linker SB, Salma J, Day K, Schuster J, Anderlid BM, Dahl N, Gage FH, Falk A | Molecular psychiatry | 28924182 | Mol Psychiatry | 2018 Jul |
| Prediction of response to drug therapy in psychiatric disorders. | Stern S, Linker S, Vadodaria KC, Marchetto MC, Gage FH | Open biology | 29794033 | Open Biol | 2018 May |
| Astroglial cells regulate the developmental timeline of human neurons differentiated from induced pluripotent stem cells. | Tang X, Zhou L, Wagner AM, Marchetto MC, Muotri AR, Gage FH, Chen G | Stem cell research | 23759711 | Stem Cell Res | 2013 Sep |
| Transcriptional and epigenetic mechanisms of cellular reprogramming to induced pluripotency. | van den Hurk M, Kenis G, Bardy C, van den Hove DL, Gage FH, Steinbusch HW, Rutten BP | Epigenomics | 27419933 | Epigenomics | 2016 Aug |
| Environment-driven somatic mosaicism in brain disorders. | Bedrosian TA, Linker S, Gage FH | Genome medicine | 27215330 | Genome Med | 2016 May 23 |
| Altered Neuronal Support and Inflammatory Response in Bipolar Disorder Patient-Derived Astrocytes. | Vadodaria KC, Mendes APD, Mei A, Racha V, Erikson G, Shokhirev MN, Oefner R, Heard KJ, McCarthy MJ, Eyler L, Kelsoe JR, Santos R, Marchetto MC, Gage FH | Stem cell reports | 33667413 | Stem Cell Reports | 2021 Apr 13 |
| Neurons derived from patients with bipolar disorder divide into intrinsically different sub-populations of neurons, predicting the patients' responsiveness to lithium. | Stern S, Santos R, Marchetto MC, Mendes APD, Rouleau GA, Biesmans S, Wang QW, Yao J, Charnay P, Bang AG, Alda M, Gage FH | Molecular psychiatry | 28242870 | Mol Psychiatry | 2018 Jun |
| Species-specific maturation profiles of human, chimpanzee and bonobo neural cells. | Marchetto MC, Hrvoj-Mihic B, Kerman BE, Yu DX, Vadodaria KC, Linker SB, Narvaiza I, Santos R, Denli AM, Mendes AP, Oefner R, Cook J, McHenry L, Grasmick JM, Heard K, Fredlender C, Randolph-Moore L, Kshirsagar R, Xenitopoulos R, Chou G, Hah N, Muotri AR, Padmanabhan K, Semendeferi K, Gage FH | eLife | 30730291 | Elife | 2019 Feb 7 |
| Mobile DNA elements in the generation of diversity and complexity in the brain. | Erwin JA, Marchetto MC, Gage FH | Nature reviews. Neuroscience | 25005482 | Nat Rev Neurosci | 2014 Aug |
| Differential L1 regulation in pluripotent stem cells of humans and apes. | Marchetto MCN, Narvaiza I, Denli AM, Benner C, Lazzarini TA, Nathanson JL, Paquola ACM, Desai KN, Herai RH, Weitzman MD, Yeo GW, Muotri AR, Gage FH | Nature | 24153179 | Nature | 2013 Nov 28 |
| Mosaic copy number variation in human neurons. | McConnell MJ, Lindberg MR, Brennand KJ, Piper JC, Voet T, Cowing-Zitron C, Shumilina S, Lasken RS, Vermeesch JR, Hall IM, Gage FH | Science (New York, N.Y.) | 24179226 | Science | 2013 Nov 1 |
| Predicting the functional states of human iPSC-derived neurons with single-cell RNA-seq and electrophysiology. | Bardy C, van den Hurk M, Kakaradov B, Erwin JA, Jaeger BN, Hernandez RV, Eames T, Paucar AA, Gorris M, Marchand C, Jappelli R, Barron J, Bryant AK, Kellogg M, Lasken RS, Rutten BP, Steinbusch HW, Yeo GW, Gage FH | Molecular psychiatry | 27698428 | Mol Psychiatry | 2016 Nov |
| Examining non-LTR retrotransposons in the context of the evolving primate brain. | Linker SB, Marchetto MC, Narvaiza I, Denli AM, Gage FH | BMC biology | 28800766 | BMC Biol | 2017 Aug 11 |
| In vivo imaging of dendritic pruning in dentate granule cells. | Gonçalves JT, Bloyd CW, Shtrahman M, Johnston ST, Schafer ST, Parylak SL, Tran T, Chang T, Gage FH | Nature neuroscience | 27135217 | Nat Neurosci | 2016 Jun |
| Using single nuclei for RNA-seq to capture the transcriptome of postmortem neurons. | Krishnaswami SR, Grindberg RV, Novotny M, Venepally P, Lacar B, Bhutani K, Linker SB, Pham S, Erwin JA, Miller JA, Hodge R, McCarthy JK, Kelder M, McCorrison J, Aevermann BD, Fuertes FD, Scheuermann RH, Lee J, Lein ES, Schork N, McConnell MJ, Gage FH, Lasken RS | Nature protocols | 26890679 | Nat Protoc | 2016 Mar |
| Emergence of a Homo sapiens-specific gene family and chromosome 16p11.2 CNV susceptibility. | Nuttle X, Giannuzzi G, Duyzend MH, Schraiber JG, Narvaiza I, Sudmant PH, Penn O, Chiatante G, Malig M, Huddleston J, Benner C, Camponeschi F, Ciofi-Baffoni S, Stessman HA, Marchetto MC, Denman L, Harshman L, Baker C, Raja A, Penewit K, Janke N, Tang WJ, Ventura M, Banci L, Antonacci F, Akey JM, Amemiya CT, Gage FH, Reymond A, Eichler EE | Nature | 27487209 | Nature | 2016 Aug 11 |
| Mitochondria, Metabolism, and Redox Mechanisms in Psychiatric Disorders. | Kim Y, Vadodaria KC, Lenkei Z, Kato T, Gage FH, Marchetto MC, Santos R | Antioxidants & redox signaling | 30585734 | Antioxid Redox Signal | 2019 Aug 1 |
| A novel environment-evoked transcriptional signature predicts reactivity in single dentate granule neurons. | Jaeger BN, Linker SB, Parylak SL, Barron JJ, Gallina IS, Saavedra CD, Fitzpatrick C, Lim CK, Schafer ST, Lacar B, Jessberger S, Gage FH | Nature communications | 30082781 | Nat Commun | 2018 Aug 6 |
| Focal adhesion is associated with lithium response in bipolar disorder: evidence from a network-based multi-omics analysis. | Niemsiri V, Rosenthal SB, Nievergelt CM, Maihofer AX, Marchetto MC, Santos R, Shekhtman T, Alliey-Rodriguez N, Anand A, Balaraman Y, Berrettini WH, Bertram H, Burdick KE, Calabrese JR, Calkin CV, Conroy C, Coryell WH, DeModena A, Eyler LT, Feeder S, Fisher C, Frazier N, Frye MA, Gao K, Garnham J, Gershon ES, Goes FS, Goto T, Harrington GJ, Jakobsen P, Kamali M, Kelly M, Leckband SG, Lohoff FW, McCarthy MJ, McInnis MG, Craig D, Millett CE, Mondimore F, Morken G, Nurnberger JI, Donovan CO, Øedegaard KJ, Ryan K, Schinagle M, Shilling PD, Slaney C, Stapp EK, Stautland A, Tarwater B, Zandi PP, Alda M, Fisch KM, Gage FH, Kelsoe JR | Molecular psychiatry | 36991131 | Mol Psychiatry | 2024 Jan |
| RNA-sequencing from single nuclei. | Grindberg RV, Yee-Greenbaum JL, McConnell MJ, Novotny M, O'Shaughnessy AL, Lambert GM, Araúzo-Bravo MJ, Lee J, Fishman M, Robbins GE, Lin X, Venepally P, Badger JH, Galbraith DW, Gage FH, Lasken RS | Proceedings of the National Academy of Sciences of the United States of America | 24248345 | Proc Natl Acad Sci U S A | 2013 Dec 3 |
| Neuronal medium that supports basic synaptic functions and activity of human neurons in vitro. | Bardy C, van den Hurk M, Eames T, Marchand C, Hernandez RV, Kellogg M, Gorris M, Galet B, Palomares V, Brown J, Bang AG, Mertens J, Böhnke L, Boyer L, Simon S, Gage FH | Proceedings of the National Academy of Sciences of the United States of America | 25870293 | Proc Natl Acad Sci U S A | 2015 May 19 |
| Pathological priming causes developmental gene network heterochronicity in autistic subject-derived neurons. | Schafer ST, Paquola ACM, Stern S, Gosselin D, Ku M, Pena M, Kuret TJM, Liyanage M, Mansour AA, Jaeger BN, Marchetto MC, Glass CK, Mertens J, Gage FH | Nature neuroscience | 30617258 | Nat Neurosci | 2019 Feb |
| A human neurodevelopmental model for Williams syndrome. | Chailangkarn T, Trujillo CA, Freitas BC, Hrvoj-Mihic B, Herai RH, Yu DX, Brown TT, Marchetto MC, Bardy C, McHenry L, Stefanacci L, Järvinen A, Searcy YM, DeWitt M, Wong W, Lai P, Ard MC, Hanson KL, Romero S, Jacobs B, Dale AM, Dai L, Korenberg JR, Gage FH, Bellugi U, Halgren E, Semendeferi K, Muotri AR | Nature | 27509850 | Nature | 2016 Aug 18 |
| Adult Hippocampal Neurogenesis: A Coming-of-Age Story. | Kuhn HG, Toda T, Gage FH | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30381404 | J Neurosci | 2018 Dec 5 |
| Creating Patient-Specific Neural Cells for the In Vitro Study of Brain Disorders. | Brennand KJ, Marchetto MC, Benvenisty N, Brüstle O, Ebert A, Izpisua Belmonte JC, Kaykas A, Lancaster MA, Livesey FJ, McConnell MJ, McKay RD, Morrow EM, Muotri AR, Panchision DM, Rubin LL, Sawa A, Soldner F, Song H, Studer L, Temple S, Vaccarino FM, Wu J, Vanderhaeghen P, Gage FH, Jaenisch R | Stem cell reports | 26610635 | Stem Cell Reports | 2015 Dec 8 |
| Conserved expression of transposon-derived non-coding transcripts in primate stem cells. | Ramsay L, Marchetto MC, Caron M, Chen SH, Busche S, Kwan T, Pastinen T, Gage FH, Bourque G | BMC genomics | 28245871 | BMC Genomics | 2017 Feb 28 |
| Molecular roadblocks for cellular reprogramming. | Vierbuchen T, Wernig M | Molecular cell | 23020854 | Mol Cell | 2012 Sep 28 |
| Induced neuronal reprogramming. | Ang CE, Wernig M | The Journal of comparative neurology | 24771471 | J Comp Neurol | 2014 Aug 15 |
| Generation of induced neuronal cells by the single reprogramming factor ASCL1. | Chanda S, Ang CE, Davila J, Pak C, Mall M, Lee QY, Ahlenius H, Jung SW, Südhof TC, Wernig M | Stem cell reports | 25254342 | Stem Cell Reports | 2014 Aug 12 |
| Pathogenic mechanism of an autism-associated neuroligin mutation involves altered AMPA-receptor trafficking. | Chanda S, Aoto J, Lee SJ, Wernig M, Südhof TC | Molecular psychiatry | 25778475 | Mol Psychiatry | 2016 Feb |
| Myt1l safeguards neuronal identity by actively repressing many non-neuronal fates. | Mall M, Kareta MS, Chanda S, Ahlenius H, Perotti N, Zhou B, Grieder SD, Ge X, Drake S, Euong Ang C, Walker BM, Vierbuchen T, Fuentes DR, Brennecke P, Nitta KR, Jolma A, Steinmetz LM, Taipale J, Südhof TC, Wernig M | Nature | 28379941 | Nature | 2017 Apr 13 |
| Generation of pure GABAergic neurons by transcription factor programming. | Yang N, Chanda S, Marro S, Ng YH, Janas JA, Haag D, Ang CE, Tang Y, Flores Q, Mall M, Wapinski O, Li M, Ahlenius H, Rubenstein JL, Chang HY, Buylla AA, Südhof TC, Wernig M | Nature methods | 28504679 | Nat Methods | 2017 Jun |
| Towards an Understanding of Synapse Formation. | Südhof TC | Neuron | 30359597 | Neuron | 2018 Oct 24 |
| Acute reduction in oxygen tension enhances the induction of neurons from human fibroblasts. | Davila J, Chanda S, Ang CE, Südhof TC, Wernig M | Journal of neuroscience methods | 23562599 | J Neurosci Methods | 2013 Jun 15 |
| In Vivo Reprogramming for Brain and Spinal Cord Repair. | Chen G, Wernig M, Berninger B, Nakafuku M, Parmar M, Zhang CL | eNeuro | 26730402 | eNeuro | 2015 Sep-Oct |
| FoxO3 regulates neuronal reprogramming of cells from postnatal and aging mice. | Ahlenius H, Chanda S, Webb AE, Yousif I, Karmazin J, Prusiner SB, Brunet A, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 27402759 | Proc Natl Acad Sci U S A | 2016 Jul 26 |
| Neurons generated by direct conversion of fibroblasts reproduce synaptic phenotype caused by autism-associated neuroligin-3 mutation. | Chanda S, Marro S, Wernig M, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 24046374 | Proc Natl Acad Sci U S A | 2013 Oct 8 |
| SPARCL1 Promotes Excitatory But Not Inhibitory Synapse Formation and Function Independent of Neurexins and Neuroligins. | Gan KJ, Südhof TC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 32973045 | J Neurosci | 2020 Oct 14 |
| Neuroligin-3 confines AMPA receptors into nanoclusters, thereby controlling synaptic strength at the calyx of Held synapses. | Han Y, Cao R, Qin L, Chen LY, Tang AH, Südhof TC, Zhang B | Science advances | 35704570 | Sci Adv | 2022 Jun 17 |
| Molecular self-avoidance in synaptic neurexin complexes. | Wang CY, Trotter JH, Liakath-Ali K, Lee SJ, Liu X, Südhof TC | Science advances | 34919427 | Sci Adv | 2021 Dec 17 |
| Induction of synapse formation by de novo neurotransmitter synthesis. | Burlingham SR, Wong NF, Peterkin L, Lubow L, Dos Santos Passos C, Benner O, Ghebrial M, Cast TP, Xu-Friedman MA, Südhof TC, Chanda S | Nature communications | 35650274 | Nat Commun | 2022 Jun 1 |
| Insights and applications of direct neuronal reprogramming. | Schaukowitch K, Janas JA, Wernig M | Current opinion in genetics & development | 37862835 | Curr Opin Genet Dev | 2023 Dec |
| Astrocytic Neuroligin-3 influences gene expression and social behavior, but is dispensable for synapse number. | Qin L, Liu Z, Guo S, Han Y, Wang X, Ren W, Chen J, Zhen H, Nie C, Xing KK, Chen T, Südhof TC, Sun Y, Zhang B | Molecular psychiatry | 39003414 | Mol Psychiatry | 2025 Jan |
| Comprehensive qPCR profiling of gene expression in single neuronal cells. | Citri A, Pang ZP, Südhof TC, Wernig M, Malenka RC | Nature protocols | 22193304 | Nat Protoc | 2011 Dec 22 |
| Generation of oligodendroglial cells by direct lineage conversion. | Yang N, Zuchero JB, Ahlenius H, Marro S, Ng YH, Vierbuchen T, Hawkins JS, Geissler R, Barres BA, Wernig M | Nature biotechnology | 23584610 | Nat Biotechnol | 2013 May |
| Cerebellins are differentially expressed in selective subsets of neurons throughout the brain. | Seigneur E, Südhof TC | The Journal of comparative neurology | 28714144 | J Comp Neurol | 2017 Oct 15 |
| Transdifferentiation of human adult peripheral blood T cells into neurons. | Tanabe K, Ang CE, Chanda S, Olmos VH, Haag D, Levinson DF, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 29866841 | Proc Natl Acad Sci U S A | 2018 Jun 19 |
| Direct Reprogramming of Human Neurons Identifies MARCKSL1 as a Pathogenic Mediator of Valproic Acid-Induced Teratogenicity. | Chanda S, Ang CE, Lee QY, Ghebrial M, Haag D, Shibuya Y, Wernig M, Südhof TC | Cell stem cell | 31155484 | Cell Stem Cell | 2019 Jul 3 |
| Specific factors in blood from young but not old mice directly promote synapse formation and NMDA-receptor recruitment. | Gan KJ, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 31160442 | Proc Natl Acad Sci U S A | 2019 Jun 18 |
| The cell biology of synapse formation. | Südhof TC | The Journal of cell biology | 34086051 | J Cell Biol | 2021 Jul 5 |
| The many roads to Rome: induction of neural precursor cells from fibroblasts. | Lujan E, Wernig M | Current opinion in genetics & development | 22868177 | Curr Opin Genet Dev | 2012 Oct |
| FOXO3 shares common targets with ASCL1 genome-wide and inhibits ASCL1-dependent neurogenesis. | Webb AE, Pollina EA, Vierbuchen T, Urbán N, Ucar D, Leeman DS, Martynoga B, Sewak M, Rando TA, Guillemot F, Wernig M, Brunet A | Cell reports | 23891001 | Cell Rep | 2013 Aug 15 |
| Human Neuropsychiatric Disease Modeling using Conditional Deletion Reveals Synaptic Transmission Defects Caused by Heterozygous Mutations in NRXN1. | Pak C, Danko T, Zhang Y, Aoto J, Anderson G, Maxeiner S, Yi F, Wernig M, Südhof TC | Cell stem cell | 26279266 | Cell Stem Cell | 2015 Sep 3 |
| Neuroligin-4 Regulates Excitatory Synaptic Transmission in Human Neurons. | Marro SG, Chanda S, Yang N, Janas JA, Valperga G, Trotter J, Zhou B, Merrill S, Yousif I, Shelby H, Vogel H, Kalani MYS, Südhof TC, Wernig M | Neuron | 31257103 | Neuron | 2019 Aug 21 |
| Neuroligin-1 Signaling Controls LTP and NMDA Receptors by Distinct Molecular Pathways. | Wu X, Morishita WK, Riley AM, Hale WD, Südhof TC, Malenka RC | Neuron | 30871858 | Neuron | 2019 May 8 |
| Deletion of Neuroligins from Astrocytes Does Not Detectably Alter Synapse Numbers or Astrocyte Cytoarchitecture by Maturity. | Golf SR, Trotter JH, Wang J, Nakahara G, Han X, Wernig M, Südhof TC | bioRxiv : the preprint server for biology | 37090508 | bioRxiv | 2025 Jan 6 |
| Direct lineage conversion of terminally differentiated hepatocytes to functional neurons. | Marro S, Pang ZP, Yang N, Tsai MC, Qu K, Chang HY, Südhof TC, Wernig M | Cell stem cell | 21962918 | Cell Stem Cell | 2011 Oct 4 |
| Induction of human neuronal cells by defined transcription factors. | Pang ZP, Yang N, Vierbuchen T, Ostermeier A, Fuentes DR, Yang TQ, Citri A, Sebastiano V, Marro S, Südhof TC, Wernig M | Nature | 21617644 | Nature | 2011 May 26 |
| Cellular reprogramming: recent advances in modeling neurological diseases. | Ming GL, Brüstle O, Muotri A, Studer L, Wernig M, Christian KM | The Journal of neuroscience : the official journal of the Society for Neuroscience | 22072658 | J Neurosci | 2011 Nov 9 |
| Direct conversion of mouse fibroblasts to self-renewing, tripotent neural precursor cells. | Lujan E, Chanda S, Ahlenius H, Südhof TC, Wernig M | Proceedings of the National Academy of Sciences of the United States of America | 22308465 | Proc Natl Acad Sci U S A | 2012 Feb 14 |
| Autism-associated neuroligin-4 mutation selectively impairs glycinergic synaptic transmission in mouse brainstem synapses. | Zhang B, Gokce O, Hale WD, Brose N, Südhof TC | The Journal of experimental medicine | 29724786 | J Exp Med | 2018 Jun 4 |
| Retinoic Acid Receptor RARα-Dependent Synaptic Signaling Mediates Homeostatic Synaptic Plasticity at the Inhibitory Synapses of Mouse Visual Cortex. | Zhong LR, Chen X, Park E, Südhof TC, Chen L | The Journal of neuroscience : the official journal of the Society for Neuroscience | 30355624 | J Neurosci | 2018 Dec 5 |
| Evolution of the Autism-Associated Neuroligin-4 Gene Reveals Broad Erosion of Pseudoautosomal Regions in Rodents. | Maxeiner S, Benseler F, Krasteva-Christ G, Brose N, Südhof TC | Molecular biology and evolution | 32011705 | Mol Biol Evol | 2020 May 1 |
| The fragile X mutation impairs homeostatic plasticity in human neurons by blocking synaptic retinoic acid signaling. | Zhang Z, Marro SG, Zhang Y, Arendt KL, Patzke C, Zhou B, Fair T, Yang N, Südhof TC, Wernig M, Chen L | Science translational medicine | 30068571 | Sci Transl Med | 2018 Aug 1 |
| Efficient generation of dopaminergic induced neuronal cells with midbrain characteristics. | Ng YH, Chanda S, Janas JA, Yang N, Kokubu Y, Südhof TC, Wernig M | Stem cell reports | 34171286 | Stem Cell Reports | 2021 Jul 13 |
| Analyses of the autism-associated neuroligin-3 R451C mutation in human neurons reveal a gain-of-function synaptic mechanism. | Wang L, Mirabella VR, Dai R, Su X, Xu R, Jadali A, Bernabucci M, Singh I, Chen Y, Tian J, Jiang P, Kwan KY, Pak C, Liu C, Comoletti D, Hart RP, Chen C, Südhof TC, Pang ZP | Molecular psychiatry | 36280753 | Mol Psychiatry | 2024 Jun |
| Distinct mechanisms control the specific synaptic functions of Neuroligin 1 and Neuroligin 2. | Wang J, Sudhof T, Wernig M | EMBO reports | 39747663 | EMBO Rep | 2025 Feb |
| Rapid single-step induction of functional neurons from human pluripotent stem cells. | Zhang Y, Pak C, Han Y, Ahlenius H, Zhang Z, Chanda S, Marro S, Patzke C, Acuna C, Covy J, Xu W, Yang N, Danko T, Chen L, Wernig M, Südhof TC | Neuron | 23764284 | Neuron | 2013 Jun 5 |
| An indirect approach to generating specific human cell types. | Lujan E, Wernig M | Nature methods | 23269377 | Nat Methods | 2013 Jan |
| Induced neuronal cells: how to make and define a neuron. | Yang N, Ng YH, Pang ZP, Südhof TC, Wernig M | Cell stem cell | 22136927 | Cell Stem Cell | 2011 Dec 2 |
| Unique versus Redundant Functions of Neuroligin Genes in Shaping Excitatory and Inhibitory Synapse Properties. | Chanda S, Hale WD, Zhang B, Wernig M, Südhof TC | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28607166 | J Neurosci | 2017 Jul 19 |
| Neuromodulator Signaling Bidirectionally Controls Vesicle Numbers in Human Synapses. | Patzke C, Brockmann MM, Dai J, Gan KJ, Grauel MK, Fenske P, Liu Y, Acuna C, Rosenmund C, Südhof TC | Cell | 31585084 | Cell | 2019 Oct 3 |
| Multiple signaling pathways are essential for synapse formation induced by synaptic adhesion molecules. | Jiang X, Sando R, Südhof TC | Proceedings of the National Academy of Sciences of the United States of America | 33431662 | Proc Natl Acad Sci U S A | 2021 Jan 19 |
| Direct lineage conversions: unnatural but useful? | Vierbuchen T, Wernig M | Nature biotechnology | 21997635 | Nat Biotechnol | 2011 Oct |
| Analysis of conditional heterozygous STXBP1 mutations in human neurons. | Patzke C, Han Y, Covy J, Yi F, Maxeiner S, Wernig M, Südhof TC | The Journal of clinical investigation | 26280581 | J Clin Invest | 2015 Sep |
| Conditional deletion of L1CAM in human neurons impairs both axonal and dendritic arborization and action potential generation. | Patzke C, Acuna C, Giam LR, Wernig M, Südhof TC | The Journal of experimental medicine | 27001749 | J Exp Med | 2016 Apr 4 |
| Autism-associated SHANK3 haploinsufficiency causes Ih channelopathy in human neurons. | Yi F, Danko T, Botelho SC, Patzke C, Pak C, Wernig M, Südhof TC | Science (New York, N.Y.) | 26966193 | Science | 2016 May 6 |
| Efficient generation of functional neurons from mouse embryonic stem cells via neurogenin-2 expression. | Liu Y, Wang J, Südhof TC, Wernig M | Nature protocols | 37596357 | Nat Protoc | 2023 Oct |
| Computational methods and challenges for large-scale circuit mapping. | Helmstaedter M, Mitra PP | Current opinion in neurobiology | 22221862 | Curr Opin Neurobiol | 2012 Feb |
| The circuit architecture of whole brains at the mesoscopic scale. | Mitra PP | Neuron | 25233311 | Neuron | 2014 Sep 17 |
| High-Throughput Method of Whole-Brain Sectioning, Using the Tape-Transfer Technique. | Pinskiy V, Jones J, Tolpygo AS, Franciotti N, Weber K, Mitra PP | PloS one | 26181725 | PLoS One | 2015 |
| Out-of-focus brain image detection in serial tissue sections. | Pollatou A, Ferrante DD | Journal of neuroscience methods | 32771371 | J Neurosci Methods | 2020 Nov 1 |
| A low-cost technique to cryo-protect and freeze rodent brains, precisely aligned to stereotaxic coordinates for whole-brain cryosectioning. | Pinskiy V, Tolpygo AS, Jones J, Weber K, Franciotti N, Mitra PP | Journal of neuroscience methods | 23541995 | J Neurosci Methods | 2013 Sep 15 |
| Frequency-selective control of cortical and subcortical networks by central thalamus. | Liu J, Lee HJ, Weitz AJ, Fang Z, Lin P, Choy M, Fisher R, Pinskiy V, Tolpygo A, Mitra P, Schiff N, Lee JH | eLife | 26652162 | Elife | 2015 Dec 10 |
| Towards a comprehensive atlas of cortical connections in a primate brain: Mapping tracer injection studies of the common marmoset into a reference digital template. | Majka P, Chaplin TA, Yu HH, Tolpygo A, Mitra PP, Wójcik DK, Rosa MG | The Journal of comparative neurology | 27099164 | J Comp Neurol | 2016 Aug 1 |
| Discovery of a proneurogenic, neuroprotective chemical. | Pieper AA, Xie S, Capota E, Estill SJ, Zhong J, Long JM, Becker GL, Huntington P, Goldman SE, Shen CH, Capota M, Britt JK, Kotti T, Ure K, Brat DJ, Williams NS, MacMillan KS, Naidoo J, Melito L, Hsieh J, De Brabander J, Ready JM, McKnight SL | Cell | 20603013 | Cell | 2010 Jul 9 |
| P7C3 neuroprotective chemicals function by activating the rate-limiting enzyme in NAD salvage. | Wang G, Han T, Nijhawan D, Theodoropoulos P, Naidoo J, Yadavalli S, Mirzaei H, Pieper AA, Ready JM, McKnight SL | Cell | 25215490 | Cell | 2014 Sep 11 |
| NPAS1 represses the generation of specific subtypes of cortical interneurons. | Stanco A, Pla R, Vogt D, Chen Y, Mandal S, Walker J, Hunt RF, Lindtner S, Erdman CA, Pieper AA, Hamilton SP, Xu D, Baraban SC, Rubenstein JL | Neuron | 25467980 | Neuron | 2014 Dec 3 |
| The P7C3 class of neuroprotective compounds exerts antidepressant efficacy in mice by increasing hippocampal neurogenesis. | Walker AK, Rivera PD, Wang Q, Chuang JC, Tran S, Osborne-Lawrence S, Estill SJ, Starwalt R, Huntington P, Morlock L, Naidoo J, Williams NS, Ready JM, Eisch AJ, Pieper AA, Zigman JM | Molecular psychiatry | 24751964 | Mol Psychiatry | 2015 Apr |
| Discovery of a neuroprotective chemical, (S)-N-(3-(3,6-dibromo-9H-carbazol-9-yl)-2-fluoropropyl)-6-methoxypyridin-2-amine [(-)-P7C3-S243], with improved druglike properties. | Naidoo J, De Jesus-Cortes H, Huntington P, Estill S, Morlock LK, Starwalt R, Mangano TJ, Williams NS, Pieper AA, Ready JM | Journal of medicinal chemistry | 24697290 | J Med Chem | 2014 May 8 |
| Neuroprotective efficacy of aminopropyl carbazoles in a mouse model of amyotrophic lateral sclerosis. | Tesla R, Wolf HP, Xu P, Drawbridge J, Estill SJ, Huntington P, McDaniel L, Knobbe W, Burket A, Tran S, Starwalt R, Morlock L, Naidoo J, Williams NS, Ready JM, McKnight SL, Pieper AA | Proceedings of the National Academy of Sciences of the United States of America | 23027932 | Proc Natl Acad Sci U S A | 2012 Oct 16 |
| P7C3 and an unbiased approach to drug discovery for neurodegenerative diseases. | Pieper AA, McKnight SL, Ready JM | Chemical Society reviews | 24514864 | Chem Soc Rev | 2014 Oct 7 |
| P7C3 neuroprotective chemicals block axonal degeneration and preserve function after traumatic brain injury. | Yin TC, Britt JK, De Jesús-Cortés H, Lu Y, Genova RM, Khan MZ, Voorhees JR, Shao J, Katzman AC, Huntington PJ, Wassink C, McDaniel L, Newell EA, Dutca LM, Naidoo J, Cui H, Bassuk AG, Harper MM, McKnight SL, Ready JM, Pieper AA | Cell reports | 25220467 | Cell Rep | 2014 Sep 25 |
| Reduced GABA neuron density in auditory cerebral cortex of subjects with major depressive disorder. | Smiley JF, Hackett TA, Bleiwas C, Petkova E, Stankov A, Mann JJ, Rosoklija G, Dwork AJ | Journal of chemical neuroanatomy | 26686292 | J Chem Neuroanat | 2016 Oct |
| Neuroprotective efficacy of a proneurogenic compound after traumatic brain injury. | Blaya MO, Bramlett HM, Naidoo J, Pieper AA, Dietrich WD | Journal of neurotrauma | 24070637 | J Neurotrauma | 2014 Mar 1 |
| Neuroprotective efficacy of aminopropyl carbazoles in a mouse model of Parkinson disease. | De Jesús-Cortés H, Xu P, Drawbridge J, Estill SJ, Huntington P, Tran S, Britt J, Tesla R, Morlock L, Naidoo J, Melito LM, Wang G, Williams NS, Ready JM, McKnight SL, Pieper AA | Proceedings of the National Academy of Sciences of the United States of America | 23027934 | Proc Natl Acad Sci U S A | 2012 Oct 16 |
| Development of proneurogenic, neuroprotective small molecules. | MacMillan KS, Naidoo J, Liang J, Melito L, Williams NS, Morlock L, Huntington PJ, Estill SJ, Longgood J, Becker GL, McKnight SL, Pieper AA, De Brabander JK, Ready JM | Journal of the American Chemical Society | 21210688 | J Am Chem Soc | 2011 Feb 9 |
| Pharmacologic rescue of motor and sensory function by the neuroprotective compound P7C3 following neonatal nerve injury. | Kemp SWP, Szynkaruk M, Stanoulis KN, Wood MD, Liu EH, Willand MP, Morlock L, Naidoo J, Williams NS, Ready JM, Mangano TJ, Beggs S, Salter MW, Gordon T, Pieper AA, Borschel GH | Neuroscience | 25313000 | Neuroscience | 2015 Jan 22 |
| Population-enriched innate immune variants may identify candidate gene targets at the intersection of cancer and cardio-metabolic disease. | Yeyeodu S, Hanafi D, Webb K, Laurie NA, Kimbro KS | Frontiers in endocrinology | 38577257 | Front Endocrinol (Lausanne) | 2023 |
| Applying a Gene Reversal Rate Computational Methodology to Identify Drugs for a Rare Cancer: Inflammatory Breast Cancer. | Ji X, Williams KP, Zheng W | Cancer informatics | 37846218 | Cancer Inform | 2023 |
| Geospatial Associations between Female Breast Cancer Mortality Rates and Environmental Socioeconomic Indicators for North Carolina. | Burwell A, Kimbro S, Mulrooney T | International journal of environmental research and public health | 37510605 | Int J Environ Res Public Health | 2023 Jul 15 |
| Identification of small molecule antagonists of sonic hedgehog/heparin binding with activity in hedgehog functional assays. | Lamson DR, Tarpley M, Addo K, Ji X, Abu Rabe D, Ehe B, Hughes M, Smith GR, Daye LR, Musso DL, Zheng W, Williams KP | Biochimica et biophysica acta. General subjects | 39151833 | Biochim Biophys Acta Gen Subj | 2024 Nov |
| Identification of Novel GANT61 Analogs with Activity in Hedgehog Functional Assays and GLI1-Dependent Cancer Cells. | Abu Rabe D, Chdid L, Lamson DR, Laudeman CP, Tarpley M, Elsayed N, Smith GR, Zheng W, Dixon MS, Williams KP | Molecules (Basel, Switzerland) | 38999049 | Molecules | 2024 Jun 28 |
| Interventions Across the Translational Research Spectrum: Addressing Disparities Among Racial and Ethnic Minoritized Youth with Type 1 Diabetes. | Ellis DA, Naar S | Endocrinology and metabolism clinics of North America | 37865475 | Endocrinol Metab Clin North Am | 2023 Dec |
| Study protocol for transforming health equity research in integrated primary care: Antiracism as a disruptive innovation. | Naar S, Pettus C, Anderson N, Pooler-Burgess M, Ralston P, Flynn H, Combs T, Baquet C, Schatschneider C, Luke D | PloS one | 38935743 | PLoS One | 2024 |
| Accommodating Serial Correlation and Sequential Design Elements in Personalized Studies and Aggregated Personalized Studies. | Schork NJ | Harvard data science review | 37032736 | Harv Data Sci Rev | 2022 |
| An R Shiny App for a Chronic Lower Back Pain Study, Personalized N-of-1 Trial. | Chandereng T | Harvard data science review | 37091071 | Harv Data Sci Rev | 2022 |
| Are Nomothetic or Ideographic Approaches Superior in Predicting Daily Exercise Behaviors? | Cheung YK, Hsueh PS, Qian M, Yoon S, Meli L, Diaz KM, Schwartz JE, Kronish IM, Davidson KW | Methods of information in medicine | 29582914 | Methods Inf Med | 2017 |
| Patients and primary care providers identify opportunities for personalized (N-of-1) trials in the mobile health era. | Kronish IM, Alcántara C, Duer-Hefele J, St Onge T, Davidson KW, Carter EJ, Medina V, Cohn E, Moise N | Journal of clinical epidemiology | 28648833 | J Clin Epidemiol | 2017 Sep |
| N-of-1 Randomized Intervention Trials in Health Psychology: A Systematic Review and Methodology Critique. | Shaffer JA, Kronish IM, Falzon L, Cheung YK, Davidson KW | Annals of behavioral medicine : a publication of the Society of Behavioral Medicine | 30124759 | Ann Behav Med | 2018 Aug 16 |
| A Series of Virtual Interventions for Chronic Lower Back Pain: A Feasibility Pilot Study for a Series of Personalized (N-of-1) Trials. | Butler M, D'Angelo S, Kaplan M, Tashnim Z, Miller D, Ahn H, Falzon L, Dominello AJ, Foroughi C, Chandereng T, Cheung K, Davidson K | Harvard data science review | 37609556 | Harv Data Sci Rev | 2022 |
| Rapid Emergence of SARS-CoV-2 in the Greater New York Metropolitan Area: Geolocation, Demographics, Positivity Rates, and Hospitalization for 46 793 Persons Tested by Northwell Health. | Reichberg SB, Mitra PP, Haghamad A, Ramrattan G, Crawford JM, Northwell COVID-19 Research Consortium, Berry GJ, Davidson KW, Drach A, Duong S, Juretschko S, Maria NI, Yang Y, Ziemba YC | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 32640030 | Clin Infect Dis | 2020 Dec 15 |
| Usefulness of Elevated Troponin to Predict Death in Patients With COVID-19 and Myocardial Injury. | Majure DT, Gruberg L, Saba SG, Kvasnovsky C, Hirsch JS, Jauhar R, Northwell Health COVID-19 Research Consortium | The American journal of cardiology | 33058800 | Am J Cardiol | 2021 Jan 1 |
| BMI as a Risk Factor for Clinical Outcomes in Patients Hospitalized with COVID-19 in New York. | Kim TS, Roslin M, Wang JJ, Kane J, Hirsch JS, Kim EJ, Northwell Health COVID-19 Research Consortium | Obesity (Silver Spring, Md.) | 33128848 | Obesity (Silver Spring) | 2021 Feb |
| An early experience on the effect of solid organ transplant status on hospitalized COVID-19 patients. | Nair V, Jandovitz N, Hirsch JS, Abate M, Satapathy SK, Roth N, Miyara SJ, Guevara S, Kressel AM, Xiang A, Wu G, Butensky SD, Lin D, Williams S, Bhaskaran MC, Majure DT, Grodstein E, Lau L, Nair G, Fahmy AE, Winnick A, Breslin N, Berlinrut I, Molmenti C, Becker LB, Malhotra P, Gautam-Goyal P, Lima B, Maybaum S, Shah SK, Takegawa R, Hayashida K, Shinozaki K, Teperman LW, Molmenti EP, Northwell Health COVID-19 Research Consortium | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 33443778 | Am J Transplant | 2021 Jul |
| Intersectional Identity and Racial Inequality During the COVID-19 Pandemic: Perspectives of Black Physician Mothers. | Louisias M, Marrast L | Journal of women's health (2002) | 32762601 | J Womens Health (Larchmt) | 2020 Sep |
| Evaluating Personalized (N-of-1) Trials in Rare Diseases: How Much Experimentation Is Enough? | Cheung K, Mitsumoto H | Harvard data science review | 38283317 | Harv Data Sci Rev | 2022 |
| Patient preferences for personalized (N-of-1) trials: a conjoint analysis. | Moise N, Wood D, Cheung YKK, Duan N, Onge TS, Duer-Hefele J, Pu T, Davidson KW, Kronish IM, Members of the “Personalized Trial Collaboratory” | Journal of clinical epidemiology | 29859242 | J Clin Epidemiol | 2018 Oct |
| Machine learning to assist clinical decision-making during the COVID-19 pandemic. | Debnath S, Barnaby DP, Coppa K, Makhnevich A, Kim EJ, Chatterjee S, Tóth V, Levy TJ, Paradis MD, Cohen SL, Hirsch JS, Zanos TP, Northwell COVID-19 Research Consortium | Bioelectronic medicine | 32665967 | Bioelectron Med | 2020 |
| Increasing the Precision of Hypertension Treatment Through Personalized Trials: a Pilot Study. | Kronish IM, Cheung YK, Shimbo D, Julian J, Gallagher B, Parsons F, Davidson KW | Journal of general internal medicine | 30859504 | J Gen Intern Med | 2019 Jun |
| Significance of Multiple Adverse Social Determinants of Health on the Diagnosis, Control, and Management of Diabetes. | Kim EJ, Abrahams S, Marrast L, Martinez J, Hanchate AD, Conigliaro J | Journal of general internal medicine | 32495092 | J Gen Intern Med | 2021 Jul |
| Experimental Designs to Optimize Treatments for Individuals: Personalized N-of-1 Trials. | Davidson KW, Silverstein M, Cheung K, Paluch RA, Epstein LH | JAMA pediatrics | 33587109 | JAMA Pediatr | 2021 Apr 1 |
| Racial and ethnic minority patient participation in N-of-1 trials: perspectives of healthcare providers and patients. | Marrast L, Conigliaro J, Chan C, Kim EJ, Duer-Hefele J, Diefenbach MA, Davidson KW | Personalized medicine | 34047197 | Per Med | 2021 Jul |
| Estimating the predictive value of negative severe acute respiratory coronavirus virus 2 (SARS-CoV-2) results: A prospective study. | Hirschwerk D, Foley M, Lesser M, Farber B, Crawford JM, Davidson KW, Berry GJ, Smith E, Kast C, Volel V, McGinn T | Infection control and hospital epidemiology | 33298203 | Infect Control Hosp Epidemiol | 2021 Oct |
| Intubated COVID-19 predictive (ICOP) score for early mortality after intubation in patients with COVID-19. | Nishikimi M, Rasul R, Sison CP, Jafari D, Shoaib M, Shinozaki K, Li T, Hayashida K, Rolston DM, Hirsch JS, Becker LB, Northwell Health COVID-19 Research Consortium | Scientific reports | 34702896 | Sci Rep | 2021 Oct 26 |
| Impact of Timing of Tocilizumab Use in Hospitalized Patients With SARS-CoV-2 Infection. | Singh AK, Oks M, Husk G, Dechario SP, Mina B, Singh K, Kirschenbaum L, Carpati CM, Mahmoud O, Gabra NI, Ishikawa O, Altschultz E, Shah V, Mahajan A, Gautam A, Birnbaum B, Antonacci AC, Raoof S | Respiratory care | 34548407 | Respir Care | 2021 Dec |
| Barriers to the Use of Clinical Decision Support for the Evaluation of Pulmonary Embolism: Qualitative Interview Study. | Richardson S, Dauber-Decker KL, McGinn T, Barnaby DP, Cattamanchi A, Pekmezaris R | JMIR human factors | 34346901 | JMIR Hum Factors | 2021 Aug 4 |
| Now is the time to assess the effects of open science practiceswith randomized control trials. | Suls J, Rothman AJ, Davidson KW | The American psychologist | 34807632 | Am Psychol | 2022 Apr |
| Clinical Mortality in a Large COVID-19 Cohort: Observational Study. | Jarrett M, Schultz S, Lyall J, Wang J, Stier L, De Geronimo M, Nelson K | Journal of medical Internet research | 32930099 | J Med Internet Res | 2020 Sep 25 |
| A Machine Learning Prediction Model of Respiratory Failure Within 48 Hours of Patient Admission for COVID-19: Model Development and Validation. | Bolourani S, Brenner M, Wang P, McGinn T, Hirsch JS, Barnaby D, Zanos TP, Northwell COVID-19 Research Consortium | Journal of medical Internet research | 33476281 | J Med Internet Res | 2021 Feb 10 |
| Clinical Usefulness of Bright White Light Therapy for Depressive Symptoms in Cancer Survivors: Results from a Series of Personalized (N-of-1) Trials. | Kronish IM, Cheung YK, Julian J, Parsons F, Lee J, Yoon S, Valdimarsdottir H, Green P, Suls J, Hershman DL, Davidson KW | Healthcare (Basel, Switzerland) | 31905890 | Healthcare (Basel) | 2019 Dec 30 |
| Mortality of Mechanically Ventilated COVID-19 Patients in Traditional versus Expanded Intensive Care Units in New York. | Nishikimi M, Jafari D, Singh N, Shinozaki K, Sison CP, Shoaib M, Gong J, Rasul R, Li T, Hayashida K, Rolston DM, Miyara SJ, Hirsch JS, Gandomi A, White MT, Jarrett MP, Lesser ML, Becker LB, Northwell Health COVID-19 Research Consortium | Annals of the American Thoracic Society | 35213292 | Ann Am Thorac Soc | 2022 Aug |
| Association of race/ethnicity with mortality in patients hospitalized with COVID-19. | Richardson S, Martinez J, Hirsch JS, Cerise J, Lesser M, Roswell RO, Davidson KW, Northwell Health COVID-19 Research Consortium | PloS one | 35925973 | PLoS One | 2022 |
| Envisioning a future for precision health psychology: innovative applied statistical approaches to N-of-1 studies. | Davidson KW, Cheung YK | Health psychology review | 28651455 | Health Psychol Rev | 2017 Sep |
| Introducing Data Sciences to N-of-1 Designs, Statistics, Use-Cases, the Future, and the Moniker 'N-of-1' Trial. | Davidson KW, Cheung YK, Friel CP, Suls J | Harvard data science review | 38009132 | Harv Data Sci Rev | 2022 |
| Protocol for randomized personalized trial for stress management compared to standard of care. | Goodwin AM, Miller D, D'Angelo S, Perrin A, Wiener R, Greene B, Romain AN, Arader L, Chandereng T, Kuen Cheung Y, Davidson KW, Butler M | Frontiers in psychology | 37794909 | Front Psychol | 2023 |
| The Family of Single-Case Experimental Designs. | Epstein LH, Dallery J | Harvard data science review | 36926648 | Harv Data Sci Rev | 2022 |
| Examination of patient characteristics and hydroxychloroquine use based on the US Food and Drug Administration's recommendation: a cross-sectional analysis in New York. | Kim EJ, Coppa K, Hirsch JS, Abrahams S, Johnson J, Lesser M, Davidson KW, Conigliaro J, Northwell Health COVID-19 Research Consortium, Northwell Health COVID-19 Research Consortium | BMJ open | 33558355 | BMJ Open | 2021 Feb 8 |
| Prevalence and Predictors of Venous Thromboembolism or Mortality in Hospitalized COVID-19 Patients. | Cohen SL, Gianos E, Barish MA, Chatterjee S, Kohn N, Lesser M, Giannis D, Coppa K, Hirsch JS, McGinn TG, Goldin ME, Spyropoulos AC, Northwell Health COVID-19 Research Consortium | Thrombosis and haemostasis | 33472255 | Thromb Haemost | 2021 Aug |
| Sex-Based Differences in COVID-19 Outcomes. | Tejpal A, Gianos E, Cerise J, Hirsch JS, Rosen S, Kohn N, Lesser M, Weinberg C, Majure D, Satapathy SK, Bernstein D, Barish MA, Spyropoulos AC, Brown RM | Journal of women's health (2002) | 33885345 | J Womens Health (Larchmt) | 2021 Apr |
| Risk factors and outcomes for acute-on-chronic liver failure in COVID-19: a large multi-center observational cohort study. | Satapathy SK, Roth NC, Kvasnovsky C, Hirsch JS, Trindade AJ, Molmenti E, Barish M, Hirschwerk D, Da BL, Bernstein D, Northwell Health COVID-19 Research Consortium | Hepatology international | 33826042 | Hepatol Int | 2021 Jun |
| Let Sleeping Patients Lie, avoiding unnecessary overnight vitals monitoring using a clinically based deep-learning model. | Tóth V, Meytlis M, Barnaby DP, Bock KR, Oppenheim MI, Al-Abed Y, McGinn T, Davidson KW, Becker LB, Hirsch JS, Zanos TP | NPJ digital medicine | 33299116 | NPJ Digit Med | 2020 Nov 13 |
| Early Experience of COVID-19 in a US Children's Hospital. | Kainth MK, Goenka PK, Williamson KA, Fishbein JS, Subramony A, Barone S, Belfer JA, Feld LM, Krief WI, Palumbo N, Rajan S, Rocker J, Scotto T, Sharma S, Sokoloff WC, Schleien C, Rubin LG, NORTHWELL HEALTH COVID-19 RESEARCH CONSORTIUM | Pediatrics | 32680880 | Pediatrics | 2020 Oct |
| COVID-19 in kidney transplant recipients. | Nair V, Jandovitz N, Hirsch JS, Nair G, Abate M, Bhaskaran M, Grodstein E, Berlinrut I, Hirschwerk D, Cohen SL, Davidson KW, Dominello AJ, Osorio GA, Richardson S, Teperman LW, Molmenti EP | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 32351040 | Am J Transplant | 2020 Jul |
| Characteristics, Cardiac Involvement, and Outcomes of Multisystem Inflammatory Syndrome of Childhood Associated with severe acute respiratory syndrome coronavirus 2 Infection. | Capone CA, Subramony A, Sweberg T, Schneider J, Shah S, Rubin L, Schleien C, Northwell Health COVID-19 Research Consortium, Epstein S, Johnson JC, Kessel A, Misra N, Mitchell E, Palumbo N, Rajan S, Rocker J, Williamson K, Davidson KW | The Journal of pediatrics | 32553873 | J Pediatr | 2020 Sep |
| Personalized (N-of-1) Trials for Depression: A Systematic Review. | Kronish IM, Hampsey M, Falzon L, Konrad B, Davidson KW | Journal of clinical psychopharmacology | 29596148 | J Clin Psychopharmacol | 2018 Jun |
| N-of-1 Trials, Their Reporting Guidelines, and the Advancement of Open Science Principles. | Porcino A, Vohra S | Harvard data science review | 38031562 | Harv Data Sci Rev | 2022 |
| Expanding Knowledge and Changing Attitudes About Poverty: An Interactive, Interprofessional Approach. | Marrast LM, Chim C, Tocco J, Coletti DJ, Nouryan C, Block L, Martinez J | Journal of primary care & community health | 35225052 | J Prim Care Community Health | 2022 Jan-Dec |
| In-Hospital 30-Day Survival Among Young Adults With Coronavirus Disease 2019: A Cohort Study. | Richardson S, Gitlin J, Kozel Z, Levy S, Rahman H, Hirsch JS, McGinn T, Diefenbach MA | Open forum infectious diseases | 34183983 | Open Forum Infect Dis | 2021 Jun |
| Series of virtual light therapy interventions for fatigue: a feasibility pilot study protocol for a series of personalised (N-of-1) trials. | Butler M, D'Angelo S, Lewis C, Miller D, Perrin A, Suls J, Chandereng T, Cheung YK, Davidson KW | BMJ open | 36283748 | BMJ Open | 2022 Oct 25 |
| Why Do I Get Side Effects? Personalized (N-of-1) Trials for Statin Intolerance and the Nocebo Effect. | Howard JP, Wood FA, Francis DP | Harvard data science review | 38344133 | Harv Data Sci Rev | 2022 |
| Using Metabolic Testing to Personalize Behavioral Obesity Treatment. | Epstein LH, Apolzan JW, Moore M, Neuwald NV, Faith MS | Obesity science & practice | 40070464 | Obes Sci Pract | 2025 Apr |
| Effectiveness of interventions targeting self-regulation to improve adherence to chronic disease medications: a meta-review of meta-analyses. | Wilson TE, Hennessy EA, Falzon L, Boyd R, Kronish IM, Birk JL | Health psychology review | 31856664 | Health Psychol Rev | 2020 Mar |
| Selected psychological comorbidities in coronary heart disease: Challenges and grand opportunities. | Davidson KW, Alcántara C, Miller GE | The American psychologist | 30394780 | Am Psychol | 2018 Nov |
| Barriers to and Facilitators for Acceptance of Comprehensive Clinical Decision Support System-Driven Care Maps for Patients With Thoracic Trauma: Interview Study Among Health Care Providers and Nurses. | Jones EK, Banks A, Melton GB, Porta CM, Tignanelli CJ | JMIR human factors | 35293873 | JMIR Hum Factors | 2022 Mar 16 |
| Accomplishing breakthroughs in behavioural medicine research. | Davidson KW, Bacon SL, Bennett GG, Brondolo E, Czajkowski SM, Diefenbach MA, Epel ES, Matthews K, Revenson TA, Ruiz JM, Segerstrom SC, Behavioral Medicine Research Council | Nature human behaviour | 34127817 | Nat Hum Behav | 2021 Jul |
| Effectiveness of SARS-CoV-2 Decontamination and Containment in a COVID-19 ICU. | Brune Z, Kuschner CE, Mootz J, Davidson KW, Pena RCF, Ghanem MH, Fischer A, Gitman M, Teperman L, Mason C, Becker LB | International journal of environmental research and public health | 33802332 | Int J Environ Res Public Health | 2021 Mar 3 |
| Prevalence of SARS-CoV-2 Antibodies in Health Care Personnel in the New York City Area. | Moscola J, Sembajwe G, Jarrett M, Farber B, Chang T, McGinn T, Davidson KW, Northwell Health COVID-19 Research Consortium | JAMA | 32780804 | JAMA | 2020 Sep 1 |
| Single case designs for early phase behavioral translational research in health psychology. | Epstein LH, Bickel WK, Czajkowski SM, Paluch RA, Moeyaert M, Davidson KW | Health psychology : official journal of the Division of Health Psychology, American Psychological Association | 34370494 | Health Psychol | 2021 Dec |
| Using Behavioral Analytics to Increase Exercise: A Randomized N-of-1 Study. | Yoon S, Schwartz JE, Burg MM, Kronish IM, Alcantara C, Julian J, Parsons F, Davidson KW, Diaz KM | American journal of preventive medicine | 29429607 | Am J Prev Med | 2018 Apr |
| A look at the increasing demographic representation within behavioral medicine. | Yoon S, Falzon L, Anderson NB, Davidson KW | Journal of behavioral medicine | 30825089 | J Behav Med | 2019 Feb |
| Presenting Characteristics, Comorbidities, and Outcomes Among 5700 Patients Hospitalized With COVID-19 in the New York City Area. | Richardson S, Hirsch JS, Narasimhan M, Crawford JM, McGinn T, Davidson KW, the Northwell COVID-19 Research Consortium, Barnaby DP, Becker LB, Chelico JD, Cohen SL, Cookingham J, Coppa K, Diefenbach MA, Dominello AJ, Duer-Hefele J, Falzon L, Gitlin J, Hajizadeh N, Harvin TG, Hirschwerk DA, Kim EJ, Kozel ZM, Marrast LM, Mogavero JN, Osorio GA, Qiu M, Zanos TP | JAMA | 32320003 | JAMA | 2020 May 26 |
| Conduct and Implementation of Personalized Trials in Research and Practice. | Kravitz RL, Duan N | Harvard data science review | 38009129 | Harv Data Sci Rev | 2022 |
| Personalized Data Science and Personalized (N-of-1) Trials: Promising Paradigms for Individualized Health Care. | Duan N, Norman D, Schmid C, Sim I, Kravitz RL | Harvard data science review | 38009133 | Harv Data Sci Rev | 2022 |
| Scientific opportunities in resilience research for cardiovascular health and wellness. Report from a National Heart, Lung, and Blood Institute workshop. | Taylor HA, Finkel T, Gao Y, Ballinger SW, Campo R, Chen R, Chen SH, Davidson K, Iruela-Arispe ML, Jaquish C, LeBrasseur NK, Odden MC, Papanicolaou GJ, Picard M, Srinivas P, Tjurmina O, Wolz M, Galis ZS | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 36322029 | FASEB J | 2022 Dec |
| A Series of Personalized Virtual Light Therapy Interventions for Fatigue: Feasibility Randomized Crossover Trial for N-of-1 Treatment. | Butler M, D'Angelo S, Ahn H, Chandereng T, Miller D, Perrin A, Romain AN, Scatoni A, Friel CP, Cheung YK, Davidson KW | JMIR formative research | 37721795 | JMIR Form Res | 2023 Sep 18 |
| A Series of Remote Melatonin Supplement Interventions for Poor Sleep: Protocol for a Feasibility Pilot Study for a Series of Personalized (N-of-1) Trials. | Butler M, D'Angelo S, Perrin A, Rodillas J, Miller D, Arader L, Chandereng T, Cheung YK, Shechter A, Davidson KW | JMIR research protocols | 37535419 | JMIR Res Protoc | 2023 Aug 3 |
| Personalized Trial Ethics and Institutional Review Board Submissions. | Samuel JP, Wootton SH | Harvard data science review | 38283318 | Harv Data Sci Rev | 2022 |
| The DNA glycosylase NEIL2 plays a vital role in combating SARS-CoV-2 infection. | Hazra T, Tapryal N, Chakraborty A, Rayavara K, Wakamiya M, Islam A, Pan L, Hsu J, Tat V, Maruyama J, Hosoki K, Sayed I, Alcantara J, Castillo V, Tindle C, Sarker A, Cardenas V, Sharma G, Alexander LC, Sur S, Ghosh G, Paessler S, Sahoo D, Ghosh P, Das S, Boldogh I, Tseng CT | Research square | 35665009 | Res Sq | 2022 May 27 |
| Microfluidics-Based Organism Isolation from Whole Blood: An Emerging Tool for Bloodstream Infection Diagnosis. | Burklund A, Zhang JXJ | Annals of biomedical engineering | 30980291 | Ann Biomed Eng | 2019 Jul |
| Biomimetic hierarchical walnut kernel-like and erythrocyte-like mesoporous silica nanomaterials: controllable synthesis and versatile applications. | Hao N, Nie Y, Zhang JXJ | Microporous and mesoporous materials : the official journal of the International Zeolite Association | 29479288 | Microporous Mesoporous Mater | 2018 May 1 |
| Advances in liquid biopsy on-chip for cancer management: Technologies, biomarkers, and clinical analysis. | Tadimety A, Closson A, Li C, Yi S, Shen T, Zhang JXJ | Critical reviews in clinical laboratory sciences | 29388456 | Crit Rev Clin Lab Sci | 2018 May |
| Ultrafast Synthesis of Multifunctional Submicrometer Hollow Silica Spheres in Microfluidic Spiral Channels. | Nie Y, Hao N, Zhang JXJ | Scientific reports | 28974729 | Sci Rep | 2017 Oct 3 |
| Patterned Plasmonic Surfaces-Theory, Fabrication, and Applications in Biosensing. | Chorsi HT, Zhu Y, Zhang JXJ | Journal of microelectromechanical systems : a joint IEEE and ASME publication on microstructures, microactuators, microsensors, and microsystems | 29276365 | J Microelectromech Syst | 2017 Aug |
| Scalable Signature-Based Molecular Diagnostics Through On-chip Biomarker Profiling Coupled with Machine Learning. | Molinski J, Tadimety A, Burklund A, Zhang JXJ | Annals of biomedical engineering | 32816167 | Ann Biomed Eng | 2020 Oct |
| Multifunctional Pacemaker Lead for Cardiac Energy Harvesting and Pressure Sensing. | Dong L, Closson AB, Jin C, Nie Y, Cabe A, Escobedo D, Huang S, Trase I, Xu Z, Chen Z, Feldman MD, Zhang JXJ | Advanced healthcare materials | 32347010 | Adv Healthc Mater | 2020 Jun |
| Flexible Piezoelectric Nanogenerators Using Metal-doped ZnO-PVDF Films. | Jin C, Hao N, Xu Z, Trase I, Nie Y, Dong L, Closson A, Chen Z, Zhang JXJ | Sensors and actuators. A, Physical | 33380776 | Sens Actuators A Phys | 2020 Apr 15 |
| Plasmonic Nanoparticle Conjugation for Nucleic Acid Biosensing. | Tadimety A, Zhang Y, Molinski JH, Palinski TJ, Tsongalis GJ, Zhang JXJ | Methods in molecular biology (Clifton, N.J.) | 34837175 | Methods Mol Biol | 2022 |
| Combined immunomagnetic capture coupled with ultrasensitive plasmonic detection of circulating tumor cells in blood. | Shen W, Song Y, Burklund A, Le B, Zhang R, Wang L, Xi Y, Qian K, Shen T, Zhang JXJ | Biomedical microdevices | 30417219 | Biomed Microdevices | 2018 Nov 12 |
| Ultrafast microfluidic synthesis of hierarchical triangular silver core-silica shell nanoplatelet toward enhanced cellular internalization. | Hao N, Nie Y, Xu Z, Zhang JXJ | Journal of colloid and interface science | 30771632 | J Colloid Interface Sci | 2019 Apr 15 |
| Microfluidics for ZnO micro-/nanomaterials development: rational design, controllable synthesis, and on-chip bioapplications. | Hao N, Zhang M, Zhang JXJ | Biomaterials science | 31965125 | Biomater Sci | 2020 Mar 31 |
| Vibration-Energy-Harvesting System: Transduction Mechanisms, Frequency Tuning Techniques, and Biomechanical Applications. | Dong L, Closson AB, Jin C, Trase I, Chen Z, Zhang JXJ | Advanced materials technologies | 33829079 | Adv Mater Technol | 2019 Oct |
| Microfluidic In Situ Patterning of Silver Nanoparticles for Surface-Enhanced Raman Spectroscopic Sensing of Biomolecules. | Nie Y, Jin C, Zhang JXJ | ACS sensors | 34148342 | ACS Sens | 2021 Jul 23 |
| Tunable Buckled Beams with Mesoporous PVDF-TrFE/SWCNT Composite Film for Energy Harvesting. | Xu Z, Liu Y, Dong L, Closson AB, Hao N, Oglesby M, Escobar GP, Fu S, Han X, Wen C, Liu J, Feldman MD, Chen Z, Zhang JXJ | ACS applied materials & interfaces | 30199624 | ACS Appl Mater Interfaces | 2018 Oct 3 |
| Microfluidic enrichment of bacteria coupled to contact-free lysis on a magnetic polymer surface for downstream molecular detection. | Burklund A, Petryk JD, Hoopes PJ, Zhang JXJ | Biomicrofluidics | 32642021 | Biomicrofluidics | 2020 May |
| Microfluidics for silica biomaterials synthesis: opportunities and challenges. | Hao N , Nie Y , Zhang JXJ | Biomaterials science | 30919847 | Biomater Sci | 2019 May 28 |
| Microfluidic continuous flow synthesis of functional hollow spherical silica with hierarchical sponge-like large porous shell. | Hao N, Nie Y, Xu Z, Closson AB, Usherwood T, J Zhang JX | Chemical engineering journal (Lausanne, Switzerland : 1996) | 31762686 | Chem Eng J | 2019 Jun 15 |
| Silver nanoparticle on zinc oxide array for label-free detection of opioids through surface-enhanced raman spectroscopy. | Zhang M, Jin C, Nie Y, Ren Y, Hao N, Xu Z, Dong L, Zhang JXJ | RSC advances | 35423637 | RSC Adv | 2021 Mar 16 |
| Microfluidics-enabled rational design of immunomagnetic nanomaterials and their shape effect on liquid biopsy. | Hao N, Nie Y, Shen T, Zhang JXJ | Lab on a chip | 29923569 | Lab Chip | 2018 Jul 10 |
| Microfluidic synthesis and on-chip enrichment application of two-dimensional hollow sandwich-like mesoporous silica nanosheet with water ripple-like surface. | Hao N, Nie Y, Closson AB, Zhang JXJ | Journal of colloid and interface science | 30576991 | J Colloid Interface Sci | 2019 Mar 15 |
| Microfluidics-enabled rapid manufacturing of hierarchical silica-magnetic microflower toward enhanced circulating tumor cell screening. | Hao N , Nie Y , Tadimety A , Shen T , Zhang JXJ | Biomaterials science | 30375583 | Biomater Sci | 2018 Nov 20 |
| Plasmonic nanosensors for point-of-care biomarker detection. | Jin C, Wu Z, Molinski JH, Zhou J, Ren Y, Zhang JXJ | Materials today. Bio | 35514435 | Mater Today Bio | 2022 Mar |
| Implantable Cardiac Kirigami-Inspired Lead-Based Energy Harvester Fabricated by Enhanced Piezoelectric Composite Film. | Xu Z, Jin C, Cabe A, Escobedo D, Gruslova A, Jenney S, Closson AB, Dong L, Chen Z, Feldman MD, Zhang JXJ | Advanced healthcare materials | 33434407 | Adv Healthc Mater | 2021 Apr |
| Microfluidics-mediated self-template synthesis of anisotropic hollow ellipsoidal mesoporous silica nanomaterials. | Hao N, Nie Y, Tadimety A, Closson AB, Zhang JXJ | Materials research letters | 30854261 | Mater Res Lett | 2017 |
| Microfluidics-enabled rational design of ZnO micro-/nanoparticles with enhanced photocatalysis, cytotoxicity, and piezoelectric properties. | Hao N, Xu Z, Nie Y, Jin C, Closson AB, Zhang M, Zhang JXJ | Chemical engineering journal (Lausanne, Switzerland : 1996) | 32831625 | Chem Eng J | 2019 Dec 15 |
| Flexible Electrostatic Transducer Array with Displacement Control for Haptic Sensing and Actuation. | Trase I, Tan HZ, Chen Z, Zhang JXJ | Sensors and actuators. A, Physical | 33380777 | Sens Actuators A Phys | 2021 Jan 1 |
| Edge effect of strained bilayer nanofilms for tunable multistability and actuation. | Hu N, Han X, Huang S, Grover HM, Yu X, Zhang LN, Trase I, Zhang JX, Zhang L, Dong LX, Chen Z | Nanoscale | 28067396 | Nanoscale | 2017 Mar 2 |
| Method for Inkjet-printing PEDOT:PSS polymer electrode arrays on piezoelectric PVDF-TrFE fibers. | Closson A, Richards H, Xu Z, Jin C, Dong L, Zhang JXJ | IEEE sensors journal | 34899077 | IEEE Sens J | 2021 Dec |
| Fibroblasts: Diverse Cells Critical to Biomaterials Integration. | Hannan RT, Peirce SM, Barker TH | ACS biomaterials science & engineering | 31440581 | ACS Biomater Sci Eng | 2018 Apr 9 |
| Detection of an Integrin-Binding Mechanoswitch within Fibronectin during Tissue Formation and Fibrosis. | Cao L, Nicosia J, Larouche J, Zhang Y, Bachman H, Brown AC, Holmgren L, Barker TH | ACS nano | 28699736 | ACS Nano | 2017 Jul 25 |
| Fibroblasts: The arbiters of extracellular matrix remodeling. | DeLeon-Pennell KY, Barker TH, Lindsey ML | Matrix biology : journal of the International Society for Matrix Biology | 32504772 | Matrix Biol | 2020 Sep |
| Feeling Things Out: Bidirectional Signaling of the Cell-ECM Interface, Implications in the Mechanobiology of Cell Spreading, Migration, Proliferation, and Differentiation. | Miller AE, Hu P, Barker TH | Advanced healthcare materials | 32037719 | Adv Healthc Mater | 2020 Apr |
| Spatial-omics: Novel approaches to probe cell heterogeneity and extracellular matrix biology. | Bingham GC, Lee F, Naba A, Barker TH | Matrix biology : journal of the International Society for Matrix Biology | 32416243 | Matrix Biol | 2020 Sep |
| Strain-dependent glutathionylation of fibronectin fibers impacts mechano-chemical behavior and primes an integrin switch. | Li W, Moretti L, Su X, Yeh CR, Torres MP, Barker TH | Nature communications | 39384749 | Nat Commun | 2024 Oct 9 |
| Citrullination of fibronectin alters integrin clustering and focal adhesion stability promoting stromal cell invasion. | Stefanelli VL, Choudhury S, Hu P, Liu Y, Schwenzer A, Yeh CR, Chambers DM, von Beck K, Li W, Segura T, Midwood KS, Torres M, Barker TH | Matrix biology : journal of the International Society for Matrix Biology | 31004743 | Matrix Biol | 2019 Sep |
| LEM domain-containing protein 3 antagonizes TGFβ-SMAD2/3 signaling in a stiffness-dependent manner in both the nucleus and cytosol. | Chambers DM, Moretti L, Zhang JJ, Cooper SW, Chambers DM, Santangelo PJ, Barker TH | The Journal of biological chemistry | 30108174 | J Biol Chem | 2018 Oct 12 |
| Multi-scale models of lung fibrosis. | Leonard-Duke J, Evans S, Hannan RT, Barker TH, Bates JHT, Bonham CA, Moore BB, Kirschner DE, Peirce SM | Matrix biology : journal of the International Society for Matrix Biology | 32438056 | Matrix Biol | 2020 Sep |
| Thy-1 in Integrin Mediated Mechanotransduction. | Hu P, Barker TH | Frontiers in cell and developmental biology | 30859101 | Front Cell Dev Biol | 2019 |
| The fibrotic tumor stroma. | Yamauchi M, Barker TH, Gibbons DL, Kurie JM | The Journal of clinical investigation | 29293090 | J Clin Invest | 2018 Jan 2 |
| αvβ3 Integrin drives fibroblast contraction and strain stiffening of soft provisional matrix during progressive fibrosis. | Fiore VF, Wong SS, Tran C, Tan C, Xu W, Sulchek T, White ES, Hagood JS, Barker TH | JCI insight | 30333317 | JCI Insight | 2018 Oct 18 |
| Macrophage and Fibroblast Interactions in Biomaterial-Mediated Fibrosis. | Witherel CE, Abebayehu D, Barker TH, Spiller KL | Advanced healthcare materials | 30658015 | Adv Healthc Mater | 2019 Feb |
| Platelets prime hematopoietic and vascular niche to drive angiocrine-mediated liver regeneration. | Shido K, Chavez D, Cao Z, Ko J, Rafii S, Ding BS | Signal transduction and targeted therapy | 29201496 | Signal Transduct Target Ther | 2017 |
| Epigenetic profiles signify cell fate plasticity in unipotent spermatogonial stem and progenitor cells. | Liu Y, Giannopoulou EG, Wen D, Falciatori I, Elemento O, Allis CD, Rafii S, Seandel M | Nature communications | 27117588 | Nat Commun | 2016 Apr 27 |
| Direct conversion of human amniotic cells into endothelial cells without transitioning through a pluripotent state. | Ginsberg M, Schachterle W, Shido K, Rafii S | Nature protocols | 26540589 | Nat Protoc | 2015 Dec |
| Sox17 drives functional engraftment of endothelium converted from non-vascular cells. | Schachterle W, Badwe CR, Palikuqi B, Kunar B, Ginsberg M, Lis R, Yokoyama M, Elemento O, Scandura JM, Rafii S | Nature communications | 28091527 | Nat Commun | 2017 Jan 16 |
| Systems Biology Analysis of Temporal Dynamics That Govern Endothelial Response to Cyclic Stretch. | Lai MW, Chow N, Checco A, Kunar B, Redmond D, Rafii S, Rabbany SY | Biomolecules | 36551265 | Biomolecules | 2022 Dec 8 |
| Angiocrine functions of organ-specific endothelial cells. | Rafii S, Butler JM, Ding BS | Nature | 26791722 | Nature | 2016 Jan 21 |
| Open the gates: vascular neurocrine signaling mobilizes hematopoietic stem and progenitor cells. | Itkin T, Gómez-Salinero JM, Rafii S | The Journal of clinical investigation | 29130939 | J Clin Invest | 2017 Dec 1 |
| Endothelial jagged-2 sustains hematopoietic stem and progenitor reconstitution after myelosuppression. | Guo P, Poulos MG, Palikuqi B, Badwe CR, Lis R, Kunar B, Ding BS, Rabbany SY, Shido K, Butler JM, Rafii S | The Journal of clinical investigation | 29058691 | J Clin Invest | 2017 Dec 1 |
| Molecular Checkpoint Decisions Made by Subverted Vascular Niche Transform Indolent Tumor Cells into Chemoresistant Cancer Stem Cells. | Cao Z, Scandura JM, Inghirami GG, Shido K, Ding BS, Rafii S | Cancer cell | 27989801 | Cancer Cell | 2017 Jan 9 |
| Conversion of adult endothelium to immunocompetent haematopoietic stem cells. | Lis R, Karrasch CC, Poulos MG, Kunar B, Redmond D, Duran JGB, Badwe CR, Schachterle W, Ginsberg M, Xiang J, Tabrizi AR, Shido K, Rosenwaks Z, Elemento O, Speck NA, Butler JM, Scandura JM, Rafii S | Nature | 28514438 | Nature | 2017 May 25 |
| Platelet-derived SDF-1 primes the pulmonary capillary vascular niche to drive lung alveolar regeneration. | Rafii S, Cao Z, Lis R, Siempos II, Chavez D, Shido K, Rabbany SY, Ding BS | Nature cell biology | 25621952 | Nat Cell Biol | 2015 Feb |
| Adaptable haemodynamic endothelial cells for organogenesis and tumorigenesis. | Palikuqi B, Nguyen DT, Li G, Schreiner R, Pellegata AF, Liu Y, Redmond D, Geng F, Lin Y, Gómez-Salinero JM, Yokoyama M, Zumbo P, Zhang T, Kunar B, Witherspoon M, Han T, Tedeschi AM, Scottoni F, Lipkin SM, Dow L, Elemento O, Xiang JZ, Shido K, Spence JR, Zhou QJ, Schwartz RE, De Coppi P, Rabbany SY, Rafii S | Nature | 32908310 | Nature | 2020 Sep |
| In vitro conversion of adult murine endothelial cells to hematopoietic stem cells. | Barcia Durán JG, Lis R, Lu TM, Rafii S | Nature protocols | 30429596 | Nat Protoc | 2018 Dec |
| Transplantation of Endothelial Cells to Mitigate Acute and Chronic Radiation Injury to Vital Organs. | Rafii S, Ginsberg M, Scandura J, Butler JM, Ding BS | Radiation research | 27459700 | Radiat Res | 2016 Aug |
| Endothelial Jak3 expression enhances pro-hematopoietic angiocrine function in mice. | Barcia Durán JG, Lu T, Houghton S, Geng F, Schreiner R, Xiang J, Rafii S, Redmond D, Lis R | Communications biology | 33767339 | Commun Biol | 2021 Mar 25 |
| Morphological characterization of Etv2 vascular explants using fractal analysis and atomic force microscopy. | Adelson RP, Palikuqi B, Weiss Z, Checco A, Schreiner R, Rafii S, Rabbany SY | Microvascular research | 34146583 | Microvasc Res | 2021 Nov |
| Mechanical adjuncts for cardiocerebral resuscitation. | Riess ML, Balzer C | Expert review of medical devices | 31353970 | Expert Rev Med Devices | 2019 Sep |
| Intralipid Increases Nitric Oxide Release from Human Endothelial Cells During Oxidative Stress. | Weihrauch D, Shumpert SD, Larson ME, McVey N, Krolikowski JG, Bamkole O, Riess ML | JPEN. Journal of parenteral and enteral nutrition | 32291784 | JPEN J Parenter Enteral Nutr | 2021 Feb |
| Opioid-induced cardioprotection. | Tanaka K, Kersten JR, Riess ML | Current pharmaceutical design | 24502571 | Curr Pharm Des | 2014 |
| Therapeutic Hypothermia in Children. | Riess ML, Aufderheide TP, Yannopoulos D | The New England journal of medicine | 26332560 | N Engl J Med | 2015 Sep 3 |
| Buffer glucose adjustment affects myocardial function after ischemia-reperfusion in long-term diabetic rat isolated hearts. | Balzer C, Cleveland WJ, Li Z, Riess ML | Physiological reports | 36324287 | Physiol Rep | 2022 Nov |
| Venous Waveform Analysis Correlates With Echocardiography in Detecting Hypovolemia in a Rat Hemorrhage Model. | Lefevre RJ, Balzer C, Baudenbacher FJ, Riess ML, Hernandez A, Eagle SS | Seminars in cardiothoracic and vascular anesthesia | 32957831 | Semin Cardiothorac Vasc Anesth | 2021 Mar |
| Noninvasively Measured Hemoglobin Concentration Reflects Arterial Hemoglobin Concentration Before but Not After Cardiopulmonary Bypass in Patients Undergoing Coronary Artery or Valve Surgery. | Riess ML, Pagel PS | Journal of cardiothoracic and vascular anesthesia | 27475734 | J Cardiothorac Vasc Anesth | 2016 Oct |
| Identifying Candidates for Advanced Hemodynamic Support After Cardiac Arrest. | Bartos JA, Doonan AL, Yannopoulos D | Circulation | 29335287 | Circulation | 2018 Jan 16 |
| Role of epinephrine and extracorporeal membrane oxygenation in the management of ischemic refractory ventricular fibrillation: a randomized trial in pigs. | Bartos JA, Voicu S, Matsuura TR, Tsangaris A, Sideris G, Oestreich BA, George SA, Olson M, Shekar KC, Rees JN, Carlson K, Sebastian P, McKnite S, Raveendran G, Aufderheide TP, Yannopoulos D | JACC. Basic to translational science | 29152600 | JACC Basic Transl Sci | 2017 Jun |
| Identifying Important Gaps in Randomized Controlled Trials of Adult Cardiac Arrest Treatments: A Systematic Review of the Published Literature. | Sinha SS, Sukul D, Lazarus JJ, Polavarapu V, Chan PS, Neumar RW, Nallamothu BK | Circulation. Cardiovascular quality and outcomes | 27756794 | Circ Cardiovasc Qual Outcomes | 2016 Nov |
| Non-invasive cardiac output monitoring during sinus surgery. | Gollapudy S, Riess ML | Journal of anesthesia | 25543335 | J Anesth | 2015 Aug |
| Total intravenous versus inhaled anesthesia in transsphenoidal tumor surgery. | Gollapudy S, Poetker DM, Sidhu J, Riess ML | American journal of otolaryngology | 30017373 | Am J Otolaryngol | 2018 Sep-Oct |
| Reperfusion injury protection during Basic Life Support improves circulation and survival outcomes in a porcine model of prolonged cardiac arrest. | Debaty G, Lurie K, Metzger A, Lick M, Bartos JA, Rees JN, McKnite S, Puertas L, Pepe P, Fowler R, Yannopoulos D | Resuscitation | 27211835 | Resuscitation | 2016 Aug |
| Poloxamer 188 Protects Isolated Adult Mouse Cardiomyocytes from Reoxygenation Injury. | Salzman MM, Bartos JA, Yannopoulos D, Riess ML | Pharmacology research & perspectives | 33073927 | Pharmacol Res Perspect | 2020 Dec |
| High central venous pressure amplitude predicts successful defibrillation in a porcine model of cardiac arrest. | Balzer C, Eagle SS, Yannopoulos D, Aufderheide TP, Riess ML | Resuscitation | 36736947 | Resuscitation | 2023 Apr |
| Venous waveform analysis detects acute right ventricular failure in a rat respiratory arrest model. | Lefevre RJ, Barajas MB, Balzer C, Baudenbacher FJ, Riess ML, Staudt G, Hernandez A, Eagle SS | Pediatric research | 36042330 | Pediatr Res | 2023 May |
| Anaesthetic Postconditioning at the Initiation of CPR Improves Myocardial and Mitochondrial Function in a Pig Model of Prolonged Untreated Ventricular Fibrillation. | Riess ML, Matsuura TR, Bartos JA, Bienengraeber M, Aldakkak M, McKnite SH, Rees JN, Aufderheide TP, Sarraf M, Neumar RW, Yannopoulos D | Resuscitation | 25281906 | Resuscitation | 2014 Dec |
| Arterial flow waveforms, vascular tone, and chronic fatigue: a case report. | Zundel MT, Pattyn M, Chelimsky TC, Riess ML | Autonomic neuroscience : basic & clinical | 25817901 | Auton Neurosci | 2015 Jul |
| Surgical Field Visualization during Functional Endoscopic Sinus Surgery: Comparison of Propofol- vs Desflurane-Based Anesthesia. | Gollapudy S, Gashkoff DA, Poetker DM, Loehrl TA, Riess ML | Otolaryngology--head and neck surgery : official journal of American Academy of Otolaryngology-Head and Neck Surgery | 32450733 | Otolaryngol Head Neck Surg | 2020 Oct |
| Early Effects of Prolonged Cardiac Arrest and Ischemic Postconditioning during Cardiopulmonary Resuscitation on Cardiac and Brain Mitochondrial Function in Pigs. | Matsuura TR, Bartos JA, Tsangaris A, Shekar KC, Olson MD, Riess ML, Bienengraeber M, Aufderheide TP, Neumar RW, Rees JN, McKnite SH, Dikalova AE, Dikalov SI, Douglas HF, Yannopoulos D | Resuscitation | 28408349 | Resuscitation | 2017 Jul |
| New Developments in Cardiac Arrest Management. | Riess ML | Advances in anesthesia | 28867873 | Adv Anesth | 2016 |
| Simulated traumatic brain injury in in-vitro mouse neuronal and brain endothelial cell culture models. | Meyer LJ, Lotze FP, Riess ML | Journal of pharmacological and toxicological methods | 35149185 | J Pharmacol Toxicol Methods | 2022 Mar-Apr |
| PPARγ-Independent Side Effects of Thiazolidinediones on Mitochondrial Redox State in Rat Isolated Hearts. | Riess ML, Elorbany R, Weihrauch D, Stowe DF, Camara AKS | Cells | 31968546 | Cells | 2020 Jan 20 |
| Poloxamer 188 Exerts Direct Protective Effects on Mouse Brain Microvascular Endothelial Cells in an In Vitro Traumatic Brain Injury Model. | Lotze FP, Riess ML | Biomedicines | 34440247 | Biomedicines | 2021 Aug 19 |
| Sodium nitroprusside enhanced cardiopulmonary resuscitation improves short term survival in a porcine model of ischemic refractory ventricular fibrillation. | Yannopoulos D, Bartos JA, George SA, Sideris G, Voicu S, Oestreich B, Matsuura T, Shekar K, Rees J, Aufderheide TP | Resuscitation | 27771299 | Resuscitation | 2017 Jan |
| Potential Effects of Poloxamer 188 on Rat Isolated Brain Mitochondria after Oxidative Stress In Vivo and In Vitro. | Pille JA, Riess ML | Brain sciences | 33477541 | Brain Sci | 2021 Jan 18 |
| Minnesota Resuscitation Consortium's Advanced Perfusion and Reperfusion Cardiac Life Support Strategy for Out-of-Hospital Refractory Ventricular Fibrillation. | Yannopoulos D, Bartos JA, Martin C, Raveendran G, Missov E, Conterato M, Frascone RJ, Trembley A, Sipprell K, John R, George S, Carlson K, Brunsvold ME, Garcia S, Aufderheide TP | Journal of the American Heart Association | 27412906 | J Am Heart Assoc | 2016 Jun 13 |
| Novelties in pharmacological management of cardiopulmonary resuscitation. | Bartos JA, Yannopoulos D | Current opinion in critical care | 23995130 | Curr Opin Crit Care | 2013 Oct |
| Increasing body mass index predicts increasing difficulty, failure rate, and time to discovery of failure of epidural anesthesia in laboring patients. | Kula AO, Riess ML, Ellinas EH | Journal of clinical anesthesia | 28235511 | J Clin Anesth | 2017 Feb |
| Sounds Impossible, but It's Knot. | Smith LE, Heath DR, Riess ML | Anesthesiology | 30632983 | Anesthesiology | 2019 May |
| Outcomes of intermediate-risk patients treated with transcatheter and surgical aortic valve replacement in the Veterans Affairs Healthcare System: A single center 20-year experience. | Garcia S, Kelly R, Mbai M, Gurevich S, Oestreich B, Yannopoulos D, Adabag S | Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions | 29316204 | Catheter Cardiovasc Interv | 2018 Aug 1 |
| Lipid emulsion enhances cardiac performance after ischemia-reperfusion in isolated hearts from summer-active arctic ground squirrels. | Salzman MM, Cheng Q, Deklotz RJ, Dulai GK, Douglas HF, Dikalova AE, Weihrauch D, Barnes BM, Riess ML | Journal of comparative physiology. B, Biochemical, systemic, and environmental physiology | 28364393 | J Comp Physiol B | 2017 Jul |
| Video laryngoscopic oral intubation in rats: a simple and effective method. | Balzer C, Cleveland WJ, Jinka TR, Riess ML | American journal of physiology. Lung cellular and molecular physiology | 32233786 | Am J Physiol Lung Cell Mol Physiol | 2020 May 1 |
| MicroRNA-21 Mediates Isoflurane-induced Cardioprotection against Ischemia-Reperfusion Injury via Akt/Nitric Oxide Synthase/Mitochondrial Permeability Transition Pore Pathway. | Qiao S, Olson JM, Paterson M, Yan Y, Zaja I, Liu Y, Riess ML, Kersten JR, Liang M, Warltier DC, Bosnjak ZJ, Ge ZD | Anesthesiology | 26259139 | Anesthesiology | 2015 Oct |
| Bundled postconditioning therapies improve hemodynamics and neurologic recovery after 17 min of untreated cardiac arrest. | Bartos JA, Matsuura TR, Sarraf M, Youngquist ST, McKnite SH, Rees JN, Sloper DT, Bates FS, Segal N, Debaty G, Lurie KG, Neumar RW, Metzger JM, Riess ML, Yannopoulos D | Resuscitation | 25447036 | Resuscitation | 2015 Feb |
| Early Access to the Cardiac Catheterization Laboratory for Patients Resuscitated From Cardiac Arrest Due to a Shockable Rhythm: The Minnesota Resuscitation Consortium Twin Cities Unified Protocol. | Garcia S, Drexel T, Bekwelem W, Raveendran G, Caldwell E, Hodgson L, Wang Q, Adabag S, Mahoney B, Frascone R, Helmer G, Lick C, Conterato M, Baran K, Bart B, Bachour F, Roh S, Panetta C, Stark R, Haugland M, Mooney M, Wesley K, Yannopoulos D | Journal of the American Heart Association | 26744380 | J Am Heart Assoc | 2016 Jan 7 |
| Design and Implementation of a Rat Ex Vivo Lung Perfusion Model. | Cleveland WJ, Hees JE, Balzer C, Douglas HF, Stevens T, Riess ML | Journal of visualized experiments : JoVE | 37306411 | J Vis Exp | 2023 May 26 |
| A new method to predict return of spontaneous circulation by peripheral intravenous analysis during cardiopulmonary resuscitation: a rat model pilot study. | Balzer C, Eagle SS, Baudenbacher FJ, Riess ML | Intensive care medicine experimental | 39531090 | Intensive Care Med Exp | 2024 Nov 12 |
| A Paper-Based Test for Screening Newborns for Sickle Cell Disease. | Piety NZ, George A, Serrano S, Lanzi MR, Patel PR, Noli MP, Kahan S, Nirenberg D, Camanda JF, Airewele G, Shevkoplyas SS | Scientific reports | 28367971 | Sci Rep | 2017 Apr 3 |
| Quantifying morphological heterogeneity: a study of more than 1 000 000 individual stored red blood cells. | Piety NZ, Gifford SC, Yang X, Shevkoplyas SS | Vox sanguinis | 25900518 | Vox Sang | 2015 Oct |
| C4d deposits on the surface of RBCs in trauma patients and interferes with their function. | Muroya T, Kannan L, Ghiran IC, Shevkoplyas SS, Paz Z, Tsokos M, Dalle Lucca JJ, Shapiro NI, Tsokos GC | Critical care medicine | 24448198 | Crit Care Med | 2014 May |
| Density-based separation in multiphase systems provides a simple method to identify sickle cell disease. | Kumar AA, Patton MR, Hennek JW, Lee SY, D'Alesio-Spina G, Yang X, Kanter J, Shevkoplyas SS, Brugnara C, Whitesides GM | Proceedings of the National Academy of Sciences of the United States of America | 25197072 | Proc Natl Acad Sci U S A | 2014 Oct 14 |
| Shape matters: the effect of red blood cell shape on perfusion of an artificial microvascular network. | Piety NZ, Reinhart WH, Pourreau PH, Abidi R, Shevkoplyas SS | Transfusion | 26711854 | Transfusion | 2016 Apr |
| Validation of a Low-Cost Paper-Based Screening Test for Sickle Cell Anemia. | Piety NZ, Yang X, Kanter J, Vignes SM, George A, Shevkoplyas SS | PloS one | 26735691 | PLoS One | 2016 |
| Influence of feeding hematocrit and perfusion pressure on hematocrit reduction (Fåhraeus effect) in an artificial microvascular network. | Reinhart WH, Piety NZ, Shevkoplyas SS | Microcirculation (New York, N.Y. : 1994) | 28801994 | Microcirculation | 2017 Nov |
| Optimal hematocrit in an artificial microvascular network. | Piety NZ, Reinhart WH, Stutz J, Shevkoplyas SS | Transfusion | 28681482 | Transfusion | 2017 Sep |
| A rapid paper-based test for quantifying sickle hemoglobin in blood samples from patients with sickle cell disease. | Piety NZ, Yang X, Lezzar D, George A, Shevkoplyas SS | American journal of hematology | 25689370 | Am J Hematol | 2015 Jun |
| Dynamics of shape recovery by stored red blood cells during washing at the single cell level. | Lu M, Shevkoplyas SS | Transfusion | 32748970 | Transfusion | 2020 Oct |
| Deep ensemble learning enables highly accurate classification of stored red blood cell morphology. | Routt AH, Yang N, Piety NZ, Lu M, Shevkoplyas SS | Scientific reports | 36823298 | Sci Rep | 2023 Feb 23 |
| Controlled incremental filtration: a simplified approach to design and fabrication of high-throughput microfluidic devices for selective enrichment of particles. | Gifford SC, Spillane AM, Vignes SM, Shevkoplyas SS | Lab on a chip | 25254358 | Lab Chip | 2014 Dec 7 |
| Washing stored red blood cells in an albumin solution improves their morphologic and hemorheologic properties. | Reinhart WH, Piety NZ, Deuel JW, Makhro A, Schulzki T, Bogdanov N, Goede JS, Bogdanova A, Abidi R, Shevkoplyas SS | Transfusion | 25752902 | Transfusion | 2015 Aug |
| Traditional and emerging technologies for washing and volume reducing blood products. | Lu M, Lezzar DL, Vörös E, Shevkoplyas SS | Journal of blood medicine | 30655711 | J Blood Med | 2019 |
| Substituting Sodium Hydrosulfite with Sodium Metabisulfite Improves Long-Term Stability of a Distributable Paper-Based Test Kit for Point-of-Care Screening for Sickle Cell Anemia. | Torabian K, Lezzar D, Piety NZ, George A, Shevkoplyas SS | Biosensors | 28930183 | Biosensors (Basel) | 2017 Sep 20 |
| Centrifugation-free washing reduces buildup of potassium and free hemoglobin in washed red blood cells after the procedure. | Vörös E, Lu M, Lezzar D, Shevkoplyas SS | American journal of hematology | 30184257 | Am J Hematol | 2018 Dec |
| A portable system for processing donated whole blood into high quality components without centrifugation. | Gifford SC, Strachan BC, Xia H, Vörös E, Torabian K, Tomasino TA, Griffin GD, Lichtiger B, Aung FM, Shevkoplyas SS | PloS one | 29346441 | PLoS One | 2018 |
| The relationship between red blood cell deformability metrics and perfusion of an artificial microvascular network. | Sosa JM, Nielsen ND, Vignes SM, Chen TG, Shevkoplyas SS | Clinical hemorheology and microcirculation | 23603326 | Clin Hemorheol Microcirc | 2014 |
| Influence of red blood cell aggregation on perfusion of an artificial microvascular network. | Reinhart WH, Piety NZ, Shevkoplyas SS | Microcirculation (New York, N.Y. : 1994) | 27647727 | Microcirculation | 2017 Jul |
| Simple paper-based test for measuring blood hemoglobin concentration in resource-limited settings. | Yang X, Piety NZ, Vignes SM, Benton MS, Kanter J, Shevkoplyas SS | Clinical chemistry | 23788584 | Clin Chem | 2013 Oct |
| Improved expansion of T cells in culture when isolated with an equipment-free, high-throughput, flow-through microfluidic module versus traditional density gradient centrifugation. | Strachan BC, Xia H, Vörös E, Gifford SC, Shevkoplyas SS | Cytotherapy | 30660490 | Cytotherapy | 2019 Feb |
| Microfluidic capillary networks are more sensitive than ektacytometry to the decline of red blood cell deformability induced by storage. | Piety NZ, Stutz J, Yilmaz N, Xia H, Yoshida T, Shevkoplyas SS | Scientific reports | 33436749 | Sci Rep | 2021 Jan 12 |
| Towards bedside washing of stored red blood cells: a prototype of a simple apparatus based on microscale sedimentation in normal gravity. | Khanal G, Huynh RA, Torabian K, Xia H, Vörös E, Shevkoplyas SS | Vox sanguinis | 29067695 | Vox Sang | 2018 Jan |
| Washing in hypotonic saline reduces the fraction of irreversibly-damaged cells in stored blood: a proof-of-concept study. | Xia H, Khanal G, Strachan BC, Vörös E, Piety NZ, Gifford SC, Shevkoplyas SS | Blood transfusion = Trasfusione del sangue | 28686152 | Blood Transfus | 2017 Sep |
| Effect of osmolality on erythrocyte rheology and perfusion of an artificial microvascular network. | Reinhart WH, Piety NZ, Goede JS, Shevkoplyas SS | Microvascular research | 25660474 | Microvasc Res | 2015 Mar |
| A high-throughput microfluidic approach for 1000-fold leukocyte reduction of platelet-rich plasma. | Xia H, Strachan BC, Gifford SC, Shevkoplyas SS | Scientific reports | 27775049 | Sci Rep | 2016 Oct 24 |
| Deterioration of red blood cell mechanical properties is reduced in anaerobic storage. | Burns JM, Yoshida T, Dumont LJ, Yang X, Piety NZ, Shevkoplyas SS | Blood transfusion = Trasfusione del sangue | 26674833 | Blood Transfus | 2016 Jan |
| Centrifugation-free washing: A novel approach for removing immunoglobulin A from stored red blood cells. | Vörös E, Piety NZ, Strachan BC, Lu M, Shevkoplyas SS | American journal of hematology | 29285804 | Am J Hematol | 2018 Aug |
| Exposing the Three-Dimensional Biogeography and Metabolic States of Pathogens in Cystic Fibrosis Sputum via Hydrogel Embedding, Clearing, and rRNA Labeling. | DePas WH, Starwalt-Lee R, Van Sambeek L, Ravindra Kumar S, Gradinaru V, Newman DK | mBio | 27677788 | mBio | 2016 Sep 27 |
| SutA is a bacterial transcription factor expressed during slow growth in Pseudomonas aeruginosa. | Babin BM, Bergkessel M, Sweredoski MJ, Moradian A, Hess S, Newman DK, Tirrell DA | Proceedings of the National Academy of Sciences of the United States of America | 26787849 | Proc Natl Acad Sci U S A | 2016 Feb 2 |
| Identification of Fitness Determinants during Energy-Limited Growth Arrest in Pseudomonas aeruginosa. | Basta DW, Bergkessel M, Newman DK | mBio | 29184024 | mBio | 2017 Nov 28 |
| Chlorate Specifically Targets Oxidant-Starved, Antibiotic-Tolerant Populations of Pseudomonas aeruginosa Biofilms. | Spero MA, Newman DK | mBio | 30254119 | mBio | 2018 Sep 25 |
| Predicting the impact of promoter variability on regulatory outputs. | Kreamer NN, Phillips R, Newman DK, Boedicker JQ | Scientific reports | 26675057 | Sci Rep | 2015 Dec 17 |
| Pediatric Cystic Fibrosis Sputum Can Be Chemically Dynamic, Anoxic, and Extremely Reduced Due to Hydrogen Sulfide Formation. | Cowley ES, Kopf SH, LaRiviere A, Ziebis W, Newman DK | mBio | 26220964 | mBio | 2015 Jul 28 |
| Sputum glucose and glycemic control in cystic fibrosis-related diabetes: a cross-sectional study. | Van Sambeek L, Cowley ES, Newman DK, Kato R | PloS one | 25803537 | PLoS One | 2015 |
| Refining the Application of Microbial Lipids as Tracers of Staphylococcus aureus Growth Rates in Cystic Fibrosis Sputum. | Neubauer C, Kasi AS, Grahl N, Sessions AL, Kopf SH, Kato R, Hogan DA, Newman DK | Journal of bacteriology | 30249710 | J Bacteriol | 2018 Dec 15 |
| Ferrous iron is a significant component of bioavailable iron in cystic fibrosis airways. | Hunter RC, Asfour F, Dingemans J, Osuna BL, Samad T, Malfroot A, Cornelis P, Newman DK | mBio | 23963183 | mBio | 2013 Aug 20 |
| Refinement of metabolite detection in cystic fibrosis sputum reveals heme correlates with lung function decline. | Glasser NR, Hunter RC, Liou TG, Newman DK, Mountain West CF Consortium Investigators | PloS one | 31851705 | PLoS One | 2019 |
| Upregulation of virulence genes promotes Vibrio cholerae biofilm hyperinfectivity. | Gallego-Hernandez AL, DePas WH, Park JH, Teschler JK, Hartmann R, Jeckel H, Drescher K, Beyhan S, Newman DK, Yildiz FH | Proceedings of the National Academy of Sciences of the United States of America | 32355001 | Proc Natl Acad Sci U S A | 2020 May 19 |
| The physiology of growth arrest: uniting molecular and environmental microbiology. | Bergkessel M, Basta DW, Newman DK | Nature reviews. Microbiology | 27510862 | Nat Rev Microbiol | 2016 Aug 11 |
| The dormancy-specific regulator, SutA, is intrinsically disordered and modulates transcription initiation in Pseudomonas aeruginosa. | Bergkessel M, Babin BM, VanderVelde D, Sweredoski MJ, Moradian A, Eggleston-Rangel R, Hess S, Tirrell DA, Artsimovitch I, Newman DK | Molecular microbiology | 31254296 | Mol Microbiol | 2019 Sep |
| Phenazine redox cycling enhances anaerobic survival in Pseudomonas aeruginosa by facilitating generation of ATP and a proton-motive force. | Glasser NR, Kern SE, Newman DK | Molecular microbiology | 24612454 | Mol Microbiol | 2014 Apr |
| Pyocyanin degradation by a tautomerizing demethylase inhibits Pseudomonas aeruginosa biofilms. | Costa KC, Glasser NR, Conway SJ, Newman DK | Science (New York, N.Y.) | 27940577 | Science | 2017 Jan 13 |
| The Pyruvate and α-Ketoglutarate Dehydrogenase Complexes of Pseudomonas aeruginosa Catalyze Pyocyanin and Phenazine-1-carboxylic Acid Reduction via the Subunit Dihydrolipoamide Dehydrogenase. | Glasser NR, Wang BX, Hoy JA, Newman DK | The Journal of biological chemistry | 28174304 | J Biol Chem | 2017 Mar 31 |
| Polyphosphate granule biogenesis is temporally and functionally tied to cell cycle exit during starvation in Pseudomonas aeruginosa. | Racki LR, Tocheva EI, Dieterle MG, Sullivan MC, Jensen GJ, Newman DK | Proceedings of the National Academy of Sciences of the United States of America | 28265086 | Proc Natl Acad Sci U S A | 2017 Mar 21 |
| Anaerobic bacteria grow within Candida albicans biofilms and induce biofilm formation in suspension cultures. | Fox EP, Cowley ES, Nobile CJ, Hartooni N, Newman DK, Johnson AD | Current biology : CB | 25308076 | Curr Biol | 2014 Oct 20 |
| Selective Proteomic Analysis of Antibiotic-Tolerant Cellular Subpopulations in Pseudomonas aeruginosa Biofilms. | Babin BM, Atangcho L, van Eldijk MB, Sweredoski MJ, Moradian A, Hess S, Tolker-Nielsen T, Newman DK, Tirrell DA | mBio | 29066549 | mBio | 2017 Oct 24 |
| The ferrous iron-responsive BqsRS two-component system activates genes that promote cationic stress tolerance. | Kreamer NN, Costa F, Newman DK | mBio | 25714721 | mBio | 2015 Feb 24 |
| Heavy water and (15) N labelling with NanoSIMS analysis reveals growth rate-dependent metabolic heterogeneity in chemostats. | Kopf SH, McGlynn SE, Green-Saxena A, Guan Y, Newman DK, Orphan VJ | Environmental microbiology | 25655651 | Environ Microbiol | 2015 Jul |
| Trace incorporation of heavy water reveals slow and heterogeneous pathogen growth rates in cystic fibrosis sputum. | Kopf SH, Sessions AL, Cowley ES, Reyes C, Van Sambeek L, Hu Y, Orphan VJ, Kato R, Newman DK | Proceedings of the National Academy of Sciences of the United States of America | 26715741 | Proc Natl Acad Sci U S A | 2016 Jan 12 |
| Peptides displayed as high density brush polymers resist proteolysis and retain bioactivity. | Blum AP, Kammeyer JK, Yin J, Crystal DT, Rush AM, Gilson MK, Gianneschi NC | Journal of the American Chemical Society | 25314576 | J Am Chem Soc | 2014 Oct 29 |
| Stimuli-responsive nanomaterials for biomedical applications. | Blum AP, Kammeyer JK, Rush AM, Callmann CE, Hahn ME, Gianneschi NC | Journal of the American Chemical Society | 25474531 | J Am Chem Soc | 2015 Feb 18 |
| Activating Peptides for Cellular Uptake via Polymerization into High Density Brushes. | Blum AP, Kammeyer JK, Gianneschi NC | Chemical science | 26925209 | Chem Sci | 2016 Feb 1 |
| Biosynthetic Polymers as Functional Materials. | Carlini AS, Adamiak L, Gianneschi NC | Macromolecules | 27375299 | Macromolecules | 2016 Jun 28 |
| Micro- and Nanoparticles for Treating Cardiovascular Disease. | Suarez S, Almutairi A, Christman KL | Biomaterials science | 26146548 | Biomater Sci | 2015 Apr |
| pH-Responsive Charge-Conversion Progelator Peptides. | Carlini AS, Choi W, McCallum NC, Gianneschi NC | Advanced functional materials | 36530181 | Adv Funct Mater | 2021 Mar 24 |
| Developing injectable nanomaterials to repair the heart. | Nguyen MM, Gianneschi NC, Christman KL | Current opinion in biotechnology | 25863496 | Curr Opin Biotechnol | 2015 Aug |
| Intramyocardial injection of hydrogel with high interstitial spread does not impact action potential propagation. | Suarez SL, Rane AA, Muñoz A, Wright AT, Zhang SX, Braden RL, Almutairi A, McCulloch AD, Christman KL | Acta biomaterialia | 26265060 | Acta Biomater | 2015 Oct |
| Enzyme-Responsive Nanoparticles for Targeted Accumulation and Prolonged Retention in Heart Tissue after Myocardial Infarction. | Nguyen MM, Carlini AS, Chien MP, Sonnenberg S, Luo C, Braden RL, Osborn KG, Li Y, Gianneschi NC, Christman KL | Advanced materials (Deerfield Beach, Fla.) | 26305446 | Adv Mater | 2015 Oct 7 |
| Degradable acetalated dextran microparticles for tunable release of an engineered hepatocyte growth factor fragment. | Suarez SL, Muñoz A, Mitchell A, Braden RL, Luo C, Cochran JR, Almutairi A, Christman KL | ACS biomaterials science & engineering | 29333489 | ACS Biomater Sci Eng | 2016 Feb 8 |
| Polymerization of a peptide-based enzyme substrate. | Hahn ME, Randolph LM, Adamiak L, Thompson MP, Gianneschi NC | Chemical communications (Cambridge, England) | 23450132 | Chem Commun (Camb) | 2013 Apr 11 |
| Designing Acellular Injectable Biomaterial Therapeutics for Treating Myocardial Infarction and Peripheral Artery Disease. | Hernandez MJ, Christman KL | JACC. Basic to translational science | 29057375 | JACC Basic Transl Sci | 2017 Apr |
| UV-responsive cyclic peptide progelator bioinks. | Carlini AS, Touve MA, Fernández-Caro H, Thompson MP, Cassidy MF, Cao W, Gianneschi NC | Faraday discussions | 31549115 | Faraday Discuss | 2019 Oct 30 |
| Enzyme-directed assembly of a nanoparticle probe in tumor tissue. | Chien MP, Thompson MP, Barback CV, Ku TH, Hall DJ, Gianneschi NC | Advanced materials (Deerfield Beach, Fla.) | 23712821 | Adv Mater | 2013 Jul 12 |
| Polymerization of Protecting-Group-Free Peptides via ROMP. | Kammeyer JK, Blum AP, Adamiak L, Hahn ME, Gianneschi NC | Polymer chemistry | 24015154 | Polym Chem | 2013 |
| Polymeric Gd-DOTA amphiphiles form spherical and fibril-shaped nanoparticle MRI contrast agents. | Randolph LM, LeGuyader CLM, Hahn ME, Andolina CM, Patterson JP, Mattrey RF, Millstone JE, Botta M, Scadeng M, Gianneschi NC | Chemical science | 30155069 | Chem Sci | 2016 Jul 1 |
| Enzyme-Targeted Nanoparticles for Delivery to Ischemic Skeletal Muscle. | Ungerleider JL, Kammeyer JK, Braden RL, Christman KL, Gianneschi NC | Polymer chemistry | 29098018 | Polym Chem | 2017 Sep 14 |
| Bioactive Peptide Brush Polymers via Photoinduced Reversible-Deactivation Radical Polymerization. | Sun H, Choi W, Zang N, Battistella C, Thompson MP, Cao W, Zhou X, Forman C, Gianneschi NC | Angewandte Chemie (International ed. in English) | 31595626 | Angew Chem Int Ed Engl | 2019 Nov 25 |
| Development of a Synthetic 3-ketosteroid Δ(1)-dehydrogenase for the Generation of a Novel Catabolic Pathway Enabling Cholesterol Degradation in Human Cells. | D'Arcy BM, Swingle MR, Schambeau L, Pannell L, Prakash A, Honkanen RE | Scientific reports | 30979909 | Sci Rep | 2019 Apr 12 |
| In vivo imaging of oligodendrocytes with sulforhodamine 101. | Hill RA, Grutzendler J | Nature methods | 25357236 | Nat Methods | 2014 Nov |
| Regional Blood Flow in the Normal and Ischemic Brain Is Controlled by Arteriolar Smooth Muscle Cell Contractility and Not by Capillary Pericytes. | Hill RA, Tong L, Yuan P, Murikinati S, Gupta S, Grutzendler J | Neuron | 26119027 | Neuron | 2015 Jul 1 |
| Modulation of oligodendrocyte generation during a critical temporal window after NG2 cell division. | Hill RA, Patel KD, Goncalves CM, Grutzendler J, Nishiyama A | Nature neuroscience | 25262495 | Nat Neurosci | 2014 Nov |
| Perturbed neural activity disrupts cerebral angiogenesis during a postnatal critical period. | Whiteus C, Freitas C, Grutzendler J | Nature | 24305053 | Nature | 2014 Jan 16 |
| Angiophagy: mechanism of microvascular recanalization independent of the fibrinolytic system. | Grutzendler J | Stroke | 23709741 | Stroke | 2013 Jun |
| In vivo imaging of cerebral microvascular plasticity from birth to death. | Harb R, Whiteus C, Freitas C, Grutzendler J | Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism | 23093067 | J Cereb Blood Flow Metab | 2013 Jan |
| Label-free in vivo imaging of myelinated axons in health and disease with spectral confocal reflectance microscopy. | Schain AJ, Hill RA, Grutzendler J | Nature medicine | 24681598 | Nat Med | 2014 Apr |
| Microglia constitute a barrier that prevents neurotoxic protofibrillar Aβ42 hotspots around plaques. | Condello C, Yuan P, Schain A, Grutzendler J | Nature communications | 25630253 | Nat Commun | 2015 Jan 29 |
| Angiophagy prevents early embolus washout but recanalizes microvessels through embolus extravasation. | Grutzendler J, Murikinati S, Hiner B, Ji L, Lam CK, Yoo T, Gupta S, Hafler BP, Adelman RA, Yuan P, Rodriguez G | Science translational medicine | 24598589 | Sci Transl Med | 2014 Mar 5 |
| TREM2 Haplodeficiency in Mice and Humans Impairs the Microglia Barrier Function Leading to Decreased Amyloid Compaction and Severe Axonal Dystrophy. | Yuan P, Condello C, Keene CD, Wang Y, Bird TD, Paul SM, Luo W, Colonna M, Baddeley D, Grutzendler J | Neuron | 27196974 | Neuron | 2016 May 18 |
| Neurovascular and Immuno-Imaging: From Mechanisms to Therapies. Proceedings of the Inaugural Symposium. | Akassoglou K, Agalliu D, Chang CJ, Davalos D, Grutzendler J, Hillman EM, Khakh BS, Kleinfeld D, McGavern DB, Nelson SJ, Zlokovic BV | Frontiers in neuroscience | 26941593 | Front Neurosci | 2016 |
| Microglia-Mediated Neuroprotection, TREM2, and Alzheimer's Disease: Evidence From Optical Imaging. | Condello C, Yuan P, Grutzendler J | Biological psychiatry | 29169609 | Biol Psychiatry | 2018 Feb 15 |
| Imaging and optogenetic modulation of vascular mural cells in the live brain. | Tong L, Hill RA, Damisah EC, Murray KN, Yuan P, Bordey A, Grutzendler J | Nature protocols | 33299155 | Nat Protoc | 2021 Jan |
| Attenuation of β-Amyloid Deposition and Neurotoxicity by Chemogenetic Modulation of Neural Activity. | Yuan P, Grutzendler J | The Journal of neuroscience : the official journal of the Society for Neuroscience | 26758850 | J Neurosci | 2016 Jan 13 |
| Correlated variability in the breathing pattern and end-expiratory lung volumes in conscious humans. | Dellaca RL, Aliverti A, Lo Mauro A, Lutchen KR, Pedotti A, Suki B | PloS one | 25803710 | PLoS One | 2015 |
| Computational modeling helps uncover mechanisms related to the progression of emphysema. | Suki B, Parameswaran H | Drug discovery today. Disease models | 24904681 | Drug Discov Today Dis Models | 2014 Jul 8 |
| Tidal stretches differently regulate the contractile and cytoskeletal elements in intact airways. | Bartolák-Suki E, LaPrad AS, Harvey BC, Suki B, Lutchen KR | PloS one | 24740101 | PLoS One | 2014 |
| Combined effects of ventilation mode and positive end-expiratory pressure on mechanics, gas exchange and the epithelium in mice with acute lung injury. | Thammanomai A, Hamakawa H, Bartolák-Suki E, Suki B | PloS one | 23326543 | PLoS One | 2013 |
| Emphysema and mechanical stress-induced lung remodeling. | Suki B, Sato S, Parameswaran H, Szabari MV, Takahashi A, Bartolák-Suki E | Physiology (Bethesda, Md.) | 24186935 | Physiology (Bethesda) | 2013 Nov |
| Microtubule dynamics regulate cyclic stretch-induced cell alignment in human airway smooth muscle cells. | Morioka M, Parameswaran H, Naruse K, Kondo M, Sokabe M, Hasegawa Y, Suki B, Ito S | PloS one | 22022610 | PLoS One | 2011 |
| Scale dependence of structure-function relationship in the emphysematous mouse lung. | Sato S, Bartolák-Suki E, Parameswaran H, Hamakawa H, Suki B | Frontiers in physiology | 26029115 | Front Physiol | 2015 |
| A computational model of the response of adherent cells to stretch and changes in substrate stiffness. | Parameswaran H, Lutchen KR, Suki B | Journal of applied physiology (Bethesda, Md. : 1985) | 24408996 | J Appl Physiol (1985) | 2014 Apr 1 |
| Proteoglycans maintain lung stability in an elastase-treated mouse model of emphysema. | Takahashi A, Majumdar A, Parameswaran H, Bartolák-Suki E, Suki B | American journal of respiratory cell and molecular biology | 24450478 | Am J Respir Cell Mol Biol | 2014 Jul |
| Homeostatic maintenance via degradation and repair of elastic fibers under tension. | Alves C, Araújo AD, Oliveira CL, Imsirovic J, Bartolák-Suki E, Andrade JS, Suki B | Scientific reports | 27279029 | Sci Rep | 2016 Jun 9 |
| The major transitions of life from a network perspective. | Suki B | Frontiers in physiology | 22514542 | Front Physiol | 2012 |
| A mechanical design principle for tissue structure and function in the airway tree. | LaPrad AS, Lutchen KR, Suki B | PLoS computational biology | 23737742 | PLoS Comput Biol | 2013 |
| Variable ventilation enhances ventilation without exacerbating injury in preterm lambs with respiratory distress syndrome. | Berry CA, Suki B, Polglase GR, Pillow JJ | Pediatric research | 22805999 | Pediatr Res | 2012 Oct |
| Monitoring the temporal changes of respiratory resistance: a novel test for the management of asthma. | Gulotta C, Suki B, Brusasco V, Pellegrino R, Gobbi A, Pedotti A, Dellacà RL | American journal of respiratory and critical care medicine | 22707741 | Am J Respir Crit Care Med | 2012 Jun 15 |
| A network model of correlated growth of tissue stiffening in pulmonary fibrosis. | Oliveira CL, Bates JH, Suki B | New journal of physics | 25484613 | New J Phys | 2014 Jun 26 |
| Aging impairs smooth muscle-mediated regulation of aortic stiffness: a defect in shock absorption function? | Gao YZ, Saphirstein RJ, Yamin R, Suki B, Morgan KG | American journal of physiology. Heart and circulatory physiology | 25128168 | Am J Physiol Heart Circ Physiol | 2014 Oct 15 |
| Fluctuation-driven mechanotransduction regulates mitochondrial-network structure and function. | Bartolák-Suki E, Imsirovic J, Parameswaran H, Wellman TJ, Martinez N, Allen PG, Frey U, Suki B | Nature materials | 26213900 | Nat Mater | 2015 Oct |
| Regulation of Gastrointestinal Smooth Muscle Function by Interstitial Cells. | Sanders KM, Kito Y, Hwang SJ, Ward SM | Physiology (Bethesda, Md.) | 27488743 | Physiology (Bethesda) | 2016 Sep |
| Lung tissue mechanics as an emergent phenomenon. | Suki B, Bates JH | Journal of applied physiology (Bethesda, Md. : 1985) | 21212247 | J Appl Physiol (1985) | 2011 Apr |
| Effects of recruitment/derecruitment dynamics on the efficacy of variable ventilation. | Ma B, Suki B, Bates JH | Journal of applied physiology (Bethesda, Md. : 1985) | 21372101 | J Appl Physiol (1985) | 2011 May |
| Epithelial and endothelial damage induced by mechanical ventilation modes. | Suki B, Hubmayr R | Current opinion in critical care | 24300621 | Curr Opin Crit Care | 2014 Feb |
| Regulatory Roles of Fluctuation-Driven Mechanotransduction in Cell Function. | Suki B, Parameswaran H, Imsirovic J, Bartolák-Suki E | Physiology (Bethesda, Md.) | 27511461 | Physiology (Bethesda) | 2016 Sep |
| A novel device to stretch multiple tissue samples with variable patterns: application for mRNA regulation in tissue-engineered constructs. | Imsirovic J, Derricks K, Buczek-Thomas JA, Rich CB, Nugent MA, Suki B | Biomatter | 23628870 | Biomatter | 2013 Jul-Sep |
| Complexity and emergent phenomena. | Suki B, Bates JH, Frey U | Comprehensive Physiology | 23737210 | Compr Physiol | 2011 Apr |
| Acute mechanical forces cause deterioration in lung structure and function in elastase-induced emphysema. | Szabari MV, Parameswaran H, Sato S, Hantos Z, Bartolák-Suki E, Suki B | American journal of physiology. Lung cellular and molecular physiology | 22865550 | Am J Physiol Lung Cell Mol Physiol | 2012 Oct 1 |
| Design of a Novel Equi-Biaxial Stretcher for Live Cellular and Subcellular Imaging. | Imsirovic J, Wellman TJ, Mondoñedo JR, Bartolák-Suki E, Suki B | PloS one | 26466363 | PLoS One | 2015 |
| Variable ventilation improves ventilation and lung compliance in preterm lambs. | Pillow JJ, Musk GC, McLean CM, Polglase GR, Dalton RG, Jobe AH, Suki B | Intensive care medicine | 21567115 | Intensive Care Med | 2011 Aug |
| Efficient formation of single-copy human artificial chromosomes. | Gambogi CW, Birchak GJ, Mer E, Brown DM, Yankson G, Kixmoeller K, Gavade JN, Espinoza JL, Kashyap P, Dupont CL, Logsdon GA, Heun P, Glass JI, Black BE | Science (New York, N.Y.) | 38513017 | Science | 2024 Mar 22 |
| Efficient Formation of Single-copy Human Artificial Chromosomes. | Gambogi CW, Mer E, Brown DM, Yankson G, Gavade JN, Logsdon GA, Heun P, Glass JI, Black BE | bioRxiv : the preprint server for biology | 37546784 | bioRxiv | 2023 Jun 30 |
| The DECON pilot project investigates predictive markers for successful bariatric surgery. | Seifert G, Fagnocchi L, Edozie M, Herrmann S, Baumann H, Panzeri I, Mewes S, Aicher D, Runkel M, Lässle C, Fink J, Marjanovic G, Fichtner-Feigl S, Pospisilik JA | Scientific reports | 37591977 | Sci Rep | 2023 Aug 17 |
| Isolation and Processing of Murine White Adipocytes for Transcriptome and Epigenome Analyses. | Yang CH, Longinotto J, Panzeri I, Arrigoni L, Wegert V, Heyne S, Seifert G, Lempradl A, Bönisch U, Pospisilik JA | Journal of visualized experiments : JoVE | 35786676 | J Vis Exp | 2022 Jun 16 |
| An acute microglial metabolic response controls metabolism and improves memory. | Drougard A, Ma EH, Wegert V, Sheldon R, Panzeri I, Vatsa N, Apostle S, Fagnocchi L, Schaf J, Gossens K, Völker J, Pang S, Bremser A, Dror E, Giacona F, Sagar S, Henderson MX, Prinz M, Jones RG, Pospisilik JA | eLife | 39625057 | Elife | 2024 Dec 3 |
| Chronic obesity does not alter cancer incidence in Trp53 (R270H/ +) mice. | Panzeri I, Madaj Z, Fagnocchi L, Apostle S, Tompkins M, Hostetter G, Pospisilik JA | bioRxiv : the preprint server for biology | 39463991 | bioRxiv | 2025 Mar 17 |
| TRIM28-dependent developmental heterogeneity determines cancer susceptibility through distinct epigenetic states. | Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Yang CH, Bergsma A, Drougard A, Dror E, PERMUTE, Chandler DP, Schramek D, Triche TJ Jr, Pospisilik JA | Nature cancer | 39856421 | Nat Cancer | 2025 Feb |
| Independent phenotypic plasticity axes define distinct obesity sub-types. | Yang CH, Fagnocchi L, Apostle S, Wegert V, Casaní-Galdón S, Landgraf K, Panzeri I, Dror E, Heyne S, Wörpel T, Chandler DP, Lu D, Yang T, Gibbons E, Guerreiro R, Bras J, Thomasen M, Grunnet LG, Vaag AA, Gillberg L, Grundberg E, Conesa A, Körner A, PERMUTE, Pospisilik JA | Nature metabolism | 36097183 | Nat Metab | 2022 Sep |
| Epigenetic dosage identifies two major and functionally distinct β cell subtypes. | Dror E, Fagnocchi L, Wegert V, Apostle S, Grimaldi B, Gruber T, Panzeri I, Heyne S, Höffler KD, Kreiner V, Ching R, Tsai-Hsiu Lu T, Semwal A, Johnson B, Senapati P, Lempradl A, Schones D, Imhof A, Shen H, Pospisilik JA | Cell metabolism | 36948185 | Cell Metab | 2023 May 2 |
| Developmental priming of cancer susceptibility. | Panzeri I, Fagnocchi L, Apostle S, Tompkins M, Wolfrum E, Madaj Z, Hostetter G, Liu Y, Schaefer K, Chih-Hsiang Y, Bergsma A, Drougard A, Dror E, PERMUTE, Chandler D, Schramek D, Triche TJ Jr, Pospisilik JA | bioRxiv : the preprint server for biology | 37745326 | bioRxiv | 2023 Sep 15 |
| Comparison of Lysis and Amplification Methodologies for Optimal 16S rRNA Gene Profiling for Human and Mouse Microbiome Studies. | Rastegari F, Driscoll M, Riordan JD, Nadeau JH, Johnson JS, Weinstock GM | International journal of molecular sciences | 39940948 | Int J Mol Sci | 2025 Jan 29 |
| An acute microglial metabolic response controls metabolism and improves memory. | Drougard A, Ma EH, Wegert V, Sheldon R, Panzeri I, Vatsa N, Apostle S, Fagnocchi L, Schaf J, Gossens K, Völker J, Pang S, Bremser A, Dror E, Giacona F, Sagar, Henderson MX, Prinz M, Jones RG, Pospisilik JA | bioRxiv : the preprint server for biology | 37066282 | bioRxiv | 2024 Apr 25 |
| Unconventional function of an Achaete-Scute homolog as a terminal selector of nociceptive neuron identity. | Masoudi N, Tavazoie S, Glenwinkel L, Ryu L, Kim K, Hobert O | PLoS biology | 29672507 | PLoS Biol | 2018 Apr |
| Regulatory and evolutionary adaptation of yeast to acute lethal ethanol stress. | Yang J, Tavazoie S | PloS one | 33170850 | PLoS One | 2020 |
| Functional genetic screen identifies ITPR3/calcium/RELB axis as a driver of colorectal cancer metastatic liver colonization. | Moy RH, Nguyen A, Loo JM, Yamaguchi N, Kajba CM, Santhanam B, Ostendorf BN, Wu YG, Tavazoie S, Tavazoie SF | Developmental cell | 35487218 | Dev Cell | 2022 May 9 |
| An inducible CRISPR interference library for genetic interrogation of Saccharomyces cerevisiae biology. | Momen-Roknabadi A, Oikonomou P, Zegans M, Tavazoie S | Communications biology | 33247197 | Commun Biol | 2020 Nov 27 |
| A Targetable Secreted Neural Protein Drives Pancreatic Cancer Metastatic Colonization and HIF1α Nuclear Retention. | Yamaguchi N, Wu YG, Ravetch E, Takahashi M, Khan AG, Hayashi A, Mei W, Hsu D, Umeda S, de Stanchina E, Lorenz IC, Iacobuzio-Donahue CA, Tavazoie SF | Cancer discovery | 39028915 | Cancer Discov | 2024 Dec 2 |
| In vivo mRNA display enables large-scale proteomics by next generation sequencing. | Oikonomou P, Salatino R, Tavazoie S | Proceedings of the National Academy of Sciences of the United States of America | 33037152 | Proc Natl Acad Sci U S A | 2020 Oct 27 |
| Genome wide analysis of 3' UTR sequence elements and proteins regulating mRNA stability during maternal-to-zygotic transition in zebrafish. | Vejnar CE, Abdel Messih M, Takacs CM, Yartseva V, Oikonomou P, Christiano R, Stoeckius M, Lau S, Lee MT, Beaudoin JD, Musaev D, Darwich-Codore H, Walther TC, Tavazoie S, Cifuentes D, Giraldez AJ | Genome research | 31227602 | Genome Res | 2019 Jul |
| Regulation of Sex-biased Gene Expression by the Ancestral X-Y Chromosomal Gene Pair Kdm5c-Kdm5d. | Malcore RM, Samanta MK, Kalantry S, Iwase S | bioRxiv : the preprint server for biology | 39484414 | bioRxiv | 2024 Oct 27 |
| Route-dependent spatial engram tagging in mouse dentate gyrus. | Wilmerding LK, Kondratyev I, Ramirez S, Hasselmo ME | Neurobiology of learning and memory | 36822466 | Neurobiol Learn Mem | 2023 Apr |
| Traumatic Brain Injury-Induced Fear Generalization in Mice Involves Hippocampal Memory Trace Dysfunction and Is Alleviated by (R,S)-Ketamine. | McGowan JC, Ladner LR, Shubeck CX, Tapia J, LaGamma CT, Anqueira-González A, DeFrancesco A, Chen BK, Hunsberger HC, Sydnor EJ, Logan RW, Yu TS, Kernie SG, Denny CA | Biological psychiatry | 37423591 | Biol Psychiatry | 2024 Jan 1 |
| Weapons of stress reduction: (R,S)-ketamine and its metabolites as prophylactics for the prevention of stress-induced psychiatric disorders. | Chen BK, Denny CA | Neuropharmacology | 36427554 | Neuropharmacology | 2023 Feb 15 |
| Social reactivation of fear engrams enhances memory recall. | Finkelstein AB, Leblanc H, Cole RH, Gallerani T, Vieira A, Zaki Y, Ramirez S | Proceedings of the National Academy of Sciences of the United States of America | 35286206 | Proc Natl Acad Sci U S A | 2022 Mar 22 |
| Fluoroethylnormemantine, A Novel Derivative of Memantine, Facilitates Extinction Learning Without Sensorimotor Deficits. | Chen BK, Le Pen G, Eckmier A, Rubinstenn G, Jay TM, Denny CA | The international journal of neuropsychopharmacology | 33631001 | Int J Neuropsychopharmacol | 2021 Jul 14 |
| GluN2B on Adult-Born Granule Cells Modulates (R,S)-Ketamine's Rapid-Acting Effects in Mice. | Bulthuis NE, McGowan JC, Ladner LR, LaGamma CT, Lim SC, Shubeck CX, Brachman RA, Sydnor E, Pavlova IP, Seo DO, Drew MR, Denny CA | The international journal of neuropsychopharmacology | 39240140 | Int J Neuropsychopharmacol | 2024 Oct 1 |
| Sex-Specific Effects of Anxiety on Cognition and Activity-Dependent Neural Networks: Insights From (Female) Mice and (Wo)men. | Hunsberger HC, Lee S, Jin M, Lanio M, Whye A, Cha J, Scarlata M, Matthews LC, Jayaseelan K, Denny CA, Alzheimer’s Disease Neuroimaging Initiative | Biological psychiatry | 39349155 | Biol Psychiatry | 2025 May 1 |
| Prophylactic (R,S)-Ketamine and (2S,6S)-Hydroxynorketamine Decrease Fear Expression by Differentially Modulating Fear Neural Ensembles. | Mastrodonato A, Jin M, Kee N, Lanio M, Tapia J, Quintana L, Muñoz Zamora A, Deng SX, Xu X, Landry DW, Denny CA | Biological psychiatry | 39389408 | Biol Psychiatry | 2025 May 1 |
| Hippocampal fear engrams modulate ethanol-induced maladaptive contextual generalization in mice. | Cincotta C, Ruesch E, Senne R, Ramirez S | Hippocampus | 35950345 | Hippocampus | 2022 Oct |
| Chronic activation of fear engrams induces extinction-like behavior in ethanol-exposed mice. | Cincotta C, Murawski NJ, Grella SL, McKissick O, Doucette E, Ramirez S | Hippocampus | 32946184 | Hippocampus | 2021 Jan |
| Social behavior in mice following chronic optogenetic stimulation of hippocampal engrams. | Doucette E, Merfeld E, Leblanc H, Monasterio A, Cincotta C, Grella SL, Logan J, Ramirez S | Neurobiology of learning and memory | 33164892 | Neurobiol Learn Mem | 2020 Dec |
| Distinct hippocampal engrams control extinction and relapse of fear memory. | Lacagnina AF, Brockway ET, Crovetti CR, Shue F, McCarty MJ, Sattler KP, Lim SC, Santos SL, Denny CA, Drew MR | Nature neuroscience | 30936555 | Nat Neurosci | 2019 May |
| Prophylactic (R,S)-Ketamine Is Effective Against Stress-Induced Behaviors in Adolescent but Not Aged Mice. | Mastrodonato A, Pavlova I, Kee NC, Pham VA, McGowan JC, Mann JJ, Denny CA | The international journal of neuropsychopharmacology | 35229871 | Int J Neuropsychopharmacol | 2022 Jun 21 |
| Propranolol Decreases Fear Expression by Modulating Fear Memory Traces. | Leal Santos S, Stackmann M, Muñoz Zamora A, Mastrodonato A, De Landri AV, Vaughan N, Chen BK, Lanio M, Denny CA | Biological psychiatry | 33766406 | Biol Psychiatry | 2021 Jun 15 |
| Behavioral and neurobiological effects of GnRH agonist treatment in mice-potential implications for puberty suppression in transgender individuals. | Anacker C, Sydnor E, Chen BK, LaGamma CC, McGowan JC, Mastrodonato A, Hunsberger HC, Shores R, Dixon RS, McEwen BS, Byne W, Meyer-Bahlburg HFL, Bockting W, Ehrhardt AA, Denny CA | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 32919399 | Neuropsychopharmacology | 2021 Apr |
| Sex-Specific Effects of Anxiety on Cognition and Activity-Dependent Neural Networks: Insights from (Female) Mice and (Wo)Men. | Hunsberger HC, Lee S, Jin M, Lanio M, Whye A, Cha J, Scarlata M, Jayaseelan K, Denny CA | bioRxiv : the preprint server for biology | 37503264 | bioRxiv | 2023 Jul 10 |
| Fluoroethylnormemantine, a Novel NMDA Receptor Antagonist, for the Prevention and Treatment of Stress-Induced Maladaptive Behavior. | Chen BK, Luna VM, Shannon ME, Hunsberger HC, Mastrodonato A, Stackmann M, McGowan JC, Rubinstenn G, Denny CA | Biological psychiatry | 34274107 | Biol Psychiatry | 2021 Oct 1 |
| A SMARTTR workflow for multi-ensemble atlas mapping and brain-wide network analysis. | Jin M, Ogundare SO, Lanio M, Sorid S, Whye AR, Santos SL, Franceschini A, Denny CA | bioRxiv : the preprint server for biology | 39071434 | bioRxiv | 2025 Feb 19 |
| The genome-wide multi-layered architecture of chromosome pairing in early Drosophila embryos. | Erceg J, AlHaj Abed J, Goloborodko A, Lajoie BR, Fudenberg G, Abdennur N, Imakaev M, McCole RB, Nguyen SC, Saylor W, Joyce EF, Senaratne TN, Hannan MA, Nir G, Dekker J, Mirny LA, Wu CT | Nature communications | 31582744 | Nat Commun | 2019 Oct 3 |
| Highly structured homolog pairing reflects functional organization of the Drosophila genome. | AlHaj Abed J, Erceg J, Goloborodko A, Nguyen SC, McCole RB, Saylor W, Fudenberg G, Lajoie BR, Dekker J, Mirny LA, Wu CT | Nature communications | 31582763 | Nat Commun | 2019 Oct 3 |
| A multiplexed DNA FISH strategy for assessing genome architecture in Caenorhabditis elegans. | Fields BD, Nguyen SC, Nir G, Kennedy S | eLife | 31084706 | Elife | 2019 May 14 |
| A structural variation reference for medical and population genetics. | Collins RL, Brand H, Karczewski KJ, Zhao X, Alföldi J, Francioli LC, Khera AV, Lowther C, Gauthier LD, Wang H, Watts NA, Solomonson M, O'Donnell-Luria A, Baumann A, Munshi R, Walker M, Whelan CW, Huang Y, Brookings T, Sharpe T, Stone MR, Valkanas E, Fu J, Tiao G, Laricchia KM, Ruano-Rubio V, Stevens C, Gupta N, Cusick C, Margolin L, Genome Aggregation Database Production Team, Genome Aggregation Database Consortium, Taylor KD, Lin HJ, Rich SS, Post WS, Chen YI, Rotter JI, Nusbaum C, Philippakis A, Lander E, Gabriel S, Neale BM, Kathiresan S, Daly MJ, Banks E, MacArthur DG, Talkowski ME | Nature | 32461652 | Nature | 2020 May |
| Transcription-mediated supercoiling regulates genome folding and loop formation. | Neguembor MV, Martin L, Castells-García Á, Gómez-García PA, Vicario C, Carnevali D, AlHaj Abed J, Granados A, Sebastian-Perez R, Sottile F, Solon J, Wu CT, Lakadamyali M, Cosma MP | Molecular cell | 34297911 | Mol Cell | 2021 Aug 5 |
| Ultraconserved Elements Occupy Specific Arenas of Three-Dimensional Mammalian Genome Organization. | McCole RB, Erceg J, Saylor W, Wu CT | Cell reports | 29996107 | Cell Rep | 2018 Jul 10 |
| OligoMiner provides a rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes. | Beliveau BJ, Kishi JY, Nir G, Sasaki HM, Saka SK, Nguyen SC, Wu CT, Yin P | Proceedings of the National Academy of Sciences of the United States of America | 29463736 | Proc Natl Acad Sci U S A | 2018 Mar 6 |
| Pericentromeric heterochromatin is hierarchically organized and spatially contacts H3K9me2 islands in euchromatin. | Lee YCG, Ogiyama Y, Martins NMC, Beliveau BJ, Acevedo D, Wu CT, Cavalli G, Karpen GH | PLoS genetics | 32203508 | PLoS Genet | 2020 Mar |
| 3D mapping and accelerated super-resolution imaging of the human genome using in situ sequencing. | Nguyen HQ, Chattoraj S, Castillo D, Nguyen SC, Nir G, Lioutas A, Hershberg EA, Martins NMC, Reginato PL, Hannan M, Beliveau BJ, Church GM, Daugharthy ER, Marti-Renom MA, Wu CT | Nature methods | 32719531 | Nat Methods | 2020 Aug |
| MiOS, an integrated imaging and computational strategy to model gene folding with nucleosome resolution. | Neguembor MV, Arcon JP, Buitrago D, Lema R, Walther J, Garate X, Martin L, Romero P, AlHaj Abed J, Gut M, Blanc J, Lakadamyali M, Wu CT, Brun Heath I, Orozco M, Dans PD, Cosma MP | Nature structural & molecular biology | 36220894 | Nat Struct Mol Biol | 2022 Oct |
| Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling. | Nir G, Farabella I, Pérez Estrada C, Ebeling CG, Beliveau BJ, Sasaki HM, Lee SD, Nguyen SC, McCole RB, Chattoraj S, Erceg J, AlHaj Abed J, Martins NMC, Nguyen HQ, Hannan MA, Russell S, Durand NC, Rao SSP, Kishi JY, Soler-Vila P, Di Pierro M, Onuchic JN, Callahan SP, Schreiner JM, Stuckey JA, Yin P, Aiden EL, Marti-Renom MA, Wu CT | PLoS genetics | 30586358 | PLoS Genet | 2018 Dec |
| Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies. | Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J, Human Genome Structural Variation Consortium, Gerstein MB, Devine SE, Marschall T, Korbel JO, Eichler EE, Chaisson MJP, Lee C, Mills RE, Brand H, Talkowski ME | American journal of human genetics | 33789087 | Am J Hum Genet | 2021 May 6 |
| Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images. | Wernersson E, Gelali E, Girelli G, Wang S, Castillo D, Mattsson Langseth C, Verron Q, Nguyen HQ, Chattoraj S, Martinez Casals A, Blom H, Lundberg E, Nilsson M, Marti-Renom MA, Wu CT, Crosetto N, Bienko M | Nature methods | 38844629 | Nat Methods | 2024 Jul |
| In Situ Super-Resolution Imaging of Genomic DNA with OligoSTORM and OligoDNA-PAINT. | Beliveau BJ, Boettiger AN, Nir G, Bintu B, Yin P, Zhuang X, Wu CT | Methods in molecular biology (Clifton, N.J.) | 28924672 | Methods Mol Biol | 2017 |
| Islands of retroelements are major components of Drosophila centromeres. | Chang CH, Chavan A, Palladino J, Wei X, Martins NMC, Santinello B, Chen CC, Erceg J, Beliveau BJ, Wu CT, Larracuente AM, Mellone BG | PLoS biology | 31086362 | PLoS Biol | 2019 May |
| Paircounting. | Nguyen HQ, Lee SD, Wu CT | Trends in genetics : TIG | 31521404 | Trends Genet | 2019 Nov |
| Spatial and temporal organization of the genome: Current state and future aims of the 4D nucleome project. | Dekker J, Alber F, Aufmkolk S, Beliveau BJ, Bruneau BG, Belmont AS, Bintu L, Boettiger A, Calandrelli R, Disteche CM, Gilbert DM, Gregor T, Hansen AS, Huang B, Huangfu D, Kalhor R, Leslie CS, Li W, Li Y, Ma J, Noble WS, Park PJ, Phillips-Cremins JE, Pollard KS, Rafelski SM, Ren B, Ruan Y, Shav-Tal Y, Shen Y, Shendure J, Shu X, Strambio-De-Castillia C, Vertii A, Zhang H, Zhong S | Molecular cell | 37419111 | Mol Cell | 2023 Aug 3 |
| Three-dimensional genome organization via triplex-forming RNAs. | Farabella I, Di Stefano M, Soler-Vila P, Marti-Marimon M, Marti-Renom MA | Nature structural & molecular biology | 34759378 | Nat Struct Mol Biol | 2021 Nov |
| A Randomized Controlled Trial of an Integrated Brain, Body, and Social Intervention for Children With ADHD. | Smith SD, Vitulano LA, Katsovich L, Li S, Moore C, Li F, Grantz H, Zheng X, Eicher V, Aktan Guloksuz S, Zheng Y, Dong J, Sukhodolsky DG, Leckman JF | Journal of attention disorders | 27178060 | J Atten Disord | 2020 Mar |
| A preliminary study of movement intensity during a Go/No-Go task and its association with ADHD outcomes and symptom severity. | Li F, Zheng Y, Smith SD, Shic F, Moore CC, Zheng X, Qi Y, Liu Z, Leckman JF | Child and adolescent psychiatry and mental health | 27999615 | Child Adolesc Psychiatry Ment Health | 2016 |
| An integrated program of computer-presented and physical cognitive training exercises for children with attention-deficit/hyperactivity disorder. | Wexler BE, Vitulano LA, Moore C, Katsovich L, Smith SD, Rush C, Grantz H, Dong J, Leckman JF | Psychological medicine | 32090720 | Psychol Med | 2021 Jul |
| Meta-Analysis: Risk of Tics Associated With Psychostimulant Use in Randomized, Placebo-Controlled Trials. | Cohen SC, Mulqueen JM, Ferracioli-Oda E, Stuckelman ZD, Coughlin CG, Leckman JF, Bloch MH | Journal of the American Academy of Child and Adolescent Psychiatry | 26299294 | J Am Acad Child Adolesc Psychiatry | 2015 Sep |
| Prenatal and Perinatal Risk Factors and the Promise of Birth Cohort Studies: Origins of Obsessive-Compulsive Disorder. | Fernandez TV, Leckman JF | JAMA psychiatry | 27706471 | JAMA Psychiatry | 2016 Nov 1 |
| Using micro-cognition biomarkers of neurosystem dysfunction to redefine ADHD subtypes: A scalable digital path to diagnosis based on brain function. | Wexler BE, Kish R | Psychiatry research | 37494880 | Psychiatry Res | 2023 Aug |
| N-Acetylcysteine in the Treatment of Pediatric Tourette Syndrome: Randomized, Double-Blind, Placebo-Controlled Add-On Trial. | Bloch MH, Panza KE, Yaffa A, Alvarenga PG, Jakubovski E, Mulqueen JM, Landeros-Weisenberger A, Leckman JF | Journal of child and adolescent psychopharmacology | 27027204 | J Child Adolesc Psychopharmacol | 2016 May |
| Effects of Integrated Brain, Body, and Social (IBBS) intervention on ERP measures of attentional control in children with ADHD. | Smith SD, Crowley MJ, Ferrey A, Ramsey K, Wexler BE, Leckman JF, Sukhodolsky DG | Psychiatry research | 31233935 | Psychiatry Res | 2019 Aug |
| Randomized Sham Controlled Double-blind Trial of Repetitive Transcranial Magnetic Stimulation for Adults With Severe Tourette Syndrome. | Landeros-Weisenberger A, Mantovani A, Motlagh MG, de Alvarenga PG, Katsovich L, Leckman JF, Lisanby SH | Brain stimulation | 25912296 | Brain Stimul | 2015 May-Jun |
| Electrophysiological signatures of inhibitory control in children with Tourette syndrome and attention-deficit/hyperactivity disorder. | Morand-Beaulieu S, Smith SD, Ibrahim K, Wu J, Leckman JF, Crowley MJ, Sukhodolsky DG | Cortex; a journal devoted to the study of the nervous system and behavior | 35042055 | Cortex | 2022 Feb |
| Stanford's Outcomes Research in Kids (STORK): a prospective study of healthy pregnant women and their babies in Northern California. | Ley C, Sanchez Mde L, Mathur A, Yang S, Sundaram V, Parsonnet J | BMJ open | 27075843 | BMJ Open | 2016 Apr 13 |
| Effect of long-term antibiotic use on weight in adolescents with acne. | Contopoulos-Ioannidis DG, Ley C, Wang W, Ma T, Olson C, Shi X, Luft HS, Hastie T, Parsonnet J | The Journal of antimicrobial chemotherapy | 26782773 | J Antimicrob Chemother | 2016 Apr |
| A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the USA. | Walters WA, Ley C, Hastie T, Ley RE, Parsonnet J | BMC medical research methodology | 38302887 | BMC Med Res Methodol | 2024 Feb 1 |
| Shared B cell memory to coronaviruses and other pathogens varies in human age groups and tissues. | Yang F, Nielsen SCA, Hoh RA, Röltgen K, Wirz OF, Haraguchi E, Jean GH, Lee JY, Pham TD, Jackson KJL, Roskin KM, Liu Y, Nguyen K, Ohgami RS, Osborne EM, Nadeau KC, Niemann CU, Parsonnet J, Boyd SD | Science (New York, N.Y.) | 33846272 | Science | 2021 May 14 |
| Crossover Control Study of the Effect of Personal Care Products Containing Triclosan on the Microbiome. | Poole AC, Pischel L, Ley C, Suh G, Goodrich JK, Haggerty TD, Ley RE, Parsonnet J | mSphere | 27303746 | mSphere | 2016 May-Jun |
| Infectious diseases in children and body mass index in young adults. | Suh G, Ley C, Parsonnet J | Emerging infectious diseases | 22932124 | Emerg Infect Dis | 2012 Sep |
| Comparison of two methods - regression predictive model and intake shift model - for adjusting self-reported dietary recall of total energy intake of populations. | Lankester J, Perry S, Parsonnet J | Frontiers in public health | 25506048 | Front Public Health | 2014 |
| Recall accuracy of weekly automated surveys of health care utilization and infectious disease symptoms among infants over the first year of life. | Ley C, Willis L, de la Luz Sanchez M, Parsonnet J | PloS one | 31846482 | PLoS One | 2019 |
| Urinary triclosan is associated with elevated body mass index in NHANES. | Lankester J, Patel C, Cullen MR, Ley C, Parsonnet J | PloS one | 24278238 | PLoS One | 2013 |
| Triclosan and triclocarban exposure and thyroid function during pregnancy-A randomized intervention. | Ley C, Pischel L, Parsonnet J | Reproductive toxicology (Elmsford, N.Y.) | 28939492 | Reprod Toxicol | 2017 Dec |
| Gestational diabetes is driven by microbiota-induced inflammation months before diagnosis. | Pinto Y, Frishman S, Turjeman S, Eshel A, Nuriel-Ohayon M, Shrossel O, Ziv O, Walters W, Parsonnet J, Ley C, Johnson EL, Kumar K, Schweitzer R, Khatib S, Magzal F, Muller E, Tamir S, Tenenbaum-Gavish K, Rautava S, Salminen S, Isolauri E, Yariv O, Peled Y, Poran E, Pardo J, Chen R, Hod M, Borenstein E, Ley RE, Schwartz B, Louzoun Y, Hadar E, Koren O | Gut | 36627187 | Gut | 2023 May |
| Shaping of infant B cell receptor repertoires by environmental factors and infectious disease. | Nielsen SCA, Roskin KM, Jackson KJL, Joshi SA, Nejad P, Lee JY, Wagar LE, Pham TD, Hoh RA, Nguyen KD, Tsunemoto HY, Patel SB, Tibshirani R, Ley C, Davis MM, Parsonnet J, Boyd SD | Science translational medicine | 30814336 | Sci Transl Med | 2019 Feb 27 |
| Household triclosan and triclocarban effects on the infant and maternal microbiome. | Ribado JV, Ley C, Haggerty TD, Tkachenko E, Bhatt AS, Parsonnet J | EMBO molecular medicine | 29030459 | EMBO Mol Med | 2017 Dec |
| Increased T Cell Differentiation and Cytolytic Function in Bangladeshi Compared to American Children. | Wagar LE, Bolen CR, Sigal N, Lopez Angel CJ, Guan L, Kirkpatrick BD, Haque R, Tibshirani RJ, Parsonnet J, Petri WA Jr, Davis MM | Frontiers in immunology | 31620139 | Front Immunol | 2019 |
| Metagenomic sequencing of stool samples in Bangladeshi infants: virome association with poliovirus shedding after oral poliovirus vaccination. | Tan SK, Granados AC, Bouquet J, Hoy-Schulz YE, Green L, Federman S, Stryke D, Haggerty TD, Ley C, Yeh MT, Jannat K, Maldonado YA, Andino R, Parsonnet J, Chiu CY | Scientific reports | 32958861 | Sci Rep | 2020 Sep 21 |
| A modified Michaelis-Menten equation estimates growth from birth to 3 years in healthy babies in the US. | Walters W, Ley C, Hastie T, Ley R, Parsonnet J | Research square | 36711501 | Res Sq | 2023 Jun 22 |
| Longitudinal comparison of the developing gut virome in infants and their mothers. | Walters WA, Granados AC, Ley C, Federman S, Stryke D, Santos Y, Haggerty T, Sotomayor-Gonzalez A, Servellita V, Ley RE, Parsonnet J, Chiu CY | Cell host & microbe | 36758519 | Cell Host Microbe | 2023 Feb 8 |
| D-SPIN constructs gene regulatory network models from multiplexed scRNA-seq data revealing organizing principles of cellular perturbation response. | Jiang J, Chen S, Tsou T, McGinnis CS, Khazaei T, Zhu Q, Park JH, Strazhnik IM, Vielmetter J, Gong Y, Hanna J, Chow ED, Sivak DA, Gartner ZJ, Thomson M | bioRxiv : the preprint server for biology | 37131803 | bioRxiv | 2024 Jun 4 |
| Unexplored regions of the protein sequence-structure map revealed at scale by a library of foldtuned language models. | Subramanian AM, Martinez ZA, Lourenço AL, Liu S, Thomson M | bioRxiv : the preprint server for biology | 38187750 | bioRxiv | 2025 Jan 13 |
| Protein CREATE enables closed-loop design of de novo synthetic protein binders. | Lourenço A, Subramanian A, Spencer R, Anaya M, Miao J, Fu W, Chow E, Thomson M | bioRxiv : the preprint server for biology | 39803556 | bioRxiv | 2025 Jan 2 |
| Identification of orphan ligand-receptor relationships using a cell-based CRISPRa enrichment screening platform. | Siepe DH, Henneberg LT, Wilson SC, Hess GT, Bassik MC, Zinn K, Garcia KC | eLife | 36178190 | Elife | 2022 Sep 30 |
| Receptor Elimination by E3 Ubiquitin Ligase Recruitment (REULR): A Targeted Protein Degradation Toolbox. | Siepe DH, Picton LK, Garcia KC | ACS synthetic biology | 37011906 | ACS Synth Biol | 2023 Apr 21 |
| TRILL: ORCHESTRATING MODULAR DEEP-LEARNING WORKFLOWS FOR DEMOCRATIZED, SCALABLE PROTEIN ANALYSIS AND ENGINEERING. | Martinez ZA, Murray RM, Thomson MW | bioRxiv : the preprint server for biology | 37986952 | bioRxiv | 2023 Nov 10 |
| AlphaFold2 enables accurate deorphanization of ligands to single-pass receptors. | Danneskiold-Samsøe NB, Kavi D, Jude KM, Nissen SB, Wat LW, Coassolo L, Zhao M, Santana-Oikawa GA, Broido BB, Garcia KC, Svensson KJ | bioRxiv : the preprint server for biology | 36993313 | bioRxiv | 2023 Dec 15 |
| Spin glasses, error correcting codes, and synchronization of human stem cell organoids. | Thomson M | Cell | 36736298 | Cell | 2023 Feb 2 |
| Deploying synthetic coevolution and machine learning to engineer protein-protein interactions. | Yang A, Jude KM, Lai B, Minot M, Kocyla AM, Glassman CR, Nishimiya D, Kim YS, Reddy ST, Khan AA, Garcia KC | Science (New York, N.Y.) | 37499032 | Science | 2023 Jul 28 |
| Crosstalk between the Rho and Rab family of small GTPases in neurodegenerative disorders. | Nik Akhtar S, Bunner WP, Brennan E, Lu Q, Szatmari EM | Frontiers in cellular neuroscience | 36779014 | Front Cell Neurosci | 2023 |
| Enabling systemic identification and functionality profiling for Cdc42 homeostatic modulators. | Malasala S, Azimian F, Chen YH, Twiss JL, Boykin C, Akhtar SN, Lu Q | Communications chemistry | 39562759 | Commun Chem | 2024 Nov 19 |
| Therapeutic Effect of Y-27632 on Tumorigenesis and Cisplatin-Induced Peripheral Sensory Loss through RhoA-NF-κB. | Zhu Y, Howard GA, Pittman K, Boykin C, Herring LE, Wilkerson EM, Verbanac K, Lu Q | Molecular cancer research : MCR | 31189689 | Mol Cancer Res | 2019 Sep |
| Selective axonal translation of the mRNA isoform encoding prenylated Cdc42 supports axon growth. | Lee SJ, Zdradzinski MD, Sahoo PK, Kar AN, Patel P, Kawaguchi R, Aguilar BJ, Lantz KD, McCain CR, Coppola G, Lu Q, Twiss JL | Journal of cell science | 33674450 | J Cell Sci | 2021 Apr 1 |
| Nanoarchitecture and molecular interactions of epithelial cell junction proteins revealed by super-resolution microscopy. | Naser AN, Guiler W, Lu Q, Chen YH | Annals of the New York Academy of Sciences | 35819053 | Ann N Y Acad Sci | 2022 Oct |
| RhoA-LIMK Signaling Axis Reveals Rostral-Caudal Plane and Spatial Dysregulation in the Brain of Alzheimer's Disease Mouse Models. | Nik Akhtar S, Lu Q | Journal of Alzheimer's disease : JAD | 37718806 | J Alzheimers Dis | 2023 |
| KHSRP-mediated Decay of Axonally Localized Prenyl-Cdc42 mRNA Slows Nerve Regeneration. | Zdradzinski MD, Vaughn LS, Matoo S, Trumbull K, Loomis A, Thames E, Lee SJ, Perrone-Bizzozero N, Lu Q, Larsen JM, Twiss JL | bioRxiv : the preprint server for biology | 39975228 | bioRxiv | 2025 Feb 8 |
| Trans-Compartmental Regulation of Tight Junction Barrier Function. | Naser AN, Lu Q, Chen YH | Tissue barriers | 36220768 | Tissue Barriers | 2023 Oct 2 |
| TRPV4: En RhoA To a Cure? | Lu Q, Chen YH | BioEssays : news and reviews in molecular, cellular and developmental biology | 35441721 | Bioessays | 2022 Jun |
| G-Protein Signaling in Alzheimer's Disease: Spatial Expression Validation of Semi-supervised Deep Learning-Based Computational Framework. | Zhang DF, Penwell T, Chen YH, Koehler A, Wu R, Nik Akhtar S, Lu Q | The Journal of neuroscience : the official journal of the Society for Neuroscience | 39327003 | J Neurosci | 2024 Nov 6 |
| Spatial and planar profiling of Rac1/Cdc42 signaling in Alzheimer's disease brain. | Akhtar SN, Tran TD, Chen YH, Lu Q | Journal of Alzheimer's disease : JAD | 39610278 | J Alzheimers Dis | 2024 Dec |
| Responsiveness to perturbations is a hallmark of transcription factors that maintain cell identity in vitro. | Mellis IA, Edelstein HI, Truitt R, Goyal Y, Beck LE, Symmons O, Dunagin MC, Linares Saldana RA, Shah PP, Pérez-Bermejo JA, Padmanabhan A, Yang W, Jain R, Raj A | Cell systems | 34352221 | Cell Syst | 2021 Sep 22 |
| Retrospective identification of cell-intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Arnett M, Yang W, Raj A | Cell systems | 38335955 | Cell Syst | 2024 Feb 21 |
| Genetic screening for single-cell variability modulators driving therapy resistance. | Torre EA, Arai E, Bayatpour S, Jiang CL, Beck LE, Emert BL, Shaffer SM, Mellis IA, Fane ME, Alicea GM, Budinich KA, Weeraratna AT, Shi J, Raj A | Nature genetics | 33398196 | Nat Genet | 2021 Jan |
| Social reprogramming in ants induces longevity-associated glia remodeling. | Sheng L, Shields EJ, Gospocic J, Glastad KM, Ratchasanmuang P, Berger SL, Raj A, Little S, Bonasio R | Science advances | 32875108 | Sci Adv | 2020 Aug |
| Spatial transcriptomics reveals influence of microenvironment on intrinsic fates in melanoma therapy resistance. | Boe RH, Triandafillou CG, Lazcano R, Wargo JA, Raj A | bioRxiv : the preprint server for biology | 39005406 | bioRxiv | 2024 Jul 2 |
| Innate Immune Memory is Stimulus Specific. | O'Farrell A, Niu Z, Li J, Van Eyndhoven LC, Sarma K, Raj A | bioRxiv : the preprint server for biology | 39896612 | bioRxiv | 2025 Jan 24 |
| An atlas of lamina-associated chromatin across twelve human cell types reveals an intermediate chromatin subtype. | Shah PP, Keough KC, Gjoni K, Santini GT, Abdill RJ, Wickramasinghe NM, Dundes CE, Karnay A, Chen A, Salomon REA, Walsh PJ, Nguyen SC, Whalen S, Joyce EF, Loh KM, Dubois N, Pollard KS, Jain R | Genome biology | 36691074 | Genome Biol | 2023 Jan 23 |
| Systematically quantifying morphological features reveals constraints on organoid phenotypes. | Beck LE, Lee J, Coté C, Dunagin MC, Lukonin I, Salla N, Chang MK, Hughes AJ, Mornin JD, Gartner ZJ, Liberali P, Raj A | Cell systems | 35705097 | Cell Syst | 2022 Jul 20 |
| Gene regulation gravitates toward either addition or multiplication when combining the effects of two signals. | Sanford EM, Emert BL, Coté A, Raj A | eLife | 33284110 | Elife | 2020 Dec 7 |
| Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations. | Kiani K, Sanford EM, Goyal Y, Raj A | Molecular systems biology | 36069349 | Mol Syst Biol | 2022 Sep |
| Cell type determination for cardiac differentiation occurs soon after seeding of human-induced pluripotent stem cells. | Jiang CL, Goyal Y, Jain N, Wang Q, Truitt RE, Coté AJ, Emert B, Mellis IA, Kiani K, Yang W, Jain R, Raj A | Genome biology | 35382863 | Genome Biol | 2022 Apr 5 |
| Post-transcriptional splicing can occur in a slow-moving zone around the gene. | Coté A, O'Farrell A, Dardani I, Dunagin M, Coté C, Wan Y, Bayatpour S, Drexler HL, Alexander KA, Chen F, Wassie AT, Patel R, Pham K, Boyden ES, Berger S, Phillips-Cremins J, Churchman LS, Raj A | eLife | 38577979 | Elife | 2024 Apr 5 |
| Diverse clonal fates emerge upon drug treatment of homogeneous cancer cells. | Goyal Y, Busch GT, Pillai M, Li J, Boe RH, Grody EI, Chelvanambi M, Dardani IP, Emert B, Bodkin N, Braun J, Fingerman D, Kaur A, Jain N, Ravindran PT, Mellis IA, Kiani K, Alicea GM, Fane ME, Ahmed SS, Li H, Chen Y, Chai C, Kaster J, Witt RG, Lazcano R, Ingram DR, Johnson SB, Wani K, Dunagin MC, Lazar AJ, Weeraratna AT, Wargo JA, Herlyn M, Raj A | Nature | 37468627 | Nature | 2023 Aug |
| AP-1 Mediates Cellular Adaptation and Memory Formation During Therapy Resistance. | Li J, Ravindran PT, O'Farrell A, Busch GT, Boe RH, Niu Z, Woo S, Dunagin MC, Jain N, Goyal Y, Sarma K, Herlyn M, Raj A | bioRxiv : the preprint server for biology | 39091739 | bioRxiv | 2024 Jul 25 |
| FZD2 Regulates Murine Hair Follicle Function and Maintenance. | Brennan-Crispi DM, Frankfurter M, Murphy C, Sheng E, Xu M, Morrisey EE, Millar SE, Leung TH | The Journal of investigative dermatology | 35051380 | J Invest Dermatol | 2022 Aug |
| Memory Sequencing Reveals Heritable Single-Cell Gene Expression Programs Associated with Distinct Cellular Behaviors. | Shaffer SM, Emert BL, Reyes Hueros RA, Cote C, Harmange G, Schaff DL, Sizemore AE, Gupte R, Torre E, Singh A, Bassett DS, Raj A | Cell | 32735851 | Cell | 2020 Aug 20 |
| Allelic correlation is a marker of trade-offs between barriers to transmission of expression variability and signal responsiveness in genetic networks. | Boe RH, Ayyappan V, Schuh L, Raj A | Cell systems | 36450286 | Cell Syst | 2022 Dec 21 |
| Retrospective identification of intrinsic factors that mark pluripotency potential in rare somatic cells. | Jain N, Goyal Y, Dunagin MC, Cote CJ, Mellis IA, Emert B, Jiang CL, Dardani IP, Reffsin S, Raj A | bioRxiv : the preprint server for biology | 36798299 | bioRxiv | 2023 Feb 10 |
| Pathogenic LMNA variants disrupt cardiac lamina-chromatin interactions and de-repress alternative fate genes. | Shah PP, Lv W, Rhoades JH, Poleshko A, Abbey D, Caporizzo MA, Linares-Saldana R, Heffler JG, Sayed N, Thomas D, Wang Q, Stanton LJ, Bedi K, Morley MP, Cappola TP, Owens AT, Margulies KB, Frank DB, Wu JC, Rader DJ, Yang W, Prosser BL, Musunuru K, Jain R | Cell stem cell | 33529599 | Cell Stem Cell | 2021 May 6 |
| Variability within rare cell states enables multiple paths toward drug resistance. | Emert BL, Cote CJ, Torre EA, Dardani IP, Jiang CL, Jain N, Shaffer SM, Raj A | Nature biotechnology | 33619394 | Nat Biotechnol | 2021 Jul |
| Picking Winners and Losers: Cell Competition in Tissue Development and Homeostasis. | Kim W, Jain R | Trends in genetics : TIG | 32418713 | Trends Genet | 2020 Jul |
| Gene Networks with Transcriptional Bursting Recapitulate Rare Transient Coordinated High Expression States in Cancer. | Schuh L, Saint-Antoine M, Sanford EM, Emert BL, Singh A, Marr C, Raj A, Goyal Y | Cell systems | 32325034 | Cell Syst | 2020 Apr 22 |
| ClampFISH 2.0 enables rapid, scalable amplified RNA detection in situ. | Dardani I, Emert BL, Goyal Y, Jiang CL, Kaur A, Lee J, Rouhanifard SH, Alicea GM, Fane ME, Xiao M, Herlyn M, Weeraratna AT, Raj A | Nature methods | 36280724 | Nat Methods | 2022 Nov |
| Single cell susceptibility to SARS-CoV-2 infection is driven by variable cell states. | Reffsin S, Miller J, Ayyanathan K, Dunagin MC, Jain N, Schultz DC, Cherry S, Raj A | bioRxiv : the preprint server for biology | 37461472 | bioRxiv | 2023 Jul 7 |
| Reversible Assembly of Proteolysis Targeting Chimeras. | Gui W, Giardina SF, Balzarini M, Barany F, Kodadek T | ACS chemical biology | 37422908 | ACS Chem Biol | 2023 Jul 21 |
| Facile Synthesis of Homodimeric Protein Ligands. | Gui W, Kodadek T | Chembiochem : a European journal of chemical biology | 37449865 | Chembiochem | 2023 Sep 15 |
| Solid-phase synthesis of DNA-encoded libraries via an "aldehyde explosion" strategy. | Paciaroni NG , Ndungu JM , Kodadek T | Chemical communications (Cambridge, England) | 32215395 | Chem Commun (Camb) | 2020 Apr 30 |
| Applications and Limitations of Oxime-Linked "Split PROTACs". | Gui W, Kodadek T | Chembiochem : a European journal of chemical biology | 35802347 | Chembiochem | 2022 Sep 16 |
| Synthesis and Screening of a DNA-Encoded Library of Non-Peptidic Macrocycles. | Koesema E, Roy A, Paciaroni NG, Coito C, Tokmina-Roszyk M, Kodadek T | Angewandte Chemie (International ed. in English) | 35192245 | Angew Chem Int Ed Engl | 2022 Apr 25 |
| Structural characterization of a peptoid-inspired conformationally constrained oligomer (PICCO) bound to streptavidin. | McEnaney P , Balzarini M , Park H , Kodadek T | Chemical communications (Cambridge, England) | 32785302 | Chem Commun (Camb) | 2020 Sep 16 |
| Chemical composition of DNA-encoded libraries, past present and future. | Dickson P, Kodadek T | Organic & biomolecular chemistry | 31017595 | Org Biomol Chem | 2019 May 15 |
| Beyond protein binding: recent advances in screening DNA-encoded libraries. | Kodadek T, Paciaroni NG, Balzarini M, Dickson P | Chemical communications (Cambridge, England) | 31633708 | Chem Commun (Camb) | 2019 Nov 18 |
| Physical and Functional Analysis of the Putative Rpn13 Inhibitor RA190. | Dickson P, Abegg D, Vinogradova E, Takaya J, An H, Simanski S, Cravatt BF, Adibekian A, Kodadek T | Cell chemical biology | 32857985 | Cell Chem Biol | 2020 Nov 19 |
| Mechanistic Studies of the Multiple Myeloma and Melanoma Cell-Selective Toxicity of the Rpn13-Binding Peptoid KDT-11. | Dickson P, Simanski S, Ngundu JM, Kodadek T | Cell chemical biology | 32857986 | Cell Chem Biol | 2020 Nov 19 |
| Hachimoji DNA and RNA: A genetic system with eight building blocks. | Hoshika S, Leal NA, Kim MJ, Kim MS, Karalkar NB, Kim HJ, Bates AM, Watkins NE Jr, SantaLucia HA, Meyer AJ, DasGupta S, Piccirilli JA, Ellington AD, SantaLucia J Jr, Georgiadis MM, Benner SA | Science (New York, N.Y.) | 30792304 | Science | 2019 Feb 22 |
| Snapshots of an evolved DNA polymerase pre- and post-incorporation of an unnatural nucleotide. | Singh I, Laos R, Hoshika S, Benner SA, Georgiadis MM | Nucleic acids research | 29986111 | Nucleic Acids Res | 2018 Sep 6 |
| Building better polymerases: Engineering the replication of expanded genetic alphabets. | Ouaray Z, Benner SA, Georgiadis MM, Richards NGJ | The Journal of biological chemistry | 33004440 | J Biol Chem | 2020 Dec 11 |
| Assessing Readability of an 8-Letter Expanded Deoxyribonucleic Acid Alphabet with Nanopores. | Thomas CA, Craig JM, Hoshika S, Brinkerhoff H, Huang JR, Abell SJ, Kim HC, Franzi MC, Carrasco JD, Kim HJ, Smith DC, Gundlach JH, Benner SA, Laszlo AH | Journal of the American Chemical Society | 37036666 | J Am Chem Soc | 2023 Apr 10 |
| Synthetic Biology Pathway to Nucleoside Triphosphates for Expanded Genetic Alphabets. | Li Y, Abraham C, Suslov O, Yaren O, Shaw RW, Kim MJ, Wan S, Marliere P, Benner SA | ACS synthetic biology | 37227319 | ACS Synth Biol | 2023 Jun 16 |
| A folding motif formed with an expanded genetic alphabet. | Wang B, Rocca JR, Hoshika S, Chen C, Yang Z, Esmaeeli R, Wang J, Pan X, Lu J, Wang KK, Cao YC, Tan W, Benner SA | Nature chemistry | 38858518 | Nat Chem | 2024 Oct |
| Electrochemical Reduction and Oxidation of Eight Unnatural 2'-Deoxynucleosides at a Pyrolytic Graphite Electrode. | Špaček J, Karalkar N, Fojta M, Wang J, Benner SA | Electrochimica acta | 33087943 | Electrochim Acta | 2020 Dec 1 |
| Ligand-Guided Selection with Artificially Expanded Genetic Information Systems against TCR-CD3ε. | Zumrut H, Yang Z, Williams N, Arizala J, Batool S, Benner SA, Mallikaratchy P | Biochemistry | 31880917 | Biochemistry | 2020 Feb 4 |
| Enzymatic synthesis and nanopore sequencing of 12-letter supernumerary DNA. | Kawabe H, Thomas CA, Hoshika S, Kim MJ, Kim MS, Miessner L, Kaplan N, Craig JM, Gundlach JH, Laszlo AH, Benner SA, Marchand JA | Nature communications | 37884513 | Nat Commun | 2023 Oct 26 |
| Aptamer Technologies in Neuroscience, Neuro-Diagnostics and Neuro-Medicine Development. | Wang B, Kobeissy F, Golpich M, Cai G, Li X, Abedi R, Haskins W, Tan W, Benner SA, Wang KKW | Molecules (Basel, Switzerland) | 38474636 | Molecules | 2024 Mar 2 |
| An Aptamer-Nanotrain Assembled from Six-Letter DNA Delivers Doxorubicin Selectively to Liver Cancer Cells. | Zhang L, Wang S, Yang Z, Hoshika S, Xie S, Li J, Chen X, Wan S, Li L, Benner SA, Tan W | Angewandte Chemie (International ed. in English) | 31650689 | Angew Chem Int Ed Engl | 2020 Jan 7 |
| Monitoring of switches in heterochromatin-induced silencing shows incomplete establishment and developmental instabilities. | Bughio F, Huckell GR, Maggert KA | Proceedings of the National Academy of Sciences of the United States of America | 31527269 | Proc Natl Acad Sci U S A | 2019 Oct 1 |
| The processivity factor Pol32 mediates nuclear localization of DNA polymerase delta and prevents chromosomal fragile site formation in Drosophila development. | Ji J, Tang X, Hu W, Maggert KA, Rong YS | PLoS genetics | 31100062 | PLoS Genet | 2019 May |
| The peculiar genetics of the ribosomal DNA blurs the boundaries of transgenerational epigenetic inheritance. | Bughio F, Maggert KA | Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology | 30511202 | Chromosome Res | 2019 Mar |
| Live analysis of position-effect variegation in Drosophila reveals different modes of action for HP1a and Su(var)3-9. | Bughio FJ, Maggert KA | Proceedings of the National Academy of Sciences of the United States of America | 35704756 | Proc Natl Acad Sci U S A | 2022 Jun 21 |
| Human rDNA copy number is unstable in metastatic breast cancers. | Valori V, Tus K, Laukaitis C, Harris DT, LeBeau L, Maggert KA | Epigenetics | 31352858 | Epigenetics | 2020 Jan-Feb |
| Under the magnifying glass: The ups and downs of rDNA copy number. | Kindelay SM, Maggert KA | Seminars in cell & developmental biology | 35595601 | Semin Cell Dev Biol | 2023 Feb 28 |
| Stress: An evolutionary mutagen. | Maggert KA | Proceedings of the National Academy of Sciences of the United States of America | 31434787 | Proc Natl Acad Sci U S A | 2019 Sep 3 |
| Chronic Menthol Does Not Change Stoichiometry or Functional Plasma Membrane Levels of Mouse α3β4-Containing Nicotinic Acetylcholine Receptors. | Bavan S, Kim CH, Henderson BJ, Lester HA | Molecular pharmacology | 30670481 | Mol Pharmacol | 2019 Apr |
| Regulation of epithelial sodium channel activity by SARS-CoV-1 and SARS-CoV-2 proteins. | Grant SN, Lester HA | Biophysical journal | 34197807 | Biophys J | 2021 Jul 20 |
| Directed Evolution of a Selective and Sensitive Serotonin Sensor via Machine Learning. | Unger EK, Keller JP, Altermatt M, Liang R, Matsui A, Dong C, Hon OJ, Yao Z, Sun J, Banala S, Flanigan ME, Jaffe DA, Hartanto S, Carlen J, Mizuno GO, Borden PM, Shivange AV, Cameron LP, Sinning S, Underhill SM, Olson DE, Amara SG, Temple Lang D, Rudnick G, Marvin JS, Lavis LD, Lester HA, Alvarez VA, Fisher AJ, Prescher JA, Kash TL, Yarov-Yarovoy V, Gradinaru V, Looger LL, Tian L | Cell | 33333022 | Cell | 2020 Dec 23 |
| Biosensors Show the Pharmacokinetics of S-Ketamine in the Endoplasmic Reticulum. | Bera K, Kamajaya A, Shivange AV, Muthusamy AK, Nichols AL, Borden PM, Grant S, Jeon J, Lin E, Bishara I, Chin TM, Cohen BN, Kim CH, Unger EK, Tian L, Marvin JS, Looger LL, Lester HA | Frontiers in cellular neuroscience | 31798415 | Front Cell Neurosci | 2019 |
| Selective Serotonin Reuptake Inhibitors within Cells: Temporal Resolution in Cytoplasm, Endoplasmic Reticulum, and Membrane. | Nichols AL, Blumenfeld Z, Luebbert L, Knox HJ, Muthusamy AK, Marvin JS, Kim CH, Grant SN, Walton DP, Cohen BN, Hammar R, Looger L, Artursson P, Dougherty DA, Lester HA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 36868853 | J Neurosci | 2023 Mar 29 |
| Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. | Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA | bioRxiv : the preprint server for biology | 36712031 | bioRxiv | 2024 Jan 18 |
| Interactive computational and experimental approaches improve the sensitivity of periplasmic binding protein-based nicotine biosensors for measurements in biofluids. | Haloi N, Huang S, Nichols AL, Fine EJ, Friesenhahn NJ, Marotta CB, Dougherty DA, Lindahl E, Howard RJ, Mayo SL, Lester HA | Protein engineering, design & selection : PEDS | 38302088 | Protein Eng Des Sel | 2024 Jan 29 |
| Proteins for increased surface expression of the α6β4 nicotinic acetylcholine receptor: nothing but good news? | Grant S, Lester HA | The Journal of clinical investigation | 33074245 | J Clin Invest | 2020 Nov 2 |
| Correction: Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands. | Nichols AL, Blumenfeld Z, Fan C, Luebbert L, Blom AEM, Cohen BN, Marvin JS, Borden PM, Kim CH, Muthusamy AK, Shivange AV, Knox HJ, Campello HR, Wang JH, Dougherty DA, Looger LL, Gallagher T, Rees DC, Lester HA | eLife | 36520038 | Elife | 2022 Dec 15 |
| Fluorescence Screens for Identifying Central Nervous System-Acting Drug-Biosensor Pairs for Subcellular and Supracellular Pharmacokinetics. | Beatty ZG, Muthusamy AK, Unger EK, Dougherty DA, Tian L, Looger LL, Shivange AV, Bera K, Lester HA, Nichols AL | Bio-protocol | 36532688 | Bio Protoc | 2022 Nov 20 |
| Antidepressants enter cells, organelles, and membranes. | Blumenfeld Z, Bera K, Castrén E, Lester HA | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 37783840 | Neuropsychopharmacology | 2024 Jan |
| Determining the pharmacokinetics of nicotinic drugs in the endoplasmic reticulum using biosensors. | Shivange AV, Borden PM, Muthusamy AK, Nichols AL, Bera K, Bao H, Bishara I, Jeon J, Mulcahy MJ, Cohen B, O'Riordan SL, Kim C, Dougherty DA, Chapman ER, Marvin JS, Looger LL, Lester HA | The Journal of general physiology | 30718376 | J Gen Physiol | 2019 Jun 3 |
| Three Mutations Convert the Selectivity of a Protein Sensor from Nicotinic Agonists to S-Methadone for Use in Cells, Organelles, and Biofluids. | Muthusamy AK, Kim CH, Virgil SC, Knox HJ, Marvin JS, Nichols AL, Cohen BN, Dougherty DA, Looger LL, Lester HA | Journal of the American Chemical Society | 35446570 | J Am Chem Soc | 2022 May 18 |
| Virus-like particle-induced protection against MRSA pneumonia is dependent on IL-13 and enhancement of phagocyte function. | Rynda-Apple A, Dobrinen E, McAlpine M, Read A, Harmsen A, Richert LE, Calverley M, Pallister K, Voyich J, Wiley JA, Johnson B, Young M, Douglas T, Harmsen AG | The American journal of pathology | 22642909 | Am J Pathol | 2012 Jul |
| Learning the pattern of epistasis linking genotype and phenotype in a protein. | Poelwijk FJ, Socolich M, Ranganathan R | Nature communications | 31527666 | Nat Commun | 2019 Sep 16 |
| Roadmap on biology in time varying environments. | Murugan A, Husain K, Rust MJ, Hepler C, Bass J, Pietsch JMJ, Swain PS, Jena SG, Toettcher JE, Chakraborty AK, Sprenger KG, Mora T, Walczak AM, Rivoire O, Wang S, Wood KB, Skanata A, Kussell E, Ranganathan R, Shih HY, Goldenfeld N | Physical biology | 33477124 | Phys Biol | 2021 May 17 |
| Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles. | Kaisanlahti A, Turunen J, Byts N, Samoylenko A, Bart G, Virtanen N, Tejesvi MV, Zhyvolozhnyi A, Sarfraz S, Kumpula S, Hekkala J, Salmi S, Will O, Korvala J, Paalanne N, Erawijantari PP, Suokas M, Medina TP, Vainio S, Medina OP, Lahti L, Tapiainen T, Reunanen J | Microbiome | 37953319 | Microbiome | 2023 Nov 13 |
| Direct visualization of electric-field-stimulated ion conduction in a potassium channel. | Lee B, White KI, Socolich M, Klureza MA, Henning R, Srajer V, Ranganathan R, Hekstra DR | Cell | 39793560 | Cell | 2025 Jan 9 |
| Chronic intermittent ethanol exposure and withdrawal leads to adaptations in nucleus accumbens core postsynaptic density proteome and dendritic spines. | Uys JD, McGuier NS, Gass JT, Griffin WC 3rd, Ball LE, Mulholland PJ | Addiction biology | 25787124 | Addict Biol | 2016 May |
| An evolution-based model for designing chorismate mutase enzymes. | Russ WP, Figliuzzi M, Stocker C, Barrat-Charlaix P, Socolich M, Kast P, Hilvert D, Monasson R, Cocco S, Weigt M, Ranganathan R | Science (New York, N.Y.) | 32703877 | Science | 2020 Jul 24 |
| RNA sectors and allosteric function within the ribosome. | Walker AS, Russ WP, Ranganathan R, Schepartz A | Proceedings of the National Academy of Sciences of the United States of America | 32747536 | Proc Natl Acad Sci U S A | 2020 Aug 18 |
| A set of experimentally validated, mutually orthogonal primers for combinatorially specifying genetic components. | Subramanian SK, Russ WP, Ranganathan R | Synthetic biology (Oxford, England) | 32995509 | Synth Biol (Oxf) | 2018 |
| Deconstruction of the Ras switching cycle through saturation mutagenesis. | Bandaru P, Shah NH, Bhattacharyya M, Barton JP, Kondo Y, Cofsky JC, Gee CL, Chakraborty AK, Kortemme T, Ranganathan R, Kuriyan J | eLife | 28686159 | Elife | 2017 Jul 7 |
| An evolutionary hotspot defines functional differences between CRYPTOCHROMES. | Rosensweig C, Reynolds KA, Gao P, Laothamatas I, Shan Y, Ranganathan R, Takahashi JS, Green CB | Nature communications | 29556064 | Nat Commun | 2018 Mar 19 |
| A Novel EGFRvIII T-Cell Bispecific Antibody for the Treatment of Glioblastoma. | Iurlaro R, Waldhauer I, Planas-Rigol E, Bonfill-Teixidor E, Arias A, Nicolini V, Freimoser-Grundschober A, Cuartas I, Martínez-Moreno A, Martínez-Ricarte F, Cordero E, Cicuendez M, Casalino S, Guardia-Reyes X, Fahrni L, Pöschinger T, Steinhart V, Richard M, Briner S, Mueller J, Osl F, Sam J, Colombetti S, Bacac M, Klein C, Pineda E, Reyes-Figueroa L, Di Somma A, González J, Nuciforo P, Carles J, Vieito M, Tabernero J, Umaña P, Seoane J | Molecular cancer therapeutics | 35915983 | Mol Cancer Ther | 2022 Oct 7 |
| Electric-field-stimulated protein mechanics. | Hekstra DR, White KI, Socolich MA, Henning RW, Šrajer V, Ranganathan R | Nature | 27926732 | Nature | 2016 Dec 15 |
| Coevolution-based inference of amino acid interactions underlying protein function. | Salinas VH, Ranganathan R | eLife | 30024376 | Elife | 2018 Jul 20 |
| Three structural solutions for bacterial adhesion pilus stability and superelasticity. | Doran MH, Baker JL, Dahlberg T, Andersson M, Bullitt E | Structure (London, England : 1993) | 37001523 | Structure | 2023 May 4 |
| (31)P-dephased, (13)C-detected REDOR for NMR crystallography at natural isotopic abundance. | Greenwood AI, Clay MC, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 28319851 | J Magn Reson | 2017 May |
| Probing cholesterol binding and translocation in P-glycoprotein. | Thangapandian S, Kapoor K, Tajkhorshid E | Biochimica et biophysica acta. Biomembranes | 31676371 | Biochim Biophys Acta Biomembr | 2020 Jan 1 |
| Microscopic Characterization of GRP1 PH Domain Interaction with Anionic Membranes. | Pant S, Tajkhorshid E | Journal of computational chemistry | 31762060 | J Comput Chem | 2020 Mar 5 |
| Serotonin transporter-ibogaine complexes illuminate mechanisms of inhibition and transport. | Coleman JA, Yang D, Zhao Z, Wen PC, Yoshioka C, Tajkhorshid E, Gouaux E | Nature | 31019304 | Nature | 2019 May |
| Exact distance measurements for structure and dynamics in solid proteins by fast-magic-angle-spinning NMR. | Grohe K, Nimerovsky E, Singh H, Vasa SK, Söldner B, Vögeli B, Rienstra CM, Linser R | Chemical communications (Cambridge, England) | 31199417 | Chem Commun (Camb) | 2019 Jul 14 |
| Ataxia-linked SLC1A3 mutations alter EAAT1 chloride channel activity and glial regulation of CNS function. | Wu Q, Akhter A, Pant S, Cho E, Zhu JX, Garner A, Ohyama T, Tajkhorshid E, van Meyel DJ, Ryan RM | The Journal of clinical investigation | 35167492 | J Clin Invest | 2022 Apr 1 |
| Molecular mechanism of prestin electromotive signal amplification. | Ge J, Elferich J, Dehghani-Ghahnaviyeh S, Zhao Z, Meadows M, von Gersdorff H, Tajkhorshid E, Gouaux E | Cell | 34390643 | Cell | 2021 Sep 2 |
| Topological Learning Approach to Characterizing Biological Membranes. | Arango AS, Park H, Tajkhorshid E | bioRxiv : the preprint server for biology | 38076911 | bioRxiv | 2023 Nov 28 |
| Differential dynamics and direct interaction of bound ligands with lipids in multidrug transporter ABCG2. | Rasouli A, Yu Q, Dehghani-Ghahnaviyeh S, Wen PC, Kowal J, Locher KP, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 36580587 | Proc Natl Acad Sci U S A | 2023 Jan 3 |
| Tuning phenylalanine fluorination to assess aromatic contributions to protein function and stability in cells. | Galles GD, Infield DT, Clark CJ, Hemshorn ML, Manikandan S, Fazan F, Rasouli A, Tajkhorshid E, Galpin JD, Cooley RB, Mehl RA, Ahern CA | Nature communications | 36599844 | Nat Commun | 2023 Jan 4 |
| Identifying mutation hotspots reveals pathogenetic mechanisms of KCNQ2 epileptic encephalopathy. | Zhang J, Kim EC, Chen C, Procko E, Pant S, Lam K, Patel J, Choi R, Hong M, Joshi D, Bolton E, Tajkhorshid E, Chung HJ | Scientific reports | 32179837 | Sci Rep | 2020 Mar 16 |
| Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes. | Gullett JM, Cuypers MG, Grace CR, Pant S, Subramanian C, Tajkhorshid E, Rock CO, White SW | The Journal of biological chemistry | 35122790 | J Biol Chem | 2022 Mar |
| Active participation of membrane lipids in inhibition of multidrug transporter P-glycoprotein. | Kapoor K, Pant S, Tajkhorshid E | Chemical science | 34084427 | Chem Sci | 2021 Apr 9 |
| Structures of the TMC-1 complex illuminate mechanosensory transduction. | Jeong H, Clark S, Goehring A, Dehghani-Ghahnaviyeh S, Rasouli A, Tajkhorshid E, Gouaux E | Nature | 36224384 | Nature | 2022 Oct |
| Twisting and tilting of a mechanosensitive molecular probe detects order in membranes. | Licari G, Strakova K, Matile S, Tajkhorshid E | Chemical science | 32864081 | Chem Sci | 2020 Jun 14 |
| Membrane surface recognition by the ASAP1 PH domain and consequences for interactions with the small GTPase Arf1. | Soubias O, Pant S, Heinrich F, Zhang Y, Roy NS, Li J, Jian X, Yohe ME, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA | Science advances | 32998886 | Sci Adv | 2020 Sep |
| Conformational changes in the nucleotide-binding domains of P-glycoprotein induced by ATP hydrolysis. | Dehghani-Ghahnaviyeh S, Kapoor K, Tajkhorshid E | FEBS letters | 33159693 | FEBS Lett | 2021 Mar |
| Solid-State NMR (13)C sensitivity at high magnetic field. | Han R, Borcik CG, Wang S, Warmuth OA, Geohring K, Mullen C, Incitti M, Stringer JA, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 38991265 | J Magn Reson | 2024 Aug |
| Membrane-bound model of the ternary complex between factor VIIa/tissue factor and factor X. | Muller MP, Mortenson A, Sedzro JC, Wen PC, Morrissey JH, Tajkhorshid E | Blood advances | 39671302 | Blood Adv | 2025 Feb 25 |
| Solid-State NMR of highly (13)C-enriched cholesterol in lipid bilayers. | Della Ripa LA, Petros ZA, Cioffi AG, Piehl DW, Courtney JM, Burke MD, Rienstra CM | Methods (San Diego, Calif.) | 29366688 | Methods | 2018 Apr 1 |
| Structural Insights into the Lipid A Transport Pathway in MsbA. | Padayatti PS, Lee SC, Stanfield RL, Wen PC, Tajkhorshid E, Wilson IA, Zhang Q | Structure (London, England : 1993) | 31130486 | Structure | 2019 Jul 2 |
| Membrane Mixer: A Toolkit for Efficient Shuffling of Lipids in Heterogeneous Biological Membranes. | Licari G, Dehghani-Ghahnaviyeh S, Tajkhorshid E | Journal of chemical information and modeling | 35104125 | J Chem Inf Model | 2022 Feb 28 |
| Fungicidal amphotericin B sponges are assemblies of staggered asymmetric homodimers encasing large void volumes. | Lewandowska A, Soutar CP, Greenwood AI, Nimerovsky E, De Lio AM, Holler JT, Hisao GS, Khandelwal A, Zhang J, SantaMaria AM, Schwieters CD, Pogorelov TV, Burke MD, Rienstra CM | Nature structural & molecular biology | 34887566 | Nat Struct Mol Biol | 2021 Dec |
| Stoichiometric analysis reveals a unique phosphatidylserine binding site in coagulation factor X. | Paul D, Morrissey JH | Journal of thrombosis and haemostasis : JTH | 34894064 | J Thromb Haemost | 2022 Mar |
| Aberrant Expression of a Non-muscle RBFOX2 Isoform Triggers Cardiac Conduction Defects in Myotonic Dystrophy. | Misra C, Bangru S, Lin F, Lam K, Koenig SN, Lubbers ER, Hedhli J, Murphy NP, Parker DJ, Dobrucki LW, Cooper TA, Tajkhorshid E, Mohler PJ, Kalsotra A | Developmental cell | 32109384 | Dev Cell | 2020 Mar 23 |
| Integrating hydrogen-deuterium exchange mass spectrometry with molecular dynamics simulations to probe lipid-modulated conformational changes in membrane proteins. | Martens C, Shekhar M, Lau AM, Tajkhorshid E, Politis A | Nature protocols | 31605097 | Nat Protoc | 2019 Nov |
| Membrane Interactions of Cy3 and Cy5 Fluorophores and Their Effects on Membrane-Protein Dynamics. | Lam K, Tajkhorshid E | Biophysical journal | 32533943 | Biophys J | 2020 Jul 7 |
| Multivalent Polymer-Peptide Conjugates-A General Platform for Inhibiting Amyloid Beta Peptide Aggregation. | Jiang X, Halmes AJ, Licari G, Smith JW, Song Y, Moore EG, Chen Q, Tajkhorshid E, Rienstra CM, Moore JS | ACS macro letters | 32149017 | ACS Macro Lett | 2019 Oct 15 |
| Mechanism of gating and partial agonist action in the glycine receptor. | Yu J, Zhu H, Lape R, Greiner T, Du J, Lü W, Sivilotti L, Gouaux E | Cell | 33567265 | Cell | 2021 Feb 18 |
| Lactadherin's Multistate Binding Predicts Stable Membrane-Bound Conformations of Factors V and VIII's C Domains. | Cheng KJ, De Lio AM, Jain R, Paul D, Morrissey JH, Pogorelov TV | Biochemistry | 37747791 | Biochemistry | 2023 Oct 17 |
| Phosphatidylthreonine is a procoagulant lipid detected in human blood and elevated in coronary artery disease. | Hajeyah AA, Protty MB, Paul D, Costa D, Omidvar N, Morgan B, Iwasaki Y, McGill B, Jenkins PV, Yousef Z, Allen-Redpath K, Soyama S, Choudhury A, Mitra R, Yaqoob P, Morrissey JH, Collins PW, O'Donnell VB | Journal of lipid research | 38103786 | J Lipid Res | 2024 Jan |
| Cross polarization stability in multidimensional NMR spectroscopy of biological solids. | Harding BD, Barclay AM, Piehl DW, Hiett A, Warmuth OA, Han R, Henzler-Wildman K, Rienstra CM | Journal of magnetic resonance (San Diego, Calif. : 1997) | 38991266 | J Magn Reson | 2024 Aug |
| Enhancing Spectrometer Performance with Unsupervised Machine Learning. | Harding BD, Hu Z, Hiett A, Delaglio F, Henzler-Wildman KA, Rienstra CM | The journal of physical chemistry. B | 39395040 | J Phys Chem B | 2024 Oct 24 |
| Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism. | Thangapandian S, Fakharzadeh A, Moradi M, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 40042900 | Proc Natl Acad Sci U S A | 2025 Mar 11 |
| Computational Dissection of Membrane Transport at a Microscopic Level. | Jiang T, Wen PC, Trebesch N, Zhao Z, Pant S, Kapoor K, Shekhar M, Tajkhorshid E | Trends in biochemical sciences | 31813734 | Trends Biochem Sci | 2020 Mar |
| Cryo-EM structures of a lipid-sensitive pentameric ligand-gated ion channel embedded in a phosphatidylcholine-only bilayer. | Kumar P, Wang Y, Zhang Z, Zhao Z, Cymes GD, Tajkhorshid E, Grosman C | Proceedings of the National Academy of Sciences of the United States of America | 31911476 | Proc Natl Acad Sci U S A | 2020 Jan 21 |
| Calcium-Induced Lipid Nanocluster Structures: Sculpturing of the Plasma Membrane. | Hallock MJ, Greenwood AI, Wang Y, Morrissey JH, Tajkhorshid E, Rienstra CM, Pogorelov TV | Biochemistry | 30456950 | Biochemistry | 2018 Dec 18 |
| Interaction of Alpha-Synuclein and Its Mutants with Rigid Lipid Vesicle Mimics of Varying Surface Curvature. | McClain SM, Ojoawo AM, Lin W, Rienstra CM, Murphy CJ | ACS nano | 32672441 | ACS Nano | 2020 Aug 25 |
| Probing key elements of teixobactin-lipid II interactions in membranes. | Wen PC, Vanegas JM, Rempe SB, Tajkhorshid E | Chemical science | 30210775 | Chem Sci | 2018 Sep 14 |
| Lipids and ions traverse the membrane by the same physical pathway in the nhTMEM16 scramblase. | Jiang T, Yu K, Hartzell HC, Tajkhorshid E | eLife | 28917060 | Elife | 2017 Sep 16 |
| Lipid specificity of the membrane binding domain of coagulation factor X. | Muller MP, Wang Y, Morrissey JH, Tajkhorshid E | Journal of thrombosis and haemostasis : JTH | 28782177 | J Thromb Haemost | 2017 Oct |
| (1)H-Detected REDOR with Fast Magic-Angle Spinning of a Deuterated Protein. | Ghosh M, Rienstra CM | The journal of physical chemistry. B | 28816462 | J Phys Chem B | 2017 Sep 14 |
| Targeting lipid-protein interaction to treat Syk-mediated acute myeloid leukemia. | Singaram I, Sharma A, Pant S, Lihan M, Park MJ, Pergande M, Buwaneka P, Hu Y, Mahmud N, Kim YM, Cologna S, Gevorgyan V, Khan I, Tajkhorshid E, Cho W | Nature chemical biology | 36229686 | Nat Chem Biol | 2023 Feb |
| Cryo-EM structures of human ABCA7 provide insights into its phospholipid translocation mechanisms. | Le LTM, Thompson JR, Dehghani-Ghahnaviyeh S, Pant S, Dang PX, French JB, Kanikeyo T, Tajkhorshid E, Alam A | The EMBO journal | 36484366 | EMBO J | 2023 Feb 1 |
| Molecular View into Preferential Binding of the Factor VII Gla Domain to Phosphatidic Acid. | Muller MP, Morrissey JH, Tajkhorshid E | Biochemistry | 35853076 | Biochemistry | 2022 Aug 16 |
| Hydrogen-deuterium exchange mass spectrometry captures distinct dynamics upon substrate and inhibitor binding to a transporter. | Jia R, Martens C, Shekhar M, Pant S, Pellowe GA, Lau AM, Findlay HE, Harris NJ, Tajkhorshid E, Booth PJ, Politis A | Nature communications | 33268777 | Nat Commun | 2020 Dec 2 |
| A serine loop in tissue factor mediates substrate selectivity by the tissue factor-factor VIIa complex. | Birkle F, Morrissey JH | Journal of thrombosis and haemostasis : JTH | 32885882 | J Thromb Haemost | 2021 Jan |
| Binding mode of SARS-CoV-2 fusion peptide to human cellular membrane. | Gorgun D, Lihan M, Kapoor K, Tajkhorshid E | Biophysical journal | 33675757 | Biophys J | 2021 Jul 20 |
| A modification of γ-encoded RN symmetry pulses for increasing the scaling factor and more accurate measurements of the strong heteronuclear dipolar couplings. | Nimerovsky E, Soutar CP | Journal of magnetic resonance (San Diego, Calif. : 1997) | 32950918 | J Magn Reson | 2020 Oct |
| Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation. | Muller MP, Jiang T, Sun C, Lihan M, Pant S, Mahinthichaichan P, Trifan A, Tajkhorshid E | Chemical reviews | 30978005 | Chem Rev | 2019 May 8 |
| Direct protein-lipid interactions shape the conformational landscape of secondary transporters. | Martens C, Shekhar M, Borysik AJ, Lau AM, Reading E, Tajkhorshid E, Booth PJ, Politis A | Nature communications | 30297844 | Nat Commun | 2018 Oct 8 |
| Myr-Arf1 conformational flexibility at the membrane surface sheds light on the interactions with ArfGAP ASAP1. | Zhang Y, Soubias O, Pant S, Heinrich F, Vogel A, Li J, Li Y, Clifton LA, Daum S, Bacia K, Huster D, Randazzo PA, Lösche M, Tajkhorshid E, Byrd RA | Nature communications | 37989735 | Nat Commun | 2023 Nov 21 |
| Asymmetric conformations and lipid interactions shape the ATP-coupled cycle of a heterodimeric ABC transporter. | Tang Q, Sinclair M, Hasdemir HS, Stein RA, Karakas E, Tajkhorshid E, Mchaourab HS | Nature communications | 37938578 | Nat Commun | 2023 Nov 8 |
| The carboxy terminus causes interfacial assembly of oleate hydratase on a membrane bilayer. | Radka CD, Grace CR, Hasdemir HS, Li Y, Rodriguez CC, Rodrigues P, Oldham ML, Qayyum MZ, Pitre A, MacCain WJ, Kalathur RC, Tajkhorshid E, Rock CO | The Journal of biological chemistry | 38211817 | J Biol Chem | 2024 Feb |
| Segmental Dynamics of Membranous Cholesterol are Coupled. | Della Ripa LA, Courtney JM, Phinney SM, Borcik CG, Burke MD, Rienstra CM, Pogorelov TV | Journal of the American Chemical Society | 37410392 | J Am Chem Soc | 2023 Jul 19 |
| Automated fibril structure calculations in Xplor-NIH. | Barclay AM, Milchberg MH, Warmuth OA, Tuttle MD, Dennis CJ, Schwieters CD, Rienstra CM | Structure (London, England : 1993) | 39662464 | Structure | 2025 Feb 6 |
| A network of phosphatidylinositol 4,5-bisphosphate binding sites regulates gating of the Ca(2+)-activated Cl(-) channel ANO1 (TMEM16A). | Yu K, Jiang T, Cui Y, Tajkhorshid E, Hartzell HC | Proceedings of the National Academy of Sciences of the United States of America | 31515451 | Proc Natl Acad Sci U S A | 2019 Oct 1 |
| Structure of the alternative complex III in a supercomplex with cytochrome oxidase. | Sun C, Benlekbir S, Venkatakrishnan P, Wang Y, Hong S, Hosler J, Tajkhorshid E, Rubinstein JL, Gennis RB | Nature | 29695868 | Nature | 2018 May |
| Microscopic view of lipids and their diverse biological functions. | Wen PC, Mahinthichaichan P, Trebesch N, Jiang T, Zhao Z, Shinn E, Wang Y, Shekhar M, Kapoor K, Chan CK, Tajkhorshid E | Current opinion in structural biology | 30048836 | Curr Opin Struct Biol | 2018 Aug |
| Peridinin Is an Exceptionally Potent and Membrane-Embedded Inhibitor of Bilayer Lipid Peroxidation. | Haley HMS, Hill AG, Greenwood AI, Woerly EM, Rienstra CM, Burke MD | Journal of the American Chemical Society | 30388000 | J Am Chem Soc | 2018 Nov 14 |
| Structural basis for the reaction cycle of DASS dicarboxylate transporters. | Sauer DB, Trebesch N, Marden JJ, Cocco N, Song J, Koide A, Koide S, Tajkhorshid E, Wang DN | eLife | 32869741 | Elife | 2020 Sep 1 |
| Aβ(1-42) tetramer and octamer structures reveal edge conductivity pores as a mechanism for membrane damage. | Ciudad S, Puig E, Botzanowski T, Meigooni M, Arango AS, Do J, Mayzel M, Bayoumi M, Chaignepain S, Maglia G, Cianferani S, Orekhov V, Tajkhorshid E, Bardiaux B, Carulla N | Nature communications | 32541820 | Nat Commun | 2020 Jun 15 |
| Polymer-Peptide Conjugates Convert Amyloid into Protein Nanobundles through Fragmentation and Lateral Association. | Smith JW, Jiang X, An H, Barclay AM, Licari G, Tajkhorshid E, Moore EG, Rienstra CM, Moore JS, Chen Q | ACS applied nano materials | 32149271 | ACS Appl Nano Mater | 2020 Feb 28 |
| An Activity-Based Sensing Approach for the Detection of Cyclooxygenase-2 in Live Cells. | Yadav AK, Reinhardt CJ, Arango AS, Huff HC, Dong L, Malkowski MG, Das A, Tajkhorshid E, Chan J | Angewandte Chemie (International ed. in English) | 31854058 | Angew Chem Int Ed Engl | 2020 Feb 17 |
| Tumor-acquired somatic mutation affects conformation to abolish ABCG2-mediated drug resistance. | Gose T, Rasouli A, Dehghani-Ghahnaviyeh S, Wen PC, Wang Y, Lynch J, Fukuda Y, Shafi T, Ford RC, Tajkhorshid E, Schuetz JD | Drug resistance updates : reviews and commentaries in antimicrobial and anticancer chemotherapy | 38387283 | Drug Resist Updat | 2024 Mar |
| Tuning sterol extraction kinetics yields a renal-sparing polyene antifungal. | Maji A, Soutar CP, Zhang J, Lewandowska A, Uno BE, Yan S, Shelke Y, Murhade G, Nimerovsky E, Borcik CG, Arango AS, Lange JD, Marin-Toledo JP, Lyu Y, Bailey KL, Roady PJ, Holler JT, Khandelwal A, SantaMaria AM, Sanchez H, Juvvadi PR, Johns G, Hageman MJ, Krise J, Gebremariam T, Youssef EG, Bartizal K, Marr KA, Steinbach WJ, Ibrahim AS, Patterson TF, Wiederhold NP, Andes DR, Pogorelov TV, Schwieters CD, Fan TM, Rienstra CM, Burke MD | Nature | 37938782 | Nature | 2023 Nov |
| Posttranslational modifications optimize the ability of SARS-CoV-2 spike for effective interaction with host cell receptors. | Kapoor K, Chen T, Tajkhorshid E | Proceedings of the National Academy of Sciences of the United States of America | 35737823 | Proc Natl Acad Sci U S A | 2022 Jul 12 |
| A cancer mutation promotes EphA4 oligomerization and signaling by altering the conformation of the SAM domain. | Light TP, Gomez-Soler M, Wang Z, Karl K, Zapata-Mercado E, Gehring MP, Lechtenberg BC, Pogorelov TV, Hristova K, Pasquale EB | The Journal of biological chemistry | 34139238 | J Biol Chem | 2021 Jul |
| PIP(2)-dependent coupling of voltage sensor and pore domains in K(v)7.2 channel. | Pant S, Zhang J, Kim EC, Lam K, Chung HJ, Tajkhorshid E | Communications biology | 34650221 | Commun Biol | 2021 Oct 14 |
| Backbone amides are determinants of Cl(-) selectivity in CLC ion channels. | Leisle L, Lam K, Dehghani-Ghahnaviyeh S, Fortea E, Galpin JD, Ahern CA, Tajkhorshid E, Accardi A | Nature communications | 36473856 | Nat Commun | 2022 Dec 6 |
| Relationship among egg quality traits in Japanese quails and prediction of egg weight and color using data mining algorithms. | Çelik Ş, Eyduran E, Şengül AY, Şengül T | Tropical animal health and production | 34195902 | Trop Anim Health Prod | 2021 Jul 1 |
| APACE: AlphaFold2 and advanced computing as a service for accelerated discovery in biophysics. | Park H, Patel P, Haas R, Huerta EA | Proceedings of the National Academy of Sciences of the United States of America | 38913887 | Proc Natl Acad Sci U S A | 2024 Jul 2 |
| Editing DNA Methylation in the Mammalian Genome. | Liu XS, Wu H, Ji X, Stelzer Y, Wu X, Czauderna S, Shu J, Dadon D, Young RA, Jaenisch R | Cell | 27662091 | Cell | 2016 Sep 22 |
| Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias. | Dunford A, Weinstock DM, Savova V, Schumacher SE, Cleary JP, Yoda A, Sullivan TJ, Hess JM, Gimelbrant AA, Beroukhim R, Lawrence MS, Getz G, Lane AA | Nature genetics | 27869828 | Nat Genet | 2017 Jan |
| Dynamic Enhancer DNA Methylation as Basis for Transcriptional and Cellular Heterogeneity of ESCs. | Song Y, van den Berg PR, Markoulaki S, Soldner F, Dall'Agnese A, Henninger JE, Drotar J, Rosenau N, Cohen MA, Young RA, Semrau S, Stelzer Y, Jaenisch R | Molecular cell | 31422875 | Mol Cell | 2019 Sep 5 |
| Cell state transition analysis identifies interventions that improve control of Mycobacterium tuberculosis infection by susceptible macrophages. | Yabaji SM, Rukhlenko OS, Chatterjee S, Bhattacharya B, Wood E, Kasaikina M, Kholodenko BN, Gimelbrant AA, Kramnik I | Science advances | 37756395 | Sci Adv | 2023 Sep 29 |
| Risk alleles of genes with monoallelic expression are enriched in gain-of-function variants and depleted in loss-of-function variants for neurodevelopmental disorders. | Savova V, Vinogradova S, Pruss D, Gimelbrant AA, Weiss LA | Molecular psychiatry | 28265118 | Mol Psychiatry | 2017 Dec |
| Establishment of human pluripotent stem cell-derived pancreatic β-like cells in the mouse pancreas. | Ma H, Wert KJ, Shvartsman D, Melton DA, Jaenisch R | Proceedings of the National Academy of Sciences of the United States of America | 29599125 | Proc Natl Acad Sci U S A | 2018 Apr 10 |
| High prevalence of clonal monoallelic expression. | Vigneau S, Vinogradova S, Savova V, Gimelbrant A | Nature genetics | 30082785 | Nat Genet | 2018 Sep |
| Genes with monoallelic expression contribute disproportionately to genetic diversity in humans. | Savova V, Chun S, Sohail M, McCole RB, Witwicki R, Gai L, Lenz TL, Wu CT, Sunyaev SR, Gimelbrant AA | Nature genetics | 26808112 | Nat Genet | 2016 Mar |
| Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. | Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA | bioRxiv : the preprint server for biology | 36798258 | bioRxiv | 2023 Feb 12 |
| Foreign RNA spike-ins enable accurate allele-specific expression analysis at scale. | Mendelevich A, Gupta S, Pakharev A, Teodosiadis A, Mironov AA, Gimelbrant AA | Bioinformatics (Oxford, England) | 37387154 | Bioinformatics | 2023 Jun 30 |
| dbMAE: the database of autosomal monoallelic expression. | Savova V, Patsenker J, Vigneau S, Gimelbrant AA | Nucleic acids research | 26503248 | Nucleic Acids Res | 2016 Jan 4 |
| Replicate sequencing libraries are important for quantification of allelic imbalance. | Mendelevich A, Vinogradova S, Gupta S, Mironov AA, Sunyaev SR, Gimelbrant AA | Nature communications | 34099647 | Nat Commun | 2021 Jun 7 |
| Rescue of Fragile X Syndrome Neurons by DNA Methylation Editing of the FMR1 Gene. | Liu XS, Wu H, Krzisch M, Wu X, Graef J, Muffat J, Hnisz D, Li CH, Yuan B, Xu C, Li Y, Vershkov D, Cacace A, Young RA, Jaenisch R | Cell | 29456084 | Cell | 2018 Feb 22 |
| RNA sequencing-based screen for reactivation of silenced alleles of autosomal genes. | Gupta S, Lafontaine DL, Vigneau S, Mendelevich A, Vinogradova S, Igarashi KJ, Bortvin A, Alves-Pereira CF, Nag A, Gimelbrant AA | G3 (Bethesda, Md.) | 35100361 | G3 (Bethesda) | 2022 Feb 4 |
| Women Are Less Likely Than Men to Be Full Professors in Cardiology: Why Does This Happen and How Can We Fix It? | Carnes M, Bairey Merz CN | Circulation | 28153988 | Circulation | 2017 Feb 7 |
| A quantitative linguistic analysis of National Institutes of Health R01 application critiques from investigators at one institution. | Kaatz A, Magua W, Zimmerman DR, Carnes M | Academic medicine : journal of the Association of American Medical Colleges | 25140529 | Acad Med | 2015 Jan |
| Providing Epistemic Support For Assessments Through Mobile-Supported Sharing Activities. | Raclaw J, Robles JS, DiDomenico SM | Research on language and social interaction | 28936031 | Res Lang Soc Interact | 2016 |
| 'Your comments are meaner than your score': score calibration talk influences intra- and inter-panel variability during scientific grant peer review. | Pier EL, Raclaw J, Kaatz A, Brauer M, Carnes M, Nathan MJ, Ford CE | Research Evaluation | 28458466 | Res Eval | 2017 Jan |
| Low agreement among reviewers evaluating the same NIH grant applications. | Pier EL, Brauer M, Filut A, Kaatz A, Raclaw J, Nathan MJ, Ford CE, Carnes M | Proceedings of the National Academy of Sciences of the United States of America | 29507248 | Proc Natl Acad Sci U S A | 2018 Mar 20 |
| Laughter and the Management of Divergent Positions in Peer Review Interactions. | Raclaw J, Ford CE | Journal of pragmatics | 29170594 | J Pragmat | 2017 May |
| Stuck in the out-group: Jennifer can't grow up, Jane's invisible, and Janet's over the hill. | Kaatz A, Carnes M | Journal of women's health (2002) | 24844292 | J Womens Health (Larchmt) | 2014 Jun |
| Parents' Expectations for and Reactions to Children's Racial Biases. | Scott KE, Shutts K, Devine PG | Child development | 30825398 | Child Dev | 2020 May |
| Stereotypes possess heterogeneous directionality: a theoretical and empirical exploration of stereotype structure and content. | Cox WT, Devine PG | PloS one | 25811181 | PLoS One | 2015 |
| Patterns of Feedback on the Bridge to Independence: A Qualitative Thematic Analysis of NIH Mentored Career Development Award Application Critiques. | Kaatz A, Dattalo M, Regner C, Filut A, Carnes M | Journal of women's health (2002) | 26418619 | J Womens Health (Larchmt) | 2016 Jan |
| A meta-analysis of procedures to change implicit measures. | Forscher PS, Lai CK, Axt JR, Ebersole CR, Herman M, Devine PG, Nosek BA | Journal of personality and social psychology | 31192631 | J Pers Soc Psychol | 2019 Sep |
| Laughter and the Chair: Social Pressures Influencing Scoring During Grant Peer Review Meetings. | Pier EL, Raclaw J, Carnes M, Ford CE, Kaatz A | Journal of general internal medicine | 30604119 | J Gen Intern Med | 2019 Apr |
| Threats to objectivity in peer review: the case of gender. | Kaatz A, Gutierrez B, Carnes M | Trends in pharmacological sciences | 25086743 | Trends Pharmacol Sci | 2014 Aug |
| Write More Articles, Get More Grants: The Impact of Department Climate on Faculty Research Productivity. | Sheridan J, Savoy JN, Kaatz A, Lee YG, Filut A, Carnes M | Journal of women's health (2002) | 28375751 | J Womens Health (Larchmt) | 2017 May |
| Fair Play: A Study of Scientific Workforce Trainers' Experience Playing an Educational Video Game about Racial Bias. | Kaatz A, Carnes M, Gutierrez B, Savoy J, Samuel C, Filut A, Pribbenow CM | CBE life sciences education | 28450447 | CBE Life Sci Educ | 2017 Summer |
| Analysis of National Institutes of Health R01 Application Critiques, Impact, and Criteria Scores: Does the Sex of the Principal Investigator Make a Difference? | Kaatz A, Lee YG, Potvien A, Magua W, Filut A, Bhattacharya A, Leatherberry R, Zhu X, Carnes M | Academic medicine : journal of the Association of American Medical Colleges | 27276003 | Acad Med | 2016 Aug |
| Are Female Applicants Disadvantaged in National Institutes of Health Peer Review? Combining Algorithmic Text Mining and Qualitative Methods to Detect Evaluative Differences in R01 Reviewers' Critiques. | Magua W, Zhu X, Bhattacharya A, Filut A, Potvien A, Leatherberry R, Lee YG, Jens M, Malikireddy D, Carnes M, Kaatz A | Journal of women's health (2002) | 28281870 | J Womens Health (Larchmt) | 2017 May |
| Little race or gender bias in an experiment of initial review of NIH R01 grant proposals. | Forscher PS, Cox WTL, Brauer M, Devine PG | Nature human behaviour | 30953009 | Nat Hum Behav | 2019 Mar |
| The motivation to express prejudice. | Forscher PS, Cox WT, Graetz N, Devine PG | Journal of personality and social psychology | 26479365 | J Pers Soc Psychol | 2015 Nov |
| Who Resembles a Scientific Leader-Jack or Jill? How Implicit Bias Could Influence Research Grant Funding. | Kolehmainen C, Carnes M | Circulation | 29459461 | Circulation | 2018 Feb 20 |
| Breaking the prejudice habit: Mechanisms, timecourse, and longevity. | Forscher PS, Mitamura C, Dix EL, Cox WTL, Devine PG | Journal of experimental social psychology | 29225371 | J Exp Soc Psychol | 2017 Sep |
| Value-Based Standards Guide Sexism Inferences for Self and Others. | Mitamura C, Erickson L, Devine PG | Journal of experimental social psychology | 29230069 | J Exp Soc Psychol | 2017 Sep |
| A Gender Bias Habit-Breaking Intervention Led to Increased Hiring of Female Faculty in STEMM Departments. | Devine PG, Forscher PS, Cox WTL, Kaatz A, Sheridan J, Carnes M | Journal of experimental social psychology | 29249837 | J Exp Soc Psychol | 2017 Nov |
| A Psychological Profile of the Alt-Right. | Forscher PS, Kteily NS | Perspectives on psychological science : a journal of the Association for Psychological Science | 31747343 | Perspect Psychol Sci | 2020 Jan |
| Inferences About Sexual Orientation: The Roles of Stereotypes, Faces, and The Gaydar Myth. | Cox WT, Devine PG, Bischmann AA, Hyde JS | Journal of sex research | 26219212 | J Sex Res | 2016 |
| Advancing Women's Health and Women's Leadership With Endowed Chairs in Women's Health. | Carnes M, Johnson P, Klein W, Jenkins M, Bairey Merz CN | Academic medicine : journal of the Association of American Medical Colleges | 27759706 | Acad Med | 2017 Feb |
| Multi-disciplinary methods to define RNA-protein interactions and regulatory networks. | Ascano M, Gerstberger S, Tuschl T | Current opinion in genetics & development | 23453689 | Curr Opin Genet Dev | 2013 Feb |
| Inhibition Mechanism of an Anti-CRISPR Suppressor AcrIIA4 Targeting SpyCas9. | Yang H, Patel DJ | Molecular cell | 28602637 | Mol Cell | 2017 Jul 6 |
| Identification of the RNA recognition element of the RBPMS family of RNA-binding proteins and their transcriptome-wide mRNA targets. | Farazi TA, Leonhardt CS, Mukherjee N, Mihailovic A, Li S, Max KE, Meyer C, Yamaji M, Cekan P, Jacobs NC, Gerstberger S, Bognanni C, Larsson E, Ohler U, Tuschl T | RNA (New York, N.Y.) | 24860013 | RNA | 2014 Jul |
| The evolutionary journey of Argonaute proteins. | Swarts DC, Makarova K, Wang Y, Nakanishi K, Ketting RF, Koonin EV, Patel DJ, van der Oost J | Nature structural & molecular biology | 25192263 | Nat Struct Mol Biol | 2014 Sep |
| Global target mRNA specification and regulation by the RNA-binding protein ZFP36. | Mukherjee N, Jacobs NC, Hafner M, Kennington EA, Nusbaum JD, Tuschl T, Blackshear PJ, Ohler U | Genome biology | 24401661 | Genome Biol | 2014 Jan 8 |
| Cryo-EM Structures Reveal Mechanism and Inhibition of DNA Targeting by a CRISPR-Cas Surveillance Complex. | Guo TW, Bartesaghi A, Yang H, Falconieri V, Rao P, Merk A, Eng ET, Raczkowski AM, Fox T, Earl LA, Patel DJ, Subramaniam S | Cell | 28985564 | Cell | 2017 Oct 5 |
| Structural basis for molecular discrimination by a 3',3'-cGAMP sensing riboswitch. | Ren A, Wang XC, Kellenberger CA, Rajashankar KR, Jones RA, Hammond MC, Patel DJ | Cell reports | 25818298 | Cell Rep | 2015 Apr 7 |
| Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP. | Vasilyev N, Polonskaia A, Darnell JC, Darnell RB, Patel DJ, Serganov A | Proceedings of the National Academy of Sciences of the United States of America | 26374839 | Proc Natl Acad Sci U S A | 2015 Sep 29 |
| SSMART: sequence-structure motif identification for RNA-binding proteins. | Munteanu A, Mukherjee N, Ohler U | Bioinformatics (Oxford, England) | 29893814 | Bioinformatics | 2018 Dec 1 |
| Detecting actively translated open reading frames in ribosome profiling data. | Calviello L, Mukherjee N, Wyler E, Zauber H, Hirsekorn A, Selbach M, Landthaler M, Obermayer B, Ohler U | Nature methods | 26657557 | Nat Methods | 2016 Feb |
| Structure and function of the bacterial decapping enzyme NudC. | Höfer K, Li S, Abele F, Frindert J, Schlotthauer J, Grawenhoff J, Du J, Patel DJ, Jäschke A | Nature chemical biology | 27428510 | Nat Chem Biol | 2016 Sep |
| Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets. | Farazi TA, Ten Hoeve JJ, Brown M, Mihailovic A, Horlings HM, van de Vijver MJ, Tuschl T, Wessels LF | Genome biology | 24398324 | Genome Biol | 2014 Jan 7 |
| The TIA1 RNA-Binding Protein Family Regulates EIF2AK2-Mediated Stress Response and Cell Cycle Progression. | Meyer C, Garzia A, Mazzola M, Gerstberger S, Molina H, Tuschl T | Molecular cell | 29429924 | Mol Cell | 2018 Feb 15 |
| Optimization of PAR-CLIP for transcriptome-wide identification of binding sites of RNA-binding proteins. | Garzia A, Meyer C, Morozov P, Sajek M, Tuschl T | Methods (San Diego, Calif.) | 27765618 | Methods | 2017 Apr 15 |
| DND1 maintains germline stem cells via recruitment of the CCR4-NOT complex to target mRNAs. | Yamaji M, Jishage M, Meyer C, Suryawanshi H, Der E, Yamaji M, Garzia A, Morozov P, Manickavel S, McFarland HL, Roeder RG, Hafner M, Tuschl T | Nature | 28297718 | Nature | 2017 Mar 23 |
| Small molecule inhibition of cGAS reduces interferon expression in primary macrophages from autoimmune mice. | Vincent J, Adura C, Gao P, Luz A, Lama L, Asano Y, Okamoto R, Imaeda T, Aida J, Rothamel K, Gogakos T, Steinberg J, Reasoner S, Aso K, Tuschl T, Patel DJ, Glickman JF, Ascano M | Nature communications | 28963528 | Nat Commun | 2017 Sep 29 |
| Recognition of distinct RNA motifs by the clustered CCCH zinc fingers of neuronal protein Unkempt. | Murn J, Teplova M, Zarnack K, Shi Y, Patel DJ | Nature structural & molecular biology | 26641712 | Nat Struct Mol Biol | 2016 Jan |
| DNA-guided DNA interference by a prokaryotic Argonaute. | Swarts DC, Jore MM, Westra ER, Zhu Y, Janssen JH, Snijders AP, Wang Y, Patel DJ, Berenguer J, Brouns SJJ, van der Oost J | Nature | 24531762 | Nature | 2014 Mar 13 |
| FMRP targets distinct mRNA sequence elements to regulate protein expression. | Ascano M Jr, Mukherjee N, Bandaru P, Miller JB, Nusbaum JD, Corcoran DL, Langlois C, Munschauer M, Dewell S, Hafner M, Williams Z, Ohler U, Tuschl T | Nature | 23235829 | Nature | 2012 Dec 20 |
| The mRNA-bound proteome of the early fly embryo. | Wessels HH, Imami K, Baltz AG, Kolinski M, Beldovskaya A, Selbach M, Small S, Ohler U, Landthaler M | Genome research | 27197210 | Genome Res | 2016 Jul |
| Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites. | Teplova M, Hafner M, Teplov D, Essig K, Tuschl T, Patel DJ | Genes & development | 23630077 | Genes Dev | 2013 Apr 15 |
| The G3BP1-Family-USP10 Deubiquitinase Complex Rescues Ubiquitinated 40S Subunits of Ribosomes Stalled in Translation from Lysosomal Degradation. | Meyer C, Garzia A, Morozov P, Molina H, Tuschl T | Molecular cell | 31981475 | Mol Cell | 2020 Mar 19 |
| The RNA-binding protein vigilin regulates VLDL secretion through modulation of Apob mRNA translation. | Mobin MB, Gerstberger S, Teupser D, Campana B, Charisse K, Heim MH, Manoharan M, Tuschl T, Stoffel M | Nature communications | 27665711 | Nat Commun | 2016 Sep 26 |
| The E3 ubiquitin ligase and RNA-binding protein ZNF598 orchestrates ribosome quality control of premature polyadenylated mRNAs. | Garzia A, Jafarnejad SM, Meyer C, Chapat C, Gogakos T, Morozov P, Amiri M, Shapiro M, Molina H, Tuschl T, Sonenberg N | Nature communications | 28685749 | Nat Commun | 2017 Jul 7 |
| Global identification of functional microRNA-mRNA interactions in Drosophila. | Wessels HH, Lebedeva S, Hirsekorn A, Wurmus R, Akalin A, Mukherjee N, Ohler U | Nature communications | 30967537 | Nat Commun | 2019 Apr 9 |
| MicroRNA target site identification by integrating sequence and binding information. | Majoros WH, Lekprasert P, Mukherjee N, Skalsky RL, Corcoran DL, Cullen BR, Ohler U | Nature methods | 23708386 | Nat Methods | 2013 Jul |
| Multicolor microRNA FISH effectively differentiates tumor types. | Renwick N, Cekan P, Masry PA, McGeary SE, Miller JB, Hafner M, Li Z, Mihailovic A, Morozov P, Brown M, Gogakos T, Mobin MB, Snorrason EL, Feilotter HE, Zhang X, Perlis CS, Wu H, Suárez-Fariñas M, Feng H, Shuda M, Moore PS, Tron VA, Chang Y, Tuschl T | The Journal of clinical investigation | 23728175 | J Clin Invest | 2013 Jun |
| A phosphate-binding pocket within the platform-PAZ-connector helix cassette of human Dicer. | Tian Y, Simanshu DK, Ma JB, Park JE, Heo I, Kim VN, Patel DJ | Molecular cell | 24486018 | Mol Cell | 2014 Feb 20 |
| Integrative classification of human coding and noncoding genes through RNA metabolism profiles. | Mukherjee N, Calviello L, Hirsekorn A, de Pretis S, Pelizzola M, Ohler U | Nature structural & molecular biology | 27870833 | Nat Struct Mol Biol | 2017 Jan |
| Simultaneous detection of the subcellular localization of RNAs and proteins in cultured cells by combined multicolor RNA-FISH and IF. | Meyer C, Garzia A, Tuschl T | Methods (San Diego, Calif.) | 27664292 | Methods | 2017 Apr 15 |
| PAM-Dependent Target DNA Recognition and Cleavage by C2c1 CRISPR-Cas Endonuclease. | Yang H, Gao P, Rajashankar KR, Patel DJ | Cell | 27984729 | Cell | 2016 Dec 15 |
| Deciphering human ribonucleoprotein regulatory networks. | Mukherjee N, Wessels HH, Lebedeva S, Sajek M, Ghanbari M, Garzia A, Munteanu A, Yusuf D, Farazi T, Hoell JI, Akat KM, Akalin A, Tuschl T, Ohler U | Nucleic acids research | 30517751 | Nucleic Acids Res | 2019 Jan 25 |
| Accommodation of Helical Imperfections in Rhodobacter sphaeroides Argonaute Ternary Complexes with Guide RNA and Target DNA. | Liu Y, Esyunina D, Olovnikov I, Teplova M, Kulbachinskiy A, Aravin AA, Patel DJ | Cell reports | 29996105 | Cell Rep | 2018 Jul 10 |
| Purification of cross-linked RNA-protein complexes by phenol-toluol extraction. | Urdaneta EC, Vieira-Vieira CH, Hick T, Wessels HH, Figini D, Moschall R, Medenbach J, Ohler U, Granneman S, Selbach M, Beckmann BM | Nature communications | 30824702 | Nat Commun | 2019 Mar 1 |
| omniCLIP: probabilistic identification of protein-RNA interactions from CLIP-seq data. | Drewe-Boss P, Wessels HH, Ohler U | Genome biology | 30384847 | Genome Biol | 2018 Nov 1 |
| Type III-A CRISPR-Cas Csm Complexes: Assembly, Periodic RNA Cleavage, DNase Activity Regulation, and Autoimmunity. | Jia N, Mo CY, Wang C, Eng ET, Marraffini LA, Patel DJ | Molecular cell | 30503773 | Mol Cell | 2019 Jan 17 |
| Human cGAS catalytic domain has an additional DNA-binding interface that enhances enzymatic activity and liquid-phase condensation. | Xie W, Lama L, Adura C, Tomita D, Glickman JF, Tuschl T, Patel DJ | Proceedings of the National Academy of Sciences of the United States of America | 31142647 | Proc Natl Acad Sci U S A | 2019 Jun 11 |
| Structural basis underlying CAC RNA recognition by the RRM domain of dimeric RNA-binding protein RBPMS. | Teplova M, Farazi TA, Tuschl T, Patel DJ | Quarterly reviews of biophysics | 26347403 | Q Rev Biophys | 2016 Jan |
| Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry. | Zhang F, Simmons CR, Gates J, Liu Y, Yan H | Angewandte Chemie (International ed. in English) | 30066355 | Angew Chem Int Ed Engl | 2018 Sep 17 |
| Nanocaged enzymes with enhanced catalytic activity and increased stability against protease digestion. | Zhao Z, Fu J, Dhakal S, Johnson-Buck A, Liu M, Zhang T, Woodbury NW, Liu Y, Walter NG, Yan H | Nature communications | 26861509 | Nat Commun | 2016 Feb 10 |
| Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. | Simmons CR, Zhang F, MacCulloch T, Fahmi N, Stephanopoulos N, Liu Y, Seeman NC, Yan H | Journal of the American Chemical Society | 28731332 | J Am Chem Soc | 2017 Aug 16 |
| Monovalent streptavidin that senses oligonucleotides. | Taylor SK, Wang J, Kostic N, Stojanovic MN | Angewandte Chemie (International ed. in English) | 23606329 | Angew Chem Int Ed Engl | 2013 May 17 |
| Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation. | Li J, Green AA, Yan H, Fan C | Nature chemistry | 29064489 | Nat Chem | 2017 Nov |
| High-Affinity Nucleic-Acid-Based Receptors for Steroids. | Yang KA, Chun H, Zhang Y, Pecic S, Nakatsuka N, Andrews AM, Worgall TS, Stojanovic MN | ACS chemical biology | 29083858 | ACS Chem Biol | 2017 Dec 15 |
| Amplification of Signal on Cell Surfaces in Molecular Cascades. | Rudchenko S, Taylor S, Milosavic N, Rudchenko M, Wedderhoff Tissi B, Mapara MY, Stojanovic MN | Cells | 38132177 | Cells | 2023 Dec 18 |
| A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo. | Li S, Jiang Q, Liu S, Zhang Y, Tian Y, Song C, Wang J, Zou Y, Anderson GJ, Han JY, Chang Y, Liu Y, Zhang C, Chen L, Zhou G, Nie G, Yan H, Ding B, Zhao Y | Nature biotechnology | 29431737 | Nat Biotechnol | 2018 Mar |
| An Integrated Microfluidic SELEX Approach Using Combined Electrokinetic and Hydrodynamic Manipulation. | Olsen T, Zhu J, Kim J, Pei R, Stojanovic MN, Lin Q | SLAS technology | 27418370 | SLAS Technol | 2017 Feb |
| Aptamer-field-effect transistors overcome Debye length limitations for small-molecule sensing. | Nakatsuka N, Yang KA, Abendroth JM, Cheung KM, Xu X, Yang H, Zhao C, Zhu B, Rim YS, Yang Y, Weiss PS, Stojanović MN, Andrews AM | Science (New York, N.Y.) | 30190311 | Science | 2018 Oct 19 |
| Autonomous molecular cascades for evaluation of cell surfaces. | Rudchenko M, Taylor S, Pallavi P, Dechkovskaia A, Khan S, Butler VP Jr, Rudchenko S, Stojanovic MN | Nature nanotechnology | 23892986 | Nat Nanotechnol | 2013 Aug |
| Integrated Microfluidic Isolation of Aptamers Using Electrophoretic Oligonucleotide Manipulation. | Kim J, Olsen TR, Zhu J, Hilton JP, Yang KA, Pei R, Stojanovic MN, Lin Q | Scientific reports | 27217242 | Sci Rep | 2016 May 24 |
| DNA origami nanostructures can exhibit preferential renal uptake and alleviate acute kidney injury. | Jiang D, Ge Z, Im HJ, England CG, Ni D, Hou J, Zhang L, Kutyreff CJ, Yan Y, Liu Y, Cho SY, Engle JW, Shi J, Huang P, Fan C, Yan H, Cai W | Nature biomedical engineering | 30505626 | Nat Biomed Eng | 2018 Nov |
| Recognition and sensing of low-epitope targets via ternary complexes with oligonucleotides and synthetic receptors. | Yang KA, Barbu M, Halim M, Pallavi P, Kim B, Kolpashchikov DM, Pecic S, Taylor S, Worgall TS, Stojanovic MN | Nature chemistry | 25343606 | Nat Chem | 2014 Nov |
| Integrated Microfluidic Aptasensor for Mass Spectrometric Detection of Vasopressin in Human Plasma Ultrafiltrate. | Yang J, Zhu J, Pei R, Oliver JA, Landry DW, Stojanovic MN, Lin Q | Analytical methods : advancing methods and applications | 28090219 | Anal Methods | 2016 Jul 14 |
| A Three-Enzyme Pathway with an Optimised Geometric Arrangement to Facilitate Substrate Transfer. | Liu M, Fu J, Qi X, Wootten S, Woodbury NW, Liu Y, Yan H | Chembiochem : a European journal of chemical biology | 26995014 | Chembiochem | 2016 Jun 16 |
| INTEGRATED MICROFLUIDIC SELEX USING FREE SOLUTION ELECTROKINETICS. | Olsen TR, Tapia-Alveal C, Yang KA, Zhang X, Pereira LJ, Farmakidis N, Pei R, Stojanovic MN, Lin Q | Journal of the Electrochemical Society | 29170564 | J Electrochem Soc | 2017 |
| Insulin Hexamer-Caged Gadolinium Ion as MRI Contrast-o-phore. | Taylor SK, Tran TH, Liu MZ, Harris PE, Sun Y, Jambawalikar SR, Tong L, Stojanovic MN | Chemistry (Weinheim an der Bergstrasse, Germany) | 29873848 | Chemistry | 2018 Jul 25 |
| In vitro selection and amplification protocols for isolation of aptameric sensors for small molecules. | Yang KA, Pei R, Stojanovic MN | Methods (San Diego, Calif.) | 27155227 | Methods | 2016 Aug 15 |
| Self-Assembly of Complex DNA Tessellations by Using Low-Symmetry Multi-arm DNA Tiles. | Zhang F, Jiang S, Li W, Hunt A, Liu Y, Yan H | Angewandte Chemie (International ed. in English) | 27276237 | Angew Chem Int Ed Engl | 2016 Jul 25 |
| Statistical analysis of molecular signal recording. | Glaser JI, Zamft BM, Marblestone AH, Moffitt JR, Tyo K, Boyden ES, Church G, Kording KP | PLoS computational biology | 23874187 | PLoS Comput Biol | 2013 |
| Rapid directed molecular evolution of fluorescent proteins in mammalian cells. | Babakhanova S, Jung EE, Namikawa K, Zhang H, Wang Y, Subach OM, Korzhenevskiy DA, Rakitina TV, Xiao X, Wang W, Shi J, Drobizhev M, Park D, Eisenhard L, Tang H, Köster RW, Subach FV, Boyden ES, Piatkevich KD | Protein science : a publication of the Protein Society | 34913537 | Protein Sci | 2022 Mar |
| Thalamic reticular nucleus induces fast and local modulation of arousal state. | Lewis LD, Voigts J, Flores FJ, Schmitt LI, Wilson MA, Halassa MM, Brown EN | eLife | 26460547 | Elife | 2015 Oct 13 |
| Quantifying Pituitary-Adrenal Dynamics and Deconvolution of Concurrent Cortisol and Adrenocorticotropic Hormone Data by Compressed Sensing. | Faghih RT, Dahleh MA, Adler GK, Klerman EB, Brown EN | IEEE transactions on bio-medical engineering | 25935025 | IEEE Trans Biomed Eng | 2015 Oct |
| Nitrous oxide-induced slow and delta oscillations. | Pavone KJ, Akeju O, Sampson AL, Ling K, Purdon PL, Brown EN | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 26118489 | Clin Neurophysiol | 2016 Jan |
| Spatiotemporal Dynamics of Dexmedetomidine-Induced Electroencephalogram Oscillations. | Akeju O, Kim SE, Vazquez R, Rhee J, Pavone KJ, Hobbs LE, Purdon PL, Brown EN | PloS one | 27711165 | PLoS One | 2016 |
| Closed-loop, ultraprecise, automated craniotomies. | Pak N, Siegle JH, Kinney JP, Denman DJ, Blanche TJ, Boyden ES | Journal of neurophysiology | 25855700 | J Neurophysiol | 2015 Jun 1 |
| Lack of Responsiveness during the Onset and Offset of Sevoflurane Anesthesia Is Associated with Decreased Awake-Alpha Oscillation Power. | Pavone KJ, Su L, Gao L, Eromo E, Vazquez R, Rhee J, Hobbs LE, Ibala R, Demircioglu G, Purdon PL, Brown EN, Akeju O | Frontiers in systems neuroscience | 28611601 | Front Syst Neurosci | 2017 |
| Robust Estimation of Sparse Narrowband Spectra from Neuronal Spiking Data. | Miran S, Purdon PL, Brown EN, Babadi B | IEEE transactions on bio-medical engineering | 28026746 | IEEE Trans Biomed Eng | 2017 Oct |
| Multi-sensory Gamma Stimulation Ameliorates Alzheimer's-Associated Pathology and Improves Cognition. | Martorell AJ, Paulson AL, Suk HJ, Abdurrob F, Drummond GT, Guan W, Young JZ, Kim DN, Kritskiy O, Barker SJ, Mangena V, Prince SM, Brown EN, Chung K, Boyden ES, Singer AC, Tsai LH | Cell | 30879788 | Cell | 2019 Apr 4 |
| Variability in pharmacologically-induced coma for treatment of refractory status epilepticus. | An J, Jonnalagadda D, Moura V Junior, Purdon PL, Brown EN, Westover MB | PloS one | 30379935 | PLoS One | 2018 |
| Reference-free harmonic regression technique to remove EEG-fMRI ballistocardiogram artifacts. | Krishnaswamy P, Bonmassar G, Purdon PL, Brown EN | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 24110963 | Annu Int Conf IEEE Eng Med Biol Soc | 2013 |
| A brain-machine interface for control of medically-induced coma. | Shanechi MM, Chemali JJ, Liberman M, Solt K, Brown EN | PLoS computational biology | 24204231 | PLoS Comput Biol | 2013 Oct |
| Activation of D1 dopamine receptors induces emergence from isoflurane general anesthesia. | Taylor NE, Chemali JJ, Brown EN, Solt K | Anesthesiology | 23221866 | Anesthesiology | 2013 Jan |
| Local cortical dynamics of burst suppression in the anaesthetized brain. | Lewis LD, Ching S, Weiner VS, Peterfreund RA, Eskandar EN, Cash SS, Brown EN, Purdon PL | Brain : a journal of neurology | 23887187 | Brain | 2013 Sep |
| Using Anesthesia to Reveal the Elements of Consciousness. | Solt K | Trends in cognitive sciences | 30104140 | Trends Cogn Sci | 2018 Nov |
| Disruption of the ascending arousal network in acute traumatic disorders of consciousness. | Snider SB, Bodien YG, Bianciardi M, Brown EN, Wu O, Edlow BL | Neurology | 31484715 | Neurology | 2019 Sep 24 |
| Population imaging of neural activity in awake behaving mice. | Piatkevich KD, Bensussen S, Tseng HA, Shroff SN, Lopez-Huerta VG, Park D, Jung EE, Shemesh OA, Straub C, Gritton HJ, Romano MF, Costa E, Sabatini BL, Fu Z, Boyden ES, Han X | Nature | 31597963 | Nature | 2019 Oct |
| An enhanced cerebral recovery index for coma prognostication following cardiac arrest. | Ghassemi MM, Amorim E, Pati SB, Mark RG, Brown EN, Purdon PL, Westover MB | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736317 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 |
| Modulation depth estimation and variable selection in state-space models for neural interfaces. | Malik WQ, Hochberg LR, Donoghue JP, Brown EN | IEEE transactions on bio-medical engineering | 25265627 | IEEE Trans Biomed Eng | 2015 Feb |
| Adaptation to elastic loads and BMI robot controls during rat locomotion examined with point-process GLMs. | Song W, Cajigas I, Brown EN, Giszter SF | Frontiers in systems neuroscience | 25972789 | Front Syst Neurosci | 2015 |
| Thalamocortical control of propofol phase-amplitude coupling. | Soplata AE, McCarthy MM, Sherfey J, Lee S, Purdon PL, Brown EN, Kopell N | PLoS computational biology | 29227992 | PLoS Comput Biol | 2017 Dec |
| Nanoscale imaging of clinical specimens using pathology-optimized expansion microscopy. | Zhao Y, Bucur O, Irshad H, Chen F, Weins A, Stancu AL, Oh EY, DiStasio M, Torous V, Glass B, Stillman IE, Schnitt SJ, Beck AH, Boyden ES | Nature biotechnology | 28714966 | Nat Biotechnol | 2017 Aug |
| Sevoflurane Induces Coherent Slow-Delta Oscillations in Rats. | Guidera JA, Taylor NE, Lee JT, Vlasov KY, Pei J, Stephen EP, Mayo JP, Brown EN, Solt K | Frontiers in neural circuits | 28725184 | Front Neural Circuits | 2017 |
| Dexmedetomidine promotes biomimetic non-rapid eye movement stage 3 sleep in humans: A pilot study. | Akeju O, Hobbs LE, Gao L, Burns SM, Pavone KJ, Plummer GS, Walsh EC, Houle TT, Kim SE, Bianchi MT, Ellenbogen JM, Brown EN | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 29154132 | Clin Neurophysiol | 2018 Jan |
| The aging brain and anesthesia. | Brown EN, Purdon PL | Current opinion in anaesthesiology | 23820102 | Curr Opin Anaesthesiol | 2013 Aug |
| Independent optical excitation of distinct neural populations. | Klapoetke NC, Murata Y, Kim SS, Pulver SR, Birdsey-Benson A, Cho YK, Morimoto TK, Chuong AS, Carpenter EJ, Tian Z, Wang J, Xie Y, Yan Z, Zhang Y, Chow BY, Surek B, Melkonian M, Jayaraman V, Constantine-Paton M, Wong GK, Boyden ES | Nature methods | 24509633 | Nat Methods | 2014 Mar |
| Probabilistic Common Spatial Patterns for Multichannel EEG Analysis. | Wu W, Chen Z, Gao X, Li Y, Brown EN, Gao S | IEEE transactions on pattern analysis and machine intelligence | 26005228 | IEEE Trans Pattern Anal Mach Intell | 2015 Mar |
| In reply. | Purdon PL, Zhou DW, Akeju O, Brown EN | Anesthesiology | 26284863 | Anesthesiology | 2015 Sep |
| Electroencephalogram signatures of ketamine anesthesia-induced unconsciousness. | Akeju O, Song AH, Hamilos AE, Pavone KJ, Flores FJ, Brown EN, Purdon PL | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 27178861 | Clin Neurophysiol | 2016 Jun |
| State-space multitaper time-frequency analysis. | Kim SE, Behr MK, Ba D, Brown EN | Proceedings of the National Academy of Sciences of the United States of America | 29255032 | Proc Natl Acad Sci U S A | 2018 Jan 2 |
| Functional and topological diversity of LOV domain photoreceptors. | Glantz ST, Carpenter EJ, Melkonian M, Gardner KH, Boyden ES, Wong GK, Chow BY | Proceedings of the National Academy of Sciences of the United States of America | 26929367 | Proc Natl Acad Sci U S A | 2016 Mar 15 |
| Rapid thalamocortical network switching mediated by cortical synchronization underlies propofol-induced EEG signatures: a biophysical model. | Soplata AE, Adam E, Brown EN, Purdon PL, McCarthy MM, Kopell N | Journal of neurophysiology | 37314079 | J Neurophysiol | 2023 Jul 1 |
| Precision Calcium Imaging of Dense Neural Populations via a Cell-Body-Targeted Calcium Indicator. | Shemesh OA, Linghu C, Piatkevich KD, Goodwin D, Celiker OT, Gritton HJ, Romano MF, Gao R, Yu CJ, Tseng HA, Bensussen S, Narayan S, Yang CT, Freifeld L, Siciliano CA, Gupta I, Wang J, Pak N, Yoon YG, Ullmann JFP, Guner-Ataman B, Noamany H, Sheinkopf ZR, Park WM, Asano S, Keating AE, Trimmer JS, Reimer J, Tolias AS, Bear MF, Tye KM, Han X, Ahrens MB, Boyden ES | Neuron | 32592656 | Neuron | 2020 Aug 5 |
| Modeling the dynamical effects of anesthesia on brain circuits. | Ching S, Brown EN | Current opinion in neurobiology | 24457211 | Curr Opin Neurobiol | 2014 Apr |
| A review of multitaper spectral analysis. | Babadi B, Brown EN | IEEE transactions on bio-medical engineering | 24759284 | IEEE Trans Biomed Eng | 2014 May |
| Anatomical substrates for direct interactions between hippocampus, medial prefrontal cortex, and the thalamic nucleus reuniens. | Varela C, Kumar S, Yang JY, Wilson MA | Brain structure & function | 23571778 | Brain Struct Funct | 2014 May |
| SAP102 regulates synaptic AMPAR function through a CNIH-2-dependent mechanism. | Liu M, Shi R, Hwang H, Han KS, Wong MH, Ren X, Lewis LD, Brown EN, Xu W | Journal of neurophysiology | 30067114 | J Neurophysiol | 2018 Oct 1 |
| Neural oscillations demonstrate that general anesthesia and sedative states are neurophysiologically distinct from sleep. | Akeju O, Brown EN | Current opinion in neurobiology | 28544930 | Curr Opin Neurobiol | 2017 Jun |
| Sensitivity to Sevoflurane anesthesia is decreased in mice with a congenital deletion of Guanylyl Cyclase-1 alpha. | Nagasaka Y, Wepler M, Thoonen R, Sips PY, Allen K, Graw JA, Yao V, Burns SM, Muenster S, Brouckaert P, Miller K, Solt K, Buys ES, Ichinose F, Zapol WM | BMC anesthesiology | 28615047 | BMC Anesthesiol | 2017 Jun 14 |
| Pharmacological Modulation of Noradrenergic Arousal Circuitry Disrupts Functional Connectivity of the Locus Ceruleus in Humans. | Song AH, Kucyi A, Napadow V, Brown EN, Loggia ML, Akeju O | The Journal of neuroscience : the official journal of the Society for Neuroscience | 28626012 | J Neurosci | 2017 Jul 19 |
| Deciphering Neural Codes of Memory during Sleep. | Chen Z, Wilson MA | Trends in neurosciences | 28390699 | Trends Neurosci | 2017 May |
| Multi-neuron intracellular recording in vivo via interacting autopatching robots. | Kodandaramaiah SB, Flores FJ, Holst GL, Singer AC, Han X, Brown EN, Boyden ES, Forest CR | eLife | 29297466 | Elife | 2018 Jan 3 |
| Corticoamygdala Transfer of Socially Derived Information Gates Observational Learning. | Allsop SA, Wichmann R, Mills F, Burgos-Robles A, Chang CJ, Felix-Ortiz AC, Vienne A, Beyeler A, Izadmehr EM, Glober G, Cum MI, Stergiadou J, Anandalingam KK, Farris K, Namburi P, Leppla CA, Weddington JC, Nieh EH, Smith AC, Ba D, Brown EN, Tye KM | Cell | 29731170 | Cell | 2018 May 31 |
| The human burst suppression electroencephalogram of deep hypothermia. | Westover MB, Ching S, Kumaraswamy VM, Akeju SO, Pierce E, Cash SS, Kilbride R, Brown EN, Purdon PL | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 25649968 | Clin Neurophysiol | 2015 Oct |
| Optogenetic activation of cholinergic neurons in the PPT or LDT induces REM sleep. | Van Dort CJ, Zachs DP, Kenny JD, Zheng S, Goldblum RR, Gelwan NA, Ramos DM, Nolan MA, Wang K, Weng FJ, Lin Y, Wilson MA, Brown EN | Proceedings of the National Academy of Sciences of the United States of America | 25548191 | Proc Natl Acad Sci U S A | 2015 Jan 13 |
| Differential requirement for NMDAR activity in SAP97β-mediated regulation of the number and strength of glutamatergic AMPAR-containing synapses. | Liu M, Lewis LD, Shi R, Brown EN, Xu W | Journal of neurophysiology | 24225540 | J Neurophysiol | 2014 Feb |
| Measuring the signal-to-noise ratio of a neuron. | Czanner G, Sarma SV, Ba D, Eden UT, Wu W, Eskandar E, Lim HH, Temereanca S, Suzuki WA, Brown EN | Proceedings of the National Academy of Sciences of the United States of America | 25995363 | Proc Natl Acad Sci U S A | 2015 Jun 9 |
| Protein-retention expansion microscopy of cells and tissues labeled using standard fluorescent proteins and antibodies. | Tillberg PW, Chen F, Piatkevich KD, Zhao Y, Yu CC, English BP, Gao L, Martorell A, Suk HJ, Yoshida F, DeGennaro EM, Roossien DH, Gong G, Seneviratne U, Tannenbaum SR, Desimone R, Cai D, Boyden ES | Nature biotechnology | 27376584 | Nat Biotechnol | 2016 Sep |
| Escape From Oblivion: Neural Mechanisms of Emergence From General Anesthesia. | Kelz MB, García PS, Mashour GA, Solt K | Anesthesia and analgesia | 30883418 | Anesth Analg | 2019 Apr |
| Novel Genetically Encoded Bright Positive Calcium Indicator NCaMP7 Based on the mNeonGreen Fluorescent Protein. | Subach OM, Sotskov VP, Plusnin VV, Gruzdeva AM, Barykina NV, Ivashkina OI, Anokhin KV, Nikolaeva AY, Korzhenevskiy DA, Vlaskina AV, Lazarenko VA, Boyko KM, Rakitina TV, Varizhuk AM, Pozmogova GE, Podgorny OV, Piatkevich KD, Boyden ES, Subach FV | International journal of molecular sciences | 32121243 | Int J Mol Sci | 2020 Feb 28 |
| Reference-free removal of EEG-fMRI ballistocardiogram artifacts with harmonic regression. | Krishnaswamy P, Bonmassar G, Poulsen C, Pierce ET, Purdon PL, Brown EN | NeuroImage | 26151100 | Neuroimage | 2016 Mar |
| Fluoxetine prevents respiratory arrest without enhancing ventilation in DBA/1 mice. | Zeng C, Long X, Cotten JF, Forman SA, Solt K, Faingold CL, Feng HJ | Epilepsy & behavior : E&B | 25771493 | Epilepsy Behav | 2015 Apr |
| A genetically encoded near-infrared fluorescent calcium ion indicator. | Qian Y, Piatkevich KD, Mc Larney B, Abdelfattah AS, Mehta S, Murdock MH, Gottschalk S, Molina RS, Zhang W, Chen Y, Wu J, Drobizhev M, Hughes TE, Zhang J, Schreiter ER, Shoham S, Razansky D, Boyden ES, Campbell RE | Nature methods | 30664778 | Nat Methods | 2019 Feb |
| Acceptability and Feasibility of eSCCIP: Results From a Pilot Study of the Electronic Surviving Cancer Competently Intervention Program. | Canter KS, Vega G, Perez Ramirez A, Munoz Osorio A, Thomas C, Lewis AM, Arasteh K, Kazak A | Journal of pediatric psychology | 36303445 | J Pediatr Psychol | 2023 Mar 20 |
| Enhancement of encoding and retrieval functions through theta phase-specific manipulation of hippocampus. | Siegle JH, Wilson MA | eLife | 25073927 | Elife | 2014 Jul 29 |
| State-dependent architecture of thalamic reticular subnetworks. | Halassa MM, Chen Z, Wimmer RD, Brunetti PM, Zhao S, Zikopoulos B, Wang F, Brown EN, Wilson MA | Cell | 25126786 | Cell | 2014 Aug 14 |
| In vivo robotics: the automation of neuroscience and other intact-system biological fields. | Kodandaramaiah SB, Boyden ES, Forest CR | Annals of the New York Academy of Sciences | 23841584 | Ann N Y Acad Sci | 2013 Dec |
| Spatial Multiplexing of Fluorescent Reporters for Imaging Signaling Network Dynamics. | Linghu C, Johnson SL, Valdes PA, Shemesh OA, Park WM, Park D, Piatkevich KD, Wassie AT, Liu Y, An B, Barnes SA, Celiker OT, Yao CC, Yu CJ, Wang R, Adamala KP, Bear MF, Keating AE, Boyden ES | Cell | 33232692 | Cell | 2020 Dec 10 |
| Gamma frequency entrainment attenuates amyloid load and modifies microglia. | Iaccarino HF, Singer AC, Martorell AJ, Rudenko A, Gao F, Gillingham TZ, Mathys H, Seo J, Kritskiy O, Abdurrob F, Adaikkan C, Canter RG, Rueda R, Brown EN, Boyden ES, Tsai LH | Nature | 27929004 | Nature | 2016 Dec 7 |
| Design, implementation, and evaluation of a physiological closed-loop control device for medically-induced coma. | Jingzhi An, Purdon PL, Solt K, Sims NM, Brown EN, Westover MB | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 29060851 | Annu Int Conf IEEE Eng Med Biol Soc | 2017 Jul |
| Dexmedetomidine Disrupts the Local and Global Efficiencies of Large-scale Brain Networks. | Hashmi JA, Loggia ML, Khan S, Gao L, Kim J, Napadow V, Brown EN, Akeju O | Anesthesiology | 28092321 | Anesthesiology | 2017 Mar |
| Assessing neuronal interactions of cell assemblies during general anesthesia. | Chen Z, Vijayan S, Ching S, Hale G, Flores FJ, Wilson MA, Brown EN | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 22255259 | Annu Int Conf IEEE Eng Med Biol Soc | 2011 |
| Physostigmine and Methylphenidate Induce Distinct Arousal States During Isoflurane General Anesthesia in Rats. | Kenny JD, Chemali JJ, Cotten JF, Van Dort CJ, Kim SE, Ba D, Taylor NE, Brown EN, Solt K | Anesthesia and analgesia | 26991753 | Anesth Analg | 2016 Nov |
| Left-Lateralized Contributions of Saccades to Cortical Activity During a One-Back Word Recognition Task. | Chang YC, Khan S, Taulu S, Kuperberg G, Brown EN, Hämäläinen MS, Temereanca S | Frontiers in neural circuits | 29867372 | Front Neural Circuits | 2018 |
| A Neurologic Examination for Anesthesiologists: Assessing Arousal Level during Induction, Maintenance, and Emergence. | Reshef ER, Schiff ND, Brown EN | Anesthesiology | 30664547 | Anesthesiology | 2019 Mar |
| Delta frequency optogenetic stimulation of the thalamic nucleus reuniens is sufficient to produce working memory deficits: relevance to schizophrenia. | Duan AR, Varela C, Zhang Y, Shen Y, Xiong L, Wilson MA, Lisman J | Biological psychiatry | 25891221 | Biol Psychiatry | 2015 Jun 15 |
| Dextroamphetamine (but Not Atomoxetine) Induces Reanimation from General Anesthesia: Implications for the Roles of Dopamine and Norepinephrine in Active Emergence. | Kenny JD, Taylor NE, Brown EN, Solt K | PloS one | 26148114 | PLoS One | 2015 |
| Ageing delays emergence from general anaesthesia in rats by increasing anaesthetic sensitivity in the brain. | Chemali JJ, Kenny JD, Olutola O, Taylor NE, Kimchi EY, Purdon PL, Brown EN, Solt K | British journal of anaesthesia | 26174302 | Br J Anaesth | 2015 Jul |
| Age-dependency of sevoflurane-induced electroencephalogram dynamics in children. | Akeju O, Pavone KJ, Thum JA, Firth PG, Westover MB, Puglia M, Shank ES, Brown EN, Purdon PL | British journal of anaesthesia | 26174303 | Br J Anaesth | 2015 Jul |
| Toward an In Vivo Neuroimaging Template of Human Brainstem Nuclei of the Ascending Arousal, Autonomic, and Motor Systems. | Bianciardi M, Toschi N, Edlow BL, Eichner C, Setsompop K, Polimeni JR, Brown EN, Kinney HC, Rosen BR, Wald LL | Brain connectivity | 26066023 | Brain Connect | 2015 Dec |
| Phase organization of network computations. | Wilson MA, Varela C, Remondes M | Current opinion in neurobiology | 25679370 | Curr Opin Neurobiol | 2015 Apr |
| Biophysical Modeling of Alpha Rhythms During Halothane-Induced Unconsciousness. | Vijayan S, Ching S, Purdon PL, Brown EN, Kopell NJ | International IEEE/EMBS Conference on Neural Engineering : [proceedings]. International IEEE EMBS Conference on Neural Engineering | 25284633 | Int IEEE EMBS Conf Neural Eng | 2013 |
| A Multitaper Frequency-Domain Bootstrap Method. | Kim SE, Ba D, Brown EN | IEEE signal processing letters | 32002009 | IEEE Signal Process Lett | 2018 Dec |
| Spatial variation in automated burst suppression detection in pharmacologically induced coma. | An J, Jonnalagadda D, Moura V, Purdon PL, Brown EN, Westover MB | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26738009 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 |
| Multimodal General Anesthesia: Theory and Practice. | Brown EN, Pavone KJ, Naranjo M | Anesthesia and analgesia | 30252709 | Anesth Analg | 2018 Nov |
| Cognitive Impairment Is Associated with Absolute Intraoperative Frontal α-Band Power but Not with Baseline α-Band Power: A Pilot Study. | Koch S, Feinkohl I, Chakravarty S, Windmann V, Lichtner G, Pischon T, Brown EN, Spies C, BioCog Study Group | Dementia and geriatric cognitive disorders | 31578031 | Dement Geriatr Cogn Disord | 2019 |
| Dense, Continuous Membrane Labeling and Expansion Microscopy Visualization of Ultrastructure in Tissues. | Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, IMAXT Grand Challenge Consortium, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES | bioRxiv : the preprint server for biology | 38496681 | bioRxiv | 2024 Mar 8 |
| Thalamocortical mechanisms for the anteriorization of α rhythms during propofol-induced unconsciousness. | Vijayan S, Ching S, Purdon PL, Brown EN, Kopell NJ | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23825412 | J Neurosci | 2013 Jul 3 |
| Electrical stimulation of the ventral tegmental area induces reanimation from general anesthesia. | Solt K, Van Dort CJ, Chemali JJ, Taylor NE, Kenny JD, Brown EN | Anesthesiology | 24398816 | Anesthesiology | 2014 Aug |
| A Bayesian nonparametric approach for uncovering rat hippocampal population codes during spatial navigation. | Linderman SW, Johnson MJ, Wilson MA, Chen Z | Journal of neuroscience methods | 26854398 | J Neurosci Methods | 2016 Apr 1 |
| Disruption of thalamic functional connectivity is a neural correlate of dexmedetomidine-induced unconsciousness. | Akeju O, Loggia ML, Catana C, Pavone KJ, Vazquez R, Rhee J, Contreras Ramirez V, Chonde DB, Izquierdo-Garcia D, Arabasz G, Hsu S, Habeeb K, Hooker JM, Napadow V, Brown EN, Purdon PL | eLife | 25432022 | Elife | 2014 Nov 28 |
| Robust spectrotemporal decomposition by iteratively reweighted least squares. | Ba D, Babadi B, Purdon PL, Brown EN | Proceedings of the National Academy of Sciences of the United States of America | 25468968 | Proc Natl Acad Sci U S A | 2014 Dec 16 |
| Optogenetic activation of dopamine neurons in the ventral tegmental area induces reanimation from general anesthesia. | Taylor NE, Van Dort CJ, Kenny JD, Pei J, Guidera JA, Vlasov KY, Lee JT, Boyden ES, Brown EN, Solt K | Proceedings of the National Academy of Sciences of the United States of America | 27791160 | Proc Natl Acad Sci U S A | 2016 Nov 8 |
| Real-Time Readout of Large-Scale Unsorted Neural Ensemble Place Codes. | Hu S, Ciliberti D, Grosmark AD, Michon F, Ji D, Penagos H, Buzsáki G, Wilson MA, Kloosterman F, Chen Z | Cell reports | 30517852 | Cell Rep | 2018 Dec 4 |
| The rostromedial tegmental nucleus: a key modulator of pain and opioid analgesia. | Taylor NE, Long H, Pei J, Kukutla P, Phero A, Hadaegh F, Abdelnabi A, Solt K, Brenner GJ | Pain | 31246732 | Pain | 2019 Nov |
| The Role of Glutamatergic and Dopaminergic Neurons in the Periaqueductal Gray/Dorsal Raphe: Separating Analgesia and Anxiety. | Taylor NE, Pei J, Zhang J, Vlasov KY, Davis T, Taylor E, Weng FJ, Van Dort CJ, Solt K, Brown EN | eNeuro | 31058210 | eNeuro | 2019 Jan-Feb |
| An easy-to-assemble, robust, and lightweight drive implant for chronic tetrode recordings in freely moving animals. | Voigts J, Newman JP, Wilson MA, Harnett MT | Journal of neural engineering | 32074511 | J Neural Eng | 2020 May 19 |
| Tuning the Sensitivity of Genetically Encoded Fluorescent Potassium Indicators through Structure-Guided and Genome Mining Strategies. | Torres Cabán CC, Yang M, Lai C, Yang L, Subach FV, Smith BO, Piatkevich KD, Boyden ES | ACS sensors | 35427452 | ACS Sens | 2022 May 27 |
| Machine learning of EEG spectra classifies unconsciousness during GABAergic anesthesia. | Abel JH, Badgeley MA, Meschede-Krasa B, Schamberg G, Garwood IC, Lecamwasam K, Chakravarty S, Zhou DW, Keating M, Purdon PL, Brown EN | PloS one | 33956800 | PLoS One | 2021 |
| Pharmacodynamic modeling of propofol-induced general anesthesia in young adults. | Chakravarty S, Nikolaeva K, Kishnan D, Flores FJ, Purdon PL, Brown EN | ... Health innovations and point-of-care technologies conference. Health innovations and point-of-care technologies conference | 32803192 | Health Innov Point Care Conf | 2017 Nov |
| Clinical Electroencephalography for Anesthesiologists: Part I: Background and Basic Signatures. | Purdon PL, Sampson A, Pavone KJ, Brown EN | Anesthesiology | 26275092 | Anesthesiology | 2015 Oct |
| Age-dependent electroencephalogram (EEG) patterns during sevoflurane general anesthesia in infants. | Cornelissen L, Kim SE, Purdon PL, Brown EN, Berde CB | eLife | 26102526 | Elife | 2015 Jun 23 |
| Robust control of burst suppression for medical coma. | Westover MB, Kim SE, Ching S, Purdon PL, Brown EN | Journal of neural engineering | 26020243 | J Neural Eng | 2015 Aug |
| A comparison of propofol- and dexmedetomidine-induced electroencephalogram dynamics using spectral and coherence analysis. | Akeju O, Pavone KJ, Westover MB, Vazquez R, Prerau MJ, Harrell PG, Hartnack KE, Rhee J, Sampson AL, Habeeb K, Gao L, Pierce ET, Walsh JL, Brown EN, Purdon PL | Anesthesiology | 25187999 | Anesthesiology | 2014 Nov |
| GABAA circuit mechanisms are associated with ether anesthesia-induced unconsciousness. | Akeju O, Hamilos AE, Song AH, Pavone KJ, Purdon PL, Brown EN | Clinical neurophysiology : official journal of the International Federation of Clinical Neurophysiology | 27178867 | Clin Neurophysiol | 2016 Jun |
| Green fluorescent genetically encoded calcium indicator based on calmodulin/M13-peptide from fungi. | Barykina NV, Subach OM, Piatkevich KD, Jung EE, Malyshev AY, Smirnov IV, Bogorodskiy AO, Borshchevskiy VI, Varizhuk AM, Pozmogova GE, Boyden ES, Anokhin KV, Enikolopov GN, Subach FV | PloS one | 28837632 | PLoS One | 2017 |
| Near-Infrared Fluorescent Proteins Engineered from Bacterial Phytochromes in Neuroimaging. | Piatkevich KD, Suk HJ, Kodandaramaiah SB, Yoshida F, DeGennaro EM, Drobizhev M, Hughes TE, Desimone R, Boyden ES, Verkhusha VV | Biophysical journal | 29017728 | Biophys J | 2017 Nov 21 |
| Thalamocortical synchronization during induction and emergence from propofol-induced unconsciousness. | Flores FJ, Hartnack KE, Fath AB, Kim SE, Wilson MA, Brown EN, Purdon PL | Proceedings of the National Academy of Sciences of the United States of America | 28743752 | Proc Natl Acad Sci U S A | 2017 Aug 8 |
| Effects of sevoflurane and propofol on frontal electroencephalogram power and coherence. | Akeju O, Westover MB, Pavone KJ, Sampson AL, Hartnack KE, Brown EN, Purdon PL | Anesthesiology | 25233374 | Anesthesiology | 2014 Nov |
| Dense, continuous membrane labeling and expansion microscopy visualization of ultrastructure in tissues. | Shin TW, Wang H, Zhang C, An B, Lu Y, Zhang E, Lu X, Karagiannis ED, Kang JS, Emenari A, Symvoulidis P, Asano S, Lin L, Costa EK, IMAXT Grand Challenge Consortium, Marblestone AH, Kasthuri N, Tsai LH, Boyden ES | Nature communications | 39939319 | Nat Commun | 2025 Feb 12 |
| Mesenchymal stem cells for the treatment of neurodegenerative disease. | Joyce N, Annett G, Wirthlin L, Olson S, Bauer G, Nolta JA | Regenerative medicine | 21082892 | Regen Med | 2010 Nov |
| Mesenchymal stem cells for the sustained in vivo delivery of bioactive factors. | Meyerrose T, Olson S, Pontow S, Kalomoiris S, Jung Y, Annett G, Bauer G, Nolta JA | Advanced drug delivery reviews | 20920540 | Adv Drug Deliv Rev | 2010 Sep 30 |
| Examination of mesenchymal stem cell-mediated RNAi transfer to Huntington's disease affected neuronal cells for reduction of huntingtin. | Olson SD, Kambal A, Pollock K, Mitchell GM, Stewart H, Kalomoiris S, Cary W, Nacey C, Pepper K, Nolta JA | Molecular and cellular neurosciences | 22198539 | Mol Cell Neurosci | 2012 Mar |
| Preclinical evaluation of mesenchymal stem cells overexpressing VEGF to treat critical limb ischemia. | Beegle JR, Magner NL, Kalomoiris S, Harding A, Zhou P, Nacey C, White JL, Pepper K, Gruenloh W, Annett G, Nolta JA, Fierro FA | Molecular therapy. Methods & clinical development | 27610394 | Mol Ther Methods Clin Dev | 2016 |
| The Complex Ethics of First In Human Stem Cell Clinical Trials. | Yarborough M, Tempkin T, Nolta J, Joyce N | AJOB neuroscience | 24273680 | AJOB Neurosci | 2012 |
| Human Mesenchymal Stem Cells Genetically Engineered to Overexpress Brain-derived Neurotrophic Factor Improve Outcomes in Huntington's Disease Mouse Models. | Pollock K, Dahlenburg H, Nelson H, Fink KD, Cary W, Hendrix K, Annett G, Torrest A, Deng P, Gutierrez J, Nacey C, Pepper K, Kalomoiris S, D Anderson J, McGee J, Gruenloh W, Fury B, Bauer G, Duffy A, Tempkin T, Wheelock V, Nolta JA | Molecular therapy : the journal of the American Society of Gene Therapy | 26765769 | Mol Ther | 2016 May |
| Comprehensive Proteomic Analysis of Mesenchymal Stem Cell Exosomes Reveals Modulation of Angiogenesis via Nuclear Factor-KappaB Signaling. | Anderson JD, Johansson HJ, Graham CS, Vesterlund M, Pham MT, Bramlett CS, Montgomery EN, Mellema MS, Bardini RL, Contreras Z, Hoon M, Bauer G, Fink KD, Fury B, Hendrix KJ, Chedin F, El-Andaloussi S, Hwang B, Mulligan MS, Lehtiö J, Nolta JA | Stem cells (Dayton, Ohio) | 26782178 | Stem Cells | 2016 Mar |
| Signaling defects in iPSC-derived fragile X premutation neurons. | Liu J, Koscielska KA, Cao Z, Hulsizer S, Grace N, Mitchell G, Nacey C, Githinji J, McGee J, Garcia-Arocena D, Hagerman RJ, Nolta J, Pessah IN, Hagerman PJ | Human molecular genetics | 22641815 | Hum Mol Genet | 2012 Sep 1 |
| Directing mesenchymal stem cells to bone to augment bone formation and increase bone mass. | Guan M, Yao W, Liu R, Lam KS, Nolta J, Jia J, Panganiban B, Meng L, Zhou P, Shahnazari M, Ritchie RO, Lane NE | Nature medicine | 22306732 | Nat Med | 2012 Feb 5 |
| Genetically engineered mesenchymal stem cells as a proposed therapeutic for Huntington's disease. | Olson SD, Pollock K, Kambal A, Cary W, Mitchell GM, Tempkin J, Stewart H, McGee J, Bauer G, Kim HS, Tempkin T, Wheelock V, Annett G, Dunbar G, Nolta JA | Molecular neurobiology | 22161544 | Mol Neurobiol | 2012 Feb |
| Clinical translation of stem cells: insight for cartilage therapies. | Lee JK, Responte DJ, Cissell DD, Hu JC, Nolta JA, Athanasiou KA | Critical reviews in biotechnology | 24083452 | Crit Rev Biotechnol | 2014 Mar |
| Human Myoblast and Mesenchymal Stem Cell Interactions Visualized by Videomicroscopy. | Black AB, Dahlenburg H, Pepper K, Nacey C, Pontow S, Kuhn MA, Belafsky PC, Nolta JA | Human gene therapy methods | 26544924 | Hum Gene Ther Methods | 2015 Dec |
| BMI1 Regulation of Self-Renewal and Multipotency in Human Mesenchymal Stem Cells. | Jung Y, Nolta JA | Current stem cell research & therapy | 26763885 | Curr Stem Cell Res Ther | 2016 |
| Preclinical translation of exosomes derived from mesenchymal stem/stromal cells. | Elahi FM, Farwell DG, Nolta JA, Anderson JD | Stem cells (Dayton, Ohio) | 31381842 | Stem Cells | 2020 Jan |
| Mesenchymal stem cells for trinucleotide repeat disorders. | Annett G, Bauer G, Nolta JA | Methods in molecular biology (Clifton, N.J.) | 23754220 | Methods Mol Biol | 2013 |
| Fibroblast Growth Factor 2 Regulates High Mobility Group A2 Expression in Human Bone Marrow-Derived Mesenchymal Stem Cells. | Kalomoiris S, Cicchetto AC, Lakatos K, Nolta JA, Fierro FA | Journal of cellular biochemistry | 26888666 | J Cell Biochem | 2016 Sep |
| Clinical trial perspective for adult and juvenile Huntington's disease using genetically-engineered mesenchymal stem cells. | Deng P, Torrest A, Pollock K, Dahlenburg H, Annett G, Nolta JA, Fink KD | Neural regeneration research | 27335539 | Neural Regen Res | 2016 May |
| Potential long-term treatment of hemophilia A by neonatal co-transplantation of cord blood-derived endothelial colony-forming cells and placental mesenchymal stromal cells. | Gao K, Kumar P, Cortez-Toledo E, Hao D, Reynaga L, Rose M, Wang C, Farmer D, Nolta J, Zhou J, Zhou P, Wang A | Stem cell research & therapy | 30670078 | Stem Cell Res Ther | 2019 Jan 22 |
| Exosomes Derived from Human Primed Mesenchymal Stem Cells Induce Mitosis and Potentiate Growth Factor Secretion. | Yuan O, Lin C, Wagner J, Archard JA, Deng P, Halmai J, Bauer G, Fink KD, Fury B, Perotti NH, Walker JE, Pollock K, Apperson M, Butters J, Belafsky P, Farwell DG, Kuhn M, Nolta J, Anderson JD | Stem cells and development | 30638129 | Stem Cells Dev | 2019 Mar 15 |
| Efficient Generation of Induced Pluripotent Stem and Neural Progenitor Cells From Acutely Harvested Dura Mater Obtained During Ventriculoperitoneal Shunt Surgery. | Cary WA, Hori CN, Pham MT, Nacey CA, McGee JL, Hamou M, Berman RF, Bauer G, Nolta JA, Waldau B | World neurosurgery | 26074438 | World Neurosurg | 2015 Nov |
| HDACs regulate the differentiation of endothelial cells from human iPSCs. | Li T, Wu H, Wang P, Kim AM, Jia J, Nolta JA, Zhou P | Cell biochemistry and function | 35789099 | Cell Biochem Funct | 2022 Aug |
| Role of MEF2C in the Endothelial Cells Derived from Human Induced Pluripotent Stem Cells. | Li T, Conroy KL, Kim AM, Halmai J, Gao K, Moreno E, Wang A, Passerini AG, Nolta JA, Zhou P | Stem cells (Dayton, Ohio) | 36639926 | Stem Cells | 2023 Apr 25 |
| Effects on proliferation and differentiation of multipotent bone marrow stromal cells engineered to express growth factors for combined cell and gene therapy. | Fierro FA, Kalomoiris S, Sondergaard CS, Nolta JA | Stem cells (Dayton, Ohio) | 21898687 | Stem Cells | 2011 Nov |
| Concise review: Induced pluripotent stem cell-derived mesenchymal stem cells: progress toward safe clinical products. | Jung Y, Bauer G, Nolta JA | Stem cells (Dayton, Ohio) | 21898694 | Stem Cells | 2012 Jan |
| Concise review: MicroRNA function in multipotent mesenchymal stromal cells. | Clark EA, Kalomoiris S, Nolta JA, Fierro FA | Stem cells (Dayton, Ohio) | 24860868 | Stem Cells | 2014 May |
| Insulin and IGFs enhance hepatocyte differentiation from human embryonic stem cells via the PI3K/AKT pathway. | Magner NL, Jung Y, Wu J, Nolta JA, Zern MA, Zhou P | Stem cells (Dayton, Ohio) | 23836547 | Stem Cells | 2013 Oct |
| Novel targeted therapy for neuroblastoma: silencing the MXD3 gene using siRNA. | Duong C, Yoshida S, Chen C, Barisone G, Diaz E, Li Y, Beckett L, Chung J, Antony R, Nolta J, Nitin N, Satake N | Pediatric research | 28419087 | Pediatr Res | 2017 Sep |
| Intravitreal Administration of Human Bone Marrow CD34+ Stem Cells in a Murine Model of Retinal Degeneration. | Moisseiev E, Smit-McBride Z, Oltjen S, Zhang P, Zawadzki RJ, Motta M, Murphy CJ, Cary W, Annett G, Nolta JA, Park SS | Investigative ophthalmology & visual science | 27537262 | Invest Ophthalmol Vis Sci | 2016 Aug 1 |
| "Next-generation" mesenchymal stem or stromal cells for the in vivo delivery of bioactive factors: progressing toward the clinic. | Nolta JA | Transfusion | 27079315 | Transfusion | 2016 Apr |
| Developing stem cell therapies for juvenile and adult-onset Huntington's disease. | Fink KD, Deng P, Torrest A, Stewart H, Pollock K, Gruenloh W, Annett G, Tempkin T, Wheelock V, Nolta JA | Regenerative medicine | 26237705 | Regen Med | 2015 |
| Hypoxic preconditioning of mesenchymal stromal cells induces metabolic changes, enhances survival, and promotes cell retention in vivo. | Beegle J, Lakatos K, Kalomoiris S, Stewart H, Isseroff RR, Nolta JA, Fierro FA | Stem cells (Dayton, Ohio) | 25702874 | Stem Cells | 2015 Jun |
| Crosstalk between adrenergic and toll-like receptors in human mesenchymal stem cells and keratinocytes: a recipe for impaired wound healing. | Dasu MR, Ramirez SR, La TD, Gorouhi F, Nguyen C, Lin BR, Mashburn C, Stewart H, Peavy TR, Nolta JA, Isseroff RR | Stem cells translational medicine | 24760207 | Stem Cells Transl Med | 2014 Jun |
| Allele-Specific Reduction of the Mutant Huntingtin Allele Using Transcription Activator-Like Effectors in Human Huntington's Disease Fibroblasts. | Fink KD, Deng P, Gutierrez J, Anderson JS, Torrest A, Komarla A, Kalomoiris S, Cary W, Anderson JD, Gruenloh W, Duffy A, Tempkin T, Annett G, Wheelock V, Segal DJ, Nolta JA | Cell transplantation | 26850319 | Cell Transplant | 2016 |
| Protective Effect of Intravitreal Administration of Exosomes Derived from Mesenchymal Stem Cells on Retinal Ischemia. | Moisseiev E, Anderson JD, Oltjen S, Goswami M, Zawadzki RJ, Nolta JA, Park SS | Current eye research | 28636406 | Curr Eye Res | 2017 Oct |
| Advances in bone marrow stem cell therapy for retinal dysfunction. | Park SS, Moisseiev E, Bauer G, Anderson JD, Grant MB, Zam A, Zawadzki RJ, Werner JS, Nolta JA | Progress in retinal and eye research | 27784628 | Prog Retin Eye Res | 2017 Jan |
| Mesenchymal stem/stromal cells genetically engineered to produce vascular endothelial growth factor for revascularization in wound healing and ischemic conditions. | Fierro FA, Magner N, Beegle J, Dahlenburg H, Logan White J, Zhou P, Pepper K, Fury B, Coleal-Bergum DP, Bauer G, Gruenloh W, Annett G, Pifer C, Nolta JA | Transfusion | 30383901 | Transfusion | 2019 Feb |
| Primed mesenchymal stem cells package exosomes with metabolites associated with immunomodulation. | Showalter MR, Wancewicz B, Fiehn O, Archard JA, Clayton S, Wagner J, Deng P, Halmai J, Fink KD, Bauer G, Fury B, Perotti NH, Apperson M, Butters J, Belafsky P, Farwell G, Kuhn M, Nolta JA, Anderson JD | Biochemical and biophysical research communications | 30926165 | Biochem Biophys Res Commun | 2019 May 14 |
| Enhancing Retention of Human Bone Marrow Mesenchymal Stem Cells with Prosurvival Factors Promotes Angiogenesis in a Mouse Model of Limb Ischemia. | Cortez-Toledo E, Rose M, Agu E, Dahlenburg H, Yao W, Nolta JA, Zhou P | Stem cells and development | 30398391 | Stem Cells Dev | 2019 Jan 15 |
| Involvement of mesenchymal stem cells in cancer progression and metastases. | Chang AI, Schwertschkow AH, Nolta JA, Wu J | Current cancer drug targets | 25619387 | Curr Cancer Drug Targets | 2015 |
| Mesenchymal Stem Cells Respond to Hypoxia by Increasing Diacylglycerols. | Lakatos K, Kalomoiris S, Merkely B, Nolta JA, Fierro FA | Journal of cellular biochemistry | 26212931 | J Cell Biochem | 2016 Feb |
| Engineered BDNF producing cells as a potential treatment for neurologic disease. | Deng P, Anderson JD, Yu AS, Annett G, Fink KD, Nolta JA | Expert opinion on biological therapy | 27159050 | Expert Opin Biol Ther | 2016 Aug |
| Novel Targeted Therapy for Precursor B Cell Acute Lymphoblastic Leukemia: anti-CD22 Antibody-MXD3 Antisense Oligonucleotide Conjugate. | Satake N, Duong C, Yoshida S, Oestergaard M, Chen C, Peralta R, Guo S, Seth PP, Li Y, Beckett L, Chung J, Nolta J, Nitin N, Tuscano JM | Molecular medicine (Cambridge, Mass.) | 27455414 | Mol Med | 2016 Oct |
| Coupling of mRNA Structure Rearrangement to Ribosome Movement during Bypassing of Non-coding Regions. | Chen J, Coakley A, O'Connor M, Petrov A, O'Leary SE, Atkins JF, Puglisi JD | Cell | 26590426 | Cell | 2015 Nov 19 |
| A simple real-time assay for in vitro translation. | Capece MC, Kornberg GL, Petrov A, Puglisi JD | RNA (New York, N.Y.) | 25525154 | RNA | 2015 Feb |
| Unraveling the dynamics of ribosome translocation. | Chen J, Tsai A, O'Leary SE, Petrov A, Puglisi JD | Current opinion in structural biology | 23142574 | Curr Opin Struct Biol | 2012 Dec |
| Nonfluorescent quenchers to correlate single-molecule conformational and compositional dynamics. | Chen J, Tsai A, Petrov A, Puglisi JD | Journal of the American Chemical Society | 22428667 | J Am Chem Soc | 2012 Apr 4 |
| Dynamics of the translational machinery. | Petrov A, Kornberg G, O'Leary S, Tsai A, Uemura S, Puglisi JD | Current opinion in structural biology | 21256733 | Curr Opin Struct Biol | 2011 Feb |
| cis-Acting RNA elements in the hepatitis C virus RNA genome. | Sagan SM, Chahal J, Sarnow P | Virus research | 25576644 | Virus Res | 2015 Aug 3 |
| Real-time observation of signal recognition particle binding to actively translating ribosomes. | Noriega TR, Chen J, Walter P, Puglisi JD | eLife | 25358118 | Elife | 2014 Oct 30 |
| Kinetic pathway of 40S ribosomal subunit recruitment to hepatitis C virus internal ribosome entry site. | Fuchs G, Petrov AN, Marceau CD, Popov LM, Chen J, O'Leary SE, Wang R, Carette JE, Sarnow P, Puglisi JD | Proceedings of the National Academy of Sciences of the United States of America | 25516984 | Proc Natl Acad Sci U S A | 2015 Jan 13 |
| Coordinated conformational and compositional dynamics drive ribosome translocation. | Chen J, Petrov A, Tsai A, O'Leary SE, Puglisi JD | Nature structural & molecular biology | 23624862 | Nat Struct Mol Biol | 2013 Jun |
| Multiple Parallel Pathways of Translation Initiation on the CrPV IRES. | Petrov A, Grosely R, Chen J, O'Leary SE, Puglisi JD | Molecular cell | 27058789 | Mol Cell | 2016 Apr 7 |
| Sequence-dependent elongation dynamics on macrolide-bound ribosomes. | Johansson M, Chen J, Tsai A, Kornberg G, Puglisi JD | Cell reports | 24836000 | Cell Rep | 2014 Jun 12 |
| Signal recognition particle-ribosome binding is sensitive to nascent chain length. | Noriega TR, Tsai A, Elvekrog MM, Petrov A, Neher SB, Chen J, Bradshaw N, Puglisi JD, Walter P | The Journal of biological chemistry | 24808175 | J Biol Chem | 2014 Jul 11 |
| Dynamic pathways of -1 translational frameshifting. | Chen J, Petrov A, Johansson M, Tsai A, O'Leary SE, Puglisi JD | Nature | 24919156 | Nature | 2014 Aug 21 |
| Heterogeneous pathways and timing of factor departure during translation initiation. | Tsai A, Petrov A, Marshall RA, Korlach J, Uemura S, Puglisi JD | Nature | 22722848 | Nature | 2012 Jul 19 |
| High-throughput platform for real-time monitoring of biological processes by multicolor single-molecule fluorescence. | Chen J, Dalal RV, Petrov AN, Tsai A, O'Leary SE, Chapin K, Cheng J, Ewan M, Hsiung PL, Lundquist P, Turner SW, Hsu DR, Puglisi JD | Proceedings of the National Academy of Sciences of the United States of America | 24379388 | Proc Natl Acad Sci U S A | 2014 Jan 14 |
| Post-termination Ribosome Intermediate Acts as the Gateway to Ribosome Recycling. | Prabhakar A, Capece MC, Petrov A, Choi J, Puglisi JD | Cell reports | 28683310 | Cell Rep | 2017 Jul 5 |
| Single-molecule analysis of translational dynamics. | Petrov A, Chen J, O'Leary S, Tsai A, Puglisi JD | Cold Spring Harbor perspectives in biology | 22798542 | Cold Spring Harb Perspect Biol | 2012 Sep 1 |
| Amino acid sequence repertoire of the bacterial proteome and the occurrence of untranslatable sequences. | Navon SP, Kornberg G, Chen J, Schwartzman T, Tsai A, Puglisi EV, Puglisi JD, Adir N | Proceedings of the National Academy of Sciences of the United States of America | 27307442 | Proc Natl Acad Sci U S A | 2016 Jun 28 |
| 2'-O-methylation in mRNA disrupts tRNA decoding during translation elongation. | Choi J, Indrisiunaite G, DeMirci H, Ieong KW, Wang J, Petrov A, Prabhakar A, Rechavi G, Dominissini D, He C, Ehrenberg M, Puglisi JD | Nature structural & molecular biology | 29459784 | Nat Struct Mol Biol | 2018 Mar |
| Cotranslational Protein Folding inside the Ribosome Exit Tunnel. | Nilsson OB, Hedman R, Marino J, Wickles S, Bischoff L, Johansson M, Müller-Lucks A, Trovato F, Puglisi JD, O'Brien EP, Beckmann R, von Heijne G | Cell reports | 26321634 | Cell Rep | 2015 Sep 8 |
| Dynamic recognition of the mRNA cap by Saccharomyces cerevisiae eIF4E. | O'Leary SE, Petrov A, Chen J, Puglisi JD | Structure (London, England : 1993) | 24183571 | Structure | 2013 Dec 3 |
| The dynamics of SecM-induced translational stalling. | Tsai A, Kornberg G, Johansson M, Chen J, Puglisi JD | Cell reports | 24836001 | Cell Rep | 2014 Jun 12 |
| The impact of aminoglycosides on the dynamics of translation elongation. | Tsai A, Uemura S, Johansson M, Puglisi EV, Marshall RA, Aitken CE, Korlach J, Ehrenberg M, Puglisi JD | Cell reports | 23416053 | Cell Rep | 2013 Feb 21 |
| N(6)-methyladenosine in mRNA disrupts tRNA selection and translation-elongation dynamics. | Choi J, Ieong KW, Demirci H, Chen J, Petrov A, Prabhakar A, O'Leary SE, Dominissini D, Rechavi G, Soltis SM, Ehrenberg M, Puglisi JD | Nature structural & molecular biology | 26751643 | Nat Struct Mol Biol | 2016 Feb |
| Natural Product Screening Reveals Naphthoquinone Complex I Bypass Factors. | Vafai SB, Mevers E, Higgins KW, Fomina Y, Zhang J, Mandinova A, Newman D, Shaw SY, Clardy J, Mootha VK | PloS one | 27622560 | PLoS One | 2016 |
| A genetically encoded tool for manipulation of NADP(+)/NADPH in living cells. | Cracan V, Titov DV, Shen H, Grabarek Z, Mootha VK | Nature chemical biology | 28805804 | Nat Chem Biol | 2017 Oct |
| Hepatic NADH reductive stress underlies common variation in metabolic traits. | Goodman RP, Markhard AL, Shah H, Sharma R, Skinner OS, Clish CB, Deik A, Patgiri A, Hsu YH, Masia R, Noh HL, Suk S, Goldberger O, Hirschhorn JN, Yellen G, Kim JK, Mootha VK | Nature | 32461692 | Nature | 2020 Jul |
| A natural fusion of flavodiiron, rubredoxin, and rubredoxin oxidoreductase domains is a self-sufficient water-forming oxidase of Trichomonas vaginalis. | Abdulaziz EN, Bell TA, Rashid B, Heacock ML, Begic T, Skinner OS, Yaseen MA, Chao LH, Mootha VK, Pierik AJ, Cracan V | The Journal of biological chemistry | 35780837 | J Biol Chem | 2022 Aug |
| Complementation of mitochondrial electron transport chain by manipulation of the NAD+/NADH ratio. | Titov DV, Cracan V, Goodman RP, Peng J, Grabarek Z, Mootha VK | Science (New York, N.Y.) | 27124460 | Science | 2016 Apr 8 |
| XRN 5'→3' exoribonucleases: structure, mechanisms and functions. | Nagarajan VK, Jones CI, Newbury SF, Green PJ | Biochimica et biophysica acta | 23517755 | Biochim Biophys Acta | 2013 Jun-Jul |
| An miRNA Expression Signature for the Human Colonic Stem Cell Niche Distinguishes Malignant from Normal Epithelia. | Viswanathan V, Damle S, Zhang T, Opdenaker L, Modarai S, Accerbi M, Schmidt S, Green P, Galileo D, Palazzo J, Fields J, Haghighat S, Rigoutsos I, Gonye G, Boman BM | Cancer research | 28487386 | Cancer Res | 2017 Jul 15 |
| Identification of SMG6 cleavage sites and a preferred RNA cleavage motif by global analysis of endogenous NMD targets in human cells. | Schmidt SA, Foley PL, Jeong DH, Rymarquis LA, Doyle F, Tenenbaum SA, Belasco JG, Green PJ | Nucleic acids research | 25429978 | Nucleic Acids Res | 2015 Jan |
| Peptide design by optimization on a data-parameterized protein interaction landscape. | Jenson JM, Xue V, Stretz L, Mandal T, Reich LL, Keating AE | Proceedings of the National Academy of Sciences of the United States of America | 30322927 | Proc Natl Acad Sci U S A | 2018 Oct 30 |
| Comparison of the peptide binding preferences of three closely related TRAF paralogs: TRAF2, TRAF3, and TRAF5. | Foight GW, Keating AE | Protein science : a publication of the Protein Society | 26779844 | Protein Sci | 2016 Jul |
| Generating High-Accuracy Peptide-Binding Data in High Throughput with Yeast Surface Display and SORTCERY. | Reich LL, Dutta S, Keating AE | Methods in molecular biology (Clifton, N.J.) | 27094295 | Methods Mol Biol | 2016 |
| SORTCERY-A High-Throughput Method to Affinity Rank Peptide Ligands. | Reich LL, Dutta S, Keating AE | Journal of molecular biology | 25311858 | J Mol Biol | 2015 Jun 5 |
| Combinatorial bZIP dimers display complex DNA-binding specificity landscapes. | Rodríguez-Martínez JA, Reinke AW, Bhimsaria D, Keating AE, Ansari AZ | eLife | 28186491 | Elife | 2017 Feb 10 |
| Measurements and implications of the membrane dipole potential. | Wang L | Annual review of biochemistry | 22443933 | Annu Rev Biochem | 2012 |
| Membrane protein reconstitution for functional and structural studies. | Wang L, Tonggu L | Science China. Life sciences | 25576454 | Sci China Life Sci | 2015 Jan |
| Random Spherically Constrained Single-Particle (RSC) Method to Study Voltage-Gated Ion Channels. | Wang L | Methods in molecular biology (Clifton, N.J.) | 29058198 | Methods Mol Biol | 2018 |
| Effects of N-glycosylation on hyperpolarization-activated cyclic nucleotide-gated (HCN) channels. | Li M, Tonggu L, Tang L, Wang L | The Biochemical journal | 25423599 | Biochem J | 2015 Feb 15 |
| Near-atomic resolution structure of the largest known Ca(2+) channel: ryanodine receptor. | Wang L | Science China. Life sciences | 25614031 | Sci China Life Sci | 2015 Feb |
| Structure of the Human BK Ion Channel in Lipid Environment. | Tonggu L, Wang L | Membranes | 36005673 | Membranes (Basel) | 2022 Jul 31 |
| Cryo-EM sample preparation method for extremely low concentration liposomes. | Tonggu L, Wang L | Ultramicroscopy | 31622807 | Ultramicroscopy | 2020 Jan |
| tRNA is a new target for cleavage by a MazF toxin. | Schifano JM, Cruz JW, Vvedenskaya IO, Edifor R, Ouyang M, Husson RN, Nickels BE, Woychik NA | Nucleic acids research | 26740583 | Nucleic Acids Res | 2016 Feb 18 |
| The mechanism of RNA 5′ capping with NAD+, NADH and desphospho-CoA. | Bird JG, Zhang Y, Tian Y, Panova N, Barvík I, Greene L, Liu M, Buckley B, Krásný L, Lee JK, Kaplan CD, Ebright RH, Nickels BE | Nature | 27383794 | Nature | 2016 Jul 21 |
| Interactions between RNA polymerase and the "core recognition element" counteract pausing. | Vvedenskaya IO, Vahedian-Movahed H, Bird JG, Knoblauch JG, Goldman SR, Zhang Y, Ebright RH, Nickels BE | Science (New York, N.Y.) | 24926020 | Science | 2014 Jun 13 |
| NanoRNAs: a class of small RNAs that can prime transcription initiation in bacteria. | Nickels BE, Dove SL | Journal of molecular biology | 21704045 | J Mol Biol | 2011 Oct 7 |
| NanoRNAs prime transcription initiation in vivo. | Goldman SR, Sharp JS, Vvedenskaya IO, Livny J, Dove SL, Nickels BE | Molecular cell | 21700226 | Mol Cell | 2011 Jun 24 |
| Preparation of cDNA libraries for high-throughput RNA sequencing analysis of RNA 5' ends. | Vvedenskaya IO, Goldman SR, Nickels BE | Methods in molecular biology (Clifton, N.J.) | 25665566 | Methods Mol Biol | 2015 |
| Growth phase-dependent control of transcription start site selection and gene expression by nanoRNAs. | Vvedenskaya IO, Sharp JS, Goldman SR, Kanabar PN, Livny J, Dove SL, Nickels BE | Genes & development | 22751503 | Genes Dev | 2012 Jul 1 |
| Massively Systematic Transcript End Readout, "MASTER": Transcription Start Site Selection, Transcriptional Slippage, and Transcript Yields. | Vvedenskaya IO, Zhang Y, Goldman SR, Valenti A, Visone V, Taylor DM, Ebright RH, Nickels BE | Molecular cell | 26626484 | Mol Cell | 2015 Dec 17 |
| A new way to start: nanoRNA-mediated priming of transcription initiation. | Nickels BE | Transcription | 23117822 | Transcription | 2012 Nov-Dec |
| Ubiquitous promoter-localization of essential virulence regulators in Francisella tularensis. | Ramsey KM, Osborne ML, Vvedenskaya IO, Su C, Nickels BE, Dove SL | PLoS pathogens | 25830507 | PLoS Pathog | 2015 Apr |
| Interactions between RNA polymerase and the core recognition element are a determinant of transcription start site selection. | Vvedenskaya IO, Vahedian-Movahed H, Zhang Y, Taylor DM, Ebright RH, Nickels BE | Proceedings of the National Academy of Sciences of the United States of America | 27162333 | Proc Natl Acad Sci U S A | 2016 May 24 |
| A Conserved Pattern of Primer-Dependent Transcription Initiation in Escherichia coli and Vibrio cholerae Revealed by 5' RNA-seq. | Druzhinin SY, Tran NT, Skalenko KS, Goldman SR, Knoblauch JG, Dove SL, Nickels BE | PLoS genetics | 26131907 | PLoS Genet | 2015 Jul |
| Breaking the diffraction barrier: super-resolution imaging of cells. | Huang B, Babcock H, Zhuang X | Cell | 21168201 | Cell | 2010 Dec 23 |
| Actin, spectrin, and associated proteins form a periodic cytoskeletal structure in axons. | Xu K, Zhong G, Zhuang X | Science (New York, N.Y.) | 23239625 | Science | 2013 Jan 25 |
| A high-density 3D localization algorithm for stochastic optical reconstruction microscopy. | Babcock H, Sigal YM, Zhuang X | Optical nanoscopy | 25431749 | Opt Nanoscopy | 2012 |
| Phosphine quenching of cyanine dyes as a versatile tool for fluorescence microscopy. | Vaughan JC, Dempsey GT, Sun E, Zhuang X | Journal of the American Chemical Society | 23311875 | J Am Chem Soc | 2013 Jan 30 |
| Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. | Zhao ZW, Roy R, Gebhardt JC, Suter DM, Chapman AR, Xie XS | Proceedings of the National Academy of Sciences of the United States of America | 24379392 | Proc Natl Acad Sci U S A | 2014 Jan 14 |
| Chromosome organization by a nucleoid-associated protein in live bacteria. | Wang W, Li GW, Chen C, Xie XS, Zhuang X | Science (New York, N.Y.) | 21903814 | Science | 2011 Sep 9 |
| Coupled, circumferential motions of the cell wall synthesis machinery and MreB filaments in B. subtilis. | Garner EC, Bernard R, Wang W, Zhuang X, Rudner DZ, Mitchison T | Science (New York, N.Y.) | 21636745 | Science | 2011 Jul 8 |
| Fast compressed sensing analysis for super-resolution imaging using L1-homotopy. | Babcock HP, Moffitt JR, Cao Y, Zhuang X | Optics express | 24514370 | Opt Express | 2013 Nov 18 |
| RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. | Chen KH, Boettiger AN, Moffitt JR, Wang S, Zhuang X | Science (New York, N.Y.) | 25858977 | Science | 2015 Apr 24 |
| Ultrabright photoactivatable fluorophores created by reductive caging. | Vaughan JC, Jia S, Zhuang X | Nature methods | 23103881 | Nat Methods | 2012 Dec |
| Spatial organization of chromatin domains and compartments in single chromosomes. | Wang S, Su JH, Beliveau BJ, Bintu B, Moffitt JR, Wu CT, Zhuang X | Science (New York, N.Y.) | 27445307 | Science | 2016 Aug 5 |
| Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. | Wang C, Han B, Zhou R, Zhuang X | Cell | 27153499 | Cell | 2016 May 5 |
| Structurally distinct Ca(2+) signaling domains of sperm flagella orchestrate tyrosine phosphorylation and motility. | Chung JJ, Shim SH, Everley RA, Gygi SP, Zhuang X, Clapham DE | Cell | 24813608 | Cell | 2014 May 8 |
| Characterization and development of photoactivatable fluorescent proteins for single-molecule-based superresolution imaging. | Wang S, Moffitt JR, Dempsey GT, Xie XS, Zhuang X | Proceedings of the National Academy of Sciences of the United States of America | 24912163 | Proc Natl Acad Sci U S A | 2014 Jun 10 |
| Super-resolution fluorescence imaging of telomeres reveals TRF2-dependent T-loop formation. | Doksani Y, Wu JY, de Lange T, Zhuang X | Cell | 24120135 | Cell | 2013 Oct 10 |
| Molecular architecture and assembly principles of Vibrio cholerae biofilms. | Berk V, Fong JC, Dempsey GT, Develioglu ON, Zhuang X, Liphardt J, Yildiz FH, Chu S | Science (New York, N.Y.) | 22798614 | Science | 2012 Jul 13 |
| Isotropic 3D Super-resolution Imaging with a Self-bending Point Spread Function. | Jia S, Vaughan JC, Zhuang X | Nature photonics | 25383090 | Nat Photonics | 2014 |
| Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. | Chen H, Shiroguchi K, Ge H, Xie XS | Molecular systems biology | 25964259 | Mol Syst Biol | 2015 May 11 |
| Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. | Chen H, Shiroguchi K, Ge H, Xie XS | Molecular systems biology | 25583150 | Mol Syst Biol | 2015 Jan 12 |
| Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging. | Sigal YM, Speer CM, Babcock HP, Zhuang X | Cell | 26435106 | Cell | 2015 Oct 8 |
| Spatial organization shapes the turnover of a bacterial transcriptome. | Moffitt JR, Pandey S, Boettiger AN, Wang S, Zhuang X | eLife | 27198188 | Elife | 2016 May 20 |
| Mechanism of transcriptional bursting in bacteria. | Chong S, Chen C, Ge H, Xie XS | Cell | 25036631 | Cell | 2014 Jul 17 |
| ISWI remodelers slide nucleosomes with coordinated multi-base-pair entry steps and single-base-pair exit steps. | Deindl S, Hwang WL, Hota SK, Blosser TR, Prasad P, Bartholomew B, Zhuang X | Cell | 23374341 | Cell | 2013 Jan 31 |
| Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. | Gebhardt JC, Suter DM, Roy R, Zhao ZW, Chapman AR, Basu S, Maniatis T, Xie XS | Nature methods | 23524394 | Nat Methods | 2013 May |
| Statistical deconvolution for superresolution fluorescence microscopy. | Mukamel EA, Babcock H, Zhuang X | Biophysical journal | 22677393 | Biophys J | 2012 May 16 |
| Dual-objective STORM reveals three-dimensional filament organization in the actin cytoskeleton. | Xu K, Babcock HP, Zhuang X | Nature methods | 22231642 | Nat Methods | 2012 Jan 8 |
| Long-range attraction in aqueous colloidal suspensions. | Zhao Q, Coult J, Pollack GH | Proceedings of SPIE--the International Society for Optical Engineering | 22065648 | Proc SPIE Int Soc Opt Eng | 2010 |
| EFFECT OF PARTICLE DIAMETER ON EXCLUSION-ZONE SIZE. | Nhan DT, Pollack GH | International journal of design & nature and ecodynamics : a transdisciplinary journal relating to nature, science and the humanities | 22389653 | Int J Des Nat Ecodyn | 2011 Jun 2 |
| Persisting water droplets on water surfaces. | Klyuzhin IS, Ienna F, Roeder B, Wexler A, Pollack GH | The journal of physical chemistry. B | 20961076 | J Phys Chem B | 2010 Nov 11 |
| High electrical permittivity of ultrapure water at the water-platinum interface. | Musumeci F, Pollack GH | Chemical physics letters | 25258452 | Chem Phys Lett | 2014 Oct 3 |
| On the driver of blood circulation beyond the heart. | Li Z, Pollack GH | PloS one | 37856567 | PLoS One | 2023 |
| Impact of Hydrophilic Surfaces on Interfacial Water Dynamics Probed with NMR Spectroscopy. | Yoo H, Paranji R, Pollack GH | The journal of physical chemistry letters | 22003430 | J Phys Chem Lett | 2011 Feb 18 |
| Light-induced effects on Brownian displacements. | Bhalerao AS, Pollack GH | Journal of biophotonics | 21287689 | J Biophotonics | 2011 Mar |
| WATER, ENERGY AND LIFE: FRESH VIEWS FROM THE WATER'S EDGE. | Pollack GH | International journal of design & nature and ecodynamics : a transdisciplinary journal relating to nature, science and the humanities | 22977460 | Int J Des Nat Ecodyn | 2010 Dec 3 |
| Exclusion-Zone Formation From Discontinuous Nafion Surfaces. | Figueroa XA, Pollack GH | International journal of design & nature and ecodynamics : a transdisciplinary journal relating to nature, science and the humanities | 24826197 | Int J Des Nat Ecodyn | 2011 Nov 30 |
| Charge-based forces at the Nafion-water interface. | Das R, Pollack GH | Langmuir : the ACS journal of surfaces and colloids | 23311934 | Langmuir | 2013 Feb 26 |
| Solute-free interfacial zones in polar liquids. | Chai B, Pollack GH | The journal of physical chemistry. B | 20369860 | J Phys Chem B | 2010 Apr 29 |
| Effect of hyperbaric oxygen conditions on the ordering of interfacial water. | Ypma RE, Pollack GH | Undersea & hyperbaric medicine : journal of the Undersea and Hyperbaric Medical Society, Inc | 26152107 | Undersea Hyperb Med | 2015 May-Jun |
| Effect of Local and General Anesthetics on Interfacial Water. | Kundacina N, Shi M, Pollack GH | PloS one | 27054588 | PLoS One | 2016 |
| UNEXPECTED PRESENCE OF SOLUTE-FREE ZONES AT METAL-WATER INTERFACES. | Chai B, Mahtani AG, Pollack GH | Contemporary materials | 23807904 | Contemp Mater | 2012 |
| Contraction-Induced Changes in Hydrogen Bonding of Muscle Hydration Water. | Yoo H, Nagornyak E, Das R, Wexler AD, Pollack GH | The journal of physical chemistry letters | 24803993 | J Phys Chem Lett | 2014 Mar 20 |
| Unexpected water flow through Nafion-tube punctures. | O'Rourke C, Klyuzhin I, Park JS, Pollack GH | Physical review. E, Statistical, nonlinear, and soft matter physics | 21728645 | Phys Rev E Stat Nonlin Soft Matter Phys | 2011 May |
| Influence of water on the work function of certain metals. | Musumeci F, Pollack GH | Chemical physics letters | 22639466 | Chem Phys Lett | 2012 May 21 |
| Particle Displacement in Aqueous Suspension Arising from Incident Radiant Energy. | Kimura KW, Pollack GH | Langmuir : the ACS journal of surfaces and colloids | 26335979 | Langmuir | 2015 Sep 29 |
| Structures of a Na+-coupled, substrate-bound MATE multidrug transporter. | Lu M, Symersky J, Radchenko M, Koide A, Guo Y, Nie R, Koide S | Proceedings of the National Academy of Sciences of the United States of America | 23341609 | Proc Natl Acad Sci U S A | 2013 Feb 5 |
| Generation of new protein functions by nonhomologous combinations and rearrangements of domains and modules. | Koide S | Current opinion in biotechnology | 19700302 | Curr Opin Biotechnol | 2009 Aug |
| Architecture of the fungal nuclear pore inner ring complex. | Stuwe T, Bley CJ, Thierbach K, Petrovic S, Schilbach S, Mayo DJ, Perriches T, Rundlet EJ, Jeon YE, Collins LN, Huber FM, Lin DH, Paduch M, Koide A, Lu V, Fischer J, Hurt E, Koide S, Kossiakoff AA, Hoelz A | Science (New York, N.Y.) | 26316600 | Science | 2015 Oct 2 |
| Selective Targeting of SH2 Domain-Phosphotyrosine Interactions of Src Family Tyrosine Kinases with Monobodies. | Kükenshöner T, Schmit NE, Bouda E, Sha F, Pojer F, Koide A, Seeliger M, Koide S, Hantschel O | Journal of molecular biology | 28347651 | J Mol Biol | 2017 May 5 |
| Structural and functional dissection of the DH and PH domains of oncogenic Bcr-Abl tyrosine kinase. | Reckel S, Gehin C, Tardivon D, Georgeon S, Kükenshöner T, Löhr F, Koide A, Buchner L, Panjkovich A, Reynaud A, Pinho S, Gerig B, Svergun D, Pojer F, Güntert P, Dötsch V, Koide S, Gavin AC, Hantschel O | Nature communications | 29235475 | Nat Commun | 2017 Dec 13 |
| Allosteric Inhibition of Bcr-Abl Kinase by High Affinity Monobody Inhibitors Directed to the Src Homology 2 (SH2)-Kinase Interface. | Wojcik J, Lamontanara AJ, Grabe G, Koide A, Akin L, Gerig B, Hantschel O, Koide S | The Journal of biological chemistry | 26912659 | J Biol Chem | 2016 Apr 15 |
| Isoform-specific monobody inhibitors of small ubiquitin-related modifiers engineered using structure-guided library design. | Gilbreth RN, Truong K, Madu I, Koide A, Wojcik JB, Li NS, Piccirilli JA, Chen Y, Koide S | Proceedings of the National Academy of Sciences of the United States of America | 21518904 | Proc Natl Acad Sci U S A | 2011 May 10 |
| A peptide tag system for facile purification and single-molecule immobilization. | Huang J, Nagy SS, Koide A, Rock RS, Koide S | Biochemistry | 19928925 | Biochemistry | 2009 Dec 22 |
| Directed network wiring identifies a key protein interaction in embryonic stem cell differentiation. | Yasui N, Findlay GM, Gish GD, Hsiung MS, Huang J, Tucholska M, Taylor L, Smith L, Boldridge WC, Koide A, Pawson T, Koide S | Molecular cell | 24910098 | Mol Cell | 2014 Jun 19 |
| Generation of high-performance binding proteins for peptide motifs by affinity clamping. | Koide S, Huang J | Methods in enzymology | 23422435 | Methods Enzymol | 2013 |
| Teaching an old scaffold new tricks: monobodies constructed using alternative surfaces of the FN3 scaffold. | Koide A, Wojcik J, Gilbreth RN, Hoey RJ, Koide S | Journal of molecular biology | 22198408 | J Mol Biol | 2012 Jan 13 |
| Target-binding proteins based on the 10th human fibronectin type III domain (¹⁰Fn3). | Koide S, Koide A, Lipovšek D | Methods in enzymology | 22230568 | Methods Enzymol | 2012 |
| Inhibition of RAS function through targeting an allosteric regulatory site. | Spencer-Smith R, Koide A, Zhou Y, Eguchi RR, Sha F, Gajwani P, Santana D, Gupta A, Jacobs M, Herrero-Garcia E, Cobbert J, Lavoie H, Smith M, Rajakulendran T, Dowdell E, Okur MN, Dementieva I, Sicheri F, Therrien M, Hancock JF, Ikura M, Koide S, O'Bryan JP | Nature chemical biology | 27820802 | Nat Chem Biol | 2017 Jan |
| Affinity maturation of single-domain antibodies by yeast surface display. | Koide A, Koide S | Methods in molecular biology (Clifton, N.J.) | 22886267 | Methods Mol Biol | 2012 |
| Allosteric modulation of a human protein kinase with monobodies. | Zorba A, Nguyen V, Koide A, Hoemberger M, Zheng Y, Kutter S, Kim C, Koide S, Kern D | Proceedings of the National Academy of Sciences of the United States of America | 31239342 | Proc Natl Acad Sci U S A | 2019 Jul 9 |
| Dissection of the BCR-ABL signaling network using highly specific monobody inhibitors to the SHP2 SH2 domains. | Sha F, Gencer EB, Georgeon S, Koide A, Yasui N, Koide S, Hantschel O | Proceedings of the National Academy of Sciences of the United States of America | 23980151 | Proc Natl Acad Sci U S A | 2013 Sep 10 |
| Rational conversion of affinity reagents into label-free sensors for Peptide motifs by designed allostery. | Huang J, Koide S | ACS chemical biology | 20143785 | ACS Chem Biol | 2010 Mar 19 |
| Structural basis for exquisite specificity of affinity clamps, synthetic binding proteins generated through directed domain-interface evolution. | Huang J, Makabe K, Biancalana M, Koide A, Koide S | Journal of molecular biology | 19646997 | J Mol Biol | 2009 Oct 9 |
| Structural insights for engineering binding proteins based on non-antibody scaffolds. | Gilbreth RN, Koide S | Current opinion in structural biology | 22749196 | Curr Opin Struct Biol | 2012 Aug |
| ETO family protein Mtgr1 mediates Prdm14 functions in stem cell maintenance and primordial germ cell formation. | Nady N, Gupta A, Ma Z, Swigut T, Koide A, Koide S, Wysocka J | eLife | 26523391 | Elife | 2015 Nov 2 |
| Targeting the α4-α5 interface of RAS results in multiple levels of inhibition. | Spencer-Smith R, Li L, Prasad S, Koide A, Koide S, O'Bryan JP | Small GTPases | 28692342 | Small GTPases | 2019 Sep |
| Biological synthesis of circular polypeptides. | Aboye TL, Camarero JA | The Journal of biological chemistry | 22707722 | J Biol Chem | 2012 Aug 3 |
| Recombinant Expression of Cyclotides Using Split Inteins. | Jagadish K, Camarero JA | Methods in molecular biology (Clifton, N.J.) | 27714609 | Methods Mol Biol | 2017 |
| In vivo Evaluation of an Engineered Cyclotide as Specific CXCR4 Imaging Reagent. | Lesniak WG, Aboye T, Chatterjee S, Camarero JA, Nimmagadda S | Chemistry (Weinheim an der Bergstrasse, Germany) | 28771849 | Chemistry | 2017 Oct 17 |
| Cyclotides, a versatile ultrastable micro-protein scaffold for biotechnological applications. | Camarero JA | Bioorganic & medicinal chemistry letters | 29110985 | Bioorg Med Chem Lett | 2017 Dec 1 |
| Backbone dynamics of cyclotide MCoTI-I free and complexed with trypsin. | Puttamadappa SS, Jagadish K, Shekhtman A, Camarero JA | Angewandte Chemie (International ed. in English) | 20715250 | Angew Chem Int Ed Engl | 2010 Sep 17 |
| Photomodulation of protein trans-splicing through backbone photocaging of the DnaE split intein. | Berrade L, Kwon Y, Camarero JA | Chembiochem : a European journal of chemical biology | 20512791 | Chembiochem | 2010 Jul 5 |
| In-cell fluorescence activation and labeling of proteins mediated by FRET-quenched split inteins. | Borra R, Dong D, Elnagar AY, Woldemariam GA, Camarero JA | Journal of the American Chemical Society | 22404648 | J Am Chem Soc | 2012 Apr 11 |
| Biosynthesis and antimicrobial evaluation of backbone-cyclized α-defensins. | Garcia AE, Tai KP, Puttamadappa SS, Shekhtman A, Ouellette AJ, Camarero JA | Biochemistry | 22040603 | Biochemistry | 2011 Dec 6 |
| Intein applications: from protein purification and labeling to metabolic control methods. | Wood DW, Camarero JA | The Journal of biological chemistry | 24700459 | J Biol Chem | 2014 May 23 |
| Legume cyclotides shed light on the genetic origin of knotted circular proteins. | Camarero JA | Proceedings of the National Academy of Sciences of the United States of America | 21653883 | Proc Natl Acad Sci U S A | 2011 Jun 21 |
| "Splicing up" drug discovery. Cell-based expression and screening of genetically-encoded libraries of backbone-cyclized polypeptides. | Sancheti H, Camarero JA | Advanced drug delivery reviews | 19628015 | Adv Drug Deliv Rev | 2009 Sep 30 |
| Cyclotides: Overview and Biotechnological Applications. | Gould A, Camarero JA | Chembiochem : a European journal of chemical biology | 28544675 | Chembiochem | 2017 Jul 18 |
| Protein Chemical Modification Inside Living Cells Using Split Inteins. | Borra R, Camarero JA | Methods in molecular biology (Clifton, N.J.) | 27714613 | Methods Mol Biol | 2017 |
| In-cell production of a genetically-encoded library based on the θ-defensin RTD-1 using a bacterial expression system. | Bi T, Li Y, Shekhtman A, Camarero JA | Bioorganic & medicinal chemistry | 28927803 | Bioorg Med Chem | 2018 Mar 15 |
| Expression of fluorescent cyclotides using protein trans-splicing for easy monitoring of cyclotide-protein interactions. | Jagadish K, Borra R, Lacey V, Majumder S, Shekhtman A, Wang L, Camarero JA | Angewandte Chemie (International ed. in English) | 23322720 | Angew Chem Int Ed Engl | 2013 Mar 11 |
| Design of a MCoTI-Based Cyclotide with Angiotensin (1-7)-Like Activity. | Aboye T, Meeks CJ, Majumder S, Shekhtman A, Rodgers K, Camarero JA | Molecules (Basel, Switzerland) | 26821010 | Molecules | 2016 Jan 26 |
| Cellular uptake of cyclotide MCoTI-I follows multiple endocytic pathways. | Contreras J, Elnagar AY, Hamm-Alvarez SF, Camarero JA | Journal of controlled release : official journal of the Controlled Release Society | 21906641 | J Control Release | 2011 Oct 30 |
| Design of a novel cyclotide-based CXCR4 antagonist with anti-human immunodeficiency virus (HIV)-1 activity. | Aboye TL, Ha H, Majumder S, Christ F, Debyser Z, Shekhtman A, Neamati N, Camarero JA | Journal of medicinal chemistry | 23151033 | J Med Chem | 2012 Dec 13 |
| Protein microarrays: novel developments and applications. | Berrade L, Garcia AE, Camarero JA | Pharmaceutical research | 21116694 | Pharm Res | 2011 Jul |
| Cyclotides, a promising molecular scaffold for peptide-based therapeutics. | Jagadish K, Camarero JA | Biopolymers | 20564025 | Biopolymers | 2010 |
| Efficient one-pot cyclization/folding of Rhesus θ-defensin-1 (RTD-1). | Aboye TL, Li Y, Majumder S, Hao J, Shekhtman A, Camarero JA | Bioorganic & medicinal chemistry letters | 22425570 | Bioorg Med Chem Lett | 2012 Apr 15 |
| Expressed protein ligation: a resourceful tool to study protein structure and function. | Berrade L, Camarero JA | Cellular and molecular life sciences : CMLS | 19685006 | Cell Mol Life Sci | 2009 Dec |
| Biosynthesis and biological screening of a genetically encoded library based on the cyclotide MCoTI-I. | Austin J, Wang W, Puttamadappa S, Shekhtman A, Camarero JA | Chembiochem : a European journal of chemical biology | 19780078 | Chembiochem | 2009 Nov 2 |
| Optimizing the future for biotechnology therapies, the key role of protein engineering. | Camarero JA | Advanced drug delivery reviews | 19735684 | Adv Drug Deliv Rev | 2009 Sep 30 |
| Recombinant expression of backbone-cyclized polypeptides. | Borra R, Camarero JA | Biopolymers | 23893781 | Biopolymers | 2013 Sep |
| In vivo activation of the p53 tumor suppressor pathway by an engineered cyclotide. | Ji Y, Majumder S, Millard M, Borra R, Bi T, Elnagar AY, Neamati N, Shekhtman A, Camarero JA | Journal of the American Chemical Society | 23848581 | J Am Chem Soc | 2013 Aug 7 |
| Changing the topology of protein backbone: the effect of backbone cyclization on the structure and dynamics of a SH3 domain. | Schumann FH, Varadan R, Tayakuniyil PP, Grossman JH, Camarero JA, Fushman D | Frontiers in chemistry | 25905098 | Front Chem | 2015 |
| Full Sequence Amino Acid Scanning of θ-Defensin RTD-1 Yields a Potent Anthrax Lethal Factor Protease Inhibitor. | Li Y, Gould A, Aboye T, Bi T, Breindel L, Shekhtman A, Camarero JA | Journal of medicinal chemistry | 28151653 | J Med Chem | 2017 Mar 9 |
| Chemical and biological production of cyclotides. | Li Y, Bi T, Camarero JA | Advances in botanical research | 27064329 | Adv Bot Res | 2015 |
| In vivo biosynthesis of an Ala-scan library based on the cyclic peptide SFTI-1. | Austin J, Kimura RH, Woo YH, Camarero JA | Amino acids | 19685144 | Amino Acids | 2010 May |
| Biological activities of natural and engineered cyclotides, a novel molecular scaffold for peptide-based therapeutics. | Garcia AE, Camarero JA | Current molecular pharmacology | 20858197 | Curr Mol Pharmacol | 2010 Nov |
| Recombinant production of rhesus θ-defensin-1 (RTD-1) using a bacterial expression system. | Gould A, Li Y, Majumder S, Garcia AE, Carlsson P, Shekhtman A, Camarero JA | Molecular bioSystems | 22327102 | Mol Biosyst | 2012 Apr |
| Cyclotides, a novel ultrastable polypeptide scaffold for drug discovery. | Gould A, Ji Y, Aboye TL, Camarero JA | Current pharmaceutical design | 22204428 | Curr Pharm Des | 2011 Dec |
| Insights into the molecular flexibility of θ-defensins by NMR relaxation analysis. | Conibear AC, Wang CK, Bi T, Rosengren KJ, Camarero JA, Craik DJ | The journal of physical chemistry. B | 25375365 | J Phys Chem B | 2014 Dec 11 |
| Rapid parallel synthesis of bioactive folded cyclotides by using a tea-bag approach. | Aboye T, Kuang Y, Neamati N, Camarero JA | Chembiochem : a European journal of chemical biology | 25663016 | Chembiochem | 2015 Mar 23 |
| Recombinant Expression and Phenotypic Screening of a Bioactive Cyclotide Against α-Synuclein-Induced Cytotoxicity in Baker's Yeast. | Jagadish K, Gould A, Borra R, Majumder S, Mushtaq Z, Shekhtman A, Camarero JA | Angewandte Chemie (International ed. in English) | 26096948 | Angew Chem Int Ed Engl | 2015 Jul 13 |
| Efficient recombinant expression of SFTI-1 in bacterial cells using intein-mediated protein trans-splicing. | Li Y, Aboye T, Breindel L, Shekhtman A, Camarero JA | Biopolymers | 27178003 | Biopolymers | 2016 Nov |
| Self-assembled nanoplatform for targeted delivery of chemotherapy agents via affinity-regulated molecular interactions. | Park S, Kang S, Veach AJ, Vedvyas Y, Zarnegar R, Kim JY, Jin MM | Biomaterials | 20667589 | Biomaterials | 2010 Oct |
| Novel strategy for selection of monoclonal antibodies against highly conserved antigens: phage library panning against ephrin-B2 displayed on yeast. | Gu X, Vedvyas Y, Chen X, Kaushik T, Hwang CI, Hu X, Nikitin AY, Jin MM | PloS one | 22292016 | PLoS One | 2012 |
| Quantitative assessment of RNA-protein interactions with high-throughput sequencing-RNA affinity profiling. | Ozer A, Tome JM, Friedman RC, Gheba D, Schroth GP, Lis JT | Nature protocols | 26182240 | Nat Protoc | 2015 Aug |
| High-throughput binding characterization of RNA aptamer selections using a microplate-based multiplex microcolumn device. | Szeto K, Reinholt SJ, Duarte FM, Pagano JM, Ozer A, Yao L, Lis JT, Craighead HG | Analytical and bioanalytical chemistry | 24553662 | Anal Bioanal Chem | 2014 Apr |
| RAPID-SELEX for RNA aptamers. | Szeto K, Latulippe DR, Ozer A, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG | PloS one | 24376564 | PLoS One | 2013 |
| Comprehensive analysis of RNA-protein interactions by high-throughput sequencing-RNA affinity profiling. | Tome JM, Ozer A, Pagano JM, Gheba D, Schroth GP, Lis JT | Nature methods | 24809628 | Nat Methods | 2014 Jun |
| Cell surface assembly of HIV gp41 six-helix bundles for facile, quantitative measurements of hetero-oligomeric interactions. | Hu X, Saha P, Chen X, Kim D, Devarasetty M, Varadarajan R, Jin MM | Journal of the American Chemical Society | 22888993 | J Am Chem Soc | 2012 Sep 12 |
| Inflamed leukocyte-mimetic nanoparticles for molecular imaging of inflammation. | Chen X, Wong R, Khalidov I, Wang AY, Leelawattanachai J, Wang Y, Jin MM | Biomaterials | 21783245 | Biomaterials | 2011 Oct |
| New Technologies Provide Quantum Changes in the Scale, Speed, and Success of SELEX Methods and Aptamer Characterization. | Ozer A, Pagano JM, Lis JT | Molecular therapy. Nucleic acids | 25093707 | Mol Ther Nucleic Acids | 2014 Aug 5 |
| Multiplexed microcolumn-based process for efficient selection of RNA aptamers. | Latulippe DR, Szeto K, Ozer A, Duarte FM, Kelly CV, Pagano JM, White BS, Shalloway D, Lis JT, Craighead HG | Analytical chemistry | 23398198 | Anal Chem | 2013 Mar 19 |
| Density-dependent cooperative non-specific binding in solid-phase SELEX affinity selection. | Ozer A, White BS, Lis JT, Shalloway D | Nucleic acids research | 23737446 | Nucleic Acids Res | 2013 Aug |
| Highly Multiplexed RNA Aptamer Selection using a Microplate-based Microcolumn Device. | Reinholt SJ, Ozer A, Lis JT, Craighead HG | Scientific reports | 27432610 | Sci Rep | 2016 Jul 19 |
| Discovering aptamers by cell-SELEX against human soluble growth factors ectopically expressed on yeast cell surface. | Meng HW, Pagano JM, White BS, Toyoda Y, Min IM, Craighead HG, Shalloway D, Lis JT, Xiao K, Jin MM | PloS one | 24675636 | PLoS One | 2014 |
| Defining NELF-E RNA binding in HIV-1 and promoter-proximal pause regions. | Pagano JM, Kwak H, Waters CT, Sprouse RO, White BS, Ozer A, Szeto K, Shalloway D, Craighead HG, Lis JT | PLoS genetics | 24453987 | PLoS Genet | 2014 Jan |
| Structural basis for conformational switching and GTP loading of the large G protein atlastin. | Byrnes LJ, Singh A, Szeto K, Benvin NM, O'Donnell JP, Zipfel WR, Sondermann H | The EMBO journal | 23334294 | EMBO J | 2013 Feb 6 |
| Myosin II controls cellular branching morphogenesis and migration in three dimensions by minimizing cell-surface curvature. | Elliott H, Fischer RS, Myers KA, Desai RA, Gao L, Chen CS, Adelstein RS, Waterman CM, Danuser G | Nature cell biology | 25621949 | Nat Cell Biol | 2015 Feb |
| FRET binding antenna reports spatiotemporal dynamics of GDI-Cdc42 GTPase interactions. | Hodgson L, Spiering D, Sabouri-Ghomi M, Dagliyan O, DerMardirossian C, Danuser G, Hahn KM | Nature chemical biology | 27501396 | Nat Chem Biol | 2016 Oct |
| Fluctuation-based imaging of nuclear Rac1 activation by protein oligomerisation. | Hinde E, Yokomori K, Gaus K, Hahn KM, Gratton E | Scientific reports | 24573109 | Sci Rep | 2014 Feb 27 |
| What's wrong with correlative experiments? | Vilela M, Danuser G | Nature cell biology | 21892139 | Nat Cell Biol | 2011 Sep 2 |
| Millisecond spatiotemporal dynamics of FRET biosensors by the pair correlation function and the phasor approach to FLIM. | Hinde E, Digman MA, Hahn KM, Gratton E | Proceedings of the National Academy of Sciences of the United States of America | 23248275 | Proc Natl Acad Sci U S A | 2013 Jan 2 |
| Knowledge-based design of a biosensor to quantify localized ERK activation in living cells. | Kummer L, Hsu CW, Dagliyan O, MacNevin C, Kaufholz M, Zimmermann B, Dokholyan NV, Hahn KM, Plückthun A | Chemistry & biology | 23790495 | Chem Biol | 2013 Jun 20 |
| Delivery of membrane impermeable cargo into CHO cells by peptide nanoparticles targeted by a protein corona. | Dittrich C, Burckhardt CJ, Danuser G | Biomaterials | 22226586 | Biomaterials | 2012 Mar |
| A RhoC biosensor reveals differences in the activation kinetics of RhoA and RhoC in migrating cells. | Zawistowski JS, Sabouri-Ghomi M, Danuser G, Hahn KM, Hodgson L | PloS one | 24224016 | PLoS One | 2013 |
| LOVTRAP: an optogenetic system for photoinduced protein dissociation. | Wang H, Vilela M, Winkler A, Tarnawski M, Schlichting I, Yumerefendi H, Kuhlman B, Liu R, Danuser G, Hahn KM | Nature methods | 27427858 | Nat Methods | 2016 Sep |
| Fluctuation analysis of activity biosensor images for the study of information flow in signaling pathways. | Vilela M, Halidi N, Besson S, Elliott H, Hahn K, Tytell J, Danuser G | Methods in enzymology | 23280114 | Methods Enzymol | 2013 |
| Manipulation of endogenous kinase activity in living cells using photoswitchable inhibitory peptides. | Yi JJ, Wang H, Vilela M, Danuser G, Hahn KM | ACS synthetic biology | 24905630 | ACS Synth Biol | 2014 Nov 21 |
| Imaging the coordination of multiple signalling activities in living cells. | Welch CM, Elliott H, Danuser G, Hahn KM | Nature reviews. Molecular cell biology | 22016058 | Nat Rev Mol Cell Biol | 2011 Oct 21 |
| Humanin, a cytoprotective peptide, is expressed in carotid atherosclerotic [corrected] plaques in humans. | Zacharias DG, Kim SG, Massat AE, Bachar AR, Oh YK, Herrmann J, Rodriguez-Porcel M, Cohen P, Lerman LO, Lerman A | PloS one | 22328926 | PLoS One | 2012 |
| Naturally occurring mitochondrial-derived peptides are age-dependent regulators of apoptosis, insulin sensitivity, and inflammatory markers. | Cobb LJ, Lee C, Xiao J, Yen K, Wong RG, Nakamura HK, Mehta HH, Gao Q, Ashur C, Huffman DM, Wan J, Muzumdar R, Barzilai N, Cohen P | Aging | 27070352 | Aging (Albany NY) | 2016 Apr |
| International collaboration: promises and challenges. | Widmer RJ, Widmer JM, Lerman A | Rambam Maimonides medical journal | 25973264 | Rambam Maimonides Med J | 2015 Apr |
| Pharmacokinetics and tissue distribution of humanin and its analogues in male rodents. | Chin YP, Keni J, Wan J, Mehta H, Anene F, Jia Y, Lue YH, Swerdloff R, Cobb LJ, Wang C, Cohen P | Endocrinology | 23836030 | Endocrinology | 2013 Oct |
| Humanin: a harbinger of mitochondrial-derived peptides? | Lee C, Yen K, Cohen P | Trends in endocrinology and metabolism: TEM | 23402768 | Trends Endocrinol Metab | 2013 May |
| The emerging role of the mitochondrial-derived peptide humanin in stress resistance. | Yen K, Lee C, Mehta H, Cohen P | Journal of molecular endocrinology | 23239898 | J Mol Endocrinol | 2013 Feb |
| The cytoprotective peptide humanin is induced and neutralizes Bax after pro-apoptotic stress in the rat testis. | Jia Y, Lue YH, Swerdloff R, Lee KW, Cobb LJ, Cohen P, Wang C | Andrology | 23686888 | Andrology | 2013 Jul |
| Effects of Sex, Strain, and Energy Intake on Hallmarks of Aging in Mice. | Mitchell SJ, Madrigal-Matute J, Scheibye-Knudsen M, Fang E, Aon M, González-Reyes JA, Cortassa S, Kaushik S, Gonzalez-Freire M, Patel B, Wahl D, Ali A, Calvo-Rubio M, Burón MI, Guiterrez V, Ward TM, Palacios HH, Cai H, Frederick DW, Hine C, Broeskamp F, Habering L, Dawson J, Beasley TM, Wan J, Ikeno Y, Hubbard G, Becker KG, Zhang Y, Bohr VA, Longo DL, Navas P, Ferrucci L, Sinclair DA, Cohen P, Egan JM, Mitchell JR, Baur JA, Allison DB, Anson RM, Villalba JM, Madeo F, Cuervo AM, Pearson KJ, Ingram DK, Bernier M, de Cabo R | Cell metabolism | 27304509 | Cell Metab | 2016 Jun 14 |
| The Mitochondrial-Derived Peptide Humanin Protects RPE Cells From Oxidative Stress, Senescence, and Mitochondrial Dysfunction. | Sreekumar PG, Ishikawa K, Spee C, Mehta HH, Wan J, Yen K, Cohen P, Kannan R, Hinton DR | Investigative ophthalmology & visual science | 26990160 | Invest Ophthalmol Vis Sci | 2016 Mar |
| Humanin preserves endothelial function and prevents atherosclerotic plaque progression in hypercholesterolemic ApoE deficient mice. | Oh YK, Bachar AR, Zacharias DG, Kim SG, Wan J, Cobb LJ, Lerman LO, Cohen P, Lerman A | Atherosclerosis | 21763658 | Atherosclerosis | 2011 Nov |
| IGF-I regulates the age-dependent signaling peptide humanin. | Lee C, Wan J, Miyazaki B, Fang Y, Guevara-Aguirre J, Yen K, Longo V, Bartke A, Cohen P | Aging cell | 25040290 | Aging Cell | 2014 Oct |
| Subcellular Fractionation for ERK Activation Upon Mitochondrial-derived Peptide Treatment. | Kim SJ, Xiao J, Cohen P, Yen K | Journal of visualized experiments : JoVE | 28994791 | J Vis Exp | 2017 Sep 25 |
| Humanin prevents intra-renal microvascular remodeling and inflammation in hypercholesterolemic ApoE deficient mice. | Zhang X, Urbieta-Caceres VH, Eirin A, Bell CC, Crane JA, Tang H, Jordan KL, Oh YK, Zhu XY, Korsmo MJ, Bachar AR, Cohen P, Lerman A, Lerman LO | Life sciences | 22820173 | Life Sci | 2012 Sep 4 |
| Humanin: Functional Interfaces with IGF-I. | Xiao J, Kim SJ, Cohen P, Yen K | Growth hormone & IGF research : official journal of the Growth Hormone Research Society and the International IGF Research Society | 27082450 | Growth Horm IGF Res | 2016 Aug |
| MOTS-c: A novel mitochondrial-derived peptide regulating muscle and fat metabolism. | Lee C, Kim KH, Cohen P | Free radical biology & medicine | 27216708 | Free Radic Biol Med | 2016 Nov |
| The association between circulating microRNA levels and coronary endothelial function. | Widmer RJ, Chung WY, Herrmann J, Jordan KL, Lerman LO, Lerman A | PloS one | 25310838 | PLoS One | 2014 |
| The Potent Humanin Analogue (HNG) Protects Germ Cells and Leucocytes While Enhancing Chemotherapy-Induced Suppression of Cancer Metastases in Male Mice. | Lue Y, Swerdloff R, Wan J, Xiao J, French S, Atienza V, Canela V, Bruhn KW, Stone B, Jia Y, Cohen P, Wang C | Endocrinology | 26384090 | Endocrinology | 2015 Dec |
| New role for the mitochondrial peptide humanin: protective agent against chemotherapy-induced side effects. | Cohen P | Journal of the National Cancer Institute | 24586106 | J Natl Cancer Inst | 2014 Mar |
| Circulating humanin levels are associated with preserved coronary endothelial function. | Widmer RJ, Flammer AJ, Herrmann J, Rodriguez-Porcel M, Wan J, Cohen P, Lerman LO, Lerman A | American journal of physiology. Heart and circulatory physiology | 23220334 | Am J Physiol Heart Circ Physiol | 2013 Feb 1 |
| Central insulin-like growth factor-1 (IGF-1) restores whole-body insulin action in a model of age-related insulin resistance and IGF-1 decline. | Huffman DM, Farias Quipildor G, Mao K, Zhang X, Wan J, Apontes P, Cohen P, Barzilai N | Aging cell | 26534869 | Aging Cell | 2016 Feb |
| The mitochondrial-derived peptide MOTS-c promotes metabolic homeostasis and reduces obesity and insulin resistance. | Lee C, Zeng J, Drew BG, Sallam T, Martin-Montalvo A, Wan J, Kim SJ, Mehta H, Hevener AL, de Cabo R, Cohen P | Cell metabolism | 25738459 | Cell Metab | 2015 Mar 3 |
| Late-life targeting of the IGF-1 receptor improves healthspan and lifespan in female mice. | Mao K, Quipildor GF, Tabrizian T, Novaj A, Guan F, Walters RO, Delahaye F, Hubbard GB, Ikeno Y, Ejima K, Li P, Allison DB, Salimi-Moosavi H, Beltran PJ, Cohen P, Barzilai N, Huffman DM | Nature communications | 29921922 | Nat Commun | 2018 Jun 19 |
| The effects of humanin and its analogues on male germ cell apoptosis induced by chemotherapeutic drugs. | Jia Y, Ohanyan A, Lue YH, Swerdloff RS, Liu PY, Cohen P, Wang C | Apoptosis : an international journal on programmed cell death | 25666707 | Apoptosis | 2015 Apr |
| Rat Humanin is encoded and translated in mitochondria and is localized to the mitochondrial compartment where it regulates ROS production. | Paharkova V, Alvarez G, Nakamura H, Cohen P, Lee KW | Molecular and cellular endocrinology | 26116236 | Mol Cell Endocrinol | 2015 Sep 15 |
| The mitochondrial-derived peptide humanin activates the ERK1/2, AKT, and STAT3 signaling pathways and has age-dependent signaling differences in the hippocampus. | Kim SJ, Guerrero N, Wassef G, Xiao J, Mehta HH, Cohen P, Yen K | Oncotarget | 27384491 | Oncotarget | 2016 Jul 26 |
| Requirement of argininosuccinate lyase for systemic nitric oxide production. | Erez A, Nagamani SC, Shchelochkov OA, Premkumar MH, Campeau PM, Chen Y, Garg HK, Li L, Mian A, Bertin TK, Black JO, Zeng H, Tang Y, Reddy AK, Summar M, O'Brien WE, Harrison DG, Mitch WE, Marini JC, Aschner JL, Bryan NS, Lee B | Nature medicine | 22081021 | Nat Med | 2011 Nov 13 |
| Argininosuccinate lyase deficiency-argininosuccinic aciduria and beyond. | Erez A, Nagamani SC, Lee B | American journal of medical genetics. Part C, Seminars in medical genetics | 21312326 | Am J Med Genet C Semin Med Genet | 2011 Feb 15 |
| Argininosuccinate lyase deficiency. | Nagamani SC, Erez A, Lee B | Genetics in medicine : official journal of the American College of Medical Genetics | 22241104 | Genet Med | 2012 May |
| Concentration- and stage-specific effects of nitrite on colon cancer cell lines. | Jiang H, Tang Y, Garg HK, Parthasarathy DK, Torregrossa AC, Hord NG, Bryan NS | Nitric oxide : biology and chemistry | 22504070 | Nitric Oxide | 2012 May 15 |
| Systemic hypertension in two patients with ASL deficiency: a result of nitric oxide deficiency? | Brunetti-Pierri N, Erez A, Shchelochkov O, Craigen W, Lee B | Molecular genetics and metabolism | 19592285 | Mol Genet Metab | 2009 Sep-Oct |
| Optimizing therapy for argininosuccinic aciduria. | Nagamani SC, Lee B, Erez A | Molecular genetics and metabolism | 22841516 | Mol Genet Metab | 2012 Sep |
| Insights into the pathogenesis and treatment of cancer from inborn errors of metabolism. | Erez A, Shchelochkov OA, Plon SE, Scaglia F, Lee B | American journal of human genetics | 21473982 | Am J Hum Genet | 2011 Apr 8 |
| Argininosuccinate lyase in enterocytes protects from development of necrotizing enterocolitis. | Premkumar MH, Sule G, Nagamani SC, Chakkalakal S, Nordin A, Jain M, Ruan MZ, Bertin T, Dawson B, Zhang J, Schady D, Bryan NS, Campeau PM, Erez A, Lee B | American journal of physiology. Gastrointestinal and liver physiology | 24904080 | Am J Physiol Gastrointest Liver Physiol | 2014 Aug 1 |
| A randomized controlled trial to evaluate the effects of high-dose versus low-dose of arginine therapy on hepatic function tests in argininosuccinic aciduria. | Nagamani SC, Shchelochkov OA, Mullins MA, Carter S, Lanpher BC, Sun Q, Kleppe S, Erez A, O'Brian Smith E, Marini JC, Members of the Urea Cycle Disorders Consortium, Lee B | Molecular genetics and metabolism | 23040521 | Mol Genet Metab | 2012 Nov |
| Nitric-oxide supplementation for treatment of long-term complications in argininosuccinic aciduria. | Nagamani SC, Campeau PM, Shchelochkov OA, Premkumar MH, Guse K, Brunetti-Pierri N, Chen Y, Sun Q, Tang Y, Palmer D, Reddy AK, Li L, Slesnick TC, Feig DI, Caudle S, Harrison D, Salviati L, Marini JC, Bryan NS, Erez A, Lee B | American journal of human genetics | 22541557 | Am J Hum Genet | 2012 May 4 |
| The mitochondrial fatty acid synthesis (mtFASII) pathway is capable of mediating nuclear-mitochondrial cross talk through the PPAR system of transcriptional activation. | Parl A, Mitchell SL, Clay HB, Reiss S, Li Z, Murdock DG | Biochemical and biophysical research communications | 24161390 | Biochem Biophys Res Commun | 2013 Nov 15 |
| Altering the Mitochondrial Fatty Acid Synthesis (mtFASII) Pathway Modulates Cellular Metabolic States and Bioactive Lipid Profiles as Revealed by Metabolomic Profiling. | Clay HB, Parl AK, Mitchell SL, Singh L, Bell LN, Murdock DG | PloS one | 26963735 | PLoS One | 2016 |
| Origins of cellular geometry. | Marshall WF | BMC biology | 21880160 | BMC Biol | 2011 Aug 31 |
| Visualizing cytoplasmic flow during single-cell wound healing in Stentor coeruleus. | Slabodnick M, Prevo B, Gross P, Sheung J, Marshall W | Journal of visualized experiments : JoVE | 24378633 | J Vis Exp | 2013 Dec 19 |
| The kinase regulator mob1 acts as a patterning protein for stentor morphogenesis. | Slabodnick MM, Ruby JG, Dunn JG, Feldman JL, DeRisi JL, Marshall WF | PLoS biology | 24823688 | PLoS Biol | 2014 May |
| The Macronuclear Genome of Stentor coeruleus Reveals Tiny Introns in a Giant Cell. | Slabodnick MM, Ruby JG, Reiff SB, Swart EC, Gosai S, Prabakaran S, Witkowska E, Larue GE, Fisher S, Freeman RM Jr, Gunawardena J, Chu W, Stover NA, Gregory BD, Nowacki M, Derisi J, Roy SW, Marshall WF, Sood P | Current biology : CB | 28190732 | Curr Biol | 2017 Feb 20 |
| Phenotypic Screening for Friedreich Ataxia Using Random shRNA Selection. | Cotticelli MG, Acquaviva F, Xia S, Kaur A, Wang Y, Wilson RB | Journal of biomolecular screening | 26286937 | J Biomol Screen | 2015 Oct |
| Introduction of mismatches in a random shRNA-encoding library improves potency for phenotypic selection. | Wang Y, Speier JS, Engram-Pearl J, Wilson RB | PloS one | 24498319 | PLoS One | 2014 |
| Prolyl hydroxylase domain protein 2 (PHD2) binds a Pro-Xaa-Leu-Glu motif, linking it to the heat shock protein 90 pathway. | Song D, Li LS, Heaton-Johnson KJ, Arsenault PR, Master SR, Lee FS | The Journal of biological chemistry | 23413029 | J Biol Chem | 2013 Apr 5 |
| Human high-altitude adaptation: forward genetics meets the HIF pathway. | Bigham AW, Lee FS | Genes & development | 25319824 | Genes Dev | 2014 Oct 15 |
| Defective Tibetan PHD2 binding to p23 links high altitude adaption to altered oxygen sensing. | Song D, Li LS, Arsenault PR, Tan Q, Bigham AW, Heaton-Johnson KJ, Master SR, Lee FS | The Journal of biological chemistry | 24711448 | J Biol Chem | 2014 May 23 |
| Identification of prolyl hydroxylation modifications in mammalian cell proteins. | Arsenault PR, Heaton-Johnson KJ, Li LS, Song D, Ferreira VS, Patel N, Master SR, Lee FS | Proteomics | 25421965 | Proteomics | 2015 Apr |
| Distinct BimBH3 (BimSAHB) stapled peptides for structural and cellular studies. | Bird GH, Gavathiotis E, LaBelle JL, Katz SG, Walensky LD | ACS chemical biology | 24358963 | ACS Chem Biol | 2014 Mar 21 |
| Targeted disruption of the EZH2-EED complex inhibits EZH2-dependent cancer. | Kim W, Bird GH, Neff T, Guo G, Kerenyi MA, Walensky LD, Orkin SH | Nature chemical biology | 23974116 | Nat Chem Biol | 2013 Oct |
| Photoreactive stapled peptides to identify and characterize BCL-2 family interaction sites by mass spectrometry. | Lee S, Braun CR, Bird GH, Walensky LD | Methods in enzymology | 24974285 | Methods Enzymol | 2014 |
| Photoreactive stapled BH3 peptides to dissect the BCL-2 family interactome. | Braun CR, Mintseris J, Gavathiotis E, Bird GH, Gygi SP, Walensky LD | Chemistry & biology | 21168768 | Chem Biol | 2010 Dec 22 |
| Inhibition of Pro-apoptotic BAX by a noncanonical interaction mechanism. | Barclay LA, Wales TE, Garner TP, Wachter F, Lee S, Guerra RM, Stewart ML, Braun CR, Bird GH, Gavathiotis E, Engen JR, Walensky LD | Molecular cell | 25684204 | Mol Cell | 2015 Mar 5 |
| Protein-protein interactions: A PUMA mechanism unfolds. | Walensky LD | Nature chemical biology | 23416398 | Nat Chem Biol | 2013 Mar |
| Direct BAKtivation. | Walensky LD | Nature structural & molecular biology | 23649360 | Nat Struct Mol Biol | 2013 May |
| Direct activation of full-length proapoptotic BAK. | Leshchiner ES, Braun CR, Bird GH, Walensky LD | Proceedings of the National Academy of Sciences of the United States of America | 23404709 | Proc Natl Acad Sci U S A | 2013 Mar 12 |
| Playing fullBAK. | Walensky LD | Cell cycle (Georgetown, Tex.) | 23588072 | Cell Cycle | 2013 May 1 |
| Chemical synthesis of hydrocarbon-stapled peptides for protein interaction research and therapeutic targeting. | Bird GH, Crannell WC, Walensky LD | Current protocols in chemical biology | 23801563 | Curr Protoc Chem Biol | 2011 Sep 1 |
| Multimodal interaction with BCL-2 family proteins underlies the proapoptotic activity of PUMA BH3. | Edwards AL, Gavathiotis E, LaBelle JL, Braun CR, Opoku-Nsiah KA, Bird GH, Walensky LD | Chemistry & biology | 23890007 | Chem Biol | 2013 Jul 25 |
| A phospho-BAD BH3 helix activates glucokinase by a mechanism distinct from that of allosteric activators. | Szlyk B, Braun CR, Ljubicic S, Patton E, Bird GH, Osundiji MA, Matschinsky FM, Walensky LD, Danial NN | Nature structural & molecular biology | 24317490 | Nat Struct Mol Biol | 2014 Jan |
| Direct inhibition of oncogenic KRAS by hydrocarbon-stapled SOS1 helices. | Leshchiner ES, Parkhitko A, Bird GH, Luccarelli J, Bellairs JA, Escudero S, Opoku-Nsiah K, Godes M, Perrimon N, Walensky LD | Proceedings of the National Academy of Sciences of the United States of America | 25624485 | Proc Natl Acad Sci U S A | 2015 Feb 10 |
| Phospho-BAD BH3 mimicry protects β cells and restores functional β cell mass in diabetes. | Ljubicic S, Polak K, Fu A, Wiwczar J, Szlyk B, Chang Y, Alvarez-Perez JC, Bird GH, Walensky LD, Garcia-Ocaña A, Danial NN | Cell reports | 25640178 | Cell Rep | 2015 Feb 3 |
| Strategies for discovering and derisking covalent, irreversible enzyme inhibitors. | Johnson DS, Weerapana E, Cravatt BF | Future medicinal chemistry | 20640225 | Future Med Chem | 2010 Jun |
| Fully functionalized small-molecule probes for integrated phenotypic screening and target identification. | Cisar JS, Cravatt BF | Journal of the American Chemical Society | 22667687 | J Am Chem Soc | 2012 Jun 27 |
| Acyl hydrazides as peptoid sub-monomers. | Sarma BK, Yousufuddin M, Kodadek T | Chemical communications (Cambridge, England) | 21892506 | Chem Commun (Camb) | 2011 Oct 14 |
| The pharmacological landscape and therapeutic potential of serine hydrolases. | Bachovchin DA, Cravatt BF | Nature reviews. Drug discovery | 22212679 | Nat Rev Drug Discov | 2012 Jan 3 |
| A liquid array platform for the multiplexed analysis of synthetic molecule-protein interactions. | Doran TM, Kodadek T | ACS chemical biology | 24245981 | ACS Chem Biol | 2014 Feb 21 |
| Enzyme inhibitor discovery by activity-based protein profiling. | Niphakis MJ, Cravatt BF | Annual review of biochemistry | 24905785 | Annu Rev Biochem | 2014 |
| Identification of selective covalent inhibitors of platelet activating factor acetylhydrolase 1B2 from the screening of an oxadiazolone-capped peptoid-azapeptoid hybrid library. | Sarma BK, Liu X, Kodadek T | Bioorganic & medicinal chemistry | 27160052 | Bioorg Med Chem | 2016 Sep 1 |
| Incorporation of heterocycles into the backbone of peptoids to generate diverse peptoid-inspired one bead one compound libraries. | Aditya A, Kodadek T | ACS combinatorial science | 22320121 | ACS Comb Sci | 2012 Mar 12 |
| Superfamily-wide portrait of serine hydrolase inhibition achieved by library-versus-library screening. | Bachovchin DA, Ji T, Li W, Simon GM, Blankman JL, Adibekian A, Hoover H, Niessen S, Cravatt BF | Proceedings of the National Academy of Sciences of the United States of America | 21084632 | Proc Natl Acad Sci U S A | 2010 Dec 7 |
| Quantitative reactivity profiling predicts functional cysteines in proteomes. | Weerapana E, Wang C, Simon GM, Richter F, Khare S, Dillon MB, Bachovchin DA, Mowen K, Baker D, Cravatt BF | Nature | 21085121 | Nature | 2010 Dec 9 |
| A Cleavable Scaffold Strategy for the Synthesis of One-Bead One-Compound Cyclic Peptoid Libraries That Can Be Sequenced By Tandem Mass Spectrometry. | Simpson LS, Kodadek T | Tetrahedron letters | 22736872 | Tetrahedron Lett | 2012 May 2 |
| Click-generated triazole ureas as ultrapotent in vivo-active serine hydrolase inhibitors. | Adibekian A, Martin BR, Wang C, Hsu KL, Bachovchin DA, Niessen S, Hoover H, Cravatt BF | Nature chemical biology | 21572424 | Nat Chem Biol | 2011 May 15 |
| Competitive activity-based protein profiling identifies aza-β-lactams as a versatile chemotype for serine hydrolase inhibition. | Zuhl AM, Mohr JT, Bachovchin DA, Niessen S, Hsu KL, Berlin JM, Dochnahl M, López-Alberca MP, Fu GC, Cravatt BF | Journal of the American Chemical Society | 22400490 | J Am Chem Soc | 2012 Mar 21 |
| Proteome-wide covalent ligand discovery in native biological systems. | Backus KM, Correia BE, Lum KM, Forli S, Horning BD, González-Páez GE, Chatterjee S, Lanning BR, Teijaro JR, Olson AJ, Wolan DW, Cravatt BF | Nature | 27309814 | Nature | 2016 Jun 23 |
| Rapid development of a potent photo-triggered inhibitor of the serine hydrolase RBBP9. | Liu X, Dix M, Speers AE, Bachovchin DA, Zuhl AM, Cravatt BF, Kodadek TJ | Chembiochem : a European journal of chemical biology | 22907802 | Chembiochem | 2012 Sep 24 |
| Solid phase synthesis of 1,3,4-oxadiazin-5 (6R)-one and 1,3,4-oxadiazol-2-one scaffolds from acyl hydrazides. | Sarma BK, Liu X, Wu H, Gao Y, Kodadek T | Organic & biomolecular chemistry | 25354697 | Org Biomol Chem | 2015 Jan 7 |
| Epistatic relationships reveal the functional organization of yeast transcription factors. | Zheng J, Benschop JJ, Shales M, Kemmeren P, Greenblatt J, Cagney G, Holstege F, Li H, Krogan NJ | Molecular systems biology | 20959818 | Mol Syst Biol | 2010 Oct 5 |
| Identification of small activating RNAs that enhance endogenous OCT4 expression in human mesenchymal stem cells. | Wang J, Huang V, Ye L, Bárcena A, Lin G, Lue TF, Li LC | Stem cells and development | 25232932 | Stem Cells Dev | 2015 Feb 1 |
| Demystifying the nuclear function of Argonaute proteins. | Huang V, Li LC | RNA biology | 24384674 | RNA Biol | 2014 |
| Chromatin remodeling by the small RNA machinery in mammalian cells. | Li LC | Epigenetics | 24149777 | Epigenetics | 2014 Jan |
| Induction of NANOG expression by targeting promoter sequence with small activating RNA antagonizes retinoic acid-induced differentiation. | Wang X, Wang J, Huang V, Place RF, Li LC | The Biochemical journal | 22339500 | Biochem J | 2012 May 1 |
| saRNA-guided Ago2 targets the RITA complex to promoters to stimulate transcription. | Portnoy V, Lin SH, Li KH, Burlingame A, Hu ZH, Li H, Li LC | Cell research | 26902284 | Cell Res | 2016 Mar |
| Targeted induction of endogenous NKX3-1 by small activating RNA inhibits prostate tumor growth. | Ren S, Kang MR, Wang J, Huang V, Place RF, Sun Y, Li LC | The Prostate | 23836514 | Prostate | 2013 Oct |
| Targeted p21WAF1/CIP1 activation by RNAa inhibits hepatocellular carcinoma cells. | Kosaka M, Kang MR, Yang G, Li LC | Nucleic acid therapeutics | 22909100 | Nucleic Acid Ther | 2012 Oct |
| Small RNA and transcriptional upregulation. | Portnoy V, Huang V, Place RF, Li LC | Wiley interdisciplinary reviews. RNA | 21823233 | Wiley Interdiscip Rev RNA | 2011 Sep-Oct |
| Adaptation and clonal selection models of castration-resistant prostate cancer: current perspective. | Ahmed M, Li LC | International journal of urology : official journal of the Japanese Urological Association | 23163774 | Int J Urol | 2013 Apr |
| Formulation of Small Activating RNA Into Lipidoid Nanoparticles Inhibits Xenograft Prostate Tumor Growth by Inducing p21 Expression. | Place RF, Wang J, Noonan EJ, Meyers R, Manoharan M, Charisse K, Duncan R, Huang V, Wang X, Li LC | Molecular therapy. Nucleic acids | 23343884 | Mol Ther Nucleic Acids | 2012 Mar 27 |
| miRNA goes nuclear. | Huang V, Li LC | RNA biology | 22336708 | RNA Biol | 2012 Mar |
| Defining features and exploring chemical modifications to manipulate RNAa activity. | Place RF, Noonan EJ, Földes-Papp Z, Li LC | Current pharmaceutical biotechnology | 20662764 | Curr Pharm Biotechnol | 2010 Aug |
| Ago1 Interacts with RNA polymerase II and binds to the promoters of actively transcribed genes in human cancer cells. | Huang V, Zheng J, Qi Z, Wang J, Place RF, Yu J, Li H, Li LC | PLoS genetics | 24086155 | PLoS Genet | 2013 |
| Inducing gene expression by targeting promoter sequences using small activating RNAs. | Wang J, Place RF, Portnoy V, Huang V, Kang MR, Kosaka M, Ho MKC, Li LC | Journal of biological methods | 25839046 | J Biol Methods | 2015 Mar 11 |
| RNAa is conserved in mammalian cells. | Huang V, Qin Y, Wang J, Wang X, Place RF, Lin G, Lue TF, Li LC | PloS one | 20107511 | PLoS One | 2010 Jan 22 |
| Small RNA and its application in andrology and urology. | Wang J, Li LC | Translational andrology and urology | 23002430 | Transl Androl Urol | 2012 |
| RNAa in action: from the exception to the norm. | Guo D, Barry L, Lin SS, Huang V, Li LC | RNA biology | 25602906 | RNA Biol | 2014 |
| Prognostic value and function of KLF4 in prostate cancer: RNAa and vector-mediated overexpression identify KLF4 as an inhibitor of tumor cell growth and migration. | Wang J, Place RF, Huang V, Wang X, Noonan EJ, Magyar CE, Huang J, Li LC | Cancer research | 21159640 | Cancer Res | 2010 Dec 15 |
| Low copy expression vectors for use in Yersinia sp. and related organisms. | Obrist MW, Miller VL | Plasmid | 22445322 | Plasmid | 2012 Jul |
| Upregulation of Cyclin B1 by miRNA and its implications in cancer. | Huang V, Place RF, Portnoy V, Wang J, Qi Z, Jia Z, Yu A, Shuman M, Yu J, Li LC | Nucleic acids research | 22053081 | Nucleic Acids Res | 2012 Feb |
| Conversion of mouse epiblast stem cells to an earlier pluripotency state by small molecules. | Zhou H, Li W, Zhu S, Joo JY, Do JT, Xiong W, Kim JB, Zhang K, Schöler HR, Ding S | The Journal of biological chemistry | 20705612 | J Biol Chem | 2010 Sep 24 |
| Integration and long distance axonal regeneration in the central nervous system from transplanted primitive neural stem cells. | Zhao J, Sun W, Cho HM, Ouyang H, Li W, Lin Y, Do J, Zhang L, Ding S, Liu Y, Lu P, Zhang K | The Journal of biological chemistry | 23155053 | J Biol Chem | 2013 Jan 4 |
| JNK inhibition reduces apoptosis and neovascularization in a murine model of age-related macular degeneration. | Du H, Sun X, Guma M, Luo J, Ouyang H, Zhang X, Zeng J, Quach J, Nguyen DH, Shaw PX, Karin M, Zhang K | Proceedings of the National Academy of Sciences of the United States of America | 23341606 | Proc Natl Acad Sci U S A | 2013 Feb 5 |
| Images in clinical medicine. Carotid-cavernous sinus fistula. | Korn BS, Zhang K | The New England journal of medicine | 21345097 | N Engl J Med | 2011 Feb 24 |
| Stem cells and eye development. | Zhang K, Ding S | The New England journal of medicine | 21793749 | N Engl J Med | 2011 Jul 28 |
| Tyrosine-mutant AAV8 delivery of human MERTK provides long-term retinal preservation in RCS rats. | Deng WT, Dinculescu A, Li Q, Boye SL, Li J, Gorbatyuk MS, Pang J, Chiodo VA, Matthes MT, Yasumura D, Liu L, Alkuraya FS, Zhang K, Vollrath D, LaVail MM, Hauswirth WW | Investigative ophthalmology & visual science | 22408006 | Invest Ophthalmol Vis Sci | 2012 Apr 6 |
| Transgenic expression of the proneural transcription factor Ascl1 in Müller glia stimulates retinal regeneration in young mice. | Ueki Y, Wilken MS, Cox KE, Chipman L, Jorstad N, Sternhagen K, Simic M, Ullom K, Nakafuku M, Reh TA | Proceedings of the National Academy of Sciences of the United States of America | 26483457 | Proc Natl Acad Sci U S A | 2015 Nov 3 |
| A transient wave of BMP signaling in the retina is necessary for Müller glial differentiation. | Ueki Y, Wilken MS, Cox KE, Chipman LB, Bermingham-McDonogh O, Reh TA | Development (Cambridge, England) | 25605781 | Development | 2015 Feb 1 |
| Complement factor H genotypes impact risk of age-related macular degeneration by interaction with oxidized phospholipids. | Shaw PX, Zhang L, Zhang M, Du H, Zhao L, Lee C, Grob S, Lim SL, Hughes G, Lee J, Bedell M, Nelson MH, Lu F, Krupa M, Luo J, Ouyang H, Tu Z, Su Z, Zhu J, Wei X, Feng Z, Duan Y, Yang Z, Ferreyra H, Bartsch DU, Kozak I, Zhang L, Lin F, Sun H, Feng H, Zhang K | Proceedings of the National Academy of Sciences of the United States of America | 22875704 | Proc Natl Acad Sci U S A | 2012 Aug 21 |
| Neural Stem Cells Derived by Small Molecules Preserve Vision. | Lu B, Morgans CW, Girman S, Luo J, Zhao J, Du H, Lim S, Ding S, Svendsen C, Zhang K, Wang S | Translational vision science & technology | 24049711 | Transl Vis Sci Technol | 2013 Jan |
| Induction of retinal progenitors and neurons from mammalian Müller glia under defined conditions. | Zhao JJ, Ouyang H, Luo J, Patel S, Xue Y, Quach J, Sfeir N, Zhang M, Fu X, Ding S, Chen S, Zhang K | The Journal of biological chemistry | 24523410 | J Biol Chem | 2014 Apr 25 |
| Bio-inspired detoxification using 3D-printed hydrogel nanocomposites. | Gou M, Qu X, Zhu W, Xiang M, Yang J, Zhang K, Wei Y, Chen S | Nature communications | 24805923 | Nat Commun | 2014 May 8 |
| Increased expression of multifunctional serine protease, HTRA1, in retinal pigment epithelium induces polypoidal choroidal vasculopathy in mice. | Jones A, Kumar S, Zhang N, Tong Z, Yang JH, Watt C, Anderson J, Amrita, Fillerup H, McCloskey M, Luo L, Yang Z, Ambati B, Marc R, Oka C, Zhang K, Fu Y | Proceedings of the National Academy of Sciences of the United States of America | 21844367 | Proc Natl Acad Sci U S A | 2011 Aug 30 |
| Induced pluripotent stem cell therapies for geographic atrophy of age-related macular degeneration. | Du H, Lim SL, Grob S, Zhang K | Seminars in ophthalmology | 21609235 | Semin Ophthalmol | 2011 May |
| High temperature requirement factor A1 (HTRA1) gene regulates angiogenesis through transforming growth factor-β family member growth differentiation factor 6. | Zhang L, Lim SL, Du H, Zhang M, Kozak I, Hannum G, Wang X, Ouyang H, Hughes G, Zhao L, Zhu X, Lee C, Su Z, Zhou X, Shaw R, Geum D, Wei X, Zhu J, Ideker T, Oka C, Wang N, Yang Z, Shaw PX, Zhang K | The Journal of biological chemistry | 22049084 | J Biol Chem | 2012 Jan 6 |
| Ciliary neurotrophic factor delivered by encapsulated cell intraocular implants for treatment of geographic atrophy in age-related macular degeneration. | Zhang K, Hopkins JJ, Heier JS, Birch DG, Halperin LS, Albini TA, Brown DM, Jaffe GJ, Tao W, Williams GA | Proceedings of the National Academy of Sciences of the United States of America | 21444807 | Proc Natl Acad Sci U S A | 2011 Apr 12 |
| Reprogramming of human primary somatic cells by OCT4 and chemical compounds. | Zhu S, Li W, Zhou H, Wei W, Ambasudhan R, Lin T, Kim J, Zhang K, Ding S | Cell stem cell | 21112560 | Cell Stem Cell | 2010 Dec 3 |
| Direct reprogramming of mouse fibroblasts to neural progenitors. | Kim J, Efe JA, Zhu S, Talantova M, Yuan X, Wang S, Lipton SA, Zhang K, Ding S | Proceedings of the National Academy of Sciences of the United States of America | 21521790 | Proc Natl Acad Sci U S A | 2011 May 10 |
| A calcineurin-independent mechanism of angiogenesis inhibition by a nonimmunosuppressive cyclosporin A analog. | Nacev BA, Low WK, Huang Z, Su TT, Su Z, Alkuraya H, Kasuga D, Sun W, Träger M, Braun M, Fischer G, Zhang K, Liu JO | The Journal of pharmacology and experimental therapeutics | 21562139 | J Pharmacol Exp Ther | 2011 Aug |
| Genome-wide methylation profiles reveal quantitative views of human aging rates. | Hannum G, Guinney J, Zhao L, Zhang L, Hughes G, Sadda S, Klotzle B, Bibikova M, Fan JB, Gao Y, Deconde R, Chen M, Rajapakse I, Friend S, Ideker T, Zhang K | Molecular cell | 23177740 | Mol Cell | 2013 Jan 24 |
| TCF7L2 variation and proliferative diabetic retinopathy. | Luo J, Zhao L, Chen AY, Zhang X, Zhu J, Zhao J, Ouyang H, Luo H, Song Y, Lee J, Patel SH, Shaw PX, Sadda S, Zhuo Y, Rosenfeld MG, Zhang K | Diabetes | 23434931 | Diabetes | 2013 Jul |
| miR-124-9-9* potentiates Ascl1-induced reprogramming of cultured Müller glia. | Wohl SG, Reh TA | Glia | 26732729 | Glia | 2016 May |
| Essential role of ELOVL4 protein in very long chain fatty acid synthesis and retinal function. | Harkewicz R, Du H, Tong Z, Alkuraya H, Bedell M, Sun W, Wang X, Hsu YH, Esteve-Rudd J, Hughes G, Su Z, Zhang M, Lopes VS, Molday RS, Williams DS, Dennis EA, Zhang K | The Journal of biological chemistry | 22199362 | J Biol Chem | 2012 Mar 30 |
| Rapid induction and long-term self-renewal of primitive neural precursors from human embryonic stem cells by small molecule inhibitors. | Li W, Sun W, Zhang Y, Wei W, Ambasudhan R, Xia P, Talantova M, Lin T, Kim J, Wang X, Kim WR, Lipton SA, Zhang K, Ding S | Proceedings of the National Academy of Sciences of the United States of America | 21525408 | Proc Natl Acad Sci U S A | 2011 May 17 |
| WNT7A and PAX6 define corneal epithelium homeostasis and pathogenesis. | Ouyang H, Xue Y, Lin Y, Zhang X, Xi L, Patel S, Cai H, Luo J, Zhang M, Zhang M, Yang Y, Li G, Li H, Jiang W, Yeh E, Lin J, Pei M, Zhu J, Cao G, Zhang L, Yu B, Chen S, Fu XD, Liu Y, Zhang K | Nature | 25030175 | Nature | 2014 Jul 17 |
| Human retinal progenitor cell transplantation preserves vision. | Luo J, Baranov P, Patel S, Ouyang H, Quach J, Wu F, Qiu A, Luo H, Hicks C, Zeng J, Zhu J, Lu J, Sfeir N, Wen C, Zhang M, Reade V, Patel S, Sinden J, Sun X, Shaw P, Young M, Zhang K | The Journal of biological chemistry | 24407289 | J Biol Chem | 2014 Mar 7 |
| WNT signaling in stem cell differentiation and tumor formation. | Ouyang H, Zhuo Y, Zhang K | The Journal of clinical investigation | 23524963 | J Clin Invest | 2013 Apr |
| Direct conversion of fibroblasts to neurons by reprogramming PTB-regulated microRNA circuits. | Xue Y, Ouyang K, Huang J, Zhou Y, Ouyang H, Li H, Wang G, Wu Q, Wei C, Bi Y, Jiang L, Cai Z, Sun H, Zhang K, Zhang Y, Chen J, Fu XD | Cell | 23313552 | Cell | 2013 Jan 17 |
| Next generation sequencing-based molecular diagnosis of retinitis pigmentosa: identification of a novel genotype-phenotype correlation and clinical refinements. | Wang F, Wang H, Tuan HF, Nguyen DH, Sun V, Keser V, Bowne SJ, Sullivan LS, Luo H, Zhao L, Wang X, Zaneveld JE, Salvo JS, Siddiqui S, Mao L, Wheaton DK, Birch DG, Branham KE, Heckenlively JR, Wen C, Flagg K, Ferreyra H, Pei J, Khan A, Ren H, Wang K, Lopez I, Qamar R, Zenteno JC, Ayala-Ramirez R, Buentello-Volante B, Fu Q, Simpson DA, Li Y, Sui R, Silvestri G, Daiger SP, Koenekoop RK, Zhang K, Chen R | Human genetics | 24154662 | Hum Genet | 2014 Mar |
| Small molecule Photoregulin3 prevents retinal degeneration in the Rho(P23H) mouse model of retinitis pigmentosa. | Nakamura PA, Shimchuk AA, Tang S, Wang Z, DeGolier K, Ding S, Reh TA | eLife | 29148976 | Elife | 2017 Nov 17 |
| Cellular reprogramming: a small molecule perspective. | Nie B, Wang H, Laurent T, Ding S | Current opinion in cell biology | 22959962 | Curr Opin Cell Biol | 2012 Dec |
| P53 is required for the developmental restriction in Müller glial proliferation in mouse retina. | Ueki Y, Karl MO, Sudar S, Pollak J, Taylor RJ, Loeffler K, Wilken MS, Reardon S, Reh TA | Glia | 22777914 | Glia | 2012 Oct |
| Pharmacological Reprogramming of Fibroblasts into Neural Stem Cells by Signaling-Directed Transcriptional Activation. | Zhang M, Lin YH, Sun YJ, Zhu S, Zheng J, Liu K, Cao N, Li K, Huang Y, Ding S | Cell stem cell | 27133794 | Cell Stem Cell | 2016 May 5 |
| Transcription Factor PAX6 (Paired Box 6) Controls Limbal Stem Cell Lineage in Development and Disease. | Li G, Xu F, Zhu J, Krawczyk M, Zhang Y, Yuan J, Patel S, Wang Y, Lin Y, Zhang M, Cai H, Chen D, Zhang M, Cao G, Yeh E, Lin D, Su Q, Li WW, Sen GL, Afshari N, Chen S, Maas RL, Fu XD, Zhang K, Liu Y, Ouyang H | The Journal of biological chemistry | 26045558 | J Biol Chem | 2015 Aug 14 |
| Chemical approaches to cell reprogramming. | Yu C, Liu K, Tang S, Ding S | Current opinion in genetics & development | 25461450 | Curr Opin Genet Dev | 2014 Oct |
| Potential of Small Molecule-Mediated Reprogramming of Rod Photoreceptors to Treat Retinitis Pigmentosa. | Nakamura PA, Tang S, Shimchuk AA, Ding S, Reh TA | Investigative ophthalmology & visual science | 27893103 | Invest Ophthalmol Vis Sci | 2016 Nov 1 |
| Genetic and environmental factors strongly influence risk, severity and progression of age-related macular degeneration. | Wang W, Gawlik K, Lopez J, Wen C, Zhu J, Wu F, Shi W, Scheibler S, Cai H, Vairavan R, Shi A, Haw W, Ferreyra H, Zhang M, Chang S, Zhang K | Signal transduction and targeted therapy | 29263899 | Signal Transduct Target Ther | 2016 |
| Small molecules, big roles -- the chemical manipulation of stem cell fate and somatic cell reprogramming. | Zhang Y, Li W, Laurent T, Ding S | Journal of cell science | 23420199 | J Cell Sci | 2012 Dec 1 |
| Common variant in VEGFA and response to anti-VEGF therapy for neovascular age-related macular degeneration. | Zhao L, Grob S, Avery R, Kimura A, Pieramici D, Lee J, Rabena M, Ortiz S, Quach J, Cao G, Luo H, Zhang M, Pei M, Song Y, Tornambe P, Goldbaum M, Ferreyra H, Kozak I, Zhang K | Current molecular medicine | 23745581 | Curr Mol Med | 2013 Jul |
| Regenerative medicine for the special senses: restoring the inputs. | Bermingham-McDonogh O, Corwin JT, Hauswirth WW, Heller S, Reed R, Reh TA | The Journal of neuroscience : the official journal of the Society for Neuroscience | 23055472 | J Neurosci | 2012 Oct 10 |
| Regulated reprogramming in the regeneration of sensory receptor cells. | Bermingham-McDonogh O, Reh TA | Neuron | 21835338 | Neuron | 2011 Aug 11 |
| Genes of the unfolded protein response pathway harbor risk alleles for primary open angle glaucoma. | Carbone MA, Chen Y, Hughes GA, Weinreb RN, Zabriskie NA, Zhang K, Anholt RR | PloS one | 21655191 | PLoS One | 2011 |
| An essential role of the cysteine-rich domain of FZD4 in Norrin/Wnt signaling and familial exudative vitreoretinopathy. | Zhang K, Harada Y, Wei X, Shukla D, Rajendran A, Tawansy K, Bedell M, Lim S, Shaw PX, He X, Yang Z | The Journal of biological chemistry | 21177847 | J Biol Chem | 2011 Mar 25 |
| Sustained axon regeneration induced by co-deletion of PTEN and SOCS3. | Sun F, Park KK, Belin S, Wang D, Lu T, Chen G, Zhang K, Yeung C, Feng G, Yankner BA, He Z | Nature | 22056987 | Nature | 2011 Nov 6 |
| Four additional natural 7-deazaguanine derivatives in phages and how to make them. | Cui L, Balamkundu S, Liu CF, Ye H, Hourihan J, Rausch A, Hauß C, Nilsson E, Hoetzinger M, Holmfeldt K, Zhang W, Martinez-Alvarez L, Peng X, Tremblay D, Moinau S, Solonenko N, Sullivan MB, Lee YJ, Mulholland A, Weigele PR, de Crécy-Lagard V, Dedon PC, Hutinet G | Nucleic acids research | 37572349 | Nucleic Acids Res | 2023 Sep 22 |
| Phosphorothioate DNA modification by BREX Type 4 systems in the human gut microbiome. | Yuan Y, DeMott MS, Byrne SR, Flores K, Poyet M, Groussin M, Microbiome Conservancy G, Berdy B, Comstock L, Alm EJ, Dedon PC | bioRxiv : the preprint server for biology | 38895356 | bioRxiv | 2024 Jun 3 |
| Nick-seq for single-nucleotide resolution genomic maps of DNA modifications and damage. | Cao B, Wu X, Zhou J, Wu H, Liu L, Zhang Q, DeMott MS, Gu C, Wang L, You D, Dedon PC | Nucleic acids research | 32484547 | Nucleic Acids Res | 2020 Jul 9 |
| PT-seq: A method for metagenomic analysis of phosphorothioate epigenetics in complex microbial communities. | Yuan Y, DeMott MS, Byrne SR, Global Microbiome Conservancy, Dedon PC | bioRxiv : the preprint server for biology | 38895297 | bioRxiv | 2024 Jun 3 |
| Protein Domain Guided Screen for Sequence Specific and Phosphorothioate-Dependent Restriction Endonucleases. | Lutz T, Czapinska H, Fomenkov A, Potapov V, Heiter DF, Cao B, Dedon P, Bochtler M, Xu SY | Frontiers in microbiology | 33013736 | Front Microbiol | 2020 |
| Strategies to Avoid Artifacts in Mass Spectrometry-Based Epitranscriptome Analyses. | Kaiser S, Byrne SR, Ammann G, Asadi Atoi P, Borland K, Brecheisen R, DeMott MS, Gehrke T, Hagelskamp F, Heiss M, Yoluç Y, Liu L, Zhang Q, Dedon PC, Cao B, Kellner S | Angewandte Chemie (International ed. in English) | 34339593 | Angew Chem Int Ed Engl | 2021 Oct 25 |
| Temporal dynamics and metagenomics of phosphorothioate epigenomes in the human gut microbiome. | Byrne SR, DeMott MS, Yuan Y, Ghanegolmohammadi F, Kaiser S, Fox JG, Alm EJ, Dedon PC | Microbiome | 40128848 | Microbiome | 2025 Mar 24 |
| tRNA modification profiling reveals epitranscriptome regulatory networks in Pseudomonas aeruginosa. | Sun J, Wu J, Yuan Y, Fan L, Chua WLP, Ling YHS, Balamkundu S, Priya D, Suen HCS, de Crécy-Lagard V, Dziergowska A, Dedon PC | bioRxiv : the preprint server for biology | 39005467 | bioRxiv | 2024 Jul 2 |
| The role of environmental exposures and the epigenome in health and disease. | Perera BPU, Faulk C, Svoboda LK, Goodrich JM, Dolinoy DC | Environmental and molecular mutagenesis | 31177562 | Environ Mol Mutagen | 2020 Jan |
| Paradoxical whole genome DNA methylation dynamics of 5'aza-deoxycytidine in chronic low-dose exposure in mice. | Colwell M, Wanner NM, Drown C, Drown M, Dolinoy DC, Faulk C | Epigenetics | 32619143 | Epigenetics | 2021 Jan-Feb |
| The evolution of CpG density and lifespan in conserved primate and mammalian promoters. | McLain AT, Faulk C | Aging | 29661983 | Aging (Albany NY) | 2018 Apr 14 |
| Genomic Tools for Environmental Epigenetics and Implications for Public Health. | Perera BPU, Svoboda L, Dolinoy DC | Current opinion in toxicology | 31763499 | Curr Opin Toxicol | 2019 Dec |
| Evolutionary conservation of DNA methylation in CpG sites within ultraconserved noncoding elements. | Colwell M, Drown M, Showel K, Drown C, Palowski A, Faulk C | Epigenetics | 29372669 | Epigenetics | 2018 |
| Somatic expression of piRNA and associated machinery in the mouse identifies short, tissue-specific piRNA. | Perera BPU, Tsai ZT, Colwell ML, Jones TR, Goodrich JM, Wang K, Sartor MA, Faulk C, Dolinoy DC | Epigenetics | 30955436 | Epigenetics | 2019 May |
| piOxi database: a web resource of germline and somatic tissue piRNAs identified by chemical oxidation. | Wang K, Perera BPU, Morgan RK, Sala-Hamrick K, Geron V, Svoboda LK, Faulk C, Dolinoy DC, Sartor MA | Database : the journal of biological databases and curation | 38204359 | Database (Oxford) | 2024 Jan 10 |
| Comparison of toxicogenomics and traditional approaches to inform mode of action and points of departure in human health risk assessment of benzo[a]pyrene in drinking water. | Moffat I, Chepelev N, Labib S, Bourdon-Lacombe J, Kuo B, Buick JK, Lemieux F, Williams A, Halappanavar S, Malik A, Luijten M, Aubrecht J, Hyduke DR, Fornace AJ Jr, Swartz CD, Recio L, Yauk CL | Critical reviews in toxicology | 25605026 | Crit Rev Toxicol | 2015 Jan |
| The human toxome project. | Bouhifd M, Andersen ME, Baghdikian C, Boekelheide K, Crofton KM, Fornace AJ Jr, Kleensang A, Li H, Livi C, Maertens A, McMullen PD, Rosenberg M, Thomas R, Vantangoli M, Yager JD, Zhao L, Hartung T | ALTEX | 25742299 | ALTEX | 2015 |
| Exploring new technologies in biomedical research. | Benam KH, Gilchrist S, Kleensang A, Satz AB, Willett C, Zhang Q | Drug discovery today | 30953865 | Drug Discov Today | 2019 Jun |
| Metabolomics in toxicology and preclinical research. | Ramirez T, Daneshian M, Kamp H, Bois FY, Clench MR, Coen M, Donley B, Fischer SM, Ekman DR, Fabian E, Guillou C, Heuer J, Hogberg HT, Jungnickel H, Keun HC, Krennrich G, Krupp E, Luch A, Noor F, Peter E, Riefke B, Seymour M, Skinner N, Smirnova L, Verheij E, Wagner S, Hartung T, van Ravenzwaay B, Leist M | ALTEX | 23665807 | ALTEX | 2013 |
| Mapping the human toxome by systems toxicology. | Bouhifd M, Hogberg HT, Kleensang A, Maertens A, Zhao L, Hartung T | Basic & clinical pharmacology & toxicology | 24443875 | Basic Clin Pharmacol Toxicol | 2014 Jul |
| Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function. | Kleensang A, Vantangoli MM, Odwin-DaCosta S, Andersen ME, Boekelheide K, Bouhifd M, Fornace AJ Jr, Li HH, Livi CB, Madnick S, Maertens A, Rosenberg M, Yager JD, Zhao L, Hartung T | Scientific reports | 27456714 | Sci Rep | 2016 Jul 26 |
| Transcriptional and metabolic adaptation of human neurons to the mitochondrial toxicant MPP(+). | Krug AK, Gutbier S, Zhao L, Pöltl D, Kullmann C, Ivanova V, Förster S, Jagtap S, Meiser J, Leparc G, Schildknecht S, Adam M, Hiller K, Farhan H, Brunner T, Hartung T, Sachinidis A, Leist M | Cell death & disease | 24810058 | Cell Death Dis | 2014 May 8 |
| The Human Toxome Collaboratorium: A Shared Environment for Multi-Omic Computational Collaboration within a Consortium. | Fasani RA, Livi CB, Choudhury DR, Kleensang A, Bouhifd M, Pendse SN, McMullen PD, Andersen ME, Hartung T, Rosenberg M | Frontiers in pharmacology | 26924983 | Front Pharmacol | 2015 |
| Metabolomic network analysis of estrogen-stimulated MCF-7 cells: a comparison of overrepresentation analysis, quantitative enrichment analysis and pathway analysis versus metabolite network analysis. | Maertens A, Bouhifd M, Zhao L, Odwin-DaCosta S, Kleensang A, Yager JD, Hartung T | Archives of toxicology | 27039105 | Arch Toxicol | 2017 Jan |
| 3D - a new dimension of in vitro research. | Hartung T | Advanced drug delivery reviews | 24721291 | Adv Drug Deliv Rev | 2014 Apr |
| Systems Toxicology: Real World Applications and Opportunities. | Hartung T, FitzGerald RE, Jennings P, Mirams GR, Peitsch MC, Rostami-Hodjegan A, Shah I, Wilks MF, Sturla SJ | Chemical research in toxicology | 28362102 | Chem Res Toxicol | 2017 Apr 17 |
| Immunotoxicology: challenges in the 21st century and in vitro opportunities. | Hartung T, Corsini E | ALTEX | 24173166 | ALTEX | 2013 |
| Integration of metabolic activation with a predictive toxicogenomics signature to classify genotoxic versus nongenotoxic chemicals in human TK6 cells. | Buick JK, Moffat I, Williams A, Swartz CD, Recio L, Hyduke DR, Li HH, Fornace AJ Jr, Aubrecht J, Yauk CL | Environmental and molecular mutagenesis | 25733247 | Environ Mol Mutagen | 2015 Jul |
| Development of a toxicogenomics signature for genotoxicity using a dose-optimization and informatics strategy in human cells. | Li HH, Hyduke DR, Chen R, Heard P, Yauk CL, Aubrecht J, Fornace AJ Jr | Environmental and molecular mutagenesis | 25733355 | Environ Mol Mutagen | 2015 Jul |
| Arsenite and cadmium promote the development of mammary tumors. | Divekar SD, Li HH, Parodi DA, Ghafouri TB, Chen R, Cyrus K, Foxworth AE, Fornace AJ, Byrne C, Martin MB | Carcinogenesis | 31646340 | Carcinogenesis | 2020 Jul 14 |
| Review: toxicometabolomics. | Bouhifd M, Hartung T, Hogberg HT, Kleensang A, Zhao L | Journal of applied toxicology : JAT | 23722930 | J Appl Toxicol | 2013 Dec |
| Integrated testing strategies for safety assessments. | Hartung T, Luechtefeld T, Maertens A, Kleensang A | ALTEX | 23338803 | ALTEX | 2013 |
| Ultrasensitive response motifs: basic amplifiers in molecular signalling networks. | Zhang Q, Bhattacharya S, Andersen ME | Open biology | 23615029 | Open Biol | 2013 Apr 24 |
| Estradiol Exposure Differentially Alters Monolayer versus Microtissue MCF-7 Human Breast Carcinoma Cultures. | Vantangoli MM, Madnick SJ, Wilson S, Boekelheide K | PloS one | 27379522 | PLoS One | 2016 |
| Application of the TGx-28.65 transcriptomic biomarker to classify genotoxic and non-genotoxic chemicals in human TK6 cells in the presence of rat liver S9. | Yauk CL, Buick JK, Williams A, Swartz CD, Recio L, Li HH, Fornace AJ Jr, Thomson EM, Aubrecht J | Environmental and molecular mutagenesis | 26946220 | Environ Mol Mutagen | 2016 May |
| Morphologic effects of estrogen stimulation on 3D MCF-7 microtissues. | Vantangoli MM, Wilson S, Madnick SJ, Huse SM, Boekelheide K | Toxicology letters | 26921789 | Toxicol Lett | 2016 Apr 25 |
| 21st Century Cell Culture for 21st Century Toxicology. | Pamies D, Hartung T | Chemical research in toxicology | 28092941 | Chem Res Toxicol | 2017 Jan 17 |
| Pathways of Toxicity. | Kleensang A, Maertens A, Rosenberg M, Fitzpatrick S, Lamb J, Auerbach S, Brennan R, Crofton KM, Gordon B, Fornace AJ Jr, Gaido K, Gerhold D, Haw R, Henney A, Ma'ayan A, McBride M, Monti S, Ochs MF, Pandey A, Sharan R, Stierum R, Tugendreich S, Willett C, Wittwehr C, Xia J, Patton GW, Arvidson K, Bouhifd M, Hogberg HT, Luechtefeld T, Smirnova L, Zhao L, Adeleye Y, Kanehisa M, Carmichael P, Andersen ME, Hartung T | ALTEX | 24127042 | ALTEX | 2014 |
| Look back in anger - what clinical studies tell us about preclinical work. | Hartung T | ALTEX | 23861075 | ALTEX | 2013 |
| Systems Toxicology: The Future of Risk Assessment. | Sauer JM, Hartung T, Leist M, Knudsen TB, Hoeng J, Hayes AW | International journal of toxicology | 25804424 | Int J Toxicol | 2015 Jul-Aug |
| MPTP's pathway of toxicity indicates central role of transcription factor SP1. | Maertens A, Luechtefeld T, Kleensang A, Hartung T | Archives of toxicology | 25851821 | Arch Toxicol | 2015 May |
| Development and validation of a high-throughput transcriptomic biomarker to address 21st century genetic toxicology needs. | Li HH, Chen R, Hyduke DR, Williams A, Frötschl R, Ellinger-Ziegelbauer H, O'Lone R, Yauk CL, Aubrecht J, Fornace AJ Jr | Proceedings of the National Academy of Sciences of the United States of America | 29203651 | Proc Natl Acad Sci U S A | 2017 Dec 19 |
| Information-dependent enrichment analysis reveals time-dependent transcriptional regulation of the estrogen pathway of toxicity. | Pendse SN, Maertens A, Rosenberg M, Roy D, Fasani RA, Vantangoli MM, Madnick SJ, Boekelheide K, Fornace AJ, Odwin SA, Yager JD, Hartung T, Andersen ME, McMullen PD | Archives of toxicology | 27592001 | Arch Toxicol | 2017 Apr |
| Mechanistic validation. | Hartung T, Hoffmann S, Stephens M | ALTEX | 23665802 | ALTEX | 2013 |
| Quality assurance of metabolomics. | Bouhifd M, Beger R, Flynn T, Guo L, Harris G, Hogberg H, Kaddurah-Daouk R, Kamp H, Kleensang A, Maertens A, Odwin-DaCosta S, Pamies D, Robertson D, Smirnova L, Sun J, Zhao L, Hartung T | ALTEX | 26536290 | ALTEX | 2015 |
| Perspectives on In Vitro to In Vivo Extrapolations. | Hartung T | Applied in vitro toxicology | 31890748 | Appl In Vitro Toxicol | 2018 Dec 1 |
| Organophosphorus flame retardants are developmental neurotoxicants in a rat primary brainsphere in vitro model. | Hogberg HT, de Cássia da Silveira E Sá R, Kleensang A, Bouhifd M, Cemiloglu Ulker O, Smirnova L, Behl M, Maertens A, Zhao L, Hartung T | Archives of toxicology | 33078273 | Arch Toxicol | 2021 Jan |
| MCF-7 Human Breast Cancer Cells Form Differentiated Microtissues in Scaffold-Free Hydrogels. | Vantangoli MM, Madnick SJ, Huse SM, Weston P, Boekelheide K | PloS one | 26267486 | PLoS One | 2015 |
| Joint Bounding of Peaks Across Samples Improves Differential Analysis in Mass Spectrometry-Based Metabolomics. | Myint L, Kleensang A, Zhao L, Hartung T, Hansen KD | Analytical chemistry | 28221771 | Anal Chem | 2017 Mar 21 |
| CAR-T Entering a New "Phase": Improving CAR-T Function by Harnessing Phase Separation. | Su X | Cancer research | 39879116 | Cancer Res | 2025 Mar 14 |
| Hyperactive PLCG1 drives non-canonical signaling to promote cell survival. | Zeng L, Zhang X, Xiong Y, Sato K, Hajicek N, Sondek J, Su X | bioRxiv : the preprint server for biology | 39763946 | bioRxiv | 2024 Dec 18 |
| Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition. | Fahlberg MD, Forward S, Assita ER, Mazzola M, Kiem A, Handley M, Yun SH, Kwok SJJ | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 39467031 | Cytometry A | 2024 Nov |
| Laser particle activated cell sorting in microfluidics. | Dannenberg PH, Kang J, Martino N, Kashiparekh A, Forward S, Wu J, Liapis AC, Wang J, Yun SH | Lab on a chip | 35621381 | Lab Chip | 2022 Jun 14 |
| Aggregation-Induced Stimulated Emission of 100% Dye Microspheres. | Kim KH, Yan H, Yun SH | Advanced optical materials | 38107448 | Adv Opt Mater | 2023 Jul 18 |
| Facile layer-by-layer fabrication of semiconductor microdisk laser particles. | Dannenberg PH, Liapis AC, Martino N, Sarkar D, Kim KH, Yun SH | APL photonics | 38031595 | APL Photonics | 2023 Feb |
| High-dimensional multi-pass flow cytometry via spectrally encoded cellular barcoding. | Kwok SJJ, Forward S, Fahlberg MD, Assita ER, Cosgriff S, Lee SH, Abbott GR, Zhu H, Minasian NH, Vote AS, Martino N, Yun SH | Nature biomedical engineering | 38036616 | Nat Biomed Eng | 2024 Mar |
| Ultrasmall InGa(As)P Dielectric and Plasmonic Nanolasers. | Sarkar D, Cho S, Yan H, Martino N, Dannenberg PH, Yun SH | ACS nano | 37523588 | ACS Nano | 2023 Aug 22 |
| Large-scale combinatorial optical barcoding of cells with laser particles. | Martino N, Yan H, Abbott G, Fahlberg M, Forward S, Kim KH, Wu Y, Zhu H, Kwok SJJ, Yun SH | Light, science & applications | 40169572 | Light Sci Appl | 2025 Apr 1 |
| Single-cell transcriptomics of a dynamic cell behavior in murine airways. | Kwok SJJ, Montoro DT, Haber AL, Yun SH, Vinarsky V | eLife | 37083555 | Elife | 2023 Apr 21 |
| Overcoming fixation and permeabilization challenges in flow cytometry by optical barcoding and multi-pass acquisition. | Fahlberg MD, Forward S, Assita ER, Mazzola M, Kiem A, Handley M, Yun SH, Kwok SJJ | bioRxiv : the preprint server for biology | 39185194 | bioRxiv | 2024 Aug 16 |
| Precise photoelectrochemical tuning of semiconductor microdisk lasers. | Sarkar D, Dannenberg PH, Martino N, Kim KH, Yun SH | Advanced photonics | 38993283 | Adv Photonics | 2023 Sep |
| Wideband Tuning and Deep-Tissue Spectral Detection of Indium Phosphide Nano-Laser Particles. | Cho S, Moon W, Martino N, Yun SH | bioRxiv : the preprint server for biology | 39677764 | bioRxiv | 2024 Dec 3 |
| Half-wave nanolasers and intracellular plasmonic lasing particles. | Cho S, Martino N, Yun SH | Nature nanotechnology | 39747602 | Nat Nanotechnol | 2025 Mar |
| Plasmonic Hinge Modes in Metal-Coated Nanolasers. | Cho S, Yang Y, Soljačić M, Yun SH | Nano letters | 39414245 | Nano Lett | 2024 Oct 30 |
| Determination of [11C]rifampin pharmacokinetics within Mycobacterium tuberculosis-infected mice by using dynamic positron emission tomography bioimaging. | DeMarco VP, Ordonez AA, Klunk M, Prideaux B, Wang H, Zhuo Z, Tonge PJ, Dannals RF, Holt DP, Lee CK, Weinstein EA, Dartois V, Dooley KE, Jain SK | Antimicrobial agents and chemotherapy | 26169396 | Antimicrob Agents Chemother | 2015 Sep |
| Computer-aided pulmonary image analysis in small animal models. | Xu Z, Bagci U, Mansoor A, Kramer-Marek G, Luna B, Kubler A, Dey B, Foster B, Papadakis GZ, Camp JV, Jonsson CB, Bishai WR, Jain S, Udupa JK, Mollura DJ | Medical physics | 26133591 | Med Phys | 2015 Jul |
| Design of Selective Substrates and Activity-Based Probes for Hydrolase Important for Pathogenesis 1 (HIP1) from Mycobacterium tuberculosis. | Lentz CS, Ordonez AA, Kasperkiewicz P, La Greca F, O'Donoghue AJ, Schulze CJ, Powers JC, Craik CS, Drag M, Jain SK, Bogyo M | ACS infectious diseases | 27739665 | ACS Infect Dis | 2016 Nov 11 |
| The biodistribution of 5-[18F]fluoropyrazinamide in Mycobacterium tuberculosis-infected mice determined by positron emission tomography. | Zhang Z, Ordonez AA, Smith-Jones P, Wang H, Gogarty KR, Daryaee F, Bambarger LE, Chang YS, Jain SK, Tonge PJ | PloS one | 28151985 | PLoS One | 2017 |
| SPECT/CT Imaging of Mycobacterium tuberculosis Infection with [(125)I]anti-C3d mAb. | Foss CA, Kulik L, Ordonez AA, Jain SK, Michael Holers V, Thurman JM, Pomper MG | Molecular imaging and biology | 29998399 | Mol Imaging Biol | 2019 Jun |
| Positron Emission Tomography Imaging with 2-[(18)F]F- p-Aminobenzoic Acid Detects Staphylococcus aureus Infections and Monitors Drug Response. | Zhang Z, Ordonez AA, Wang H, Li Y, Gogarty KR, Weinstein EA, Daryaee F, Merino J, Yoon GE, Kalinda AS, Mease RC, Iuliano JN, Smith-Jones PM, Jain SK, Tonge PJ | ACS infectious diseases | 30067329 | ACS Infect Dis | 2018 Nov 9 |
| Matrix Metalloproteinases in Pulmonary and Central Nervous System Tuberculosis-A Review. | Rohlwink UK, Walker NF, Ordonez AA, Li YJ, Tucker EW, Elkington PT, Wilkinson RJ, Wilkinson KA | International journal of molecular sciences | 30889803 | Int J Mol Sci | 2019 Mar 18 |
| Novel vaccine strategies against tuberculosis: a road less travelled. | Pokkali S, Jain S | Expert review of vaccines | 24195477 | Expert Rev Vaccines | 2013 Dec |
| Radiosynthesis and validation of [Carboxy-(11) C]4-Aminobenzoic acid ([(11) C]PABA), a PET radiotracer for imaging bacterial infections. | Holt DP, Kalinda AS, Bambarger LE, Jain SK, Dannals RF | Journal of labelled compounds & radiopharmaceuticals | 30089334 | J Labelled Comp Radiopharm | 2019 Jan |
| Radiosynthesis and PET Bioimaging of (76)Br-Bedaquiline in a Murine Model of Tuberculosis. | Ordonez AA, Carroll LS, Abhishek S, Mota F, Ruiz-Bedoya CA, Klunk MH, Singh AK, Freundlich JS, Mease RC, Jain SK | ACS infectious diseases | 31345032 | ACS Infect Dis | 2019 Dec 13 |
| Extensively drug-resistant tuberculosis in a young child after travel to India. | Salazar-Austin N, Ordonez AA, Hsu AJ, Benson JE, Mahesh M, Menachery E, Razeq JH, Salfinger M, Starke JR, Milstone AM, Parrish N, Nuermberger EL, Jain SK | The Lancet. Infectious diseases | 26607130 | Lancet Infect Dis | 2015 Dec |
| Balancing the Risks of Radiation and Anesthesia in Pediatric Patients. | Tucker EW, Jain SK, Mahesh M | Journal of the American College of Radiology : JACR | 28750847 | J Am Coll Radiol | 2017 Nov |
| Imaging Enterobacterales infections in patients using pathogen-specific positron emission tomography. | Ordonez AA, Wintaco LM, Mota F, Restrepo AF, Ruiz-Bedoya CA, Reyes CF, Uribe LG, Abhishek S, D'Alessio FR, Holt DP, Dannals RF, Rowe SP, Castillo VR, Pomper MG, Granados U, Jain SK | Science translational medicine | 33853931 | Sci Transl Med | 2021 Apr 14 |
| Radiotracer Development for Bacterial Imaging. | Mota F, Ordonez AA, Firth G, Ruiz-Bedoya CA, Ma MT, Jain SK | Journal of medicinal chemistry | 32048838 | J Med Chem | 2020 Mar 12 |
| Advanced imaging tools for childhood tuberculosis: potential applications and research needs. | Jain SK, Andronikou S, Goussard P, Antani S, Gomez-Pastrana D, Delacourt C, Starke JR, Ordonez AA, Jean-Philippe P, Browning RS, Perez-Velez CM | The Lancet. Infectious diseases | 32589869 | Lancet Infect Dis | 2020 Nov |
| Visualizing the dynamics of tuberculosis pathology using molecular imaging. | Ordonez AA, Tucker EW, Anderson CJ, Carter CL, Ganatra S, Kaushal D, Kramnik I, Lin PL, Madigan CA, Mendez S, Rao J, Savic RM, Tobin DM, Walzl G, Wilkinson RJ, Lacourciere KA, Via LE, Jain SK | The Journal of clinical investigation | 33645551 | J Clin Invest | 2021 Mar 1 |
| The integrated stress response mediates necrosis in murine Mycobacterium tuberculosis granulomas. | Bhattacharya B, Xiao S, Chatterjee S, Urbanowski M, Ordonez A, Ihms EA, Agrahari G, Lun S, Berland R, Pichugin A, Gao Y, Connor J, Ivanov AR, Yan BS, Kobzik L, Koo BB, Jain S, Bishai W, Kramnik I | The Journal of clinical investigation | 33301427 | J Clin Invest | 2021 Feb 1 |
| Caspase-Based PET for Evaluating Pro-Apoptotic Treatments in a Tuberculosis Mouse Model. | Ordonez AA, Abhishek S, Singh AK, Klunk MH, Azad BB, Aboagye EO, Carroll L, Jain SK | Molecular imaging and biology | 32232626 | Mol Imaging Biol | 2020 Dec |
| Radiosynthesis and Biodistribution of (18)F-Linezolid in Mycobacterium tuberculosis-Infected Mice Using Positron Emission Tomography. | Mota F, Jadhav R, Ruiz-Bedoya CA, Ordonez AA, Klunk MH, Freundlich JS, Jain SK | ACS infectious diseases | 32243132 | ACS Infect Dis | 2020 May 8 |
| Capsules for biomedical image segmentation. | LaLonde R, Xu Z, Irmakci I, Jain S, Bagci U | Medical image analysis | 33246227 | Med Image Anal | 2021 Feb |
| High-dose rifampin improves bactericidal activity without increased intracerebral inflammation in animal models of tuberculous meningitis. | Ruiz-Bedoya CA, Mota F, Tucker EW, Mahmud FJ, Reyes-Mantilla MI, Erice C, Bahr M, Flavahan K, de Jesus P, Kim J, Foss CA, Peloquin CA, Hammoud DA, Ordonez AA, Pardo CA, Jain SK | The Journal of clinical investigation | 35085105 | J Clin Invest | 2022 Mar 15 |
| 11C-Para-aminobenzoic acid PET imaging of S. aureus and MRSA infection in preclinical models and humans. | Ordonez AA, Parker MF, Miller RJ, Plyku D, Ruiz-Bedoya CA, Tucker EW, Luu JM, Dikeman DA, Lesniak WG, Holt DP, Dannals RF, Miller LS, Rowe SP, Wilson DM, Jain SK | JCI insight | 35014627 | JCI Insight | 2022 Jan 11 |
| A Systematic Approach for Developing Bacteria-Specific Imaging Tracers. | Ordonez AA, Weinstein EA, Bambarger LE, Saini V, Chang YS, DeMarco VP, Klunk MH, Urbanowski ME, Moulton KL, Murawski AM, Pokkali S, Kalinda AS, Jain SK | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 27635025 | J Nucl Med | 2017 Jan |
| Polymeric nanofiber coating with tunable combinatorial antibiotic delivery prevents biofilm-associated infection in vivo. | Ashbaugh AG, Jiang X, Zheng J, Tsai AS, Kim WS, Thompson JM, Miller RJ, Shahbazian JH, Wang Y, Dillen CA, Ordonez AA, Chang YS, Jain SK, Jones LC, Sterling RS, Mao HQ, Miller LS | Proceedings of the National Academy of Sciences of the United States of America | 27791154 | Proc Natl Acad Sci U S A | 2016 Nov 8 |
| Joint solution for PET image segmentation, denoising, and partial volume correction. | Xu Z, Gao M, Papadakis GZ, Luna B, Jain S, Mollura DJ, Bagci U | Medical image analysis | 29627687 | Med Image Anal | 2018 May |
| [(11)C]Para-Aminobenzoic Acid: A Positron Emission Tomography Tracer Targeting Bacteria-Specific Metabolism. | Mutch CA, Ordonez AA, Qin H, Parker M, Bambarger LE, Villanueva-Meyer JE, Blecha J, Carroll V, Taglang C, Flavell R, Sriram R, VanBrocklin H, Rosenberg O, Ohliger MA, Jain SK, Neumann KD, Wilson DM | ACS infectious diseases | 29712422 | ACS Infect Dis | 2018 Jul 13 |
| Tuberculous meningitis: a roadmap for advancing basic and translational research. | Jain SK, Tobin DM, Tucker EW, Venketaraman V, Ordonez AA, Jayashankar L, Siddiqi OK, Hammoud DA, Prasadarao NV, Sandor M, Hafner R, Fabry Z, NIH Tuberculous Meningitis Writing Group | Nature immunology | 29777209 | Nat Immunol | 2018 Jun |
| Matrix Metalloproteinase Inhibition in a Murine Model of Cavitary Tuberculosis Paradoxically Worsens Pathology. | Ordonez AA, Pokkali S, Sanchez-Bautista J, Klunk MH, Urbanowski ME, Kübler A, Bishai WR, Elkington PT, Jain SK | The Journal of infectious diseases | 29920600 | J Infect Dis | 2019 Jan 29 |
| In vivo prediction of tuberculosis-associated cavity formation in rabbits. | Luna B, Kubler A, Larsson C, Foster B, Bagci U, Mollura DJ, Jain SK, Bishai WR | The Journal of infectious diseases | 25117755 | J Infect Dis | 2015 Feb 1 |
| Efficient ribcage segmentation from CT scans using shape features. | Xu Z, Bagci U, Jonsson C, Jain S, Mollura DJ | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 25570597 | Annu Int Conf IEEE Eng Med Biol Soc | 2014 |
| Imaging Chronic Tuberculous Lesions Using Sodium [(18)F]Fluoride Positron Emission Tomography in Mice. | Ordonez AA, DeMarco VP, Klunk MH, Pokkali S, Jain SK | Molecular imaging and biology | 25750032 | Mol Imaging Biol | 2015 Oct |
| Molecular imaging of bacterial infections: Overcoming the barriers to clinical translation. | Ordonez AA, Sellmyer MA, Gowrishankar G, Ruiz-Bedoya CA, Tucker EW, Palestro CJ, Hammoud DA, Jain SK | Science translational medicine | 31484790 | Sci Transl Med | 2019 Sep 4 |
| Flagging Bacteria with Radiolabeled d-Amino Acids. | Mota F, Jain SK | ACS central science | 32123728 | ACS Cent Sci | 2020 Feb 26 |
| Kit-based synthesis of 2-deoxy-2-[(18)F]-fluoro-D-sorbitol for bacterial imaging. | Mota F, De Jesus P, Jain SK | Nature protocols | 34686858 | Nat Protoc | 2021 Nov |
| Molecular Imaging: a Novel Tool To Visualize Pathogenesis of Infections In Situ. | Gordon O, Ruiz-Bedoya CA, Ordonez AA, Tucker EW, Jain SK | mBio | 31662452 | mBio | 2019 Oct 29 |
| Stability and Viability of SARS-CoV-2. | Rubens JH, Karakousis PC, Jain SK | The New England journal of medicine | 32283575 | N Engl J Med | 2020 May 14 |
| Dynamic imaging in patients with tuberculosis reveals heterogeneous drug exposures in pulmonary lesions. | Ordonez AA, Wang H, Magombedze G, Ruiz-Bedoya CA, Srivastava S, Chen A, Tucker EW, Urbanowski ME, Pieterse L, Fabian Cardozo E, Lodge MA, Shah MR, Holt DP, Mathews WB, Dannals RF, Gobburu JVS, Peloquin CA, Rowe SP, Gumbo T, Ivaturi VD, Jain SK | Nature medicine | 32066976 | Nat Med | 2020 Apr |
| Successful cure of extensively drug-resistant pulmonary tuberculosis in a young child. | Salazar-Austin N, Akinboyo I, Jain SK | The Lancet. Infectious diseases | 28845790 | Lancet Infect Dis | 2017 Sep |
| Mouse model of pulmonary cavitary tuberculosis and expression of matrix metalloproteinase-9. | Ordonez AA, Tasneen R, Pokkali S, Xu Z, Converse PJ, Klunk MH, Mollura DJ, Nuermberger EL, Jain SK | Disease models & mechanisms | 27482816 | Dis Model Mech | 2016 Jul 1 |
| Noninvasive (11)C-rifampin positron emission tomography reveals drug biodistribution in tuberculous meningitis. | Tucker EW, Guglieri-Lopez B, Ordonez AA, Ritchie B, Klunk MH, Sharma R, Chang YS, Sanchez-Bautista J, Frey S, Lodge MA, Rowe SP, Holt DP, Gobburu JVS, Peloquin CA, Mathews WB, Dannals RF, Pardo CA, Kannan S, Ivaturi VD, Jain SK | Science translational medicine | 30518610 | Sci Transl Med | 2018 Dec 5 |
| Molecular Imaging of Diabetic Foot Infections: New Tools for Old Questions. | Ruiz-Bedoya CA, Gordon O, Mota F, Abhishek S, Tucker EW, Ordonez AA, Jain SK | International journal of molecular sciences | 31795077 | Int J Mol Sci | 2019 Nov 28 |
| Cavitary tuberculosis: the gateway of disease transmission. | Urbanowski ME, Ordonez AA, Ruiz-Bedoya CA, Jain SK, Bishai WR | The Lancet. Infectious diseases | 32482293 | Lancet Infect Dis | 2020 Jun |
| (11)C-PABA as a PET Radiotracer for Functional Renal Imaging: Preclinical and First-in-Human Study. | Ruiz-Bedoya CA, Ordonez AA, Werner RA, Plyku D, Klunk MH, Leal J, Lesniak WG, Holt DP, Dannals RF, Higuchi T, Rowe SP, Jain SK | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 32198314 | J Nucl Med | 2020 Nov |
| Imaging Macrophage-associated Inflammation. | Foss CA, Sanchez-Bautista J, Jain SK | Seminars in nuclear medicine | 29626941 | Semin Nucl Med | 2018 May |
| Imaging Pulmonary Foreign Body Reaction Using [(125)I]iodo-DPA-713 SPECT/CT in Mice. | Sanchez-Bautista J, Foss CA, Ordonez AA, Klunk MH, Jain SK | Molecular imaging and biology | 29987615 | Mol Imaging Biol | 2019 Apr |
| Pathogen-Specific Bacterial Imaging in Nuclear Medicine. | Ordonez AA, Jain SK | Seminars in nuclear medicine | 29452620 | Semin Nucl Med | 2018 Mar |
| Pharmacokinetics of rifapentine and rifampin in a rabbit model of tuberculosis and correlation with clinical trial data. | Rifat D, Prideaux B, Savic RM, Urbanowski ME, Parsons TL, Luna B, Marzinke MA, Ordonez AA, DeMarco VP, Jain SK, Dartois V, Bishai WR, Dooley KE | Science translational medicine | 29618565 | Sci Transl Med | 2018 Apr 4 |
| Dynamic PET-facilitated modeling and high-dose rifampin regimens for Staphylococcus aureus orthopedic implant-associated infections. | Gordon O, Lee DE, Liu B, Langevin B, Ordonez AA, Dikeman DA, Shafiq B, Thompson JM, Sponseller PD, Flavahan K, Lodge MA, Rowe SP, Dannals RF, Ruiz-Bedoya CA, Read TD, Peloquin CA, Archer NK, Miller LS, Davis KM, Gobburu JVS, Jain SK | Science translational medicine | 34851697 | Sci Transl Med | 2021 Dec |
| Microglia activation in a pediatric rabbit model of tuberculous meningitis. | Tucker EW, Pokkali S, Zhang Z, DeMarco VP, Klunk M, Smith ES, Ordonez AA, Penet MF, Bhujwalla Z, Jain SK, Kannan S | Disease models & mechanisms | 27935825 | Dis Model Mech | 2016 Dec 1 |
| The Promise of Molecular Imaging in the Study and Treatment of Infectious Diseases. | Jain SK | Molecular imaging and biology | 28155078 | Mol Imaging Biol | 2017 Jun |
| Delamanid Central Nervous System Pharmacokinetics in Tuberculous Meningitis in Rabbits and Humans. | Tucker EW, Pieterse L, Zimmerman MD, Udwadia ZF, Peloquin CA, Gler MT, Ganatra S, Tornheim JA, Chawla P, Caoili JC, Ritchie B, Jain SK, Dartois V, Dooley KE | Antimicrobial agents and chemotherapy | 31383662 | Antimicrob Agents Chemother | 2019 Oct |
| Rabbit model of Staphylococcus aureus implant-associated spinal infection. | Gordon O, Miller RJ, Thompson JM, Ordonez AA, Klunk MH, Dikeman DA, Joyce DP, Ruiz-Bedoya CA, Miller LS, Jain SK | Disease models & mechanisms | 32586832 | Dis Model Mech | 2020 Jul 28 |
| Re: Increased 18F-2-Fluorodeoxysorbitol (18F-FDS) Activity in a Pituitary Spindle Cell Carcinoma. | Javadi MS, Ordonez AA, Jain SK | Clinical nuclear medicine | 28319504 | Clin Nucl Med | 2017 Aug |
| PET/CT imaging of CSF1R in a mouse model of tuberculosis. | Foss CA, Ordonez AA, Naik R, Das D, Hall A, Wu Y, Dannals RF, Jain SK, Pomper MG, Horti AG | European journal of nuclear medicine and molecular imaging | 35713665 | Eur J Nucl Med Mol Imaging | 2022 Oct |
| Toehold switches: de-novo-designed regulators of gene expression. | Green AA, Silver PA, Collins JJ, Yin P | Cell | 25417166 | Cell | 2014 Nov 6 |
| Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes. | Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT | Nature communications | 25962338 | Nat Commun | 2015 May 12 |
| 124-Color Super-resolution Imaging by Engineering DNA-PAINT Blinking Kinetics. | Wade OK, Woehrstein JB, Nickels PC, Strauss S, Stehr F, Stein J, Schueder F, Strauss MT, Ganji M, Schnitzbauer J, Grabmayr H, Yin P, Schwille P, Jungmann R | Nano letters | 30864449 | Nano Lett | 2019 Apr 10 |
| SABER amplifies FISH: enhanced multiplexed imaging of RNA and DNA in cells and tissues. | Kishi JY, Lapan SW, Beliveau BJ, West ER, Zhu A, Sasaki HM, Saka SK, Wang Y, Cepko CL, Yin P | Nature methods | 31110282 | Nat Methods | 2019 Jun |
| Imaging RNA polymerase III transcription using a photostable RNA-fluorophore complex. | Song W, Filonov GS, Kim H, Hirsch M, Li X, Moon JD, Jaffrey SR | Nature chemical biology | 28945233 | Nat Chem Biol | 2017 Nov |
| Multiplexed 3D cellular super-resolution imaging with DNA-PAINT and Exchange-PAINT. | Jungmann R, Avendaño MS, Woehrstein JB, Dai M, Shih WM, Yin P | Nature methods | 24487583 | Nat Methods | 2014 Mar |
| A Compact DNA Cube with Side Length 10 nm. | Scheible MB, Ong LL, Woehrstein JB, Jungmann R, Yin P, Simmel FC | Small (Weinheim an der Bergstrasse, Germany) | 26294348 | Small | 2015 Oct 21 |
| Ribocomputing: Cellular Logic Computation Using RNA Devices. | Kim J, Yin P, Green AA | Biochemistry | 29256603 | Biochemistry | 2018 Feb 13 |
| The emerging landscape of single-molecule protein sequencing technologies. | Alfaro JA, Bohländer P, Dai M, Filius M, Howard CJ, van Kooten XF, Ohayon S, Pomorski A, Schmid S, Aksimentiev A, Anslyn EV, Bedran G, Cao C, Chinappi M, Coyaud E, Dekker C, Dittmar G, Drachman N, Eelkema R, Goodlett D, Hentz S, Kalathiya U, Kelleher NL, Kelly RT, Kelman Z, Kim SH, Kuster B, Rodriguez-Larrea D, Lindsay S, Maglia G, Marcotte EM, Marino JP, Masselon C, Mayer M, Samaras P, Sarthak K, Sepiashvili L, Stein D, Wanunu M, Wilhelm M, Yin P, Meller A, Joo C | Nature methods | 34099939 | Nat Methods | 2021 Jun |
| Sub-100-nm metafluorophores with digitally tunable optical properties self-assembled from DNA. | Woehrstein JB, Strauss MT, Ong LL, Wei B, Zhang DY, Jungmann R, Yin P | Science advances | 28691083 | Sci Adv | 2017 Jun |
| Complex cellular logic computation using ribocomputing devices. | Green AA, Kim J, Ma D, Silver PA, Collins JJ, Yin P | Nature | 28746304 | Nature | 2017 Aug 3 |
| Axial plane single-molecule super-resolution microscopy of whole cells. | An S, Ziegler KF, Zhang P, Wang Y, Kwok T, Xu F, Bi C, Matosevic S, Yin P, Li T, Huang F | Biomedical optics express | 32010528 | Biomed Opt Express | 2020 Jan 1 |
| Quantitative super-resolution imaging with qPAINT. | Jungmann R, Avendaño MS, Dai M, Woehrstein JB, Agasti SS, Feiger Z, Rodal A, Yin P | Nature methods | 27018580 | Nat Methods | 2016 May |
| Single-stranded DNA and RNA origami. | Han D, Qi X, Myhrvold C, Wang B, Dai M, Jiang S, Bates M, Liu Y, An B, Zhang F, Yan H, Yin P | Science (New York, N.Y.) | 29242318 | Science | 2017 Dec 15 |
| Polyhedra self-assembled from DNA tripods and characterized with 3D DNA-PAINT. | Iinuma R, Ke Y, Jungmann R, Schlichthaerle T, Woehrstein JB, Yin P | Science (New York, N.Y.) | 24625926 | Science | 2014 Apr 4 |
| Multiplexed Exchange-PAINT imaging reveals ligand-dependent EGFR and Met interactions in the plasma membrane. | Werbin JL, Avendaño MS, Becker V, Jungmann R, Yin P, Danuser G, Sorger PK | Scientific reports | 28939861 | Sci Rep | 2017 Sep 22 |
| A DNA nanoscope via auto-cycling proximity recording. | Schaus TE, Woo S, Xuan F, Chen X, Yin P | Nature communications | 28947733 | Nat Commun | 2017 Sep 25 |
| Universal Super-Resolution Multiplexing by DNA Exchange. | Schueder F, Strauss MT, Hoerl D, Schnitzbauer J, Schlichthaerle T, Strauss S, Yin P, Harz H, Leonhardt H, Jungmann R | Angewandte Chemie (International ed. in English) | 28256790 | Angew Chem Int Ed Engl | 2017 Mar 27 |
| Programmable autonomous synthesis of single-stranded DNA. | Kishi JY, Schaus TE, Gopalkrishnan N, Xuan F, Yin P | Nature chemistry | 29359755 | Nat Chem | 2018 Feb |
| Design space for complex DNA structures. | Wei B, Dai M, Myhrvold C, Ke Y, Jungmann R, Yin P | Journal of the American Chemical Society | 24256506 | J Am Chem Soc | 2013 Dec 4 |
| Super-resolution labelling with Action-PAINT. | Liu N, Dai M, Saka SK, Yin P | Nature chemistry | 31527848 | Nat Chem | 2019 Nov |
| Super-resolution Geometric Barcoding for Multiplexed miRNA Profiling. | Xu W, Yin P, Dai M | Angewandte Chemie (International ed. in English) | 30182521 | Angew Chem Int Ed Engl | 2018 Oct 22 |
| Multiplexed 3D super-resolution imaging of whole cells using spinning disk confocal microscopy and DNA-PAINT. | Schueder F, Lara-Gutiérrez J, Beliveau BJ, Saka SK, Sasaki HM, Woehrstein JB, Strauss MT, Grabmayr H, Yin P, Jungmann R | Nature communications | 29233999 | Nat Commun | 2017 Dec 12 |
| Three-dimensional nanoscopy of whole cells and tissues with in situ point spread function retrieval. | Xu F, Ma D, MacPherson KP, Liu S, Bu Y, Wang Y, Tang Y, Bi C, Kwok T, Chubykin AA, Yin P, Calve S, Landreth GE, Huang F | Nature methods | 32371980 | Nat Methods | 2020 May |
| DNA-barcoded labeling probes for highly multiplexed Exchange-PAINT imaging. | Agasti SS, Wang Y, Schueder F, Sukumar A, Jungmann R, Yin P | Chemical science | 28451377 | Chem Sci | 2017 Apr 1 |
| Optical imaging of individual biomolecules in densely packed clusters. | Dai M, Jungmann R, Yin P | Nature nanotechnology | 27376244 | Nat Nanotechnol | 2016 Sep |
| Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components. | Ong LL, Hanikel N, Yaghi OK, Grun C, Strauss MT, Bron P, Lai-Kee-Him J, Schueder F, Wang B, Wang P, Kishi JY, Myhrvold C, Zhu A, Jungmann R, Bellot G, Ke Y, Yin P | Nature | 29219968 | Nature | 2017 Dec 6 |
| Reconfigurable Three-Dimensional Gold Nanorod Plasmonic Nanostructures Organized on DNA Origami Tripod. | Zhan P, Dutta PK, Wang P, Song G, Dai M, Zhao SX, Wang ZG, Yin P, Zhang W, Ding B, Ke Y | ACS nano | 28056172 | ACS Nano | 2017 Feb 28 |
| Characterization of Lactate Sensors Based on Lactate Oxidase and Palladium Benzoporphyrin Immobilized in Hydrogels. | Andrus LP, Unruh R, Wisniewski NA, McShane MJ | Biosensors | 26198251 | Biosensors (Basel) | 2015 Jul 7 |
| Near-Infrared Optical Nanosensors for Continuous Detection of Glucose. | Le LV, Chendke GS, Gamsey S, Wisniewski N, Desai TA | Journal of diabetes science and technology | 31709808 | J Diabetes Sci Technol | 2020 Mar |
| Preclinical Evaluation of Poly(HEMA-co-acrylamide) Hydrogels Encapsulating Glucose Oxidase and Palladium Benzoporphyrin as Fully Implantable Glucose Sensors. | Unruh RM, Roberts JR, Nichols SP, Gamsey S, Wisniewski NA, McShane MJ | Journal of diabetes science and technology | 26085565 | J Diabetes Sci Technol | 2015 Jun 17 |
| Tissue-Integrating Oxygen Sensors: Continuous Tracking of Tissue Hypoxia. | Wisniewski NA, Nichols SP, Gamsey SJ, Pullins S, Au-Yeung KY, Klitzman B, Helton KL | Advances in experimental medicine and biology | 28685468 | Adv Exp Med Biol | 2017 |
| Composite Hydrogels with Engineered Microdomains for Optical Glucose Sensing at Low Oxygen Conditions. | Bornhoeft LR, Biswas A, McShane MJ | Biosensors | 28117762 | Biosensors (Basel) | 2017 Jan 22 |
| Enzymatic Glucose Sensor Compensation for Variations in Ambient Oxygen Concentration. | Collier BB, McShane MJ | Proceedings of SPIE--the International Society for Optical Engineering | 26257458 | Proc SPIE Int Soc Opt Eng | 2015 Feb |
| A Versatile Multichannel Instrument for Measurement of Ratiometric Fluorescence Intensity and Phosphorescence Lifetime. | Zavareh AT, Ko B, Roberts J, Elahi S, McShane MJ | IEEE access : practical innovations, open solutions | 34858770 | IEEE Access | 2021 |
| The First-in-Man "Si Se Puede" Study for the use of micro-oxygen sensors (MOXYs) to determine dynamic relative oxygen indices in the feet of patients with limb-threatening ischemia during endovascular therapy. | Montero-Baker MF, Au-Yeung KY, Wisniewski NA, Gamsey S, Morelli-Alvarez L, Mills JL Sr, Campos M, Helton KL | Journal of vascular surgery | 26004327 | J Vasc Surg | 2015 Jun |
| Long-Term In Vivo Oxygen Sensors for Peripheral Artery Disease Monitoring. | Nichols SP, Balaconis MK, Gant RM, Au-Yeung KY, Wisniewski NA | Advances in experimental medicine and biology | 30178370 | Adv Exp Med Biol | 2018 |
| Continuous monitoring of interstitial tissue oxygen using subcutaneous oxygen microsensors: In vivo characterization in healthy volunteers. | Kanick SC, Schneider PA, Klitzman B, Wisniewski NA, Rebrin K | Microvascular research | 30742844 | Microvasc Res | 2019 Jul |
| A Design Full of Holes: Functional Nanofilm-Coated Microdomains in Alginate Hydrogels. | Roberts JR, Ritter DW, McShane MJ | Journal of materials chemistry. B | 24040514 | J Mater Chem B | 2013 |
| Temperature Compensation of Oxygen Sensing Films Utilizing a Dynamic Dual Lifetime Calculation Technique. | Collier BB, McShane MJ | IEEE sensors journal | 26566384 | IEEE Sens J | 2014 Aug |
| Inorganic-Organic Interpenetrating Network Hydrogels as Tissue-Integrating Luminescent Implants: Physicochemical Characterization and Preclinical Evaluation. | Unruh RM, Bornhoeft LR, Nichols SP, Wisniewski NA, McShane MJ | Macromolecular bioscience | 34847287 | Macromol Biosci | 2022 Mar |
| Modification of PEGylated enzyme with glutaraldehyde can enhance stability while avoiding intermolecular crosslinking. | Ritter DW, Newton JM, McShane MJ | RSC advances | 26052433 | RSC Adv | 2014 |
| Fluorescence imaging of cellular metabolites with RNA. | Paige JS, Nguyen-Duc T, Song W, Jaffrey SR | Science (New York, N.Y.) | 22403384 | Science | 2012 Mar 9 |
| Imaging bacterial protein expression using genetically encoded RNA sensors. | Song W, Strack RL, Jaffrey SR | Nature methods | 23872791 | Nat Methods | 2013 Sep |
| Imaging metabolite dynamics in living cells using a Spinach-based riboswitch. | You M, Litke JL, Jaffrey SR | Proceedings of the National Academy of Sciences of the United States of America | 25964329 | Proc Natl Acad Sci U S A | 2015 May 26 |
| Designing optogenetically controlled RNA for regulating biological systems. | You M, Jaffrey SR | Annals of the New York Academy of Sciences | 25758022 | Ann N Y Acad Sci | 2015 Sep |
| Detection of Low-Abundance Metabolites in Live Cells Using an RNA Integrator. | You M, Litke JL, Wu R, Jaffrey SR | Cell chemical biology | 30773480 | Cell Chem Biol | 2019 Apr 18 |
| Plug-and-play fluorophores extend the spectral properties of Spinach. | Song W, Strack RL, Svensen N, Jaffrey SR | Journal of the American Chemical Society | 24393009 | J Am Chem Soc | 2014 Jan 29 |
| Broccoli: rapid selection of an RNA mimic of green fluorescent protein by fluorescence-based selection and directed evolution. | Filonov GS, Moon JD, Svensen N, Jaffrey SR | Journal of the American Chemical Society | 25337688 | J Am Chem Soc | 2014 Nov 19 |
| A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. | Strack RL, Disney MD, Jaffrey SR | Nature methods | 24162923 | Nat Methods | 2013 Dec |
| In-gel imaging of RNA processing using broccoli reveals optimal aptamer expression strategies. | Filonov GS, Kam CW, Song W, Jaffrey SR | Chemistry & biology | 26000751 | Chem Biol | 2015 May 21 |
| Spectral Tuning by a Single Nucleotide Controls the Fluorescence Properties of a Fluorogenic Aptamer. | Filonov GS, Song W, Jaffrey SR | Biochemistry | 30838859 | Biochemistry | 2019 Mar 26 |
| Peptide Synthesis on a Next-Generation DNA Sequencing Platform. | Svensen N, Peersen OB, Jaffrey SR | Chembiochem : a European journal of chemical biology | 27385640 | Chembiochem | 2016 Sep 2 |
| Structure and Mechanism of RNA Mimics of Green Fluorescent Protein. | You M, Jaffrey SR | Annual review of biophysics | 26098513 | Annu Rev Biophys | 2015 |
| New approaches for sensing metabolites and proteins in live cells using RNA. | Strack RL, Jaffrey SR | Current opinion in chemical biology | 23746618 | Curr Opin Chem Biol | 2013 Aug |
| Rapid Selection of RNA Aptamers that Activate Fluorescence of Small Molecules. | Filonov GS | Methods in molecular biology (Clifton, N.J.) | 28255887 | Methods Mol Biol | 2017 |
| Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells. | Litke JL, You M, Jaffrey SR | Methods in enzymology | 27241761 | Methods Enzymol | 2016 |
| Using Spinach-based sensors for fluorescence imaging of intracellular metabolites and proteins in living bacteria. | Strack RL, Song W, Jaffrey SR | Nature protocols | 24356773 | Nat Protoc | 2014 Jan |
| RNA-Based Fluorescent Biosensors for Detecting Metabolites in vitro and in Living Cells. | Jaffrey SR | Advances in pharmacology (San Diego, Calif.) | 29413520 | Adv Pharmacol | 2018 |
| RNA Imaging with Dimeric Broccoli in Live Bacterial and Mammalian Cells. | Filonov GS, Jaffrey SR | Current protocols in chemical biology | 26995352 | Curr Protoc Chem Biol | 2016 Mar 16 |
| Enhancing protease activity assay in droplet-based microfluidics using a biomolecule concentrator. | Chen CH, Sarkar A, Song YA, Miller MA, Kim SJ, Griffith LG, Lauffenburger DA, Han J | Journal of the American Chemical Society | 21671557 | J Am Chem Soc | 2011 Jul 13 |
| Adaptive growth factor delivery from a polyelectrolyte coating promotes synergistic bone tissue repair and reconstruction. | Shah NJ, Hyder MN, Quadir MA, Dorval Courchesne NM, Seeherman HJ, Nevins M, Spector M, Hammond PT | Proceedings of the National Academy of Sciences of the United States of America | 25136093 | Proc Natl Acad Sci U S A | 2014 Sep 2 |
| On-demand dissolution of modular, synthetic extracellular matrix reveals local epithelial-stromal communication networks. | Valdez J, Cook CD, Ahrens CC, Wang AJ, Brown A, Kumar M, Stockdale L, Rothenberg D, Renggli K, Gordon E, Lauffenburger D, White F, Griffith L | Biomaterials | 28371736 | Biomaterials | 2017 Jun |
| Osteotropic therapy via targeted layer-by-layer nanoparticles. | Morton SW, Shah NJ, Quadir MA, Deng ZJ, Poon Z, Hammond PT | Advanced healthcare materials | 24124132 | Adv Healthc Mater | 2014 Jun |
| Engineering fibronectin-based binding proteins by yeast surface display. | Chen TF, de Picciotto S, Hackel BJ, Wittrup KD | Methods in enzymology | 23422436 | Methods Enzymol | 2013 |
| Multiplexed protease activity assay for low-volume clinical samples using droplet-based microfluidics and its application to endometriosis. | Chen CH, Miller MA, Sarkar A, Beste MT, Isaacson KB, Lauffenburger DA, Griffith LG, Han J | Journal of the American Chemical Society | 23157326 | J Am Chem Soc | 2013 Feb 6 |
| Engineering liver. | Griffith LG, Wells A, Stolz DB | Hepatology (Baltimore, Md.) | 24668880 | Hepatology | 2014 Oct |
| Microfluidic probe for single-cell analysis in adherent tissue culture. | Sarkar A, Kolitz S, Lauffenburger DA, Han J | Nature communications | 24594667 | Nat Commun | 2014 Mar 5 |
| ADAM9 inhibition increases membrane activity of ADAM10 and controls α-secretase processing of amyloid precursor protein. | Moss ML, Powell G, Miller MA, Edwards L, Qi B, Sang QX, De Strooper B, Tesseur I, Lichtenthaler SF, Taverna M, Zhong JL, Dingwall C, Ferdous T, Schlomann U, Zhou P, Griffith LG, Lauffenburger DA, Petrovich R, Bartsch JW | The Journal of biological chemistry | 21956108 | J Biol Chem | 2011 Nov 25 |
| Helix versus coil polypeptide macromers: gel networks with decoupled stiffness and permeability. | Oelker AM, Morey SM, Griffith LG, Hammond PT | Soft matter | 24575148 | Soft Matter | 2012 Nov 14 |
| Targeting tumor cell motility as a strategy against invasion and metastasis. | Wells A, Grahovac J, Wheeler S, Ma B, Lauffenburger D | Trends in pharmacological sciences | 23571046 | Trends Pharmacol Sci | 2013 May |
| Growth factor regulation of proliferation and survival of multipotential stromal cells. | Rodrigues M, Griffith LG, Wells A | Stem cell research & therapy | 20977782 | Stem Cell Res Ther | 2010 Oct 26 |
| Proteolytic Activity Matrix Analysis (PrAMA) for simultaneous determination of multiple protease activities. | Miller MA, Barkal L, Jeng K, Herrlich A, Moss M, Griffith LG, Lauffenburger DA | Integrative biology : quantitative biosciences from nano to macro | 21180771 | Integr Biol (Camb) | 2011 Apr |
| Co-regulation of primary mouse hepatocyte viability and function by oxygen and matrix. | Buck LD, Inman SW, Rusyn I, Griffith LG | Biotechnology and bioengineering | 24222008 | Biotechnol Bioeng | 2014 May |
| High resolution stereolithography fabrication of perfusable scaffolds to enable long-term meso-scale hepatic culture for disease modeling. | Sphabmixay P, Raredon MSB, Wang AJ, Lee H, Hammond PT, Fang NX, Griffith LG | Biofabrication | 34479229 | Biofabrication | 2021 Sep 21 |
| Models of signalling networks - what cell biologists can gain from them and give to them. | Janes KA, Lauffenburger DA | Journal of cell science | 23720376 | J Cell Sci | 2013 May 1 |
| Endothelial cell phenotypic behaviors cluster into dynamic state transition programs modulated by angiogenic and angiostatic cytokines. | Rimchala T, Kamm RD, Lauffenburger DA | Integrative biology : quantitative biosciences from nano to macro | 23303249 | Integr Biol (Camb) | 2013 Mar |
| The dormancy dilemma: quiescence versus balanced proliferation. | Wells A, Griffith L, Wells JZ, Taylor DP | Cancer research | 23794703 | Cancer Res | 2013 Jul 1 |
| Closed-loop feedback control for microfluidic systems through automated capacitive fluid height sensing. | Soenksen LR, Kassis T, Noh M, Griffith LG, Trumper DL | Lab on a chip | 29437172 | Lab Chip | 2018 Mar 13 |
| Transport and shear in a microfluidic membrane bilayer device for cell culture. | Inamdar NK, Griffith LG, Borenstein JT | Biomicrofluidics | 21799719 | Biomicrofluidics | 2011 Jun |
| Hepatic nonparenchymal cells drive metastatic breast cancer outgrowth and partial epithelial to mesenchymal transition. | Taylor DP, Clark A, Wheeler S, Wells A | Breast cancer research and treatment | 24610032 | Breast Cancer Res Treat | 2014 Apr |
| Dual responsiveness of a tunable thermo-sensitive polypeptide. | Chopko CM, Lowden EL, Engler AC, Griffith LG, Hammond PT | ACS macro letters | 24883233 | ACS Macro Lett | 2012 Jun 19 |
| Molecular network analysis of endometriosis reveals a role for c-Jun-regulated macrophage activation. | Beste MT, Pfäffle-Doyle N, Prentice EA, Morris SN, Lauffenburger DA, Isaacson KB, Griffith LG | Science translational medicine | 24500404 | Sci Transl Med | 2014 Feb 5 |
| Approaches to in vitro tissue regeneration with application for human disease modeling and drug development. | Ebrahimkhani MR, Young CL, Lauffenburger DA, Griffith LG, Borenstein JT | Drug discovery today | 24793141 | Drug Discov Today | 2014 Jun |
| Equilibrium and dynamic design principles for binding molecules engineered for reagentless biosensors. | de Picciotto S, Imperiali B, Griffith LG, Wittrup KD | Analytical biochemistry | 24814226 | Anal Biochem | 2014 Sep 1 |
| FRET-capture: a sensitive method for the detection of dynamic protein interactions. | Socher E, Imperiali B | Chembiochem : a European journal of chemical biology | 23239458 | Chembiochem | 2013 Jan 2 |
| Two-photon fluorescence spectroscopy and imaging of 4-dimethylaminonaphthalimide peptide and protein conjugates. | McLean AM, Socher E, Varnavski O, Clark TB, Imperiali B, Goodson T 3rd | The journal of physical chemistry. B | 24245815 | J Phys Chem B | 2013 Dec 19 |
| Insights into proteomic immune cell signaling and communication via data-driven modeling. | Benedict KF, Lauffenburger DA | Current topics in microbiology and immunology | 22878785 | Curr Top Microbiol Immunol | 2013 |
| Measurement and modeling of signaling at the single-cell level. | Kolitz SE, Lauffenburger DA | Biochemistry | 22954137 | Biochemistry | 2012 Sep 25 |
| Design Principles for SuCESsFul Biosensors: Specific Fluorophore/Analyte Binding and Minimization of Fluorophore/Scaffold Interactions. | de Picciotto S, Dickson PM, Traxlmayr MW, Marques BS, Socher E, Zhao S, Cheung S, Kiefer JD, Wand AJ, Griffith LG, Imperiali B, Wittrup KD | Journal of molecular biology | 27448945 | J Mol Biol | 2016 Oct 9 |
| Development and Application of the Metalloprotease Activity Multiplexed Bead-Based Immunoassay (MAMBI). | Ahrens CC, Chiswick EL, Ravindra KC, Miller MA, Ramseier JY, Isaacson KB, Lauffenburger DA, Griffith LG | Biochemistry | 31474112 | Biochemistry | 2019 Sep 24 |
| Engineering Modular 3D Liver Culture Microenvironments In Vitro to Parse the Interplay between Biophysical and Biochemical Microenvironment Cues on Hepatic Phenotypes. | Wang AJ, Allen A, Sofman M, Sphabmixay P, Yildiz E, Griffith LG | Advanced nanobiomed research | 35872804 | Adv Nanobiomed Res | 2022 Jan |
| ADAM-10 and -17 regulate endometriotic cell migration via concerted ligand and receptor shedding feedback on kinase signaling. | Miller MA, Meyer AS, Beste MT, Lasisi Z, Reddy S, Jeng KW, Chen CH, Han J, Isaacson K, Griffith LG, Lauffenburger DA | Proceedings of the National Academy of Sciences of the United States of America | 23674691 | Proc Natl Acad Sci U S A | 2013 May 28 |
| Modeling boundary conditions for balanced proliferation in metastatic latency. | Taylor DP, Wells JZ, Savol A, Chennubhotla C, Wells A | Clinical cancer research : an official journal of the American Association for Cancer Research | 23329811 | Clin Cancer Res | 2013 Mar 1 |
| Matrikine and matricellular regulators of EGF receptor signaling on cancer cell migration and invasion. | Grahovac J, Wells A | Laboratory investigation; a journal of technical methods and pathology | 24247562 | Lab Invest | 2014 Jan |
| Bioreactor technologies to support liver function in vitro. | Ebrahimkhani MR, Neiman JA, Raredon MS, Hughes DJ, Griffith LG | Advanced drug delivery reviews | 24607703 | Adv Drug Deliv Rev | 2014 Apr |
| The matrikine tenascin-C protects multipotential stromal cells/mesenchymal stem cells from death cytokines such as FasL. | Rodrigues M, Yates CC, Nuschke A, Griffith L, Wells A | Tissue engineering. Part A | 23541003 | Tissue Eng Part A | 2013 Sep |
| Matrix control of scarring. | Yates CC, Bodnar R, Wells A | Cellular and molecular life sciences : CMLS | 21390544 | Cell Mol Life Sci | 2011 Jun |
| Uncharged Helical Modular Polypeptide Hydrogels for Cellular Scaffolds. | Ahrens CC, Welch ME, Griffith LG, Hammond PT | Biomacromolecules | 26461932 | Biomacromolecules | 2015 Dec 14 |
| Chemoproteomics of matrix metalloproteases in a model of cartilage degeneration suggests functional biomarkers associated with posttraumatic osteoarthritis. | Ravindra KC, Ahrens CC, Wang Y, Ramseier JY, Wishnok JS, Griffith LG, Grodzinsky AJ, Tannenbaum SR | The Journal of biological chemistry | 29794029 | J Biol Chem | 2018 Jul 20 |
| Covalent Modification of Synthetic Hydrogels with Bioactive Proteins via Sortase-Mediated Ligation. | Cambria E, Renggli K, Ahrens CC, Cook CD, Kroll C, Krueger AT, Imperiali B, Griffith LG | Biomacromolecules | 26098148 | Biomacromolecules | 2015 Aug 10 |
| Synchronized time-lens source for coherent Raman scattering microscopy. | Wang K, Freudiger CW, Lee JH, Saar BG, Xie XS, Xu C | Optics express | 21164749 | Opt Express | 2010 Nov 8 |
| RNAi screening for fat regulatory genes with SRS microscopy. | Wang MC, Min W, Freudiger CW, Ruvkun G, Xie XS | Nature methods | 21240281 | Nat Methods | 2011 Feb |
| Quantitative chemical imaging with multiplex stimulated Raman scattering microscopy. | Fu D, Lu FK, Zhang X, Freudiger C, Pernik DR, Holtom G, Xie XS | Journal of the American Chemical Society | 22316340 | J Am Chem Soc | 2012 Feb 29 |
| Coherent nonlinear optical imaging: beyond fluorescence microscopy. | Min W, Freudiger CW, Lu S, Xie XS | Annual review of physical chemistry | 21453061 | Annu Rev Phys Chem | 2011 |
| Multicolor stimulated Raman scattering (SRS) microscopy. | Lu FK, Ji M, Fu D, Ni X, Freudiger CW, Holtom G, Xie XS | Molecular physics | 23504195 | Mol Phys | 2012 Aug |
| Olfactory sensory neurons transiently express multiple olfactory receptors during development. | Tan L, Li Q, Xie XS | Molecular systems biology | 26646940 | Mol Syst Biol | 2015 Dec 8 |
| Rare event of histone demethylation can initiate singular gene expression of olfactory receptors. | Tan L, Zong C, Xie XS | Proceedings of the National Academy of Sciences of the United States of America | 24344257 | Proc Natl Acad Sci U S A | 2013 Dec 24 |
| Fiber optical parametric oscillator for coherent anti-Stokes Raman scattering microscopy. | Lamb ES, Lefrancois S, Ji M, Wadsworth WJ, Xie XS, Wise FW | Optics letters | 24321947 | Opt Lett | 2013 Oct 15 |
| Video-rate molecular imaging in vivo with stimulated Raman scattering. | Saar BG, Freudiger CW, Reichman J, Stanley CM, Holtom GR, Xie XS | Science (New York, N.Y.) | 21127249 | Science | 2010 Dec 3 |
| High-power picosecond fiber source for coherent Raman microscopy. | Kieu K, Saar BG, Holtom GR, Xie XS, Wise FW | Optics letters | 19571996 | Opt Lett | 2009 Jul 1 |
| Label-free DNA imaging in vivo with stimulated Raman scattering microscopy. | Lu FK, Basu S, Igras V, Hoang MP, Ji M, Fu D, Holtom GR, Neel VA, Freudiger CW, Fisher DE, Xie XS | Proceedings of the National Academy of Sciences of the United States of America | 26324899 | Proc Natl Acad Sci U S A | 2015 Sep 15 |
| Imaging the intracellular distribution of tyrosine kinase inhibitors in living cells with quantitative hyperspectral stimulated Raman scattering. | Fu D, Zhou J, Zhu WS, Manley PW, Wang YK, Hood T, Wylie A, Xie XS | Nature chemistry | 24950332 | Nat Chem | 2014 Jul |
| Optical heterodyne-detected Raman-induced Kerr effect (OHD-RIKE) microscopy. | Freudiger CW, Roeffaers MB, Zhang X, Saar BG, Min W, Xie XS | The journal of physical chemistry. B | 21504149 | J Phys Chem B | 2011 May 12 |
| Coherent Raman scanning fiber endoscopy. | Saar BG, Johnston RS, Freudiger CW, Xie XS, Seibel EJ | Optics letters | 21725423 | Opt Lett | 2011 Jul 1 |
| In vivo metabolic fingerprinting of neutral lipids with hyperspectral stimulated Raman scattering microscopy. | Fu D, Yu Y, Folick A, Currie E, Farese RV Jr, Tsai TH, Xie XS, Wang MC | Journal of the American Chemical Society | 24869754 | J Am Chem Soc | 2014 Jun 18 |
| Hyperspectral imaging with stimulated Raman scattering by chirped femtosecond lasers. | Fu D, Holtom G, Freudiger C, Zhang X, Xie XS | The journal of physical chemistry. B | 23256635 | J Phys Chem B | 2013 Apr 25 |
| Rapid, label-free detection of brain tumors with stimulated Raman scattering microscopy. | Ji M, Orringer DA, Freudiger CW, Ramkissoon S, Liu X, Lau D, Golby AJ, Norton I, Hayashi M, Agar NY, Young GS, Spino C, Santagata S, Camelo-Piragua S, Ligon KL, Sagher O, Xie XS | Science translational medicine | 24005159 | Sci Transl Med | 2013 Sep 4 |
| Rapid intraoperative histology of unprocessed surgical specimens via fibre-laser-based stimulated Raman scattering microscopy. | Orringer DA, Pandian B, Niknafs YS, Hollon TC, Boyle J, Lewis S, Garrard M, Hervey-Jumper SL, Garton HJL, Maher CO, Heth JA, Sagher O, Wilkinson DA, Snuderl M, Venneti S, Ramkissoon SH, McFadden KA, Fisher-Hubbard A, Lieberman AP, Johnson TD, Xie XS, Trautman JK, Freudiger CW, Camelo-Piragua S | Nature biomedical engineering | 28955599 | Nat Biomed Eng | 2017 |
| Label-free live-cell imaging of nucleic acids using stimulated Raman scattering microscopy. | Zhang X, Roeffaers MB, Basu S, Daniele JR, Fu D, Freudiger CW, Holtom GR, Xie XS | Chemphyschem : a European journal of chemical physics and physical chemistry | 22368112 | Chemphyschem | 2012 Mar |
| Multicolored stain-free histopathology with coherent Raman imaging. | Freudiger CW, Pfannl R, Orringer DA, Saar BG, Ji M, Zeng Q, Ottoboni L, Wei Y, Waeber C, Sims JR, De Jager PL, Sagher O, Philbert MA, Xu X, Kesari S, Xie XS, Young GS | Laboratory investigation; a journal of technical methods and pathology | 22906986 | Lab Invest | 2012 Oct |
| Monitoring peripheral nerve degeneration in ALS by label-free stimulated Raman scattering imaging. | Tian F, Yang W, Mordes DA, Wang JY, Salameh JS, Mok J, Chew J, Sharma A, Leno-Duran E, Suzuki-Uematsu S, Suzuki N, Han SS, Lu FK, Ji M, Zhang R, Liu Y, Strominger J, Shneider NA, Petrucelli L, Xie XS, Eggan K | Nature communications | 27796305 | Nat Commun | 2016 Oct 31 |
| Multicolor stimulated Raman scattering microscopy with a rapidly tunable optical parametric oscillator. | Kong L, Ji M, Holtom GR, Fu D, Freudiger CW, Xie XS | Optics letters | 23454943 | Opt Lett | 2013 Jan 15 |
| Highly specific label-free molecular imaging with spectrally tailored excitation stimulated Raman scattering (STE-SRS) microscopy. | Freudiger CW, Min W, Holtom GR, Xu B, Dantus M, Xie XS | Nature photonics | 23015809 | Nat Photonics | 2011 |
| Imaging drug delivery to skin with stimulated Raman scattering microscopy. | Saar BG, Contreras-Rojas LR, Xie XS, Guy RH | Molecular pharmaceutics | 21548600 | Mol Pharm | 2011 Jun 6 |
| Detection of human brain tumor infiltration with quantitative stimulated Raman scattering microscopy. | Ji M, Lewis S, Camelo-Piragua S, Ramkissoon SH, Snuderl M, Venneti S, Fisher-Hubbard A, Garrard M, Fu D, Wang AC, Heth JA, Maher CO, Sanai N, Johnson TD, Freudiger CW, Sagher O, Xie XS, Orringer DA | Science translational medicine | 26468325 | Sci Transl Med | 2015 Oct 14 |
| Improving the accuracy of brain tumor surgery via Raman-based technology. | Hollon T, Lewis S, Freudiger CW, Sunney Xie X, Orringer DA | Neurosurgical focus | 26926067 | Neurosurg Focus | 2016 Mar |
| A Near-Complete Spatial Map of Olfactory Receptors in the Mouse Main Olfactory Epithelium. | Tan L, Xie XS | Chemical senses | 29796642 | Chem Senses | 2018 Jul 5 |
| A stochastic single-molecule event triggers phenotype switching of a bacterial cell. | Choi PJ, Cai L, Frieda K, Xie XS | Science (New York, N.Y.) | 18927393 | Science | 2008 Oct 17 |
| Mapping DNA polymerase errors by single-molecule sequencing. | Lee DF, Lu J, Chang S, Loparo JJ, Xie XS | Nucleic acids research | 27185891 | Nucleic Acids Res | 2016 Jul 27 |
| Stimulated Raman Scattering Microscopy with a Robust Fibre Laser Source. | Freudiger CW, Yang W, Holtom GR, Peyghambarian N, Xie XS, Kieu KQ | Nature photonics | 25313312 | Nat Photonics | 2014 Feb 1 |
| Innate immune pathway modulator screen identifies STING pathway activation as a strategy to inhibit multiple families of arbo and respiratory viruses. | Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Castillo Cario S, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells MS, Ramaiah A, Arumugaswami V | Cell reports. Medicine | 37119814 | Cell Rep Med | 2023 May 16 |
| Low complexity domains of the nucleocapsid protein of SARS-CoV-2 form amyloid fibrils. | Tayeb-Fligelman E, Bowler JT, Tai CE, Sawaya MR, Jiang YX, Garcia G Jr, Griner SL, Cheng X, Salwinski L, Lutter L, Seidler PM, Lu J, Rosenberg GM, Hou K, Abskharon R, Pan H, Zee CT, Boyer DR, Li Y, Anderson DH, Murray KA, Falcon G, Cascio D, Saelices L, Damoiseaux R, Arumugaswami V, Guo F, Eisenberg DS | Nature communications | 37185252 | Nat Commun | 2023 Apr 25 |
| Comparative Analysis of Molecular Pathogenic Mechanisms and Antiviral Development Targeting Old and New World Hantaviruses. | Jeyachandran AV, Irudayam JI, Dubey S, Chakravarty N, Konda B, Shah A, Su B, Wang C, Cui Q, Williams KJ, Srikanth S, Shi Y, Deb A, Damoiseaux R, Stripp BR, Ramaiah A, Arumugaswami V | bioRxiv : the preprint server for biology | 37577539 | bioRxiv | 2023 Aug 5 |
| Neurological pathophysiology of SARS-CoV-2 and pandemic potential RNA viruses: a comparative analysis. | Chakravarty N, Senthilnathan T, Paiola S, Gyani P, Castillo Cario S, Urena E, Jeysankar A, Jeysankar P, Ignatius Irudayam J, Natesan Subramanian S, Lavretsky H, Joshi S, Garcia G Jr, Ramaiah A, Arumugaswami V | FEBS letters | 34757622 | FEBS Lett | 2021 Dec |
| The Apolipoprotein E neutralizing antibody inhibits SARS-CoV-2 infection by blocking cellular entry of lipoviral particles. | Cui Q, Jeyachandran AV, Garcia G, Qin C, Zhou Y, Zhang M, Wang C, Sun G, Liu W, Zhou T, Feng L, Palmer C, Li Z, Aziz A, Gomperts BN, Feng P, Arumugaswami V, Shi Y | MedComm | 37822714 | MedComm (2020) | 2023 Oct |
| Differential Susceptibility of Ex Vivo Primary Glioblastoma Tumors to Oncolytic Effect of Modified Zika Virus. | Garcia G Jr, Chakravarty N, Paiola S, Urena E, Gyani P, Tse C, French SW, Danielpour M, Breunig JJ, Nathanson DA, Arumugaswami V | Cells | 37830597 | Cells | 2023 Sep 29 |
| ORAI1 Limits SARS-CoV-2 Infection by Regulating Tonic Type I IFN Signaling. | Wu B, Ramaiah A, Garcia G Jr, Hasiakos S, Arumugaswami V, Srikanth S | Journal of immunology (Baltimore, Md. : 1950) | 34819389 | J Immunol | 2022 Jan 1 |
| Longitudinal Evaluation of Antibody Persistence in Mother-Infant Dyads After Severe Acute Respiratory Syndrome Coronavirus 2 Infection in Pregnancy. | Cambou MC, Liu CM, Mok T, Fajardo-Martinez V, Paiola SG, Ibarrondo FJ, Kerin T, Fuller T, Tobin NH, Garcia G, Bhattacharya D, Aldrovandi GM, Arumugaswami V, Foo SS, Jung JU, Vasconcelos Z, Brasil P, Brendolin M, Yang OO, Rao R, Nielsen-Saines K | The Journal of infectious diseases | 36082433 | J Infect Dis | 2023 Jan 11 |
| Replication-Deficient Zika Vector-Based Vaccine Provides Maternal and Fetal Protection in Mouse Model. | Garcia G Jr, Chakravarty N, Abu AE, Jeyachandran AV, Takano KA, Brown R, Morizono K, Arumugaswami V | Microbiology spectrum | 36169338 | Microbiol Spectr | 2022 Oct 26 |
| A ketogenic diet can mitigate SARS-CoV-2 induced systemic reprogramming and inflammation. | Palermo A, Li S, Ten Hoeve J, Chellappa A, Morris A, Dillon B, Ma F, Wang Y, Cao E, Shabane B, Acín-Perez R, Petcherski A, Lusis AJ, Hazen S, Shirihai OS, Pellegrini M, Arumugaswami V, Graeber TG, Deb A | Communications biology | 37923961 | Commun Biol | 2023 Nov 3 |
| Fibroblasts in heart scar tissue directly regulate cardiac excitability and arrhythmogenesis. | Wang Y, Li Q, Tao B, Angelini M, Ramadoss S, Sun B, Wang P, Krokhaleva Y, Ma F, Gu Y, Espinoza A, Yamauchi K, Pellegrini M, Novitch B, Olcese R, Qu Z, Song Z, Deb A | Science (New York, N.Y.) | 37769108 | Science | 2023 Sep 29 |
| Development of a blocker of the universal phosphatidylserine- and phosphatidylethanolamine-dependent viral entry pathways. | Song DH, Garcia G Jr, Situ K, Chua BA, Hong MLO, Do EA, Ramirez CM, Harui A, Arumugaswami V, Morizono K | Virology | 34020328 | Virology | 2021 Aug |
| Targeting the coronavirus nucleocapsid protein through GSK-3 inhibition. | Liu X, Verma A, Garcia G Jr, Ramage H, Lucas A, Myers RL, Michaelson JJ, Coryell W, Kumar A, Charney AW, Kazanietz MG, Rader DJ, Ritchie MD, Berrettini WH, Schultz DC, Cherry S, Damoiseaux R, Arumugaswami V, Klein PS | Proceedings of the National Academy of Sciences of the United States of America | 34593624 | Proc Natl Acad Sci U S A | 2021 Oct 19 |
| In Silico Genome Analysis Reveals the Evolution and Potential Impact of SARS-CoV-2 Omicron Structural Changes on Host Immune Evasion and Antiviral Therapeutics. | Chauhan D, Chakravarty N, Jeyachandran AV, Jayakarunakaran A, Sinha S, Mishra R, Arumugaswami V, Ramaiah A | Viruses | 36366559 | Viruses | 2022 Nov 6 |
| Hippo signaling pathway activation during SARS-CoV-2 infection contributes to host antiviral response. | Garcia G Jr, Jeyachandran AV, Wang Y, Irudayam JI, Cario SC, Sen C, Li S, Li Y, Kumar A, Nielsen-Saines K, French SW, Shah PS, Morizono K, Gomperts BN, Deb A, Ramaiah A, Arumugaswami V | PLoS biology | 36346780 | PLoS Biol | 2022 Nov |
| Broad-spectrum antiviral inhibitors targeting pandemic potential RNA viruses. | Garcia G Jr, Irudayam JI, Jeyachandran AV, Dubey S, Chang C, Cario SC, Price N, Arumugam S, Marquez AL, Shah A, Fanaei A, Chakravarty N, Joshi S, Sinha S, French SW, Parcells M, Ramaiah A, Arumugaswami V | bioRxiv : the preprint server for biology | 36711787 | bioRxiv | 2023 Jan 20 |
| Mpox Virus and its ocular surface manifestations. | Chakravarty N, Hemani D, Paravastu R, Ahmad Z, Palani SN, Arumugaswami V, Kumar A | The ocular surface | 38972544 | Ocul Surf | 2024 Oct |
| Differential Susceptibility of Fetal Retinal Pigment Epithelial Cells, hiPSC- Retinal Stem Cells, and Retinal Organoids to Zika Virus Infection. | Contreras D, Garcia G Jr, Jones MK, Martinez LE, Jayakarunakaran A, Gangalapudi V, Tang J, Wu Y, Zhao JJ, Chen Z, Ramaiah A, Tsui I, Kumar A, Nielsen-Saines K, Wang S, Arumugaswami V | Viruses | 36680182 | Viruses | 2023 Jan 1 |
| Cardiomyocytes disrupt pyrimidine biosynthesis in nonmyocytes to regulate heart repair. | Li S, Yokota T, Wang P, Ten Hoeve J, Ma F, Le TM, Abt ER, Zhou Y, Wu R, Nanthavongdouangsy M, Rodriguez A, Wang Y, Lin YJ, Muranaka H, Sharpley M, Braddock DT, MacRae VE, Banerjee U, Chiou PY, Seldin M, Huang D, Teitell M, Gertsman I, Jung M, Bensinger SJ, Damoiseaux R, Faull K, Pellegrini M, Lusis AJ, Graeber TG, Radu CG, Deb A | The Journal of clinical investigation | 34813507 | J Clin Invest | 2022 Jan 18 |
| Hippo Signaling Pathway Activation during SARS-CoV-2 Infection Contributes to Host Antiviral Response. | Garcia G Jr, Wang Y, Ignatius Irudayam J, Jeyachandran AV, Cario SC, Sen C, Li S, Li Y, Kumar A, Nielsen-Saines K, French SW, Shah PS, Morizono K, Gomperts B, Deb A, Ramaiah A, Arumugaswami V | bioRxiv : the preprint server for biology | 35441167 | bioRxiv | 2022 Apr 8 |
| SARS-CoV-2 and its beta variant of concern infect human conjunctival epithelial cells and induce differential antiviral innate immune response. | Singh S, Garcia G Jr, Shah R, Kramerov AA, Wright RE 3rd, Spektor TM, Ljubimov AV, Arumugaswami V, Kumar A | The ocular surface | 34583089 | Ocul Surf | 2022 Jan |
| Regulation of insulin and adipokinetic hormone/glucagon production in flies. | Ahmad M, He L, Perrimon N | Wiley interdisciplinary reviews. Developmental biology | 31379062 | Wiley Interdiscip Rev Dev Biol | 2020 Mar |
| Proximity labeling reveals non-centrosomal microtubule-organizing center components required for microtubule growth and localization. | Sanchez AD, Branon TC, Cote LE, Papagiannakis A, Liang X, Pickett MA, Shen K, Jacobs-Wagner C, Ting AY, Feldman JL | Current biology : CB | 34242576 | Curr Biol | 2021 Aug 23 |
| Repairing the blood-brain barrier. | McMahon AP, Ichida JK | Science (New York, N.Y.) | 35175806 | Science | 2022 Feb 18 |
| Split-TurboID enables contact-dependent proximity labeling in cells. | Cho KF, Branon TC, Rajeev S, Svinkina T, Udeshi ND, Thoudam T, Kwak C, Rhee HW, Lee IK, Carr SA, Ting AY | Proceedings of the National Academy of Sciences of the United States of America | 32424107 | Proc Natl Acad Sci U S A | 2020 Jun 2 |
| RNA-protein interaction mapping via MS2- or Cas13-based APEX targeting. | Han S, Zhao BS, Myers SA, Carr SA, He C, Ting AY | Proceedings of the National Academy of Sciences of the United States of America | 32839320 | Proc Natl Acad Sci U S A | 2020 Sep 8 |
| Protein phosphatase 1 regulates core PCP signaling. | Song S, Cho B, Weiner AT, Nissen SB, Ojeda Naharros I, Sanchez Bosch P, Suyama K, Hu Y, He L, Svinkina T, Udeshi ND, Carr SA, Perrimon N, Axelrod JD | EMBO reports | 37975164 | EMBO Rep | 2023 Dec 6 |
| Protein phosphatase 1 regulates core PCP signaling. | Song S, Cho B, Weiner AT, Nissen SB, Naharros IO, Bosch PS, Suyama K, Hu Y, He L, Svinkina T, Udeshi ND, Carr SA, Perrimon N, Axelrod JD | bioRxiv : the preprint server for biology | 37745534 | bioRxiv | 2023 Sep 13 |
| Engineered allostery in light-regulated LOV-Turbo enables precise spatiotemporal control of proximity labeling in living cells. | Lee SY, Cheah JS, Zhao B, Xu C, Roh H, Kim CK, Cho KF, Udeshi ND, Carr SA, Ting AY | Nature methods | 37188954 | Nat Methods | 2023 Jun |
| Proteomics of protein trafficking by in vivo tissue-specific labeling. | Droujinine IA, Meyer AS, Wang D, Udeshi ND, Hu Y, Rocco D, McMahon JA, Yang R, Guo J, Mu L, Carey DK, Svinkina T, Zeng R, Branon T, Tabatabai A, Bosch JA, Asara JM, Ting AY, Carr SA, McMahon AP, Perrimon N | Nature communications | 33888706 | Nat Commun | 2021 Apr 22 |
| Cell-Surface Proteomic Profiling in the Fly Brain Uncovers Wiring Regulators. | Li J, Han S, Li H, Udeshi ND, Svinkina T, Mani DR, Xu C, Guajardo R, Xie Q, Li T, Luginbuhl DJ, Wu B, McLaughlin CN, Xie A, Kaewsapsak P, Quake SR, Carr SA, Ting AY, Luo L | Cell | 31955847 | Cell | 2020 Jan 23 |
| Proximal tubule responses to injury: interrogation by single-cell transcriptomics. | Cippà PE, McMahon AP | Current opinion in nephrology and hypertension | 37074682 | Curr Opin Nephrol Hypertens | 2023 Jul 1 |
| Spatiotemporally-resolved mapping of RNA binding proteins via functional proximity labeling reveals a mitochondrial mRNA anchor promoting stress recovery. | Qin W, Myers SA, Carey DK, Carr SA, Ting AY | Nature communications | 34404792 | Nat Commun | 2021 Aug 17 |
| Coordination of tumor growth and host wasting by tumor-derived Upd3. | Ding G, Xiang X, Hu Y, Xiao G, Chen Y, Binari R, Comjean A, Li J, Rushworth E, Fu Z, Mohr SE, Perrimon N, Song W | Cell reports | 34407411 | Cell Rep | 2021 Aug 17 |
| Transcription factor Acj6 controls dendrite targeting via a combinatorial cell-surface code. | Xie Q, Li J, Li H, Udeshi ND, Svinkina T, Orlin D, Kohani S, Guajardo R, Mani DR, Xu C, Li T, Han S, Wei W, Shuster SA, Luginbuhl DJ, Quake SR, Murthy SE, Ting AY, Carr SA, Luo L | Neuron | 35613619 | Neuron | 2022 Jul 20 |
| Shared and Distinctive Neighborhoods of Emerin and Lamin B Receptor Revealed by Proximity Labeling and Quantitative Proteomics. | Cheng LC, Zhang X, Abhinav K, Nguyen JA, Baboo S, Martinez-Bartolomé S, Branon TC, Ting AY, Loose E, Yates JR 3rd, Gerace L | Journal of proteome research | 35972904 | J Proteome Res | 2022 Sep 2 |
| In situ cell-type-specific cell-surface proteomic profiling in mice. | Shuster SA, Li J, Chon U, Sinantha-Hu MC, Luginbuhl DJ, Udeshi ND, Carey DK, Takeo YH, Xie Q, Xu C, Mani DR, Han S, Ting AY, Carr SA, Luo L | Neuron | 36220098 | Neuron | 2022 Dec 7 |
| Identifying Common Molecular Mechanisms in Experimental and Human Acute Kidney Injury. | Gerhardt LMS, McMahon AP | Seminars in nephrology | 36402654 | Semin Nephrol | 2022 May |
| Dietary Amino Acids Promote Glucagon-like Hormone Release to Generate Novel Calcium Waves in Adipose Tissues. | He L, Ahmad M, Wu S, Luo S, Shi W, Guo X, Cao Y, Perrimon N | Research square | 38947048 | Res Sq | 2024 Jun 12 |
| Cell-death induced immune response and coagulopathy promote cachexia in Drosophila. | Singh A, Hu Y, Lopes RF, Lane L, Woldemichael H, Xu C, Udeshi ND, Carr SA, Perrimon N | bioRxiv : the preprint server for biology | 39829769 | bioRxiv | 2025 Feb 10 |
| A genetic model for in vivo proximity labelling of the mammalian secretome. | Yang R, Meyer AS, Droujinine IA, Udeshi ND, Hu Y, Guo J, McMahon JA, Carey DK, Xu C, Fang Q, Sha J, Qin S, Rocco D, Wohlschlegel J, Ting AY, Carr SA, Perrimon N, McMahon AP | Open biology | 35946312 | Open Biol | 2022 Aug |
| Deciphering molecular interactions by proximity labeling. | Qin W, Cho KF, Cavanagh PE, Ting AY | Nature methods | 33432242 | Nat Methods | 2021 Feb |
| Proximity-dependent labeling methods for proteomic profiling in living cells: An update. | Bosch JA, Chen CL, Perrimon N | Wiley interdisciplinary reviews. Developmental biology | 32909689 | Wiley Interdiscip Rev Dev Biol | 2021 Jan |
| Proximity-Labeling Reveals Novel Host and Parasite Proteins at the Toxoplasma Parasitophorous Vacuole Membrane. | Cygan AM, Jean Beltran PM, Mendoza AG, Branon TC, Ting AY, Carr SA, Boothroyd JC | mBio | 34749525 | mBio | 2021 Dec 21 |
| Proximity labeling in mammalian cells with TurboID and split-TurboID. | Cho KF, Branon TC, Udeshi ND, Myers SA, Carr SA, Ting AY | Nature protocols | 33139955 | Nat Protoc | 2020 Dec |
| Dynamic mapping of proteome trafficking within and between living cells by TransitID. | Qin W, Cheah JS, Xu C, Messing J, Freibaum BD, Boeynaems S, Taylor JP, Udeshi ND, Carr SA, Ting AY | Cell | 37385249 | Cell | 2023 Jul 20 |
| Molecular and cellular mechanisms of teneurin signaling in synaptic partner matching. | Xu C, Li Z, Lyu C, Hu Y, McLaughlin CN, Wong KKL, Xie Q, Luginbuhl DJ, Li H, Udeshi ND, Svinkina T, Mani DR, Han S, Li T, Li Y, Guajardo R, Ting AY, Carr SA, Li J, Luo L | Cell | 38996528 | Cell | 2024 Sep 5 |
| Gold nanoparticles and tilt pairs to assess protein flexibility by cryo-electron microscopy. | Jagota M, Townshend RJL, Kang LW, Bushnell DA, Dror RO, Kornberg RD, Azubel M | Ultramicroscopy | 34062386 | Ultramicroscopy | 2021 Aug |
| Taf2 mediates DNA binding of Taf14. | Klein BJ, Feigerle JT, Zhang J, Ebmeier CC, Fan L, Singh RK, Wang WW, Schmitt LR, Lee T, Hansen KC, Liu WR, Wang YX, Strahl BD, Anthony Weil P, Kutateladze TG | Nature communications | 35676274 | Nat Commun | 2022 Jun 8 |
| 3D genomics across the tree of life reveals condensin II as a determinant of architecture type. | Hoencamp C, Dudchenko O, Elbatsh AMO, Brahmachari S, Raaijmakers JA, van Schaik T, Sedeño Cacciatore Á, Contessoto VG, van Heesbeen RGHP, van den Broek B, Mhaskar AN, Teunissen H, St Hilaire BG, Weisz D, Omer AD, Pham M, Colaric Z, Yang Z, Rao SSP, Mitra N, Lui C, Yao W, Khan R, Moroz LL, Kohn A, St Leger J, Mena A, Holcroft K, Gambetta MC, Lim F, Farley E, Stein N, Haddad A, Chauss D, Mutlu AS, Wang MC, Young ND, Hildebrandt E, Cheng HH, Knight CJ, Burnham TLU, Hovel KA, Beel AJ, Mattei PJ, Kornberg RD, Warren WC, Cary G, Gómez-Skarmeta JL, Hinman V, Lindblad-Toh K, Di Palma F, Maeshima K, Multani AS, Pathak S, Nel-Themaat L, Behringer RR, Kaur P, Medema RH, van Steensel B, de Wit E, Onuchic JN, Di Pierro M, Lieberman Aiden E, Rowland BD | Science (New York, N.Y.) | 34045355 | Science | 2021 May 28 |
| Structure of mitotic chromosomes. | Beel AJ, Azubel M, Matteï PJ, Kornberg RD | Molecular cell | 34520722 | Mol Cell | 2021 Nov 4 |
| Primary Role of the Nucleosome. | Kornberg RD, Lorch Y | Molecular cell | 32763226 | Mol Cell | 2020 Aug 6 |
| Simple biochemical features underlie transcriptional activation domain diversity and dynamic, fuzzy binding to Mediator. | Sanborn AL, Yeh BT, Feigerle JT, Hao CV, Townshend RJ, Lieberman Aiden E, Dror RO, Kornberg RD | eLife | 33904398 | Elife | 2021 Apr 27 |
| A conserved Bacteroidetes antigen induces anti-inflammatory intestinal T lymphocytes. | Bousbaine D, Fisch LI, London M, Bhagchandani P, Rezende de Castro TB, Mimee M, Olesen S, Reis BS, VanInsberghe D, Bortolatto J, Poyet M, Cheloha RW, Sidney J, Ling J, Gupta A, Lu TK, Sette A, Alm EJ, Moon JJ, Victora GD, Mucida D, Ploegh HL, Bilate AM | Science (New York, N.Y.) | 35926021 | Science | 2022 Aug 5 |
| Microbiota modulate sympathetic neurons via a gut-brain circuit. | Muller PA, Schneeberger M, Matheis F, Wang P, Kerner Z, Ilanges A, Pellegrino K, Del Mármol J, Castro TBR, Furuichi M, Perkins M, Han W, Rao A, Pickard AJ, Cross JR, Honda K, de Araujo I, Mucida D | Nature | 32641826 | Nature | 2020 Jul |
| Microbiota-modulated CART(+) enteric neurons autonomously regulate blood glucose. | Muller PA, Matheis F, Schneeberger M, Kerner Z, Jové V, Mucida D | Science (New York, N.Y.) | 32855216 | Science | 2020 Oct 16 |
| Gut macrophages: key players in intestinal immunity and tissue physiology. | Muller PA, Matheis F, Mucida D | Current opinion in immunology | 31841704 | Curr Opin Immunol | 2020 Feb |
| Enteric pathogens induce tissue tolerance and prevent neuronal loss from subsequent infections. | Ahrends T, Aydin B, Matheis F, Classon CH, Marchildon F, Furtado GC, Lira SA, Mucida D | Cell | 34717799 | Cell | 2021 Nov 11 |
| Adrenergic Signaling in Muscularis Macrophages Limits Infection-Induced Neuronal Loss. | Matheis F, Muller PA, Graves CL, Gabanyi I, Kerner ZJ, Costa-Borges D, Ahrends T, Rosenstiel P, Mucida D | Cell | 31923400 | Cell | 2020 Jan 9 |
| Tunable dynamics of B cell selection in gut germinal centres. | Nowosad CR, Mesin L, Castro TBR, Wichmann C, Donaldson GP, Araki T, Schiepers A, Lockhart AAK, Bilate AM, Mucida D, Victora GD | Nature | 33116306 | Nature | 2020 Dec |
| Rationale redesign of type III secretion systems: toward the development of non-pathogenic E. coli for in vivo delivery of therapeutic payloads. | González-Prieto C, Lesser CF | Current opinion in microbiology | 29141238 | Curr Opin Microbiol | 2018 Feb |
| In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. | Srivastava R, González-Prieto C, Lynch JP, Muscolo ME, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF | PNAS nexus | 39262854 | PNAS Nexus | 2024 Sep |
| Emerging strategies for engineering Escherichia coli Nissle 1917-based therapeutics. | Lynch JP, Goers L, Lesser CF | Trends in pharmacological sciences | 35232591 | Trends Pharmacol Sci | 2022 Sep |
| Citrobacter rodentium(ϕStx2dact), a murine infection model for enterohemorrhagic Escherichia coli. | Thorpe CM, Pulsifer AR, Osburne MS, Vanaja SK, Leong JM | Current opinion in microbiology | 34929548 | Curr Opin Microbiol | 2022 Feb |
| Living Engineered Bacterial Therapeutics: Emerging Affordable Precision Interventions. | Srivastava R, Lesser CF | Microbial biotechnology | 39579048 | Microb Biotechnol | 2024 Nov |
| PROT(3)EcT, engineered Escherichia coli for the targeted delivery of therapeutics. | González-Prieto C, Lynch JP, Lesser CF | Trends in molecular medicine | 37574350 | Trends Mol Med | 2023 Nov |
| Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917. | Gelfat I, Aqeel Y, Tremblay JM, Jaskiewicz JJ, Shrestha A, Lee JN, Hu S, Qian X, Magoun L, Sheoran A, Bedenice D, Giem C, Manjula-Basavanna A, Pulsifer AR, Tu HX, Li X, Minus ML, Osburne MS, Tzipori S, Shoemaker CB, Leong JM, Joshi NS | PLoS pathogens | 36107831 | PLoS Pathog | 2022 Sep |
| A host metabolite promotes Salmonella survival. | Lynch JP, Lesser CF | Science (New York, N.Y.) | 33479138 | Science | 2021 Jan 22 |
| Engineered Escherichia coli for the in situ secretion of therapeutic nanobodies in the gut. | Lynch JP, González-Prieto C, Reeves AZ, Bae S, Powale U, Godbole NP, Tremblay JM, Schmidt FI, Ploegh HL, Kansra V, Glickman JN, Leong JM, Shoemaker CB, Garrett WS, Lesser CF | Cell host & microbe | 37003258 | Cell Host Microbe | 2023 Apr 12 |
| In situ deposition of nanobodies by an engineered commensal microbe promotes survival in a mouse model of enterohemorrhagic E. coli. | Srivastava R, González-Prieto C, Lynch JP, Muscolo M, Lin CY, Brown MA, Lemos L, Shrestha A, Osburne MS, Leong JM, Lesser CF | bioRxiv : the preprint server for biology | 39131305 | bioRxiv | 2024 Jul 30 |
| Growth and stress response mechanisms underlying post-feeding regenerative organ growth in the Burmese python. | Andrew AL, Perry BW, Card DC, Schield DR, Ruggiero RP, McGaugh SE, Choudhary A, Secor SM, Castoe TA | BMC genomics | 28464824 | BMC Genomics | 2017 May 2 |
| Native Zinc Catalyzes Selective and Traceless Release of Small Molecules in β-Cells. | Lee M, Maji B, Manna D, Kahraman S, Elgamal RM, Small J, Kokkonda P, Vetere A, Goldberg JM, Lippard SJ, Kulkarni RN, Wagner BK, Choudhary A | Journal of the American Chemical Society | 32175731 | J Am Chem Soc | 2020 Apr 8 |
| Engineering designer beta cells with a CRISPR-Cas9 conjugation platform. | Lim D, Sreekanth V, Cox KJ, Law BK, Wagner BK, Karp JM, Choudhary A | Nature communications | 32792475 | Nat Commun | 2020 Aug 13 |
| Rational Design of Silicon-Based Zinc Ionophores. | Yamada K, Deb A, Shoba VM, Lim D, Maji B, Modell AE, Choudhary A | Angewandte Chemie (International ed. in English) | 35385189 | Angew Chem Int Ed Engl | 2022 Jun 7 |
| A 3D culture platform enables development of zinc-binding prodrugs for targeted proliferation of β cells. | Yang K, Lee M, Jones PA, Liu SS, Zhou A, Xu J, Sreekanth V, Wu JLY, Vo L, Lee EA, Pop R, Lee Y, Wagner BK, Melton DA, Choudhary A, Karp JM | Science advances | 33208361 | Sci Adv | 2020 Nov |
| Excess pancreatic elastase alters acinar-β cell communication by impairing the mechano-signaling and the PAR2 pathways. | Basile G, Vetere A, Hu J, Ijaduola O, Zhang Y, Liu KC, Eltony AM, De Jesus DF, Fukuda K, Doherty G, Leech CA, Chepurny OG, Holz GG, Yun SH, Andersson O, Choudhary A, Wagner BK, Kulkarni RN | Cell metabolism | 37339634 | Cell Metab | 2023 Jul 11 |
| A new microphysiological system shows hypoxia primes human ISCs for interleukin-dependent rescue of stem cell activity. | Rivera KR, Bliton RJ, Burclaff J, Czerwinski MJ, Liu J, Trueblood JM, Hinesley CM, Breau KA, Joshi S, Pozdin VA, Yao M, Ziegler AL, Blikslager AT, Daniele MA, Magness ST | bioRxiv : the preprint server for biology | 36778265 | bioRxiv | 2023 Feb 1 |
| In Vitro Generation of Mouse Colon Crypts. | Wang Y, Gunasekara DB, Attayek PJ, Reed MI, DiSalvo M, Nguyen DL, Dutton JS, Lebhar MS, Bultman SJ, Sims CE, Magness ST, Allbritton NL | ACS biomaterials science & engineering | 30854421 | ACS Biomater Sci Eng | 2017 Oct 9 |
| Primary Cell-Derived Intestinal Models: Recapitulating Physiology. | Dutton JS, Hinman SS, Kim R, Wang Y, Allbritton NL | Trends in biotechnology | 30591184 | Trends Biotechnol | 2019 Jul |
| Reserve Stem Cells in Intestinal Homeostasis and Injury. | Bankaitis ED, Ha A, Kuo CJ, Magness ST | Gastroenterology | 30118745 | Gastroenterology | 2018 Nov |
| Formation of Human Colonic Crypt Array by Application of Chemical Gradients Across a Shaped Epithelial Monolayer. | Wang Y, Kim R, Gunasekara DB, Reed MI, DiSalvo M, Nguyen DL, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29693040 | Cell Mol Gastroenterol Hepatol | 2018 |
| Interplay between diet, gut microbiota, epigenetic events, and colorectal cancer. | Bultman SJ | Molecular nutrition & food research | 27138454 | Mol Nutr Food Res | 2017 Jan |
| Magnetically-propelled fecal surrogates for modeling the impact of solid-induced shear forces on primary colonic epithelial cells. | Hinman SS, Huling J, Wang Y, Wang H, Bretherton RC, DeForest CA, Allbritton NL | Biomaterials | 34412014 | Biomaterials | 2021 Sep |
| TGFB1 induces fetal reprogramming and enhances intestinal regeneration. | Chen L, Qiu X, Dupre A, Pellon-Cardenas O, Fan X, Xu X, Rout P, Walton KD, Burclaff J, Zhang R, Fang W, Ofer R, Logerfo A, Vemuri K, Bandyopadhyay S, Wang J, Barbet G, Wang Y, Gao N, Perekatt AO, Hu W, Magness ST, Spence JR, Verzi MP | Cell stem cell | 37865088 | Cell Stem Cell | 2023 Nov 2 |
| In vitro generation of self-renewing human intestinal epithelia over planar and shaped collagen hydrogels. | Hinman SS, Wang Y, Kim R, Allbritton NL | Nature protocols | 33299154 | Nat Protoc | 2021 Jan |
| "Fix and Click" for Assay of Sphingolipid Signaling in Single Primary Human Intestinal Epithelial Cells. | Gallion LA, Wang Y, Massaro A, Yao M, Petersen BV, Zhang Q, Huang W, Carr AJ, Zhang Q, Allbritton NL | Analytical chemistry | 35020354 | Anal Chem | 2022 Jan 25 |
| Nonsteroidal Anti-Inflammatory Drug-Induced Leaky Gut Modeled Using Polarized Monolayers of Primary Human Intestinal Epithelial Cells. | Bhatt AP, Gunasekara DB, Speer J, Reed MI, Peña AN, Midkiff BR, Magness ST, Bultman SJ, Allbritton NL, Redinbo MR | ACS infectious diseases | 29094594 | ACS Infect Dis | 2018 Jan 12 |
| An in vitro intestinal platform with a self-sustaining oxygen gradient to study the human gut/microbiome interface. | Kim R, Attayek PJ, Wang Y, Furtado KL, Tamayo R, Sims CE, Allbritton NL | Biofabrication | 31519008 | Biofabrication | 2019 Nov 6 |
| Recombination drives the evolution of mutational robustness. | Singhal S, Gomez SM, Burch CL | Current opinion in systems biology | 31572829 | Curr Opin Syst Biol | 2019 Feb |
| Building a Thick Mucus Hydrogel Layer to Improve the Physiological Relevance of In Vitro Primary Colonic Epithelial Models. | Wang Y, Kim R, Sims CE, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 31356887 | Cell Mol Gastroenterol Hepatol | 2019 |
| Enterochromaffin Cell-Enriched Monolayer Platform for Assaying Serotonin Release from Human Primary Intestinal Cells. | Wang Y, Sims CE, Allbritton NL | Analytical chemistry | 32819098 | Anal Chem | 2020 Sep 15 |
| Butyrate consumption of differentiated colonocytes in the upper crypt promotes homeostatic proliferation of stem and progenitor cells near the crypt base. | Bultman SJ | Translational cancer research | 30568890 | Transl Cancer Res | 2016 Sep |
| Analysis of Interleukin 8 Secretion by a Stem-Cell-Derived Human-Intestinal-Epithelial-Monolayer Platform. | Wang Y, Kim R, Hwang SJ, Dutton J, Sims CE, Allbritton NL | Analytical chemistry | 30199234 | Anal Chem | 2018 Oct 2 |
| "Fix and assay": separating in-cellulo sphingolipid reactions from analytical assay in time and space using an aldehyde-based fixative. | Proctor A , Allbritton NL | The Analyst | 30207332 | Analyst | 2019 Jan 28 |
| Genomewide CRISPR knockout screen identified PLAC8 as an essential factor for SADS-CoVs infection. | Tse LV, Meganck RM, Araba KC, Yount BL, Shaffer KM, Hou YJ, Munt JE, Adams LE, Wykoff JA, Morowitz JM, Dong S, Magness ST, Marzluff WF, Gonzalez LM, Ehre C, Baric RS | Proceedings of the National Academy of Sciences of the United States of America | 35476513 | Proc Natl Acad Sci U S A | 2022 May 3 |
| Design of 8-mer peptides that block Clostridioides difficile toxin A in intestinal cells. | Sarma S, Catella CM, San Pedro ET, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK | Communications biology | 37634026 | Commun Biol | 2023 Aug 26 |
| A leaky human colon model reveals uncoupled apical/basal cytotoxicity in early Clostridioides difficile toxin exposure. | Ok MT, Liu J, Bliton RJ, Hinesley CM, San Pedro EET, Breau KA, Gomez-Martinez I, Burclaff J, Magness ST | American journal of physiology. Gastrointestinal and liver physiology | 36749911 | Am J Physiol Gastrointest Liver Physiol | 2023 Apr 1 |
| Hyperglycemia minimally alters primary self-renewing human colonic epithelial cells while TNFα-promotes severe intestinal epithelial dysfunction. | Dutton JS, Hinman SS, Kim R, Attayek PJ, Maurer M, Sims CS, Allbritton NL | Integrative biology : quantitative biosciences from nano to macro | 33989405 | Integr Biol (Camb) | 2021 Jun 15 |
| Self-renewing Monolayer of Primary Colonic or Rectal Epithelial Cells. | Wang Y, DiSalvo M, Gunasekara DB, Dutton J, Proctor A, Lebhar MS, Williamson IA, Speer J, Howard RL, Smiddy NM, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29204504 | Cell Mol Gastroenterol Hepatol | 2017 Jul |
| The microbiome and its potential as a cancer preventive intervention. | Bultman SJ | Seminars in oncology | 26970128 | Semin Oncol | 2016 Feb |
| A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. | Williamson IA, Arnold JW, Samsa LA, Gaynor L, DiSalvo M, Cocchiaro JL, Carroll I, Azcarate-Peril MA, Rawls JF, Allbritton NL, Magness ST | Cellular and molecular gastroenterology and hepatology | 30123820 | Cell Mol Gastroenterol Hepatol | 2018 |
| Microphysiological System Design: Simplicity Is Elegance. | Hinman SS, Kim R, Wang Y, Phillips KS, Attayek PJ, Allbritton NL | Current opinion in biomedical engineering | 32095672 | Curr Opin Biomed Eng | 2020 Mar |
| The role of the microbiome in cancer development and therapy. | Bhatt AP, Redinbo MR, Bultman SJ | CA: a cancer journal for clinicians | 28481406 | CA Cancer J Clin | 2017 Jul 8 |
| Development of Arrayed Colonic Organoids for Screening of Secretagogues Associated with Enterotoxins. | Gunasekara DB, DiSalvo M, Wang Y, Nguyen DL, Reed MI, Speer J, Sims CE, Magness ST, Allbritton NL | Analytical chemistry | 29281259 | Anal Chem | 2018 Feb 6 |
| Hypoxia Primes Human ISCs for Interleukin-Dependent Rescue of Stem Cell Activity. | Rivera KR, Bliton RJ, Burclaff J, Czerwinski MJ, Liu J, Trueblood JM, Hinesley CM, Breau KA, Deal HE, Joshi S, Pozdin VA, Yao M, Ziegler AL, Blikslager AT, Daniele MA, Magness ST | Cellular and molecular gastroenterology and hepatology | 37562653 | Cell Mol Gastroenterol Hepatol | 2023 |
| Efficient transgenesis and homology-directed gene targeting in monolayers of primary human small intestinal and colonic epithelial stem cells. | Breau KA, Ok MT, Gomez-Martinez I, Burclaff J, Kohn NP, Magness ST | Stem cell reports | 35523179 | Stem Cell Reports | 2022 Jun 14 |
| Stem/Proliferative and Differentiated Cells within Primary Murine Colonic Epithelium Display Distinct Intracellular Free Ca(2+) Signal Codes. | Mestril S, Kim R, Hinman SS, Gomez SM, Allbritton NL | Advanced healthcare materials | 34510822 | Adv Healthc Mater | 2021 Nov |
| Design of 8-mer Peptides that Block Clostridioides difficile Toxin A in Intestinal Cells. | Sarma S, Catella CM, Pedro ETS, Xiao X, Durmusoglu D, Menegatti S, Crook N, Magness ST, Hall CK | bioRxiv : the preprint server for biology | 36711911 | bioRxiv | 2023 Jan 12 |
| Bioengineered Systems and Designer Matrices That Recapitulate the Intestinal Stem Cell Niche. | Wang Y, Kim R, Hinman SS, Zwarycz B, Magness ST, Allbritton NL | Cellular and molecular gastroenterology and hepatology | 29675459 | Cell Mol Gastroenterol Hepatol | 2018 Mar |
| Formation of arrays of planar, murine, intestinal crypts possessing a stem/proliferative cell compartment and differentiated cell zone. | Kim R, Wang Y, Hwang SJ, Attayek PJ, Smiddy NM, Reed MI, Sims CE, Allbritton NL | Lab on a chip | 29944153 | Lab Chip | 2018 Jul 24 |
| A Monolayer of Primary Colonic Epithelium Generated on a Scaffold with a Gradient of Stiffness for Drug Transport Studies. | Gunasekara DB, Speer J, Wang Y, Nguyen DL, Reed MI, Smiddy NM, Parker JS, Fallon JK, Smith PC, Sims CE, Magness ST, Allbritton NL | Analytical chemistry | 30350627 | Anal Chem | 2018 Nov 20 |
| Molecular transport through primary human small intestinal monolayers by culture on a collagen scaffold with a gradient of chemical cross-linking. | Speer JE, Gunasekara DB, Wang Y, Fallon JK, Attayek PJ, Smith PC, Sims CE, Allbritton NL | Journal of biological engineering | 31061676 | J Biol Eng | 2019 |
| Photopatterned Membranes and Chemical Gradients Enable Scalable Phenotypic Organization of Primary Human Colon Epithelial Models. | Hinman SS, Wang Y, Allbritton NL | Analytical chemistry | 31692334 | Anal Chem | 2019 Dec 3 |
| Integrative microphysiological tissue systems of cancer metastasis to the liver. | Clark AM, Allbritton NL, Wells A | Seminars in cancer biology | 32580025 | Semin Cancer Biol | 2021 Jun |
| A Planar Culture Model of Human Absorptive Enterocytes Reveals Metformin Increases Fatty Acid Oxidation and Export. | Gomez-Martinez I, Bliton RJ, Breau KA, Czerwinski MJ, Williamson IA, Wen J, Rawls JF, Magness ST | Cellular and molecular gastroenterology and hepatology | 35489715 | Cell Mol Gastroenterol Hepatol | 2022 |
| A microengineered collagen scaffold for generating a polarized crypt-villus architecture of human small intestinal epithelium. | Wang Y, Gunasekara DB, Reed MI, DiSalvo M, Bultman SJ, Sims CE, Magness ST, Allbritton NL | Biomaterials | 28288348 | Biomaterials | 2017 Jun |
| Use of liquid lithography to form in vitro intestinal crypts with varying microcurvature surrounding the stem cell niche. | Logan Howard R, Wang Y, Allbritton NL | Journal of micromechanics and microengineering : structures, devices, and systems | 35241878 | J Micromech Microeng | 2021 Dec |
| A Proximal-to-Distal Survey of Healthy Adult Human Small Intestine and Colon Epithelium by Single-Cell Transcriptomics. | Burclaff J, Bliton RJ, Breau KA, Ok MT, Gomez-Martinez I, Ranek JS, Bhatt AP, Purvis JE, Woosley JT, Magness ST | Cellular and molecular gastroenterology and hepatology | 35176508 | Cell Mol Gastroenterol Hepatol | 2022 |
| An in vitro platform for quantifying cell cycle phase lengths in primary human intestinal stem cells. | Cotton MJ, Ariel P, Chen K, Walcott VA, Dixit M, Breau KA, Hinesley CM, Kedziora K, Tang CY, Zheng A, Magness ST, Burclaff J | bioRxiv : the preprint server for biology | 37873351 | bioRxiv | 2023 Oct 10 |
| Prospective functional classification of all possible missense variants in PPARG. | Majithia AR, Tsuda B, Agostini M, Gnanapradeepan K, Rice R, Peloso G, Patel KA, Zhang X, Broekema MF, Patterson N, Duby M, Sharpe T, Kalkhoven E, Rosen ED, Barroso I, Ellard S, UK Monogenic Diabetes Consortium, Kathiresan S, Myocardial Infarction Genetics Consortium, O'Rahilly S, UK Congenital Lipodystrophy Consortium, Chatterjee K, Florez JC, Mikkelsen T, Savage DB, Altshuler D | Nature genetics | 27749844 | Nat Genet | 2016 Dec |
| In vivo genome editing using Staphylococcus aureus Cas9. | Ran FA, Cong L, Yan WX, Scott DA, Gootenberg JS, Kriz AJ, Zetsche B, Shalem O, Wu X, Makarova KS, Koonin EV, Sharp PA, Zhang F | Nature | 25830891 | Nature | 2015 Apr 9 |
| Genome-scale CRISPR-Cas9 knockout screening in human cells. | Shalem O, Sanjana NE, Hartenian E, Shi X, Scott DA, Mikkelson T, Heckl D, Ebert BL, Root DE, Doench JG, Zhang F | Science (New York, N.Y.) | 24336571 | Science | 2014 Jan 3 |
| A Pungent and Painful Toxin. | Green D, Dong X | Cell | 31474364 | Cell | 2019 Sep 5 |
| Genome Editing in Human Pluripotent Stem Cells: Approaches, Pitfalls, and Solutions. | Hendriks WT, Warren CR, Cowan CA | Cell stem cell | 26748756 | Cell Stem Cell | 2016 Jan 7 |
| Genome-Edited Human Pluripotent Stem Cell-Derived Macrophages as a Model of Reverse Cholesterol Transport--Brief Report. | Gupta RM, Meissner TB, Cowan CA, Musunuru K | Arteriosclerosis, thrombosis, and vascular biology | 26543098 | Arterioscler Thromb Vasc Biol | 2016 Jan |
| Humanity in a Dish: Population Genetics with iPSCs. | Warren CR, Cowan CA | Trends in cell biology | 29054332 | Trends Cell Biol | 2018 Jan |
| Improved vectors and genome-wide libraries for CRISPR screening. | Sanjana NE, Shalem O, Zhang F | Nature methods | 25075903 | Nat Methods | 2014 Aug |
| Patient hiPSCs Identify Vascular Smooth Muscle Arylacetamide Deacetylase as Protective against Atherosclerosis. | Toyohara T, Roudnicky F, Florido MHC, Nakano T, Yu H, Katsuki S, Lee M, Meissner T, Friesen M, Davidow LS, Ptaszek L, Abe T, Rubin LL, Pereira AC, Aikawa M, Cowan CA | Cell stem cell | 32413331 | Cell Stem Cell | 2020 Jul 2 |
| [Leukocyte count of puerperal sows]. | Mäde D, Wujanz G | Berliner und Munchener tierarztliche Wochenschrift | 9054332 | Berl Munch Tierarztl Wochenschr | 1996 Sep |
| Common genetic variants modulate pathogen-sensing responses in human dendritic cells. | Lee MN, Ye C, Villani AC, Raj T, Li W, Eisenhaure TM, Imboywa SH, Chipendo PI, Ran FA, Slowikowski K, Ward LD, Raddassi K, McCabe C, Lee MH, Frohlich IY, Hafler DA, Kellis M, Raychaudhuri S, Zhang F, Stranger BE, Benoist CO, De Jager PL, Regev A, Hacohen N | Science (New York, N.Y.) | 24604203 | Science | 2014 Mar 7 |
| Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells. | Wu X, Scott DA, Kriz AJ, Chiu AC, Hsu PD, Dadon DB, Cheng AW, Trevino AE, Konermann S, Chen S, Jaenisch R, Zhang F, Sharp PA | Nature biotechnology | 24752079 | Nat Biotechnol | 2014 Jul |
| Efficient CRISPR-Cas9-mediated genome editing in Plasmodium falciparum. | Wagner JC, Platt RJ, Goldfless SJ, Zhang F, Niles JC | Nature methods | 25108687 | Nat Methods | 2014 Sep |
| Efficient ablation of genes in human hematopoietic stem and effector cells using CRISPR/Cas9. | Mandal PK, Ferreira LM, Collins R, Meissner TB, Boutwell CL, Friesen M, Vrbanac V, Garrison BS, Stortchevoi A, Bryder D, Musunuru K, Brand H, Tager AM, Allen TM, Talkowski ME, Rossi DJ, Cowan CA | Cell stem cell | 25517468 | Cell Stem Cell | 2014 Nov 6 |
| A distant trophoblast-specific enhancer controls HLA-G expression at the maternal-fetal interface. | Ferreira LM, Meissner TB, Mikkelsen TS, Mallard W, O'Donnell CW, Tilburgs T, Gomes HA, Camahort R, Sherwood RI, Gifford DK, Rinn JL, Cowan CA, Strominger JL | Proceedings of the National Academy of Sciences of the United States of America | 27078102 | Proc Natl Acad Sci U S A | 2016 May 10 |
| White-to-brown metabolic conversion of human adipocytes by JAK inhibition. | Moisan A, Lee YK, Zhang JD, Hudak CS, Meyer CA, Prummer M, Zoffmann S, Truong HH, Ebeling M, Kiialainen A, Gérard R, Xia F, Schinzel RT, Amrein KE, Cowan CA | Nature cell biology | 25487280 | Nat Cell Biol | 2015 Jan |
| Fattening chips: hypertrophy, feeding, and fasting of human white adipocytes in vitro. | Pope BD, Warren CR, Dahl MO, Pizza CV, Henze DE, Sinatra NR, Gonzalez GM, Chang H, Liu Q, Glieberman AL, Ferrier JP Jr, Cowan CA, Parker KK | Lab on a chip | 33034335 | Lab Chip | 2020 Nov 10 |
| Low incidence of off-target mutations in individual CRISPR-Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing. | Veres A, Gosis BS, Ding Q, Collins R, Ragavendran A, Brand H, Erdin S, Cowan CA, Talkowski ME, Musunuru K | Cell stem cell | 24996167 | Cell Stem Cell | 2014 Jul 3 |
| CRISPR-mediated direct mutation of cancer genes in the mouse liver. | Xue W, Chen S, Yin H, Tammela T, Papagiannakopoulos T, Joshi NS, Cai W, Yang G, Bronson R, Crowley DG, Zhang F, Anderson DG, Sharp PA, Jacks T | Nature | 25119044 | Nature | 2014 Oct 16 |
| Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs. | Ding Q, Regan SN, Xia Y, Oostrom LA, Cowan CA, Musunuru K | Cell stem cell | 23561441 | Cell Stem Cell | 2013 Apr 4 |
| DNA targeting specificity of RNA-guided Cas9 nucleases. | Hsu PD, Scott DA, Weinstein JA, Ran FA, Konermann S, Agarwala V, Li Y, Fine EJ, Wu X, Shalem O, Cradick TJ, Marraffini LA, Bao G, Zhang F | Nature biotechnology | 23873081 | Nat Biotechnol | 2013 Sep |
| Induced Pluripotent Stem Cell Differentiation Enables Functional Validation of GWAS Variants in Metabolic Disease. | Warren CR, O'Sullivan JF, Friesen M, Becker CE, Zhang X, Liu P, Wakabayashi Y, Morningstar JE, Shi X, Choi J, Xia F, Peters DT, Florido MHC, Tsankov AM, Duberow E, Comisar L, Shay J, Jiang X, Meissner A, Musunuru K, Kathiresan S, Daheron L, Zhu J, Gerszten RE, Deo RC, Vasan RS, O'Donnell CJ, Cowan CA | Cell stem cell | 28388431 | Cell Stem Cell | 2017 Apr 6 |
| Microenvironmental Control of Adipocyte Fate and Function. | Pope BD, Warren CR, Parker KK, Cowan CA | Trends in cell biology | 27268909 | Trends Cell Biol | 2016 Oct |
| Asialoglycoprotein receptor 1 is a specific cell-surface marker for isolating hepatocytes derived from human pluripotent stem cells. | Peters DT, Henderson CA, Warren CR, Friesen M, Xia F, Becker CE, Musunuru K, Cowan CA | Development (Cambridge, England) | 27143754 | Development | 2016 May 1 |
| GPR146 Deficiency Protects against Hypercholesterolemia and Atherosclerosis. | Yu H, Rimbert A, Palmer AE, Toyohara T, Xia Y, Xia F, Ferreira LMR, Chen Z, Chen T, Loaiza N, Horwitz NB, Kacergis MC, Zhao L, BIOS Consortium, Soukas AA, Kuivenhoven JA, Kathiresan S, Cowan CA | Cell | 31778654 | Cell | 2019 Nov 27 |
| Minireview: Genome Editing of Human Pluripotent Stem Cells for Modeling Metabolic Disease. | Yu H, Cowan CA | Molecular endocrinology (Baltimore, Md.) | 27075706 | Mol Endocrinol | 2016 Jun |
| Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity. | Ran FA, Hsu PD, Lin CY, Gootenberg JS, Konermann S, Trevino AE, Scott DA, Inoue A, Matoba S, Zhang Y, Zhang F | Cell | 23992846 | Cell | 2013 Sep 12 |
| A TALEN genome-editing system for generating human stem cell-based disease models. | Ding Q, Lee YK, Schaefer EA, Peters DT, Veres A, Kim K, Kuperwasser N, Motola DL, Meissner TB, Hendriks WT, Trevisan M, Gupta RM, Moisan A, Banks E, Friesen M, Schinzel RT, Xia F, Tang A, Xia Y, Figueroa E, Wann A, Ahfeldt T, Daheron L, Zhang F, Rubin LL, Peng LF, Chung RT, Musunuru K, Cowan CA | Cell stem cell | 23246482 | Cell Stem Cell | 2013 Feb 7 |
| Genome engineering using the CRISPR-Cas9 system. | Ran FA, Hsu PD, Wright J, Agarwala V, Scott DA, Zhang F | Nature protocols | 24157548 | Nat Protoc | 2013 Nov |
| Permanent alteration of PCSK9 with in vivo CRISPR-Cas9 genome editing. | Ding Q, Strong A, Patel KM, Ng SL, Gosis BS, Regan SN, Cowan CA, Rader DJ, Musunuru K | Circulation research | 24916110 | Circ Res | 2014 Aug 15 |
| Genome-wide CRISPR screen in a mouse model of tumor growth and metastasis. | Chen S, Sanjana NE, Zheng K, Shalem O, Lee K, Shi X, Scott DA, Song J, Pan JQ, Weissleder R, Lee H, Zhang F, Sharp PA | Cell | 25748654 | Cell | 2015 Mar 12 |
| CRISPR-Cas9 knockin mice for genome editing and cancer modeling. | Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F | Cell | 25263330 | Cell | 2014 Oct 9 |
| Mitoregulin Controls β-Oxidation in Human and Mouse Adipocytes. | Friesen M, Warren CR, Yu H, Toyohara T, Ding Q, Florido MHC, Sayre C, Pope BD, Goff LA, Rinn JL, Cowan CA | Stem cell reports | 32243843 | Stem Cell Reports | 2020 Apr 14 |
| Generation of vascular endothelial and smooth muscle cells from human pluripotent stem cells. | Patsch C, Challet-Meylan L, Thoma EC, Urich E, Heckel T, O'Sullivan JF, Grainger SJ, Kapp FG, Sun L, Christensen K, Xia Y, Florido MH, He W, Pan W, Prummer M, Warren CR, Jakob-Roetne R, Certa U, Jagasia R, Freskgård PO, Adatto I, Kling D, Huang P, Zon LI, Chaikof EL, Gerszten RE, Graf M, Iacone R, Cowan CA | Nature cell biology | 26214132 | Nat Cell Biol | 2015 Aug |
| The reconstituted 'humanized liver' in TK-NOG mice is mature and functional. | Hasegawa M, Kawai K, Mitsui T, Taniguchi K, Monnai M, Wakui M, Ito M, Suematsu M, Peltz G, Nakamura M, Suemizu H | Biochemical and biophysical research communications | 21238430 | Biochem Biophys Res Commun | 2011 Feb 18 |
| A better prognosis for genetic association studies in mice. | Zheng M, Dill D, Peltz G | Trends in genetics : TIG | 22118772 | Trends Genet | 2012 Feb |
| Identification of drug targets by chemogenomic and metabolomic profiling in yeast. | Wu M, Zheng M, Zhang W, Suresh S, Schlecht U, Fitch WL, Aronova S, Baumann S, Davis R, St Onge R, Dill DL, Peltz G | Pharmacogenetics and genomics | 23076370 | Pharmacogenet Genomics | 2012 Dec |
| Can 'humanized' mice improve drug development in the 21st century? | Peltz G | Trends in pharmacological sciences | 23602782 | Trends Pharmacol Sci | 2013 May |
| Next-generation computational genetic analysis: multiple complement alleles control survival after Candida albicans infection. | Peltz G, Zaas AK, Zheng M, Solis NV, Zhang MX, Liu HH, Hu Y, Boxx GM, Phan QT, Dill D, Filler SG | Infection and immunity | 21875959 | Infect Immun | 2011 Nov |
| Cd14 SNPs regulate the innate immune response. | Liu HH, Hu Y, Zheng M, Suhoski MM, Engleman EG, Dill DL, Hudnall M, Wang J, Spolski R, Leonard WJ, Peltz G | Molecular immunology | 22445606 | Mol Immunol | 2012 Jun |
| Liquid chromatography/mass spectrometry methods for measuring dipeptide abundance in non-small-cell lung cancer. | Wu M, Xu Y, Fitch WL, Zheng M, Merritt RE, Shrager JB, Zhang W, Dill DL, Peltz G, Hoang CD | Rapid communications in mass spectrometry : RCM | 23943330 | Rapid Commun Mass Spectrom | 2013 Sep 30 |
| Computational genetic discoveries that could improve perioperative medicine. | Zheng M, Dill D, Clark JD, Peltz G | Current opinion in anaesthesiology | 22647490 | Curr Opin Anaesthesiol | 2012 Aug |
| Using chimeric mice with humanized livers to predict human drug metabolism and a drug-drug interaction. | Nishimura T, Hu Y, Wu M, Pham E, Suemizu H, Elazar M, Liu M, Idilman R, Yurdaydin C, Angus P, Stedman C, Murphy B, Glenn J, Nakamura M, Nomura T, Chen Y, Zheng M, Fitch WL, Peltz G | The Journal of pharmacology and experimental therapeutics | 23143674 | J Pharmacol Exp Ther | 2013 Feb |
| Opiate-induced changes in brain adenosine levels and narcotic drug responses. | Wu M, Sahbaie P, Zheng M, Lobato R, Boison D, Clark JD, Peltz G | Neuroscience | 23098802 | Neuroscience | 2013 Jan 3 |
| The role of Abcb5 alleles in susceptibility to haloperidol-induced toxicity in mice and humans. | Zheng M, Zhang H, Dill DL, Clark JD, Tu S, Yablonovitch AL, Tan MH, Zhang R, Rujescu D, Wu M, Tessarollo L, Vieira W, Gottesman MM, Deng S, Eberlin LS, Zare RN, Billard JM, Gillet JP, Li JB, Peltz G | PLoS medicine | 25647612 | PLoS Med | 2015 Feb |
| Metabolomic-derived novel cyst fluid biomarkers for pancreatic cysts: glucose and kynurenine. | Park WG, Wu M, Bowen R, Zheng M, Fitch WL, Pai RK, Wodziak D, Visser BC, Poultsides GA, Norton JA, Banerjee S, Chen AM, Friedland S, Scott BA, Pasricha PJ, Lowe AW, Peltz G | Gastrointestinal endoscopy | 23566642 | Gastrointest Endosc | 2013 Aug |
| Helicobacter pylori and esophageal disease: wake-up call? | Blaser MJ | Gastroenterology | 21029801 | Gastroenterology | 2010 Dec |
| The human microbiome: at the interface of health and disease. | Cho I, Blaser MJ | Nature reviews. Genetics | 22411464 | Nat Rev Genet | 2012 Mar 13 |
| Infant antibiotic exposures and early-life body mass. | Trasande L, Blustein J, Liu M, Corwin E, Cox LM, Blaser MJ | International journal of obesity (2005) | 22907693 | Int J Obes (Lond) | 2013 Jan |
| Helicobacter pylori and the birth cohort effect: evidence for stabilized colonization rates in childhood. | den Hoed CM, Vila AJ, Holster IL, Perez-Perez GI, Blaser MJ, de Jongste JC, Kuipers EJ | Helicobacter | 21923687 | Helicobacter | 2011 Oct |
| The impact of Helicobacter pylori on atopic disorders in childhood. | Holster IL, Vila AM, Caudri D, den Hoed CM, Perez-Perez GI, Blaser MJ, de Jongste JC, Kuipers EJ | Helicobacter | 22515362 | Helicobacter | 2012 Jun |
| The microbiome revolution. | Blaser MJ | The Journal of clinical investigation | 25271724 | J Clin Invest | 2014 Oct |
| Intergenerational reduction in Helicobacter pylori prevalence is similar between different ethnic groups living in a Western city. | den Hollander WJ, Holster IL, van Gilst B, van Vuuren AJ, Jaddoe VW, Hofman A, Perez-Perez GI, Kuipers EJ, Moll HA, Blaser MJ | Gut | 25192563 | Gut | 2015 Aug |
| Antibiotics in early life and obesity. | Cox LM, Blaser MJ | Nature reviews. Endocrinology | 25488483 | Nat Rev Endocrinol | 2015 Mar |
| Loss of HDAC6 alters gut microbiota and worsens obesity. | Lieber AD, Beier UH, Xiao H, Wilkins BJ, Jiao J, Li XS, Schugar RC, Strauch CM, Wang Z, Brown JM, Hazen SL, Bokulich NA, Ruggles KV, Akimova T, Hancock WW, Blaser MJ | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 30102568 | FASEB J | 2019 Jan |
| Association of caesarean delivery with child adiposity from age 6 weeks to 15 years. | Blustein J, Attina T, Liu M, Ryan AM, Cox LM, Blaser MJ, Trasande L | International journal of obesity (2005) | 23670220 | Int J Obes (Lond) | 2013 Jul |
| Antibiotic exposure and the development of coeliac disease: a nationwide case-control study. | Mårild K, Ye W, Lebwohl B, Green PH, Blaser MJ, Card T, Ludvigsson JF | BMC gastroenterology | 23834758 | BMC Gastroenterol | 2013 Jul 8 |
| Helicobacter pylori lipids can form ordered membrane domains (rafts). | Huang Z, Zhang XS, Blaser MJ, London E | Biochimica et biophysica acta. Biomembranes | 31449801 | Biochim Biophys Acta Biomembr | 2019 Nov 1 |
| Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course. | Ventura RE, Iizumi T, Battaglia T, Liu M, Perez-Perez GI, Herbert J, Blaser MJ | Scientific reports | 31705027 | Sci Rep | 2019 Nov 8 |
| Severe lung disease characterized by lymphocytic bronchiolitis, alveolar ductitis, and emphysema (BADE) in industrial machine-manufacturing workers. | Cummings KJ, Stanton ML, Nett RJ, Segal LN, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Green BJ, LeBouf RF, Blaser MJ, Weissman DN | American journal of industrial medicine | 31461179 | Am J Ind Med | 2019 Nov |
| Celecoxib does not alter intestinal microbiome in a longitudinal diet-controlled study. | Bokulich NA, Battaglia T, Aleman JO, Walker JM, Blaser MJ, Holt PR | Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases | 26806255 | Clin Microbiol Infect | 2016 May |
| Antibiotics, birth mode, and diet shape microbiome maturation during early life. | Bokulich NA, Chung J, Battaglia T, Henderson N, Jay M, Li H, D Lieber A, Wu F, Perez-Perez GI, Chen Y, Schweizer W, Zheng X, Contreras M, Dominguez-Bello MG, Blaser MJ | Science translational medicine | 27306664 | Sci Transl Med | 2016 Jun 15 |
| Links between environment, diet, and the hunter-gatherer microbiome. | Fragiadakis GK, Smits SA, Sonnenburg ED, Van Treuren W, Reid G, Knight R, Manjurano A, Changalucha J, Dominguez-Bello MG, Leach J, Sonnenburg JL | Gut microbes | 30118385 | Gut Microbes | 2019 |
| Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. | Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL | mBio | 27178263 | mBio | 2016 May 13 |
| Helminth infection promotes colonization resistance via type 2 immunity. | Ramanan D, Bowcutt R, Lee SC, Tang MS, Kurtz ZD, Ding Y, Honda K, Gause WC, Blaser MJ, Bonneau RA, Lim YA, Loke P, Cadwell K | Science (New York, N.Y.) | 27080105 | Science | 2016 Apr 29 |
| Joint modeling of zero-inflated longitudinal proportions and time-to-event data with application to a gut microbiome study. | Hu J, Wang C, Blaser MJ, Li H | Biometrics | 34213763 | Biometrics | 2022 Dec |
| The impact of early-life sub-therapeutic antibiotic treatment (STAT) on excessive weight is robust despite transfer of intestinal microbes. | Schulfer AF, Schluter J, Zhang Y, Brown Q, Pathmasiri W, McRitchie S, Sumner S, Li H, Xavier JB, Blaser MJ | The ISME journal | 30651608 | ISME J | 2019 May |
| Role of childhood infection in the sequelae of H. pylori disease. | Harris PR, Smythies LE, Smith PD, Perez-Perez GI | Gut microbes | 24275060 | Gut Microbes | 2013 Nov-Dec |
| Development of the human gastrointestinal microbiota and insights from high-throughput sequencing. | Dominguez-Bello MG, Blaser MJ, Ley RE, Knight R | Gastroenterology | 21530737 | Gastroenterology | 2011 May |
| Decreased Fecal Bacterial Diversity and Altered Microbiome in Children Colonized With Clostridium difficile. | Chen LA, Hourigan SK, Grigoryan Z, Gao Z, Clemente JC, Rideout JR, Chirumamilla S, Rabidazeh S, Saeed S, Elson CO, Oliva-Hemker M, Blaser MJ, Sears CL | Journal of pediatric gastroenterology and nutrition | 30540709 | J Pediatr Gastroenterol Nutr | 2019 Apr |
| Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice. | Schulfer AF, Battaglia T, Alvarez Y, Bijnens L, Ruiz VE, Ho M, Robinson S, Ward T, Cox LM, Rogers AB, Knights D, Sartor RB, Blaser MJ | Nature microbiology | 29180726 | Nat Microbiol | 2018 Feb |
| The theory of disappearing microbiota and the epidemics of chronic diseases. | Blaser MJ | Nature reviews. Immunology | 28749457 | Nat Rev Immunol | 2017 Jul 27 |
| Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota. | den Hartigh LJ, Gao Z, Goodspeed L, Wang S, Das AK, Burant CF, Chait A, Blaser MJ | The Journal of nutrition | 29659960 | J Nutr | 2018 Apr 1 |
| Description of two novel members of the family Erysipelotrichaceae: Ileibacterium valens gen. nov., sp. nov. and Dubosiella newyorkensis, gen. nov., sp. nov., from the murine intestine, and emendation to the description of Faecalibaculum rodentium. | Cox LM, Sohn J, Tyrrell KL, Citron DM, Lawson PA, Patel NB, Iizumi T, Perez-Perez GI, Goldstein EJC, Blaser MJ | International journal of systematic and evolutionary microbiology | 28100298 | Int J Syst Evol Microbiol | 2017 May |
| Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences. | Cox LM, Yamanishi S, Sohn J, Alekseyenko AV, Leung JM, Cho I, Kim SG, Li H, Gao Z, Mahana D, Zárate Rodriguez JG, Rogers AB, Robine N, Loke P, Blaser MJ | Cell | 25126780 | Cell | 2014 Aug 14 |
| Enteric hyperoxaluria: role of microbiota and antibiotics. | Liu M, Nazzal L | Current opinion in nephrology and hypertension | 31145706 | Curr Opin Nephrol Hypertens | 2019 Jul |
| The effects of trans-resveratrol on insulin resistance, inflammation, and microbiota in men with the metabolic syndrome: A pilot randomized, placebo-controlled clinical trial. | Walker JM, Eckardt P, Aleman JO, da Rosa JC, Liang Y, Iizumi T, Etheve S, Blaser MJ, L Breslow J, Holt PR | Journal of clinical and translational research | 30873501 | J Clin Transl Res | 2019 Jan 10 |
| Work-related adverse respiratory health outcomes at a machine manufacturing facility with a cluster of bronchiolitis, alveolar ductitis and emphysema (BADE). | Cummings KJ, Stanton ML, Kreiss K, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Edwards NT, Segal LN, Blaser MJ, Weissman DN, Nett RJ | Occupational and environmental medicine | 32132182 | Occup Environ Med | 2020 Jun |
| Effect of antibiotic treatment on Oxalobacter formigenes colonization of the gut microbiome and urinary oxalate excretion. | Nazzal L, Francois F, Henderson N, Liu M, Li H, Koh H, Wang C, Gao Z, Perez GP, Asplin JR, Goldfarb DS, Blaser MJ | Scientific reports | 34385560 | Sci Rep | 2021 Aug 12 |
| The Jeremiah Metzger Lecture: Global warming redux: the disappearing microbiota and epidemic obesity. | Blaser MJ | Transactions of the American Clinical and Climatological Association | 23303990 | Trans Am Clin Climatol Assoc | 2012 |
| Ethnicity is a strong predictor for Helicobacter pylori infection in young women in a multi-ethnic European city. | den Hollander WJ, Holster IL, den Hoed CM, van Deurzen F, van Vuuren AJ, Jaddoe VW, Hofman A, Perez Perez GI, Blaser MJ, Moll HA, Kuipers EJ | Journal of gastroenterology and hepatology | 23808840 | J Gastroenterol Hepatol | 2013 Nov |
| Partial restoration of the microbiota of cesarean-born infants via vaginal microbial transfer. | Dominguez-Bello MG, De Jesus-Laboy KM, Shen N, Cox LM, Amir A, Gonzalez A, Bokulich NA, Song SJ, Hoashi M, Rivera-Vinas JI, Mendez K, Knight R, Clemente JC | Nature medicine | 26828196 | Nat Med | 2016 Mar |
| The Intestinal Microbiome and Estrogen Receptor-Positive Female Breast Cancer. | Kwa M, Plottel CS, Blaser MJ, Adams S | Journal of the National Cancer Institute | 27107051 | J Natl Cancer Inst | 2016 Aug |
| Asthma: Undoing millions of years of coevolution in early life? | Dominguez-Bello MG, Blaser MJ | Science translational medicine | 26424565 | Sci Transl Med | 2015 Sep 30 |
| Helicobacter pylori in children with asthmatic conditions at school age, and their mothers. | den Hollander WJ, Sonnenschein-van der Voort AM, Holster IL, de Jongste JC, Jaddoe VW, Hofman A, Perez-Perez GI, Moll HA, Blaser MJ, Duijts L, Kuipers EJ | Alimentary pharmacology & therapeutics | 26932510 | Aliment Pharmacol Ther | 2016 Apr |
| Oxalobacter formigenes-associated host features and microbial community structures examined using the American Gut Project. | Liu M, Koh H, Kurtz ZD, Battaglia T, PeBenito A, Li H, Nazzal L, Blaser MJ | Microbiome | 28841836 | Microbiome | 2017 Aug 25 |
| Helminth colonization is associated with increased diversity of the gut microbiota. | Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, Gundra UM, Cho I, Bonneau R, Blaser MJ, Chua KH, Loke P | PLoS neglected tropical diseases | 24851867 | PLoS Negl Trop Dis | 2014 May |
| Association between Helicobacter pylori and mortality in the NHANES III study. | Chen Y, Segers S, Blaser MJ | Gut | 23303440 | Gut | 2013 Sep |
| Distinct cutaneous bacterial assemblages in a sampling of South American Amerindians and US residents. | Blaser MJ, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Estrada I, Gao Z, Clemente JC, Costello EK, Knight R | The ISME journal | 22895161 | ISME J | 2013 Jan |
| Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation. | Segal LN, Alekseyenko AV, Clemente JC, Kulkarni R, Wu B, Gao Z, Chen H, Berger KI, Goldring RM, Rom WN, Blaser MJ, Weiden MD | Microbiome | 24450871 | Microbiome | 2013 Jul 1 |
| The Human Microbiome before Birth. | Blaser MJ, Dominguez-Bello MG | Cell host & microbe | 27832586 | Cell Host Microbe | 2016 Nov 9 |
| A multivariate distance-based analytic framework for microbial interdependence association test in longitudinal study. | Zhang Y, Han SW, Cox LM, Li H | Genetic epidemiology | 28872698 | Genet Epidemiol | 2017 Dec |
| Seasonal cycling in the gut microbiome of the Hadza hunter-gatherers of Tanzania. | Smits SA, Leach J, Sonnenburg ED, Gonzalez CG, Lichtman JS, Reid G, Knight R, Manjurano A, Changalucha J, Elias JE, Dominguez-Bello MG, Sonnenburg JL | Science (New York, N.Y.) | 28839072 | Science | 2017 Aug 25 |
| Antibiotics in early life alter the murine colonic microbiome and adiposity. | Cho I, Yamanishi S, Cox L, Methé BA, Zavadil J, Li K, Gao Z, Mahana D, Raju K, Teitler I, Li H, Alekseyenko AV, Blaser MJ | Nature | 22914093 | Nature | 2012 Aug 30 |
| Predominance of Lactobacillus spp. Among Patients Who Do Not Acquire Multidrug-Resistant Organisms. | Araos R, Tai AK, Snyder GM, Blaser MJ, D'Agata EMC | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 27358350 | Clin Infect Dis | 2016 Oct 1 |
| Randomised, double-blind, placebo-controlled trial with azithromycin selects for anti-inflammatory microbial metabolites in the emphysematous lung. | Segal LN, Clemente JC, Wu BG, Wikoff WR, Gao Z, Li Y, Ko JP, Rom WN, Blaser MJ, Weiden MD | Thorax | 27486204 | Thorax | 2017 Jan |
| Enrichment of the lung microbiome with oral taxa is associated with lung inflammation of a Th17 phenotype. | Segal LN, Clemente JC, Tsay JC, Koralov SB, Keller BC, Wu BG, Li Y, Shen N, Ghedin E, Morris A, Diaz P, Huang L, Wikoff WR, Ubeda C, Artacho A, Rom WN, Sterman DH, Collman RG, Blaser MJ, Weiden MD | Nature microbiology | 27572644 | Nat Microbiol | 2016 Apr 4 |
| Harnessing the Early-Life Microbiota to Protect Children with Cystic Fibrosis. | Segal LN, Blaser MJ | The Journal of pediatrics | 25934071 | J Pediatr | 2015 Jul |
| Antibiotic use and its consequences for the normal microbiome. | Blaser MJ | Science (New York, N.Y.) | 27126037 | Science | 2016 Apr 29 |
| Sparse and compositionally robust inference of microbial ecological networks. | Kurtz ZD, Müller CL, Miraldi ER, Littman DR, Blaser MJ, Bonneau RA | PLoS computational biology | 25950956 | PLoS Comput Biol | 2015 May |
| Longitudinal changes of microbiome composition and microbial metabolomics after surgical weight loss in individuals with obesity. | Shen N, Caixàs A, Ahlers M, Patel K, Gao Z, Dutia R, Blaser MJ, Clemente JC, Laferrère B | Surgery for obesity and related diseases : official journal of the American Society for Bariatric Surgery | 31296445 | Surg Obes Relat Dis | 2019 Aug |
| Comparative prevalence of Oxalobacter formigenes in three human populations. | PeBenito A, Nazzal L, Wang C, Li H, Jay M, Noya-Alarcon O, Contreras M, Lander O, Leach J, Dominguez-Bello MG, Blaser MJ | Scientific reports | 30679485 | Sci Rep | 2019 Jan 24 |
| Metabolic and metagenomic outcomes from early-life pulsed antibiotic treatment. | Nobel YR, Cox LM, Kirigin FF, Bokulich NA, Yamanishi S, Teitler I, Chung J, Sohn J, Barber CM, Goldfarb DS, Raju K, Abubucker S, Zhou Y, Ruiz VE, Li H, Mitreva M, Alekseyenko AV, Weinstock GM, Sodergren E, Blaser MJ | Nature communications | 26123276 | Nat Commun | 2015 Jun 30 |
| A bitter aftertaste: unintended effects of artificial sweeteners on the gut microbiome. | Bokulich NA, Blaser MJ | Cell metabolism | 25440050 | Cell Metab | 2014 Nov 4 |
| A highly adaptive microbiome-based association test for survival traits. | Koh H, Livanos AE, Blaser MJ, Li H | BMC genomics | 29558893 | BMC Genomics | 2018 Mar 20 |
| Fecal microbiota and bile acid interactions with systemic and adipose tissue metabolism in diet-induced weight loss of obese postmenopausal women. | Alemán JO, Bokulich NA, Swann JR, Walker JM, De Rosa JC, Battaglia T, Costabile A, Pechlivanis A, Liang Y, Breslow JL, Blaser MJ, Holt PR | Journal of translational medicine | 30176893 | J Transl Med | 2018 Sep 3 |
| Risk of Clostridium difficile Infection in Patients With Celiac Disease: A Population-Based Study. | Lebwohl B, Nobel YR, Green PHR, Blaser MJ, Ludvigsson JF | The American journal of gastroenterology | 29087398 | Am J Gastroenterol | 2017 Dec |
| Estimating and testing the microbial causal mediation effect with high-dimensional and compositional microbiome data. | Wang C, Hu J, Blaser MJ, Li H | Bioinformatics (Oxford, England) | 31329243 | Bioinformatics | 2020 Jan 15 |
| Are we using too many antibiotics during pregnancy? | Ledger WJ, Blaser MJ | BJOG : an international journal of obstetrics and gynaecology | 24118809 | BJOG | 2013 Nov |
| The nonfermentable dietary fiber hydroxypropyl methylcellulose modulates intestinal microbiota. | Cox LM, Cho I, Young SA, Anderson WH, Waters BJ, Hung SC, Gao Z, Mahana D, Bihan M, Alekseyenko AV, Methé BA, Blaser MJ | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23154883 | FASEB J | 2013 Feb |
| Pathways in microbe-induced obesity. | Cox LM, Blaser MJ | Cell metabolism | 23747247 | Cell Metab | 2013 Jun 4 |
| Candida krusei colonization in patients with gastrointestinal diseases. | Huong DT, Zhao Y, Nguyet NT, Loan TT, Binh NT, Thinh NV, Hanh NT, Perez-Perez GI, Perlin DS | Medical mycology | 23815437 | Med Mycol | 2013 Nov |
| A brave new world: the lung microbiota in an era of change. | Segal LN, Blaser MJ | Annals of the American Thoracic Society | 24437400 | Ann Am Thorac Soc | 2014 Jan |
| Association between gastric Helicobacter pylori colonization and glycated hemoglobin levels. | Chen Y, Blaser MJ | The Journal of infectious diseases | 22427676 | J Infect Dis | 2012 Apr 15 |
| Host demise as a beneficial function of indigenous microbiota in human hosts. | Blaser MJ, Webb GF | mBio | 25516618 | mBio | 2014 Dec 16 |
| Helicobacter pylori colonization and pregnancies complicated by preeclampsia, spontaneous prematurity, and small for gestational age birth. | den Hollander WJ, Schalekamp-Timmermans S, Holster IL, Jaddoe VW, Hofman A, Moll HA, Perez-Perez GI, Blaser MJ, Steegers EA, Kuipers EJ | Helicobacter | 27786400 | Helicobacter | 2017 Apr |
| The Role of CagA in the Gastric Biology of Helicobacter pylori. | Backert S, Blaser MJ | Cancer research | 27655809 | Cancer Res | 2016 Jul 15 |
| Antibiotic perturbation of the murine gut microbiome enhances the adiposity, insulin resistance, and liver disease associated with high-fat diet. | Mahana D, Trent CM, Kurtz ZD, Bokulich NA, Battaglia T, Chung J, Müller CL, Li H, Bonneau RA, Blaser MJ | Genome medicine | 27124954 | Genome Med | 2016 Apr 27 |
| A single early-in-life macrolide course has lasting effects on murine microbial network topology and immunity. | Ruiz VE, Battaglia T, Kurtz ZD, Bijnens L, Ou A, Engstrand I, Zheng X, Iizumi T, Mullins BJ, Müller CL, Cadwell K, Bonneau R, Perez-Perez GI, Blaser MJ | Nature communications | 28894149 | Nat Commun | 2017 Sep 11 |
| The gut microbiota influences skeletal muscle mass and function in mice. | Lahiri S, Kim H, Garcia-Perez I, Reza MM, Martin KA, Kundu P, Cox LM, Selkrig J, Posma JM, Zhang H, Padmanabhan P, Moret C, Gulyás B, Blaser MJ, Auwerx J, Holmes E, Nicholson J, Wahli W, Pettersson S | Science translational medicine | 31341063 | Sci Transl Med | 2019 Jul 24 |
| Microbiome and malignancy. | Plottel CS, Blaser MJ | Cell host & microbe | 22018233 | Cell Host Microbe | 2011 Oct 20 |
| The effect of H. pylori eradication on meal-associated changes in plasma ghrelin and leptin. | Francois F, Roper J, Joseph N, Pei Z, Chhada A, Shak JR, de Perez AZ, Perez-Perez GI, Blaser MJ | BMC gastroenterology | 21489301 | BMC Gastroenterol | 2011 Apr 14 |
| Detecting a bacterial protein to understand cancer risk. | Blaser MJ | Clinical chemistry | 21586641 | Clin Chem | 2011 Sep |
| Maturation of the gut microbiome and risk of asthma in childhood. | Stokholm J, Blaser MJ, Thorsen J, Rasmussen MA, Waage J, Vinding RK, Schoos AM, Kunøe A, Fink NR, Chawes BL, Bønnelykke K, Brejnrod AD, Mortensen MS, Al-Soud WA, Sørensen SJ, Bisgaard H | Nature communications | 29321519 | Nat Commun | 2018 Jan 10 |
| Evidence for Environmental-Human Microbiota Transfer at a Manufacturing Facility with Novel Work-related Respiratory Disease. | Wu BG, Kapoor B, Cummings KJ, Stanton ML, Nett RJ, Kreiss K, Abraham JL, Colby TV, Franko AD, Green FHY, Sanyal S, Clemente JC, Gao Z, Coffre M, Meyn P, Heguy A, Li Y, Sulaiman I, Borbet TC, Koralov SB, Tallaksen RJ, Wendland D, Bachelder VD, Boylstein RJ, Park JH, Cox-Ganser JM, Virji MA, Crawford JA, Edwards NT, Veillette M, Duchaine C, Warren K, Lundeen S, Blaser MJ, Segal LN | American journal of respiratory and critical care medicine | 32673495 | Am J Respir Crit Care Med | 2020 Dec 15 |
| The Presence of Oxalobacter formigenes in the Microbiome of Healthy Young Adults. | Barnett C, Nazzal L, Goldfarb DS, Blaser MJ | The Journal of urology | 26292041 | J Urol | 2016 Feb |
| Risks of Antibiotic Exposures Early in Life on the Developing Microbiome. | Schulfer A, Blaser MJ | PLoS pathogens | 26135581 | PLoS Pathog | 2015 Jul |
| A powerful microbiome-based association test and a microbial taxa discovery framework for comprehensive association mapping. | Koh H, Blaser MJ, Li H | Microbiome | 28438217 | Microbiome | 2017 Apr 24 |
| Microbially Produced Acetate: A "Missing Link" in Understanding Obesity? | Trent CM, Blaser MJ | Cell metabolism | 27411005 | Cell Metab | 2016 Jul 12 |
| Development of the Human Mycobiome over the First Month of Life and across Body Sites. | Ward TL, Dominguez-Bello MG, Heisel T, Al-Ghalith G, Knights D, Gale CA | mSystems | 29546248 | mSystems | 2018 May-Jun |
| Partial convergence of the human vaginal and rectal maternal microbiota in late gestation and early post-partum. | Shin H, Martinez KA 2nd, Henderson N, Jay M, Schweizer W, Bogaert D, Park G, Bokulich NA, Blaser MJ, Dominguez-Bello MG | NPJ biofilms and microbiomes | 37311781 | NPJ Biofilms Microbiomes | 2023 Jun 13 |
| Computational analysis of Rho GTPase cycling. | Falkenberg CV, Loew LM | PLoS computational biology | 23326220 | PLoS Comput Biol | 2013 |
| G Protein-regulated inducer of neurite outgrowth (GRIN) modulates Sprouty protein repression of mitogen-activated protein kinase (MAPK) activation by growth factor stimulation. | Hwangpo TA, Jordan JD, Premsrirut PK, Jayamaran G, Licht JD, Iyengar R, Neves SR | The Journal of biological chemistry | 22383529 | J Biol Chem | 2012 Apr 20 |
| Systems biology of kidney diseases. | He JC, Chuang PY, Ma'ayan A, Iyengar R | Kidney international | 21881558 | Kidney Int | 2012 Jan |
| ERK regulation of phosphodiesterase 4 enhances dopamine-stimulated AMPA receptor membrane insertion. | Song RS, Massenburg B, Wenderski W, Jayaraman V, Thompson L, Neves SR | Proceedings of the National Academy of Sciences of the United States of America | 23986500 | Proc Natl Acad Sci U S A | 2013 Sep 17 |
| Compartmentalized PDE4A5 Signaling Impairs Hippocampal Synaptic Plasticity and Long-Term Memory. | Havekes R, Park AJ, Tolentino RE, Bruinenberg VM, Tudor JC, Lee Y, Hansen RT, Guercio LA, Linton E, Neves-Zaph SR, Meerlo P, Baillie GS, Houslay MD, Abel T | The Journal of neuroscience : the official journal of the Society for Neuroscience | 27559174 | J Neurosci | 2016 Aug 24 |
| Modeling of spatially-restricted intracellular signaling. | Neves SR | Wiley interdisciplinary reviews. Systems biology and medicine | 21766466 | Wiley Interdiscip Rev Syst Biol Med | 2012 Jan-Feb |
| Obtaining and estimating kinetic parameters from the literature. | Neves SR | Science signaling | 21934111 | Sci Signal | 2011 Sep 13 |
| Developing models in virtual cell. | Neves SR | Science signaling | 21954293 | Sci Signal | 2011 Sep 20 |
| Interconnected network motifs control podocyte morphology and kidney function. | Azeloglu EU, Hardy SV, Eungdamrong NJ, Chen Y, Jayaraman G, Chuang PY, Fang W, Xiong H, Neves SR, Jain MR, Li H, Ma'ayan A, Gordon RE, He JC, Iyengar R | Science signaling | 24497609 | Sci Signal | 2014 Feb 4 |
| A biomimetic gelatin-based platform elicits a pro-differentiation effect on podocytes through mechanotransduction. | Hu M, Azeloglu EU, Ron A, Tran-Ba KH, Calizo RC, Tavassoly I, Bhattacharya S, Jayaraman G, Chen Y, Rabinovich V, Iyengar R, Hone JC, He JC, Kaufman LJ | Scientific reports | 28262745 | Sci Rep | 2017 Mar 6 |
| Pleomorphic ensembles: formation of large clusters composed of weakly interacting multivalent molecules. | Falkenberg CV, Blinov ML, Loew LM | Biophysical journal | 24314076 | Biophys J | 2013 Dec 3 |
| Cell shape information is transduced through tension-independent mechanisms. | Ron A, Azeloglu EU, Calizo RC, Hu M, Bhattacharya S, Chen Y, Jayaraman G, Lee S, Neves-Zaph SR, Li H, Gordon RE, He JC, Hone JC, Iyengar R | Nature communications | 29247198 | Nat Commun | 2017 Dec 15 |
| Modeling of spatial intracellular signaling events in neurons. | Wenderski WC, Neves SR | Methods in enzymology | 22289450 | Methods Enzymol | 2012 |
| Cross-regulation of Phosphodiesterase 1 and Phosphodiesterase 2 Activities Controls Dopamine-mediated Striatal α-Amino-3-hydroxy-5-methyl-4-isoxazolepropionic Acid (AMPA) Receptor Trafficking. | Song RS, Tolentino R, Sobie EA, Neves-Zaph SR | The Journal of biological chemistry | 27605670 | J Biol Chem | 2016 Oct 28 |
| Insulin action and resistance in obesity and type 2 diabetes. | Czech MP | Nature medicine | 28697184 | Nat Med | 2017 Jul 11 |
| Gene silencing in adipose tissue macrophages regulates whole-body metabolism in obese mice. | Aouadi M, Tencerova M, Vangala P, Yawe JC, Nicoloro SM, Amano SU, Cohen JL, Czech MP | Proceedings of the National Academy of Sciences of the United States of America | 23630254 | Proc Natl Acad Sci U S A | 2013 May 14 |
| Glucan particles for selective delivery of siRNA to phagocytic cells in mice. | Tesz GJ, Aouadi M, Prot M, Nicoloro SM, Boutet E, Amano SU, Goller A, Wang M, Guo CA, Salomon WE, Virbasius JV, Baum RA, O'Connor MJ Jr, Soto E, Ostroff GR, Czech MP | The Biochemical journal | 21418037 | Biochem J | 2011 Jun 1 |
| Activation of the Nlrp3 inflammasome in infiltrating macrophages by endocannabinoids mediates beta cell loss in type 2 diabetes. | Jourdan T, Godlewski G, Cinar R, Bertola A, Szanda G, Liu J, Tam J, Han T, Mukhopadhyay B, Skarulis MC, Ju C, Aouadi M, Czech MP, Kunos G | Nature medicine | 23955712 | Nat Med | 2013 Sep |
| Activated Kupffer cells inhibit insulin sensitivity in obese mice. | Tencerova M, Aouadi M, Vangala P, Nicoloro SM, Yawe JC, Cohen JL, Shen Y, Garcia-Menendez L, Pedersen DJ, Gallagher-Dorval K, Perugini RA, Gupta OT, Czech MP | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 25805830 | FASEB J | 2015 Jul |
| RNAi-based therapeutic strategies for metabolic disease. | Czech MP, Aouadi M, Tesz GJ | Nature reviews. Endocrinology | 21502982 | Nat Rev Endocrinol | 2011 Apr 19 |
| Lipid storage by adipose tissue macrophages regulates systemic glucose tolerance. | Aouadi M, Vangala P, Yawe JC, Tencerova M, Nicoloro SM, Cohen JL, Shen Y, Czech MP | American journal of physiology. Endocrinology and metabolism | 24986598 | Am J Physiol Endocrinol Metab | 2014 Aug 15 |
| A population of Langerin-positive dendritic cells in murine Peyer's patches involved in sampling β-glucan microparticles. | De Jesus M, Ostroff GR, Levitz SM, Bartling TR, Mantis NJ | PloS one | 24632738 | PLoS One | 2014 |
| CD40 deficiency in mice exacerbates obesity-induced adipose tissue inflammation, hepatic steatosis, and insulin resistance. | Guo CA, Kogan S, Amano SU, Wang M, Dagdeviren S, Friedline RH, Aouadi M, Kim JK, Czech MP | American journal of physiology. Endocrinology and metabolism | 23482447 | Am J Physiol Endocrinol Metab | 2013 May 1 |
| Local proliferation of macrophages contributes to obesity-associated adipose tissue inflammation. | Amano SU, Cohen JL, Vangala P, Tencerova M, Nicoloro SM, Yawe JC, Shen Y, Czech MP, Aouadi M | Cell metabolism | 24374218 | Cell Metab | 2014 Jan 7 |
| Insulin signalling mechanisms for triacylglycerol storage. | Czech MP, Tencerova M, Pedersen DJ, Aouadi M | Diabetologia | 23443243 | Diabetologia | 2013 May |
| Peptide- and Amine-Modified Glucan Particles for the Delivery of Therapeutic siRNA. | Cohen JL, Shen Y, Aouadi M, Vangala P, Tencerova M, Amano SU, Nicoloro SM, Yawe JC, Czech MP | Molecular pharmaceutics | 26815386 | Mol Pharm | 2016 Mar 7 |
| IL-1 signaling in obesity-induced hepatic lipogenesis and steatosis. | Negrin KA, Roth Flach RJ, DiStefano MT, Matevossian A, Friedline RH, Jung D, Kim JK, Czech MP | PloS one | 25216251 | PLoS One | 2014 |
| β-Catenin-driven cancers require a YAP1 transcriptional complex for survival and tumorigenesis. | Rosenbluh J, Nijhawan D, Cox AG, Li X, Neal JT, Schafer EJ, Zack TI, Wang X, Tsherniak A, Schinzel AC, Shao DD, Schumacher SE, Weir BA, Vazquez F, Cowley GS, Root DE, Mesirov JP, Beroukhim R, Kuo CJ, Goessling W, Hahn WC | Cell | 23245941 | Cell | 2012 Dec 21 |
| Reversible cell-cycle entry in adult kidney podocytes through regulated control of telomerase and Wnt signaling. | Shkreli M, Sarin KY, Pech MF, Papeta N, Chang W, Brockman SA, Cheung P, Lee E, Kuhnert F, Olson JL, Kuo CJ, Gharavi AG, D'Agati VD, Artandi SE | Nature medicine | 22138751 | Nat Med | 2011 Dec 4 |
| Matrix interactions modulate neurotrophin-mediated neurite outgrowth and pathfinding. | Madl CM, Heilshorn SC | Neural regeneration research | 26170800 | Neural Regen Res | 2015 Apr |
| Injectable Hydrogels with In Situ Double Network Formation Enhance Retention of Transplanted Stem Cells. | Cai L, Dewi RE, Heilshorn SC | Advanced functional materials | 26273242 | Adv Funct Mater | 2015 Mar 4 |
| Organoid modeling for cancer precision medicine. | Cantrell MA, Kuo CJ | Genome medicine | 25825593 | Genome Med | 2015 |
| Chemotaxis of human induced pluripotent stem cell-derived endothelial cells. | Huang NF, Dewi RE, Okogbaa J, Lee JC, Jalilrufaihah A, Heilshorn SC, Cooke JP | American journal of translational research | 23977410 | Am J Transl Res | 2013 |
| Partial proteasome inhibitors induce hair follicle growth by stabilizing β-catenin. | Yucel G, Van Arnam J, Means PC, Huntzicker E, Altindag B, Lara MF, Yuan J, Kuo C, Oro AE | Stem cells (Dayton, Ohio) | 23963711 | Stem Cells | 2014 Jan |
| Organoids as Models for Neoplastic Transformation. | Neal JT, Kuo CJ | Annual review of pathology | 26907527 | Annu Rev Pathol | 2016 May 23 |
| Dual-stage growth factor release within 3D protein-engineered hydrogel niches promotes adipogenesis. | Greenwood-Goodwin M, Teasley ES, Heilshorn SC | Biomaterials science | 25309741 | Biomater Sci | 2014 Nov 1 |
| Hybrid elastin-like polypeptide-polyethylene glycol (ELP-PEG) hydrogels with improved transparency and independent control of matrix mechanics and cell ligand density. | Wang H, Cai L, Paul A, Enejder A, Heilshorn SC | Biomacromolecules | 25111283 | Biomacromolecules | 2014 Sep 8 |
| Oncogenic transformation of diverse gastrointestinal tissues in primary organoid culture. | Li X, Nadauld L, Ootani A, Corney DC, Pai RK, Gevaert O, Cantrell MA, Rack PG, Neal JT, Chan CW, Yeung T, Gong X, Yuan J, Wilhelmy J, Robine S, Attardi LD, Plevritis SK, Hung KE, Chen CZ, Ji HP, Kuo CJ | Nature medicine | 24859528 | Nat Med | 2014 Jul |
| The intestinal stem cell markers Bmi1 and Lgr5 identify two functionally distinct populations. | Yan KS, Chia LA, Li X, Ootani A, Su J, Lee JY, Su N, Luo Y, Heilshorn SC, Amieva MR, Sangiorgi E, Capecchi MR, Kuo CJ | Proceedings of the National Academy of Sciences of the United States of America | 22190486 | Proc Natl Acad Sci U S A | 2012 Jan 10 |
| Improving viability of stem cells during syringe needle flow through the design of hydrogel cell carriers. | Aguado BA, Mulyasasmita W, Su J, Lampe KJ, Heilshorn SC | Tissue engineering. Part A | 22011213 | Tissue Eng Part A | 2012 Apr |
| Avidity-controlled delivery of angiogenic peptides from injectable molecular-recognition hydrogels. | Mulyasasmita W, Cai L, Hori Y, Heilshorn SC | Tissue engineering. Part A | 24490588 | Tissue Eng Part A | 2014 Aug |
| Avidity-controlled hydrogels for injectable co-delivery of induced pluripotent stem cell-derived endothelial cells and growth factors. | Mulyasasmita W, Cai L, Dewi RE, Jha A, Ullmann SD, Luong RH, Huang NF, Heilshorn SC | Journal of controlled release : official journal of the Controlled Release Society | 24848744 | J Control Release | 2014 Oct 10 |
| Designing ECM-mimetic materials using protein engineering. | Cai L, Heilshorn SC | Acta biomaterialia | 24365704 | Acta Biomater | 2014 Apr |
| Protein-engineered scaffolds for in vitro 3D culture of primary adult intestinal organoids. | DiMarco RL, Dewi RE, Bernal G, Kuo C, Heilshorn SC | Biomaterials science | 26371971 | Biomater Sci | 2015 Oct 15 |
| Protein-engineered hydrogel encapsulation for 3-D culture of murine cochlea. | Chang DT, Chai R, DiMarco R, Heilshorn SC, Cheng AG | Otology & neurotology : official publication of the American Otological Society, American Neurotology Society [and] European Academy of Otology and Neurotology | 25111520 | Otol Neurotol | 2015 Mar |
| Small-molecule axon-polarization studies enabled by a shear-free microfluidic gradient generator. | Xu H, Ferreira MM, Heilshorn SC | Lab on a chip | 24781157 | Lab Chip | 2014 Jun 21 |
| Engineering of three-dimensional microenvironments to promote contractile behavior in primary intestinal organoids. | DiMarco RL, Su J, Yan KS, Dewi R, Kuo CJ, Heilshorn SC | Integrative biology : quantitative biosciences from nano to macro | 24343706 | Integr Biol (Camb) | 2014 Feb |
| Multifunctional materials through modular protein engineering. | DiMarco RL, Heilshorn SC | Advanced materials (Deerfield Beach, Fla.) | 22730248 | Adv Mater | 2012 Aug 2 |
| Sustained in vitro intestinal epithelial culture within a Wnt-dependent stem cell niche. | Ootani A, Li X, Sangiorgi E, Ho QT, Ueno H, Toda S, Sugihara H, Fujimoto K, Weissman IL, Capecchi MR, Kuo CJ | Nature medicine | 19398967 | Nat Med | 2009 Jun |
| One-pot Synthesis of Elastin-like Polypeptide Hydrogels with Grafted VEGF-Mimetic Peptides. | Cai L, Dinh CB, Heilshorn SC | Biomaterials science | 24729868 | Biomater Sci | 2014 May 1 |
| Spontaneous cardiomyocyte differentiation of mouse embryoid bodies regulated by hydrogel crosslink density. | Chung C, Pruitt BL, Heilshorn SC | Biomaterials science | 24748962 | Biomater Sci | 2013 Oct 1 |
| Molecular-level engineering of protein physical hydrogels for predictive sol-gel phase behavior. | Mulyasasmita W, Lee JS, Heilshorn SC | Biomacromolecules | 21861461 | Biomacromolecules | 2011 Oct 10 |
| Interfollicular epidermal stem cells self-renew via autocrine Wnt signaling. | Lim X, Tan SH, Koh WL, Chau RM, Yan KS, Kuo CJ, van Amerongen R, Klein AM, Nusse R | Science (New York, N.Y.) | 24311688 | Science | 2013 Dec 6 |
| Presentation of BMP-2 mimicking peptides in 3D hydrogels directs cell fate commitment in osteoblasts and mesenchymal stem cells. | Madl CM, Mehta M, Duda GN, Heilshorn SC, Mooney DJ | Biomacromolecules | 24400664 | Biomacromolecules | 2014 Feb 10 |
| Adaptable hydrogel networks with reversible linkages for tissue engineering. | Wang H, Heilshorn SC | Advanced materials (Deerfield Beach, Fla.) | 25989348 | Adv Mater | 2015 Jul 1 |
| Regulation of self-renewal and differentiation by the intestinal stem cell niche. | Yeung TM, Chia LA, Kosinski CM, Kuo CJ | Cellular and molecular life sciences : CMLS | 21509540 | Cell Mol Life Sci | 2011 Aug |
| Matrix RGD ligand density and L1CAM-mediated Schwann cell interactions synergistically enhance neurite outgrowth. | Romano NH, Madl CM, Heilshorn SC | Acta biomaterialia | 25308870 | Acta Biomater | 2015 Jan |
| Microfluidic gradients reveal enhanced neurite outgrowth but impaired guidance within 3D matrices with high integrin ligand densities. | Romano NH, Lampe KJ, Xu H, Ferreira MM, Heilshorn SC | Small (Weinheim an der Bergstrasse, Germany) | 25315156 | Small | 2015 Feb 11 |
| Coproduction of healthcare service. | Batalden M, Batalden P, Margolis P, Seid M, Armstrong G, Opipari-Arrigan L, Hartung H | BMJ quality & safety | 26376674 | BMJ Qual Saf | 2016 Jul |
| Using a network organisational architecture to support the development of Learning Healthcare Systems. | Britto MT, Fuller SC, Kaplan HC, Kotagal U, Lannon C, Margolis PA, Muething SE, Schoettker PJ, Seid M | BMJ quality & safety | 29438072 | BMJ Qual Saf | 2018 Nov |
| Co-Designing a Collaborative Chronic Care Network (C3N) for Inflammatory Bowel Disease: Development of Methods. | Seid M, Dellal G, Peterson LE, Provost L, Gloor PA, Fore DL, Margolis PA | JMIR human factors | 29472173 | JMIR Hum Factors | 2018 Feb 22 |
| Collaborative Chronic Care Networks (C3Ns) to transform chronic illness care. | Margolis PA, Peterson LE, Seid M | Pediatrics | 23729764 | Pediatrics | 2013 Jun |
| Appreciating the Nuance of Daily Symptom Variation to Individualize Patient Care. | Adler J, Saeed SA, Eslick IS, Provost L, Margolis PA, Kaplan HC | EGEMS (Washington, DC) | 27376097 | EGEMS (Wash DC) | 2016 |
| Learning Health Systems as Facilitators of Precision Medicine. | Ramsey LB, Mizuno T, Vinks AA, Margolis PA | Clinical pharmacology and therapeutics | 27984650 | Clin Pharmacol Ther | 2017 Mar |
| Engagement, peer production, and the learning healthcare system. | Seid M, Margolis PA, Opipari-Arrigan L | JAMA pediatrics | 24446048 | JAMA Pediatr | 2014 Mar |
| What's in a name generator? Choosing the right name generators for social network surveys in healthcare quality and safety research. | Burt RS, Meltzer DO, Seid M, Borgert A, Chung JW, Colletti RB, Dellal G, Kahn SA, Kaplan HC, Peterson LE, Margolis P | BMJ quality & safety | 22942400 | BMJ Qual Saf | 2012 Dec |
| Health services innovation: the time is now. | Zuckerman B, Margolis PA, Mate KS | JAMA | 23512055 | JAMA | 2013 Mar 20 |
| Pilot Development of an Electronic Pediatric Inflammatory Bowel Disease Quiz Game. | Tung J, Grunow JE, Jacobs N | Journal of pediatric gastroenterology and nutrition | 25793902 | J Pediatr Gastroenterol Nutr | 2015 Sep |
| A maturity grid assessment tool for learning networks. | Lannon C, Schuler CL, Seid M, Provost LP, Fuller S, Purcell D, Forrest CB, Margolis PA | Learning health systems | 33889737 | Learn Health Syst | 2021 Apr |
| Measuring engagement in a collaborative learning health system: The case of ImproveCareNow. | Hartley DM, Keck C, Havens M, Margolis PA, Seid M | Learning health systems | 33889734 | Learn Health Syst | 2021 Apr |
| Improved outcomes in a quality improvement collaborative for pediatric inflammatory bowel disease. | Crandall WV, Margolis PA, Kappelman MD, King EC, Pratt JM, Boyle BM, Duffy LF, Grunow JE, Kim SC, Leibowitz I, Schoen BT, Colletti RB, ImproveCareNow Collaborative | Pediatrics | 22412030 | Pediatrics | 2012 Apr |
| "A Guide to Gutsy Living": Patient-Driven Development of a Pediatric Ostomy Toolkit. | David JG, Jofriet A, Seid M, Margolis PA, ImproveCareNow Pediatric IBD Learning Health System | Pediatrics | 29610402 | Pediatrics | 2018 May |
| Plasticity of basal cells during postnatal development in the rat epididymis. | Shum WW, Hill E, Brown D, Breton S | Reproduction (Cambridge, England) | 23960170 | Reproduction | 2013 |
| High-resolution helium ion microscopy of epididymal epithelial cells and their interaction with spermatozoa. | Păunescu TG, Shum WW, Huynh C, Lechner L, Goetze B, Brown D, Breton S | Molecular human reproduction | 25015675 | Mol Hum Reprod | 2014 Oct |
| Establishment of cell-cell cross talk in the epididymis: control of luminal acidification. | Shum WW, Ruan YC, Da Silva N, Breton S | Journal of andrology | 21441423 | J Androl | 2011 Nov-Dec |
| ROS1 signaling regulates epithelial differentiation in the epididymis. | Jun HJ, Roy J, Smith TB, Wood LB, Lane K, Woolfenden S, Punko D, Bronson RT, Haigis KM, Breton S, Charest A | Endocrinology | 24971615 | Endocrinology | 2014 Sep |
| Epithelial basal cells are distinct from dendritic cells and macrophages in the mouse epididymis. | Shum WW, Smith TB, Cortez-Retamozo V, Grigoryeva LS, Roy JW, Hill E, Pittet MJ, Breton S, Da Silva N | Biology of reproduction | 24648397 | Biol Reprod | 2014 May |
| A dense network of dendritic cells populates the murine epididymis. | Da Silva N, Cortez-Retamozo V, Reinecker HC, Wildgruber M, Hill E, Brown D, Swirski FK, Pittet MJ, Breton S | Reproduction (Cambridge, England) | 21310816 | Reproduction | 2011 May |
| In vivo imaging of tracheal epithelial cells in mice during airway regeneration. | Kim JK, Vinarsky V, Wain J, Zhao R, Jung K, Choi J, Lam A, Pardo-Saganta A, Breton S, Rajagopal J, Yun SH | American journal of respiratory cell and molecular biology | 22984086 | Am J Respir Cell Mol Biol | 2012 Dec |
| Transepithelial projections from basal cells are luminal sensors in pseudostratified epithelia. | Shum WW, Da Silva N, McKee M, Smith PJ, Brown D, Breton S | Cell | 19070580 | Cell | 2008 Dec 12 |
| Quantitative and stoichiometric analysis of the microRNA content of exosomes. | Chevillet JR, Kang Q, Ruf IK, Briggs HA, Vojtech LN, Hughes SM, Cheng HH, Arroyo JD, Meredith EK, Gallichotte EN, Pogosova-Agadjanyan EL, Morrissey C, Stirewalt DL, Hladik F, Yu EY, Higano CS, Tewari M | Proceedings of the National Academy of Sciences of the United States of America | 25267620 | Proc Natl Acad Sci U S A | 2014 Oct 14 |
| Ultra-Specific Isolation of Circulating Tumor Cells Enables Rare-Cell RNA Profiling. | Jack RM, Grafton MM, Rodrigues D, Giraldez MD, Griffith C, Cieslak R, Zeinali M, Kumar Sinha C, Azizi E, Wicha M, Tewari M, Simeone DM, Nagrath S | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 27711257 | Adv Sci (Weinh) | 2016 Sep |
| Tumor characterization by ultrasound-release of multiple protein and microRNA biomarkers, preclinical and clinical evidence. | D'Souza AL, Chevillet JR, Ghanouni P, Yan X, Tewari M, Gambhir SS | PloS one | 29547636 | PLoS One | 2018 |
| Absolute quantification by droplet digital PCR versus analog real-time PCR. | Hindson CM, Chevillet JR, Briggs HA, Gallichotte EN, Ruf IK, Hindson BJ, Vessella RL, Tewari M | Nature methods | 23995387 | Nat Methods | 2013 Oct |
| A functional extracellular transcriptome in animals? Implications for biology, disease and medicine. | Tewari M | Genome biology | 25723626 | Genome Biol | 2015 Feb 26 |
| Circulating microRNAs and treatment response in the Phase II SWOG S0925 study for patients with new metastatic hormone-sensitive prostate cancer. | Cheng HH, Plets M, Li H, Higano CS, Tangen CM, Agarwal N, Vogelzang NJ, Hussain M, Thompson IM Jr, Tewari M, Yu EY | The Prostate | 29105802 | Prostate | 2018 Feb |
| Design and Analysis for Studying microRNAs in Human Disease: A Primer on -Omic Technologies. | Nair VS, Pritchard CC, Tewari M, Ioannidis JP | American journal of epidemiology | 24966218 | Am J Epidemiol | 2014 Jul 15 |
| Blood cell origin of circulating microRNAs: a cautionary note for cancer biomarker studies. | Pritchard CC, Kroh E, Wood B, Arroyo JD, Dougherty KJ, Miyaji MM, Tait JF, Tewari M | Cancer prevention research (Philadelphia, Pa.) | 22158052 | Cancer Prev Res (Phila) | 2012 Mar |
| Exosomes in human semen carry a distinctive repertoire of small non-coding RNAs with potential regulatory functions. | Vojtech L, Woo S, Hughes S, Levy C, Ballweber L, Sauteraud RP, Strobl J, Westerberg K, Gottardo R, Tewari M, Hladik F | Nucleic acids research | 24838567 | Nucleic Acids Res | 2014 Jun |
| Post-transcriptional generation of miRNA variants by multiple nucleotidyl transferases contributes to miRNA transcriptome complexity. | Wyman SK, Knouf EC, Parkin RK, Fritz BR, Lin DW, Dennis LM, Krouse MA, Webster PJ, Tewari M | Genome research | 21813625 | Genome Res | 2011 Sep |
| Intact microRNA analysis using high resolution mass spectrometry. | Kullolli M, Knouf E, Arampatzidou M, Tewari M, Pitteri SJ | Journal of the American Society for Mass Spectrometry | 24174127 | J Am Soc Mass Spectrom | 2014 Jan |
| Plasma processing conditions substantially influence circulating microRNA biomarker levels. | Cheng HH, Yi HS, Kim Y, Kroh EM, Chien JW, Eaton KD, Goodman MT, Tait JF, Tewari M, Pritchard CC | PloS one | 23762257 | PLoS One | 2013 |
| Mutant DNA quantification by digital PCR can be confounded by heating during DNA fragmentation. | Kang Q, Parkin B, Giraldez MD, Tewari M | BioTechniques | 27071606 | Biotechniques | 2016 Apr |
| Argonaute2 complexes carry a population of circulating microRNAs independent of vesicles in human plasma. | Arroyo JD, Chevillet JR, Kroh EM, Ruf IK, Pritchard CC, Gibson DF, Mitchell PS, Bennett CF, Pogosova-Agadjanyan EL, Stirewalt DL, Tait JF, Tewari M | Proceedings of the National Academy of Sciences of the United States of America | 21383194 | Proc Natl Acad Sci U S A | 2011 Mar 22 |
| Systematic design and functional analysis of artificial microRNAs. | Arroyo JD, Gallichotte EN, Tewari M | Nucleic acids research | 24598260 | Nucleic Acids Res | 2014 May |
| The human TUT1 nucleotidyl transferase as a global regulator of microRNA abundance. | Knouf EC, Wyman SK, Tewari M | PloS one | 23874977 | PLoS One | 2013 |
| MicroRNA profiling: approaches and considerations. | Pritchard CC, Cheng HH, Tewari M | Nature reviews. Genetics | 22510765 | Nat Rev Genet | 2012 Apr 18 |
| Kinetic fingerprinting to identify and count single nucleic acids. | Johnson-Buck A, Su X, Giraldez MD, Zhao M, Tewari M, Walter NG | Nature biotechnology | 26098451 | Nat Biotechnol | 2015 Jul |
| Droplet Digital PCR for Absolute Quantification of Extracellular MicroRNAs in Plasma and Serum: Quantification of the Cancer Biomarker hsa-miR-141. | Giraldez MD, Chevillet JR, Tewari M | Methods in molecular biology (Clifton, N.J.) | 29717459 | Methods Mol Biol | 2018 |
| Evaluating Serum Markers for Hormone Receptor-Negative Breast Cancer. | Schummer M, Thorpe J, Giraldez MD, Bergan L, Tewari M, Urban N | PloS one | 26565788 | PLoS One | 2015 |
| Circulating microRNA profiling identifies a subset of metastatic prostate cancer patients with evidence of cancer-associated hypoxia. | Cheng HH, Mitchell PS, Kroh EM, Dowell AE, Chéry L, Siddiqui J, Nelson PS, Vessella RL, Knudsen BS, Chinnaiyan AM, Pienta KJ, Morrissey C, Tewari M | PloS one | 23935962 | PLoS One | 2013 |
| Release of Cell-free MicroRNA Tumor Biomarkers into the Blood Circulation with Pulsed Focused Ultrasound: A Noninvasive, Anatomically Localized, Molecular Liquid Biopsy. | Chevillet JR, Khokhlova TD, Giraldez MD, Schade GR, Starr F, Wang YN, Gallichotte EN, Wang K, Hwang JH, Tewari M | Radiology | 27802108 | Radiology | 2017 Apr |
| Rapid, ultra low coverage copy number profiling of cell-free DNA as a precision oncology screening strategy. | Hovelson DH, Liu CJ, Wang Y, Kang Q, Henderson J, Gursky A, Brockman S, Ramnath N, Krauss JC, Talpaz M, Kandarpa M, Chugh R, Tuck M, Herman K, Grasso CS, Quist MJ, Feng FY, Haakenson C, Langmore J, Kamberov E, Tesmer T, Husain H, Lonigro RJ, Robinson D, Smith DC, Alva AS, Hussain MH, Chinnaiyan AM, Tewari M, Mills RE, Morgan TM, Tomlins SA | Oncotarget | 29163793 | Oncotarget | 2017 Oct 27 |
| Platelet-Synthesized Testosterone in Men with Prostate Cancer Induces Androgen Receptor Signaling. | Zaslavsky AB, Gloeckner-Kalousek A, Adams M, Putluri N, Venghatakrishnan H, Li H, Morgan TM, Feng FY, Tewari M, Sreekumar A, Palapattu GS | Neoplasia (New York, N.Y.) | 26152357 | Neoplasia | 2015 Jun |
| Evaluation of combination therapy against hepatitis C virus infection in human liver chimeric mice. | de Jong YP, Rice CM, Ploss A | Journal of hepatology | 21145816 | J Hepatol | 2011 May |
| Antisense gets a grip on miR-122 in chimpanzees. | Branch AD, Rice CM | Science translational medicine | 20371461 | Sci Transl Med | 2010 Jan 6 |
| New horizons for studying human hepatotropic infections. | de Jong YP, Rice CM, Ploss A | The Journal of clinical investigation | 20179350 | J Clin Invest | 2010 Mar |
| Persistent hepatitis C virus infection in microscale primary human hepatocyte cultures. | Ploss A, Khetani SR, Jones CT, Syder AJ, Trehan K, Gaysinskaya VA, Mu K, Ritola K, Rice CM, Bhatia SN | Proceedings of the National Academy of Sciences of the United States of America | 20133632 | Proc Natl Acad Sci U S A | 2010 Feb 16 |
| Human hepatocyte PNPLA3-148M exacerbates rapid non-alcoholic fatty liver disease development in chimeric mice. | Kabbani M, Michailidis E, Steensels S, Fulmer CG, Luna JM, Le Pen J, Tardelli M, Razooky B, Ricardo-Lax I, Zou C, Zeck B, Stenzel AF, Quirk C, Foquet L, Ashbrook AW, Schneider WM, Belkaya S, Lalazar G, Liang Y, Pittman M, Devisscher L, Suemizu H, Theise ND, Chiriboga L, Cohen DE, Copenhaver R, Grompe M, Meuleman P, Ersoy BA, Rice CM, de Jong YP | Cell reports | 36103835 | Cell Rep | 2022 Sep 13 |
| New Methods in Tissue Engineering: Improved Models for Viral Infection. | Ramanan V, Scull MA, Sheahan TP, Rice CM, Bhatia SN | Annual review of virology | 25893203 | Annu Rev Virol | 2014 Nov |
| Development of a multiplex phenotypic cell-based high throughput screening assay to identify novel hepatitis C virus antivirals. | Kim HY, Li X, Jones CT, Rice CM, Garcia JM, Genovesio A, Hansen MA, Windisch MP | Antiviral research | 23660623 | Antiviral Res | 2013 Jul |
| Pluripotent stem cell-derived hepatocyte-like cells. | Schwartz RE, Fleming HE, Khetani SR, Bhatia SN | Biotechnology advances | 24440487 | Biotechnol Adv | 2014 Mar-Apr |
| Expression of heterologous proteins flanked by NS3-4A cleavage sites within the hepatitis C virus polyprotein. | Horwitz JA, Dorner M, Friling T, Donovan BM, Vogt A, Loureiro J, Oh T, Rice CM, Ploss A | Virology | 23485372 | Virology | 2013 Apr 25 |
| Degradable hydrogels derived from PEG-diacrylamide for hepatic tissue engineering. | Stevens KR, Miller JS, Blakely BL, Chen CS, Bhatia SN | Journal of biomedical materials research. Part A | 25851120 | J Biomed Mater Res A | 2015 Oct |
| Modeling host interactions with hepatitis B virus using primary and induced pluripotent stem cell-derived hepatocellular systems. | Shlomai A, Schwartz RE, Ramanan V, Bhatta A, de Jong YP, Bhatia SN, Rice CM | Proceedings of the National Academy of Sciences of the United States of America | 25092305 | Proc Natl Acad Sci U S A | 2014 Aug 19 |
| Hepatitis C virus induces interferon-λ and interferon-stimulated genes in primary liver cultures. | Marukian S, Andrus L, Sheahan TP, Jones CT, Charles ED, Ploss A, Rice CM, Dustin LB | Hepatology (Baltimore, Md.) | 21800339 | Hepatology | 2011 Dec |
| Micropatterned cell-cell interactions enable functional encapsulation of primary hepatocytes in hydrogel microtissues. | Li CY, Stevens KR, Schwartz RE, Alejandro BS, Huang JH, Bhatia SN | Tissue engineering. Part A | 24498910 | Tissue Eng Part A | 2014 Aug |
| Development of human CD4+FoxP3+ regulatory T cells in human stem cell factor-, granulocyte-macrophage colony-stimulating factor-, and interleukin-3-expressing NOD-SCID IL2Rγ(null) humanized mice. | Billerbeck E, Barry WT, Mu K, Dorner M, Rice CM, Ploss A | Blood | 21252091 | Blood | 2011 Mar 17 |
| Mopping up miRNA: An integrated HBV transcript disrupts liver homeostasis by sequestering miR-122. | Luna JM, Michailidis E, Rice CM | Journal of hepatology | 26541590 | J Hepatol | 2016 Feb |
| Micropatterned coculture of primary human hepatocytes and supportive cells for the study of hepatotropic pathogens. | March S, Ramanan V, Trehan K, Ng S, Galstian A, Gural N, Scull MA, Shlomai A, Mota MM, Fleming HE, Khetani SR, Rice CM, Bhatia SN | Nature protocols | 26584444 | Nat Protoc | 2015 Dec |
| In situ expansion of engineered human liver tissue in a mouse model of chronic liver disease. | Stevens KR, Scull MA, Ramanan V, Fortin CL, Chaturvedi RR, Knouse KA, Xiao JW, Fung C, Mirabella T, Chen AX, McCue MG, Yang MT, Fleming HE, Chung K, de Jong YP, Chen CS, Rice CM, Bhatia SN | Science translational medicine | 28724577 | Sci Transl Med | 2017 Jul 19 |
| Cell and tissue engineering for liver disease. | Bhatia SN, Underhill GH, Zaret KS, Fox IJ | Science translational medicine | 25031271 | Sci Transl Med | 2014 Jul 16 |
| InVERT molding for scalable control of tissue microarchitecture. | Stevens KR, Ungrin MD, Schwartz RE, Ng S, Carvalho B, Christine KS, Chaturvedi RR, Li CY, Zandstra PW, Chen CS, Bhatia SN | Nature communications | 23673632 | Nat Commun | 2013 |
| Characterization of nonprimate hepacivirus and construction of a functional molecular clone. | Scheel TK, Kapoor A, Nishiuchi E, Brock KV, Yu Y, Andrus L, Gu M, Renshaw RW, Dubovi EJ, McDonough SP, Van de Walle GR, Lipkin WI, Divers TJ, Tennant BC, Rice CM | Proceedings of the National Academy of Sciences of the United States of America | 25646476 | Proc Natl Acad Sci U S A | 2015 Feb 17 |
| Identification of small molecules for human hepatocyte expansion and iPS differentiation. | Shan J, Schwartz RE, Ross NT, Logan DJ, Thomas D, Duncan SA, North TE, Goessling W, Carpenter AE, Bhatia SN | Nature chemical biology | 23728495 | Nat Chem Biol | 2013 Aug |
| Viral genome imaging of hepatitis C virus to probe heterogeneous viral infection and responses to antiviral therapies. | Ramanan V, Trehan K, Ong ML, Luna JM, Hoffmann HH, Espiritu C, Sheahan TP, Chandrasekar H, Schwartz RE, Christine KS, Rice CM, van Oudenaarden A, Bhatia SN | Virology | 27128351 | Virology | 2016 Jul |
| Pan-Genotype Hepatitis E Virus Replication in Stem Cell-Derived Hepatocellular Systems. | Wu X, Dao Thi VL, Liu P, Takacs CN, Xiang K, Andrus L, Gouttenoire J, Moradpour D, Rice CM | Gastroenterology | 29277559 | Gastroenterology | 2018 Feb |
| A genetically humanized mouse model for hepatitis C virus infection. | Dorner M, Horwitz JA, Robbins JB, Barry WT, Feng Q, Mu K, Jones CT, Schoggins JW, Catanese MT, Burton DR, Law M, Rice CM, Ploss A | Nature | 21654804 | Nature | 2011 Jun 8 |
| Barriers of hepatitis C virus interspecies transmission. | Sandmann L, Ploss A | Virology | 23217617 | Virology | 2013 Jan 5 |
| Characterization of human antiviral adaptive immune responses during hepatotropic virus infection in HLA-transgenic human immune system mice. | Billerbeck E, Horwitz JA, Labitt RN, Donovan BM, Vega K, Budell WC, Koo GC, Rice CM, Ploss A | Journal of immunology (Baltimore, Md. : 1950) | 23833235 | J Immunol | 2013 Aug 15 |
| Interferon lambda alleles predict innate antiviral immune responses and hepatitis C virus permissiveness. | Sheahan T, Imanaka N, Marukian S, Dorner M, Liu P, Ploss A, Rice CM | Cell host & microbe | 24528865 | Cell Host Microbe | 2014 Feb 12 |
| Real-time imaging of hepatitis C virus infection using a fluorescent cell-based reporter system. | Jones CT, Catanese MT, Law LM, Khetani SR, Syder AJ, Ploss A, Oh TS, Schoggins JW, MacDonald MR, Bhatia SN, Rice CM | Nature biotechnology | 20118917 | Nat Biotechnol | 2010 Feb |
| Bioengineering methods for analysis of cells in vitro. | Underhill GH, Galie P, Chen CS, Bhatia SN | Annual review of cell and developmental biology | 23057744 | Annu Rev Cell Dev Biol | 2012 |
| Advances and challenges in studying hepatitis C virus in its native environment. | Sheahan T, Jones CT, Ploss A | Expert review of gastroenterology & hepatology | 20932139 | Expert Rev Gastroenterol Hepatol | 2010 Oct |
| Teaching new tricks to an old foe: murinizing hepatitis C virus. | Gerold G, Rice CM, Ploss A | Hepatology (Baltimore, Md.) | 21105113 | Hepatology | 2010 Dec |
| Modeling hepatitis C virus infection using human induced pluripotent stem cells. | Schwartz RE, Trehan K, Andrus L, Sheahan TP, Ploss A, Duncan SA, Rice CM, Bhatia SN | Proceedings of the National Academy of Sciences of the United States of America | 22308485 | Proc Natl Acad Sci U S A | 2012 Feb 14 |
| Hepatitis C virus infects rhesus macaque hepatocytes and simianized mice. | Scull MA, Shi C, de Jong YP, Gerold G, Ries M, von Schaewen M, Donovan BM, Labitt RN, Horwitz JA, Gaska JM, Hrebikova G, Xiao JW, Flatley B, Fung C, Chiriboga L, Walker CM, Evans DT, Rice CM, Ploss A | Hepatology (Baltimore, Md.) | 25820364 | Hepatology | 2015 Jul |
| Expansion, in vivo-ex vivo cycling, and genetic manipulation of primary human hepatocytes. | Michailidis E, Vercauteren K, Mancio-Silva L, Andrus L, Jahan C, Ricardo-Lax I, Zou C, Kabbani M, Park P, Quirk C, Pyrgaki C, Razooky B, Verhoye L, Zoluthkin I, Lu WY, Forbes SJ, Chiriboga L, Theise ND, Herzog RW, Suemizu H, Schneider WM, Shlomai A, Meuleman P, Bhatia SN, Rice CM, de Jong YP | Proceedings of the National Academy of Sciences of the United States of America | 31915293 | Proc Natl Acad Sci U S A | 2020 Jan 21 |
| Targeting BCL-XL in fibrolamellar hepatocellular carcinoma. | Shebl B, Ng D, Lalazar G, Rosemore C, Finkelstein TM, Migler RD, Zheng G, Zhang P, Jiang CS, Qureshi A, Vaughan R, Yarchoan M, de Jong YP, Rice CM, Coffino P, Ortiz MV, Zhou D, Simon SM | JCI insight | 36073545 | JCI Insight | 2022 Sep 8 |
| Mouse characteristics that affect establishing xenografts from hepatocellular carcinoma patient biopsies in the United States. | Zou C, El Dika I, Vercauteren KOA, Capanu M, Chou J, Shia J, Pilet J, Quirk C, Lalazar G, Andrus L, Kabbani M, Yaqubie A, Khalil D, Mergoub T, Chiriboga L, Rice CM, Abou-Alfa GK, de Jong YP | Cancer medicine | 34951132 | Cancer Med | 2022 Feb |
| Understanding the hepatitis C virus life cycle paves the way for highly effective therapies. | Scheel TK, Rice CM | Nature medicine | 23836234 | Nat Med | 2013 Jul |
| The ins and outs of hepatitis C virus entry and assembly. | Lindenbach BD, Rice CM | Nature reviews. Microbiology | 24018384 | Nat Rev Microbiol | 2013 Oct |
| Using goal-directed design to create a novel system for improving chronic illness care. | Fore D, Goldenhar LM, Margolis PA, Seid M | JMIR research protocols | 24168835 | JMIR Res Protoc | 2013 Oct 29 |
| Single cell analysis of HCV-infected patient hepatocytes: the science is no longer science fiction. | Sheahan TP, Rice CM | Gastroenterology | 24176873 | Gastroenterology | 2013 Dec |
| Insufficient interleukin-12 signalling favours differentiation of human CD4(+) and CD8(+) T cells into GATA-3(+) and GATA-3(+) T-bet(+) subsets in humanized mice. | Billerbeck E, Labitt RN, Vega K, Frias-Staheli N, Dorner M, Xiao JW, Rice CM, Ploss A | Immunology | 24766459 | Immunology | 2014 Oct |
| Virus associated malignancies: the role of viral hepatitis in hepatocellular carcinoma. | Shlomai A, de Jong YP, Rice CM | Seminars in cancer biology | 24457013 | Semin Cancer Biol | 2014 Jun |
| Expression of paramyxovirus V proteins promotes replication and spread of hepatitis C virus in cultures of primary human fetal liver cells. | Andrus L, Marukian S, Jones CT, Catanese MT, Sheahan TP, Schoggins JW, Barry WT, Dustin LB, Trehan K, Ploss A, Bhatia SN, Rice CM | Hepatology (Baltimore, Md.) | 22144107 | Hepatology | 2011 Dec |
| Identification, molecular cloning, and analysis of full-length hepatitis C virus transmitted/founder genotypes 1, 3, and 4. | Stoddard MB, Li H, Wang S, Saeed M, Andrus L, Ding W, Jiang X, Learn GH, von Schaewen M, Wen J, Goepfert PA, Hahn BH, Ploss A, Rice CM, Shaw GM | mBio | 25714714 | mBio | 2015 Feb 24 |
| Analysis of Hepatitis C Virus Particle Heterogeneity in Immunodeficient Human Liver Chimeric fah-/- Mice. | Andreo U, de Jong YP, Scull MA, Xiao JW, Vercauteren K, Quirk C, Mommersteeg MC, Bergaya S, Menon A, Fisher EA, Rice CM | Cellular and molecular gastroenterology and hepatology | 28936471 | Cell Mol Gastroenterol Hepatol | 2017 Nov |
| A Combination of Human Broadly Neutralizing Antibodies against Hepatitis B Virus HBsAg with Distinct Epitopes Suppresses Escape Mutations. | Wang Q, Michailidis E, Yu Y, Wang Z, Hurley AM, Oren DA, Mayer CT, Gazumyan A, Liu Z, Zhou Y, Schoofs T, Yao KH, Nieke JP, Wu J, Jiang Q, Zou C, Kabbani M, Quirk C, Oliveira T, Chhosphel K, Zhang Q, Schneider WM, Jahan C, Ying T, Horowitz J, Caskey M, Jankovic M, Robbiani DF, Wen Y, de Jong YP, Rice CM, Nussenzweig MC | Cell host & microbe | 32504577 | Cell Host Microbe | 2020 Aug 12 |
| Identification of Novel Therapeutic Targets for Fibrolamellar Carcinoma Using Patient-Derived Xenografts and Direct-from-Patient Screening. | Lalazar G, Requena D, Ramos-Espiritu L, Ng D, Bhola PD, de Jong YP, Wang R, Narayan NJC, Shebl B, Levin S, Michailidis E, Kabbani M, Vercauteren KOA, Hurley AM, Farber BA, Hammond WJ, Saltsman JA 3rd, Weinberg EM, Glickman JF, Lyons BA, Ellison J, Schadde E, Hertl M, Leiting JL, Truty MJ, Smoot RL, Tierney F, Kato T, Wendel HG, LaQuaglia MP, Rice CM, Letai A, Coffino P, Torbenson MS, Ortiz MV, Simon SM | Cancer discovery | 34127480 | Cancer Discov | 2021 Oct |
| Rapid casting of patterned vascular networks for perfusable engineered three-dimensional tissues. | Miller JS, Stevens KR, Yang MT, Baker BM, Nguyen DH, Cohen DM, Toro E, Chen AA, Galie PA, Yu X, Chaturvedi R, Bhatia SN, Chen CS | Nature materials | 22751181 | Nat Mater | 2012 Sep |
| Development of humanized mouse models to study human malaria parasite infection. | Vaughan AM, Kappe SH, Ploss A, Mikolajczak SA | Future microbiology | 22568719 | Future Microbiol | 2012 May |
| Superior In vivo Transduction of Human Hepatocytes Using Engineered AAV3 Capsid. | Vercauteren K, Hoffman BE, Zolotukhin I, Keeler GD, Xiao JW, Basner-Tschakarjan E, High KA, Ertl HC, Rice CM, Srivastava A, de Jong YP, Herzog RW | Molecular therapy : the journal of the American Society of Gene Therapy | 27019999 | Mol Ther | 2016 Jun |
| Humanized mice efficiently engrafted with fetal hepatoblasts and syngeneic immune cells develop human monocytes and NK cells. | Billerbeck E, Mommersteeg MC, Shlomai A, Xiao JW, Andrus L, Bhatta A, Vercauteren K, Michailidis E, Dorner M, Krishnan A, Charlton MR, Chiriboga L, Rice CM, de Jong YP | Journal of hepatology | 27151182 | J Hepatol | 2016 Aug |
| Insulin regulation of monoamine signaling: pathway to obesity. | Niswender KD, Daws LC, Avison MJ, Galli A | Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology | 21116253 | Neuropsychopharmacology | 2011 Jan |
| Disruption of Daily Rhythms by High-Fat Diet Is Reversible. | Branecky KL, Niswender KD, Pendergast JS | PloS one | 26366733 | PLoS One | 2015 |
| Neuronal ablation of p-Akt at Ser473 leads to altered 5-HT1A/2A receptor function. | Saunders C, Siuta M, Robertson SD, Davis AR, Sauer J, Matthies HJG, Gresch PJ, Airey D, Lindsley CW, Schetz JA, Niswender KD, Veenstra-Vanderweele JM, Galli A | Neurochemistry international | 24090638 | Neurochem Int | 2014 Jul |
| Period determination in the food-entrainable and methamphetamine-sensitive circadian oscillator(s). | Pendergast JS, Oda GA, Niswender KD, Yamazaki S | Proceedings of the National Academy of Sciences of the United States of America | 22891330 | Proc Natl Acad Sci U S A | 2012 Aug 28 |
| Imbalance in Resting State Functional Connectivity is Associated with Eating Behaviors and Adiposity in Children. | Chodkowski BA, Cowan RL, Niswender KD | Heliyon | 26878067 | Heliyon | 2016 Jan |
| Disgust proneness and associated neural substrates in obesity. | Watkins TJ, Di Iorio CR, Olatunji BO, Benningfield MM, Blackford JU, Dietrich MS, Bhatia M, Theiss JD, Salomon RM, Niswender K, Cowan RL | Social cognitive and affective neuroscience | 26454815 | Soc Cogn Affect Neurosci | 2016 Mar |
| The complex relationship between the light-entrainable and methamphetamine-sensitive circadian oscillators: evidence from behavioral studies of Period-mutant mice. | Pendergast JS, Niswender KD, Yamazaki S | The European journal of neuroscience | 23869717 | Eur J Neurosci | 2013 Oct |
| Rictor/mTORC2 facilitates central regulation of energy and glucose homeostasis. | Kocalis HE, Hagan SL, George L, Turney MK, Siuta MA, Laryea GN, Morris LC, Muglia LJ, Printz RL, Stanwood GD, Niswender KD | Molecular metabolism | 24944899 | Mol Metab | 2014 Jul |
| Neuron-specific deletion of peroxisome proliferator-activated receptor delta (PPARδ) in mice leads to increased susceptibility to diet-induced obesity. | Kocalis HE, Turney MK, Printz RL, Laryea GN, Muglia LJ, Davies SS, Stanwood GD, McGuinness OP, Niswender KD | PloS one | 22916190 | PLoS One | 2012 |
| Moving beyond energy homeostasis: new roles for glucagon-like peptide-1 in food and drug reward. | Reddy IA, Stanwood GD, Galli A | Neurochemistry international | 24140429 | Neurochem Int | 2014 Jul |
| Exendin-4 decreases amphetamine-induced locomotor activity. | Erreger K, Davis AR, Poe AM, Greig NH, Stanwood GD, Galli A | Physiology & behavior | 22465309 | Physiol Behav | 2012 Jun 25 |
| Central nervous system neuropeptide Y regulates mediators of hepatic phospholipid remodeling and very low-density lipoprotein triglyceride secretion via sympathetic innervation. | Rojas JM, Bruinstroop E, Printz RL, Alijagic-Boers A, Foppen E, Turney MK, George L, Beck-Sickinger AG, Kalsbeek A, Niswender KD | Molecular metabolism | 25737956 | Mol Metab | 2015 Mar |
| Dysregulation of the norepinephrine transporter sustains cortical hypodopaminergia and schizophrenia-like behaviors in neuronal rictor null mice. | Siuta MA, Robertson SD, Kocalis H, Saunders C, Gresch PJ, Khatri V, Shiota C, Kennedy JP, Lindsley CW, Daws LC, Polley DB, Veenstra-Vanderweele J, Stanwood GD, Magnuson MA, Niswender KD, Galli A | PLoS biology | 20543991 | PLoS Biol | 2010 Jun 8 |
| Wheel-running activity modulates circadian organization and the daily rhythm of eating behavior. | Pendergast JS, Branecky KL, Huang R, Niswender KD, Yamazaki S | Frontiers in psychology | 24624109 | Front Psychol | 2014 |
| GLP-1 analog attenuates cocaine reward. | Graham DL, Erreger K, Galli A, Stanwood GD | Molecular psychiatry | 23089631 | Mol Psychiatry | 2013 Sep |
| High-fat diet acutely affects circadian organisation and eating behavior. | Pendergast JS, Branecky KL, Yang W, Ellacott KL, Niswender KD, Yamazaki S | The European journal of neuroscience | 23331763 | Eur J Neurosci | 2013 Apr |
| Brief exposure to obesogenic diet disrupts brain dopamine networks. | Barry RL, Byun NE, Williams JM, Siuta MA, Tantawy MN, Speed NK, Saunders C, Galli A, Niswender KD, Avison MJ | PloS one | 29698491 | PLoS One | 2018 |
| Insulin signaling and addiction. | Daws LC, Avison MJ, Robertson SD, Niswender KD, Galli A, Saunders C | Neuropharmacology | 21420985 | Neuropharmacology | 2011 Dec |
| Tissue-specific function of Period3 in circadian rhythmicity. | Pendergast JS, Niswender KD, Yamazaki S | PloS one | 22253927 | PLoS One | 2012 |
| Impaired striatal Akt signaling disrupts dopamine homeostasis and increases feeding. | Speed N, Saunders C, Davis AR, Owens WA, Matthies HJ, Saadat S, Kennedy JP, Vaughan RA, Neve RL, Lindsley CW, Russo SJ, Daws LC, Niswender KD, Galli A | PloS one | 21969871 | PLoS One | 2011 |
| Role for mTOR signaling and neuronal activity in morphine-induced adaptations in ventral tegmental area dopamine neurons. | Mazei-Robison MS, Koo JW, Friedman AK, Lansink CS, Robison AJ, Vinish M, Krishnan V, Kim S, Siuta MA, Galli A, Niswender KD, Appasani R, Horvath MC, Neve RL, Worley PF, Snyder SH, Hurd YL, Cheer JF, Han MH, Russo SJ, Nestler EJ | Neuron | 22196333 | Neuron | 2011 Dec 22 |
| The mouse lymph node as an ectopic transplantation site for multiple tissues. | Komori J, Boone L, DeWard A, Hoppo T, Lagasse E | Nature biotechnology | 23000933 | Nat Biotechnol | 2012 Oct |
| Ectopic transplantation sites for cell-based therapy. | DeWard AD, Komori J, Lagasse E | Current opinion in organ transplantation | 24480968 | Curr Opin Organ Transplant | 2014 Apr |
| Hyperthermia enhances mapatumumab-induced apoptotic death through ubiquitin-mediated degradation of cellular FLIP(long) in human colon cancer cells. | Song X, Kim SY, Zhou Z, Lagasse E, Kwon YT, Lee YJ | Cell death & disease | 23559011 | Cell Death Dis | 2013 Apr 4 |
| Towards Organs on Demand: Breakthroughs and Challenges in Models of Organogenesis. | Francipane MG, Lagasse E | Current pathobiology reports | 28979828 | Curr Pathobiol Rep | 2016 Sep |
| Identification of a candidate stem cell in human gallbladder. | Manohar R, Li Y, Fohrer H, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E | Stem cell research | 25765520 | Stem Cell Res | 2015 May |
| Adult hepatocytes direct liver organogenesis through non-parenchymal cell recruitment in the kidney. | Utoh R, Komori J, Kuge H, Tatsumi K, Yamada M, Hirohashi S, Tsutsumi M, Amanuma T, Yoshioka A, Nakajima Y, Wake K, Okano T, Lagasse E, Ohashi K | Journal of hepatology | 29288124 | J Hepatol | 2018 Apr |
| Identification and expansion of a unique stem cell population from adult mouse gallbladder. | Manohar R, Komori J, Guzik L, Stolz DB, Chandran UR, LaFramboise WA, Lagasse E | Hepatology (Baltimore, Md.) | 21793026 | Hepatology | 2011 Nov |
| Potential barriers to human hepatocyte transplantation in MUP-uPAtg(⁺/⁺)Rag2⁻/⁻γC⁻/⁻ mice. | Komori J, DeWard AD, Gramignoli R, Strom SC, Fontes P, Lagasse E | Cell transplantation | 23998208 | Cell Transplant | 2014 |
| Deletion of Ptp4a3 reduces clonogenicity and tumor-initiation ability of colitis-associated cancer cells in mice. | Cramer JM, Zimmerman MW, Thompson T, Homanics GE, Lazo JS, Lagasse E | Stem cell research | 24950307 | Stem Cell Res | 2014 Jul |
| Pluripotent Stem Cells to Rebuild a Kidney: The Lymph Node as a Possible Developmental Niche. | Francipane MG, Lagasse E | Cell transplantation | 26160801 | Cell Transplant | 2016 |
| Maturation of embryonic tissues in a lymph node: a new approach for bioengineering complex organs. | Francipane MG, Lagasse E | Organogenesis | 25531035 | Organogenesis | 2014 |
| Regenerating a kidney in a lymph node. | Francipane MG, Lagasse E | Pediatric nephrology (Berlin, Germany) | 26686504 | Pediatr Nephrol | 2016 Oct |
| Kidney-in-a-lymph node: A novel organogenesis assay to model human renal development and test nephron progenitor cell fates. | Francipane MG, Han B, Oxburgh L, Sims-Lucas S, Li Z, Lagasse E | Journal of tissue engineering and regenerative medicine | 31267702 | J Tissue Eng Regen Med | 2019 Sep |
| Cancer Stem Cells: A Moving Target. | Francipane MG, Chandler J, Lagasse E | Current pathobiology reports | 23914341 | Curr Pathobiol Rep | 2013 Jun 1 |
| Distinct human stem cell populations in small and large intestine. | Cramer JM, Thompson T, Geskin A, LaFramboise W, Lagasse E | PloS one | 25751518 | PLoS One | 2015 |
| Rescue of lethal hepatic failure by hepatized lymph nodes in mice. | Hoppo T, Komori J, Manohar R, Stolz DB, Lagasse E | Gastroenterology | 21070777 | Gastroenterology | 2011 Feb |
| Cellular heterogeneity in the mouse esophagus implicates the presence of a nonquiescent epithelial stem cell population. | DeWard AD, Cramer J, Lagasse E | Cell reports | 25373907 | Cell Rep | 2014 Oct 23 |
| The lymph node as a new site for kidney organogenesis. | Francipane MG, Lagasse E | Stem cells translational medicine | 25646529 | Stem Cells Transl Med | 2015 Mar |
| The cancer chemotherapeutic 5-fluorouracil is a potent Fusobacterium nucleatum inhibitor and its activity is modified by intratumoral microbiota. | LaCourse KD, Zepeda-Rivera M, Kempchinsky AG, Baryiames A, Minot SS, Johnston CD, Bullman S | Cell reports | 36384132 | Cell Rep | 2022 Nov 15 |
| Biosensor libraries harness large classes of binding domains for construction of allosteric transcriptional regulators. | Juárez JF, Lecube-Azpeitia B, Brown SL, Johnston CD, Church GM | Nature communications | 30082754 | Nat Commun | 2018 Aug 6 |
| A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche. | Zepeda-Rivera M, Minot SS, Bouzek H, Wu H, Blanco-Míguez A, Manghi P, Jones DS, LaCourse KD, Wu Y, McMahon EF, Park SN, Lim YK, Kempchinsky AG, Willis AD, Cotton SL, Yost SC, Sicinska E, Kook JK, Dewhirst FE, Segata N, Bullman S, Johnston CD | Nature | 38509359 | Nature | 2024 Apr |
| Expanding the rumen Prevotella collection: The description of Prevotella communis, sp. nov. of ovine origin. | Grabner E, Stare E, Fanedl L, Zorec M, Jones DS, Johnston CD, Avguštin G, Accetto T | Systematic and applied microbiology | 37295348 | Syst Appl Microbiol | 2023 Jul |
| Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts. | Bor B, Collins AJ, Murugkar PP, Balasubramanian S, To TT, Hendrickson EL, Bedree JK, Bidlack FB, Johnston CD, Shi W, McLean JS, He X, Dewhirst FE | Journal of dental research | 32075512 | J Dent Res | 2020 Jun |
| INVADEseq to identify cell-adherent or invasive bacteria and the associated host transcriptome at single-cell-level resolution. | Galeano Niño JL, Wu H, LaCourse KD, Srinivasan H, Fitzgibbon M, Minot SS, Sather C, Johnston CD, Bullman S | Nature protocols | 37789194 | Nat Protoc | 2023 Nov |
| Helicobacter pylori Chronic Infection Selects for Effective Colonizers of Metaplastic Glands. | O'Brien VP, Jackson LK, Frick JP, Rodriguez Martinez AE, Jones DS, Johnston CD, Salama NR | mBio | 36598261 | mBio | 2023 Feb 28 |
| The relationship between gastrointestinal cancers and the microbiota. | LaCourse KD, Johnston CD, Bullman S | The lancet. Gastroenterology & hepatology | 33743198 | Lancet Gastroenterol Hepatol | 2021 Jun |
| Systematic evasion of the restriction-modification barrier in bacteria. | Johnston CD, Cotton SL, Rittling SR, Starr JR, Borisy GG, Dewhirst FE, Lemon KP | Proceedings of the National Academy of Sciences of the United States of America | 31097593 | Proc Natl Acad Sci U S A | 2019 Jun 4 |
| Corrigendum to "Expanding the rumen Prevotella collection: the description of Prevotella communis, sp. nov. of ovine origin" [Syst. Appl. Microbiol. 46(4) (2023) 126437]. | Grabner E, Stare E, Fanedl L, Zorec M, Jones DS, Johnston CD, Avguštin G, Accetto T | Systematic and applied microbiology | 37669882 | Syst Appl Microbiol | 2023 Sep |
| Fusobacterium sphaericum sp. nov. , isolated from a human colon tumor, adheres to colonic epithelial cells and induces IL-8 secretion. | Zepeda-Rivera MA, Eisele Y, Baryiames A, Wu H, Mengoni C, Piccinno G, McMahon EF, LaCourse KD, Jones DS, Hauner H, Minot SS, Segata N, Dewhirst FE, Johnston CD, Bullman S | bioRxiv : the preprint server for biology | 37398369 | bioRxiv | 2024 Aug 28 |
| Genomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome. | Flores Ramos S, Brugger SD, Escapa IF, Skeete CA, Cotton SL, Eslami SM, Gao W, Bomar L, Tran TH, Jones DS, Minot S, Roberts RJ, Johnston CD, Lemon KP | mSystems | 34546072 | mSystems | 2021 Oct 26 |
| Harnessing the microbiome to restore immunotherapy response. | Bullman S, Eggermont A, Johnston CD, Zitvogel L | Nature cancer | 35121929 | Nat Cancer | 2021 Dec |
| Complete Genome Sequence of Morganella morganii CTX51T, Isolated from a Human Cecal Adenocarcinoma. | Stepanovica M, Zepeda-Rivera MA, McGlinchey AS, Baryiames AA, Jones DS, LaCourse KD, Bullman S, Johnston CD | Microbiology resource announcements | 35254123 | Microbiol Resour Announc | 2022 Apr 21 |
| Effect of the intratumoral microbiota on spatial and cellular heterogeneity in cancer. | Galeano Niño JL, Wu H, LaCourse KD, Kempchinsky AG, Baryiames A, Barber B, Futran N, Houlton J, Sather C, Sicinska E, Taylor A, Minot SS, Johnston CD, Bullman S | Nature | 36385528 | Nature | 2022 Nov |
| Complete Genome Sequence of Clostridium cadaveris IFB3C5, Isolated from a Human Colonic Adenocarcinoma. | McGlinchey AS, Zepeda-Rivera MA, Stepanovica M, Baryiames AA, Jones DS, LaCourse KD, Bullman S, Johnston CD | Microbiology resource announcements | 35234492 | Microbiol Resour Announc | 2022 Mar 17 |
| The tumour-associated microbiome. | Johnston CD, Bullman S | Nature reviews. Gastroenterology & hepatology | 35361914 | Nat Rev Gastroenterol Hepatol | 2022 Jun |
| Complete Genome Sequence of Arachnia rubra Strain DSM 100122(T), a Cultured Member of the Human Oral Microbiome. | Ouellette M, Bejian AA, Chen T, Jones DS, Johnston CD, Dewhirst FE | Microbiology resource announcements | 34854708 | Microbiol Resour Announc | 2021 Dec 2 |
| Complete Genome Sequences and Methylome Analyses of Cutibacterium acnes subsp. acnes Strains DSM 16379 and DSM 1897(T). | Deptula P, Laine P, Paulin L, Auvinen P, Roberts RJ, Johnston CD, Varmanen P | Microbiology resource announcements | 32675190 | Microbiol Resour Announc | 2020 Jul 16 |
| Enhanced transformation efficiency in Treponema denticola enabled by SyngenicDNA-based plasmids lacking restriction-modification target motifs. | Johnston CD, Goetting-Minesky MP, Kennedy K, Godovikova V, Zayed SM, Roberts RJ, Fenno JC | Molecular oral microbiology | 37880921 | Mol Oral Microbiol | 2023 Dec |
| The hidden fitness of the male zebra finch courtship song. | Alam D, Zia F, Roberts TF | Nature | 38509376 | Nature | 2024 Apr |
| AVN: A Deep Learning Approach for the Analysis of Birdsong. | Koch TMI, Marks ES, Roberts TF | bioRxiv : the preprint server for biology | 39229184 | bioRxiv | 2024 Aug 24 |
| Bayesian semiparametric Markov renewal mixed models for vocalization syntax. | Wu Y, Jarvis ED, Sarkar A | Biostatistics (Oxford, England) | 36583955 | Biostatistics | 2024 Jul 1 |
| A humanized NOVA1 splicing factor alters mouse vocal communications. | Tajima Y, Vargas CDM, Ito K, Wang W, Luo JD, Xing J, Kuru N, Machado LC, Siepel A, Carroll TS, Jarvis ED, Darnell RB | Nature communications | 39966351 | Nat Commun | 2025 Feb 18 |
| Deconstructing Odorant Identity via Primacy in Dual Networks. | Kepple DR, Giaffar H, Rinberg D, Koulakov AA | Neural computation | 30764743 | Neural Comput | 2019 Apr |
| Mosaic representations of odors in the input and output layers of the mouse olfactory bulb. | Chae H, Kepple DR, Bast WG, Murthy VN, Koulakov AA, Albeanu DF | Nature neuroscience | 31332371 | Nat Neurosci | 2019 Aug |
| High-throughput sequencing of single neuron projections reveals spatial organization in the olfactory cortex. | Chen Y, Chen X, Baserdem B, Zhan H, Li Y, Davis MB, Kebschull JM, Zador AM, Koulakov AA, Albeanu DF | Cell | 36306734 | Cell | 2022 Oct 27 |
| Simultaneous mapping of 3D structure and nascent RNAs argues against nuclear compartments that preclude transcription. | Goronzy IN, Quinodoz SA, Jachowicz JW, Ollikainen N, Bhat P, Guttman M | Cell reports | 36450242 | Cell Rep | 2022 Nov 29 |
| SPIDR: a highly multiplexed method for mapping RNA-protein interactions uncovers a potential mechanism for selective translational suppression upon cellular stress. | Wolin E, Guo JK, Blanco MR, Perez AA, Goronzy IN, Abdou AA, Gorhe D, Guttman M, Jovanovic M | bioRxiv : the preprint server for biology | 37333139 | bioRxiv | 2023 Jun 7 |
| Xist spatially amplifies SHARP/SPEN recruitment to balance chromosome-wide silencing and specificity to the X chromosome. | Jachowicz JW, Strehle M, Banerjee AK, Blanco MR, Thai J, Guttman M | Nature structural & molecular biology | 35301492 | Nat Struct Mol Biol | 2022 Mar |
| Denaturing purifications demonstrate that PRC2 and other widely reported chromatin proteins do not appear to bind directly to RNA in vivo. | Guo JK, Blanco MR, Walkup WG 4th, Bonesteele G, Urbinati CR, Banerjee AK, Chow A, Ettlin O, Strehle M, Peyda P, Amaya E, Trinh V, Guttman M | Molecular cell | 38387462 | Mol Cell | 2024 Apr 4 |
| Genome organization around nuclear speckles drives mRNA splicing efficiency. | Bhat P, Chow A, Emert B, Ettlin O, Quinodoz SA, Strehle M, Takei Y, Burr A, Goronzy IN, Chen AW, Huang W, Ferrer JLM, Soehalim E, Goh ST, Chari T, Sullivan DK, Blanco MR, Guttman M | Nature | 38720076 | Nature | 2024 May |
| ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements. | Perez AA, Goronzy IN, Blanco MR, Yeh BT, Guo JK, Lopes CS, Ettlin O, Burr A, Guttman M | Nature genetics | 39587360 | Nat Genet | 2024 Dec |
| Technology Roadmap for Flexible Sensors. | Luo Y, Abidian MR, Ahn JH, Akinwande D, Andrews AM, Antonietti M, Bao Z, Berggren M, Berkey CA, Bettinger CJ, Chen J, Chen P, Cheng W, Cheng X, Choi SJ, Chortos A, Dagdeviren C, Dauskardt RH, Di CA, Dickey MD, Duan X, Facchetti A, Fan Z, Fang Y, Feng J, Feng X, Gao H, Gao W, Gong X, Guo CF, Guo X, Hartel MC, He Z, Ho JS, Hu Y, Huang Q, Huang Y, Huo F, Hussain MM, Javey A, Jeong U, Jiang C, Jiang X, Kang J, Karnaushenko D, Khademhosseini A, Kim DH, Kim ID, Kireev D, Kong L, Lee C, Lee NE, Lee PS, Lee TW, Li F, Li J, Liang C, Lim CT, Lin Y, Lipomi DJ, Liu J, Liu K, Liu N, Liu R, Liu Y, Liu Y, Liu Z, Liu Z, Loh XJ, Lu N, Lv Z, Magdassi S, Malliaras GG, Matsuhisa N, Nathan A, Niu S, Pan J, Pang C, Pei Q, Peng H, Qi D, Ren H, Rogers JA, Rowe A, Schmidt OG, Sekitani T, Seo DG, Shen G, Sheng X, Shi Q, Someya T, Song Y, Stavrinidou E, Su M, Sun X, Takei K, Tao XM, Tee BCK, Thean AV, Trung TQ, Wan C, Wang H, Wang J, Wang M, Wang S, Wang T, Wang ZL, Weiss PS, Wen H, Xu S, Xu T, Yan H, Yan X, Yang H, Yang L, Yang S, Yin L, Yu C, Yu G, Yu J, Yu SH, Yu X, Zamburg E, Zhang H, Zhang X, Zhang X, Zhang X, Zhang Y, Zhang Y, Zhao S, Zhao X, Zheng Y, Zheng YQ, Zheng Z, Zhou T, Zhu B, Zhu M, Zhu R, Zhu Y, Zhu Y, Zou G, Chen X | ACS nano | 36892156 | ACS Nano | 2023 Mar 28 |
| Differential Charging in Photoemission from Mercurated DNA Monolayers on Ferromagnetic Films. | Stemer DM, Abendroth JM, Cheung KM, Ye M, El Hadri MS, Fullerton EE, Weiss PS | Nano letters | 31960675 | Nano Lett | 2020 Feb 12 |
| Detecting DNA and RNA and Differentiating Single-Nucleotide Variations via Field-Effect Transistors. | Cheung KM, Abendroth JM, Nakatsuka N, Zhu B, Yang Y, Andrews AM, Weiss PS | Nano letters | 32706969 | Nano Lett | 2020 Aug 12 |
| Lipid Bicelle Micropatterning Using Chemical Lift-Off Lithography. | Belling JN, Cheung KM, Jackman JA, Sut TN, Allen M, Park JH, Jonas SJ, Cho NJ, Weiss PS | ACS applied materials & interfaces | 32092250 | ACS Appl Mater Interfaces | 2020 Mar 18 |
| Simultaneous serotonin and dopamine monitoring across timescales by rapid pulse voltammetry with partial least squares regression. | Movassaghi CS, Perrotta KA, Yang H, Iyer R, Cheng X, Dagher M, Fillol MA, Andrews AM | Analytical and bioanalytical chemistry | 34686897 | Anal Bioanal Chem | 2021 Nov |
| Conformal Ultrathin Film Metal-Organic Framework Analogues: Characterization of Growth, Porosity, and Electronic Transport. | Lau J, Trojniak AE, Maraugha MJ, VanZanten AJ, Osterbaan AJ, Serino AC, Ohnsorg ML, Cheung KM, Ashby DS, Weiss PS, Dunn BS, Anderson ME | Chemistry of materials : a publication of the American Chemical Society | 32536746 | Chem Mater | 2019 Nov 12 |
| Chemical Lift-Off Lithography of Metal and Semiconductor Surfaces. | Cheung KM, Stemer DM, Zhao C, Young TD, Belling JN, Andrews AM, Weiss PS | ACS materials letters | 32405626 | ACS Mater Lett | 2020 Jan 6 |
| Scalable Fabrication of Quasi-One-Dimensional Gold Nanoribbons for Plasmonic Sensing. | Zhao C, Xu X, Ferhan AR, Chiang N, Jackman JA, Yang Q, Liu W, Andrews AM, Cho NJ, Weiss PS | Nano letters | 32027140 | Nano Lett | 2020 Mar 11 |
| Narrower Nanoribbon Biosensors Fabricated by Chemical Lift-off Lithography Show Higher Sensitivity. | Zhao C, Liu Q, Cheung KM, Liu W, Yang Q, Xu X, Man T, Weiss PS, Zhou C, Andrews AM | ACS nano | 33337135 | ACS Nano | 2021 Jan 26 |
| Flexible and Implantable Polyimide Aptamer-Field-Effect Transistor Biosensors. | Zhao C, Man T, Cao Y, Weiss PS, Monbouquette HG, Andrews AM | ACS sensors | 36399772 | ACS Sens | 2022 Dec 23 |
| Maximizing Electrochemical Information: A Perspective on Background-Inclusive Fast Voltammetry. | Movassaghi CS, Alcañiz Fillol M, Kishida KT, McCarty G, Sombers LA, Wassum KM, Andrews AM | Analytical chemistry | 38597398 | Anal Chem | 2024 Apr 23 |
| Dark Classics in Chemical Neuroscience: 3,4-Methylenedioxymethamphetamine. | Dunlap LE, Andrews AM, Olson DE | ACS chemical neuroscience | 30001118 | ACS Chem Neurosci | 2018 Oct 17 |
| Large-Area, Ultrathin Metal-Oxide Semiconductor Nanoribbon Arrays Fabricated by Chemical Lift-Off Lithography. | Zhao C, Xu X, Bae SH, Yang Q, Liu W, Belling JN, Cheung KM, Rim YS, Yang Y, Andrews AM, Weiss PS | Nano letters | 30060654 | Nano Lett | 2018 Sep 12 |
| Small-Molecule Patterning via Prefunctionalized Alkanethiols. | Cao HH, Nakatsuka N, Deshayes S, Abendroth JM, Yang H, Weiss PS, Kasko AM, Andrews AM | Chemistry of materials : a publication of the American Chemical Society | 30828130 | Chem Mater | 2018 Jun 26 |
| Phenylalanine Monitoring via Aptamer-Field-Effect Transistor Sensors. | Cheung KM, Yang KA, Nakatsuka N, Zhao C, Ye M, Jung ME, Yang H, Weiss PS, Stojanović MN, Andrews AM | ACS sensors | 31631652 | ACS Sens | 2019 Dec 27 |
| Aptamer Recognition of Multiplexed Small-Molecule-Functionalized Substrates. | Nakatsuka N, Cao HH, Deshayes S, Melkonian AL, Kasko AM, Weiss PS, Andrews AM | ACS applied materials & interfaces | 29851335 | ACS Appl Mater Interfaces | 2018 Jul 18 |
| Spin-Dependent Ionization of Chiral Molecular Films. | Abendroth JM, Cheung KM, Stemer DM, El Hadri MS, Zhao C, Fullerton EE, Weiss PS | Journal of the American Chemical Society | 30734553 | J Am Chem Soc | 2019 Mar 6 |
| A functional group-guided approach to aptamers for small molecules. | Yang K, Mitchell NM, Banerjee S, Cheng Z, Taylor S, Kostic AM, Wong I, Sajjath S, Zhang Y, Stevens J, Mohan S, Landry DW, Worgall TS, Andrews AM, Stojanovic MN | Science (New York, N.Y.) | 37262137 | Science | 2023 Jun 2 |
| Wearable aptamer-field-effect transistor sensing system for noninvasive cortisol monitoring. | Wang B, Zhao C, Wang Z, Yang KA, Cheng X, Liu W, Yu W, Lin S, Zhao Y, Cheung KM, Lin H, Hojaiji H, Weiss PS, Stojanović MN, Tomiyama AJ, Andrews AM, Emaminejad S | Science advances | 34985954 | Sci Adv | 2022 Jan 7 |
| Interfacing with the Brain: How Nanotechnology Can Contribute. | Ahmed AAA, Alegret N, Almeida B, Alvarez-Puebla R, Andrews AM, Ballerini L, Barrios-Capuchino JJ, Becker C, Blick RH, Bonakdar S, Chakraborty I, Chen X, Cheon J, Chilla G, Coelho Conceicao AL, Delehanty J, Dulle M, Efros AL, Epple M, Fedyk M, Feliu N, Feng M, Fernández-Chacón R, Fernandez-Cuesta I, Fertig N, Förster S, Garrido JA, George M, Guse AH, Hampp N, Harberts J, Han J, Heekeren HR, Hofmann UG, Holzapfel M, Hosseinkazemi H, Huang Y, Huber P, Hyeon T, Ingebrandt S, Ienca M, Iske A, Kang Y, Kasieczka G, Kim DH, Kostarelos K, Lee JH, Lin KW, Liu S, Liu X, Liu Y, Lohr C, Mailänder V, Maffongelli L, Megahed S, Mews A, Mutas M, Nack L, Nakatsuka N, Oertner TG, Offenhäusser A, Oheim M, Otange B, Otto F, Patrono E, Peng B, Picchiotti A, Pierini F, Pötter-Nerger M, Pozzi M, Pralle A, Prato M, Qi B, Ramos-Cabrer P, Genger UR, Ritter N, Rittner M, Roy S, Santoro F, Schuck NW, Schulz F, Şeker E, Skiba M, Sosniok M, Stephan H, Wang R, Wang T, Wegner KD, Weiss PS, Xu M, Yang C, Zargarian SS, Zeng Y, Zhou Y, Zhu D, Zierold R, Parak WJ | ACS nano | 40063703 | ACS Nano | 2025 Mar 25 |
| Polyserotonin Nanoparticles as Multifunctional Materials for Biomedical Applications. | Nakatsuka N, Hasani-Sadrabadi MM, Cheung KM, Young TD, Bahlakeh G, Moshaverinia A, Weiss PS, Andrews AM | ACS nano | 29664607 | ACS Nano | 2018 May 22 |
| Optogenetic Stimulation of Midbrain Dopamine Neurons Produces Striatal Serotonin Release. | Dagher M, Perrotta KA, Erwin SA, Hachisuka A, Iyer R, Masmanidis SC, Yang H, Andrews AM | ACS chemical neuroscience | 35312275 | ACS Chem Neurosci | 2022 Apr 6 |
| Implantable aptamer-field-effect transistor neuroprobes for in vivo neurotransmitter monitoring. | Zhao C, Cheung KM, Huang IW, Yang H, Nakatsuka N, Liu W, Cao Y, Man T, Weiss PS, Monbouquette HG, Andrews AM | Science advances | 34818033 | Sci Adv | 2021 Nov 26 |
| Divalent Cation Dependence Enhances Dopamine Aptamer Biosensing. | Nakatsuka N, Abendroth JM, Yang KA, Andrews AM | ACS applied materials & interfaces | 33410656 | ACS Appl Mater Interfaces | 2021 Mar 3 |
| Lipid-Bicelle-Coated Microfluidics for Intracellular Delivery with Reduced Fouling. | Belling JN, Heidenreich LK, Park JH, Kawakami LM, Takahashi J, Frost IM, Gong Y, Young TD, Jackman JA, Jonas SJ, Cho NJ, Weiss PS | ACS applied materials & interfaces | 32940030 | ACS Appl Mater Interfaces | 2020 Oct 14 |
| Photothermal Intracellular Delivery Using Gold Nanodisk Arrays. | Zhao C, Man T, Xu X, Yang Q, Liu W, Jonas SJ, Teitell MA, Chiou PY, Weiss PS | ACS materials letters | 34708213 | ACS Mater Lett | 2020 Nov 2 |
| Flexible Multiplexed In(2)O(3) Nanoribbon Aptamer-Field-Effect Transistors for Biosensing. | Liu Q, Zhao C, Chen M, Liu Y, Zhao Z, Wu F, Li Z, Weiss PS, Andrews AM, Zhou C | iScience | 33083757 | iScience | 2020 Sep 25 |
| SeroWare: An Open-Source Software Suite for Voltammetry Data Acquisition and Analysis. | Movassaghi CS, Iyer R, Curry ME, Wesely ME, Fillol MA, Andrews AM | ACS chemical neuroscience | 39993240 | ACS Chem Neurosci | 2025 Mar 5 |
| Synthesis of PEG-grafted boron doped Si nanocrystals. | Greenhagen JR, Andaraarachchi HP, Li Z, Kortshagen UR | The Journal of chemical physics | 31822090 | J Chem Phys | 2019 Dec 7 |
| Cortical column and whole-brain imaging with molecular contrast and nanoscale resolution. | Gao R, Asano SM, Upadhyayula S, Pisarev I, Milkie DE, Liu TL, Singh V, Graves A, Huynh GH, Zhao Y, Bogovic J, Colonell J, Ott CM, Zugates C, Tappan S, Rodriguez A, Mosaliganti KR, Sheu SH, Pasolli HA, Pang S, Xu CS, Megason SG, Hess H, Lippincott-Schwartz J, Hantman A, Rubin GM, Kirchhausen T, Saalfeld S, Aso Y, Boyden ES, Betzig E | Science (New York, N.Y.) | 30655415 | Science | 2019 Jan 18 |
| Structures and topological defects in pressure-driven lyotropic chromonic liquid crystals. | Zhang Q, Zhang R, Ge B, Yaqoob Z, So PTC, Bischofberger I | Proceedings of the National Academy of Sciences of the United States of America | 34446562 | Proc Natl Acad Sci U S A | 2021 Aug 31 |
| Single-Shot Quantitative Polarization Imaging of Complex Birefringent Structure Dynamics. | Ge B, Zhang Q, Zhang R, Lin JT, Tseng PH, Chang CW, Dong CY, Zhou R, Yaqoob Z, Bischofberger I, So PTC | ACS photonics | 37292495 | ACS Photonics | 2021 Dec 15 |
| Distance-dependent resonance energy transfer in alkyl-terminated Si nanocrystal solids. | Li Z, Robinson ZL, Elvati P, Violi A, Kortshagen UR | The Journal of chemical physics | 35364875 | J Chem Phys | 2022 Mar 28 |
| Fast light-field 3D microscopy with out-of-distribution detection and adaptation through Conditional Normalizing Flows. | Vizcaíno JP, Symvoulidis P, Wang Z, Jelten J, Favaro P, Boyden ES, Lasser T | ArXiv | 37396615 | ArXiv | 2023 Jun 14 |
| In vivo visualization of butterfly scale cell morphogenesis in Vanessa cardui. | McDougal AD, Kang S, Yaqoob Z, So PTC, Kolle M | Proceedings of the National Academy of Sciences of the United States of America | 34845021 | Proc Natl Acad Sci U S A | 2021 Dec 7 |
| Recording of cellular physiological histories along optically readable self-assembling protein chains. | Linghu C, An B, Shpokayte M, Celiker OT, Shmoel N, Zhang R, Zhang C, Park D, Park WM, Ramirez S, Boyden ES | Nature biotechnology | 36593405 | Nat Biotechnol | 2023 May |
| Aerosol-Phase Synthesis and Processing of Luminescent Silicon Nanocrystals. | Li Z, Kortshagen UR | Chemistry of materials : a publication of the American Chemical Society | 34163100 | Chem Mater | 2019 Sep 19 |
| A highly homogeneous polymer composed of tetrahedron-like monomers for high-isotropy expansion microscopy. | Gao R, Yu CJ, Gao L, Piatkevich KD, Neve RL, Munro JB, Upadhyayula S, Boyden ES | Nature nanotechnology | 33782587 | Nat Nanotechnol | 2021 Jun |
| In situ genome sequencing resolves DNA sequence and structure in intact biological samples. | Payne AC, Chiang ZD, Reginato PL, Mangiameli SM, Murray EM, Yao CC, Markoulaki S, Earl AS, Labade AS, Jaenisch R, Church GM, Boyden ES, Buenrostro JD, Chen F | Science (New York, N.Y.) | 33384301 | Science | 2021 Feb 26 |
| Improved genetically encoded near-infrared fluorescent calcium ion indicators for in vivo imaging. | Qian Y, Cosio DMO, Piatkevich KD, Aufmkolk S, Su WC, Celiker OT, Schohl A, Murdock MH, Aggarwal A, Chang YF, Wiseman PW, Ruthazer ES, Boyden ES, Campbell RE | PLoS biology | 33232322 | PLoS Biol | 2020 Nov |
| Water-Soluble Luminescent Silicon Nanocrystals by Plasma-Induced Acrylic Acid Grafting and PEGylation. | Li Z, Mahajan A, Andaraarachchi HP, Lee Y, Kortshagen UR | ACS applied bio materials | 35014827 | ACS Appl Bio Mater | 2022 Jan 17 |
| Multisensory gamma stimulation promotes glymphatic clearance of amyloid. | Murdock MH, Yang CY, Sun N, Pao PC, Blanco-Duque C, Kahn MC, Kim T, Lavoie NS, Victor MB, Islam MR, Galiana F, Leary N, Wang S, Bubnys A, Ma E, Akay LA, Sneve M, Qian Y, Lai C, McCarthy MM, Kopell N, Kellis M, Piatkevich KD, Boyden ES, Tsai LH | Nature | 38418876 | Nature | 2024 Mar |
| Mapping nanoscale topographic features in thick tissues with speckle diffraction tomography. | Kang S, Zhou R, Brelen M, Mak HK, Lin Y, So PTC, Yaqoob Z | Light, science & applications | 37607903 | Light Sci Appl | 2023 Aug 22 |
| Dynamics of microcompartment formation at the mitosis-to-G1 transition. | Goel VY, Aboreden NG, Jusuf JM, Zhang H, Mori LP, Mirny LA, Blobel GA, Banigan EJ, Hansen AS | bioRxiv : the preprint server for biology | 39345388 | bioRxiv | 2024 Sep 16 |
| LDB1 establishes multi-enhancer networks to regulate gene expression. | Aboreden NG, Lam JC, Goel VY, Wang S, Wang X, Midla SC, Quijano A, Keller CA, Giardine BM, Hardison RC, Zhang H, Hansen AS, Blobel GA | bioRxiv : the preprint server for biology | 39229045 | bioRxiv | 2024 Aug 24 |
| Genome-wide absolute quantification of chromatin looping. | Jusuf JM, Grosse-Holz S, Gabriele M, Mach P, Flyamer IM, Zechner C, Giorgetti L, Mirny LA, Hansen AS | bioRxiv : the preprint server for biology | 39935886 | bioRxiv | 2025 Jan 15 |
| Enhancer selectivity in space and time: from enhancer-promoter interactions to promoter activation. | Yang JH, Hansen AS | Nature reviews. Molecular cell biology | 38413840 | Nat Rev Mol Cell Biol | 2024 Jul |
| Molecular models of bidirectional promoter regulation. | Nemsick S, Hansen AS | Current opinion in structural biology | 38905929 | Curr Opin Struct Biol | 2024 Aug |
| Catalytic Protein Inhibitors. | Kodadek T | Angewandte Chemie (International ed. in English) | 38064411 | Angew Chem Int Ed Engl | 2024 Mar 11 |
| Juneteenth in STEMM and the barriers to equitable science. | Mays A, Byars-Winston A, Hinton A Jr, Marshall AG, Kirabo A, August A, Marlin BJ, Riggs B, Tolbert B, Wanjalla C, Womack C, Evans CS, Barnes C, Starbird C, Williams C, Reynolds C, Taabazuing C, Cameron CE, Murray DD, Applewhite D, Morton DJ, Lee D, Williams DW, Lynch D, Brady D, Lynch E, Rutaganira FUN, Silva GM, Shuler H, Saboor IA, Davis J, Dzirasa K, Hammonds-Odie L, Reyes L, Sweetwyne MT, McReynolds MR, Johnson MDL, Smith NA, Pittman N, Ajijola OA, Smith Q, Robinson RAS, Lewis SC, Murray SA, Black S, Neal SE, Andrisse S, Townsend S, Damo SM, Griffith TN, Lambert WM, Clemons WM Jr | Cell | 37295396 | Cell | 2023 Jun 8 |
| RASopathy mutations open new insights into the mechanism of BRAF activation. | Dar AC, Brady DC | Molecular cell | 36400004 | Mol Cell | 2022 Nov 17 |
| Reorganization of pancreas circadian transcriptome with aging. | Sharma D, Wessel CR, Mahdavinia M, Preuss F, Bishehsari F | Aging | 37647013 | Aging (Albany NY) | 2023 Aug 29 |
| Alcohol Drinking Without Meals Is Associated With Risk of Gastrointestinal Cancers, Including Early-Onset Cases. | Shi M, Ahmedin NJ, Zong X, Yilmaz ӦH, Bishehsari F, Cao Y | Gastroenterology | 37977310 | Gastroenterology | 2024 Feb |
| Circadian transcriptome of pancreatic adenocarcinoma unravels chronotherapeutic targets. | Sharma D, Adnan D, Abdel-Reheem MK, Anafi RC, Leary DD, Bishehsari F | JCI insight | 38716727 | JCI Insight | 2024 May 8 |
| Early-onset Colon Cancer Shows a Distinct Intestinal Microbiome and a Host-Microbe Interaction. | Adnan D, Trinh JQ, Sharma D, Alsayid M, Bishehsari F | Cancer prevention research (Philadelphia, Pa.) | 37967575 | Cancer Prev Res (Phila) | 2024 Jan 4 |
| Patient-Derived Organoids as Therapy Screening Platforms in Cancer Patients. | Khorsandi D, Yang JW, Foster S, Khosravi S, Hosseinzadeh Kouchehbaghi N, Zarei F, Lee YB, Runa F, Gangrade A, Voskanian L, Adnan D, Zhu Y, Wang Z, Jucaud V, Dokmeci MR, Shen X, Bishehsari F, Kelber JA, Khademhosseini A, de Barros NR | Advanced healthcare materials | 38359321 | Adv Healthc Mater | 2024 Aug |
| Protein design and variant prediction using autoregressive generative models. | Shin JE, Riesselman AJ, Kollasch AW, McMahon C, Simon E, Sander C, Manglik A, Kruse AC, Marks DS | Nature communications | 33893299 | Nat Commun | 2021 Apr 23 |
| The M3 Muscarinic Acetylcholine Receptor Can Signal through Multiple G Protein Families. | Smith JS, Hilibrand AS, Skiba MA, Dates AN, Calvillo-Miranda VG, Kruse AC | Molecular pharmacology | 38641412 | Mol Pharmacol | 2024 May 17 |
| Proteome-wide model for human disease genetics. | Orenbuch R, Shearer CA, Kollasch AW, Spinner HD, Hopf TA, van Niekerk L, Franceschi D, Dias M, Frazer J, Marks DS | medRxiv : the preprint server for health sciences | 38076790 | medRxiv | 2025 Mar 14 |
| Deep generative modeling of the human proteome reveals over a hundred novel genes involved in rare genetic disorders. | Orenbuch R, Kollasch AW, Spinner HD, Shearer CA, Hopf TA, Franceschi D, Dias M, Frazer J, Marks DS | Research square | 38260496 | Res Sq | 2024 Jan 4 |
| Rapidly inducible yeast surface display for antibody evolution with OrthoRep. | Paulk AM, Williams RL, Liu CC | bioRxiv : the preprint server for biology | 38826191 | bioRxiv | 2024 May 24 |
| Evolutionary-Scale Enzymology Enables Biochemical Constant Prediction Across a Multi-Peaked Catalytic Landscape. | Muir DF, Asper GPR, Notin P, Posner JA, Marks DS, Keiser MJ, Pinney MM | bioRxiv : the preprint server for biology | 39484523 | bioRxiv | 2024 Oct 25 |
| Continuous evolution of user-defined genes at 1 million times the genomic mutation rate. | Rix G, Williams RL, Hu VJ, Spinner A, Pisera AO, Marks DS, Liu CC | Science (New York, N.Y.) | 39509492 | Science | 2024 Nov 8 |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | bioRxiv : the preprint server for biology | 33200136 | bioRxiv | 2020 Nov 11 |
| An Atlas of Variant Effects to understand the genome at nucleotide resolution. | Fowler DM, Adams DJ, Gloyn AL, Hahn WC, Marks DS, Muffley LA, Neal JT, Roth FP, Rubin AF, Starita LM, Hurles ME | Genome biology | 37394429 | Genome Biol | 2023 Jul 3 |
| An in silico method to assess antibody fragment polyreactivity. | Harvey EP, Shin JE, Skiba MA, Nemeth GR, Hurley JD, Wellner A, Shaw AY, Miranda VG, Min JK, Liu CC, Marks DS, Kruse AC | Nature communications | 36477674 | Nat Commun | 2022 Dec 7 |
| Learning from prepandemic data to forecast viral escape. | Thadani NN, Gurev S, Notin P, Youssef N, Rollins NJ, Ritter D, Sander C, Gal Y, Marks DS | Nature | 37821700 | Nature | 2023 Oct |
| Epitope-directed selection of GPCR nanobody ligands with evolvable function. | Skiba MA, Canavan C, Nemeth GR, Liu J, Kanso A, Kruse AC | Proceedings of the National Academy of Sciences of the United States of America | 40067891 | Proc Natl Acad Sci U S A | 2025 Mar 18 |
| Interaction specificity of clustered protocadherins inferred from sequence covariation and structural analysis. | Nicoludis JM, Green AG, Walujkar S, May EJ, Sotomayor M, Marks DS, Gaudet R | Proceedings of the National Academy of Sciences of the United States of America | 31431536 | Proc Natl Acad Sci U S A | 2019 Sep 3 |
| Antibodies Expand the Scope of Angiotensin Receptor Pharmacology. | Skiba MA, Sterling SM, Rawson S, Gilman MSA, Xu H, Nemeth GR, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Wingler LM, Kruse AC | bioRxiv : the preprint server for biology | 37662341 | bioRxiv | 2023 Aug 24 |
| Continuous evolution of user-defined genes at 1-million-times the genomic mutation rate. | Rix G, Williams RL, Spinner H, Hu VJ, Marks DS, Liu CC | bioRxiv : the preprint server for biology | 38014077 | bioRxiv | 2023 Nov 14 |
| The relaxin receptor RXFP1 signals through a mechanism of autoinhibition. | Erlandson SC, Rawson S, Osei-Owusu J, Brock KP, Liu X, Paulo JA, Mintseris J, Gygi SP, Marks DS, Cong X, Kruse AC | Nature chemical biology | 37081311 | Nat Chem Biol | 2023 Aug |
| Guidelines for releasing a variant effect predictor. | Livesey BJ, Badonyi M, Dias M, Frazer J, Kumar S, Lindorff-Larsen K, McCandlish DM, Orenbuch R, Shearer CA, Muffley L, Foreman J, Glazer AM, Lehner B, Marks DS, Roth FP, Rubin AF, Starita LM, Marsh JA | ArXiv | 38699161 | ArXiv | 2024 Apr 16 |
| Ultra-Efficient Integration of Gene Libraries onto Yeast Cytosolic Plasmids. | Pisera A, Yu Y, Williams RL, Liu CC | bioRxiv : the preprint server for biology | 39651169 | bioRxiv | 2024 Nov 30 |
| Co-evolution of interacting proteins through non-contacting and non-specific mutations. | Ding D, Green AG, Wang B, Lite TV, Weinstein EN, Marks DS, Laub MT | Nature ecology & evolution | 35361892 | Nat Ecol Evol | 2022 May |
| Rapid generation of potent antibodies by autonomous hypermutation in yeast. | Wellner A, McMahon C, Gilman MSA, Clements JR, Clark S, Nguyen KM, Ho MH, Hu VJ, Shin JE, Feldman J, Hauser BM, Caradonna TM, Wingler LM, Schmidt AG, Marks DS, Abraham J, Kruse AC, Liu CC | Nature chemical biology | 34168368 | Nat Chem Biol | 2021 Oct |
| Antibodies expand the scope of angiotensin receptor pharmacology. | Skiba MA, Sterling SM, Rawson S, Zhang S, Xu H, Jiang H, Nemeth GR, Gilman MSA, Hurley JD, Shen P, Staus DP, Kim J, McMahon C, Lehtinen MK, Rockman HA, Barth P, Wingler LM, Kruse AC | Nature chemical biology | 38744986 | Nat Chem Biol | 2024 Dec |
| Discovery of VH domains that allosterically inhibit ENPP1. | Solomon PE, Bracken CJ, Carozza JA, Wang H, Young EP, Wellner A, Liu CC, Sweet-Cordero EA, Li L, Wells JA | Nature chemical biology | 37400538 | Nat Chem Biol | 2024 Jan |
| Protein design using structure-based residue preferences. | Ding D, Shaw AY, Sinai S, Rollins N, Prywes N, Savage DF, Laub MT, Marks DS | Nature communications | 38388493 | Nat Commun | 2024 Feb 22 |
| ProteinNPT: Improving Protein Property Prediction and Design with Non-Parametric Transformers. | Notin P, Marks DS, Weitzman R, Gal Y | bioRxiv : the preprint server for biology | 38106034 | bioRxiv | 2023 Dec 7 |
| ProteinGym: Large-Scale Benchmarks for Protein Design and Fitness Prediction. | Notin P, Kollasch AW, Ritter D, van Niekerk L, Paul S, Spinner H, Rollins N, Shaw A, Weitzman R, Frazer J, Dias M, Franceschi D, Orenbuch R, Gal Y, Marks DS | bioRxiv : the preprint server for biology | 38106144 | bioRxiv | 2023 Dec 8 |
| C. elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. | Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL | bioRxiv : the preprint server for biology | 37790392 | bioRxiv | 2024 Jan 24 |
| Caenorhabditis elegans Dicer acts with the RIG-I-like helicase DRH-1 and RDE-4 to cleave dsRNA. | Consalvo CD, Aderounmu AM, Donelick HM, Aruscavage PJ, Eckert DM, Shen PS, Bass BL | eLife | 38747717 | Elife | 2024 May 15 |
| The competitive landscape of the dsRNA world. | Cottrell KA, Andrews RJ, Bass BL | Molecular cell | 38118451 | Mol Cell | 2024 Jan 4 |
| Structural homology screens reveal poxvirus-encoded proteins impacting inflammasome-mediated defenses. | Boys IN, Johnson AG, Quinlan M, Kranzusch PJ, Elde NC | bioRxiv : the preprint server for biology | 36909515 | bioRxiv | 2023 Apr 3 |
| Thg1 family 3'-5' RNA polymerases as tools for targeted RNA synthesis. | Jayasinghe MI, Patel KJ, Jackman JE | RNA (New York, N.Y.) | 38997129 | RNA | 2024 Sep 16 |
| Ancestral protein reconstruction reveals evolutionary events governing variation in Dicer helicase function. | Aderounmu AM, Aruscavage PJ, Kolaczkowski B, Bass BL | eLife | 37068011 | Elife | 2023 Apr 17 |
| Structural homology screens reveal host-derived poxvirus protein families impacting inflammasome activity. | Boys IN, Johnson AG, Quinlan MR, Kranzusch PJ, Elde NC | Cell reports | 37494187 | Cell Rep | 2023 Aug 29 |
| Ancestral characterization of 1018 cancer cell lines highlights disparities and reveals gene expression and mutational differences. | Kessler MD, Bateman NW, Conrads TP, Maxwell GL, Dunning Hotopp JC, O'Connor TD | Cancer | 30865299 | Cancer | 2019 Jun 15 |
| The Complexities and Nuances of Analyzing the Genome of Drosophila ananassae and Its Wolbachia Endosymbiont. | Dunning Hotopp JC, Klasson L | G3 (Bethesda, Md.) | 29301977 | G3 (Bethesda) | 2018 Jan 4 |
| Pim kinase inhibitor co-treatment decreases alternative non-homologous end-joining DNA repair and genomic instability induced by topoisomerase 2 inhibitors in cells with FLT3 internal tandem duplication. | Scarpa M, Kapoor S, Tvedte ES, Doshi KA, Zou YS, Singh P, Lee JK, Chatterjee A, Ali MKM, Bromley RE, Hotopp JCD, Rassool FV, Baer MR | Oncotarget | 34504649 | Oncotarget | 2021 Aug 31 |
| Aligner optimization increases accuracy and decreases compute times in multi-species sequence data. | Robinson KM, Hawkins AS, Santana-Cruz I, Adkins RS, Shetty AC, Nagaraj S, Sadzewicz L, Tallon LJ, Rasko DA, Fraser CM, Mahurkar A, Silva JC, Dunning Hotopp JC | Microbial genomics | 29114401 | Microb Genom | 2017 Sep |
| Lateral gene transfer between prokaryotes and eukaryotes. | Sieber KB, Bromley RE, Dunning Hotopp JC | Experimental cell research | 28189637 | Exp Cell Res | 2017 Sep 15 |
| Modeling the integration of bacterial rRNA fragments into the human cancer genome. | Sieber KB, Gajer P, Dunning Hotopp JC | BMC bioinformatics | 27001685 | BMC Bioinformatics | 2016 Mar 21 |
| Accumulation of endosymbiont genomes in an insect autosome followed by endosymbiont replacement. | Tvedte ES, Gasser M, Zhao X, Tallon LJ, Sadzewicz L, Bromley RE, Chung M, Mattick J, Sparklin BC, Dunning Hotopp JC | Current biology : CB | 35671755 | Curr Biol | 2022 Jun 20 |
| Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data. | Robinson KM, Crabtree J, Mattick JS, Anderson KE, Dunning Hotopp JC | Microbiome | 28118849 | Microbiome | 2017 Jan 25 |
| Cost effective, experimentally robust differential-expression analysis for human/mammalian, pathogen and dual-species transcriptomics. | Shetty AC, Mattick J, Chung M, McCracken C, Mahurkar A, Filler SG, Fraser CM, Rasko DA, Bruno VM, Dunning Hotopp JC | Microbial genomics | 31851607 | Microb Genom | 2020 Jan |
| Grafting or pruning in the animal tree: lateral gene transfer and gene loss? | Dunning Hotopp JC | BMC genomics | 29914363 | BMC Genomics | 2018 Jun 18 |
| Complete Genome Sequence of wAna, the Wolbachia Endosymbiont of Drosophila ananassae. | Gasser MT, Chung M, Bromley RE, Nadendla S, Dunning Hotopp JC | Microbiology resource announcements | 31649084 | Microbiol Resour Announc | 2019 Oct 24 |
| Comparison of long-read sequencing technologies in interrogating bacteria and fly genomes. | Tvedte ES, Gasser M, Sparklin BC, Michalski J, Hjelmen CE, Johnston JS, Zhao X, Bromley R, Tallon LJ, Sadzewicz L, Rasko DA, Dunning Hotopp JC | G3 (Bethesda, Md.) | 33768248 | G3 (Bethesda) | 2021 Jun 17 |
| TwinBLAST: When Two Is Better than One. | Dunning Hotopp JC, Matsumura J, Bromley RE, Riley DR, Agrawal S, Sparklin B, Mattick J, Crabtree J, Mahurkar A | Microbiology resource announcements | 31467106 | Microbiol Resour Announc | 2019 Aug 29 |
| Best Practices for Successfully Writing and Publishing a Genome Announcement in Microbiology Resource Announcements. | Dunning Hotopp JC, Baltrus DA, Bruno VM, Dennehy JJ, Gill SR, Maresca JA, Matthijnssens J, Newton ILG, Putonti C, Rasko DA, Rokas A, Roux S, Stajich JE, Stedman KM, Stewart FJ, Thrash JC | Microbiology resource announcements | 32883786 | Microbiol Resour Announc | 2020 Sep 3 |
| Updated annotation and meta-analysis of Brugia malayi transcriptomics data reveals consistent transcriptional profiles across time and space with some study-specific differences in adult female worm transcriptional profiles. | Holt CI, Dunning Hotopp JC | PLoS neglected tropical diseases | 39325836 | PLoS Negl Trop Dis | 2024 Sep |
| Lutetium background radiation in total-body PET-A simulation study on opportunities and challenges in PET attenuation correction. | Omidvari N, Cheng L, Leung EK, Abdelhafez YG, Badawi RD, Ma T, Qi J, Cherry SR | Frontiers in nuclear medicine | 36172601 | Front Nucl Med | 2022 |
| Total-Body (18)F-FDG PET/CT in Autoimmune Inflammatory Arthritis at Ultra-Low Dose: Initial Observations. | Abdelhafez Y, Raychaudhuri SP, Mazza D, Sarkar S, Hunt HL, McBride K, Nguyen M, Caudle DT, Spencer BA, Omidvari N, Bang H, Cherry SR, Nardo L, Badawi RD, Chaudhari AJ | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 35589405 | J Nucl Med | 2022 Oct |
| Total-body PET/CT - First Clinical Experiences and Future Perspectives. | Ng QK, Triumbari EKA, Omidvari N, Cherry SR, Badawi RD, Nardo L | Seminars in nuclear medicine | 35272853 | Semin Nucl Med | 2022 May |
| First Human Imaging Studies with the EXPLORER Total-Body PET Scanner. | Badawi RD, Shi H, Hu P, Chen S, Xu T, Price PM, Ding Y, Spencer BA, Nardo L, Liu W, Bao J, Jones T, Li H, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 30733314 | J Nucl Med | 2019 Mar |
| Mini EXPLORER II: a prototype high-sensitivity PET/CT scanner for companion animal whole body and human brain scanning. | Lv Y, Lv X, Liu W, Judenhofer MS, Zwingenberger A, Wisner E, Berg E, McKenney S, Leung E, Spencer BA, Cherry SR, Badawi RD | Physics in medicine and biology | 30620929 | Phys Med Biol | 2019 Mar 21 |
| Performance assessment of a software-based coincidence processor for the EXPLORER total-body PET scanner. | Leung EK, Judenhofer MS, Cherry SR, Badawi RD | Physics in medicine and biology | 30152793 | Phys Med Biol | 2018 Sep 19 |
| Subsecond total-body imaging using ultrasensitive positron emission tomography. | Zhang X, Cherry SR, Xie Z, Shi H, Badawi RD, Qi J | Proceedings of the National Academy of Sciences of the United States of America | 31964808 | Proc Natl Acad Sci U S A | 2020 Feb 4 |
| PennPET Explorer: Human Imaging on a Whole-Body Imager. | Pantel AR, Viswanath V, Daube-Witherspoon ME, Dubroff JG, Muehllehner G, Parma MJ, Pryma DA, Schubert EK, Mankoff DA, Karp JS | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31562224 | J Nucl Med | 2020 Jan |
| Development and Evaluation of mini-EXPLORER: A Long Axial Field-of-View PET Scanner for Nonhuman Primate Imaging. | Berg E, Zhang X, Bec J, Judenhofer MS, Patel B, Peng Q, Kapusta M, Schmand M, Casey ME, Tarantal AF, Qi J, Badawi RD, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 29419483 | J Nucl Med | 2018 Jun |
| Optimization-derived blood input function using a kernel method and its evaluation with total-body PET for brain parametric imaging. | Zhu Y, Tran Q, Wang Y, Badawi RD, Cherry SR, Qi J, Abbaszadeh S, Wang G | NeuroImage | 38643890 | Neuroimage | 2024 Jun |
| Performance Characteristics of Long Axial Field-of-View PET Scanners with Axial Gaps. | Daube-Witherspoon ME, Viswanath V, Werner ME, Karp JS | IEEE transactions on radiation and plasma medical sciences | 34179595 | IEEE Trans Radiat Plasma Med Sci | 2021 May |
| Clinical Implementation of Total-Body PET/CT at University of California, Davis. | Nardo L, Abdelhafez YG, Spencer BA, Badawi RD | PET clinics | 33218600 | PET Clin | 2021 Jan |
| Scanner Design Considerations for Long Axial Field-of-View PET Systems. | Daube-Witherspoon ME, Cherry SR | PET clinics | 33160929 | PET Clin | 2021 Jan |
| 3D/4D Reconstruction and Quantitative Total Body Imaging. | Qi J, Matej S, Wang G, Zhang X | PET clinics | 33218603 | PET Clin | 2021 Jan |
| Oncologic Applications of Long Axial Field-of-View PET/Computed Tomography. | Nardo L, Pantel AR | PET clinics | 33218605 | PET Clin | 2021 Jan |
| Cloud-based serverless computing enables accelerated monte carlo simulations for nuclear medicine imaging. | Bayerlein R, Swarnakar V, Selfridge A, Spencer BA, Nardo L, Badawi RD | Biomedical physics & engineering express | 38876087 | Biomed Phys Eng Express | 2024 Jun 25 |
| The role of brown adipose tissue in branched-chain amino acid clearance in people. | Abdelhafez YG, Wang G, Li S, Pellegrinelli V, Chaudhari AJ, Ramirez A, Sen F, Vidal-Puig A, Sidossis LS, Klein S, Badawi RD, Chondronikola M | iScience | 39175781 | iScience | 2024 Aug 16 |
| Quantitative PET imaging and modeling of molecular blood-brain barrier permeability. | Chung KJ, Abdelhafez YG, Spencer BA, Jones T, Tran Q, Nardo L, Chen MS Jr, Sarkar S, Medici V, Lyo V, Badawi RD, Cherry SR, Wang G | Nature communications | 40159510 | Nat Commun | 2025 Mar 30 |
| Reaching 200-ps timing resolution in a time-of-flight and depth-of-interaction positron emission tomography detector using phosphor-coated crystals and high-density silicon photomultipliers. | Kwon SI, Ferri A, Gola A, Berg E, Piemonte C, Cherry SR, Roncali E | Journal of medical imaging (Bellingham, Wash.) | 27921069 | J Med Imaging (Bellingham) | 2016 Oct |
| Numerical observer study of lesion detectability for a long axial field-of-view whole-body PET imager using the PennPET Explorer. | Viswanath V, Daube Witherspoon ME, Karp JS, Surti S | Physics in medicine and biology | 31816616 | Phys Med Biol | 2020 Jan 24 |
| Practical joint reconstruction of activity and attenuation with autonomous scaling for time-of-flight PET. | Li Y, Matej S, Karp JS | Physics in medicine and biology | 32340014 | Phys Med Biol | 2020 Dec 23 |
| PET Parametric Imaging: Past, Present, and Future. | Wang G, Rahmim A, Gunn RN | IEEE transactions on radiation and plasma medical sciences | 33763624 | IEEE Trans Radiat Plasma Med Sci | 2020 Nov |
| Analysis of Four-Dimensional Data for Total Body PET Imaging. | Viswanath V, Chitalia R, Pantel AR, Karp JS, Mankoff DA | PET clinics | 33218604 | PET Clin | 2021 Jan |
| Quantitative accuracy in total-body imaging using the uEXPLORER PET/CT scanner. | Leung EK, Berg E, Omidvari N, Spencer BA, Li E, Abdelhafez YG, Schmall JP, Liu W, He L, Tang S, Liu Y, Dong Y, Jones T, Cherry SR, Badawi RD | Physics in medicine and biology | 34544074 | Phys Med Biol | 2021 Oct 11 |
| Performance Evaluation of the uEXPLORER Total-Body PET/CT Scanner Based on NEMA NU 2-2018 with Additional Tests to Characterize PET Scanners with a Long Axial Field of View. | Spencer BA, Berg E, Schmall JP, Omidvari N, Leung EK, Abdelhafez YG, Tang S, Deng Z, Dong Y, Lv Y, Bao J, Liu W, Li H, Jones T, Badawi RD, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 33008932 | J Nucl Med | 2021 Jun 1 |
| Total-Body Quantitative Parametric Imaging of Early Kinetics of (18)F-FDG. | Feng T, Zhao Y, Shi H, Li H, Zhang X, Wang G, Price PM, Badawi RD, Cherry SR, Jones T | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 32948679 | J Nucl Med | 2021 May 10 |
| Impact of event positioning algorithm on performance of a whole-body PET scanner using one-to-one coupled detectors. | Surti S, Karp JS | Physics in medicine and biology | 29411709 | Phys Med Biol | 2018 Mar 2 |
| Total-Body PET: Maximizing Sensitivity to Create New Opportunities for Clinical Research and Patient Care. | Cherry SR, Jones T, Karp JS, Qi J, Moses WW, Badawi RD | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 28935835 | J Nucl Med | 2018 Jan |
| Exploring Vessel Wall Biology In Vivo by Ultrasensitive Total-Body PET. | Derlin T, Spencer BA, Mamach M, Abdelhafez Y, Nardo L, Badawi RD, Cherry SR, Bengel FM | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 36175139 | J Nucl Med | 2023 Mar |
| EXPLORing Arthritis with Total-body Positron Emission Tomography. | Chaudhari AJ, Abdelhafez YG, Nardo L, Raychaudhuri SP | Seminars in musculoskeletal radiology | 37935209 | Semin Musculoskelet Radiol | 2023 Dec |
| Total-body Dynamic Imaging and Kinetic Modeling of (18)F-AraG in Healthy Individuals and a Non-Small Cell Lung Cancer Patient Undergoing Anti-PD-1 Immunotherapy. | Omidvari N, Levi J, Abdelhafez YG, Wang Y, Nardo L, Daly ME, Wang G, Cherry SR | medRxiv : the preprint server for health sciences | 37790461 | medRxiv | 2023 Nov 1 |
| Numerical investigation reveals challenges in measuring the contrast recovery coefficients in PET. | Bayerlein R, Spencer BA, Abdelhafez YG, Cherry SR, Badawi RD, Omidvari N | Physics in medicine and biology | 37802064 | Phys Med Biol | 2023 Oct 26 |
| First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody. | Omidvari N, Jones T, Price PM, Ferre AL, Lu J, Abdelhafez YG, Sen F, Cohen SH, Schmiedehausen K, Badawi RD, Shacklett BL, Wilson I, Cherry SR | medRxiv : the preprint server for health sciences | 36993568 | medRxiv | 2023 Mar 20 |
| Total-Body Multiparametric PET Quantification of (18) F-FDG Delivery and Metabolism in the Study of COVID-19 Recovery. | Wang Y, Nardo L, Spencer BA, Abdelhafez YG, Li EJ, Omidvari N, Chaudhari AJ, Badawi RD, Jones T, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 37034643 | medRxiv | 2023 Mar 30 |
| High-Temporal-Resolution Lung Kinetic Modeling Using Total-Body Dynamic PET with Time-Delay and Dispersion Corrections. | Wang Y, Spencer BA, Schmall J, Li E, Badawi RD, Jones T, Cherry SR, Wang G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37116916 | J Nucl Med | 2023 Jul |
| Quantitative PET imaging and modeling of molecular blood-brain barrier permeability. | Chung KJ, Abdelhafez YG, Spencer BA, Jones T, Tran Q, Nardo L, Chen MS Jr, Sarkar S, Medici V, Lyo V, Badawi RD, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 39108503 | medRxiv | 2024 Jul 27 |
| Quantitative Total-Body Imaging of Blood Flow with High Temporal Resolution Early Dynamic (18)F-Fluorodeoxyglucose PET Kinetic Modeling. | Chung KJ, Chaudhari AJ, Nardo L, Jones T, Chen MS Jr, Badawi RD, Cherry SR, Wang G | medRxiv : the preprint server for health sciences | 39252929 | medRxiv | 2024 Aug 31 |
| Role of Total Body PET/CT in Inflammatory Disorders. | Zoghi S, Mingels C, Badawi RD, Spencer BA, Yarbrough TL, Nardo L, Chaudhari AJ | Seminars in nuclear medicine | 39578110 | Semin Nucl Med | 2025 Jan |
| Total Body PET: Why, How, What for? | Surti S, Pantel AR, Karp JS | IEEE transactions on radiation and plasma medical sciences | 33134653 | IEEE Trans Radiat Plasma Med Sci | 2020 May |
| Quantitative image reconstruction for total-body PET imaging using the 2-meter long EXPLORER scanner. | Zhang X, Zhou J, Cherry SR, Badawi RD, Qi J | Physics in medicine and biology | 28240215 | Phys Med Biol | 2017 Mar 21 |
| PennPET Explorer: Design and Preliminary Performance of a Whole-Body Imager. | Karp JS, Viswanath V, Geagan MJ, Muehllehner G, Pantel AR, Parma MJ, Perkins AE, Schmall JP, Werner ME, Daube-Witherspoon ME | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31227573 | J Nucl Med | 2020 Jan |
| Total-Body Multiparametric PET Quantification of (18)F-FDG Delivery and Metabolism in the Study of Coronavirus Disease 2019 Recovery. | Wang Y, Nardo L, Spencer BA, Abdelhafez YG, Li EJ, Omidvari N, Chaudhari AJ, Badawi RD, Jones T, Cherry SR, Wang G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37591539 | J Nucl Med | 2023 Nov |
| Facial Anonymization and Privacy Concerns in Total-Body PET/CT. | Selfridge AR, Spencer BA, Abdelhafez YG, Nakagawa K, Tupin JD, Badawi RD | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37268426 | J Nucl Med | 2023 Aug |
| Total-Body PET Kinetic Modeling and Potential Opportunities Using Deep Learning. | Wang Y, Li E, Cherry SR, Wang G | PET clinics | 34353745 | PET Clin | 2021 Oct |
| Relating(18)F-FDG image signal-to-noise ratio to time-of-flight noise-equivalent count rate in total-body PET using the uEXPLORER scanner. | Leung EK, Abdelhafez YG, Berg E, Xie Z, Zhang X, Bayerlein R, Spencer B, Li E, Omidvari N, Selfridge A, Cherry SR, Qi J, Badawi RD | Physics in medicine and biology | 35609588 | Phys Med Biol | 2022 Jun 10 |
| Multimodal positron emission tomography (PET) imaging in non-oncologic musculoskeletal radiology. | Kogan F, Yoon D, Teeter MG, Chaudhari AJ, Hales L, Barbieri M, Gold GE, Vainberg Y, Goyal A, Watkins L | Skeletal radiology | 38492029 | Skeletal Radiol | 2024 Sep |
| Theoretical study of the benefit of long axial field-of-view PET on region of interest quantification. | Zhang X, Badawi RD, Cherry SR, Qi J | Physics in medicine and biology | 29799814 | Phys Med Biol | 2018 Jun 27 |
| Innovations in Instrumentation for Positron Emission Tomography. | Berg E, Cherry SR | Seminars in nuclear medicine | 29852942 | Semin Nucl Med | 2018 Jul |
| Quantitative PET in the 2020s: a roadmap. | Meikle SR, Sossi V, Roncali E, Cherry SR, Banati R, Mankoff D, Jones T, James M, Sutcliffe J, Ouyang J, Petibon Y, Ma C, El Fakhri G, Surti S, Karp JS, Badawi RD, Yamaya T, Akamatsu G, Schramm G, Rezaei A, Nuyts J, Fulton R, Kyme A, Lois C, Sari H, Price J, Boellaard R, Jeraj R, Bailey DL, Eslick E, Willowson KP, Dutta J | Physics in medicine and biology | 33339012 | Phys Med Biol | 2021 Mar 12 |
| Update on the PennPET Explorer: A Whole-body Imager with Scalable Axial Field-of-View. | Pantel AR, Viswanath V, Karp JS | PET clinics | 33218602 | PET Clin | 2021 Jan |
| Parallax error in long-axial field-of-view PET scanners-a simulation study. | Schmall JP, Karp JS, Werner M, Surti S | Physics in medicine and biology | 27367971 | Phys Med Biol | 2016 Jul 21 |
| Total-body imaging: Transforming the role of positron emission tomography. | Cherry SR, Badawi RD, Karp JS, Moses WW, Price P, Jones T | Science translational medicine | 28298419 | Sci Transl Med | 2017 Mar 15 |
| Total-Body Dynamic Reconstruction and Parametric Imaging on the uEXPLORER. | Zhang X, Xie Z, Berg E, Judenhofer MS, Liu W, Xu T, Ding Y, Lv Y, Dong Y, Deng Z, Tang S, Shi H, Hu P, Chen S, Bao J, Li H, Zhou J, Wang G, Cherry SR, Badawi RD, Qi J | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 31302637 | J Nucl Med | 2020 Feb |
| Advances in PET Diagnostics for Guiding Targeted Cancer Therapy and Studying In Vivo Cancer Biology. | Mankoff DA, Pantel AR, Viswanath V, Karp JS | Current pathobiology reports | 37092138 | Curr Pathobiol Rep | 2019 Sep |
| First-in-human immunoPET imaging of COVID-19 convalescent patients using dynamic total-body PET and a CD8-targeted minibody. | Omidvari N, Jones T, Price PM, Ferre AL, Lu J, Abdelhafez YG, Sen F, Cohen SH, Schmiedehausen K, Badawi RD, Shacklett BL, Wilson I, Cherry SR | Science advances | 37824612 | Sci Adv | 2023 Oct 13 |
| Total-Body Perfusion Imaging with [(11)C]-Butanol. | Li EJ, López JE, Spencer BA, Abdelhafez Y, Badawi RD, Wang G, Cherry SR | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 37652544 | J Nucl Med | 2023 Nov |
| Synthetic biology approaches to engineer T cells. | Wu CY, Rupp LJ, Roybal KT, Lim WA | Current opinion in immunology | 26218616 | Curr Opin Immunol | 2015 Aug |
| Engineering T Cells with Customized Therapeutic Response Programs Using Synthetic Notch Receptors. | Roybal KT, Williams JZ, Morsut L, Rupp LJ, Kolinko I, Choe JH, Walker WJ, McNally KA, Lim WA | Cell | 27693353 | Cell | 2016 Oct 6 |
| Synthetic Immunology: Hacking Immune Cells to Expand Their Therapeutic Capabilities. | Roybal KT, Lim WA | Annual review of immunology | 28446063 | Annu Rev Immunol | 2017 Apr 26 |
| Engineering Therapeutic T Cells: From Synthetic Biology to Clinical Trials. | Esensten JH, Bluestone JA, Lim WA | Annual review of pathology | 27959633 | Annu Rev Pathol | 2017 Jan 24 |
| CRISPR/Cas9-mediated PD-1 disruption enhances anti-tumor efficacy of human chimeric antigen receptor T cells. | Rupp LJ, Schumann K, Roybal KT, Gate RE, Ye CJ, Lim WA, Marson A | Scientific reports | 28389661 | Sci Rep | 2017 Apr 7 |
| Synthetic cytokine circuits that drive T cells into immune-excluded tumors. | Allen GM, Frankel NW, Reddy NR, Bhargava HK, Yoshida MA, Stark SR, Purl M, Lee J, Yee JL, Yu W, Li AW, Garcia KC, El-Samad H, Roybal KT, Spitzer MH, Lim WA | Science (New York, N.Y.) | 36520915 | Science | 2022 Dec 16 |
| Engineering cytokines and cytokine circuits. | Li AW, Lim WA | Science (New York, N.Y.) | 33243875 | Science | 2020 Nov 27 |
| T cell circuits that sense antigen density with an ultrasensitive threshold. | Hernandez-Lopez RA, Yu W, Cabral KA, Creasey OA, Lopez Pazmino MDP, Tonai Y, De Guzman A, Mäkelä A, Saksela K, Gartner ZJ, Lim WA | Science (New York, N.Y.) | 33632893 | Science | 2021 Mar 12 |
| Remote control of therapeutic T cells through a small molecule-gated chimeric receptor. | Wu CY, Roybal KT, Puchner EM, Onuffer J, Lim WA | Science (New York, N.Y.) | 26405231 | Science | 2015 Oct 16 |
| Precise T cell recognition programs designed by transcriptionally linking multiple receptors. | Williams JZ, Allen GM, Shah D, Sterin IS, Kim KH, Garcia VP, Shavey GE, Yu W, Puig-Saus C, Tsoi J, Ribas A, Roybal KT, Lim WA | Science (New York, N.Y.) | 33243890 | Science | 2020 Nov 27 |
| T cells selectively filter oscillatory signals on the minutes timescale. | O'Donoghue GP, Bugaj LJ, Anderson W, Daniels KG, Rawlings DJ, Lim WA | Proceedings of the National Academy of Sciences of the United States of America | 33627405 | Proc Natl Acad Sci U S A | 2021 Mar 2 |
| SynNotch-CAR T cells overcome challenges of specificity, heterogeneity, and persistence in treating glioblastoma. | Choe JH, Watchmaker PB, Simic MS, Gilbert RD, Li AW, Krasnow NA, Downey KM, Yu W, Carrera DA, Celli A, Cho J, Briones JD, Duecker JM, Goretsky YE, Dannenfelser R, Cardarelli L, Troyanskaya O, Sidhu SS, Roybal KT, Okada H, Lim WA | Science translational medicine | 33910979 | Sci Transl Med | 2021 Apr 28 |
| The Principles of Engineering Immune Cells to Treat Cancer. | Lim WA, June CH | Cell | 28187291 | Cell | 2017 Feb 9 |
| Engineering Customized Cell Sensing and Response Behaviors Using Synthetic Notch Receptors. | Morsut L, Roybal KT, Xiong X, Gordley RM, Coyle SM, Thomson M, Lim WA | Cell | 26830878 | Cell | 2016 Feb 11 |
| Precision Tumor Recognition by T Cells With Combinatorial Antigen-Sensing Circuits. | Roybal KT, Rupp LJ, Morsut L, Walker WJ, McNally KA, Park JS, Lim WA | Cell | 26830879 | Cell | 2016 Feb 11 |
| Discriminatory Power of Combinatorial Antigen Recognition in Cancer T Cell Therapies. | Dannenfelser R, Allen GM, VanderSluis B, Koegel AK, Levinson S, Stark SR, Yao V, Tadych A, Troyanskaya OG, Lim WA | Cell systems | 32916097 | Cell Syst | 2020 Sep 23 |
| Modular engineering of cellular signaling proteins and networks. | Gordley RM, Bugaj LJ, Lim WA | Current opinion in structural biology | 27423114 | Curr Opin Struct Biol | 2016 Aug |
| Choosing the Right Tool for the Job: RNAi, TALEN, or CRISPR. | Boettcher M, McManus MT | Molecular cell | 26000843 | Mol Cell | 2015 May 21 |
| A Mechanical Switch Couples T Cell Receptor Triggering to the Cytoplasmic Juxtamembrane Regions of CD3ζζ. | Lee MS, Glassman CR, Deshpande NR, Badgandi HB, Parrish HL, Uttamapinant C, Stawski PS, Ting AY, Kuhns MS | Immunity | 26231119 | Immunity | 2015 Aug 18 |
| An Approach to Spatiotemporally Resolve Protein Interaction Networks in Living Cells. | Lobingier BT, Hüttenhain R, Eichel K, Miller KB, Ting AY, von Zastrow M, Krogan NJ | Cell | 28388416 | Cell | 2017 Apr 6 |
| Atlas of Subcellular RNA Localization Revealed by APEX-Seq. | Fazal FM, Han S, Parker KR, Kaewsapsak P, Xu J, Boettiger AN, Chang HY, Ting AY | Cell | 31230715 | Cell | 2019 Jul 11 |
| Spatially resolved proteomic mapping in living cells with the engineered peroxidase APEX2. | Hung V, Udeshi ND, Lam SS, Loh KH, Cox KJ, Pedram K, Carr SA, Ting AY | Nature protocols | 26866790 | Nat Protoc | 2016 Mar |
| Proximity labeling: spatially resolved proteomic mapping for neurobiology. | Han S, Li J, Ting AY | Current opinion in neurobiology | 29125959 | Curr Opin Neurobiol | 2018 Jun |
| Proximity labeling of protein complexes and cell-type-specific organellar proteomes in Arabidopsis enabled by TurboID. | Mair A, Xu SL, Branon TC, Ting AY, Bergmann DC | eLife | 31535972 | Elife | 2019 Sep 19 |
| Correction to Directed Evolution of Split APEX2 Peroxidase. | Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A | ACS chemical biology | 31657543 | ACS Chem Biol | 2019 Dec 20 |
| Electron microscopy using the genetically encoded APEX2 tag in cultured mammalian cells. | Martell JD, Deerinck TJ, Lam SS, Ellisman MH, Ting AY | Nature protocols | 28796234 | Nat Protoc | 2017 Sep |
| Proximity Biotinylation as a Method for Mapping Proteins Associated with mtDNA in Living Cells. | Han S, Udeshi ND, Deerinck TJ, Svinkina T, Ellisman MH, Carr SA, Ting AY | Cell chemical biology | 28238724 | Cell Chem Biol | 2017 Mar 16 |
| Directed Evolution of Split APEX2 Peroxidase. | Han Y, Branon TC, Martell JD, Boassa D, Shechner D, Ellisman MH, Ting A | ACS chemical biology | 30848125 | ACS Chem Biol | 2019 Apr 19 |
| Mapping the signaling network of BIN2 kinase using TurboID-mediated biotin labeling and phosphoproteomics. | Kim TW, Park CH, Hsu CC, Kim YW, Ko YW, Zhang Z, Zhu JY, Hsiao YC, Branon T, Kaasik K, Saldivar E, Li K, Pasha A, Provart NJ, Burlingame AL, Xu SL, Ting AY, Wang ZY | The Plant cell | 36660928 | Plant Cell | 2023 Mar 15 |
| Efficient proximity labeling in living cells and organisms with TurboID. | Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY | Nature biotechnology | 30125270 | Nat Biotechnol | 2018 Oct |
| Live-cell mapping of organelle-associated RNAs via proximity biotinylation combined with protein-RNA crosslinking. | Kaewsapsak P, Shechner DM, Mallard W, Rinn JL, Ting AY | eLife | 29239719 | Elife | 2017 Dec 14 |
| Author Correction: Efficient proximity labeling in living cells and organisms with TurboID. | Branon TC, Bosch JA, Sanchez AD, Udeshi ND, Svinkina T, Carr SA, Feldman JL, Perrimon N, Ting AY | Nature biotechnology | 31748691 | Nat Biotechnol | 2020 Jan |
| A split horseradish peroxidase for the detection of intercellular protein-protein interactions and sensitive visualization of synapses. | Martell JD, Yamagata M, Deerinck TJ, Phan S, Kwa CG, Ellisman MH, Sanes JR, Ting AY | Nature biotechnology | 27240195 | Nat Biotechnol | 2016 Jul |
| Proteomic mapping of cytosol-facing outer mitochondrial and ER membranes in living human cells by proximity biotinylation. | Hung V, Lam SS, Udeshi ND, Svinkina T, Guzman G, Mootha VK, Carr SA, Ting AY | eLife | 28441135 | Elife | 2017 Apr 25 |
| Proteomic Analysis of Unbounded Cellular Compartments: Synaptic Clefts. | Loh KH, Stawski PS, Draycott AS, Udeshi ND, Lehrman EK, Wilton DK, Svinkina T, Deerinck TJ, Ellisman MH, Stevens B, Carr SA, Ting AY | Cell | 27565350 | Cell | 2016 Aug 25 |
| Reversibly switchable fluorescence microscopy with enhanced resolution and image contrast. | Yao J, Shcherbakova DM, Li C, Krumholz A, Lorca RA, Reinl E, England SK, Verkhusha VV, Wang LV | Journal of biomedical optics | 25144452 | J Biomed Opt | 2014 Aug |
| Label-free intraoperative histology of bone tissue via deep-learning-assisted ultraviolet photoacoustic microscopy. | Cao R, Nelson SD, Davis S, Liang Y, Luo Y, Zhang Y, Crawford B, Wang LV | Nature biomedical engineering | 36123403 | Nat Biomed Eng | 2023 Feb |
| Bessel-beam Grueneisen relaxation photoacoustic microscopy with extended depth of field. | Shi J, Wang L, Noordam C, Wang LV | Journal of biomedical optics | 26524679 | J Biomed Opt | 2015 Nov |
| Dependence of optical scattering from Intralipid in gelatin-gel based tissue-mimicking phantoms on mixing temperature and time. | Lai P, Xu X, Wang LV | Journal of biomedical optics | 24604534 | J Biomed Opt | 2014 Mar |
| Photoacoustic Brain Imaging: from Microscopic to Macroscopic Scales. | Yao J, Wang LV | Neurophotonics | 25401121 | Neurophotonics | 2014 May 28 |
| Photoacoustically guided wavefront shaping for enhanced optical focusing in scattering media. | Lai P, Wang L, Tay JW, Wang LV | Nature photonics | 25914725 | Nat Photonics | 2015 Feb |
| Multiscale Functional and Molecular Photoacoustic Tomography. | Yao J, Xia J, Wang LV | Ultrasonic imaging | 25933617 | Ultrason Imaging | 2016 Jan |
| Multiview Hilbert transformation for full-view photoacoustic computed tomography using a linear array. | Li G, Li L, Zhu L, Xia J, Wang LV | Journal of biomedical optics | 26112369 | J Biomed Opt | 2015 Jun |
| Label-free high-throughput detection and quantification of circulating melanoma tumor cell clusters by linear-array-based photoacoustic tomography. | Hai P, Zhou Y, Zhang R, Ma J, Li Y, Shao JY, Wang LV | Journal of biomedical optics | 27832253 | J Biomed Opt | 2017 Apr 1 |
| Noninvasive photoacoustic microscopy of methemoglobin in vivo. | Tang M, Zhou Y, Zhang R, Wang LV | Journal of biomedical optics | 25760655 | J Biomed Opt | 2015 Mar |
| Use of a single xenon flash lamp for photoacoustic computed tomography of multiple-centimeter-thick biological tissue ex vivo and a whole mouse body in vivo. | Wong TT, Zhou Y, Garcia-Uribe A, Li L, Maslov K, Lin L, Wang LV | Journal of biomedical optics | 27775747 | J Biomed Opt | 2017 Apr 1 |
| Dry coupling for whole-body small-animal photoacoustic computed tomography. | Yeh C, Li L, Zhu L, Xia J, Li C, Chen W, Garcia-Uribe A, Maslov KI, Wang LV | Journal of biomedical optics | 28241305 | J Biomed Opt | 2017 Apr 1 |
| Direct measurement of hypoxia in a xenograft multiple myeloma model by optical-resolution photoacoustic microscopy. | Imai T, Muz B, Yeh CH, Yao J, Zhang R, Azab AK, Wang L | Cancer biology & therapy | 28045569 | Cancer Biol Ther | 2017 Feb |
| Single-shot ultrafast optical imaging. | Liang J, Wang LV | Optica | 30820445 | Optica | 2018 Sep 20 |
| High-throughput ultraviolet photoacoustic microscopy with multifocal excitation. | Imai T, Shi J, Wong TTW, Li L, Zhu L, Wang LV | Journal of biomedical optics | 29546734 | J Biomed Opt | 2018 Mar |
| Photoacoustic tomography of vascular compliance in humans. | Hai P, Zhou Y, Liang J, Li C, Wang LV | Journal of biomedical optics | 26720875 | J Biomed Opt | 2015 |
| Focusing light through biological tissue and tissue-mimicking phantoms up to 9.6 cm in thickness with digital optical phase conjugation. | Shen Y, Liu Y, Ma C, Wang LV | Journal of biomedical optics | 27533439 | J Biomed Opt | 2016 Aug 1 |
| Grueneisen relaxation photoacoustic microscopy. | Wang L, Zhang C, Wang LV | Physical review letters | 25379919 | Phys Rev Lett | 2014 Oct 24 |
| Label-free automated three-dimensional imaging of whole organs by microtomy-assisted photoacoustic microscopy. | Wong TTW, Zhang R, Zhang C, Hsu HC, Maslov KI, Wang L, Shi J, Chen R, Shung KK, Zhou Q, Wang LV | Nature communications | 29123109 | Nat Commun | 2017 Nov 9 |
| Single-breath-hold photoacoustic computed tomography of the breast. | Lin L, Hu P, Shi J, Appleton CM, Maslov K, Li L, Zhang R, Wang LV | Nature communications | 29907740 | Nat Commun | 2018 Jun 15 |
| Sub-Nyquist sampling boosts targeted light transport through opaque scattering media. | Shen Y, Liu Y, Ma C, Wang LV | Optica | 28670607 | Optica | 2017 Jan 20 |
| Focusing light through scattering media by polarization modulation based generalized digital optical phase conjugation. | Yang J, Shen Y, Liu Y, Hemphill AS, Wang LV | Applied physics letters | 29203931 | Appl Phys Lett | 2017 Nov 13 |
| A review of snapshot multidimensional optical imaging: measuring photon tags in parallel. | Gao L, Wang LV | Physics reports | 27134340 | Phys Rep | 2016 Feb 29 |
| Single-shot time-reversed optical focusing into and through scattering media. | Cheng Z, Yang J, Wang LV | ACS photonics | 34337103 | ACS Photonics | 2020 Oct 21 |
| Photoacoustic Computed Tomography of Breast Cancer in Response to Neoadjuvant Chemotherapy. | Lin L, Tong X, Hu P, Invernizzi M, Lai L, Wang LV | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 33854889 | Adv Sci (Weinh) | 2021 Apr |
| Intelligently optimized digital optical phase conjugation with particle swarm optimization. | Cheng Z, Yang J, Wang LV | Optics letters | 32747844 | Opt Lett | 2020 Jan 15 |
| Angular-spectrum modeling of focusing light inside scattering media by optical phase conjugation. | Yang J, Li J, He S, Wang LV | Optica | 32025534 | Optica | 2019 Mar 20 |
| Spatio-temporal-spectral imaging of non-repeatable dissipative soliton dynamics. | Jing JC, Wei X, Wang LV | Nature communications | 32345966 | Nat Commun | 2020 Apr 28 |
| Wave of single-impulse-stimulated fast initial dip in single vessels of mouse brains imaged by high-speed functional photoacoustic microscopy. | He Y, Shi J, Maslov KI, Cao R, Wang LV | Journal of biomedical optics | 32529816 | J Biomed Opt | 2020 Jun |
| Label-free imaging of lipid-rich biological tissues by mid-infrared photoacoustic microscopy. | He Y, Shi J, Pleitez MA, Maslov K, Wagenaar DA, Wang LV | Journal of biomedical optics | 33118344 | J Biomed Opt | 2020 Oct |
| Transcranial photoacoustic computed tomography based on a layered back-projection method. | Na S, Yuan X, Lin L, Isla J, Garrett D, Wang LV | Photoacoustics | 33134081 | Photoacoustics | 2020 Dec |
| Single-shot photoacoustic imaging with single-element transducer through a spatiotemporal encoder. | Zhao Y, Wang LV | Journal of biomedical optics | 37065647 | J Biomed Opt | 2023 Apr |
| Integration of Multitargeted Polymer-Based Contrast Agents with Photoacoustic Computed Tomography: An Imaging Technique to Visualize Breast Cancer Intratumor Heterogeneity. | Li L, Patil D, Petruncio G, Harnden KK, Somasekharan JV, Paige M, Wang LV, Salvador-Morales C | ACS nano | 33464827 | ACS Nano | 2021 Feb 23 |
| Harnessing a multi-dimensional fibre laser using genetic wavefront shaping. | Wei X, Jing JC, Shen Y, Wang LV | Light, science & applications | 32884678 | Light Sci Appl | 2020 |
| Multifocal photoacoustic microscopy using a single-element ultrasonic transducer through an ergodic relay. | Li Y, Wong TTW, Shi J, Hsu HC, Wang LV | Light, science & applications | 32793336 | Light Sci Appl | 2020 |
| Calibration-free absolute quantification of particle concentration by statistical analyses of photoacoustic signals in vivo. | Zhou Y, Yao J, Maslov KI, Wang LV | Journal of biomedical optics | 24589987 | J Biomed Opt | 2014 Mar |
| Small near-infrared photochromic protein for photoacoustic multi-contrast imaging and detection of protein interactions in vivo. | Li L, Shemetov AA, Baloban M, Hu P, Zhu L, Shcherbakova DM, Zhang R, Shi J, Yao J, Wang LV, Verkhusha VV | Nature communications | 30013153 | Nat Commun | 2018 Jul 16 |
| Single-exposure optical focusing inside scattering media using binarized time-reversed adapted perturbation. | Ma C, Zhou F, Liu Y, Wang LV | Optica | 30221184 | Optica | 2015 Oct |
| In vivo characterization of connective tissue remodeling using infrared photoacoustic spectra. | Qu Y, Hu P, Shi J, Maslov K, Zhao P, Li C, Ma J, Garcia-Uribe A, Meyers K, Diveley E, Pizzella S, Muench L, Punyamurthy N, Goldstein N, Onwumere O, Alisio M, Meyenburg K, Maynard J, Helm K, Altieri E, Slaughter J, Barber S, Burger T, Kramer C, Chubiz J, Anderson M, McCarthy R, England SK, Macones GA, Stout MJ, Tuuli M, Wang LV | Journal of biomedical optics | 30520275 | J Biomed Opt | 2018 Dec |
| Fast label-free multilayered histology-like imaging of human breast cancer by photoacoustic microscopy. | Wong TTW, Zhang R, Hai P, Zhang C, Pleitez MA, Aft RL, Novack DV, Wang LV | Science advances | 28560329 | Sci Adv | 2017 May |
| Hybridized wavefront shaping for high-speed, high-efficiency focusing through dynamic diffusive media. | Hemphill AS, Tay JW, Wang LV | Journal of biomedical optics | 27626770 | J Biomed Opt | 2016 Dec 1 |
| Recent progress in photoacoustic molecular imaging. | Yao J, Wang LV | Current opinion in chemical biology | 29631120 | Curr Opin Chem Biol | 2018 Aug |
| Dual-axis illumination for virtually augmenting the detection view of optical-resolution photoacoustic microscopy. | Hsu HC, Li L, Yao J, Wong TTW, Shi J, Chen R, Zhou Q, Wang L | Journal of biomedical optics | 29981225 | J Biomed Opt | 2018 Jul |
| High-speed photoacoustic microscopy of mouse cortical microhemodynamics. | Lin L, Yao J, Zhang R, Chen CC, Huang CH, Li Y, Wang L, Chapman W, Zou J, Wang LV | Journal of biophotonics | 28009098 | J Biophotonics | 2017 Jun |
| Sensitivity of photoacoustic microscopy. | Yao J, Wang LV | Photoacoustics | 25302158 | Photoacoustics | 2014 Jun |
| Near-infrared optical-resolution photoacoustic microscopy. | Hai P, Yao J, Maslov KI, Zhou Y, Wang LV | Optics letters | 25166107 | Opt Lett | 2014 Sep 1 |
| Breakthrough in Photonics 2013: Photoacoustic Tomography in Biomedicine. | Yao J, Wang LV | IEEE photonics journal | 25383143 | IEEE Photonics J | 2014 Apr |
| Handheld photoacoustic probe to detect both melanoma depth and volume at high speed in vivo. | Zhou Y, Li G, Zhu L, Li C, Cornelius LA, Wang LV | Journal of biophotonics | 25676898 | J Biophotonics | 2015 Nov |
| Optical drug monitoring: photoacoustic imaging of nanosensors to monitor therapeutic lithium in vivo. | Cash KJ, Li C, Xia J, Wang LV, Clark HA | ACS nano | 25588028 | ACS Nano | 2015 Feb 24 |
| High-speed label-free functional photoacoustic microscopy of mouse brain in action. | Yao J, Wang L, Yang JM, Maslov KI, Wong TT, Li L, Huang CH, Zou J, Wang LV | Nature methods | 25822799 | Nat Methods | 2015 May |
| Three-dimensional photoacoustic endoscopic imaging of the rabbit esophagus. | Yang JM, Favazza C, Yao J, Chen R, Zhou Q, Shung KK, Wang LV | PloS one | 25874640 | PLoS One | 2015 |
| In vivo deep brain imaging of rats using oral-cavity illuminated photoacoustic computed tomography. | Lin L, Xia J, Wong TT, Li L, Wang LV | Journal of biomedical optics | 25611865 | J Biomed Opt | 2015 Jan |
| High-resolution, high-contrast mid-infrared imaging of fresh biological samples with ultraviolet-localized photoacoustic microscopy. | Shi J, Wong TTW, He Y, Li L, Zhang R, Yung CS, Hwang J, Maslov K, Wang LV | Nature photonics | 31440304 | Nat Photonics | 2019 Sep |
| A microrobotic system guided by photoacoustic computed tomography for targeted navigation in intestines in vivo. | Wu Z, Li L, Yang Y, Hu P, Li Y, Yang SY, Wang LV, Gao W | Science robotics | 32632399 | Sci Robot | 2019 Jul 31 |
| Photoacoustic topography through an ergodic relay for functional imaging and biometric application in vivo. | Li Y, Li L, Zhu L, Shi J, Maslov K, Wang LV | Journal of biomedical optics | 32648387 | J Biomed Opt | 2020 Jul |
| Dichroism-sensitive photoacoustic computed tomography. | Qu Y, Li L, Shen Y, Wei X, Wong TTW, Hu P, Yao J, Maslov K, Wang LV | Optica | 30820444 | Optica | 2018 Apr 20 |
| Real-time frequency-encoded spatiotemporal focusing through scattering media using a programmable 2D ultrafine optical frequency comb. | Wei X, Shen Y, Jing JC, Hemphill AS, Yang C, Xu S, Yang Z, Wang LV | Science advances | 32128401 | Sci Adv | 2020 Feb |
| Snapshot Photoacoustic Topography Through an Ergodic Relay for High-throughput Imaging of Optical Absorption. | Li Y, Li L, Zhu L, Maslov K, Shi J, Hu P, Bo E, Yao J, Liang J, Wang L, Wang LV | Nature photonics | 34178097 | Nat Photonics | 2020 Mar |
| Multiscale Photoacoustic Tomography of a Genetically Encoded Near-Infrared FRET Biosensor. | Li L, Hsu HC, Verkhusha VV, Wang LV, Shcherbakova DM | Advanced science (Weinheim, Baden-Wurttemberg, Germany) | 34533889 | Adv Sci (Weinh) | 2021 Nov |
| In vivo photoacoustic tomography of myoglobin oxygen saturation. | Lin L, Yao J, Li L, Wang LV | Journal of biomedical optics | 26719943 | J Biomed Opt | 2016 Jun |
| Photoacoustic microscopy of arteriovenous shunts and blood diffusion in early-stage tumors. | Yeh C, Liang J, Zhou Y, Hu S, Sohn RE, Arbeit JM, Wang LV | Journal of biomedical optics | 26882446 | J Biomed Opt | 2016 Feb |
| Lock-in camera based heterodyne holography for ultrasound-modulated optical tomography inside dynamic scattering media. | Liu Y, Shen Y, Ma C, Shi J, Wang LV | Applied physics letters | 27493275 | Appl Phys Lett | 2016 Jun 6 |
| Grueneisen relaxation photoacoustic microscopy in vivo. | Ma J, Shi J, Hai P, Zhou Y, Wang LV | Journal of biomedical optics | 27272096 | J Biomed Opt | 2016 Jun 1 |
| Quantitative photoacoustic elastography in humans. | Hai P, Zhou Y, Gong L, Wang LV | Journal of biomedical optics | 27304419 | J Biomed Opt | 2016 Jun 1 |
| Tutorial on photoacoustic tomography. | Zhou Y, Yao J, Wang LV | Journal of biomedical optics | 27086868 | J Biomed Opt | 2016 Jun |
| Focusing light through scattering media by full-polarization digital optical phase conjugation. | Shen Y, Liu Y, Ma C, Wang LV | Optics letters | 26977651 | Opt Lett | 2016 Mar 15 |
| Single-shot compressed ultrafast photography at one hundred billion frames per second. | Gao L, Liang J, Li C, Wang LV | Nature | 25471883 | Nature | 2014 Dec 4 |
| Single-shot stereo-polarimetric compressed ultrafast photography for light-speed observation of high-dimensional optical transients with picosecond resolution. | Liang J, Wang P, Zhu L, Wang LV | Nature communications | 33067438 | Nat Commun | 2020 Oct 16 |
| Single-shot real-time video recording of a photonic Mach cone induced by a scattered light pulse. | Liang J, Ma C, Zhu L, Chen Y, Gao L, Wang LV | Science advances | 28116357 | Sci Adv | 2017 Jan |
| Handheld optical-resolution photoacoustic microscopy. | Lin L, Zhang P, Xu S, Shi J, Li L, Yao J, Wang L, Zou J, Wang LV | Journal of biomedical optics | 27775746 | J Biomed Opt | 2017 Apr 1 |
| Optical-resolution photoacoustic microscopy for volumetric and spectral analysis of histological and immunochemical samples. | Zhang YS, Yao J, Zhang C, Li L, Wang LV, Xia Y | Angewandte Chemie (International ed. in English) | 24961608 | Angew Chem Int Ed Engl | 2014 Jul 28 |
| Handheld photoacoustic microscopy to detect melanoma depth in vivo. | Zhou Y, Xing W, Maslov KI, Cornelius LA, Wang LV | Optics letters | 25121860 | Opt Lett | 2014 Aug 15 |
| Three-dimensional arbitrary trajectory scanning photoacoustic microscopy. | Yeh C, Soetikno B, Hu S, Maslov KI, Wang LV | Journal of biophotonics | 25077689 | J Biophotonics | 2015 Apr |
| High-speed three-dimensional photoacoustic computed tomography for preclinical research and clinical translation. | Lin L, Hu P, Tong X, Na S, Cao R, Yuan X, Garrett DC, Shi J, Maslov K, Wang LV | Nature communications | 33563996 | Nat Commun | 2021 Feb 9 |
| Label-free photoacoustic tomography of whole mouse brain structures ex vivo. | Li L, Xia J, Li G, Garcia-Uribe A, Sheng Q, Anastasio MA, Wang LV | Neurophotonics | 29181425 | Neurophotonics | 2016 Jul |
| Focusing light inside dynamic scattering media with millisecond digital optical phase conjugation. | Liu Y, Ma C, Shen Y, Shi J, Wang LV | Optica | 28815194 | Optica | 2017 Feb |
| Multiview Hilbert transformation in full-ring transducer array-based photoacoustic computed tomography. | Li L, Zhu L, Shen Y, Wang LV | Journal of biomedical optics | 28745385 | J Biomed Opt | 2017 Jul 1 |
| Photoacoustic lymphatic imaging with high spatial-temporal resolution. | Martel C, Yao J, Huang CH, Zou J, Randolph GJ, Wang LV | Journal of biomedical optics | 25408958 | J Biomed Opt | 2014 Nov |
| Microvascular quantification based on contour-scanning photoacoustic microscopy. | Yeh C, Soetikno B, Hu S, Maslov KI, Wang LV | Journal of biomedical optics | 25223708 | J Biomed Opt | 2014 Sep |
| Photoacoustic elastography. | Hai P, Yao J, Li G, Li C, Wang LV | Optics letters | 26872173 | Opt Lett | 2016 Feb 15 |
| A practical guide to photoacoustic tomography in the life sciences. | Wang LV, Yao J | Nature methods | 27467726 | Nat Methods | 2016 Jul 28 |
| Ultrasonic-heating-encoded photoacoustic tomography with virtually augmented detection view. | Wang L, Li G, Xia J, Wang LV | Optica | 25984555 | Optica | 2015 |
| Optical-resolution photoacoustic endomicroscopy in vivo. | Yang JM, Li C, Chen R, Rao B, Yao J, Yeh CH, Danielli A, Maslov K, Zhou Q, Shung KK, Wang LV | Biomedical optics express | 25798315 | Biomed Opt Express | 2015 Mar 1 |
| Transvaginal fast-scanning optical-resolution photoacoustic endoscopy. | Qu Y, Li C, Shi J, Chen R, Xu S, Rafsanjani H, Maslov K, Krigman H, Garvey L, Hu P, Zhao P, Meyers K, Diveley E, Pizzella S, Muench L, Punyamurthy N, Goldstein N, Onwumere O, Alisio M, Meyenburg K, Maynard J, Helm K, Slaughter J, Barber S, Burger T, Kramer C, Chubiz J, Anderson M, McCarthy R, England SK, Macones GA, Zhou Q, Shung KK, Zou J, Stout MJ, Tuuli M, Wang LV | Journal of biomedical optics | 30520276 | J Biomed Opt | 2018 Dec |
| High-throughput, label-free, single-cell photoacoustic microscopy of intratumoral metabolic heterogeneity. | Hai P, Imai T, Xu S, Zhang R, Aft RL, Zou J, Wang LV | Nature biomedical engineering | 30936431 | Nat Biomed Eng | 2019 May |
| Nonlinear photoacoustic spectroscopy of hemoglobin. | Danielli A, Maslov K, Favazza CP, Xia J, Wang LV | Applied physics letters | 26045627 | Appl Phys Lett | 2015 May 18 |
| Time-reversed adapted-perturbation (TRAP) optical focusing onto dynamic objects inside scattering media. | Ma C, Xu X, Liu Y, Wang LV | Nature photonics | 25530797 | Nat Photonics | 2014 Dec |
| Photoacoustic tomography: principles and advances. | Xia J, Yao J, Wang LV | Electromagnetic waves (Cambridge, Mass.) | 25642127 | Electromagn Waves (Camb) | 2014 |
| Tripling the detection view of high-frequency linear-array-based photoacoustic computed tomography by using two planar acoustic reflectors. | Li G, Xia J, Wang K, Maslov K, Anastasio MA, Wang LV | Quantitative imaging in medicine and surgery | 25694954 | Quant Imaging Med Surg | 2015 Feb |
| In vivo photoacoustic flowmetry at depths of the diffusive regime based on saline injection. | Zhou Y, Poudel J, Li G, Wang LV | Journal of biomedical optics | 26267364 | J Biomed Opt | 2015 Aug |
| alphaVbeta3-targeted copper nanoparticles incorporating an Sn 2 lipase-labile fumagillin prodrug for photoacoustic neovascular imaging and treatment. | Zhang R, Pan D, Cai X, Yang X, Senpan A, Allen JS, Lanza GM, Wang LV | Theranostics | 25553103 | Theranostics | 2015 |
| Encrypted Three-dimensional Dynamic Imaging using Snapshot Time-of-flight Compressed Ultrafast Photography. | Liang J, Gao L, Hai P, Li C, Wang LV | Scientific reports | 26503834 | Sci Rep | 2015 Oct 27 |
| Label-free high-throughput photoacoustic tomography of suspected circulating melanoma tumor cells in patients in vivo. | Hai P, Qu Y, Li Y, Zhu L, Shmuylovich L, Cornelius LA, Wang LV | Journal of biomedical optics | 32170857 | J Biomed Opt | 2020 Mar |
| Spatiotemporal Antialiasing in Photoacoustic Computed Tomography. | Hu P, Li L, Lin L, Wang LV | IEEE transactions on medical imaging | 32746101 | IEEE Trans Med Imaging | 2020 Nov |
| Space- and intensity-constrained reconstruction for compressed ultrafast photography. | Zhu L, Chen Y, Liang J, Xu Q, Gao L, Ma C, Wang LV | Optica | 28775997 | Optica | 2016 Jul |
| Label-free cell nuclear imaging by Grüneisen relaxation photoacoustic microscopy. | Liu X, Wong TTW, Shi J, Ma J, Yang Q, Wang LV | Optics letters | 29444034 | Opt Lett | 2018 Feb 15 |
| In vivo photoacoustic microscopy of human cuticle microvasculature with single-cell resolution. | Hsu HC, Wang L, Wang LV | Journal of biomedical optics | 27207113 | J Biomed Opt | 2016 May 1 |
| Multiscale photoacoustic tomography using reversibly switchable bacterial phytochrome as a near-infrared photochromic probe. | Yao J, Kaberniuk AA, Li L, Shcherbakova DM, Zhang R, Wang L, Li G, Verkhusha VV, Wang LV | Nature methods | 26550774 | Nat Methods | 2016 Jan |
| Fighting against fast speckle decorrelation for light focusing inside live tissue by photon frequency shifting. | Yang J, Li L, Li J, Cheng Z, Liu Y, Wang LV | ACS photonics | 34113691 | ACS Photonics | 2020 Mar 18 |
| Continuous scanning of a time-reversed ultrasonically encoded optical focus by reflection-mode digital phase conjugation. | Suzuki Y, Tay JW, Yang Q, Wang LV | Optics letters | 24978506 | Opt Lett | 2014 Jun 15 |
| Label-free photoacoustic nanoscopy. | Danielli A, Maslov K, Garcia-Uribe A, Winkler AM, Li C, Wang L, Chen Y, Dorn GW 2nd, Wang LV | Journal of biomedical optics | 25104412 | J Biomed Opt | 2014 Aug |
| Microcirculatory changes identified by photoacoustic microscopy in patients with complex regional pain syndrome type I after stellate ganglion blocks. | Zhou Y, Yi X, Xing W, Hu S, Maslov KI, Wang LV | Journal of biomedical optics | 25144451 | J Biomed Opt | 2014 Aug |
| Dual-Modality Photoacoustic and Ultrasound Imaging System for Noninvasive Sentinel Lymph Node Detection in Patients with Breast Cancer. | Garcia-Uribe A, Erpelding TN, Krumholz A, Ke H, Maslov K, Appleton C, Margenthaler JA, Wang LV | Scientific reports | 26510774 | Sci Rep | 2015 Oct 29 |
| Cuffing-based photoacoustic flowmetry in humans in the optical diffusive regime. | Zhou Y, Liang J, Wang LV | Journal of biophotonics | 26515158 | J Biophotonics | 2016 Mar |
| High-resolution deep functional imaging of the whole mouse brain by photoacoustic computed tomography in vivo. | Zhang P, Li L, Lin L, Hu P, Shi J, He Y, Zhu L, Zhou Y, Wang LV | Journal of biophotonics | 28635056 | J Biophotonics | 2018 Jan |
| Optical focusing deep inside dynamic scattering media with near-infrared time-reversed ultrasonically encoded (TRUE) light. | Liu Y, Lai P, Ma C, Xu X, Grabar AA, Wang LV | Nature communications | 25556918 | Nat Commun | 2015 Jan 5 |
| Multi-view optical resolution photoacoustic microscopy. | Zhu L, Li L, Gao L, Wang LV | Optica | 25558469 | Optica | 2014 |
| Photoacoustic microscopy: superdepth, superresolution, and superb contrast. | Yao J, Song L, Wang LV | IEEE pulse | 25974913 | IEEE Pulse | 2015 May-Jun |
| In vivo label-free photoacoustic flow cytography and on-the-spot laser killing of single circulating melanoma cells. | He Y, Wang L, Shi J, Yao J, Li L, Zhang R, Huang CH, Zou J, Wang LV | Scientific reports | 28000788 | Sci Rep | 2016 Dec 21 |
| Noninvasive Determination of Melanoma Depth using a Handheld Photoacoustic Probe. | Zhou Y, Tripathi SV, Rosman I, Ma J, Hai P, Linette GP, Council ML, Fields RC, Wang LV, Cornelius LA | The Journal of investigative dermatology | 28163070 | J Invest Dermatol | 2017 Jun |
| Focusing light inside live tissue using reversibly switchable bacterial phytochrome as a genetically encoded photochromic guide star. | Yang J, Li L, Shemetov AA, Lee S, Zhao Y, Liu Y, Shen Y, Li J, Oka Y, Verkhusha VV, Wang LV | Science advances | 31844671 | Sci Adv | 2019 Dec |
| High-speed alignment optimization of digital optical phase conjugation systems based on autocovariance analysis in conjunction with orthonormal rectangular polynomials. | Hemphill AS, Shen Y, Hwang J, Wang LV | Journal of biomedical optics | 30156064 | J Biomed Opt | 2018 Aug |
| Snapshot photoacoustic topography through an ergodic relay of optical absorption in vivo. | Li L, Li Y, Zhang Y, Wang LV | Nature protocols | 33846630 | Nat Protoc | 2021 May |
| Single-impulse Panoramic Photoacoustic Computed Tomography of Small-animal Whole-body Dynamics at High Spatiotemporal Resolution. | Li L, Zhu L, Ma C, Lin L, Yao J, Wang L, Maslov K, Zhang R, Chen W, Shi J, Wang LV | Nature biomedical engineering | 29333331 | Nat Biomed Eng | 2017 |
| Dual-view photoacoustic microscopy for quantitative cell nuclear imaging. | Cai D, Wong TTW, Zhu L, Shi J, Chen SL, Wang LV | Optics letters | 30320772 | Opt Lett | 2018 Oct 15 |
| Photoacoustic computed tomography of human extremities. | Wray P, Lin L, Hu P, Wang LV | Journal of biomedical optics | 30784244 | J Biomed Opt | 2019 Feb |
| Single-shot real-time femtosecond imaging of temporal focusing. | Liang J, Zhu L, Wang LV | Light, science & applications | 30839588 | Light Sci Appl | 2018 |
| In vivo superresolution photoacoustic computed tomography by localization of single dyed droplets. | Zhang P, Li L, Lin L, Shi J, Wang LV | Light, science & applications | 30962922 | Light Sci Appl | 2019 |
| Single-shot ultrafast imaging attaining 70 trillion frames per second. | Wang P, Liang J, Wang LV | Nature communications | 32350256 | Nat Commun | 2020 Apr 29 |
| Amplitude-masked photoacoustic wavefront shaping and application in flowmetry. | Tay JW, Liang J, Wang LV | Optics letters | 25360912 | Opt Lett | 2014 Oct 1 |
| Bit-efficient, sub-millisecond wavefront measurement using a lock-in camera for time-reversal based optical focusing inside scattering media. | Liu Y, Ma C, Shen Y, Wang LV | Optics letters | 27192226 | Opt Lett | 2016 Apr 1 |
| Motionless volumetric photoacoustic microscopy with spatially invariant resolution. | Yang J, Gong L, Xu X, Hai P, Shen Y, Suzuki Y, Wang LV | Nature communications | 28974681 | Nat Commun | 2017 Oct 3 |
| High-speed single-shot optical focusing through dynamic scattering media with full-phase wavefront shaping. | Hemphill AS, Shen Y, Liu Y, Wang LV | Applied physics letters | 29249832 | Appl Phys Lett | 2017 Nov 27 |
| Dual-polarization analog optical phase conjugation for focusing light through scattering media. | Cheng Z, Yang J, Wang LV | Applied physics letters | 31312071 | Appl Phys Lett | 2019 Jun 10 |
| LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control. | Wang J, Telese F, Tan Y, Li W, Jin C, He X, Basnet H, Ma Q, Merkurjev D, Zhu X, Liu Z, Zhang J, Ohgi K, Taylor H, White RR, Tazearslan C, Suh Y, Macfarlan TS, Pfaff SL, Rosenfeld MG | Nature neuroscience | 26214369 | Nat Neurosci | 2015 Sep |
| Enhancer RNAs and regulated transcriptional programs. | Lam MT, Li W, Rosenfeld MG, Glass CK | Trends in biochemical sciences | 24674738 | Trends Biochem Sci | 2014 Apr |
| Enhancer-bound LDB1 regulates a corticotrope promoter-pausing repression program. | Zhang F, Tanasa B, Merkurjev D, Lin C, Song X, Li W, Tan Y, Liu Z, Zhang J, Ohgi KA, Krones A, Skowronska-Krawczyk D, Rosenfeld MG | Proceedings of the National Academy of Sciences of the United States of America | 25605944 | Proc Natl Acad Sci U S A | 2015 Feb 3 |
| lncRNA-dependent mechanisms of androgen-receptor-regulated gene activation programs. | Yang L, Lin C, Jin C, Yang JC, Tanasa B, Li W, Merkurjev D, Ohgi KA, Meng D, Zhang J, Evans CP, Rosenfeld MG | Nature | 23945587 | Nature | 2013 Aug 29 |
| Tissue damage drives co-localization of NF-κB, Smad3, and Nrf2 to direct Rev-erb sensitive wound repair in mouse macrophages. | Eichenfield DZ, Troutman TD, Link VM, Lam MT, Cho H, Gosselin D, Spann NJ, Lesch HP, Tao J, Muto J, Gallo RL, Evans RM, Glass CK | eLife | 27462873 | Elife | 2016 Jul 27 |
| Genetic and genomic approaches to understanding macrophage identity and function. | Glass CK | Arteriosclerosis, thrombosis, and vascular biology | 25745059 | Arterioscler Thromb Vasc Biol | 2015 Apr |
| Required enhancer-matrin-3 network interactions for a homeodomain transcription program. | Skowronska-Krawczyk D, Ma Q, Schwartz M, Scully K, Li W, Liu Z, Taylor H, Tollkuhn J, Ohgi KA, Notani D, Kohwi Y, Kohwi-Shigematsu T, Rosenfeld MG | Nature | 25119036 | Nature | 2014 Oct 9 |
| Epigenomic control of the innate immune response. | Stender JD, Glass CK | Current opinion in pharmacology | 23816801 | Curr Opin Pharmacol | 2013 Aug |
| Histone demethylase LSD1 regulates hematopoietic stem cells homeostasis and protects from death by endotoxic shock. | Wang J, Saijo K, Skola D, Jin C, Ma Q, Merkurjev D, Glass CK, Rosenfeld MG | Proceedings of the National Academy of Sciences of the United States of America | 29263096 | Proc Natl Acad Sci U S A | 2018 Jan 9 |
| Molecular control of activation and priming in macrophages. | Glass CK, Natoli G | Nature immunology | 26681459 | Nat Immunol | 2016 Jan |
| Vespucci: a system for building annotated databases of nascent transcripts. | Allison KA, Kaikkonen MU, Gaasterland T, Glass CK | Nucleic acids research | 24304890 | Nucleic Acids Res | 2014 Feb |
| Brd4 and JMJD6-associated anti-pause enhancers in regulation of transcriptional pause release. | Liu W, Ma Q, Wong K, Li W, Ohgi K, Zhang J, Aggarwal A, Rosenfeld MG | Cell | 24360279 | Cell | 2013 Dec 19 |
| Mutant Huntingtin promotes autonomous microglia activation via myeloid lineage-determining factors. | Crotti A, Benner C, Kerman BE, Gosselin D, Lagier-Tourenne C, Zuccato C, Cattaneo E, Gage FH, Cleveland DW, Glass CK | Nature neuroscience | 24584051 | Nat Neurosci | 2014 Apr |
| Mechanisms Underlying the Selection and Function of Macrophage-Specific Enhancers. | Link VM, Gosselin D, Glass CK | Cold Spring Harbor symposia on quantitative biology | 26582787 | Cold Spring Harb Symp Quant Biol | 2015 |
| Patient-derived xenograft (PDX) models in basic and translational breast cancer research. | Dobrolecki LE, Airhart SD, Alferez DG, Aparicio S, Behbod F, Bentires-Alj M, Brisken C, Bult CJ, Cai S, Clarke RB, Dowst H, Ellis MJ, Gonzalez-Suarez E, Iggo RD, Kabos P, Li S, Lindeman GJ, Marangoni E, McCoy A, Meric-Bernstam F, Piwnica-Worms H, Poupon MF, Reis-Filho J, Sartorius CA, Scabia V, Sflomos G, Tu Y, Vaillant F, Visvader JE, Welm A, Wicha MS, Lewis MT | Cancer metastasis reviews | 28025748 | Cancer Metastasis Rev | 2016 Dec |
| Epigenomics of macrophages. | Gosselin D, Glass CK | Immunological reviews | 25319330 | Immunol Rev | 2014 Nov |
| Ligand-dependent enhancer activation regulated by topoisomerase-I activity. | Puc J, Kozbial P, Li W, Tan Y, Liu Z, Suter T, Ohgi KA, Zhang J, Aggarwal AK, Rosenfeld MG | Cell | 25619691 | Cell | 2015 Jan 29 |
| Epigenomics: Roadmap for regulation. | Romanoski CE, Glass CK, Stunnenberg HG, Wilson L, Almouzni G | Nature | 25693562 | Nature | 2015 Feb 19 |
| LRP8-Reelin-Regulated Neuronal Enhancer Signature Underlying Learning and Memory Formation. | Telese F, Ma Q, Perez PM, Notani D, Oh S, Li W, Comoletti D, Ohgi KA, Taylor H, Rosenfeld MG | Neuron | 25892301 | Neuron | 2015 May 6 |
| Structural and Molecular Mechanisms of Cytokine-Mediated Endocrine Resistance in Human Breast Cancer Cells. | Stender JD, Nwachukwu JC, Kastrati I, Kim Y, Strid T, Yakir M, Srinivasan S, Nowak J, Izard T, Rangarajan ES, Carlson KE, Katzenellenbogen JA, Yao XQ, Grant BJ, Leong HS, Lin CY, Frasor J, Nettles KW, Glass CK | Molecular cell | 28306507 | Mol Cell | 2017 Mar 16 |
| Phase separation of ligand-activated enhancers licenses cooperative chromosomal enhancer assembly. | Nair SJ, Yang L, Meluzzi D, Oh S, Yang F, Friedman MJ, Wang S, Suter T, Alshareedah I, Gamliel A, Ma Q, Zhang J, Hu Y, Tan Y, Ohgi KA, Jayani RS, Banerjee PR, Aggarwal AK, Rosenfeld MG | Nature structural & molecular biology | 30833784 | Nat Struct Mol Biol | 2019 Mar |
| SREBP1 Contributes to Resolution of Pro-inflammatory TLR4 Signaling by Reprogramming Fatty Acid Metabolism. | Oishi Y, Spann NJ, Link VM, Muse ED, Strid T, Edillor C, Kolar MJ, Matsuzaka T, Hayakawa S, Tao J, Kaikkonen MU, Carlin AF, Lam MT, Manabe I, Shimano H, Saghatelian A, Glass CK | Cell metabolism | 28041958 | Cell Metab | 2017 Feb 7 |
| Towards an understanding of cell-specific functions of signal-dependent transcription factors. | Zhang DX, Glass CK | Journal of molecular endocrinology | 24130129 | J Mol Endocrinol | 2013 Dec |
| Functional roles of enhancer RNAs for oestrogen-dependent transcriptional activation. | Li W, Notani D, Ma Q, Tanasa B, Nunez E, Chen AY, Merkurjev D, Zhang J, Ohgi K, Song X, Oh S, Kim HS, Glass CK, Rosenfeld MG | Nature | 23728302 | Nature | 2013 Jun 27 |
| Genome-Wide Approaches to Defining Macrophage Identity and Function. | Fonseca GJ, Seidman JS, Glass CK | Microbiology spectrum | 28087927 | Microbiol Spectr | 2016 Oct |
| Tyrosine phosphorylation of histone H2A by CK2 regulates transcriptional elongation. | Basnet H, Su XB, Tan Y, Meisenhelder J, Merkurjev D, Ohgi KA, Hunter T, Pillus L, Rosenfeld MG | Nature | 25252977 | Nature | 2014 Dec 11 |
| Affinity and dose of TCR engagement yield proportional enhancer and gene activity in CD4+ T cells. | Allison KA, Sajti E, Collier JG, Gosselin D, Troutman TD, Stone EL, Hedrick SM, Glass CK | eLife | 27376549 | Elife | 2016 Jul 4 |
| Enhancer activation requires trans-recruitment of a mega transcription factor complex. | Liu Z, Merkurjev D, Yang F, Li W, Oh S, Friedman MJ, Song X, Zhang F, Ma Q, Ohgi KA, Krones A, Rosenfeld MG | Cell | 25303530 | Cell | 2014 Oct 9 |
| Analysis of Genetically Diverse Macrophages Reveals Local and Domain-wide Mechanisms that Control Transcription Factor Binding and Function. | Link VM, Duttke SH, Chun HB, Holtman IR, Westin E, Hoeksema MA, Abe Y, Skola D, Romanoski CE, Tao J, Fonseca GJ, Troutman TD, Spann NJ, Strid T, Sakai M, Yu M, Hu R, Fang R, Metzler D, Ren B, Glass CK | Cell | 29779944 | Cell | 2018 Jun 14 |
| Dismissal of RNA Polymerase II Underlies a Large Ligand-Induced Enhancer Decommissioning Program. | Tan Y, Jin C, Ma W, Hu Y, Tanasa B, Oh S, Gamliel A, Ma Q, Yao L, Zhang J, Ohgi K, Liu W, Aggarwal AK, Rosenfeld MG | Molecular cell | 30118678 | Mol Cell | 2018 Aug 16 |
| Effect of natural genetic variation on enhancer selection and function. | Heinz S, Romanoski CE, Benner C, Allison KA, Kaikkonen MU, Orozco LD, Glass CK | Nature | 24121437 | Nature | 2013 Nov 28 |
| Remodeling of the enhancer landscape during macrophage activation is coupled to enhancer transcription. | Kaikkonen MU, Spann NJ, Heinz S, Romanoski CE, Allison KA, Stender JD, Chun HB, Tough DF, Prinjha RK, Benner C, Glass CK | Molecular cell | 23932714 | Mol Cell | 2013 Aug 8 |
| Rev-Erbs repress macrophage gene expression by inhibiting enhancer-directed transcription. | Lam MT, Cho H, Lesch HP, Gosselin D, Heinz S, Tanaka-Oishi Y, Benner C, Kaikkonen MU, Kim AS, Kosaka M, Lee CY, Watt A, Grossman TR, Rosenfeld MG, Evans RM, Glass CK | Nature | 23728303 | Nature | 2013 Jun 27 |
| Chem-seq permits identification of genomic targets of drugs against androgen receptor regulation selected by functional phenotypic screens. | Jin C, Yang L, Xie M, Lin C, Merkurjev D, Yang JC, Tanasa B, Oh S, Zhang J, Ohgi KA, Zhou H, Li W, Evans CP, Ding S, Rosenfeld MG | Proceedings of the National Academy of Sciences of the United States of America | 24928520 | Proc Natl Acad Sci U S A | 2014 Jun 24 |
| Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. | Gosselin D, Link VM, Romanoski CE, Fonseca GJ, Eichenfield DZ, Spann NJ, Stender JD, Chun HB, Garner H, Geissmann F, Glass CK | Cell | 25480297 | Cell | 2014 Dec 4 |
| Control of VEGF-A transcriptional programs by pausing and genomic compartmentalization. | Kaikkonen MU, Niskanen H, Romanoski CE, Kansanen E, Kivelä AM, Laitalainen J, Heinz S, Benner C, Glass CK, Ylä-Herttuala S | Nucleic acids research | 25352550 | Nucleic Acids Res | 2014 Nov 10 |
| Condensin I and II Complexes License Full Estrogen Receptor α-Dependent Enhancer Activation. | Li W, Hu Y, Oh S, Ma Q, Merkurjev D, Song X, Zhou X, Liu Z, Tanasa B, He X, Chen AY, Ohgi K, Zhang J, Liu W, Rosenfeld MG | Molecular cell | 26166704 | Mol Cell | 2015 Jul 16 |
| Exploiting genomics and natural genetic variation to decode macrophage enhancers. | Romanoski CE, Link VM, Heinz S, Glass CK | Trends in immunology | 26298065 | Trends Immunol | 2015 Sep |
| The selection and function of cell type-specific enhancers. | Heinz S, Romanoski CE, Benner C, Glass CK | Nature reviews. Molecular cell biology | 25650801 | Nat Rev Mol Cell Biol | 2015 Mar |
| Glucocorticoid Receptor:MegaTrans Switching Mediates the Repression of an ERα-Regulated Transcriptional Program. | Yang F, Ma Q, Liu Z, Li W, Tan Y, Jin C, Ma W, Hu Y, Shen J, Ohgi KA, Telese F, Liu W, Rosenfeld MG | Molecular cell | 28475868 | Mol Cell | 2017 May 4 |
| Adoptive cell therapy for sarcoma. | Mata M, Gottschalk S | Immunotherapy | 25572477 | Immunotherapy | 2015 |
| Man's Best Friend: Utilizing Naturally Occurring Tumors in Dogs to Improve Chimeric Antigen Receptor T-cell Therapy for Human Cancers. | Mata M, Gottschalk S | Molecular therapy : the journal of the American Society of Gene Therapy | 27687136 | Mol Ther | 2016 Sep |
| Radiotherapy induces responses of lung cancer to CTLA-4 blockade. | Formenti SC, Rudqvist NP, Golden E, Cooper B, Wennerberg E, Lhuillier C, Vanpouille-Box C, Friedman K, Ferrari de Andrade L, Wucherpfennig KW, Heguy A, Imai N, Gnjatic S, Emerson RO, Zhou XK, Zhang T, Chachoua A, Demaria S | Nature medicine | 30397353 | Nat Med | 2018 Dec |
| Genetically modified T cells to target glioblastoma. | Krebs S, Rodríguez-Cruz TG, Derenzo C, Gottschalk S | Frontiers in oncology | 24427741 | Front Oncol | 2013 Dec 31 |
| The Landscape of CAR T Cells Beyond Acute Lymphoblastic Leukemia for Pediatric Solid Tumors. | DeRenzo C, Krenciute G, Gottschalk S | American Society of Clinical Oncology educational book. American Society of Clinical Oncology. Annual Meeting | 30231350 | Am Soc Clin Oncol Educ Book | 2018 May 23 |
| A Cancer Cell Program Promotes T Cell Exclusion and Resistance to Checkpoint Blockade. | Jerby-Arnon L, Shah P, Cuoco MS, Rodman C, Su MJ, Melms JC, Leeson R, Kanodia A, Mei S, Lin JR, Wang S, Rabasha B, Liu D, Zhang G, Margolais C, Ashenberg O, Ott PA, Buchbinder EI, Haq R, Hodi FS, Boland GM, Sullivan RJ, Frederick DT, Miao B, Moll T, Flaherty KT, Herlyn M, Jenkins RW, Thummalapalli R, Kowalczyk MS, Cañadas I, Schilling B, Cartwright ANR, Luoma AM, Malu S, Hwu P, Bernatchez C, Forget MA, Barbie DA, Shalek AK, Tirosh I, Sorger PK, Wucherpfennig K, Van Allen EM, Schadendorf D, Johnson BE, Rotem A, Rozenblatt-Rosen O, Garraway LA, Yoon CH, Izar B, Regev A | Cell | 30388455 | Cell | 2018 Nov 1 |
| Transgenic Expression of IL15 Improves Antiglioma Activity of IL13Rα2-CAR T Cells but Results in Antigen Loss Variants. | Krenciute G, Prinzing BL, Yi Z, Wu MF, Liu H, Dotti G, Balyasnikova IV, Gottschalk S | Cancer immunology research | 28550091 | Cancer Immunol Res | 2017 Jul |
| A major chromatin regulator determines resistance of tumor cells to T cell-mediated killing. | Pan D, Kobayashi A, Jiang P, Ferrari de Andrade L, Tay RE, Luoma AM, Tsoucas D, Qiu X, Lim K, Rao P, Long HW, Yuan GC, Doench J, Brown M, Liu XS, Wucherpfennig KW | Science (New York, N.Y.) | 29301958 | Science | 2018 Feb 16 |
| Discovering cancer immunotherapy targets in vivo. | Zhou P, Wucherpfennig KW | Oncoimmunology | 25050218 | Oncoimmunology | 2014 |
| Deleting DNMT3A in CAR T cells prevents exhaustion and enhances antitumor activity. | Prinzing B, Zebley CC, Petersen CT, Fan Y, Anido AA, Yi Z, Nguyen P, Houke H, Bell M, Haydar D, Brown C, Boi SK, Alli S, Crawford JC, Riberdy JM, Park JJ, Zhou S, Velasquez MP, DeRenzo C, Lazzarotto CR, Tsai SQ, Vogel P, Pruett-Miller SM, Langfitt DM, Gottschalk S, Youngblood B, Krenciute G | Science translational medicine | 34788079 | Sci Transl Med | 2021 Nov 17 |
| MyD88/CD40 signaling retains CAR T cells in a less differentiated state. | Prinzing B, Schreiner P, Bell M, Fan Y, Krenciute G, Gottschalk S | JCI insight | 33148882 | JCI Insight | 2020 Nov 5 |
| The microRNA miR-31 inhibits CD8(+) T cell function in chronic viral infection. | Moffett HF, Cartwright ANR, Kim HJ, Godec J, Pyrdol J, Äijö T, Martinez GJ, Rao A, Lu J, Golub TR, Cantor H, Sharpe AH, Novina CD, Wucherpfennig KW | Nature immunology | 28530712 | Nat Immunol | 2017 Jul |
| RASA2 ablation in T cells boosts antigen sensitivity and long-term function. | Carnevale J, Shifrut E, Kale N, Nyberg WA, Blaeschke F, Chen YY, Li Z, Bapat SP, Diolaiti ME, O'Leary P, Vedova S, Belk J, Daniel B, Roth TL, Bachl S, Anido AA, Prinzing B, Ibañez-Vega J, Lange S, Haydar D, Luetke-Eversloh M, Born-Bony M, Hegde B, Kogan S, Feuchtinger T, Okada H, Satpathy AT, Shannon K, Gottschalk S, Eyquem J, Krenciute G, Ashworth A, Marson A | Nature | 36002574 | Nature | 2022 Sep |
| Tissue-Resident T Cells in Clinical Response and Immune-Related Adverse Events of Immune Checkpoint Blockade. | Zhao Y, Wucherpfennig KW | Clinical cancer research : an official journal of the American Association for Cancer Research | 39404858 | Clin Cancer Res | 2024 Dec 16 |
| Design and development of therapies using chimeric antigen receptor-expressing T cells. | Dotti G, Gottschalk S, Savoldo B, Brenner MK | Immunological reviews | 24329793 | Immunol Rev | 2014 Jan |
| CAR T cells for solid tumors: armed and ready to go? | Kakarla S, Gottschalk S | Cancer journal (Sudbury, Mass.) | 24667962 | Cancer J | 2014 Mar-Apr |
| Genetically modified T-cell therapy for osteosarcoma. | DeRenzo C, Gottschalk S | Advances in experimental medicine and biology | 24924183 | Adv Exp Med Biol | 2014 |
| In vivo discovery of immunotherapy targets in the tumour microenvironment. | Zhou P, Shaffer DR, Alvarez Arias DA, Nakazaki Y, Pos W, Torres AJ, Cremasco V, Dougan SK, Cowley GS, Elpek K, Brogdon J, Lamb J, Turley SJ, Ploegh HL, Root DE, Love JC, Dranoff G, Hacohen N, Cantor H, Wucherpfennig KW | Nature | 24476824 | Nature | 2014 Feb 6 |
| Genetically Modified T-Cell Therapy for Osteosarcoma: Into the Roaring 2020s. | DeRenzo C, Gottschalk S | Advances in experimental medicine and biology | 32483735 | Adv Exp Med Biol | 2020 |
| Constitutive Signaling from an Engineered IL7 Receptor Promotes Durable Tumor Elimination by Tumor-Redirected T Cells. | Shum T, Omer B, Tashiro H, Kruse RL, Wagner DL, Parikh K, Yi Z, Sauer T, Liu D, Parihar R, Castillo P, Liu H, Brenner MK, Metelitsa LS, Gottschalk S, Rooney CM | Cancer discovery | 28830878 | Cancer Discov | 2017 Nov |
| Genetically Modified T-cell Therapy for the Treatment of Osteosarcoma: An Update. | DeRenzo C, Gottschalk S | Journal of clinical & cellular immunology | 27313973 | J Clin Cell Immunol | 2016 Apr |
| Engager T cells: a new class of antigen-specific T cells that redirect bystander T cells. | Iwahori K, Kakarla S, Velasquez MP, Yu F, Yi Z, Gerken C, Song XT, Gottschalk S | Molecular therapy : the journal of the American Society of Gene Therapy | 25142939 | Mol Ther | 2015 Jan |
| Genetic screens to study the immune system in cancer. | Wucherpfennig KW, Cartwright AN | Current opinion in immunology | 27309352 | Curr Opin Immunol | 2016 Aug |
| Engineering for Success: Approaches to Improve Chimeric Antigen Receptor T Cell Therapy for Solid Tumors. | Mata M, Gottschalk S | Drugs | 30796733 | Drugs | 2019 Mar |
| T-Scan: A Genome-wide Method for the Systematic Discovery of T Cell Epitopes. | Kula T, Dezfulian MH, Wang CI, Abdelfattah NS, Hartman ZC, Wucherpfennig KW, Lyerly HK, Elledge SJ | Cell | 31398327 | Cell | 2019 Aug 8 |
| Characterization and Functional Analysis of scFv-based Chimeric Antigen Receptors to Redirect T Cells to IL13Rα2-positive Glioma. | Krenciute G, Krebs S, Torres D, Wu MF, Liu H, Dotti G, Li XN, Lesniak MS, Balyasnikova IV, Gottschalk S | Molecular therapy : the journal of the American Society of Gene Therapy | 26514825 | Mol Ther | 2016 Feb |
| Antibody-mediated inhibition of MICA and MICB shedding promotes NK cell-driven tumor immunity. | Ferrari de Andrade L, Tay RE, Pan D, Luoma AM, Ito Y, Badrinath S, Tsoucas D, Franz B, May KF Jr, Harvey CJ, Kobold S, Pyrdol JW, Yoon C, Yuan GC, Hodi FS, Dranoff G, Wucherpfennig KW | Science (New York, N.Y.) | 29599246 | Science | 2018 Mar 30 |
| Genetic Modification Strategies to Enhance CAR T Cell Persistence for Patients With Solid Tumors. | DeRenzo C, Gottschalk S | Frontiers in immunology | 30828333 | Front Immunol | 2019 |
| Inducible Activation of MyD88 and CD40 in CAR T Cells Results in Controllable and Potent Antitumor Activity in Preclinical Solid Tumor Models. | Mata M, Gerken C, Nguyen P, Krenciute G, Spencer DM, Gottschalk S | Cancer discovery | 28801306 | Cancer Discov | 2017 Nov |
| Tissue-resident memory and circulating T cells are early responders to pre-surgical cancer immunotherapy. | Luoma AM, Suo S, Wang Y, Gunasti L, Porter CBM, Nabilsi N, Tadros J, Ferretti AP, Liao S, Gurer C, Chen YH, Criscitiello S, Ricker CA, Dionne D, Rozenblatt-Rosen O, Uppaluri R, Haddad RI, Ashenberg O, Regev A, Van Allen EM, MacBeath G, Schoenfeld JD, Wucherpfennig KW | Cell | 35803260 | Cell | 2022 Aug 4 |
| In vivo functional microangiography by visible-light optical coherence tomography. | Yi J, Chen S, Backman V, Zhang HF | Biomedical optics express | 25360376 | Biomed Opt Express | 2014 Oct 1 |
| Dynamic transcription factor activity and networks during ErbB2 breast oncogenesis and targeted therapy. | Weiss MS, Peñalver Bernabé B, Shin S, Asztalos S, Dubbury SJ, Mui MD, Bellis AD, Bluver D, Tonetti DA, Saez-Rodriguez J, Broadbelt LJ, Jeruss JS, Shea LD | Integrative biology : quantitative biosciences from nano to macro | 25303361 | Integr Biol (Camb) | 2014 Dec |
| Tissue Engineering Approaches to Modulate the Inflammatory Milieu following Spinal Cord Injury. | Dumont CM, Margul DJ, Shea LD | Cells, tissues, organs | 27701152 | Cells Tissues Organs | 2016 |
| Detection of extracellular matrix modification in cancer models with inverse spectroscopic optical coherence tomography. | Spicer GL, Azarin SM, Yi J, Young ST, Ellis R, Bauer GM, Shea LD, Backman V | Physics in medicine and biology | 27618507 | Phys Med Biol | 2016 Oct 7 |
| Theoretical model for optical oximetry at the capillary level: exploring hemoglobin oxygen saturation through backscattering of single red blood cells. | Liu R, Spicer G, Chen S, Zhang HF, Yi J, Backman V | Journal of biomedical optics | 28157244 | J Biomed Opt | 2017 Feb 1 |
| Polysaccharide-modified scaffolds for controlled lentivirus delivery in vitro and after spinal cord injury. | Thomas AM, Shea LD | Journal of controlled release : official journal of the Controlled Release Society | 23791981 | J Control Release | 2013 Sep 28 |
| Precision health for breast cancer metastasis: biomaterial scaffolds as an engineered metastatic niche to define, study, and monitor metastatic progression. | Bushnell GG, Wicha MS, Jeruss JS, Shea LD | Oncoscience | 31984215 | Oncoscience | 2019 Nov |
| Sponge-mediated lentivirus delivery to acute and chronic spinal cord injuries. | Thomas AM, Palma JL, Shea LD | Journal of controlled release : official journal of the Controlled Release Society | 25724274 | J Control Release | 2015 Apr 28 |
| Retrievable hydrogels for ovarian follicle transplantation and oocyte collection. | Rios PD, Kniazeva E, Lee HC, Xiao S, Oakes RS, Saito E, Jeruss JS, Shikanov A, Woodruff TK, Shea LD | Biotechnology and bioengineering | 29704433 | Biotechnol Bioeng | 2018 Aug |
| Engineering the pre-metastatic niche. | Aguado BA, Bushnell GG, Rao SS, Jeruss JS, Shea LD | Nature biomedical engineering | 28989814 | Nat Biomed Eng | 2017 |
| Sonic hedgehog and neurotrophin-3 increase oligodendrocyte numbers and myelination after spinal cord injury. | Thomas AM, Seidlits SK, Goodman AG, Kukushliev TV, Hassani DM, Cummings BJ, Anderson AJ, Shea LD | Integrative biology : quantitative biosciences from nano to macro | 24873988 | Integr Biol (Camb) | 2014 Jul 24 |
| Transforming growth factor-beta 1 delivery from microporous scaffolds decreases inflammation post-implant and enhances function of transplanted islets. | Liu JMH, Zhang J, Zhang X, Hlavaty KA, Ricci CF, Leonard JN, Shea LD, Gower RM | Biomaterials | 26701143 | Biomaterials | 2016 Feb |
| Fractal Characterization of Chromatin Decompaction in Live Cells. | Yi J, Stypula-Cyrus Y, Blaha CS, Roy HK, Backman V | Biophysical journal | 26636933 | Biophys J | 2015 Dec 1 |
| Biomaterial Scaffolds as Pre-metastatic Niche Mimics Systemically Alter the Primary Tumor and Tumor Microenvironment. | Aguado BA, Hartfield RM, Bushnell GG, Decker JT, Azarin SM, Nanavati D, Schipma MJ, Rao SS, Oakes RS, Zhang Y, Jeruss JS, Shea LD | Advanced healthcare materials | 29521008 | Adv Healthc Mater | 2018 May |
| Dynamic microRNA activity identifies therapeutic targets in trastuzumab-resistant HER2(+) breast cancer. | Decker JT, Hall MS, Blaisdell RB, Schwark K, Jeruss JS, Shea LD | Biotechnology and bioengineering | 29981261 | Biotechnol Bioeng | 2018 Oct |
| Heparin-chitosan nanoparticle functionalization of porous poly(ethylene glycol) hydrogels for localized lentivirus delivery of angiogenic factors. | Thomas AM, Gomez AJ, Palma JL, Yap WT, Shea LD | Biomaterials | 25023395 | Biomaterials | 2014 Oct |
| High Frequency Spectral Ultrasound Imaging to Detect Metastasis in Implanted Biomaterial Scaffolds. | Bushnell GG, Hong X, Hartfield RM, Zhang Y, Oakes RS, Rao SS, Jeruss JS, Stegemann JP, Deng CX, Shea LD | Annals of biomedical engineering | 31549327 | Ann Biomed Eng | 2020 Jan |
| Biomaterial Scaffolds Recruit an Aggressive Population of Metastatic Tumor Cells In Vivo. | Bushnell GG, Hardas TP, Hartfield RM, Zhang Y, Oakes RS, Ronquist S, Chen H, Rajapakse I, Wicha MS, Jeruss JS, Shea LD | Cancer research | 30808673 | Cancer Res | 2019 Apr 15 |
| Spectral contrast optical coherence tomography angiography enables single-scan vessel imaging. | Winkelmann JA, Eid A, Spicer G, Almassalha LM, Nguyen TQ, Backman V | Light, science & applications | 30651982 | Light Sci Appl | 2019 |
| Systems analysis of dynamic transcription factor activity identifies targets for treatment in Olaparib resistant cancer cells. | Decker JT, Hobson EC, Zhang Y, Shin S, Thomas AL, Jeruss JS, Arnold KB, Shea LD | Biotechnology and bioengineering | 28322442 | Biotechnol Bioeng | 2017 Sep |
| Lentivirus delivery of IL-10 to promote and sustain macrophage polarization towards an anti-inflammatory phenotype. | Boehler RM, Kuo R, Shin S, Goodman AG, Pilecki MA, Gower RM, Leonard JN, Shea LD | Biotechnology and bioengineering | 24375008 | Biotechnol Bioeng | 2014 Jun |
| Modulation of leukocyte infiltration and phenotype in microporous tissue engineering scaffolds via vector induced IL-10 expression. | Gower RM, Boehler RM, Azarin SM, Ricci CF, Leonard JN, Shea LD | Biomaterials | 24309498 | Biomaterials | 2014 Feb |
| Enhanced Survival with Implantable Scaffolds That Capture Metastatic Breast Cancer Cells In Vivo. | Rao SS, Bushnell GG, Azarin SM, Spicer G, Aguado BA, Stoehr JR, Jiang EJ, Backman V, Shea LD, Jeruss JS | Cancer research | 27635043 | Cancer Res | 2016 Sep 15 |
| Apoptosis-induced CXCL5 accelerates inflammation and growth of prostate tumor metastases in bone. | Roca H, Jones JD, Purica MC, Weidner S, Koh AJ, Kuo R, Wilkinson JE, Wang Y, Daignault-Newton S, Pienta KJ, Morgan TM, Keller ET, Nör JE, Shea LD, McCauley LK | The Journal of clinical investigation | 29202471 | J Clin Invest | 2018 Jan 2 |
| Embryonic stem cell secreted factors decrease invasiveness of triple-negative breast cancer cells through regulome modulation. | Tarasewicz E, Oakes RS, Aviles MO, Straehla J, Chilton KM, Decker JT, Wu J, Shea LD, Jeruss JS | Cancer biology & therapy | 29053396 | Cancer Biol Ther | 2018 Apr 3 |
| Reducing neuroinflammation by delivery of IL-10 encoding lentivirus from multiple-channel bridges. | Margul DJ, Park J, Boehler RM, Smith DR, Johnson MA, McCreedy DA, He T, Ataliwala A, Kukushliev TV, Liang J, Sohrabi A, Goodman AG, Walthers CM, Shea LD, Seidlits SK | Bioengineering & translational medicine | 27981242 | Bioeng Transl Med | 2016 Jun |
| A PLG/HAp composite scaffold for lentivirus delivery. | Boehler RM, Shin S, Fast AG, Gower RM, Shea LD | Biomaterials | 23602363 | Biomaterials | 2013 Jul |
| Quantitative quality-control metrics for in vivo oximetry in small vessels by visible light optical coherence tomography angiography. | Liu R, Song W, Backman V, Yi J | Biomedical optics express | 30800493 | Biomed Opt Express | 2019 Feb 1 |
| Metastatic Conditioning of Myeloid Cells at a Subcutaneous Synthetic Niche Reflects Disease Progression and Predicts Therapeutic Outcomes. | Oakes RS, Bushnell GG, Orbach SM, Kandagatla P, Zhang Y, Morris AH, Hall MS, LaFaire P, Decker JT, Hartfield RM, Brooks MD, Wicha MS, Jeruss JS, Shea LD | Cancer research | 31662327 | Cancer Res | 2020 Feb 1 |
| In vivo capture and label-free detection of early metastatic cells. | Azarin SM, Yi J, Gower RM, Aguado BA, Sullivan ME, Goodman AG, Jiang EJ, Rao SS, Ren Y, Tucker SL, Backman V, Jeruss JS, Shea LD | Nature communications | 26348915 | Nat Commun | 2015 Sep 8 |
| Label free localization of nanoparticles in live cancer cells using spectroscopic microscopy. | Spicer GLC , Almassalha L , Martinez IA , Ellis R , Chandler JE , Gladstein S , Zhang D , Nguyen TQ , Feder S , Subramanian H , de la Rica R , Thompson SA , Backman V | Nanoscale | 30298892 | Nanoscale | 2018 Oct 18 |
| Cryotemplation for the Rapid Fabrication of Porous, Patternable Photopolymerized Hydrogels. | Thomas AM, Shea LD | Journal of materials chemistry. B | 25083293 | J Mater Chem B | 2014 Jul 28 |
| Extracellular matrix mediators of metastatic cell colonization characterized using scaffold mimics of the pre-metastatic niche. | Aguado BA, Caffe JR, Nanavati D, Rao SS, Bushnell GG, Azarin SM, Shea LD | Acta biomaterialia | 26844426 | Acta Biomater | 2016 Mar |
| Plakophilin-2 loss promotes TGF-β1/p38 MAPK-dependent fibrotic gene expression in cardiomyocytes. | Dubash AD, Kam CY, Aguado BA, Patel DM, Delmar M, Shea LD, Green KJ | The Journal of cell biology | 26858265 | J Cell Biol | 2016 Feb 15 |
| Secretome identification of immune cell factors mediating metastatic cell homing. | Aguado BA, Wu JJ, Azarin SM, Nanavati D, Rao SS, Bushnell GG, Medicherla CB, Shea LD | Scientific reports | 26634905 | Sci Rep | 2015 Dec 4 |
| Microporous scaffolds loaded with immunomodulatory lentivirus to study the contribution of immune cell populations to tumor cell recruitment in vivo. | Bushnell GG, Rao SS, Hartfield RM, Zhang Y, Oakes RS, Jeruss JS, Shea LD | Biotechnology and bioengineering | 31544959 | Biotechnol Bioeng | 2020 Jan |
| Single capillary oximetry and tissue ultrastructural sensing by dual-band dual-scan inverse spectroscopic optical coherence tomography. | Liu R, Winkelmann JA, Spicer G, Zhu Y, Eid A, Ameer GA, Backman V, Yi J | Light, science & applications | 30839641 | Light Sci Appl | 2018 |
| Controlled release strategies for modulating immune responses to promote tissue regeneration. | Dumont CM, Park J, Shea LD | Journal of controlled release : official journal of the Controlled Release Society | 26264833 | J Control Release | 2015 Dec 10 |
| Targeted delivery of cisplatin to lung cancer using ScFvEGFR-heparin-cisplatin nanoparticles. | Peng XH, Wang Y, Huang D, Wang Y, Shin HJ, Chen Z, Spewak MB, Mao H, Wang X, Wang Y, Chen ZG, Nie S, Shin DM | ACS nano | 22032622 | ACS Nano | 2011 Dec 27 |
| Detection of circulating tumor cells in human peripheral blood using surface-enhanced Raman scattering nanoparticles. | Wang X, Qian X, Beitler JJ, Chen ZG, Khuri FR, Lewis MM, Shin HJ, Nie S, Shin DM | Cancer research | 21212408 | Cancer Res | 2011 Mar 1 |
| Intraoperative Molecular Imaging of Lung Adenocarcinoma Can Identify Residual Tumor Cells at the Surgical Margins. | Keating JJ, Okusanya OT, De Jesus E, Judy R, Jiang J, Deshpande C, Nie S, Low P, Singhal S | Molecular imaging and biology | 26228697 | Mol Imaging Biol | 2016 Apr |
| SERS Nanoparticles in Medicine: From Label-Free Detection to Spectroscopic Tagging. | Lane LA, Qian X, Nie S | Chemical reviews | 26313254 | Chem Rev | 2015 Oct 14 |
| Stimuli-responsive nanoparticles for targeting the tumor microenvironment. | Du J, Lane LA, Nie S | Journal of controlled release : official journal of the Controlled Release Society | 26341694 | J Control Release | 2015 Dec 10 |
| Intraoperative Spectroscopy with Ultrahigh Sensitivity for Image-Guided Surgery of Malignant Brain Tumors. | Kairdolf BA, Bouras A, Kaluzova M, Sharma AK, Wang MD, Hadjipanayis CG, Nie S | Analytical chemistry | 26587976 | Anal Chem | 2016 Jan 5 |
| Near-infrared Intraoperative Molecular Imaging Can Identify Metastatic Lymph Nodes in Prostate Cancer. | Xia L, Zeh R, Mizelle J, Newton A, Predina J, Nie S, Singhal S, Guzzo TJ | Urology | 28438626 | Urology | 2017 Aug |
| Detection of blur artifacts in histopathological whole-slide images of endomyocardial biopsies. | Hang Wu, Phan JH, Bhatia AK, Cundiff CA, Shehata BM, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26736365 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 |
| The More Exotic Shapes of Semiconductor Nanocrystals: Emerging Applications in Bioimaging. | Lim SJ, Smith A, Nie S | Current opinion in chemical engineering | 24982823 | Curr Opin Chem Eng | 2014 May 1 |
| Intraoperative near-infrared imaging can identify pulmonary nodules. | Okusanya OT, Holt D, Heitjan D, Deshpande C, Venegas O, Jiang J, Judy R, DeJesus E, Madajewski B, Oh K, Wang M, Albelda SM, Nie S, Singhal S | The Annals of thoracic surgery | 25106680 | Ann Thorac Surg | 2014 Oct |
| Intraoperative imaging identifies thymoma margins following neoadjuvant chemotherapy. | Keating JJ, Nims S, Venegas O, Jiang J, Holt D, Kucharczuk JC, Deshpande C, Singhal S | Oncotarget | 26689990 | Oncotarget | 2016 Jan 19 |
| Deep learning based feature-level integration of multi-omics data for breast cancer patients survival analysis. | Tong L, Mitchel J, Chatlin K, Wang MD | BMC medical informatics and decision making | 32933515 | BMC Med Inform Decis Mak | 2020 Sep 15 |
| Anchoring molecular chromophores to colloidal gold nanocrystals: surface-enhanced Raman evidence for strong electronic coupling and irreversible structural locking. | Qian X, Emory SR, Nie S | Journal of the American Chemical Society | 22257217 | J Am Chem Soc | 2012 Feb 1 |
| uPAR-targeted optical imaging contrasts as theranostic agents for tumor margin detection. | Yang L, Sajja HK, Cao Z, Qian W, Bender L, Marcus AI, Lipowska M, Wood WC, Wang YA | Theranostics | 24396518 | Theranostics | 2013 |
| Eliminating tissue-fold artifacts in histopathological whole-slide images for improved image-based prediction of cancer grade. | Kothari S, Phan JH, Wang MD | Journal of pathology informatics | 24083057 | J Pathol Inform | 2013 |
| Micro-Inversions In Human Cancer Genomes. | Qu L, Zhu H, Wang M | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 30440635 | Annu Int Conf IEEE Eng Med Biol Soc | 2018 Jul |
| Combination of an Integrin-Targeting NIR Tracer and an Ultrasensitive Spectroscopic Device for Intraoperative Detection of Head and Neck Tumor Margins and Metastatic Lymph Nodes. | Yoon Y, Mohs AM, Mancini MC, Nie S, Shim H | Tomography (Ann Arbor, Mich.) | 27738656 | Tomography | 2016 Sep |
| Development of Receptor Targeted Magnetic Iron Oxide Nanoparticles for Efficient Drug Delivery and Tumor Imaging. | Yang L, Cao Z, Sajja HK, Mao H, Wang L, Geng H, Xu H, Jiang T, Wood WC, Nie S, Wang YA | Journal of biomedical nanotechnology | 25152701 | J Biomed Nanotechnol | 2008 Dec 1 |
| Compact and blinking-suppressed quantum dots for single-particle tracking in live cells. | Lane LA, Smith AM, Lian T, Nie S | The journal of physical chemistry. B | 25157589 | J Phys Chem B | 2014 Dec 11 |
| Pathology imaging informatics for quantitative analysis of whole-slide images. | Kothari S, Phan JH, Stokes TH, Wang MD | Journal of the American Medical Informatics Association : JAMIA | 23959844 | J Am Med Inform Assoc | 2013 Nov-Dec |
| Targeted Drug Delivery and Image-Guided Therapy of Heterogeneous Ovarian Cancer Using HER2-Targeted Theranostic Nanoparticles. | Satpathy M, Wang L, Zielinski RJ, Qian W, Wang YA, Mohs AM, Kairdolf BA, Ji X, Capala J, Lipowska M, Nie S, Mao H, Yang L | Theranostics | 30809308 | Theranostics | 2019 |
| Predicting Heart Rejection Using Histopathological Whole-Slide Imaging and Deep Neural Network with Dropout. | Tong L, Hoffman R, Deshpande SR, Wang MD | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 32601619 | IEEE EMBS Int Conf Biomed Health Inform | 2017 Feb |
| Prediction of Heart Transplant Rejection Using Histopathological Whole-Slide Imaging. | Dooley AE, Tong L, Deshpande SR, Wang MD | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 32551442 | IEEE EMBS Int Conf Biomed Health Inform | 2018 Mar |
| A Novel Temporal Similarity Measure for Patients Based on Irregularly Measured Data in Electronic Health Records. | Sha Y, Venugopalan J, Wang MD | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 32577627 | ACM BCB | 2016 Oct |
| Near-infrared operating lamp for intraoperative molecular imaging of a mediastinal tumor. | Keating J, Judy R, Newton A, Singhal S | BMC medical imaging | 26883511 | BMC Med Imaging | 2016 Feb 17 |
| Semiconductor quantum dots for bioimaging and biodiagnostic applications. | Kairdolf BA, Smith AM, Stokes TH, Wang MD, Young AN, Nie S | Annual review of analytical chemistry (Palo Alto, Calif.) | 23527547 | Annu Rev Anal Chem (Palo Alto Calif) | 2013 |
| Theranostic nanoparticles with controlled release of gemcitabine for targeted therapy and MRI of pancreatic cancer. | Lee GY, Qian WP, Wang L, Wang YA, Staley CA, Satpathy M, Nie S, Mao H, Yang L | ACS nano | 23402593 | ACS Nano | 2013 Mar 26 |
| Feasibility of multiplex quantum dot stain using primary antibodies from four distinct host animals. | Tran JK, Hubbard EN, Stokes TH, Moffitt RA, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 23367436 | Annu Int Conf IEEE Eng Med Biol Soc | 2012 |
| Histological image classification using biologically interpretable shape-based features. | Kothari S, Phan JH, Young AN, Wang MD | BMC medical imaging | 23497380 | BMC Med Imaging | 2013 Mar 13 |
| Improving Personalized Clinical Risk Prediction Based on Causality-Based Association Rules. | Cheng CW, Wang MD | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 27532063 | ACM BCB | 2015 Sep |
| Models for Predicting Stage in Head and Neck Squamous Cell Carcinoma Using Proteomic and Transcriptomic Data. | Kaddi CD, Wang MD | IEEE journal of biomedical and health informatics | 26462248 | IEEE J Biomed Health Inform | 2017 Jan |
| Comparison of RNA-seq and microarray-based models for clinical endpoint prediction. | Zhang W, Yu Y, Hertwig F, Thierry-Mieg J, Zhang W, Thierry-Mieg D, Wang J, Furlanello C, Devanarayan V, Cheng J, Deng Y, Hero B, Hong H, Jia M, Li L, Lin SM, Nikolsky Y, Oberthuer A, Qing T, Su Z, Volland R, Wang C, Wang MD, Ai J, Albanese D, Asgharzadeh S, Avigad S, Bao W, Bessarabova M, Brilliant MH, Brors B, Chierici M, Chu TM, Zhang J, Grundy RG, He MM, Hebbring S, Kaufman HL, Lababidi S, Lancashire LJ, Li Y, Lu XX, Luo H, Ma X, Ning B, Noguera R, Peifer M, Phan JH, Roels F, Rosswog C, Shao S, Shen J, Theissen J, Tonini GP, Vandesompele J, Wu PY, Xiao W, Xu J, Xu W, Xuan J, Yang Y, Ye Z, Dong Z, Zhang KK, Yin Y, Zhao C, Zheng Y, Wolfinger RD, Shi T, Malkas LH, Berthold F, Wang J, Tong W, Shi L, Peng Z, Fischer M | Genome biology | 26109056 | Genome Biol | 2015 Jun 25 |
| Intraoperative molecular imaging can identify lung adenocarcinomas during pulmonary resection. | Okusanya OT, DeJesus EM, Jiang JX, Judy RP, Venegas OG, Deshpande CG, Heitjan DF, Nie S, Low PS, Singhal S | The Journal of thoracic and cardiovascular surgery | 26126457 | J Thorac Cardiovasc Surg | 2015 Jul |
| Molecular imaging to identify tumor recurrence following chemoradiation in a hostile surgical environment. | Okusanya OT, Deshpande C, Barbosa EM Jr, Aggarwal C, Simone CB 2nd, Jiang J, Judy R, DeJesus E, Albelda S, Nie S, Low PS, Singhal S | Molecular imaging | 25442640 | Mol Imaging | 2014 |
| Variance Regularized Counterfactual Risk Minimizationvia Variational Divergence Minimization. | Wu H, Wang MD | Proceedings of machine learning research | 32789292 | Proc Mach Learn Res | 2018 |
| InterVisAR: An Interactive Visualization for Association Rule Search. | Cheng CW, Sha Y, Wang MD | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 32789305 | ACM BCB | 2016 Oct |
| Intraoperative near-infrared imaging can distinguish cancer from normal tissue but not inflammation. | Holt D, Okusanya O, Judy R, Venegas O, Jiang J, DeJesus E, Eruslanov E, Quatromoni J, Bhojnagarwala P, Deshpande C, Albelda S, Nie S, Singhal S | PloS one | 25072388 | PLoS One | 2014 |
| Removing batch effects from histopathological images for enhanced cancer diagnosis. | Kothari S, Phan JH, Stokes TH, Osunkoya AO, Young AN, Wang MD | IEEE journal of biomedical and health informatics | 24808220 | IEEE J Biomed Health Inform | 2014 May |
| Small portable interchangeable imager of fluorescence for fluorescence guided surgery and research. | Okusanya OT, Madajewski B, Segal E, Judy BF, Venegas OG, Judy RP, Quatromoni JG, Wang MD, Nie S, Singhal S | Technology in cancer research & treatment | 24354756 | Technol Cancer Res Treat | 2015 Apr |
| Targeted delivery of siRNA-generating DNA nanocassettes using multifunctional nanoparticles. | Cho YS, Lee GY, Sajja HK, Qian W, Cao Z, He W, Karna P, Chen X, Mao H, Wang YA, Yang L | Small (Weinheim an der Bergstrasse, Germany) | 23292656 | Small | 2013 Jun 10 |
| Local recurrence following lung cancer surgery: incidence, risk factors, and outcomes. | Fedor D, Johnson WR, Singhal S | Surgical oncology | 23702313 | Surg Oncol | 2013 Sep |
| Impact of RNA-seq data analysis algorithms on gene expression estimation and downstream prediction. | Tong L, Wu PY, Phan JH, Hassazadeh HR, SEQC Consortium, Tong W, Wang MD | Scientific reports | 33087762 | Sci Rep | 2020 Oct 21 |
| Bioconjugated Nanoparticles for Biosensing, in Vivo Imaging, and Medical Diagnostics. | Kairdolf BA, Qian X, Nie S | Analytical chemistry | 28043119 | Anal Chem | 2017 Jan 17 |
| icuARM-II: improving the reliability of personalized risk prediction in pediatric intensive care units. | Cheng CW, Chanani N, Maher K, Wang | ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine | 27532061 | ACM BCB | 2014 Sep |
| A High-Resolution Tile-Based Approach for Classifying Biological Regions in Whole-Slide Histopathological Images. | Hoffman RA, Kothari S, Phan JH, Wang MD | IFMBE proceedings | 27532012 | IFMBE Proc | 2014 |
| Intraoperative Near-infrared Imaging Can Identify Neoplasms and Aid in Real-time Margin Assessment During Pancreatic Resection. | Newton AD, Predina JD, Shin MH, Frenzel-Sulyok LG, Vollmer CM, Drebin JA, Singhal S, Lee MK 4th | Annals of surgery | 31188797 | Ann Surg | 2019 Jul |
| Physical chemistry of nanomedicine: understanding the complex behaviors of nanoparticles in vivo. | Lane LA, Qian X, Smith AM, Nie S | Annual review of physical chemistry | 25622189 | Annu Rev Phys Chem | 2015 Apr |
| An integrated widefield imaging and spectroscopy system for contrast-enhanced, image-guided resection of tumors. | Mohs AM, Mancini MC, Provenzale JM, Saba CF, Cornell KK, Howerth EW, Nie S | IEEE transactions on bio-medical engineering | 25585410 | IEEE Trans Biomed Eng | 2015 May |
| Intraoperative near-infrared fluorescence imaging and spectroscopy identifies residual tumor cells in wounds. | Holt D, Parthasarathy AB, Okusanya O, Keating J, Venegas O, Deshpande C, Karakousis G, Madajewski B, Durham A, Nie S, Yodh AG, Singhal S | Journal of biomedical optics | 26160347 | J Biomed Opt | 2015 Jul |
| Integrating multi-omics data by learning modality invariant representations for improved prediction of overall survival of cancer. | Tong L, Wu H, Wang MD | Methods (San Diego, Calif.) | 32763377 | Methods | 2021 May |
| Emergence of two near-infrared windows for in vivo and intraoperative SERS. | Lane LA, Xue R, Nie S | Current opinion in chemical biology | 29631122 | Curr Opin Chem Biol | 2018 Aug |
| Exploration of Genomic, Proteomic, and Histopathological Image Data Integration Methods for Clinical Prediction. | Poruthoor A, Phan JH, Kothari S, Wang MD | IEEE China Summit & International Conference on Signal and Information Processing. IEEE China Summit & International Conference on Signal and Information Processing | 28393144 | IEEE China Summit Int Conf Signal Inf Process | 2013 Jul |
| Comparison of Folate Receptor Targeted Optical Contrast Agents for Intraoperative Molecular Imaging. | De Jesus E, Keating JJ, Kularatne SA, Jiang J, Judy R, Predina J, Nie S, Low P, Singhal S | International journal of molecular imaging | 26491562 | Int J Mol Imaging | 2015 |
| CAESNet: Convolutional AutoEncoder based Semi-supervised Network for improving multiclass classification of endomicroscopic images. | Tong L, Wu H, Wang MD | Journal of the American Medical Informatics Association : JAMIA | 31260038 | J Am Med Inform Assoc | 2019 Nov 1 |
| A fast least-squares algorithm for population inference. | Parry RM, Wang MD | BMC bioinformatics | 23343408 | BMC Bioinformatics | 2013 Jan 23 |
| Mapping the spatial distribution of charge carriers in quantum-confined heterostructures. | Smith AM, Lane LA, Nie S | Nature communications | 25080298 | Nat Commun | 2014 Jul 31 |
| Compact quantum dots for single-molecule imaging. | Smith AM, Nie S | Journal of visualized experiments : JoVE | 23093375 | J Vis Exp | 2012 Oct 9 |
| Intraoperative near-infrared imaging of surgical wounds after tumor resections can detect residual disease. | Madajewski B, Judy BF, Mouchli A, Kapoor V, Holt D, Wang MD, Nie S, Singhal S | Clinical cancer research : an official journal of the American Association for Cancer Research | 22932668 | Clin Cancer Res | 2012 Oct 15 |
| Integrating image analysis algorithms in a web interface for the quantification of microtubule dynamics. | Kong KY, Marcus AI, Giannakakou P, Wang MD | International journal of computational biology and drug design | 23013655 | Int J Comput Biol Drug Des | 2012 |
| Scale normalization of histopathological images for batch invariant cancer diagnostic models. | Kothari S, Phan JH, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 23366904 | Annu Int Conf IEEE Eng Med Biol Soc | 2012 |
| -Omic and Electronic Health Record Big Data Analytics for Precision Medicine. | Wu PY, Cheng CW, Kaddi CD, Venugopalan J, Hoffman R, Wang MD | IEEE transactions on bio-medical engineering | 27740470 | IEEE Trans Biomed Eng | 2017 Feb |
| Near-Infrared Intraoperative Molecular Imaging Can Locate Metastases to the Lung. | Keating J, Newton A, Venegas O, Nims S, Zeh R, Predina J, Deshpande C, Kucharczuk J, Nie S, Delikatny EJ, Singhal S | The Annals of thoracic surgery | 27793401 | Ann Thorac Surg | 2017 Feb |
| PEPCOR - A Risk Prediction Model for Pediatric Intensive Care Units Utilizing Ventilator Days and Length of Stay. | Pethiyagoda T, Chanani N, Cheng C, Wang MD | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 28164175 | IEEE EMBS Int Conf Biomed Health Inform | 2016 Feb |
| MotifMark: Finding regulatory motifs in DNA sequences. | Hassanzadeh HR, Kolhe P, Isbell CL, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 29060747 | Annu Int Conf IEEE Eng Med Biol Soc | 2017 Jul |
| Near-infrared imaging and optical coherence tomography for intraoperative visualization of tumors. | Holt D, Singhal S, Selmic LE | Veterinary surgery : VS | 31609011 | Vet Surg | 2020 Jan |
| Improved Prediction on Heart Transplant Rejection Using Convolutional Autoencoder and Multiple Instance Learning on Whole-Slide Imaging. | Zhu Y, Wang MD, Tong L, Deshpande SR | ... IEEE-EMBS International Conference on Biomedical and Health Informatics. IEEE-EMBS International Conference on Biomedical and Health Informatics | 32577622 | IEEE EMBS Int Conf Biomed Health Inform | 2019 May |
| Emerging technologies and their impact on regulatory science. | Anklam E, Bahl MI, Ball R, Beger RD, Cohen J, Fitzpatrick S, Girard P, Halamoda-Kenzaoui B, Hinton D, Hirose A, Hoeveler A, Honma M, Hugas M, Ishida S, Kass GE, Kojima H, Krefting I, Liachenko S, Liu Y, Masters S, Marx U, McCarthy T, Mercer T, Patri A, Pelaez C, Pirmohamed M, Platz S, Ribeiro AJ, Rodricks JV, Rusyn I, Salek RM, Schoonjans R, Silva P, Svendsen CN, Sumner S, Sung K, Tagle D, Tong L, Tong W, Eijnden-van-Raaij JVD, Vary N, Wang T, Waterton J, Wang M, Wen H, Wishart D, Yuan Y, Slikker W Jr | Experimental biology and medicine (Maywood, N.J.) | 34783606 | Exp Biol Med (Maywood) | 2022 Jan |
| An optimized disaggregation method for human lung tumors that preserves the phenotype and function of the immune cells. | Quatromoni JG, Singhal S, Bhojnagarwala P, Hancock WW, Albelda SM, Eruslanov E | Journal of leukocyte biology | 25359999 | J Leukoc Biol | 2015 Jan |
| Tumor-associated neutrophils stimulate T cell responses in early-stage human lung cancer. | Eruslanov EB, Bhojnagarwala PS, Quatromoni JG, Stephen TL, Ranganathan A, Deshpande C, Akimova T, Vachani A, Litzky L, Hancock WW, Conejo-Garcia JR, Feldman M, Albelda SM, Singhal S | The Journal of clinical investigation | 25384214 | J Clin Invest | 2014 Dec |
| Smart Superstructures with Ultrahigh pH-Sensitivity for Targeting Acidic Tumor Microenvironment: Instantaneous Size Switching and Improved Tumor Penetration. | Li HJ, Du JZ, Liu J, Du XJ, Shen S, Zhu YH, Wang X, Ye X, Nie S, Wang J | ACS nano | 27244096 | ACS Nano | 2016 Jul 26 |
| CD38-Expressing Myeloid-Derived Suppressor Cells Promote Tumor Growth in a Murine Model of Esophageal Cancer. | Karakasheva TA, Waldron TJ, Eruslanov E, Kim SB, Lee JS, O'Brien S, Hicks PD, Basu D, Singhal S, Malavasi F, Rustgi AK | Cancer research | 26294209 | Cancer Res | 2015 Oct 1 |
| Effect of low-expression gene filtering on detection of differentially expressed genes in RNA-seq data. | Sha Y, Phan JH, Wang MD | Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference | 26737772 | Annu Int Conf IEEE Eng Med Biol Soc | 2015 |
| Integration of multimodal RNA-seq data for prediction of kidney cancer survival. | Schwartzi M, Parkl M, Phanl JH, Wang MD | Proceedings. IEEE International Conference on Bioinformatics and Biomedicine | 27532026 | Proceedings (IEEE Int Conf Bioinformatics Biomed) | 2015 Nov |
| Mechanism by which a recently discovered allosteric inhibitor blocks glutamine metabolism in transformed cells. | Stalnecker CA, Ulrich SM, Li Y, Ramachandran S, McBrayer MK, DeBerardinis RJ, Cerione RA, Erickson JW | Proceedings of the National Academy of Sciences of the United States of America | 25548170 | Proc Natl Acad Sci U S A | 2015 Jan 13 |
| Tissue stiffness regulates serine/arginine-rich protein-mediated splicing of the extra domain B-fibronectin isoform in tumors. | Bordeleau F, Califano JP, Negrón Abril YL, Mason BN, LaValley DJ, Shin SJ, Weiss RS, Reinhart-King CA | Proceedings of the National Academy of Sciences of the United States of America | 26106154 | Proc Natl Acad Sci U S A | 2015 Jul 7 |
| Growth pattern analysis of murine lung neoplasms by advanced semi-automated quantification of micro-CT images. | Li M, Jirapatnakul A, Biancardi A, Riccio ML, Weiss RS, Reeves AP | PloS one | 24376755 | PLoS One | 2013 |
| Assessment of SIRT2 Inhibitors in Mouse Models of Cancer. | Negrón Abril YL, Fernández I, Weiss RS | Methods in molecular biology (Clifton, N.J.) | 31087297 | Methods Mol Biol | 2019 |
| Mechanistic Basis of Glutaminase Activation: A KEY ENZYME THAT PROMOTES GLUTAMINE METABOLISM IN CANCER CELLS. | Li Y, Erickson JW, Stalnecker CA, Katt WP, Huang Q, Cerione RA, Ramachandran S | The Journal of biological chemistry | 27542409 | J Biol Chem | 2016 Sep 30 |
| A SIRT2-Selective Inhibitor Promotes c-Myc Oncoprotein Degradation and Exhibits Broad Anticancer Activity. | Jing H, Hu J, He B, Negrón Abril YL, Stupinski J, Weiser K, Carbonaro M, Chiang YL, Southard T, Giannakakou P, Weiss RS, Lin H | Cancer cell | 26977881 | Cancer Cell | 2016 Mar 14 |
| Metabolic characterization of a Sirt5 deficient mouse model. | Yu J, Sadhukhan S, Noriega LG, Moullan N, He B, Weiss RS, Lin H, Schoonjans K, Auwerx J | Scientific reports | 24076663 | Sci Rep | 2013 Sep 30 |
| Therapeutic strategies impacting cancer cell glutamine metabolism. | Lukey MJ, Wilson KF, Cerione RA | Future medicinal chemistry | 24047273 | Future Med Chem | 2013 Sep |
| The oncogenic transcription factor c-Jun regulates glutaminase expression and sensitizes cells to glutaminase-targeted therapy. | Lukey MJ, Greene KS, Erickson JW, Wilson KF, Cerione RA | Nature communications | 27089238 | Nat Commun | 2016 Apr 18 |
| Sirtuin inhibitors as anticancer agents. | Hu J, Jing H, Lin H | Future medicinal chemistry | 24962284 | Future Med Chem | 2014 May |
| Pharmacological and genetic perturbation establish SIRT5 as a promising target in breast cancer. | Abril YLN, Fernandez IR, Hong JY, Chiang YL, Kutateladze DA, Zhao Q, Yang M, Hu J, Sadhukhan S, Li B, He B, Remick B, Bai JJ, Mullmann J, Wang F, Maymi V, Dhawan R, Auwerx J, Southard T, Cerione RA, Lin H, Weiss RS | Oncogene | 33479498 | Oncogene | 2021 Mar |
| Matrix stiffening promotes a tumor vasculature phenotype. | Bordeleau F, Mason BN, Lollis EM, Mazzola M, Zanotelli MR, Somasegar S, Califano JP, Montague C, LaValley DJ, Huynh J, Mencia-Trinchant N, Negrón Abril YL, Hassane DC, Bonassar LJ, Butcher JT, Weiss RS, Reinhart-King CA | Proceedings of the National Academy of Sciences of the United States of America | 28034921 | Proc Natl Acad Sci U S A | 2017 Jan 17 |
| Metabolomics-assisted proteomics identifies succinylation and SIRT5 as important regulators of cardiac function. | Sadhukhan S, Liu X, Ryu D, Nelson OD, Stupinski JA, Li Z, Chen W, Zhang S, Weiss RS, Locasale JW, Auwerx J, Lin H | Proceedings of the National Academy of Sciences of the United States of America | 27051063 | Proc Natl Acad Sci U S A | 2016 Apr 19 |
| The bicyclic intermediate structure provides insights into the desuccinylation mechanism of human sirtuin 5 (SIRT5). | Zhou Y, Zhang H, He B, Du J, Lin H, Cerione RA, Hao Q | The Journal of biological chemistry | 22767592 | J Biol Chem | 2012 Aug 17 |
| Protein lysine acylation and cysteine succination by intermediates of energy metabolism. | Lin H, Su X, He B | ACS chemical biology | 22571489 | ACS Chem Biol | 2012 Jun 15 |
| Targeting the undruggable: immunotherapy meets personalized oncology in the genomic era. | Martin SD, Coukos G, Holt RA, Nelson BH | Annals of oncology : official journal of the European Society for Medical Oncology | 26371284 | Ann Oncol | 2015 Dec |
| Development, optimization, and validation of novel anti-TEM1/CD248 affinity agent for optical imaging in cancer. | Li C, Wang J, Hu J, Feng Y, Hasegawa K, Peng X, Duan X, Zhao A, Mikitsh JL, Muzykantov VR, Chacko AM, Pryma DA, Dunn SM, Coukos G | Oncotarget | 25051365 | Oncotarget | 2014 Aug 30 |
| Antibody-based tumor vascular theranostics targeting endosialin/TEM1 in a new mouse tumor vascular model. | Li C, Chacko AM, Hu J, Hasegawa K, Swails J, Grasso L, El-Deiry WS, Nicolaides N, Muzykantov VR, Divgi CR, Coukos G | Cancer biology & therapy | 24553243 | Cancer Biol Ther | 2014 Apr |
| Tumor endothelium FasL establishes a selective immune barrier promoting tolerance in tumors. | Motz GT, Santoro SP, Wang LP, Garrabrant T, Lastra RR, Hagemann IS, Lal P, Feldman MD, Benencia F, Coukos G | Nature medicine | 24793239 | Nat Med | 2014 Jun |
| T cells bearing a chimeric antigen receptor against prostate-specific membrane antigen mediate vascular disruption and result in tumor regression. | Santoro SP, Kim S, Motz GT, Alatzoglou D, Li C, Irving M, Powell DJ Jr, Coukos G | Cancer immunology research | 25358763 | Cancer Immunol Res | 2015 Jan |
| Mass spectrometry-based antigen discovery for cancer immunotherapy. | Bassani-Sternberg M, Coukos G | Current opinion in immunology | 27155075 | Curr Opin Immunol | 2016 Aug |
| Shikonin-loaded antibody-armed nanoparticles for targeted therapy of ovarian cancer. | Matthaiou EI, Barar J, Sandaltzopoulos R, Li C, Coukos G, Omidi Y | International journal of nanomedicine | 24790428 | Int J Nanomedicine | 2014 |
| Deciphering and reversing tumor immune suppression. | Motz GT, Coukos G | Immunity | 23890064 | Immunity | 2013 Jul 25 |
| Targeting the tumor vasculature to enhance T cell activity. | Lanitis E, Irving M, Coukos G | Current opinion in immunology | 25665467 | Curr Opin Immunol | 2015 Apr |
| T-cell and NK-cell infiltration into solid tumors: a key limiting factor for efficacious cancer immunotherapy. | Melero I, Rouzaut A, Motz GT, Coukos G | Cancer discovery | 24795012 | Cancer Discov | 2014 May |
| Development of 124I immuno-PET targeting tumor vascular TEM1/endosialin. | Chacko AM, Li C, Nayak M, Mikitsh JL, Hu J, Hou C, Grasso L, Nicolaides NC, Muzykantov VR, Divgi CR, Coukos G | Journal of nuclear medicine : official publication, Society of Nuclear Medicine | 24525208 | J Nucl Med | 2014 Mar |
| Interrogating open issues in cancer precision medicine with patient-derived xenografts. | Byrne AT, Alférez DG, Amant F, Annibali D, Arribas J, Biankin AV, Bruna A, Budinská E, Caldas C, Chang DK, Clarke RB, Clevers H, Coukos G, Dangles-Marie V, Eckhardt SG, Gonzalez-Suarez E, Hermans E, Hidalgo M, Jarzabek MA, de Jong S, Jonkers J, Kemper K, Lanfrancone L, Mælandsmo GM, Marangoni E, Marine JC, Medico E, Norum JH, Palmer HG, Peeper DS, Pelicci PG, Piris-Gimenez A, Roman-Roman S, Rueda OM, Seoane J, Serra V, Soucek L, Vanhecke D, Villanueva A, Vinolo E, Bertotti A, Trusolino L | Nature reviews. Cancer | 28104906 | Nat Rev Cancer | 2017 Apr |
| Combine and Conquer: Double CTLA-4 and PD-1 Blockade Combined with Whole Tumor Antigen Vaccine Cooperate to Eradicate Tumors. | Homicsko K, Duraiswamy J, Doucey MA, Coukos G | Cancer research | 27909064 | Cancer Res | 2016 Dec 1 |
| Correction to: Characterization of the first fully human anti-TEM1 scFv in models of solid tumor imaging and immunotoxin-based therapy. | Yuan X, Yang M, Chen X, Zhang X, Sukhadia S, Musolino N, Bao H, Chen T, Xu C, Wang Q, Santoro S, Ricklin D, Hu J, Lin R, Yang W, Li Z, Qin W, Zhao A, Scholler N, Coukos G | Cancer immunology, immunotherapy : CII | 29313073 | Cancer Immunol Immunother | 2018 Feb |
| A fusion-protein approach enabling mammalian cell production of tumor targeting protein domains for therapeutic development. | Hu J, Chen X, Zhang X, Yuan X, Yang M, Dai H, Yang W, Zhou Q, Wen W, Wang Q, Qin W, Zhao A | Protein science : a publication of the Protein Society | 29500915 | Protein Sci | 2018 May |
| Tumour endothelial marker 1/endosialin-mediated targeting of human sarcoma. | Guo Y, Hu J, Wang Y, Peng X, Min J, Wang J, Matthaiou E, Cheng Y, Sun K, Tong X, Fan Y, Zhang PJ, Kandalaft LE, Irving M, Coukos G, Li C | European journal of cancer (Oxford, England : 1990) | 29304474 | Eur J Cancer | 2018 Feb |
| Targeted chromatin profiling reveals novel enhancers in Ig H and Ig L chain Loci. | Predeus AV, Gopalakrishnan S, Huang Y, Tang J, Feeney AJ, Oltz EM, Artyomov MN | Journal of immunology (Baltimore, Md. : 1950) | 24353267 | J Immunol | 2014 Feb 1 |
| Loss of synergistic transcriptional feedback loops drives diverse B-cell cancers. | Andrews JM, Pyfrom SC, Schmidt JA, Koues OI, Kowalewski RA, Grams NR, Sun JJ, Berman LR, Duncavage EJ, Lee YS, Cashen AF, Oltz EM, Payton JE | EBioMedicine | 34461601 | EBioMedicine | 2021 Sep |
| Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. | Gu J, Stevens M, Xing X, Li D, Zhang B, Payton JE, Oltz EM, Jarvis JN, Jiang K, Cicero T, Costello JF, Wang T | G3 (Bethesda, Md.) | 26888867 | G3 (Bethesda) | 2016 Apr 7 |
| Targeted epigenetic repression of a lymphoma oncogene by sequence-specific histone modifiers induces apoptosis in DLBCL. | Luo H, Schmidt JA, Lee YS, Oltz EM, Payton JE | Leukemia & lymphoma | 27268204 | Leuk Lymphoma | 2017 Feb |
| NKG2D-NKG2D Ligand Interaction Inhibits the Outgrowth of Naturally Arising Low-Grade B Cell Lymphoma In Vivo. | Raju S, Kretzmer LZ, Koues OI, Payton JE, Oltz EM, Cashen A, Polic B, Schreiber RD, Shaw AS, Markiewicz MA | Journal of immunology (Baltimore, Md. : 1950) | 27183590 | J Immunol | 2016 Jun 1 |
| cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer Independent. | Huang Y, Koues OI, Zhao JY, Liu R, Pyfrom SC, Payton JE, Oltz EM | Cell reports | 28329684 | Cell Rep | 2017 Mar 21 |
| Two forms of loops generate the chromatin conformation of the immunoglobulin heavy-chain gene locus. | Guo C, Gerasimova T, Hao H, Ivanova I, Chakraborty T, Selimyan R, Oltz EM, Sen R | Cell | 21982154 | Cell | 2011 Oct 14 |
| Unifying model for molecular determinants of the preselection Vβ repertoire. | Gopalakrishnan S, Majumder K, Predeus A, Huang Y, Koues OI, Verma-Gaur J, Loguercio S, Su AI, Feeney AJ, Artyomov MN, Oltz EM | Proceedings of the National Academy of Sciences of the United States of America | 23918392 | Proc Natl Acad Sci U S A | 2013 Aug 20 |
| Short-Circuiting Gene Regulatory Networks: Origins of B Cell Lymphoma. | Koues OI, Oltz EM, Payton JE | Trends in genetics : TIG | 26604030 | Trends Genet | 2015 Dec |
| Enhancer sequence variants and transcription-factor deregulation synergize to construct pathogenic regulatory circuits in B-cell lymphoma. | Koues OI, Kowalewski RA, Chang LW, Pyfrom SC, Schmidt JA, Luo H, Sandoval LE, Hughes TB, Bednarski JJ, Cashen AF, Payton JE, Oltz EM | Immunity | 25607463 | Immunity | 2015 Jan 20 |
| BCALM (AC099524.1) Is a Human B Lymphocyte-Specific Long Noncoding RNA That Modulates B Cell Receptor-Mediated Calcium Signaling. | Pyfrom SC, Quinn CC, Dorando HK, Luo H, Payton JE | Journal of immunology (Baltimore, Md. : 1950) | 32571842 | J Immunol | 2020 Aug 1 |
| PLAIDOH: a novel method for functional prediction of long non-coding RNAs identifies cancer-specific LncRNA activities. | Pyfrom SC, Luo H, Payton JE | BMC genomics | 30767760 | BMC Genomics | 2019 Feb 15 |
| Human hemato-lymphoid system mice: current use and future potential for medicine. | Rongvaux A, Takizawa H, Strowig T, Willinger T, Eynon EE, Flavell RA, Manz MG | Annual review of immunology | 23330956 | Annu Rev Immunol | 2013 |
| Development and function of human innate immune cells in a humanized mouse model. | Rongvaux A, Willinger T, Martinek J, Strowig T, Gearty SV, Teichmann LL, Saito Y, Marches F, Halene S, Palucka AK, Manz MG, Flavell RA | Nature biotechnology | 24633240 | Nat Biotechnol | 2014 Apr |
| Type II NKT-TFH cells against Gaucher lipids regulate B-cell immunity and inflammation. | Nair S, Boddupalli CS, Verma R, Liu J, Yang R, Pastores GM, Mistry PK, Dhodapkar MV | Blood | 25499455 | Blood | 2015 Feb 19 |
| inv(16) and NPM1mut AMLs engraft human cytokine knock-in mice. | Ellegast JM, Rauch PJ, Kovtonyuk LV, Müller R, Wagner U, Saito Y, Wildner-Verhey van Wijk N, Fritz C, Rafiei A, Lysenko V, Dudkiewicz E, Theocharides AP, Soldini D, Goede JS, Flavell RA, Manz MG | Blood | 27581357 | Blood | 2016 Oct 27 |
| Microenvironment-dependent growth of preneoplastic and malignant plasma cells in humanized mice. | Das R, Strowig T, Verma R, Koduru S, Hafemann A, Hopf S, Kocoglu MH, Borsotti C, Zhang L, Branagan A, Eynon E, Manz MG, Flavell RA, Dhodapkar MV | Nature medicine | 27723723 | Nat Med | 2016 Nov |
| BRAFV 600E or mutant MAP2K1 human CD34+ cells establish Langerhans cell-like histiocytosis in immune-deficient mice. | Rafiei A, Wilk CM, Helbling PM, Myburgh R, Saito Y, Haralambieva E, Soldini D, Chakraborty R, Merad M, Allen CE, Nombela-Arrieta C, Manz MG | Blood advances | 33035332 | Blood Adv | 2020 Oct 13 |
| Humanized hemato-lymphoid system mice. | Theocharides AP, Rongvaux A, Fritsch K, Flavell RA, Manz MG | Haematologica | 26721800 | Haematologica | 2016 Jan |
| A highly efficient and faithful MDS patient-derived xenotransplantation model for pre-clinical studies. | Song Y, Rongvaux A, Taylor A, Jiang T, Tebaldi T, Balasubramanian K, Bagale A, Terzi YK, Gbyli R, Wang X, Fu X, Gao Y, Zhao J, Podoltsev N, Xu M, Neparidze N, Wong E, Torres R, Bruscia EM, Kluger Y, Manz MG, Flavell RA, Halene S | Nature communications | 30664659 | Nat Commun | 2019 Jan 21 |
| Nanoparticle-mediated combinatorial targeting of multiple human dendritic cell (DC) subsets leads to enhanced T cell activation via IL-15-dependent DC crosstalk. | Sehgal K, Ragheb R, Fahmy TM, Dhodapkar MV, Dhodapkar KM | Journal of immunology (Baltimore, Md. : 1950) | 25080481 | J Immunol | 2014 Sep 1 |
| Peripheral blood CD34(+) cells efficiently engraft human cytokine knock-in mice. | Saito Y, Ellegast JM, Rafiei A, Song Y, Kull D, Heikenwalder M, Rongvaux A, Halene S, Flavell RA, Manz MG | Blood | 27543436 | Blood | 2016 Oct 6 |
| Clonal Immunoglobulin against Lysolipids in the Origin of Myeloma. | Nair S, Branagan AR, Liu J, Boddupalli CS, Mistry PK, Dhodapkar MV | The New England journal of medicine | 26863356 | N Engl J Med | 2016 Feb 11 |
| Targeting human dendritic cells in situ to improve vaccines. | Sehgal K, Dhodapkar KM, Dhodapkar MV | Immunology letters | 25072116 | Immunol Lett | 2014 Nov |
| A novel humanized mouse model with significant improvement of class-switched, antigen-specific antibody production. | Yu H, Borsotti C, Schickel JN, Zhu S, Strowig T, Eynon EE, Frleta D, Gurer C, Murphy AJ, Yancopoulos GD, Meffre E, Manz MG, Flavell RA | Blood | 28077418 | Blood | 2017 Feb 23 |
| A pilot test of the acceptability and efficacy of narrative and non-narrative health education materials in a low health literacy population. | Moran MB, Frank LB, Chatterjee JS, Murphy ST, Baezconde-Garbanati L | Journal of communication in healthcare | 27872657 | J Commun Healthc | 2016 |
| Narrative versus Non-narrative: The Role of Identification, Transportation and Emotion in Reducing Health Disparities. | Murphy ST, Frank LB, Chatterjee JS, Baezconde-Garbanati L | The Journal of communication | 24347679 | J Commun | 2013 Feb |
| Reducing the Excess Burden of Cervical Cancer Among Latinas: Translating Science into Health Promotion Initiatives. | Baezconde-Garbanati L, Murphy ST, Moran MB, Cortessis VK | Californian journal of health promotion | 24587769 | Calif J Health Promot | 2013 |
| Portrayals of reproductive and sexual health on prime-time television. | Pariera KL, Hether HJ, Murphy ST, Buffington Sde C, Baezconde-Garbanati L | Health communication | 24156468 | Health Commun | 2014 |
| The Ability of Narrative Communication to Address Health-related Social Norms. | Moran MB, Murphy ST, Frank L, Baezconde-Garbanati L | International Review of Social Research | 24179677 | Int Rev Soc Res | 2013 Feb |
| Public Diplomacy in Prime Time: Exploring the Potential of Entertainment Education in International Public Diplomacy. | Murphy ST, Hether HJ, Felt LJ, de Castro Buffington S | American journal of media psychology | 24489980 | Am J Media Psychol | 2012 |
| Implementation of HPV vaccination guidelines in a diverse population in Los Angeles: Results from an environmental scan of local HPV resources and needs. | Baezconde-Garbanati L, Lienemann BA, Robles M, Johnson E, Sanchez K, Singhal R, Steinberg J, Jaque JM, Pentz MA, Gruber S | Vaccine | 28774559 | Vaccine | 2017 Sep 5 |
| Using a Culturally Tailored Narrative to Increase Cervical Cancer Detection Among Spanish-Speaking Mexican-American Women. | Ochoa CY, Murphy ST, Frank LB, Baezconde-Garbanati LA | Journal of cancer education : the official journal of the American Association for Cancer Education | 31020621 | J Cancer Educ | 2020 Aug |
| Self-Construal as a Predictor of Korean American Women's Intention to Vaccinate Daughters against Human Papillomavirus. | Zhao N, Huh J, Murphy ST, Chatterjee JS, Baezconde-Garbanati L | Asian American journal of psychology | 25558309 | Asian Am J Psychol | 2014 Jan |
| Telling stories, saving lives: creating narrative health messages. | Frank LB, Murphy ST, Chatterjee JS, Moran MB, Baezconde-Garbanati L | Health communication | 25470440 | Health Commun | 2015 |
| Barriers and innovative interventions for early detection of cervical cancer. | Baezconde-Garbanati L, Agurto I, Gravitt PE, Luciani S, Murphy S, Ochoa C, Gallegos K, Barahona R, Rodríguez Y | Salud publica de Mexico | 31430087 | Salud Publica Mex | 2019 Jul-Aug |
| Information scanning and vaccine safety concerns among African American, Mexican American, and non-Hispanic White women. | Moran MB, Frank LB, Chatterjee JS, Murphy ST, Baezconde-Garbanati L | Patient education and counseling | 26321294 | Patient Educ Couns | 2016 Jan |
| Assessing impact of a community-based screening campaign to address social determinants of cervical cancer. | Po J, Bookstein A, Lee W, Barahona R, Baezconde-Garbanati L | JNCI cancer spectrum | 39888858 | JNCI Cancer Spectr | 2025 Jan 3 |
| Comparing the Relative Efficacy of Narrative vs Nonnarrative Health Messages in Reducing Health Disparities Using a Randomized Trial. | Murphy ST, Frank LB, Chatterjee JS, Moran MB, Zhao N, Amezola de Herrera P, Baezconde-Garbanati LA | American journal of public health | 25905845 | Am J Public Health | 2015 Oct |
| Each Medium Tells a Different Story: The Effect of Message Channel on Narrative Persuasion. | Walter N, Murphy ST, Frank LB, Baezconde-Garbanati L | Communication research reports : CRR | 30739986 | Commun Res Rep | 2017 |
| Susceptibility of Human Endogenous Retrovirus Type K to Reverse Transcriptase Inhibitors. | Contreras-Galindo R, Dube D, Fujinaga K, Kaplan MH, Markovitz DM | Journal of virology | 28931682 | J Virol | 2017 Dec 1 |
| Distinct splice variants and pathway enrichment in the cell-line models of aggressive human breast cancer subtypes. | Menon R, Im H, Zhang EY, Wu SL, Chen R, Snyder M, Hancock WS, Omenn GS | Journal of proteome research | 24111759 | J Proteome Res | 2014 Jan 3 |
| The strategy, organization, and progress of the HUPO Human Proteome Project. | Omenn GS | Journal of proteomics | 24145142 | J Proteomics | 2014 Apr 4 |
| Rapid molecular assays to study human centromere genomics. | Contreras-Galindo R, Fischer S, Saha AK, Lundy JD, Cervantes PW, Mourad M, Wang C, Qian B, Dai M, Meng F, Chinnaiyan A, Omenn GS, Kaplan MH, Markovitz DM | Genome research | 29141960 | Genome Res | 2017 Dec |
| Genomic flexibility of human endogenous retrovirus type K. | Dube D, Contreras-Galindo R, He S, King SR, Gonzalez-Hernandez MJ, Gitlin SD, Kaplan MH, Markovitz DM | Journal of virology | 24920813 | J Virol | 2014 Sep 1 |
| "Reverse genomics" and human endogenous retroviruses. | Markovitz DM | Transactions of the American Clinical and Climatological Association | 25125718 | Trans Am Clin Climatol Assoc | 2014 |
| Expression of human endogenous retrovirus type K (HML-2) is activated by the Tat protein of HIV-1. | Gonzalez-Hernandez MJ, Swanson MD, Contreras-Galindo R, Cookinham S, King SR, Noel RJ Jr, Kaplan MH, Markovitz DM | Journal of virology | 22593154 | J Virol | 2012 Aug |
| Discovery of selective bioactive small molecules by targeting an RNA dynamic ensemble. | Stelzer AC, Frank AT, Kratz JD, Swanson MD, Gonzalez-Hernandez MJ, Lee J, Andricioaei I, Markovitz DM, Al-Hashimi HM | Nature chemical biology | 21706033 | Nat Chem Biol | 2011 Jun 26 |
| Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity. | Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, André S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM | Cell | 26496612 | Cell | 2015 Oct 22 |
| Expansion of a novel endogenous retrovirus throughout the pericentromeres of modern humans. | Zahn J, Kaplan MH, Fischer S, Dai M, Meng F, Saha AK, Cervantes P, Chan SM, Dube D, Omenn GS, Markovitz DM, Contreras-Galindo R | Genome biology | 25886262 | Genome Biol | 2015 Apr 12 |
| Human Endogenous Retrovirus Type K (HERV-K) Particles Package and Transmit HERV-K-Related Sequences. | Contreras-Galindo R, Kaplan MH, Dube D, Gonzalez-Hernandez MJ, Chan S, Meng F, Dai M, Omenn GS, Gitlin SD, Markovitz DM | Journal of virology | 25926654 | J Virol | 2015 Jul |
| Regulation of the human endogenous retrovirus K (HML-2) transcriptome by the HIV-1 Tat protein. | Gonzalez-Hernandez MJ, Cavalcoli JD, Sartor MA, Contreras-Galindo R, Meng F, Dai M, Dube D, Saha AK, Gitlin SD, Omenn GS, Kaplan MH, Markovitz DM | Journal of virology | 24872592 | J Virol | 2014 Aug |
| The Genomic Landscape of Centromeres in Cancers. | Saha AK, Mourad M, Kaplan MH, Chefetz I, Malek SN, Buckanovich R, Markovitz DM, Contreras-Galindo R | Scientific reports | 31375789 | Sci Rep | 2019 Aug 2 |
| HIV infection reveals widespread expansion of novel centromeric human endogenous retroviruses. | Contreras-Galindo R, Kaplan MH, He S, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Kappes F, Dube D, Chan SM, Robinson D, Meng F, Dai M, Gitlin SD, Chinnaiyan AM, Omenn GS, Markovitz DM | Genome research | 23657884 | Genome Res | 2013 Sep |
| Human endogenous retrovirus K Gag coassembles with HIV-1 Gag and reduces the release efficiency and infectivity of HIV-1. | Monde K, Contreras-Galindo R, Kaplan MH, Markovitz DM, Ono A | Journal of virology | 22855497 | J Virol | 2012 Oct |
| Metrics for the Human Proteome Project 2013-2014 and strategies for finding missing proteins. | Lane L, Bairoch A, Beavis RC, Deutsch EW, Gaudet P, Lundberg E, Omenn GS | Journal of proteome research | 24364385 | J Proteome Res | 2014 Jan 3 |
| Strategies for Genomic and Proteomic Profiling of Cancers. | Omenn GS | Statistics in biosciences | 27594925 | Stat Biosci | 2016 Jun |
| Characterization of human endogenous retroviral elements in the blood of HIV-1-infected individuals. | Contreras-Galindo R, Kaplan MH, Contreras-Galindo AC, Gonzalez-Hernandez MJ, Ferlenghi I, Giusti F, Lorenzo E, Gitlin SD, Dosik MH, Yamamura Y, Markovitz DM | Journal of virology | 22031938 | J Virol | 2012 Jan |
| A new class of protein cancer biomarker candidates: differentially expressed splice variants of ERBB2 (HER2/neu) and ERBB1 (EGFR) in breast cancer cell lines. | Omenn GS, Guan Y, Menon R | Journal of proteomics | 24802673 | J Proteomics | 2014 Jul 31 |
| Innovations in proteomic profiling of cancers: alternative splice variants as a new class of cancer biomarker candidates and bridging of proteomics with structural biology. | Omenn GS, Menon R, Zhang Y | Journal of proteomics | 23603631 | J Proteomics | 2013 Sep 2 |
| NGSQC: cross-platform quality analysis pipeline for deep sequencing data. | Dai M, Thompson RC, Maher C, Contreras-Galindo R, Kaplan MH, Markovitz DM, Omenn G, Meng F | BMC genomics | 21143816 | BMC Genomics | 2010 Dec 2 |
| Genetic Variants in Epigenetic Pathways and Risks of Multiple Cancers in the GAME-ON Consortium. | Toth R, Scherer D, Kelemen LE, Risch A, Hazra A, Balavarca Y, Issa JJ, Moreno V, Eeles RA, Ogino S, Wu X, Ye Y, Hung RJ, Goode EL, Ulrich CM, OCAC, CORECT, TRICL, ELLIPSE, DRIVE, and GAME-ON consortia | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 28115406 | Cancer Epidemiol Biomarkers Prev | 2017 Jun |
| Identifying Novel Susceptibility Genes for Colorectal Cancer Risk From a Transcriptome-Wide Association Study of 125,478 Subjects. | Guo X, Lin W, Wen W, Huyghe J, Bien S, Cai Q, Harrison T, Chen Z, Qu C, Bao J, Long J, Yuan Y, Wang F, Bai M, Abecasis GR, Albanes D, Berndt SI, Bézieau S, Bishop DT, Brenner H, Buch S, Burnett-Hartman A, Campbell PT, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Cho SH, Conti DV, Chapelle A, Feskens EJM, Gallinger SJ, Giles GG, Goodman PJ, Gsur A, Guinter M, Gunter MJ, Hampe J, Hampel H, Hayes RB, Hoffmeister M, Kampman E, Kang HM, Keku TO, Kim HR, Le Marchand L, Lee SC, Li CI, Li L, Lindblom A, Lindor N, Milne RL, Moreno V, Murphy N, Newcomb PA, Nickerson DA, Offit K, Pearlman R, Pharoah PDP, Platz EA, Potter JD, Rennert G, Sakoda LC, Schafmayer C, Schmit SL, Schoen RE, Schumacher FR, Slattery ML, Su YR, Tangen CM, Ulrich CM, van Duijnhoven FJB, Van Guelpen B, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Wang X, White E, Wolk A, Woods MO, Casey G, Hsu L, Jenkins MA, Gruber SB, Peters U, Zheng W | Gastroenterology | 33058866 | Gastroenterology | 2021 Mar |
| Nonadditive Effects of Common Genetic Variants Have a Negligent Contribution to Cancer Heritability. | Hammermeister Suger A, Harrison TA, Henning B, Turman C, Kraft P, Lindström S | Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology | 39018351 | Cancer Epidemiol Biomarkers Prev | 2024 Oct 2 |
| A Germline Variant on Chromosome 4q31.1 Associates with Susceptibility to Developing Colon Cancer Metastasis. | Markowitz SD, Nock NL, Schmit SL, Stadler ZK, Joseph V, Zhang L, Willis JE, Scacheri P, Veigl M, Adams MD, Raskin L, Sullivan JF, Stratton K, Shia J, Ellis N, Rennert HS, Manschreck C, Li L, Offit K, Elston RC, Rennert G, Gruber SB | PloS one | 26751797 | PLoS One | 2016 |
| Novel Common Genetic Susceptibility Loci for Colorectal Cancer. | Schmit SL, Edlund CK, Schumacher FR, Gong J, Harrison TA, Huyghe JR, Qu C, Melas M, Van Den Berg DJ, Wang H, Tring S, Plummer SJ, Albanes D, Alonso MH, Amos CI, Anton K, Aragaki AK, Arndt V, Barry EL, Berndt SI, Bezieau S, Bien S, Bloomer A, Boehm J, Boutron-Ruault MC, Brenner H, Brezina S, Buchanan DD, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castelao JE, Chan AT, Chang-Claude J, Chanock SJ, Cheng I, Cheng YW, Chin LS, Church JM, Church T, Coetzee GA, Cotterchio M, Cruz Correa M, Curtis KR, Duggan D, Easton DF, English D, Feskens EJM, Fischer R, FitzGerald LM, Fortini BK, Fritsche LG, Fuchs CS, Gago-Dominguez M, Gala M, Gallinger SJ, Gauderman WJ, Giles GG, Giovannucci EL, Gogarten SM, Gonzalez-Villalpando C, Gonzalez-Villalpando EM, Grady WM, Greenson JK, Gsur A, Gunter M, Haiman CA, Hampe J, Harlid S, Harju JF, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Huang SC, Huerta JM, Hudson TJ, Hunter DJ, Idos GE, Iwasaki M, Jackson RD, Jacobs EJ, Jee SH, Jenkins MA, Jia WH, Jiao S, Joshi AD, Kolonel LN, Kono S, Kooperberg C, Krogh V, Kuehn T, Küry S, LaCroix A, Laurie CA, Lejbkowicz F, Lemire M, Lenz HJ, Levine D, Li CI, Li L, Lieb W, Lin Y, Lindor NM, Liu YR, Loupakis F, Lu Y, Luh F, Ma J, Mancao C, Manion FJ, Markowitz SD, Martin V, Matsuda K, Matsuo K, McDonnell KJ, McNeil CE, Milne R, Molina AJ, Mukherjee B, Murphy N, Newcomb PA, Offit K, Omichessan H, Palli D, Cotoré JPP, Pérez-Mayoral J, Pharoah PD, Potter JD, Qu C, Raskin L, Rennert G, Rennert HS, Riggs BM, Schafmayer C, Schoen RE, Sellers TA, Seminara D, Severi G, Shi W, Shibata D, Shu XO, Siegel EM, Slattery ML, Southey M, Stadler ZK, Stern MC, Stintzing S, Taverna D, Thibodeau SN, Thomas DC, Trichopoulou A, Tsugane S, Ulrich CM, van Duijnhoven FJB, van Guelpan B, Vijai J, Virtamo J, Weinstein SJ, White E, Win AK, Wolk A, Woods M, Wu AH, Wu K, Xiang YB, Yen Y, Zanke BW, Zeng YX, Zhang B, Zubair N, Kweon SS, Figueiredo JC, Zheng W, Marchand LL, Lindblom A, Moreno V, Peters U, Casey G, Hsu L, Conti DV, Gruber SB | Journal of the National Cancer Institute | 29917119 | J Natl Cancer Inst | 2019 Feb 1 |
| Shared heritability and functional enrichment across six solid cancers. | Jiang X, Finucane HK, Schumacher FR, Schmit SL, Tyrer JP, Han Y, Michailidou K, Lesseur C, Kuchenbaecker KB, Dennis J, Conti DV, Casey G, Gaudet MM, Huyghe JR, Albanes D, Aldrich MC, Andrew AS, Andrulis IL, Anton-Culver H, Antoniou AC, Antonenkova NN, Arnold SM, Aronson KJ, Arun BK, Bandera EV, Barkardottir RB, Barnes DR, Batra J, Beckmann MW, Benitez J, Benlloch S, Berchuck A, Berndt SI, Bickeböller H, Bien SA, Blomqvist C, Boccia S, Bogdanova NV, Bojesen SE, Bolla MK, Brauch H, Brenner H, Brenton JD, Brook MN, Brunet J, Brunnström H, Buchanan DD, Burwinkel B, Butzow R, Cadoni G, Caldés T, Caligo MA, Campbell I, Campbell PT, Cancel-Tassin G, Cannon-Albright L, Campa D, Caporaso N, Carvalho AL, Chan AT, Chang-Claude J, Chanock SJ, Chen C, Christiani DC, Claes KBM, Claessens F, Clements J, Collée JM, Correa MC, Couch FJ, Cox A, Cunningham JM, Cybulski C, Czene K, Daly MB, deFazio A, Devilee P, Diez O, Gago-Dominguez M, Donovan JL, Dörk T, Duell EJ, Dunning AM, Dwek M, Eccles DM, Edlund CK, Edwards DRV, Ellberg C, Evans DG, Fasching PA, Ferris RL, Liloglou T, Figueiredo JC, Fletcher O, Fortner RT, Fostira F, Franceschi S, Friedman E, Gallinger SJ, Ganz PA, Garber J, García-Sáenz JA, Gayther SA, Giles GG, Godwin AK, Goldberg MS, Goldgar DE, Goode EL, Goodman MT, Goodman G, Grankvist K, Greene MH, Gronberg H, Gronwald J, Guénel P, Håkansson N, Hall P, Hamann U, Hamdy FC, Hamilton RJ, Hampe J, Haugen A, Heitz F, Herrero R, Hillemanns P, Hoffmeister M, Høgdall E, Hong YC, Hopper JL, Houlston R, Hulick PJ, Hunter DJ, Huntsman DG, Idos G, Imyanitov EN, Ingles SA, Isaacs C, Jakubowska A, James P, Jenkins MA, Johansson M, Johansson M, John EM, Joshi AD, Kaneva R, Karlan BY, Kelemen LE, Kühl T, Khaw KT, Khusnutdinova E, Kibel AS, Kiemeney LA, Kim J, Kjaer SK, Knight JA, Kogevinas M, Kote-Jarai Z, Koutros S, Kristensen VN, Kupryjanczyk J, Lacko M, Lam S, Lambrechts D, Landi MT, Lazarus P, Le ND, Lee E, Lejbkowicz F, Lenz HJ, Leslie G, Lessel D, Lester J, Levine DA, Li L, Li CI, Lindblom A, Lindor NM, Liu G, Loupakis F, Lubiński J, Maehle L, Maier C, Mannermaa A, Marchand LL, Margolin S, May T, McGuffog L, Meindl A, Middha P, Miller A, Milne RL, MacInnis RJ, Modugno F, Montagna M, Moreno V, Moysich KB, Mucci L, Muir K, Mulligan AM, Nathanson KL, Neal DE, Ness AR, Neuhausen SL, Nevanlinna H, Newcomb PA, Newcomb LF, Nielsen FC, Nikitina-Zake L, Nordestgaard BG, Nussbaum RL, Offit K, Olah E, Olama AAA, Olopade OI, Olshan AF, Olsson H, Osorio A, Pandha H, Park JY, Pashayan N, Parsons MT, Pejovic T, Penney KL, Peters WHM, Phelan CM, Phipps AI, Plaseska-Karanfilska D, Pring M, Prokofyeva D, Radice P, Stefansson K, Ramus SJ, Raskin L, Rennert G, Rennert HS, van Rensburg EJ, Riggan MJ, Risch HA, Risch A, Roobol MJ, Rosenstein BS, Rossing MA, De Ruyck K, Saloustros E, Sandler DP, Sawyer EJ, Schabath MB, Schleutker J, Schmidt MK, Setiawan VW, Shen H, Siegel EM, Sieh W, Singer CF, Slattery ML, Sorensen KD, Southey MC, Spurdle AB, Stanford JL, Stevens VL, Stintzing S, Stone J, Sundfeldt K, Sutphen R, Swerdlow AJ, Tajara EH, Tangen CM, Tardon A, Taylor JA, Teare MD, Teixeira MR, Terry MB, Terry KL, Thibodeau SN, Thomassen M, Bjørge L, Tischkowitz M, Toland AE, Torres D, Townsend PA, Travis RC, Tung N, Tworoger SS, Ulrich CM, Usmani N, Vachon CM, Van Nieuwenhuysen E, Vega A, Aguado-Barrera ME, Wang Q, Webb PM, Weinberg CR, Weinstein S, Weissler MC, Weitzel JN, West CML, White E, Whittemore AS, Wichmann HE, Wiklund F, Winqvist R, Wolk A, Woll P, Woods M, Wu AH, Wu X, Yannoukakos D, Zheng W, Zienolddiny S, Ziogas A, Zorn KK, Lane JM, Saxena R, Thomas D, Hung RJ, Diergaarde B, McKay J, Peters U, Hsu L, García-Closas M, Eeles RA, Chenevix-Trench G, Brennan PJ, Haiman CA, Simard J, Easton DF, Gruber SB, Pharoah PDP, Price AL, Pasaniuc B, Amos CI, Kraft P, Lindström S | Nature communications | 30683880 | Nat Commun | 2019 Jan 25 |
| IgG-seq identifies immune-reactive enteric bacteria in Crohn's disease with spondyloarthritis. | Maldarelli GA, Metz M, Oguntunmibi S, Tran N, Xiang G, Lukin D, Scherl EJ, Longman RS | Gut microbes | 39949039 | Gut Microbes | 2025 Dec |
| Integrative detection of genome-wide translation using iRibo. | Turcan A, Lee J, Wacholder A, Carvunis AR | STAR protocols | 38217852 | STAR Protoc | 2024 Mar 15 |
| GitHub is an effective platform for collaborative and reproducible laboratory research. | Chen KY, Toro-Moreno M, Subramaniam AR | ArXiv | 39990799 | ArXiv | 2025 Feb 10 |
| GitHub enables collaborative and reproducible laboratory research. | Chen KY, Toro-Moreno M, Subramaniam AR | PLoS biology | 39951468 | PLoS Biol | 2025 Feb |
| Immunopeptidomics for autoimmunity: unlocking the chamber of immune secrets. | Arshad S, Cameron B, Joglekar AV | NPJ systems biology and applications | 39833247 | NPJ Syst Biol Appl | 2025 Jan 17 |
| High-quality peptide evidence for annotating non-canonical open reading frames as human proteins. | Deutsch EW, Kok LW, Mudge JM, Ruiz-Orera J, Fierro-Monti I, Sun Z, Abelin JG, Alba MM, Aspden JL, Bazzini AA, Bruford EA, Brunet MA, Calviello L, Carr SA, Carvunis AR, Chothani S, Clauwaert J, Dean K, Faridi P, Frankish A, Hubner N, Ingolia NT, Magrane M, Martin MJ, Martinez TF, Menschaert G, Ohler U, Orchard S, Rackham O, Roucou X, Slavoff SA, Valen E, Wacholder A, Weissman JS, Wu W, Xie Z, Choudhary J, Bassani-Sternberg M, Vizcaíno JA, Ternette N, Moritz RL, Prensner JR, van Heesch S | bioRxiv : the preprint server for biology | 39314370 | bioRxiv | 2024 Sep 9 |
| Single-cell massively-parallel multiplexed microbial sequencing (M3-seq) identifies rare bacterial populations and profiles phage infection. | Wang B, Lin AE, Yuan J, Novak KE, Koch MD, Wingreen NS, Adamson B, Gitai Z | Nature microbiology | 37653008 | Nat Microbiol | 2023 Oct |
| Pseudomonas aeruginosa modulates both Caenorhabditis elegans attraction and pathogenesis by regulating nitrogen assimilation. | Marogi JG, Murphy CT, Myhrvold C, Gitai Z | Nature communications | 39256376 | Nat Commun | 2024 Sep 10 |
| Pseudomonas fluorescens 15 small RNA Pfs1 mediates transgenerational epigenetic inheritance of pathogen avoidance in C. elegans through the Ephrin receptor VAB-1. | Seto R, Brown R, Kaletsky R, Parsons LR, Moore RS, Murphy CT | bioRxiv : the preprint server for biology | 38826453 | bioRxiv | 2024 May 23 |
| CeLab, a microfluidic platform for the study of life history traits, reveals metformin and SGK-1 regulation of longevity and reproductive span. | Sohrabi S, Cota V, Murphy CT | Lab on a chip | 37221962 | Lab Chip | 2023 Jun 13 |
| A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. | Sengupta T, St Ange J, Moore R, Kaletsky R, Marogi J, Myhrvold C, Gitai Z, Murphy CT | bioRxiv : the preprint server for biology | 37503135 | bioRxiv | 2023 Oct 17 |
| P. aeruginosa controls both C. elegans attraction and pathogenesis by regulating nitrogen assimilation. | Marogi JG, Murphy CT, Myhrvold C, Gitai Z | bioRxiv : the preprint server for biology | 38077073 | bioRxiv | 2023 Nov 29 |
| A natural bacterial pathogen of C. elegans uses a small RNA to induce transgenerational inheritance of learned avoidance. | Sengupta T, St Ange J, Kaletsky R, Moore RS, Seto RJ, Marogi J, Myhrvold C, Gitai Z, Murphy CT | PLoS genetics | 38547071 | PLoS Genet | 2024 Mar |
| A Critical Role for Fas-Mediated Off-Target Tumor Killing in T-cell Immunotherapy. | Upadhyay R, Boiarsky JA, Pantsulaia G, Svensson-Arvelund J, Lin MJ, Wroblewska A, Bhalla S, Scholler N, Bot A, Rossi JM, Sadek N, Parekh S, Lagana A, Baccarini A, Merad M, Brown BD, Brody JD | Cancer discovery | 33334730 | Cancer Discov | 2021 Mar |
| Spatial CRISPR genomics identifies regulators of the tumor microenvironment. | Dhainaut M, Rose SA, Akturk G, Wroblewska A, Nielsen SR, Park ES, Buckup M, Roudko V, Pia L, Sweeney R, Le Berichel J, Wilk CM, Bektesevic A, Lee BH, Bhardwaj N, Rahman AH, Baccarini A, Gnjatic S, Pe'er D, Merad M, Brown BD | Cell | 35290801 | Cell | 2022 Mar 31 |
| Pattern recognition receptor agonists in pathogen vaccines mediate antitumor T-cell cross-priming. | Aleynick M, Svensson-Arvelund J, Pantsulaia G, Kim K, Rose SA, Upadhyay R, Yellin M, Marsh H, Oreper D, Jhunjhunwala S, Moussion CC, Merad M, Brown BD, Brody JD | Journal for immunotherapy of cancer | 37487664 | J Immunother Cancer | 2023 Jul |
| Hepatic stellate cells maintain liver homeostasis through paracrine neurotrophin-3 signaling that induces hepatocyte proliferation. | Trinh VQ, Lee TF, Lemoinne S, Ray KC, Ybanez MD, Tsuchida T, Carter JK, Agudo J, Brown BD, Akat KM, Friedman SL, Lee YA | Science signaling | 37253090 | Sci Signal | 2023 May 30 |
| Ovarian cancer-derived IL-4 promotes immunotherapy resistance. | Mollaoglu G, Tepper A, Falcomatà C, Potak HT, Pia L, Amabile A, Mateus-Tique J, Rabinovich N, Park MD, LaMarche NM, Brody R, Browning L, Lin JR, Zamarin D, Sorger PK, Santagata S, Merad M, Baccarini A, Brown BD | Cell | 39481380 | Cell | 2024 Dec 26 |
| A microRNA expression and regulatory element activity atlas of the mouse immune system. | Rose SA, Wroblewska A, Dhainaut M, Yoshida H, Shaffer JM, Bektesevic A, Ben-Zvi B, Rhoads A, Kim EY, Yu B, Lavin Y, Merad M, Buenrostro JD, Brown BD, Immunological Genome Consortium | Nature immunology | 34099919 | Nat Immunol | 2021 Jul |
| Tissue-resident macrophages provide a pro-tumorigenic niche to early NSCLC cells. | Casanova-Acebes M, Dalla E, Leader AM, LeBerichel J, Nikolic J, Morales BM, Brown M, Chang C, Troncoso L, Chen ST, Sastre-Perona A, Park MD, Tabachnikova A, Dhainaut M, Hamon P, Maier B, Sawai CM, Agulló-Pascual E, Schober M, Brown BD, Reizis B, Marron T, Kenigsberg E, Moussion C, Benaroch P, Aguirre-Ghiso JA, Merad M | Nature | 34135508 | Nature | 2021 Jul |
| Lung-resident alveolar macrophages regulate the timing of breast cancer metastasis. | Dalla E, Papanicolaou M, Park MD, Barth N, Hou R, Segura-Villalobos D, Valencia Salazar L, Sun D, Forrest ARR, Casanova-Acebes M, Entenberg D, Merad M, Aguirre-Ghiso JA | Cell | 39378878 | Cell | 2024 Nov 14 |
| 3D reconstruction and standardization of the rat facial nucleus for precise mapping of vibrissal motor networks. | Guest JM, Seetharama MM, Wendel ES, Strick PL, Oberlaender M | Neuroscience | 28958919 | Neuroscience | 2018 Jan 1 |
| Ribbon scanning confocal for high-speed high-resolution volume imaging of brain. | Watson AM, Rose AH, Gibson GA, Gardner CL, Sun C, Reed DS, Lam LKM, St Croix CM, Strick PL, Klimstra WB, Watkins SC | PloS one | 28686653 | PLoS One | 2017 |
| Multiple areas of the cerebral cortex influence the stomach. | Levinthal DJ, Strick PL | Proceedings of the National Academy of Sciences of the United States of America | 32434910 | Proc Natl Acad Sci U S A | 2020 Jun 9 |
| Holographic Reconstruction of Axonal Pathways in the Human Brain. | Petersen MV, Mlakar J, Haber SN, Parent M, Smith Y, Strick PL, Griswold MA, McIntyre CC | Neuron | 31708306 | Neuron | 2019 Dec 18 |
| The Cortical Motor Areas and the Emergence of Motor Skills: A Neuroanatomical Perspective. | Strick PL, Dum RP, Rathelot JA | Annual review of neuroscience | 33863253 | Annu Rev Neurosci | 2021 Jul 8 |
| The mind-body problem: Circuits that link the cerebral cortex to the adrenal medulla. | Dum RP, Levinthal DJ, Strick PL | Proceedings of the National Academy of Sciences of the United States of America | 31871146 | Proc Natl Acad Sci U S A | 2019 Dec 26 |
| Semantic segmentation of microscopic neuroanatomical data by combining topological priors with encoder-decoder deep networks. | Banerjee S, Magee L, Wang D, Li X, Huo BX, Jayakumar J, Matho K, Lin MK, Ram K, Sivaprakasam M, Huang J, Wang Y, Mitra PP | Nature machine intelligence | 34604701 | Nat Mach Intell | 2020 Oct |
| Cortical basis for skilled vocalization. | Cerkevich CM, Rathelot JA, Strick PL | Proceedings of the National Academy of Sciences of the United States of America | 35507879 | Proc Natl Acad Sci U S A | 2022 May 10 |
| Population Density Modulates the Duration of Reproduction of C. elegans. | Wong SS, Yu J, Schroeder FC, Kim DH | Current biology : CB | 32442457 | Curr Biol | 2020 Jul 6 |
| Nematode signaling molecules derived from multimodular assembly of primary metabolic building blocks. | Yim JJ, Bose N, Meyer JM, Sommer RJ, Schroeder FC | Organic letters | 25782998 | Org Lett | 2015 Apr 3 |
| Plant metabolism of nematode pheromones mediates plant-nematode interactions. | Manohar M, Tenjo-Castano F, Chen S, Zhang YK, Kumari A, Williamson VM, Wang X, Klessig DF, Schroeder FC | Nature communications | 31924834 | Nat Commun | 2020 Jan 10 |
| Bite-size introduction to canine hematologic malignancies. | Atherton MJ, Mason NJ | Blood advances | 35316831 | Blood Adv | 2022 Jul 12 |
| Generation and Validation of an Antibody to Canine CD19 for Diagnostic and Future Therapeutic Purposes. | Haran KP, Lockhart A, Xiong A, Radaelli E, Savickas PJ, Posey A, Mason NJ | Veterinary pathology | 32081102 | Vet Pathol | 2020 Mar |
| Genetic re-direction of canine primary T cells for clinical trial use in pet dogs with spontaneous cancer. | Rotolo A, Atherton MJ, Kasper BT, Haran KP, Mason NJ | STAR protocols | 34746864 | STAR Protoc | 2021 Dec 17 |
| Redefining differentiation: Reshaping our ends. | Blau HM | Nature cell biology | 22643873 | Nat Cell Biol | 2012 May 30 |
| The central role of muscle stem cells in regenerative failure with aging. | Blau HM, Cosgrove BD, Ho AT | Nature medicine | 26248268 | Nat Med | 2015 Aug |
| Therapeutic Transdifferentiation: A Novel Approach for Ischemic Syndromes. | Connell JP, Kodali S, Cooke JP | Methodist DeBakey cardiovascular journal | 26634026 | Methodist Debakey Cardiovasc J | 2015 Jul-Sep |
| Human induced pluripotent stem cell-derived cardiomyocytes recapitulate the predilection of breast cancer patients to doxorubicin-induced cardiotoxicity. | Burridge PW, Li YF, Matsa E, Wu H, Ong SG, Sharma A, Holmström A, Chang AC, Coronado MJ, Ebert AD, Knowles JW, Telli ML, Witteles RM, Blau HM, Bernstein D, Altman RB, Wu JC | Nature medicine | 27089514 | Nat Med | 2016 May |
| Rejuvenation of the muscle stem cell population restores strength to injured aged muscles. | Cosgrove BD, Gilbert PM, Porpiglia E, Mourkioti F, Lee SP, Corbel SY, Llewellyn ME, Delp SL, Blau HM | Nature medicine | 24531378 | Nat Med | 2014 Mar |
| Humanizing the mdx mouse model of DMD: the long and the short of it. | Yucel N, Chang AC, Day JW, Rosenthal N, Blau HM | NPJ Regenerative medicine | 29479480 | NPJ Regen Med | 2018 |
| Bioengineering strategies to accelerate stem cell therapeutics. | Madl CM, Heilshorn SC, Blau HM | Nature | 29769665 | Nature | 2018 May |
| Increased tissue stiffness triggers contractile dysfunction and telomere shortening in dystrophic cardiomyocytes. | Chang ACY, Pardon G, Chang ACH, Wu H, Ong SG, Eguchi A, Ancel S, Holbrook C, Ramunas J, Ribeiro AJS, LaGory EL, Wang H, Koleckar K, Giaccia A, Mack DL, Childers MK, Denning C, Day JW, Wu JC, Pruitt BL, Blau HM | Stem cell reports | 34019816 | Stem Cell Reports | 2021 Sep 14 |
| A critical role for AID in the initiation of reprogramming to induced pluripotent stem cells. | Bhutani N, Decker MN, Brady JJ, Bussat RT, Burns DM, Corbel SY, Blau HM | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 23212122 | FASEB J | 2013 Mar |
| Tumor suppressors: enhancers or suppressors of regeneration? | Pomerantz JH, Blau HM | Development (Cambridge, England) | 23715544 | Development | 2013 Jun |
| Therapeutic angiogenesis due to balanced single-vector delivery of VEGF and PDGF-BB. | Banfi A, von Degenfeld G, Gianni-Barrera R, Reginato S, Merchant MJ, McDonald DM, Blau HM | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 22391130 | FASEB J | 2012 Jun |
| An In Vitro Model for Identifying Cardiac Side Effects of Anesthetics. | Chang ACY, Chang ACH, Nicin L, Weber GJ, Holbrook C, Davies MF, Blau HM, Bertaccini EJ | Anesthesia and analgesia | 30198930 | Anesth Analg | 2020 Jan |
| Prostaglandin E2 is essential for efficacious skeletal muscle stem-cell function, augmenting regeneration and strength. | Ho ATV, Palla AR, Blake MR, Yucel ND, Wang YX, Magnusson KEG, Holbrook CA, Kraft PE, Delp SL, Blau HM | Proceedings of the National Academy of Sciences of the United States of America | 28607093 | Proc Natl Acad Sci U S A | 2017 Jun 27 |
| Long telomeres protect against age-dependent cardiac disease caused by NOTCH1 haploinsufficiency. | Theodoris CV, Mourkioti F, Huang Y, Ranade SS, Liu L, Blau HM, Srivastava D | The Journal of clinical investigation | 28346225 | J Clin Invest | 2017 May 1 |
| Transient delivery of modified mRNA encoding TERT rapidly extends telomeres in human cells. | Ramunas J, Yakubov E, Brady JJ, Corbel SY, Holbrook C, Brandt M, Stein J, Santiago JG, Cooke JP, Blau HM | FASEB journal : official publication of the Federation of American Societies for Experimental Biology | 25614443 | FASEB J | 2015 May |
| Telomere shortening and metabolic compromise underlie dystrophic cardiomyopathy. | Chang AC, Ong SG, LaGory EL, Kraft PE, Giaccia AJ, Wu JC, Blau HM | Proceedings of the National Academy of Sciences of the United States of America | 27799523 | Proc Natl Acad Sci U S A | 2016 Nov 15 |
| Telomere shortening is a hallmark of genetic cardiomyopathies. | Chang ACY, Chang ACH, Kirillova A, Sasagawa K, Su W, Weber G, Lin J, Termglinchan V, Karakikes I, Seeger T, Dainis AM, Hinson JT, Seidman J, Seidman CE, Day JW, Ashley E, Wu JC, Blau HM | Proceedings of the National Academy of Sciences of the United States of America | 30150400 | Proc Natl Acad Sci U S A | 2018 Sep 11 |
| Modelling diastolic dysfunction in induced pluripotent stem cell-derived cardiomyocytes from hypertrophic cardiomyopathy patients. | Wu H, Yang H, Rhee JW, Zhang JZ, Lam CK, Sallam K, Chang ACY, Ma N, Lee J, Zhang H, Blau HM, Bers DM, Wu JC | European heart journal | 31219556 | Eur Heart J | 2019 Dec 1 |
| Telomerase Therapy to Reverse Cardiovascular Senescence. | Nazari-Shafti TZ, Cooke JP | Methodist DeBakey cardiovascular journal | 26634025 | Methodist Debakey Cardiovasc J | 2015 Jul-Sep |
| Direct evaluation of myocardial viability and stem cell engraftment demonstrates salvage of the injured myocardium. | Kim PJ, Mahmoudi M, Ge X, Matsuura Y, Toma I, Metzler S, Kooreman NG, Ramunas J, Holbrook C, McConnell MV, Blau H, Harnish P, Rulifson E, Yang PC | Circulation research | 25654979 | Circ Res | 2015 Mar 27 |
| Reversibility of Defective Hematopoiesis Caused by Telomere Shortening in Telomerase Knockout Mice. | Raval A, Behbehani GK, Nguyen le XT, Thomas D, Kusler B, Garbuzov A, Ramunas J, Holbrook C, Park CY, Blau H, Nolan GP, Artandi SE, Mitchell BS | PloS one | 26133370 | PLoS One | 2015 |
| Short telomeres - A hallmark of heritable cardiomyopathies. | Chang ACY, Blau HM | Differentiation; research in biological diversity | 29482077 | Differentiation | 2018 Mar-Apr |
| Cell-derived matrices for tissue engineering and regenerative medicine applications. | Fitzpatrick LE, McDevitt TC | Biomaterials science | 25530850 | Biomater Sci | 2015 Jan |
| Hydrolysis and Sulfation Pattern Effects on Release of Bioactive Bone Morphogenetic Protein-2 from Heparin-Based Microparticles. | Tellier LE, Miller T, McDevitt TC, Temenoff JS | Journal of materials chemistry. B | 27785363 | J Mater Chem B | 2015 Oct 28 |
| A rapid method for determining protein diffusion through hydrogels for regenerative medicine applications. | Hettiaratchi MH, Schudel A, Rouse T, García AJ, Thomas SN, Guldberg RE, McDevitt TC | APL bioengineering | 31069307 | APL Bioeng | 2018 Jun |
| Competitive Protein Binding Influences Heparin-Based Modulation of Spatial Growth Factor Delivery for Bone Regeneration. | Hettiaratchi MH, Chou C, Servies N, Smeekens JM, Cheng A, Esancy C, Wu R, McDevitt TC, Guldberg RE, Krishnan L | Tissue engineering. Part A | 28338419 | Tissue Eng Part A | 2017 Jul |
| Emerging strategies for spatiotemporal control of stem cell fate and morphogenesis. | Kinney MA, McDevitt TC | Trends in biotechnology | 23219200 | Trends Biotechnol | 2013 Feb |
| Microparticle-mediated sequestration of cell-secreted proteins to modulate chondrocytic differentiation. | Rinker TE, Philbrick BD, Hettiaratchi MH, Smalley DM, McDevitt TC, Temenoff JS | Acta biomaterialia | 29292168 | Acta Biomater | 2018 Mar 1 |
| Materials as stem cell regulators. | Murphy WL, McDevitt TC, Engler AJ | Nature materials | 24845994 | Nat Mater | 2014 Jun |
| Heparin microparticle effects on presentation and bioactivity of bone morphogenetic protein-2. | Hettiaratchi MH, Miller T, Temenoff JS, Guldberg RE, McDevitt TC | Biomaterials | 24881028 | Biomaterials | 2014 Aug |
| Engineering three-dimensional stem cell morphogenesis for the development of tissue models and scalable regenerative therapeutics. | Kinney MA, Hookway TA, Wang Y, McDevitt TC | Annals of biomedical engineering | 24297495 | Ann Biomed Eng | 2014 Feb |
| The effect of desulfation of chondroitin sulfate on interactions with positively charged growth factors and upregulation of cartilaginous markers in encapsulated MSCs. | Lim JJ, Temenoff JS | Biomaterials | 23570717 | Biomaterials | 2013 Jul |
| Molecular engineering of glycosaminoglycan chemistry for biomolecule delivery. | Miller T, Goude MC, McDevitt TC, Temenoff JS | Acta biomaterialia | 24121191 | Acta Biomater | 2014 Apr |
| Design Principles for Engineering of Tissues from Human Pluripotent Stem Cells. | Matthys OB, Hookway TA, McDevitt TC | Current stem cell reports | 27330934 | Curr Stem Cell Rep | 2016 Mar |
| Chondroitin sulfate microparticles modulate transforming growth factor-β1-induced chondrogenesis of human mesenchymal stem cell spheroids. | Goude MC, McDevitt TC, Temenoff JS | Cells, tissues, organs | 25413333 | Cells Tissues Organs | 2014 |
| Enhanced in vivo retention of low dose BMP-2 via heparin microparticle delivery does not accelerate bone healing in a critically sized femoral defect. | Hettiaratchi MH, Rouse T, Chou C, Krishnan L, Stevens HY, Li MA, McDevitt TC, Guldberg RE | Acta biomaterialia | 28645809 | Acta Biomater | 2017 Sep 1 |
| Heparin-mediated delivery of bone morphogenetic protein-2 improves spatial localization of bone regeneration. | Hettiaratchi MH, Krishnan L, Rouse T, Chou C, McDevitt TC, Guldberg RE | Science advances | 31922007 | Sci Adv | 2020 Jan |
| Skin autonomous antibody production regulates host-microbiota interactions. | Gribonika I, Band VI, Chi L, Perez-Chaparro PJ, Link VM, Ansaldo E, Oguz C, Bousbaine D, Fischbach MA, Belkaid Y | Nature | 39662506 | Nature | 2025 Feb |
| Immune recall improves antibody durability and breadth to SARS-CoV-2 variants. | Chen Y, Tong P, Whiteman N, Sanjari Moghaddam A, Zarghami M, Zuiani A, Habibi S, Gautam A, Keerti, Bi C, Xiao T, Cai Y, Chen B, Neuberg D, Wesemann DR | Science immunology | 35549298 | Sci Immunol | 2022 Dec 23 |
| Whence and wherefore IgE? | Rahman RS, Wesemann DR | Immunological reviews | 39041740 | Immunol Rev | 2024 Sep |
| Structural and functional impact by SARS-CoV-2 Omicron spike mutations. | Zhang J, Cai Y, Lavine CL, Peng H, Zhu H, Anand K, Tong P, Gautam A, Mayer ML, Rits-Volloch S, Wang S, Sliz P, Wesemann DR, Yang W, Seaman MS, Lu J, Xiao T, Chen B | Cell reports | 35452593 | Cell Rep | 2022 Apr 26 |
| Omicron's message on vaccines: Boosting begets breadth. | Wesemann DR | Cell | 35065712 | Cell | 2022 Feb 3 |
| Antibody-mediated SARS-CoV-2 entry in cultured cells. | Kibria MG, Lavine CL, Tang W, Wang S, Gao H, Shi W, Zhu H, Voyer J, Rits-Volloch S, Keerti, Bi C, Peng H, Wesemann DR, Lu J, Xie H, Seaman MS, Chen B | EMBO reports | 38277394 | EMBO Rep | 2023 Dec 6 |
| Germline-encoded amino acid-binding motifs drive immunodominant public antibody responses. | Shrock EL, Timms RT, Kula T, Mena EL, West AP Jr, Guo R, Lee IH, Cohen AA, McKay LGA, Bi C, Leng Y, Fujimura E, Horns F, Li M, Wesemann DR, Griffiths A, Gewurz BE, Bjorkman PJ, Elledge SJ | Science (New York, N.Y.) | 37023193 | Science | 2023 Apr 7 |
| Predicting differentially methylated cytosines in TET and DNMT3 knockout mutants via a large language model. | Sereshki S, Lonardi S | Briefings in bioinformatics | 40079264 | Brief Bioinform | 2025 Mar 4 |
| Babesia duncani multi-omics identifies virulence factors and drug targets. | Singh P, Lonardi S, Liang Q, Vydyam P, Khabirova E, Fang T, Gihaz S, Thekkiniath J, Munshi M, Abel S, Ciampossin L, Batugedara G, Gupta M, Lu XM, Lenz T, Chakravarty S, Cornillot E, Hu Y, Ma W, Gonzalez LM, Sánchez S, Estrada K, Sánchez-Flores A, Montero E, Harb OS, Le Roch KG, Mamoun CB | Nature microbiology | 37055610 | Nat Microbiol | 2023 May |
| Predicting Differentially Methylated Cytosines in TET and DNMT3 Knockout Mutants via a Large Language Model. | Sereshki S, Lonardi S | bioRxiv : the preprint server for biology | 39282350 | bioRxiv | 2024 Sep 4 |
| Machine learning in postgenomic biology and personalized medicine. | Ray A | Wiley interdisciplinary reviews. Data mining and knowledge discovery | 35966173 | Wiley Interdiscip Rev Data Min Knowl Discov | 2022 Mar-Apr |
| A single-administration therapeutic interfering particle reduces SARS-CoV-2 viral shedding and pathogenesis in hamsters. | Chaturvedi S, Beutler N, Vasen G, Pablo M, Chen X, Calia G, Buie L, Rodick R, Smith D, Rogers T, Weinberger LS | Proceedings of the National Academy of Sciences of the United States of America | 36074824 | Proc Natl Acad Sci U S A | 2022 Sep 27 |
| Identification of a therapeutic interfering particle-A single-dose SARS-CoV-2 antiviral intervention with a high barrier to resistance. | Chaturvedi S, Vasen G, Pablo M, Chen X, Beutler N, Kumar A, Tanner E, Illouz S, Rahgoshay D, Burnett J, Holguin L, Chen PY, Ndjamen B, Ott M, Rodick R, Rogers T, Smith DM, Weinberger LS | Cell | 34838159 | Cell | 2021 Dec 9 |
| Ingested (Oral) Adrenocorticotropic Hormone Inhibits IL-17 in the Central Nervous System in the Mouse Model of Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis. | Dittel LJ, Dittel BN, Brod SA | ImmunoHorizons | 35868840 | Immunohorizons | 2022 Jul 22 |
| Characterization of Definitive Regulatory B Cell Subsets by Cell Surface Phenotype, Function and Context. | Neu SD, Dittel BN | Frontiers in immunology | 34987513 | Front Immunol | 2021 |
| Gut IgA-antibody secreting cells segregate into four Blimp1+ subsets based on differential expression of IgA and Ki-67 and are retained following prolonged αCD20 B cell depletion in mice. | Neu SD, Gurski CJ, Meinhardt NJ, Jennings KC, Dittel BN | Journal of immunology (Baltimore, Md. : 1950) | 40073093 | J Immunol | 2025 Mar 5 |
| Conserved Gammaherpesvirus Protein Kinase Counters the Antiviral Effects of Myeloid Cell-Specific STAT1 Expression To Promote the Establishment of Splenic B Cell Latency. | Sylvester PA, Jondle CN, Stoltz KP, Lanham J, Dittel BN, Tarakanova VL | Journal of virology | 34132573 | J Virol | 2021 Aug 10 |
| Targeting transmembrane-domain-less MOG expression to platelets prevents disease development in experimental autoimmune encephalomyelitis. | Cai Y, Schroeder JA, Jing W, Gurski C, Williams CB, Wang S, Dittel BN, Shi Q | Frontiers in immunology | 36389708 | Front Immunol | 2022 |
| Myeloperoxidase Inhibition Ameliorates Plaque Psoriasis in Mice. | Neu SD, Strzepa A, Martin D, Sorci-Thomas MG, Pritchard KA Jr, Dittel BN | Antioxidants (Basel, Switzerland) | 34572970 | Antioxidants (Basel) | 2021 Aug 25 |
| T Cell-Specific STAT1 Expression Promotes Lytic Replication and Supports the Establishment of Gammaherpesvirus Latent Reservoir in Splenic B Cells. | Sylvester PA, Jondle CN, Schmalzriedt DL, Dittel BN, Tarakanova VL | mBio | 35968944 | mBio | 2022 Aug 30 |
| Myeloperoxidase as a Marker to Differentiate Mouse Monocyte/Macrophage Subsets. | Gurski CJ, Dittel BN | International journal of molecular sciences | 35897821 | Int J Mol Sci | 2022 Jul 26 |
| Negative Data, Oh No What Should I Do? How Publication of Negative Data Removes Roadblocks to Productive Research from the Perspective of Scientists Who Perform the Experiments. | Beltrame AK, Caldon JJ, Gurski CJ, Hajiyeva Z, Meinhardt NJ, Sommers KC, Neu SD, Dittel BN | ImmunoHorizons | 37252801 | Immunohorizons | 2023 May 1 |
| Stabilizing the return to normal behavior in an epidemic. | Berry T, Ferrari M, Sauer T, Greybush SJ, Ebeigbe D, Whalen AJ, Schiff SJ | medRxiv : the preprint server for health sciences | 36993470 | medRxiv | 2023 Oct 23 |
| Brain growth after surgical treatment for infant postinfectious hydrocephalus in Sub-Saharan Africa: 2-year results of a randomized trial. | Schiff SJ, Kulkarni AV, Mbabazi-Kabachelor E, Mugamba J, Ssenyonga P, Donnelly R, Levenbach J, Monga V, Peterson M, Cherukuri V, Warf BC | Journal of neurosurgery. Pediatrics | 34243157 | J Neurosurg Pediatr | 2021 Sep 1 |
| Paenibacillus spp infection among infants with postinfectious hydrocephalus in Uganda: an observational case-control study. | Morton SU, Hehnly C, Burgoine K, Ssentongo P, Ericson JE, Kumar MS, Hagmann C, Fronterre C, Smith J, Movassagh M, Streck N, Bebell LM, Bazira J, Kumbakumba E, Bajunirwe F, Mulondo R, Mbabazi-Kabachelor E, Nsubuga BK, Natukwatsa D, Nalule E, Magombe J, Erickson T, Ngonzi J, Ochora M, Olupot-Olupot P, Onen J, Ssenyonga P, Mugamba J, Warf BC, Kulkarni AV, Lane J, Whalen AJ, Zhang L, Sheldon K, Meier FA, Kiwanuka J, Broach JR, Paulson JN, Schiff SJ | The Lancet. Microbe | 37348522 | Lancet Microbe | 2023 Aug |
| The Problem of Microbial Dark Matter in Neonatal Sepsis. | Sinnar SA, Schiff SJ | Emerging infectious diseases | 33080169 | Emerg Infect Dis | 2020 Nov |
| Tracking and predicting the African COVID-19 pandemic. | Ssentongo P, Fronterre C, Geronimo A, Greybush SJ, Mbabazi PK, Muvawala J, Nahalamba SB, Omadi PO, Opar BT, Sinnar SA, Wang Y, Whalen AJ, Held L, Jewell C, Muwanguzi AJB, Greatrex H, Norton MM, Diggle P, Schiff SJ | medRxiv : the preprint server for health sciences | 33236036 | medRxiv | 2020 Nov 16 |
| Gun violence incidence during the COVID-19 pandemic is higher than before the pandemic in the United States. | Ssentongo P, Fronterre C, Ssentongo AE, Advani S, Heilbrunn ES, Hazelton JP, Oh JS, McCall-Hosenfeld JS, Chinchilli VM | Scientific reports | 34675321 | Sci Rep | 2021 Oct 21 |
| Engineering Principles and Bioengineering in Global Health. | Harper JR, Schiff SJ | Neurosurgery clinics of North America | 39244320 | Neurosurg Clin N Am | 2024 Oct |
| Vaginal microbiome topic modeling of laboring Ugandan women with and without fever. | Movassagh M, Bebell LM, Burgoine K, Hehnly C, Zhang L, Moran K, Sheldon K, Sinnar SA, Mbabazi-Kabachelor E, Kumbakumba E, Bazira J, Ochora M, Mulondo R, Nsubuga BK, Weeks AD, Gladstone M, Olupot-Olupot P, Ngonzi J, Roberts DJ, Meier FA, Irizarry RA, Broach JR, Schiff SJ, Paulson JN | NPJ biofilms and microbiomes | 34508087 | NPJ Biofilms Microbiomes | 2021 Sep 10 |
| Paenibacillus infection with frequent viral coinfection contributes to postinfectious hydrocephalus in Ugandan infants. | Paulson JN, Williams BL, Hehnly C, Mishra N, Sinnar SA, Zhang L, Ssentongo P, Mbabazi-Kabachelor E, Wijetunge DSS, von Bredow B, Mulondo R, Kiwanuka J, Bajunirwe F, Bazira J, Bebell LM, Burgoine K, Couto-Rodriguez M, Ericson JE, Erickson T, Ferrari M, Gladstone M, Guo C, Haran M, Hornig M, Isaacs AM, Kaaya BN, Kangere SM, Kulkarni AV, Kumbakumba E, Li X, Limbrick DD Jr, Magombe J, Morton SU, Mugamba J, Ng J, Olupot-Olupot P, Onen J, Peterson MR, Roy F, Sheldon K, Townsend R, Weeks AD, Whalen AJ, Quackenbush J, Ssenyonga P, Galperin MY, Almeida M, Atkins H, Warf BC, Lipkin WI, Broach JR, Schiff SJ | Science translational medicine | 32998967 | Sci Transl Med | 2020 Sep 30 |
| Neonatal Paenibacilliosis: Paenibacillus Infection as a Novel Cause of Sepsis in Term Neonates With High Risk of Sequelae in Uganda. | Ericson JE, Burgoine K, Kumbakumba E, Ochora M, Hehnly C, Bajunirwe F, Bazira J, Fronterre C, Hagmann C, Kulkarni AV, Kumar MS, Magombe J, Mbabazi-Kabachelor E, Morton SU, Movassagh M, Mugamba J, Mulondo R, Natukwatsa D, Kaaya BN, Olupot-Olupot P, Onen J, Sheldon K, Smith J, Ssentongo P, Ssenyonga P, Warf B, Wegoye E, Zhang L, Kiwanuka J, Paulson JN, Broach JR, Schiff SJ | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 37279589 | Clin Infect Dis | 2023 Sep 11 |
| IDENTIFIABILITY OF INFECTION MODEL PARAMETERS EARLY IN AN EPIDEMIC. | Sauer T, Berry T, Ebeigbe D, Norton MM, Whalen AJ, Schiff SJ | SIAM journal on control and optimization | 36338855 | SIAM J Control Optim | 2022 |
| Type IV Pili Are a Critical Virulence Factor in Clinical Isolates of Paenibacillus thiaminolyticus. | Hehnly C, Shi A, Ssentongo P, Zhang L, Isaacs A, Morton SU, Streck N, Erdmann-Gilmore P, Tolstoy I, Townsend RR, Limbrick DD, Paulson JN, Ericson JE, Galperin MY, Schiff SJ, Broach JR | mBio | 36374038 | mBio | 2022 Dec 20 |
| Brain imaging with portable low-field MRI. | Kimberly WT, Sorby-Adams AJ, Webb AG, Wu EX, Beekman R, Bowry R, Schiff SJ, de Havenon A, Shen FX, Sze G, Schaefer P, Iglesias JE, Rosen MS, Sheth KN | Nature reviews bioengineering | 37705717 | Nat Rev Bioeng | 2023 Sep |
| Poisson Kalman filter for disease surveillance. | Ebeigbe D, Berry T, Schiff SJ, Sauer T | Physical review research | 39211287 | Phys Rev Res | 2020 Oct-Dec |
| Verification of operational numerical weather prediction model forecasts of precipitation using satellite rainfall estimates over Africa. | Wang Y, Gueye M, Greybush SJ, Greatrex H, Whalen AJ, Ssentongo P, Zhang F, Jenkins GS, Schiff SJ | Meteorological applications | 39554903 | Meteorol Appl | 2023 Jan-Feb |
| A Generalized Unscented Transformation for Probability Distributions. | Ebeigbe D, Berry T, Norton MM, Whalen AJ, Simon D, Sauer T, Schiff SJ | ArXiv | 33850954 | ArXiv | 2021 Apr 5 |
| Exome sequencing implicates genetic disruption of prenatal neuro-gliogenesis in sporadic congenital hydrocephalus. | Jin SC, Dong W, Kundishora AJ, Panchagnula S, Moreno-De-Luca A, Furey CG, Allocco AA, Walker RL, Nelson-Williams C, Smith H, Dunbar A, Conine S, Lu Q, Zeng X, Sierant MC, Knight JR, Sullivan W, Duy PQ, DeSpenza T, Reeves BC, Karimy JK, Marlier A, Castaldi C, Tikhonova IR, Li B, Peña HP, Broach JR, Kabachelor EM, Ssenyonga P, Hehnly C, Ge L, Keren B, Timberlake AT, Goto J, Mangano FT, Johnston JM, Butler WE, Warf BC, Smith ER, Schiff SJ, Limbrick DD Jr, Heuer G, Jackson EM, Iskandar BJ, Mane S, Haider S, Guclu B, Bayri Y, Sahin Y, Duncan CC, Apuzzo MLJ, DiLuna ML, Hoffman EJ, Sestan N, Ment LR, Alper SL, Bilguvar K, Geschwind DH, Günel M, Lifton RP, Kahle KT | Nature medicine | 33077954 | Nat Med | 2020 Nov |
| mbQTL: an R/Bioconductor package for microbial quantitative trait loci (QTL) estimation. | Movassagh M, Schiff SJ, Paulson JN | Bioinformatics (Oxford, England) | 37707523 | Bioinformatics | 2023 Sep 2 |
| Infection diagnosis in hydrocephalus CT images: a domain enriched attention learning approach. | Yu M, Peterson MR, Cherukuri V, Hehnly C, Mbabazi-Kabachelor E, Mulondo R, Nsubuga Kaaya B, Broach JR, Schiff SJ, Monga V | Journal of neural engineering | 37253355 | J Neural Eng | 2023 Jun 16 |
| Short-term and Long-term Rates of Postacute Sequelae of SARS-CoV-2 Infection: A Systematic Review. | Groff D, Sun A, Ssentongo AE, Ba DM, Parsons N, Poudel GR, Lekoubou A, Oh JS, Ericson JE, Ssentongo P, Chinchilli VM | JAMA network open | 34643720 | JAMA Netw Open | 2021 Oct 1 |
| Normal childhood brain growth and a universal sex and anthropomorphic relationship to cerebrospinal fluid. | Peterson MR, Cherukuri V, Paulson JN, Ssentongo P, Kulkarni AV, Warf BC, Monga V, Schiff SJ | Journal of neurosurgery. Pediatrics | 34243147 | J Neurosurg Pediatr | 2021 Oct 1 |
| Inflammation in acquired hydrocephalus: pathogenic mechanisms and therapeutic targets. | Karimy JK, Reeves BC, Damisah E, Duy PQ, Antwi P, David W, Wang K, Schiff SJ, Limbrick DD Jr, Alper SL, Warf BC, Nedergaard M, Simard JM, Kahle KT | Nature reviews. Neurology | 32152460 | Nat Rev Neurol | 2020 May |
| mirTarRnaSeq: An R/Bioconductor Statistical Package for miRNA-mRNA Target Identification and Interaction Analysis. | Movassagh M, Morton SU, Hehnly C, Smith J, Doan TT, Irizarry R, Broach JR, Schiff SJ, Bailey JA, Paulson JN | BMC genomics | 35698050 | BMC Genomics | 2022 Jun 13 |
| Cytomegalovirus infections in infants in Uganda: Newborn-mother pairs, neonates with sepsis, and infants with hydrocephalus. | Hehnly C, Ssentongo P, Bebell LM, Burgoine K, Bazira J, Fronterre C, Kumbakumba E, Mulondo R, Mbabazi-Kabachelor E, Morton SU, Ngonzi J, Ochora M, Olupot-Olupot P, Mugamba J, Onen J, Roberts DJ, Sheldon K, Sinnar SA, Smith J, Ssenyonga P, Kiwanuka J, Paulson JN, Meier FA, Ericson JE, Broach JR, Schiff SJ | International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases | 35150915 | Int J Infect Dis | 2022 May |
| Differential richness inference for 16S rRNA marker gene surveys. | Kumar MS, Slud EV, Hehnly C, Zhang L, Broach J, Irizarry RA, Schiff SJ, Paulson JN | Genome biology | 35915508 | Genome Biol | 2022 Aug 1 |
| Pan-African evolution of within- and between-country COVID-19 dynamics. | Ssentongo P, Fronterre C, Geronimo A, Greybush SJ, Mbabazi PK, Muvawala J, Nahalamba SB, Omadi PO, Opar BT, Sinnar SA, Wang Y, Whalen AJ, Held L, Jewell C, Muwanguzi AJB, Greatrex H, Norton MM, Diggle PJ, Schiff SJ | Proceedings of the National Academy of Sciences of the United States of America | 34187879 | Proc Natl Acad Sci U S A | 2021 Jul 13 |
| Prevalence and determinants of cervical cancer screening in five sub-Saharan African countries: A population-based study. | Ba DM, Ssentongo P, Musa J, Agbese E, Diakite B, Traore CB, Wang S, Maiga M | Cancer epidemiology | 33756434 | Cancer Epidemiol | 2021 Jun |
| Congenital Cytomegalovirus Infection Burden and Epidemiologic Risk Factors in Countries With Universal Screening: A Systematic Review and Meta-analysis. | Ssentongo P, Hehnly C, Birungi P, Roach MA, Spady J, Fronterre C, Wang M, Murray-Kolb LE, Al-Shaar L, Chinchilli VM, Broach JR, Ericson JE, Schiff SJ | JAMA network open | 34424308 | JAMA Netw Open | 2021 Aug 2 |
| Rates and risk factors for suicidal ideation, suicide attempts and suicide deaths in persons with HIV: a systematic review and meta-analysis. | Pelton M, Ciarletta M, Wisnousky H, Lazzara N, Manglani M, Ba DM, Chinchillli VM, Du P, Ssentongo AE, Ssentongo P | General psychiatry | 33912798 | Gen Psychiatr | 2021 |
| Identification of White Matter Hyperintensities in Routine Emergency Department Visits Using Portable Bedside Magnetic Resonance Imaging. | de Havenon A, Parasuram NR, Crawford AL, Mazurek MH, Chavva IR, Yadlapalli V, Iglesias JE, Rosen MS, Falcone GJ, Payabvash S, Sze G, Sharma R, Schiff SJ, Safdar B, Wira C, Kimberly WT, Sheth KN | Journal of the American Heart Association | 37218590 | J Am Heart Assoc | 2023 Jun 6 |
| Correction to Lancet Microbe 2023; published online June 19. https://doi.org/10.1016/S2666-5247(23)00106-4. | The Lancet. Microbe | 37414068 | Lancet Microbe | 2023 Aug | |
| Meiotic Cas9 expression mediates gene conversion in the male and female mouse germline. | Weitzel AJ, Grunwald HA, Weber C, Levina R, Gantz VM, Hedrick SM, Bier E, Cooper KL | PLoS biology | 34941868 | PLoS Biol | 2021 Dec |
| The Imperative to Vaccinate. | Hedrick SM | The Journal of pediatrics | 30054163 | J Pediatr | 2018 Oct |
| A key control point in the T cell response to chronic infection and neoplasia: FOXO1. | Marcel N, Hedrick SM | Current opinion in immunology | 32135399 | Curr Opin Immunol | 2020 Apr |
| Understanding Immunity through the Lens of Disease Ecology. | Hedrick SM | Trends in immunology | 28882454 | Trends Immunol | 2017 Dec |
| Active genetics comes alive: Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives): Exploring the broad applications of CRISPR-based selfish genetic elements (or gene-drives). | Gantz VM, Bier E | BioEssays : news and reviews in molecular, cellular and developmental biology | 35686327 | Bioessays | 2022 Aug |
| A Bcl6 Intronic Element Regulates T Follicular Helper Cell Differentiation. | Lai CY, Marcel N, Yaldiko AW, Delpoux A, Hedrick SM | Journal of immunology (Baltimore, Md. : 1950) | 35948398 | J Immunol | 2022 Sep 15 |
| RIP3 induces apoptosis independent of pronecrotic kinase activity. | Mandal P, Berger SB, Pillay S, Moriwaki K, Huang C, Guo H, Lich JD, Finger J, Kasparcova V, Votta B, Ouellette M, King BW, Wisnoski D, Lakdawala AS, DeMartino MP, Casillas LN, Haile PA, Sehon CA, Marquis RW, Upton J, Daley-Bauer LP, Roback L, Ramia N, Dovey CM, Carette JE, Chan FK, Bertin J, Gough PJ, Mocarski ES, Kaiser WJ | Molecular cell | 25459880 | Mol Cell | 2014 Nov 20 |
| Herpes simplex virus suppresses necroptosis in human cells. | Guo H, Omoto S, Harris PA, Finger JN, Bertin J, Gough PJ, Kaiser WJ, Mocarski ES | Cell host & microbe | 25674983 | Cell Host Microbe | 2015 Feb 11 |
| Suppression of RIP3-dependent necroptosis by human cytomegalovirus. | Omoto S, Guo H, Talekar GR, Roback L, Kaiser WJ, Mocarski ES | The Journal of biological chemistry | 25778401 | J Biol Chem | 2015 May 1 |
| Retinoic Acid Inducible Gene 1 Protein (RIG1)-Like Receptor Pathway Is Required for Efficient Nuclear Reprogramming. | Sayed N, Ospino F, Himmati F, Lee J, Chanda P, Mocarski ES, Cooke JP | Stem cells (Dayton, Ohio) | 28276156 | Stem Cells | 2017 May |
| Species-independent contribution of ZBP1/DAI/DLM-1-triggered necroptosis in host defense against HSV1. | Guo H, Gilley RP, Fisher A, Lane R, Landsteiner VJ, Ragan KB, Dovey CM, Carette JE, Upton JW, Mocarski ES, Kaiser WJ | Cell death & disease | 30050136 | Cell Death Dis | 2018 Jul 26 |
| Caspase-8 and RIP kinases regulate bacteria-induced innate immune responses and cell death. | Weng D, Marty-Roix R, Ganesan S, Proulx MK, Vladimer GI, Kaiser WJ, Mocarski ES, Pouliot K, Chan FK, Kelliher MA, Harris PA, Bertin J, Gough PJ, Shayakhmetov DM, Goguen JD, Fitzgerald KA, Silverman N, Lien E | Proceedings of the National Academy of Sciences of the United States of America | 24799678 | Proc Natl Acad Sci U S A | 2014 May 20 |
| Manipulation of apoptosis and necroptosis signaling by herpesviruses. | Guo H, Kaiser WJ, Mocarski ES | Medical microbiology and immunology | 25828583 | Med Microbiol Immunol | 2015 Jun |
| Caspase-8 as an Effector and Regulator of NLRP3 Inflammasome Signaling. | Antonopoulos C, Russo HM, El Sanadi C, Martin BN, Li X, Kaiser WJ, Mocarski ES, Dubyak GR | The Journal of biological chemistry | 26100631 | J Biol Chem | 2015 Aug 14 |
| TNFR1-dependent cell death drives inflammation in Sharpin-deficient mice. | Rickard JA, Anderton H, Etemadi N, Nachbur U, Darding M, Peltzer N, Lalaoui N, Lawlor KE, Vanyai H, Hall C, Bankovacki A, Gangoda L, Wong WW, Corbin J, Huang C, Mocarski ES, Murphy JM, Alexander WS, Voss AK, Vaux DL, Kaiser WJ, Walczak H, Silke J | eLife | 25443632 | Elife | 2014 Dec 2 |
| Remarkably Robust Antiviral Immune Response despite Combined Deficiency in Caspase-8 and RIPK3. | Feng Y, Livingston-Rosanoff D, Roback L, Sundararajan A, Speck SH, Mocarski ES, Daley-Bauer LP | Journal of immunology (Baltimore, Md. : 1950) | 30194111 | J Immunol | 2018 Oct 15 |
| Caspase-8 modulates dectin-1 and complement receptor 3-driven IL-1β production in response to β-glucans and the fungal pathogen, Candida albicans. | Ganesan S, Rathinam VAK, Bossaller L, Army K, Kaiser WJ, Mocarski ES, Dillon CP, Green DR, Mayadas TN, Levitz SM, Hise AG, Silverman N, Fitzgerald KA | Journal of immunology (Baltimore, Md. : 1950) | 25063877 | J Immunol | 2014 Sep 1 |
| Cutting Edge: RIP1 kinase activity is dispensable for normal development but is a key regulator of inflammation in SHARPIN-deficient mice. | Berger SB, Kasparcova V, Hoffman S, Swift B, Dare L, Schaeffer M, Capriotti C, Cook M, Finger J, Hughes-Earle A, Harris PA, Kaiser WJ, Mocarski ES, Bertin J, Gough PJ | Journal of immunology (Baltimore, Md. : 1950) | 24821972 | J Immunol | 2014 Jun 15 |
| Mouse cytomegalovirus M36 and M45 death suppressors cooperate to prevent inflammation resulting from antiviral programmed cell death pathways. | Daley-Bauer LP, Roback L, Crosby LN, McCormick AL, Feng Y, Kaiser WJ, Mocarski ES | Proceedings of the National Academy of Sciences of the United States of America | 28292903 | Proc Natl Acad Sci U S A | 2017 Mar 28 |
| T cell-intrinsic ASC critically promotes T(H)17-mediated experimental autoimmune encephalomyelitis. | Martin BN, Wang C, Zhang CJ, Kang Z, Gulen MF, Zepp JA, Zhao J, Bian G, Do JS, Min B, Pavicic PG Jr, El-Sanadi C, Fox PL, Akitsu A, Iwakura Y, Sarkar A, Wewers MD, Kaiser WJ, Mocarski ES, Rothenberg ME, Hise AG, Dubyak GR, Ransohoff RM, Li X | Nature immunology | 26998763 | Nat Immunol | 2016 May |
| Caspase-8 restricts natural killer cell accumulation during MCMV Infection. | Feng Y, Daley-Bauer LP, Roback L, Potempa M, Lanier LL, Mocarski ES | Medical microbiology and immunology | 31115653 | Med Microbiol Immunol | 2019 Aug |
| Caspase-8 restricts antiviral CD8 T cell hyperaccumulation. | Feng Y, Daley-Bauer LP, Roback L, Guo H, Koehler HS, Potempa M, Lanier LL, Mocarski ES | Proceedings of the National Academy of Sciences of the United States of America | 31285326 | Proc Natl Acad Sci U S A | 2019 Jul 23 |
| Caspase-8 Collaborates with Caspase-11 to Drive Tissue Damage and Execution of Endotoxic Shock. | Mandal P, Feng Y, Lyons JD, Berger SB, Otani S, DeLaney A, Tharp GK, Maner-Smith K, Burd EM, Schaeffer M, Hoffman S, Capriotti C, Roback L, Young CB, Liang Z, Ortlund EA, DiPaolo NC, Bosinger S, Bertin J, Gough PJ, Brodsky IE, Coopersmith CM, Shayakhmetov DM, Mocarski ES | Immunity | 30021146 | Immunity | 2018 Jul 17 |
| Proteasome inhibition blocks necroptosis by attenuating death complex aggregation. | Ali M, Mocarski ES | Cell death & disease | 29497034 | Cell Death Dis | 2018 Mar 1 |
| RIP1 suppresses innate immune necrotic as well as apoptotic cell death during mammalian parturition. | Kaiser WJ, Daley-Bauer LP, Thapa RJ, Mandal P, Berger SB, Huang C, Sundararajan A, Guo H, Roback L, Speck SH, Bertin J, Gough PJ, Balachandran S, Mocarski ES | Proceedings of the National Academy of Sciences of the United States of America | 24821786 | Proc Natl Acad Sci U S A | 2014 May 27 |
| Herpes simplex virus 1 ICP6 impedes TNF receptor 1-induced necrosome assembly during compartmentalization to detergent-resistant membrane vesicles. | Ali M, Roback L, Mocarski ES | The Journal of biological chemistry | 30504227 | J Biol Chem | 2019 Jan 18 |
| RIPK3 Activates Parallel Pathways of MLKL-Driven Necroptosis and FADD-Mediated Apoptosis to Protect against Influenza A Virus. | Nogusa S, Thapa RJ, Dillon CP, Liedmann S, Oguin TH 3rd, Ingram JP, Rodriguez DA, Kosoff R, Sharma S, Sturm O, Verbist K, Gough PJ, Bertin J, Hartmann BM, Sealfon SC, Kaiser WJ, Mocarski ES, López CB, Thomas PG, Oberst A, Green DR, Balachandran S | Cell host & microbe | 27321907 | Cell Host Microbe | 2016 Jul 13 |
| Caspase-8 scaffolding function and MLKL regulate NLRP3 inflammasome activation downstream of TLR3. | Kang S, Fernandes-Alnemri T, Rogers C, Mayes L, Wang Y, Dillon C, Roback L, Kaiser W, Oberst A, Sagara J, Fitzgerald KA, Green DR, Zhang J, Mocarski ES, Alnemri ES | Nature communications | 26104484 | Nat Commun | 2015 Jun 24 |
| Inhibition of DAI-dependent necroptosis by the Z-DNA binding domain of the vaccinia virus innate immune evasion protein, E3. | Koehler H, Cotsmire S, Langland J, Kibler KV, Kalman D, Upton JW, Mocarski ES, Jacobs BL | Proceedings of the National Academy of Sciences of the United States of America | 29073079 | Proc Natl Acad Sci U S A | 2017 Oct 24 |
| Energy metabolic pathways control the fate and function of myeloid immune cells. | Al-Khami AA, Rodriguez PC, Ochoa AC | Journal of leukocyte biology | 28515225 | J Leukoc Biol | 2017 Aug |
| Metabolic reprogramming of myeloid-derived suppressor cells (MDSC) in cancer. | Al-Khami AA, Rodriguez PC, Ochoa AC | Oncoimmunology | 27622069 | Oncoimmunology | 2016 Aug |
| Subpopulations of myeloid-derived suppressor cells impair T cell responses through independent nitric oxide-related pathways. | Raber PL, Thevenot P, Sierra R, Wyczechowska D, Halle D, Ramirez ME, Ochoa AC, Fletcher M, Velasco C, Wilk A, Reiss K, Rodriguez PC | International journal of cancer | 24259296 | Int J Cancer | 2014 Jun 15 |
| l-Arginine depletion blunts antitumor T-cell responses by inducing myeloid-derived suppressor cells. | Fletcher M, Ramirez ME, Sierra RA, Raber P, Thevenot P, Al-Khami AA, Sanchez-Pino D, Hernandez C, Wyczechowska DD, Ochoa AC, Rodriguez PC | Cancer research | 25406192 | Cancer Res | 2015 Jan 15 |
| Exogenous lipid uptake induces metabolic and functional reprogramming of tumor-associated myeloid-derived suppressor cells. | Al-Khami AA, Zheng L, Del Valle L, Hossain F, Wyczechowska D, Zabaleta J, Sanchez MD, Dean MJ, Rodriguez PC, Ochoa AC | Oncoimmunology | 29123954 | Oncoimmunology | 2017 |
| Expression of arginase I in myeloid cells limits control of residual disease after radiation therapy of tumors in mice. | Crittenden MR, Savage T, Cottam B, Baird J, Rodriguez PC, Newell P, Young K, Jackson AM, Gough MJ | Radiation research | 24992164 | Radiat Res | 2014 Aug |
| The antimicrobial agent C31G is effective for therapy for HSV-1 ocular keratitis in the rabbit eye model. | Hill JM, Stern EM, Bhattacharjee PS, Malamud D, Clement C, Rodriguez P, Lukiw WJ, Ochoa AC, Foster TP, Velasco C, McFerrin HE Jr | Antiviral research | 23860013 | Antiviral Res | 2013 Oct |
| Rescue of notch-1 signaling in antigen-specific CD8+ T cells overcomes tumor-induced T-cell suppression and enhances immunotherapy in cancer. | Sierra RA, Thevenot P, Raber PL, Cui Y, Parsons C, Ochoa AC, Trillo-Tinoco J, Del Valle L, Rodriguez PC | Cancer immunology research | 24830414 | Cancer Immunol Res | 2014 Aug |
| Herpes Simplex Virus-1 Induced Serotonin-Associated Metabolic Pathways Correlate With Severity of Virus- and Inflammation-Associated Ocular Disease. | Battaglia DM, Sanchez-Pino MD, Nichols CD, Foster TP | Frontiers in microbiology | 35391733 | Front Microbiol | 2022 |
| Development and evaluation of SYBR Green-I based quantitative PCR assays for herpes simplex virus type 1 whole transcriptome analysis. | Garvey CE, McGowin CL, Foster TP | Journal of virological methods | 24607486 | J Virol Methods | 2014 Jun |
| Design, validation and evaluation of a SYBR green-based quantitative PCR array for comprehensive analysis of adenovirus type 5 transcriptional patterns. | Nebeluk N, Foster TP | Journal of virological methods | 32413477 | J Virol Methods | 2020 Jul |
| Development and evaluation of a host-targeted antiviral that abrogates herpes simplex virus replication through modulation of arginine-associated metabolic pathways. | Sanchez MD, Ochoa AC, Foster TP | Antiviral research | 27192555 | Antiviral Res | 2016 Aug |
| Inhibition of Fatty Acid Oxidation Modulates Immunosuppressive Functions of Myeloid-Derived Suppressor Cells and Enhances Cancer Therapies. | Hossain F, Al-Khami AA, Wyczechowska D, Hernandez C, Zheng L, Reiss K, Valle LD, Trillo-Tinoco J, Maj T, Zou W, Rodriguez PC, Ochoa AC | Cancer immunology research | 26025381 | Cancer Immunol Res | 2015 Nov |
| Arginase I levels are decreased in the plasma of pediatric patients with atopic dermatitis. | Dimitriades V, Rodriguez PC, Zabaleta J, Ochoa AC | Annals of allergy, asthma & immunology : official publication of the American College of Allergy, Asthma, & Immunology | 25027824 | Ann Allergy Asthma Immunol | 2014 Sep |
| Fuelling the mechanisms of asthma: Increased fatty acid oxidation in inflammatory immune cells may represent a novel therapeutic target. | Al-Khami AA, Ghonim MA, Del Valle L, Ibba SV, Zheng L, Pyakurel K, Okpechi SC, Garay J, Wyczechowska D, Sanchez-Pino MD, Rodriguez PC, Boulares AH, Ochoa AC | Clinical and experimental allergy : journal of the British Society for Allergy and Clinical Immunology | 28456994 | Clin Exp Allergy | 2017 Sep |
| Molecular and Structural Traits of Insulin Receptor Substrate 1/LC3 Nuclear Structures and Their Role in Autophagy Control and Tumor Cell Survival. | Lassak A, Dean M, Wyczechowska D, Wilk A, Marrero L, Trillo-Tinoco J, Boulares AH, Sarkaria JN, Del Valle L, Peruzzi F, Ochoa A, Reiss K | Molecular and cellular biology | 29483302 | Mol Cell Biol | 2018 May 15 |
| Arginine Metabolism in Myeloid Cells Shapes Innate and Adaptive Immunity. | Rodriguez PC, Ochoa AC, Al-Khami AA | Frontiers in immunology | 28223985 | Front Immunol | 2017 |
| Antibiotics and the gut microbiota. | Modi SR, Collins JJ, Relman DA | The Journal of clinical investigation | 25271726 | J Clin Invest | 2014 Oct |
| Multidomain analyses of a longitudinal human microbiome intestinal cleanout perturbation experiment. | Fukuyama J, Rumker L, Sankaran K, Jeganathan P, Dethlefsen L, Relman DA, Holmes SP | PLoS computational biology | 28821012 | PLoS Comput Biol | 2017 Aug |
| Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data. | Davis NM, Proctor DM, Holmes SP, Relman DA, Callahan BJ | Microbiome | 30558668 | Microbiome | 2018 Dec 17 |
| Microbiome as a tool and a target in the effort to address antimicrobial resistance. | Relman DA, Lipsitch M | Proceedings of the National Academy of Sciences of the United States of America | 30559176 | Proc Natl Acad Sci U S A | 2018 Dec 18 |
| REPRODUCIBLE RESEARCH WORKFLOW IN R FOR THE ANALYSIS OF PERSONALIZED HUMAN MICROBIOME DATA. | Callahan B, Proctor D, Relman D, Fukuyama J, Holmes S | Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing | 26776185 | Pac Symp Biocomput | 2016 |
| Tracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation. | Yaffe E, Relman DA | Nature microbiology | 31873203 | Nat Microbiol | 2020 Feb |
| Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses. | Callahan BJ, Sankaran K, Fukuyama JA, McMurdie PJ, Holmes SP | F1000Research | 27508062 | F1000Res | 2016 |
| Interpreting Prevotella and Bacteroides as biomarkers of diet and lifestyle. | Gorvitovskaia A, Holmes SP, Huse SM | Microbiome | 27068581 | Microbiome | 2016 Apr 12 |
| Measuring multivariate association and beyond. | Josse J, Holmes S | Statistics surveys | 29081877 | Stat Surv | 2016 |
| Latent variable modeling for the microbiome. | Sankaran K, Holmes SP | Biostatistics (Oxford, England) | 29868846 | Biostatistics | 2019 Oct 1 |
| Interactive Visualization of Hierarchically Structured Data. | Sankaran K, Holmes S | Journal of computational and graphical statistics : a joint publication of American Statistical Association, Institute of Mathematical Statistics, Interface Foundation of North America | 30416327 | J Comput Graph Stat | 2018 |
| Bayesian Nonparametric Ordination for the Analysis of Microbial Communities. | Ren B, Bacallado S, Favaro S, Holmes S, Trippa L | Journal of the American Statistical Association | 29430070 | J Am Stat Assoc | 2017 |
| A Statistical Perspective on the Challenges in Molecular Microbial Biology. | Jeganathan P, Holmes SP | Journal of agricultural, biological, and environmental statistics | 36398283 | J Agric Biol Environ Stat | 2021 Jun |
| Unrest at home: diarrheal disease and microbiota disturbance. | Bik EM, Relman DA | Genome biology | 25002208 | Genome Biol | 2014 Jun 27 |
| Ten quick tips for effective dimensionality reduction. | Nguyen LH, Holmes S | PLoS computational biology | 31220072 | PLoS Comput Biol | 2019 Jun |
| Bayesian Unidimensional Scaling for visualizing uncertainty in high dimensional datasets with latent ordering of observations. | Nguyen LH, Holmes S | BMC bioinformatics | 28929970 | BMC Bioinformatics | 2017 Sep 13 |
| Thinking about the microbiome as a causal factor in human health and disease: philosophical and experimental considerations. | Relman DA | Current opinion in microbiology | 32114367 | Curr Opin Microbiol | 2020 Apr |
| Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention. | Grembi JA, Nguyen LH, Haggerty TD, Gardner CD, Holmes SP, Parsonnet J | Scientific reports | 31996717 | Sci Rep | 2020 Jan 29 |
| DADA2: High-resolution sample inference from Illumina amplicon data. | Callahan BJ, McMurdie PJ, Rosen MJ, Han AW, Johnson AJ, Holmes SP | Nature methods | 27214047 | Nat Methods | 2016 Jul |
| Old and new: recent innovations in vaccine biology and skin T cells. | Kupper TS | The Journal of investigative dermatology | 22237702 | J Invest Dermatol | 2012 Mar |
| Skin infection generates non-migratory memory CD8+ T(RM) cells providing global skin immunity. | Jiang X, Clark RA, Liu L, Wagers AJ, Fuhlbrigge RC, Kupper TS | Nature | 22388819 | Nature | 2012 Feb 29 |
| Common clonal origin of central and resident memory T cells following skin immunization. | Gaide O, Emerson RO, Jiang X, Gulati N, Nizza S, Desmarais C, Robins H, Krueger JG, Clark RA, Kupper TS | Nature medicine | 25962122 | Nat Med | 2015 Jun |
| Human skin is protected by four functionally and phenotypically discrete populations of resident and recirculating memory T cells. | Watanabe R, Gehad A, Yang C, Scott LL, Teague JE, Schlapbach C, Elco CP, Huang V, Matos TR, Kupper TS, Clark RA | Science translational medicine | 25787765 | Sci Transl Med | 2015 Mar 18 |
| IL-1R Type 1-Deficient Mice Demonstrate an Impaired Host Immune Response against Cutaneous Vaccinia Virus Infection. | Tian T, Jin MQ, Dubin K, King SL, Hoetzenecker W, Murphy GF, Chen CA, Kupper TS, Fuhlbrigge RC | Journal of immunology (Baltimore, Md. : 1950) | 28468973 | J Immunol | 2017 Jun 1 |
| A primary role for human central memory cells in tissue immunosurveillance. | Gehad A, Teague JE, Matos TR, Huang V, Yang C, Watanabe R, O'Malley JT, Trimble CL, Kupper TS, Clark RA | Blood advances | 29437556 | Blood Adv | 2018 Feb 13 |
| Human skin in the game. | Clark RA | Science translational medicine | 24068735 | Sci Transl Med | 2013 Sep 25 |
| Human TH9 cells are skin-tropic and have autocrine and paracrine proinflammatory capacity. | Schlapbach C, Gehad A, Yang C, Watanabe R, Guenova E, Teague JE, Campbell L, Yawalkar N, Kupper TS, Clark RA | Science translational medicine | 24431112 | Sci Transl Med | 2014 Jan 15 |
| Vascular E-selectin expression correlates with CD8 lymphocyte infiltration and improved outcome in Merkel cell carcinoma. | Afanasiev OK, Nagase K, Simonson W, Vandeven N, Blom A, Koelle DM, Clark R, Nghiem P | The Journal of investigative dermatology | 23353989 | J Invest Dermatol | 2013 Aug |
| Staged development of long-lived T-cell receptor αβ T(H)17 resident memory T-cell population to Candida albicans after skin infection. | Park CO, Fu X, Jiang X, Pan Y, Teague JE, Collins N, Tian T, O'Malley JT, Emerson RO, Kim JH, Jung Y, Watanabe R, Fuhlbrigge RC, Carbone FR, Gebhardt T, Clark RA, Lin CP, Kupper TS | The Journal of allergy and clinical immunology | 29128674 | J Allergy Clin Immunol | 2018 Aug |
| Human epidermal Langerhans cells maintain immune homeostasis in skin by activating skin resident regulatory T cells. | Seneschal J, Clark RA, Gehad A, Baecher-Allan CM, Kupper TS | Immunity | 22560445 | Immunity | 2012 May 25 |
| Dermal γδ T Cells Do Not Freely Re-Circulate Out of Skin and Produce IL-17 to Promote Neutrophil Infiltration during Primary Contact Hypersensitivity. | Jiang X, Park CO, Geddes Sweeney J, Yoo MJ, Gaide O, Kupper TS | PloS one | 28081153 | PLoS One | 2017 |
| Skin CD4(+) memory T cells exhibit combined cluster-mediated retention and equilibration with the circulation. | Collins N, Jiang X, Zaid A, Macleod BL, Li J, Park CO, Haque A, Bedoui S, Heath WR, Mueller SN, Kupper TS, Gebhardt T, Carbone FR | Nature communications | 27160938 | Nat Commun | 2016 May 10 |
| Central memory T cells are the most effective precursors of resident memory T cells in human skin. | Matos TR, Gehad A, Teague JE, Dyring-Andersen B, Benezeder T, Dowlatshahi M, Crouch J, Watanabe Y, O'Malley JT, Kupper TS, Yang C, Watanabe R, Clark RA | Science immunology | 35452256 | Sci Immunol | 2022 Apr 22 |
| Galectin-1 inhibits the viability, proliferation, and Th1 cytokine production of nonmalignant T cells in patients with leukemic cutaneous T-cell lymphoma. | Cedeno-Laurent F, Watanabe R, Teague JE, Kupper TS, Clark RA, Dimitroff CJ | Blood | 22383798 | Blood | 2012 Apr 12 |
| Skin effector memory T cells do not recirculate and provide immune protection in alemtuzumab-treated CTCL patients. | Clark RA, Watanabe R, Teague JE, Schlapbach C, Tawa MC, Adams N, Dorosario AA, Chaney KS, Cutler CS, Leboeuf NR, Carter JB, Fisher DC, Kupper TS | Science translational medicine | 22261031 | Sci Transl Med | 2012 Jan 18 |
| Intramuscular therapeutic vaccination targeting HPV16 induces T cell responses that localize in mucosal lesions. | Maldonado L, Teague JE, Morrow MP, Jotova I, Wu TC, Wang C, Desmarais C, Boyer JD, Tycko B, Robins HS, Clark RA, Trimble CL | Science translational medicine | 24477000 | Sci Transl Med | 2014 Jan 29 |
| Alemtuzumab therapy for leukemic cutaneous T-cell lymphoma: diffuse erythema as a positive predictor of complete remission. | Watanabe R, Teague JE, Fisher DC, Kupper TS, Clark RA | JAMA dermatology | 24760312 | JAMA Dermatol | 2014 Jul |
| Acute rejection in vascularized composite allotransplantation. | Fischer S, Lian CG, Kueckelhaus M, Strom TB, Edelman ER, Clark RA, Murphy GF, Chandraker AK, Riella LV, Tullius SG, Pomahac B | Current opinion in organ transplantation | 25333831 | Curr Opin Organ Transplant | 2014 Dec |
| IL-4 abrogates T(H)17 cell-mediated inflammation by selective silencing of IL-23 in antigen-presenting cells. | Guenova E, Skabytska Y, Hoetzenecker W, Weindl G, Sauer K, Tham M, Kim KW, Park JH, Seo JH, Ignatova D, Cozzio A, Levesque MP, Volz T, Köberle M, Kaesler S, Thomas P, Mailhammer R, Ghoreschi K, Schäkel K, Amarov B, Eichner M, Schaller M, Clark RA, Röcken M, Biedermann T | Proceedings of the National Academy of Sciences of the United States of America | 25646481 | Proc Natl Acad Sci U S A | 2015 Feb 17 |
| Resident memory T cells in human health and disease. | Clark RA | Science translational medicine | 25568072 | Sci Transl Med | 2015 Jan 7 |
| TCR sequencing facilitates diagnosis and identifies mature T cells as the cell of origin in CTCL. | Kirsch IR, Watanabe R, O'Malley JT, Williamson DW, Scott LL, Elco CP, Teague JE, Gehad A, Lowry EL, LeBoeuf NR, Krueger JG, Robins HS, Kupper TS, Clark RA | Science translational medicine | 26446955 | Sci Transl Med | 2015 Oct 7 |
| Mucin 1 is a potential therapeutic target in cutaneous T-cell lymphoma. | Jain S, Stroopinsky D, Yin L, Rosenblatt J, Alam M, Bhargava P, Clark RA, Kupper TS, Palmer K, Coll MD, Rajabi H, Pyzer A, Bar-Natan M, Luptakova K, Arnason J, Joyce R, Kufe D, Avigan D | Blood | 26048911 | Blood | 2015 Jul 16 |
| The emerging role of resident memory T cells in protective immunity and inflammatory disease. | Park CO, Kupper TS | Nature medicine | 26121195 | Nat Med | 2015 Jul |
| Survival of tissue-resident memory T cells requires exogenous lipid uptake and metabolism. | Pan Y, Tian T, Park CO, Lofftus SY, Mei S, Liu X, Luo C, O'Malley JT, Gehad A, Teague JE, Divito SJ, Fuhlbrigge R, Puigserver P, Krueger JG, Hotamisligil GS, Clark RA, Kupper TS | Nature | 28219080 | Nature | 2017 Mar 9 |
| CD8(+) T cells in the lesional skin of atopic dermatitis and psoriasis patients are an important source of IFN-γ, IL-13, IL-17, and IL-22. | Hijnen D, Knol EF, Gent YY, Giovannone B, Beijn SJ, Kupper TS, Bruijnzeel-Koomen CA, Clark RA | The Journal of investigative dermatology | 23223131 | J Invest Dermatol | 2013 Apr |
| TH2 cytokines from malignant cells suppress TH1 responses and enforce a global TH2 bias in leukemic cutaneous T-cell lymphoma. | Guenova E, Watanabe R, Teague JE, Desimone JA, Jiang Y, Dowlatshahi M, Schlapbach C, Schaekel K, Rook AH, Tawa M, Fisher DC, Kupper TS, Clark RA | Clinical cancer research : an official journal of the American Association for Cancer Research | 23785046 | Clin Cancer Res | 2013 Jul 15 |
| Decitabine Priming Enhances Mucin 1 Inhibition Mediated Disruption of Redox Homeostasis in Cutaneous T-Cell Lymphoma. | Jain S, Washington A, Leaf RK, Bhargava P, Clark RA, Kupper TS, Stroopinsky D, Pyzer A, Cole L, Nahas M, Apel A, Rosenblatt J, Arnason J, Kufe D, Avigan D | Molecular cancer therapeutics | 28729399 | Mol Cancer Ther | 2017 Oct |
| Tumor-specific T cells in human Merkel cell carcinomas: a possible role for Tregs and T-cell exhaustion in reducing T-cell responses. | Dowlatshahi M, Huang V, Gehad AE, Jiang Y, Calarese A, Teague JE, Dorosario AA, Cheng J, Nghiem P, Schanbacher CF, Thakuria M, Schmults CD, Wang LC, Clark RA | The Journal of investigative dermatology | 23419694 | J Invest Dermatol | 2013 Jul |
| Topical resiquimod can induce disease regression and enhance T-cell effector functions in cutaneous T-cell lymphoma. | Rook AH, Gelfand JM, Wysocka M, Troxel AB, Benoit B, Surber C, Elenitsas R, Buchanan MA, Leahy DS, Watanabe R, Kirsch IR, Kim EJ, Clark RA | Blood | 26228486 | Blood | 2015 Sep 17 |
| Nonapoptotic and extracellular activity of granzyme B mediates resistance to regulatory T cell (Treg) suppression by HLA-DR-CD25hiCD127lo Tregs in multiple sclerosis and in response to IL-6. | Bhela S, Kempsell C, Manohar M, Dominguez-Villar M, Griffin R, Bhatt P, Kivisakk-Webb P, Fuhlbrigge R, Kupper T, Weiner H, Baecher-Allan C | Journal of immunology (Baltimore, Md. : 1950) | 25637022 | J Immunol | 2015 Mar 1 |
| Langerin+ dermal DC, but not Langerhans cells, are required for effective CD8-mediated immune responses after skin scarification with vaccinia virus. | Seneschal J, Jiang X, Kupper TS | The Journal of investigative dermatology | 24126845 | J Invest Dermatol | 2014 Mar |
| Regulation of gene expression in autoimmune disease loci and the genetic basis of proliferation in CD4+ effector memory T cells. | Hu X, Kim H, Raj T, Brennan PJ, Trynka G, Teslovich N, Slowikowski K, Chen WM, Onengut S, Baecher-Allan C, De Jager PL, Rich SS, Stranger BE, Brenner MB, Raychaudhuri S | PLoS genetics | 24968232 | PLoS Genet | 2014 Jun |
| Robust tumor immunity to melanoma mediated by interleukin-9-producing T cells. | Purwar R, Schlapbach C, Xiao S, Kang HS, Elyaman W, Jiang X, Jetten AM, Khoury SJ, Fuhlbrigge RC, Kuchroo VK, Clark RA, Kupper TS | Nature medicine | 22772464 | Nat Med | 2012 Aug |
| Clinically resolved psoriatic lesions contain psoriasis-specific IL-17-producing αβ T cell clones. | Matos TR, O'Malley JT, Lowry EL, Hamm D, Kirsch IR, Robins HS, Kupper TS, Krueger JG, Clark RA | The Journal of clinical investigation | 28945199 | J Clin Invest | 2017 Nov 1 |
| Nitric oxide-producing myeloid-derived suppressor cells inhibit vascular E-selectin expression in human squamous cell carcinomas. | Gehad AE, Lichtman MK, Schmults CD, Teague JE, Calarese AW, Jiang Y, Watanabe R, Clark RA | The Journal of investigative dermatology | 22718118 | J Invest Dermatol | 2012 Nov |
| Disruption of TNF-α/TNFR1 function in resident skin cells impairs host immune response against cutaneous vaccinia virus infection. | Tian T, Dubin K, Jin Q, Qureshi A, King SL, Liu L, Jiang X, Murphy GF, Kupper TS, Fuhlbrigge RC | The Journal of investigative dermatology | 22318381 | J Invest Dermatol | 2012 May |
| Skin-resident natural killer T cells participate in cutaneous allergic inflammation in atopic dermatitis. | Sun Z, Kim JH, Kim SH, Kim HR, Zhang K, Pan Y, Ko MK, Kim BM, Chu H, Lee HR, Kim HL, Kim JH, Fu X, Hyun YM, Yun KN, Kim JY, Lee DW, Song SY, Lin CP, Clark RA, Lee KH, Kupper TS, Park CO | The Journal of allergy and clinical immunology | 33516870 | J Allergy Clin Immunol | 2021 May |
| Using T. brucei as a biological epitope-display platform to elicit specific antibody responses. | Stavropoulos P, Papavasiliou FN | Journal of immunological methods | 20800596 | J Immunol Methods | 2010 Oct 31 |
| A trypanosome-derived immunotherapeutics platform elicits potent high-affinity antibodies, negating the effects of the synthetic opioid fentanyl. | Triller G, Vlachou EP, Hashemi H, van Straaten M, Zeelen JP, Kelemen Y, Baehr C, Marker CL, Ruf S, Svirina A, Chandra M, Urban K, Gkeka A, Kruse S, Baumann A, Miller AK, Bartel M, Pravetoni M, Stebbins CE, Papavasiliou FN, Verdi JP | Cell reports | 36719797 | Cell Rep | 2023 Feb 28 |
| The in vivo dynamics of antigenic variation in Trypanosoma brucei. | Mugnier MR, Cross GA, Papavasiliou FN | Science (New York, N.Y.) | 25814582 | Science | 2015 Mar 27 |
| Masters of Disguise: Antigenic Variation and the VSG Coat in Trypanosoma brucei. | Mugnier MR, Stebbins CE, Papavasiliou FN | PLoS pathogens | 27583379 | PLoS Pathog | 2016 Sep |
| Variant surface glycoprotein density defines an immune evasion threshold for African trypanosomes undergoing antigenic variation. | Pinger J, Chowdhury S, Papavasiliou FN | Nature communications | 29018220 | Nat Commun | 2017 Oct 10 |
| A Host-Pathogen Interaction Reduced to First Principles: Antigenic Variation in T. brucei. | Hovel-Miner G, Mugnier M, Papavasiliou FN, Pinger J, Schulz D | Results and problems in cell differentiation | 26537376 | Results Probl Cell Differ | 2015 |
| Immunization with Genetically Modified Trypanosomes Provides Protection against Transmissible Spongiform Encephalopathies. | Triller G, Garyfallos DA, Papavasiliou FN, Sklaviadis T, Stavropoulos P, Xanthopoulos K | International journal of molecular sciences | 36142526 | Int J Mol Sci | 2022 Sep 13 |
| Immunogenicity of novel consensus-based DNA vaccines against avian influenza. | Laddy DJ, Yan J, Corbitt N, Kobinger GP, Weiner DB | Vaccine | 17306909 | Vaccine | 2007 Apr 20 |
| A synthetic consensus anti-spike protein DNA vaccine induces protective immunity against Middle East respiratory syndrome coronavirus in nonhuman primates. | Muthumani K, Falzarano D, Reuschel EL, Tingey C, Flingai S, Villarreal DO, Wise M, Patel A, Izmirly A, Aljuaid A, Seliga AM, Soule G, Morrow M, Kraynyak KA, Khan AS, Scott DP, Feldmann F, LaCasse R, Meade-White K, Okumura A, Ugen KE, Sardesai NY, Kim JJ, Kobinger G, Feldmann H, Weiner DB | Science translational medicine | 26290414 | Sci Transl Med | 2015 Aug 19 |
| DNA vaccination protects mice against Zika virus-induced damage to the testes. | Griffin BD, Muthumani K, Warner BM, Majer A, Hagan M, Audet J, Stein DR, Ranadheera C, Racine T, De La Vega MA, Piret J, Kucas S, Tran KN, Frost KL, De Graff C, Soule G, Scharikow L, Scott J, McTavish G, Smid V, Park YK, Maslow JN, Sardesai NY, Kim JJ, Yao XJ, Bello A, Lindsay R, Boivin G, Booth SA, Kobasa D, Embury-Hyatt C, Safronetz D, Weiner DB, Kobinger GP | Nature communications | 28589934 | Nat Commun | 2017 Jun 7 |
| Pandemic Swine-Origin H1N1 Influenza Virus Replicates to Higher Levels and Induces More Fever and Acute Inflammatory Cytokines in Cynomolgus versus Rhesus Monkeys and Can Replicate in Common Marmosets. | Mooij P, Koopman G, Mortier D, van Heteren M, Oostermeijer H, Fagrouch Z, de Laat R, Kobinger G, Li Y, Remarque EJ, Kondova I, Verschoor EJ, Bogers WM | PloS one | 25946071 | PLoS One | 2015 |
| Protective immunity to H7N9 influenza viruses elicited by synthetic DNA vaccine. | Yan J, Villarreal DO, Racine T, Chu JS, Walters JN, Morrow MP, Khan AS, Sardesai NY, Kim JJ, Kobinger GP, Weiner DB | Vaccine | 24631084 | Vaccine | 2014 May 19 |
| A highly optimized DNA vaccine confers complete protective immunity against high-dose lethal lymphocytic choriomeningitis virus challenge. | Shedlock DJ, Talbott KT, Cress C, Ferraro B, Tuyishme S, Mallilankaraman K, Cisper NJ, Morrow MP, Wu SJ, Kawalekar OU, Khan AS, Sardesai NY, Muthumani K, Shen H, Weiner DB | Vaccine | 21238574 | Vaccine | 2011 Sep 9 |
| Immunogenicity of novel consensus-based DNA vaccines against Chikungunya virus. | Muthumani K, Lankaraman KM, Laddy DJ, Sundaram SG, Chung CW, Sako E, Wu L, Khan A, Sardesai N, Kim JJ, Vijayachari P, Weiner DB | Vaccine | 18471943 | Vaccine | 2008 Sep 19 |
| Safety and Immunogenicity of an Anti-Zika Virus DNA Vaccine. | Tebas P, Roberts CC, Muthumani K, Reuschel EL, Kudchodkar SB, Zaidi FI, White S, Khan AS, Racine T, Choi H, Boyer J, Park YK, Trottier S, Remigio C, Krieger D, Spruill SE, Bagarazzi M, Kobinger GP, Weiner DB, Maslow JN | The New England journal of medicine | 34525286 | N Engl J Med | 2021 Sep 16 |
| Induction of broad cytotoxic T cells by protective DNA vaccination against Marburg and Ebola. | Shedlock DJ, Aviles J, Talbott KT, Wong G, Wu SJ, Villarreal DO, Myles DJ, Croyle MA, Yan J, Kobinger GP, Weiner DB | Molecular therapy : the journal of the American Society of Gene Therapy | 23670573 | Mol Ther | 2013 Jul |
| Synthetic DNA vaccine strategies against persistent viral infections. | Villarreal DO, Talbott KT, Choo DK, Shedlock DJ, Weiner DB | Expert review of vaccines | 23659301 | Expert Rev Vaccines | 2013 May |
| A novel multivalent tuberculosis vaccine confers protection in a mouse model of tuberculosis. | Griffiths KL, Villarreal DO, Weiner DB, Khader SA | Human vaccines & immunotherapeutics | 27322875 | Hum Vaccin Immunother | 2016 Oct 2 |
| Progression of hydrocephalus during corticosteroid therapy for neurosarcoidosis. | Foley KT, Howell JD, Junck L | Postgraduate medical journal | 2602241 | Postgrad Med J | 1989 Jul |
| Molecular adjuvant HMGB1 enhances anti-influenza immunity during DNA vaccination. | Fagone P, Shedlock DJ, Bao H, Kawalekar OU, Yan J, Gupta D, Morrow MP, Patel A, Kobinger GP, Muthumani K, Weiner DB | Gene therapy | 21544096 | Gene Ther | 2011 Nov |
| HIV-mediated phosphatidylinositol 3-kinase/serine-threonine kinase activation in APCs leads to programmed death-1 ligand upregulation and suppression of HIV-specific CD8 T cells. | Muthumani K, Shedlock DJ, Choo DK, Fagone P, Kawalekar OU, Goodman J, Bian CB, Ramanathan AA, Atman P, Tebas P, Chattergoon MA, Choo AY, Weiner DB | Journal of immunology (Baltimore, Md. : 1950) | 21856939 | J Immunol | 2011 Sep 15 |
| Clinical applications of DNA vaccines: current progress. | Ferraro B, Morrow MP, Hutnick NA, Shin TH, Lucke CE, Weiner DB | Clinical infectious diseases : an official publication of the Infectious Diseases Society of America | 21765081 | Clin Infect Dis | 2011 Aug 1 |
| Combined effects of IL-12 and electroporation enhances the potency of DNA vaccination in macaques. | Hirao LA, Wu L, Khan AS, Hokey DA, Yan J, Dai A, Betts MR, Draghia-Akli R, Weiner DB | Vaccine | 18430495 | Vaccine | 2008 Jun 13 |
| Synthetic DNA vaccines: improved vaccine potency by electroporation and co-delivered genetic adjuvants. | Flingai S, Czerwonko M, Goodman J, Kudchodkar SB, Muthumani K, Weiner DB | Frontiers in immunology | 24204366 | Front Immunol | 2013 Nov 4 |
| Selected approaches for increasing HIV DNA vaccine immunogenicity in vivo. | Hutnick NA, Myles DJ, Bian CB, Muthumani K, Weiner DB | Current opinion in virology | 22440782 | Curr Opin Virol | 2011 Oct |
| Immunotherapy against HPV16/18 generates potent TH1 and cytotoxic cellular immune responses. | Bagarazzi ML, Yan J, Morrow MP, Shen X, Parker RL, Lee JC, Giffear M, Pankhong P, Khan AS, Broderick KE, Knott C, Lin F, Boyer JD, Draghia-Akli R, White CJ, Kim JJ, Weiner DB, Sardesai NY | Science translational medicine | 23052295 | Sci Transl Med | 2012 Oct 10 |
| Characterization of a Bivalent Vaccine Capable of Inducing Protection Against Both Ebola and Cross-clade H5N1 Influenza in Mice. | Wong G, Qiu X, Ebihara H, Feldmann H, Kobinger GP | The Journal of infectious diseases | 26022441 | J Infect Dis | 2015 Oct 1 |
| Plant-derived H7 VLP vaccine elicits protective immune response against H7N9 influenza virus in mice and ferrets. | Pillet S, Racine T, Nfon C, Di Lenardo TZ, Babiuk S, Ward BJ, Kobinger GP, Landry N | Vaccine | 26432915 | Vaccine | 2015 Nov 17 |
| Vaccination with synthetic constructs expressing cytomegalovirus immunogens is highly T cell immunogenic in mice. | Shedlock DJ, Talbott KT, Wu SJ, Wilson CM, Muthumani K, Boyer JD, Sardesai NY, Awasthi S, Weiner DB | Human vaccines & immunotherapeutics | 23151448 | Hum Vaccin Immunother | 2012 Nov 1 |
| Ki-67 staining for determination of rhesus macaque T cell proliferative responses ex vivo. | Shedlock DJ, Talbott KT, Morrow MP, Ferraro B, Hokey DA, Muthumani K, Weiner DB | Cytometry. Part A : the journal of the International Society for Analytical Cytology | 20104580 | Cytometry A | 2010 Mar |
| Synthetic DNA immunogen encoding hepatitis B core antigen drives immune response in liver. | Obeng-Adjei N, Choo DK, Saini J, Yan J, Pankhong P, Parikh A, Chu JS, Weiner DB | Cancer gene therapy | 23037809 | Cancer Gene Ther | 2012 Nov |
| DNA vaccines: crossing a line in the sand. Introduction to special issue. | Weiner DB | Vaccine | 18652867 | Vaccine | 2008 Sep 19 |
| Molecular adjuvant IL-33 enhances the potency of a DNA vaccine in a lethal challenge model. | Villarreal DO, Svoronos N, Wise MC, Shedlock DJ, Morrow MP, Conejo-Garcia JR, Weiner DB | Vaccine | 25887087 | Vaccine | 2015 Aug 20 |
| DNA vaccines for targeting bacterial infections. | Ingolotti M, Kawalekar O, Shedlock DJ, Muthumani K, Weiner DB | Expert review of vaccines | 20624048 | Expert Rev Vaccines | 2010 Jul |
| Rapid and Long-Term Immunity Elicited by DNA-Encoded Antibody Prophylaxis and DNA Vaccination Against Chikungunya Virus. | Muthumani K, Block P, Flingai S, Muruganantham N, Chaaithanya IK, Tingey C, Wise M, Reuschel EL, Chung C, Muthumani A, Sarangan G, Srikanth P, Khan AS, Vijayachari P, Sardesai NY, Kim JJ, Ugen KE, Weiner DB | The Journal of infectious diseases | 27001960 | J Infect Dis | 2016 Aug 1 |
| Novel synthetic plasmid and Doggybone DNA vaccines induce neutralizing antibodies and provide protection from lethal influenza challenge in mice. | Scott VL, Patel A, Villarreal DO, Hensley SE, Ragwan E, Yan J, Sardesai NY, Rothwell PJ, Extance JP, Caproni LJ, Weiner DB | Human vaccines & immunotherapeutics | 26091432 | Hum Vaccin Immunother | 2015 |
| Probing spatial organization of DNA strands using enzyme-free hairpin assembly circuits. | Li B, Jiang Y, Chen X, Ellington AD | Journal of the American Chemical Society | 22894754 | J Am Chem Soc | 2012 Aug 29 |
| DNA circuits as amplifiers for the detection of nucleic acids on a paperfluidic platform. | Allen PB, Arshad SA, Li B, Chen X, Ellington AD | Lab on a chip | 22729075 | Lab Chip | 2012 Aug 21 |
| Adapting enzyme-free DNA circuits to the detection of loop-mediated isothermal amplification reactions. | Li B, Chen X, Ellington AD | Analytical chemistry | 22947054 | Anal Chem | 2012 Oct 2 |
| Mismatches improve the performance of strand-displacement nucleic Acid circuits. | Jiang YS, Bhadra S, Li B, Ellington AD | Angewandte Chemie (International ed. in English) | 24402831 | Angew Chem Int Ed Engl | 2014 Feb 10 |
| Using RecA protein to enhance kinetic rates of DNA circuits. | Milligan JN, Ellington AD | Chemical communications (Cambridge, England) | 25967118 | Chem Commun (Camb) | 2015 Jun 11 |
| Stacking nonenzymatic circuits for high signal gain. | Chen X, Briggs N, McLain JR, Ellington AD | Proceedings of the National Academy of Sciences of the United States of America | 23509255 | Proc Natl Acad Sci U S A | 2013 Apr 2 |
| A general RNA motif for cellular transfection. | Magalhães ML, Byrom M, Yan A, Kelly L, Li N, Furtado R, Palliser D, Ellington AD, Levy M | Molecular therapy : the journal of the American Society of Gene Therapy | 22233578 | Mol Ther | 2012 Mar |
| Rational, modular adaptation of enzyme-free DNA circuits to multiple detection methods. | Li B, Ellington AD, Chen X | Nucleic acids research | 21693555 | Nucleic Acids Res | 2011 Sep 1 |
| Library generation by gene shuffling. | Meyer AJ, Ellefson JW, Ellington AD | Current protocols in molecular biology | 24510437 | Curr Protoc Mol Biol | 2014 Jan 6 |
| Coupling two different nucleic acid circuits in an enzyme-free amplifier. | Jiang Y, Li B, Chen X, Ellington AD | Molecules (Basel, Switzerland) | 23132138 | Molecules | 2012 Nov 6 |
| A primerless molecular diagnostic: phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP). | Jung C, Ellington AD | Analytical and bioanalytical chemistry | 27032410 | Anal Bioanal Chem | 2016 Dec |
| Real-time detection of isothermal amplification reactions with thermostable catalytic hairpin assembly. | Jiang YS, Li B, Milligan JN, Bhadra S, Ellington AD | Journal of the American Chemical Society | 23647466 | J Am Chem Soc | 2013 May 22 |
| Expanding the rule set of DNA circuitry with associative toehold activation. | Chen X | Journal of the American Chemical Society | 22129141 | J Am Chem Soc | 2012 Jan 11 |
| Emergence of Pseudomonas aeruginosa strains producing high levels of persister cells in patients with cystic fibrosis. | Mulcahy LR, Burns JL, Lory S, Lewis K | Journal of bacteriology | 20935098 | J Bacteriol | 2010 Dec |
| Regulation of the Escherichia coli HipBA toxin-antitoxin system by proteolysis. | Hansen S, Vulić M, Min J, Yen TJ, Schumacher MA, Brennan RG, Lewis K | PloS one | 22720069 | PLoS One | 2012 |
| Borrelia burgdorferi, the Causative Agent of Lyme Disease, Forms Drug-Tolerant Persister Cells. | Sharma B, Brown AV, Matluck NE, Hu LT, Lewis K | Antimicrobial agents and chemotherapy | 26014929 | Antimicrob Agents Chemother | 2015 Aug |
| Lassomycin, a ribosomally synthesized cyclic peptide, kills mycobacterium tuberculosis by targeting the ATP-dependent protease ClpC1P1P2. | Gavrish E, Sit CS, Cao S, Kandror O, Spoering A, Peoples A, Ling L, Fetterman A, Hughes D, Bissell A, Torrey H, Akopian T, Mueller A, Epstein S, Goldberg A, Clardy J, Lewis K | Chemistry & biology | 24684906 | Chem Biol | 2014 Apr 24 |
| Pseudomonas aeruginosa biofilms in disease. | Mulcahy LR, Isabella VM, Lewis K | Microbial ecology | 24096885 | Microb Ecol | 2014 Jul |
| Persister-promoting bacterial toxin TisB produces anion-selective pores in planar lipid bilayers. | Gurnev PA, Ortenberg R, Dörr T, Lewis K, Bezrukov SM | FEBS letters | 22728134 | FEBS Lett | 2012 Jul 30 |
| Staphylococcus aureus persisters tolerant to bactericidal antibiotics. | Lechner S, Lewis K, Bertram R | Journal of molecular microbiology and biotechnology | 22986269 | J Mol Microbiol Biotechnol | 2012 |
| Potentiation of azole antifungals by 2-adamantanamine. | Lafleur MD, Sun L, Lister I, Keating J, Nantel A, Long L, Ghannoum M, North J, Lee RE, Coleman K, Dahl T, Lewis K | Antimicrobial agents and chemotherapy | 23689724 | Antimicrob Agents Chemother | 2013 Aug |
| HipBA-promoter structures reveal the basis of heritable multidrug tolerance. | Schumacher MA, Balani P, Min J, Chinnam NB, Hansen S, Vulić M, Lewis K, Brennan RG | Nature | 26222023 | Nature | 2015 Aug 6 |
| High Persister Mutants in Mycobacterium tuberculosis. | Torrey HL, Keren I, Via LE, Lee JS, Lewis K | PloS one | 27176494 | PLoS One | 2016 |
| Killing by bactericidal antibiotics does not depend on reactive oxygen species. | Keren I, Wu Y, Inocencio J, Mulcahy LR, Lewis K | Science (New York, N.Y.) | 23471410 | Science | 2013 Mar 8 |
| A new antibiotic kills pathogens without detectable resistance. | Ling LL, Schneider T, Peoples AJ, Spoering AL, Engels I, Conlon BP, Mueller A, Schäberle TF, Hughes DE, Epstein S, Jones M, Lazarides L, Steadman VA, Cohen DR, Felix CR, Fetterman KA, Millett WP, Nitti AG, Zullo AM, Chen C, Lewis K | Nature | 25561178 | Nature | 2015 Jan 22 |
| Activated ClpP kills persisters and eradicates a chronic biofilm infection. | Conlon BP, Nakayasu ES, Fleck LE, LaFleur MD, Isabella VM, Coleman K, Leonard SN, Smith RD, Adkins JN, Lewis K | Nature | 24226776 | Nature | 2013 Nov 21 |
| A screen for and validation of prodrug antimicrobials. | Fleck LE, North EJ, Lee RE, Mulcahy LR, Casadei G, Lewis K | Antimicrobial agents and chemotherapy | 24342644 | Antimicrob Agents Chemother | 2014 |
| Genetic basis of persister tolerance to aminoglycosides in Escherichia coli. | Shan Y, Lazinski D, Rowe S, Camilli A, Lewis K | mBio | 25852159 | mBio | 2015 Apr 7 |
| Role of oxidative stress in persister tolerance. | Wu Y, Vulić M, Keren I, Lewis K | Antimicrobial agents and chemotherapy | 22777047 | Antimicrob Agents Chemother | 2012 Sep |
| Characterization and transcriptome analysis of Mycobacterium tuberculosis persisters. | Keren I, Minami S, Rubin E, Lewis K | mBio | 21673191 | mBio | 2011 |
| In vitro and in vivo activity of frenolicin B against Plasmodium falciparum and P berghei. | Fitzgerald JT, Henrich PP, O'Brien C, Krause M, Ekland EH, Mattheis C, Sá JM, Fidock D, Khosla C | The Journal of antibiotics | 22008701 | J Antibiot (Tokyo) | 2011 Dec |
| An integrated strategy for efficient vector construction and multi-gene expression in Plasmodium falciparum. | Wagner JC, Goldfless SJ, Ganesan SM, Lee MC, Fidock DA, Niles JC | Malaria journal | 24160265 | Malar J | 2013 Oct 26 |
| A key role for lipoic acid synthesis during Plasmodium liver stage development. | Falkard B, Kumar TR, Hecht LS, Matthews KA, Henrich PP, Gulati S, Lewis RE, Manary MJ, Winzeler EA, Sinnis P, Prigge ST, Heussler V, Deschermeier C, Fidock D | Cellular microbiology | 23490300 | Cell Microbiol | 2013 Sep |
| Parasite-induced ER stress response in hepatocytes facilitates Plasmodium liver stage infection. | Inácio P, Zuzarte-Luís V, Ruivo MT, Falkard B, Nagaraj N, Rooijers K, Mann M, Mair G, Fidock DA, Mota MM | EMBO reports | 26113366 | EMBO Rep | 2015 Aug |
| Targeting Plasmodium PI(4)K to eliminate malaria. | McNamara CW, Lee MC, Lim CS, Lim SH, Roland J, Simon O, Yeung BK, Chatterjee AK, McCormack SL, Manary MJ, Zeeman AM, Dechering KJ, Kumar TS, Henrich PP, Gagaring K, Ibanez M, Kato N, Kuhen KL, Fischli C, Nagle A, Rottmann M, Plouffe DM, Bursulaya B, Meister S, Rameh L, Trappe J, Haasen D, Timmerman M, Sauerwein RW, Suwanarusk R, Russell B, Renia L, Nosten F, Tully DC, Kocken CH, Glynne RJ, Bodenreider C, Fidock DA, Diagana TT, Winzeler EA | Nature | 24284631 | Nature | 2013 Dec 12 |
| Characterization of the ATG8-conjugation system in 2 Plasmodium species with special focus on the liver stage: possible linkage between the apicoplastic and autophagic systems? | Jayabalasingham B, Voss C, Ehrenman K, Romano JD, Smith ME, Fidock DA, Bosch J, Coppens I | Autophagy | 24342964 | Autophagy | 2014 Feb |
| Plasmodium falciparum LipB mutants display altered redox and carbon metabolism in asexual stages and cannot complete sporogony in Anopheles mosquitoes. | Biddau M, Santha Kumar TR, Henrich P, Laine LM, Blackburn GJ, Chokkathukalam A, Li T, Lee Sim K, King L, Hoffman SL, Barrett MP, Coombs GH, McFadden GI, Fidock DA, Müller S, Sheiner L | International journal for parasitology | 33713652 | Int J Parasitol | 2021 May |
| Yeast-based high-throughput screen identifies Plasmodium falciparum equilibrative nucleoside transporter 1 inhibitors that kill malaria parasites. | Frame IJ, Deniskin R, Rinderspacher A, Katz F, Deng SX, Moir RD, Adjalley SH, Coburn-Flynn O, Fidock DA, Willis IM, Landry DW, Akabas MH | ACS chemical biology | 25602169 | ACS Chem Biol | 2015 Mar 20 |
| Profiling the Essential Nature of Lipid Metabolism in Asexual Blood and Gametocyte Stages of Plasmodium falciparum. | Gulati S, Ekland EH, Ruggles KV, Chan RB, Jayabalasingham B, Zhou B, Mantel PY, Lee MC, Spottiswoode N, Coburn-Flynn O, Hjelmqvist D, Worgall TS, Marti M, Di Paolo G, Fidock DA | Cell host & microbe | 26355219 | Cell Host Microbe | 2015 Sep 9 |
| Multicolor bioluminescence boosts malaria research: quantitative dual-color assay and single-cell imaging in Plasmodium falciparum parasites. | Cevenini L, Camarda G, Michelini E, Siciliano G, Calabretta MM, Bona R, Kumar TR, Cara A, Branchini BR, Fidock DA, Roda A, Alano P | Analytical chemistry | 25102353 | Anal Chem | 2014 Sep 2 |
| Discrimination of potent inhibitors of Toxoplasma gondii enoyl-acyl carrier protein reductase by a thermal shift assay. | Afanador GA, Muench SP, McPhillie M, Fomovska A, Schön A, Zhou Y, Cheng G, Stec J, Freundlich JS, Shieh HM, Anderson JW, Jacobus DP, Fidock DA, Kozikowski AP, Fishwick CW, Rice DW, Freire E, McLeod R, Prigge ST | Biochemistry | 24295325 | Biochemistry | 2013 Dec 23 |
| Type II fatty acid biosynthesis is essential for Plasmodium falciparum sporozoite development in the midgut of Anopheles mosquitoes. | van Schaijk BC, Kumar TR, Vos MW, Richman A, van Gemert GJ, Li T, Eappen AG, Williamson KC, Morahan BJ, Fishbaugher M, Kennedy M, Camargo N, Khan SM, Janse CJ, Sim KL, Hoffman SL, Kappe SH, Sauerwein RW, Fidock DA, Vaughan AM | Eukaryotic cell | 24297444 | Eukaryot Cell | 2014 May |
| Recent insights into fatty acid acquisition and metabolism in malarial parasites. | Jayabalasingham B, Menard R, Fidock DA | F1000 biology reports | 20948809 | F1000 Biol Rep | 2010 Mar 25 |
| How can we identify parasite genes that underlie antimalarial drug resistance? | Anderson T, Nkhoma S, Ecker A, Fidock D | Pharmacogenomics | 21174623 | Pharmacogenomics | 2011 Jan |
| Rapid mRNA-display selection of an IL-6 inhibitor using continuous-flow magnetic separation. | Olson CA, Adams JD, Takahashi TT, Qi H, Howell SM, Wu TT, Roberts RW, Sun R, Soh HT | Angewandte Chemie (International ed. in English) | 21761516 | Angew Chem Int Ed Engl | 2011 Aug 29 |
| Single-round, multiplexed antibody mimetic design through mRNA display. | Olson CA, Nie J, Diep J, Al-Shyoukh I, Takahashi TT, Al-Mawsawi LQ, Bolin JM, Elwell AL, Swanson S, Stewart R, Thomson JA, Soh HT, Roberts RW, Sun R | Angewandte Chemie (International ed. in English) | 23125174 | Angew Chem Int Ed Engl | 2012 Dec 7 |
| Recombinant probes reveal dynamic localization of CaMKIIα within somata of cortical neurons. | Mora RJ, Roberts RW, Arnold DB | The Journal of neuroscience : the official journal of the Society for Neuroscience | 24005308 | J Neurosci | 2013 Sep 4 |
| α1-FANGs: Protein Ligands Selective for the α-Bungarotoxin Site of the α1-Nicotinic Acetylcholine Receptor. | Nichols AL, Noridomi K, Hughes CR, Jalali-Yazdi F, Eaton JB, Lai LH, Advani G, Lukas RJ, Lester HA, Chen L, Roberts RW | ACS chemical biology | 30059207 | ACS Chem Biol | 2018 Sep 21 |
| Recombinant probes for visualizing endogenous synaptic proteins in living neurons. | Gross GG, Junge JA, Mora RJ, Kwon HB, Olson CA, Takahashi TT, Liman ER, Ellis-Davies GC, McGee AW, Sabatini BL, Roberts RW, Arnold DB | Neuron | 23791193 | Neuron | 2013 Jun 19 |
| An E3-ligase-based method for ablating inhibitory synapses. | Gross GG, Straub C, Perez-Sanchez J, Dempsey WP, Junge JA, Roberts RW, Trinh le A, Fraser SE, De Koninck Y, De Koninck P, Sabatini BL, Arnold DB | Nature methods | 27271196 | Nat Methods | 2016 Aug |
| A comprehensive biophysical description of pairwise epistasis throughout an entire protein domain. | Olson CA, Wu NC, Sun R | Current biology : CB | 25455030 | Curr Biol | 2014 Nov 17 |
| Robust, quantitative analysis of proteins using peptide immunoreagents, in vitro translation, and an ultrasensitive acoustic resonant sensor. | Jalali-Yazdi F, Corbin JM, Takahashi TT, Roberts RW | Analytical chemistry | 24749546 | Anal Chem | 2014 May 20 |
| Particle display: a quantitative screening method for generating high-affinity aptamers. | Wang J, Gong Q, Maheshwari N, Eisenstein M, Arcila ML, Kosik KS, Soh HT | Angewandte Chemie (International ed. in English) | 24644057 | Angew Chem Int Ed Engl | 2014 May 5 |
| Importance of controlling nanotube density for highly sensitive and reliable biosensors functional in physiological conditions. | Ishikawa FN, Curreli M, Olson CA, Liao HI, Sun R, Roberts RW, Cote RJ, Thompson ME, Zhou C | ACS nano | 21028792 | ACS Nano | 2010 Nov 23 |
| Serum stable natural peptides designed by mRNA display. | Howell SM, Fiacco SV, Takahashi TT, Jalali-Yazdi F, Millward SW, Hu B, Wang P, Roberts RW | Scientific reports | 25234472 | Sci Rep | 2014 Sep 19 |
| High-Throughput Measurement of Binding Kinetics by mRNA Display and Next-Generation Sequencing. | Jalali-Yazdi F, Lai LH, Takahashi TT, Roberts RW | Angewandte Chemie (International ed. in English) | 26914638 | Angew Chem Int Ed Engl | 2016 Mar 14 |
| General, Label-Free Method for Determining K(d) and Ligand Concentration Simultaneously. | Jalali-Yazdi F, Takahashi TT, Roberts RW | Analytical chemistry | 26485531 | Anal Chem | 2015 Dec 1 |
| Immune defense mechanisms in the Caenorhabditis elegans intestinal epithelium. | Pukkila-Worley R, Ausubel FM | Current opinion in immunology | 22236697 | Curr Opin Immunol | 2012 Feb |
| Mitochondrial UPR-regulated innate immunity provides resistance to pathogen infection. | Pellegrino MW, Nargund AM, Kirienko NV, Gillis R, Fiorese CJ, Haynes CM | Nature | 25274306 | Nature | 2014 Dec 18 |
| Insect-derived cecropins display activity against Acinetobacter baumannii in a whole-animal high-throughput Caenorhabditis elegans model. | Jayamani E, Rajamuthiah R, Larkins-Ford J, Fuchs BB, Conery AL, Vilcinskas A, Ausubel FM, Mylonakis E | Antimicrobial agents and chemotherapy | 25583713 | Antimicrob Agents Chemother | 2015 Mar |
| Host translational inhibition by Pseudomonas aeruginosa Exotoxin A Triggers an immune response in Caenorhabditis elegans. | McEwan DL, Kirienko NV, Ausubel FM | Cell host & microbe | 22520464 | Cell Host Microbe | 2012 Apr 19 |
| Pseudomonas aeruginosa disrupts Caenorhabditis elegans iron homeostasis, causing a hypoxic response and death. | Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM | Cell host & microbe | 23601103 | Cell Host Microbe | 2013 Apr 17 |
| Aberrant Activation of p38 MAP Kinase-Dependent Innate Immune Responses Is Toxic to Caenorhabditis elegans. | Cheesman HK, Feinbaum RL, Thekkiniath J, Dowen RH, Conery AL, Pukkila-Worley R | G3 (Bethesda, Md.) | 26818074 | G3 (Bethesda) | 2016 Jan 27 |
| A High-Content, Phenotypic Screen Identifies Fluorouridine as an Inhibitor of Pyoverdine Biosynthesis and Pseudomonas aeruginosa Virulence. | Kirienko DR, Revtovich AV, Kirienko NV | mSphere | 27579370 | mSphere | 2016 Jul-Aug |
| The evolutionarily conserved mediator subunit MDT-15/MED15 links protective innate immune responses and xenobiotic detoxification. | Pukkila-Worley R, Feinbaum RL, McEwan DL, Conery AL, Ausubel FM | PLoS pathogens | 24875643 | PLoS Pathog | 2014 May |
| Stimulation of host immune defenses by a small molecule protects C. elegans from bacterial infection. | Pukkila-Worley R, Feinbaum R, Kirienko NV, Larkins-Ford J, Conery AL, Ausubel FM | PLoS genetics | 22719261 | PLoS Genet | 2012 |
| Genome-wide identification of Pseudomonas aeruginosa virulence-related genes using a Caenorhabditis elegans infection model. | Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR, Ausubel FM | PLoS pathogens | 22911607 | PLoS Pathog | 2012 |
| Antibacterial properties of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile. | Rajamuthiah R, Jayamani E, Majed H, Conery AL, Kim W, Kwon B, Fuchs BB, Kelso MJ, Ausubel FM, Mylonakis E | Bioorganic & medicinal chemistry letters | 26459212 | Bioorg Med Chem Lett | 2015 Nov 15 |
| Investment in secreted enzymes during nutrient-limited growth is utility dependent. | Cezairliyan B, Ausubel FM | Proceedings of the National Academy of Sciences of the United States of America | 28847943 | Proc Natl Acad Sci U S A | 2017 Sep 12 |
| Pseudomonas aeruginosa RhlR is required to neutralize the cellular immune response in a Drosophila melanogaster oral infection model. | Limmer S, Haller S, Drenkard E, Lee J, Yu S, Kocks C, Ausubel FM, Ferrandon D | Proceedings of the National Academy of Sciences of the United States of America | 21987808 | Proc Natl Acad Sci U S A | 2011 Oct 18 |
| An image analysis toolbox for high-throughput C. elegans assays. | Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O'Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE | Nature methods | 22522656 | Nat Methods | 2012 Apr 22 |
| RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS. | Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE | Proceedings. IEEE International Symposium on Biomedical Imaging | 21383863 | Proc IEEE Int Symp Biomed Imaging | 2010 Jun 21 |
| Morphology-guided graph search for untangling objects: C. elegans analysis. | Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C | Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention | 20879454 | Med Image Comput Comput Assist Interv | 2010 |
| Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants. | Djonović S, Urbach JM, Drenkard E, Bush J, Feinbaum R, Ausubel JL, Traficante D, Risech M, Kocks C, Fischbach MA, Priebe GP, Ausubel FM | PLoS pathogens | 23505373 | PLoS Pathog | 2013 Mar |
| Repurposing salicylanilide anthelmintic drugs to combat drug resistant Staphylococcus aureus. | Rajamuthiah R, Fuchs BB, Conery AL, Kim W, Jayamani E, Kwon B, Ausubel FM, Mylonakis E | PloS one | 25897961 | PLoS One | 2015 |
| A Defensin from the Model Beetle Tribolium castaneum Acts Synergistically with Telavancin and Daptomycin against Multidrug Resistant Staphylococcus aureus. | Rajamuthiah R, Jayamani E, Conery AL, Fuchs BB, Kim W, Johnston T, Vilcinskas A, Ausubel FM, Mylonakis E | PloS one | 26062137 | PLoS One | 2015 |
| Mitophagy confers resistance to siderophore-mediated killing by Pseudomonas aeruginosa. | Kirienko NV, Ausubel FM, Ruvkun G | Proceedings of the National Academy of Sciences of the United States of America | 25624506 | Proc Natl Acad Sci U S A | 2015 Feb 10 |
| Quorum-sensing regulator RhlR but not its autoinducer RhlI enables Pseudomonas to evade opsonization. | Haller S, Franchet A, Hakkim A, Chen J, Drenkard E, Yu S, Schirmeier S, Li Z, Martins N, Ausubel FM, Liégeois S, Ferrandon D | EMBO reports | 29523648 | EMBO Rep | 2018 May |
| Identification of Pseudomonas aeruginosa phenazines that kill Caenorhabditis elegans. | Cezairliyan B, Vinayavekhin N, Grenfell-Lee D, Yuen GJ, Saghatelian A, Ausubel FM | PLoS pathogens | 23300454 | PLoS Pathog | 2013 Jan |
| Assessing Pseudomonas virulence with a nonmammalian host: Drosophila melanogaster. | Haller S, Limmer S, Ferrandon D | Methods in molecular biology (Clifton, N.J.) | 24818946 | Methods Mol Biol | 2014 |
| High-throughput screening for novel anti-infectives using a C. elegans pathogenesis model. | Conery AL, Larkins-Ford J, Ausubel FM, Kirienko NV | Current protocols in chemical biology | 24652621 | Curr Protoc Chem Biol | 2014 Mar 14 |
| Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway. | McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM | BMC biology | 27927200 | BMC Biol | 2016 Dec 7 |
| The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans. | Vasquez-Rifo A, Veksler-Lublinsky I, Cheng Z, Ausubel FM, Ambros V | Genome biology | 31823826 | Genome Biol | 2019 Dec 10 |
| ABCDs of the Relative Contributions of Pseudomonas aeruginosa Quorum Sensing Systems to Virulence in Diverse Nonvertebrate Hosts. | Vasquez-Rifo A, Cook J, McEwan DL, Shikara D, Ausubel FM, Di Cara F, Cheng Z | mBio | 35311532 | mBio | 2022 Apr 26 |
| Somatic STAT3 mutations in large granular lymphocytic leukemia. | Koskela HL, Eldfors S, Ellonen P, van Adrichem AJ, Kuusanmäki H, Andersson EI, Lagström S, Clemente MJ, Olson T, Jalkanen SE, Majumder MM, Almusa H, Edgren H, Lepistö M, Mattila P, Guinta K, Koistinen P, Kuittinen T, Penttinen K, Parsons A, Knowles J, Saarela J, Wennerberg K, Kallioniemi O, Porkka K, Loughran TP Jr, Heckman CA, Maciejewski JP, Mustjoki S | The New England journal of medicine | 22591296 | N Engl J Med | 2012 May 17 |
| Discovery of somatic STAT5b mutations in large granular lymphocytic leukemia. | Rajala HL, Eldfors S, Kuusanmäki H, van Adrichem AJ, Olson T, Lagström S, Andersson EI, Jerez A, Clemente MJ, Yan Y, Zhang D, Awwad A, Ellonen P, Kallioniemi O, Wennerberg K, Porkka K, Maciejewski JP, Loughran TP Jr, Heckman C, Mustjoki S | Blood | 23596048 | Blood | 2013 May 30 |
| Activating somatic mutations outside the SH2-domain of STAT3 in LGL leukemia. | Andersson E, Kuusanmäki H, Bortoluzzi S, Lagström S, Parsons A, Rajala H, van Adrichem A, Eldfors S, Olson T, Clemente MJ, Laasonen A, Ellonen P, Heckman C, Loughran TP, Maciejewski JP, Mustjoki S | Leukemia | 26419508 | Leukemia | 2016 May |
| High incidence of activating STAT5B mutations in CD4-positive T-cell large granular lymphocyte leukemia. | Andersson EI, Tanahashi T, Sekiguchi N, Gasparini VR, Bortoluzzi S, Kawakami T, Matsuda K, Mitsui T, Eldfors S, Bortoluzzi S, Coppe A, Binatti A, Lagström S, Ellonen P, Fukushima N, Nishina S, Senoo N, Sakai H, Nakazawa H, Kwong YL, Loughran TP, Maciejewski JP, Mustjoki S, Ishida F | Blood | 27697773 | Blood | 2016 Nov 17 |
| Novel somatic mutations in large granular lymphocytic leukemia affecting the STAT-pathway and T-cell activation. | Andersson EI, Rajala HL, Eldfors S, Ellonen P, Olson T, Jerez A, Clemente MJ, Kallioniemi O, Porkka K, Heckman C, Loughran TP Jr, Maciejewski JP, Mustjoki S | Blood cancer journal | 24317090 | Blood Cancer J | 2013 Dec 6 |
| Efficacy of rabbit anti-thymocyte globulin in severe aplastic anemia. | Afable MG 2nd, Shaik M, Sugimoto Y, Elson P, Clemente M, Makishima H, Sekeres MA, Lichtin A, Advani A, Kalaycio M, Tiu RV, O'Keefe CL, Maciejewski JP | Haematologica | 21606164 | Haematologica | 2011 Sep |
| The analysis of clonal diversity and therapy responses using STAT3 mutations as a molecular marker in large granular lymphocytic leukemia. | Rajala HL, Olson T, Clemente MJ, Lagström S, Ellonen P, Lundan T, Hamm DE, Zaman SA, Lopez Marti JM, Andersson EI, Jerez A, Porkka K, Maciejewski JP, Loughran TP, Mustjoki S | Haematologica | 25281507 | Haematologica | 2015 Jan |
| Returns of the living dead: therapeutic action of irradiated and mitotically inactivated embryonic stem cells. | Gold JD, Wu JC | Circulation research | 23104873 | Circ Res | 2012 Oct 26 |
| Bioluminescence reporter gene imaging characterize human embryonic stem cell-derived teratoma formation. | Su W, Zhou M, Zheng Y, Fan Y, Wang L, Han Z, Kong D, Zhao RC, Wu JC, Xiang R, Li Z | Journal of cellular biochemistry | 21328457 | J Cell Biochem | 2011 Mar |
| Microfluidic single-cell real-time PCR for comparative analysis of gene expression patterns. | Sanchez-Freire V, Ebert AD, Kalisky T, Quake SR, Wu JC | Nature protocols | 22481529 | Nat Protoc | 2012 Apr 5 |
| Persistent donor cell gene expression among human induced pluripotent stem cells contributes to differences with human embryonic stem cells. | Ghosh Z, Wilson KD, Wu Y, Hu S, Quertermous T, Wu JC | PloS one | 20126639 | PLoS One | 2010 Feb 1 |
| Control of Immune Response to Allogeneic Embryonic Stem Cells by CD3 Antibody-Mediated Operational Tolerance Induction. | Calderon D, Prot M, You S, Marquet C, Bellamy V, Bruneval P, Valette F, de Almeida P, Wu JC, Pucéat M, Menasché P, Chatenoud L | American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons | 26492394 | Am J Transplant | 2016 Feb |
| Gene correction in human embryonic and induced pluripotent stem cells: promises and challenges ahead. | Narsinh KH, Wu JC | Molecular therapy : the journal of the American Society of Gene Therapy | 20514030 | Mol Ther | 2010 Jun |
| Comparison of human induced pluripotent and embryonic stem cells: fraternal or identical twins? | Narsinh KH, Plews J, Wu JC | Molecular therapy : the journal of the American Society of Gene Therapy | 21455209 | Mol Ther | 2011 Apr |
| Effects of long-term culture on human embryonic stem cell aging. | Xie X, Hiona A, Lee AS, Cao F, Huang M, Li Z, Cherry A, Pei X, Wu JC | Stem cells and development | 20629482 | Stem Cells Dev | 2011 Jan |
| In vivo directed differentiation of pluripotent stem cells for skeletal regeneration. | Levi B, Hyun JS, Montoro DT, Lo DD, Chan CK, Hu S, Sun N, Lee M, Grova M, Connolly AJ, Wu JC, Gurtner GC, Weissman IL, Wan DC, Longaker MT | Proceedings of the National Academy of Sciences of the United States of America | 23169671 | Proc Natl Acad Sci U S A | 2012 Dec 11 |
| Human Engineered Heart Muscles Engraft and Survive Long Term in a Rodent Myocardial Infarction Model. | Riegler J, Tiburcy M, Ebert A, Tzatzalos E, Raaz U, Abilez OJ, Shen Q, Kooreman NG, Neofytou E, Chen VC, Wang M, Meyer T, Tsao PS, Connolly AJ, Couture LA, Gold JD, Zimmermann WH, Wu JC | Circulation research | 26291556 | Circ Res | 2015 Sep 25 |
| Engraftment of embryonic stem cells and differentiated progeny by host conditioning with total lymphoid irradiation and regulatory T cells. | Pan Y, Leveson-Gower DB, de Almeida PE, Pierini A, Baker J, Florek M, Nishikii H, Kim BS, Ke R, Wu JC, Negrin RS | Cell reports | 25801020 | Cell Rep | 2015 Mar 24 |
| Alloimmune Responses of Humanized Mice to Human Pluripotent Stem Cell Therapeutics. | Kooreman NG, de Almeida PE, Stack JP, Nelakanti RV, Diecke S, Shao NY, Swijnenburg RJ, Sanchez-Freire V, Matsa E, Liu C, Connolly AJ, Hamming JF, Quax PHA, Brehm MA, Greiner DL, Shultz LD, Wu JC | Cell reports | 28834758 | Cell Rep | 2017 Aug 22 |
| Dissecting the oncogenic and tumorigenic potential of differentiated human induced pluripotent stem cells and human embryonic stem cells. | Ghosh Z, Huang M, Hu S, Wilson KD, Dey D, Wu JC | Cancer research | 21646469 | Cancer Res | 2011 Jul 15 |
| Pluripotent stem cells: immune to the immune system? | Pearl JI, Kean LS, Davis MM, Wu JC | Science translational medicine | 23241742 | Sci Transl Med | 2012 Dec 12 |
| Immunogenicity of pluripotent stem cells and their derivatives. | de Almeida PE, Ransohoff JD, Nahid A, Wu JC | Circulation research | 23371903 | Circ Res | 2013 Feb 1 |
| Short-term immunosuppression promotes engraftment of embryonic and induced pluripotent stem cells. | Pearl JI, Lee AS, Leveson-Gower DB, Sun N, Ghosh Z, Lan F, Ransohoff J, Negrin RS, Davis MM, Wu JC | Cell stem cell | 21362570 | Cell Stem Cell | 2011 Mar 4 |
| Single cell transcriptional profiling reveals heterogeneity of human induced pluripotent stem cells. | Narsinh KH, Sun N, Sanchez-Freire V, Lee AS, Almeida P, Hu S, Jan T, Wilson KD, Leong D, Rosenberg J, Yao M, Robbins RC, Wu JC | The Journal of clinical investigation | 21317531 | J Clin Invest | 2011 Mar |
| Costimulation-adhesion blockade is superior to cyclosporine A and prednisone immunosuppressive therapy for preventing rejection of differentiated human embryonic stem cells following transplantation. | Huber BC, Ransohoff JD, Ransohoff KJ, Riegler J, Ebert A, Kodo K, Gong Y, Sanchez-Freire V, Dey D, Kooreman NG, Diecke S, Zhang WY, Odegaard J, Hu S, Gold JD, Robbins RC, Wu JC | Stem cells (Dayton, Ohio) | 24038578 | Stem Cells | 2013 Nov |
| Transplanted terminally differentiated induced pluripotent stem cells are accepted by immune mechanisms similar to self-tolerance. | de Almeida PE, Meyer EH, Kooreman NG, Diecke S, Dey D, Sanchez-Freire V, Hu S, Ebert A, Odegaard J, Mordwinkin NM, Brouwer TP, Lo D, Montoro DT, Longaker MT, Negrin RS, Wu JC | Nature communications | 24875164 | Nat Commun | 2014 May 30 |
| Systemic Upregulation of IL-10 (Interleukin-10) Using a Nonimmunogenic Vector Reduces Growth and Rate of Dissecting Abdominal Aortic Aneurysm. | Adam M, Kooreman NG, Jagger A, Wagenhäuser MU, Mehrkens D, Wang Y, Kayama Y, Toyama K, Raaz U, Schellinger IN, Maegdefessel L, Spin JM, Hamming JF, Quax PHA, Baldus S, Wu JC, Tsao PS | Arteriosclerosis, thrombosis, and vascular biology | 29880489 | Arterioscler Thromb Vasc Biol | 2018 Aug |
| Immunization-induced antigen archiving enhances local memory CD8+ T cell responses following an unrelated viral infection. | Doan TA, Forward TS, Schafer JB, Lucas ED, Fleming I, Uecker-Martin A, Ayala E, Guthmiller JJ, Hesselberth JR, Morrison TE, Tamburini BAJ | NPJ vaccines | 38514656 | NPJ Vaccines | 2024 Mar 21 |
| Co-regulator activity of Mediator of DNA Damage Checkpoint 1 (MDC1) is associated with DNA repair dysfunction and PARP inhibitor sensitivity in lobular carcinoma of the breast. | Sottnik JL, Shackleford MT, Nesiba CS, Richer AL, Fleischmann Z, Swartz JM, Rowland CE, Musick M, Fu R, Myler LR, Opresko PL, Mehrotra S, Sokol ES, Hesselberth JR, Diamond JR, Sikora MJ | bioRxiv : the preprint server for biology | 39677775 | bioRxiv | 2025 Mar 17 |
| GPR182 is a lipoprotein receptor for dietary fat absorption. | Sun Z, Torphy RJ, Miller EN, Darehshouri A, Vigil I, Terai T, Eck E, Sun Y, Guo Y, Yee EJ, Hu J, Kedl RM, Lasda EL, Hesselberth JR, MacLean P, Bruce KD, Randolph GJ, Schulick RD, Zhu Y | bioRxiv : the preprint server for biology | 39975353 | bioRxiv | 2025 Feb 7 |
| Molecular tracking devices quantify antigen distribution and archiving in the murine lymph node. | Walsh SM, Sheridan RM, Lucas ED, Doan TA, Ware BC, Schafer J, Fu R, Burchill MA, Hesselberth JR, Tamburini BAJ | eLife | 33843587 | Elife | 2021 Apr 12 |
| Islet-antigen reactive B cells display a unique phenotype and BCR repertoire in autoantibody positive and recent-onset type 1 diabetes patients. | Nicholas CA, Tensun FA, Evans SA, Toole KP, Broncucia H, Hesselberth JR, Gottlieb PA, Wells KL, Smith MJ | bioRxiv : the preprint server for biology | 38979376 | bioRxiv | 2024 Jun 25 |
| A specific gene expression program underlies antigen archiving by lymphatic endothelial cells in mammalian lymph nodes. | Tamburini B, Sheridan R, Doan T, Lucas C, Forward T, Fleming I, Uecker-Martin A, Morrison T, Hesselberth J | Research square | 39711554 | Res Sq | 2024 Dec 10 |
| Simultaneous measurement of biochemical phenotypes and gene expression in single cells. | Richer AL, Riemondy KA, Hardie L, Hesselberth JR | Nucleic acids research | 32286626 | Nucleic Acids Res | 2020 Jun 4 |
| Chikungunya virus infection disrupts lymph node lymphatic endothelial cell composition and function via MARCO. | Lucas CJ, Sheridan RM, Reynoso GV, Davenport BJ, McCarthy MK, Martin A, Hesselberth JR, Hickman HD, Tamburini BA, Morrison TE | JCI insight | 38194268 | JCI Insight | 2024 Jan 9 |
| MARCO(+) lymphatic endothelial cells sequester arthritogenic alphaviruses to limit viremia and viral dissemination. | Carpentier KS, Sheridan RM, Lucas CJ, Davenport BJ, Li FS, Lucas ED, McCarthy MK, Reynoso GV, May NA, Tamburini BAJ, Hesselberth JR, Hickman HD, Morrison TE | The EMBO journal | 34618370 | EMBO J | 2021 Nov 15 |
| A specific and portable gene expression program underlies antigen archiving by lymphatic endothelial cells. | Sheridan RM, Doan TA, Lucas C, Forward TS, Uecker-Martin A, Morrison TE, Hesselberth JR, Tamburini BAJ | bioRxiv : the preprint server for biology | 38617225 | bioRxiv | 2024 Apr 2 |
| Genomic Mosaicism Formed by Somatic Variation in the Aging and Diseased Brain. | Costantino I, Nicodemus J, Chun J | Genes | 34356087 | Genes (Basel) | 2021 Jul 14 |
| Human brain small extracellular vesicles contain selectively packaged, full-length mRNA. | Ransom LS, Liu CS, Dunsmore E, Palmer CR, Nicodemus J, Ziomek D, Williams N, Chun J | Cell reports | 38578831 | Cell Rep | 2024 Apr 23 |
| CAQK, a peptide associating with extracellular matrix components targets sites of demyelinating injuries. | Abi-Ghanem C, Jonnalagadda D, Chun J, Kihara Y, Ranscht B | Frontiers in cellular neuroscience | 36072569 | Front Cell Neurosci | 2022 |
| Altered cell and RNA isoform diversity in aging Down syndrome brains. | Palmer CR, Liu CS, Romanow WJ, Lee MH, Chun J | Proceedings of the National Academy of Sciences of the United States of America | 34795060 | Proc Natl Acad Sci U S A | 2021 Nov 23 |
| Somatic genomic mosaicism in the brain: Identified mutations provide challenges and opportunities for the clinic. | Chun J | Med (New York, N.Y.) | 36242998 | Med | 2022 Oct 14 |
| RNA Isoform Diversity in Human Neurodegenerative Diseases. | Liu CS, Park C, Ngo T, Saikumar J, Palmer CR, Shahnaee A, Romanow WJ, Chun J | eNeuro | 39658200 | eNeuro | 2024 Dec |
| Modeling the Aging Human Lung: Generation of a Senescent Human Lung Organoid Culture System. | Aspal M, Pushlar N, Melameka M, McVicar RN, Smith E, Ogunyamoju T, Kumar M, Marth JD, Chun J, Snyder EY, Leibel SL | bioRxiv : the preprint server for biology | 40060424 | bioRxiv | 2025 Feb 26 |
| Extraction and Purification of Single Nuclei from Frozen Human Brain Tissue. | Palmer CR, Chun J | Methods in molecular biology (Clifton, N.J.) | 36399263 | Methods Mol Biol | 2023 |
| Nucleoside Reverse Transcriptase Inhibitor Exposure Is Associated with Lower Alzheimer's Disease Risk: A Retrospective Cohort Proof-of-Concept Study. | Chow TW, Raupp M, Reynolds MW, Li S, Kaeser GE, Chun J | Pharmaceuticals (Basel, Switzerland) | 38675371 | Pharmaceuticals (Basel) | 2024 Mar 22 |
| Genetic architecture of natural variation of cardiac performance from flies to humans. | Saha S, Spinelli L, Castro Mondragon JA, Kervadec A, Lynott M, Kremmer L, Roder L, Krifa S, Torres M, Brun C, Vogler G, Bodmer R, Colas AR, Ocorr K, Perrin L | eLife | 36383075 | Elife | 2022 Nov 16 |
| Mitochondrial MICOS complex genes, implicated in hypoplastic left heart syndrome, maintain cardiac contractility and actomyosin integrity. | Birker K, Ge S, Kirkland NJ, Theis JL, Marchant J, Fogarty ZC, Missinato MA, Kalvakuri S, Grossfeld P, Engler AJ, Ocorr K, Nelson TJ, Colas AR, Olson TM, Vogler G, Bodmer R | eLife | 37404133 | Elife | 2023 Jul 5 |
| Multiplatform modeling of atrial fibrillation identifies phospholamban as a central regulator of cardiac rhythm. | Kervadec A, Kezos J, Ni H, Yu M, Marchant J, Spiering S, Kannan S, Kwon C, Andersen P, Bodmer R, Grandi E, Ocorr K, Colas AR | Disease models & mechanisms | 37293707 | Dis Model Mech | 2023 Jul 1 |
| Conserved transcription factors promote cell fate stability and restrict reprogramming potential in differentiated cells. | Missinato MA, Murphy S, Lynott M, Yu MS, Kervadec A, Chang YL, Kannan S, Loreti M, Lee C, Amatya P, Tanaka H, Huang CT, Puri PL, Kwon C, Adams PD, Qian L, Sacco A, Andersen P, Colas AR | Nature communications | 36973293 | Nat Commun | 2023 Mar 27 |
| A torpor-like state (TLS) in mice slows blood epigenetic aging and prolongs healthspan. | Jayne L, Lavin-Peter A, Roessler J, Tyshkovskiy A, Antoszewski M, Ren E, Markovski A, Sun S, Yao H, Sankaran VG, Gladyshev VN, Brooke RT, Horvath S, Griffith EC, Hrvatin S | bioRxiv : the preprint server for biology | 38585858 | bioRxiv | 2024 Mar 25 |
| COVID-19 is an emergent disease of aging. | Santesmasses D, Castro JP, Zenin AA, Shindyapina AV, Gerashchenko MV, Zhang B, Kerepesi C, Yim SH, Fedichev PO, Gladyshev VN | Aging cell | 33006233 | Aging Cell | 2020 Oct |
| Ectopic cervical thymi and no thymic involution until midlife in naked mole rats. | Emmrich S, Tolibzoda Zakusilo F, Trapp A, Zhou X, Zhang Q, Irving EM, Drage MG, Zhang Z, Gladyshev VN, Seluanov A, Gorbunova V | Aging cell | 34596321 | Aging Cell | 2021 Oct |
| Causality-enriched epigenetic age uncouples damage and adaptation. | Ying K, Liu H, Tarkhov AE, Sadler MC, Lu AT, Moqri M, Horvath S, Kutalik Z, Shen X, Gladyshev VN | Nature aging | 38243142 | Nat Aging | 2024 Feb |
| Age-associated clonal B cells drive B cell lymphoma in mice. | Castro JP, Shindyapina AV, Barbieri A, Ying K, Strelkova OS, Paulo JA, Tyshkovskiy A, Meinl R, Kerepesi C, Petrashen AP, Mariotti M, Meer MV, Hu Y, Karamyshev A, Losyev G, Galhardo M, Logarinho E, Indzhykulian AA, Gygi SP, Sedivy JM, Manis JP, Gladyshev VN | Nature aging | 39117982 | Nat Aging | 2024 Oct |
| Multi-omic rejuvenation and life span extension on exposure to youthful circulation. | Zhang B, Lee DE, Trapp A, Tyshkovskiy A, Lu AT, Bareja A, Kerepesi C, McKay LK, Shindyapina AV, Dmitriev SE, Baht GS, Horvath S, Gladyshev VN, White JP | Nature aging | 37500973 | Nat Aging | 2023 Aug |
| Molecular Damage in Aging. | Gladyshev VN, Kritchevsky SB, Clarke SG, Cuervo AM, Fiehn O, de Magalhães JP, Mau T, Maes M, Moritz R, Niedernhofer LJ, Van Schaftingen E, Tranah GJ, Walsh K, Yura Y, Zhang B, Cummings SR | Nature aging | 36846190 | Nat Aging | 2021 Dec |
| Biological age is increased by stress and restored upon recovery. | Poganik JR, Zhang B, Baht GS, Tyshkovskiy A, Deik A, Kerepesi C, Yim SH, Lu AT, Haghani A, Gong T, Hedman AM, Andolf E, Pershagen G, Almqvist C, Clish CB, Horvath S, White JP, Gladyshev VN | Cell metabolism | 37086720 | Cell Metab | 2023 May 2 |
| Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. | Mitchell W, Goeminne LJE, Tyshkovskiy A, Zhang S, Chen JY, Paulo JA, Pierce KA, Choy AH, Clish CB, Gygi SP, Gladyshev VN | eLife | 38517750 | Elife | 2024 Mar 22 |
| A torpor-like state in mice slows blood epigenetic aging and prolongs healthspan. | Jayne L, Lavin-Peter A, Roessler J, Tyshkovskiy A, Antoszewski M, Ren E, Markovski A, Sun S, Yao H, Sankaran VG, Gladyshev VN, Brooke RT, Horvath S, Griffith EC, Hrvatin S | Nature aging | 40055478 | Nat Aging | 2025 Mar |
| On the cause of aging and control of lifespan: heterogeneity leads to inevitable damage accumulation, causing aging; control of damage composition and rate of accumulation define lifespan. | Gladyshev VN | BioEssays : news and reviews in molecular, cellular and developmental biology | 22915358 | Bioessays | 2012 Nov |
| Using DNA Methylation Profiling to Evaluate Biological Age and Longevity Interventions. | Petkovich DA, Podolskiy DI, Lobanov AV, Lee SG, Miller RA, Gladyshev VN | Cell metabolism | 28380383 | Cell Metab | 2017 Apr 4 |
| DNA methylation networks underlying mammalian traits. | Haghani A, Li CZ, Robeck TR, Zhang J, Lu AT, Ablaeva J, Acosta-Rodríguez VA, Adams DM, Alagaili AN, Almunia J, Aloysius A, Amor NMS, Ardehali R, Arneson A, Baker CS, Banks G, Belov K, Bennett NC, Black P, Blumstein DT, Bors EK, Breeze CE, Brooke RT, Brown JL, Carter G, Caulton A, Cavin JM, Chakrabarti L, Chatzistamou I, Chavez AS, Chen H, Cheng K, Chiavellini P, Choi OW, Clarke S, Cook JA, Cooper LN, Cossette ML, Day J, DeYoung J, Dirocco S, Dold C, Dunnum JL, Ehmke EE, Emmons CK, Emmrich S, Erbay E, Erlacher-Reid C, Faulkes CG, Fei Z, Ferguson SH, Finno CJ, Flower JE, Gaillard JM, Garde E, Gerber L, Gladyshev VN, Goya RG, Grant MJ, Green CB, Hanson MB, Hart DW, Haulena M, Herrick K, Hogan AN, Hogg CJ, Hore TA, Huang T, Izpisua Belmonte JC, Jasinska AJ, Jones G, Jourdain E, Kashpur O, Katcher H, Katsumata E, Kaza V, Kiaris H, Kobor MS, Kordowitzki P, Koski WR, Krützen M, Kwon SB, Larison B, Lee SG, Lehmann M, Lemaître JF, Levine AJ, Li X, Li C, Lim AR, Lin DTS, Lindemann DM, Liphardt SW, Little TJ, Macoretta N, Maddox D, Matkin CO, Mattison JA, McClure M, Mergl J, Meudt JJ, Montano GA, Mozhui K, Munshi-South J, Murphy WJ, Naderi A, Nagy M, Narayan P, Nathanielsz PW, Nguyen NB, Niehrs C, Nyamsuren B, O'Brien JK, Ginn PO, Odom DT, Ophir AG, Osborn S, Ostrander EA, Parsons KM, Paul KC, Pedersen AB, Pellegrini M, Peters KJ, Petersen JL, Pietersen DW, Pinho GM, Plassais J, Poganik JR, Prado NA, Reddy P, Rey B, Ritz BR, Robbins J, Rodriguez M, Russell J, Rydkina E, Sailer LL, Salmon AB, Sanghavi A, Schachtschneider KM, Schmitt D, Schmitt T, Schomacher L, Schook LB, Sears KE, Seifert AW, Shafer ABA, Shindyapina AV, Simmons M, Singh K, Sinha I, Slone J, Snell RG, Soltanmohammadi E, Spangler ML, Spriggs M, Staggs L, Stedman N, Steinman KJ, Stewart DT, Sugrue VJ, Szladovits B, Takahashi JS, Takasugi M, Teeling EC, Thompson MJ, Van Bonn B, Vernes SC, Villar D, Vinters HV, Vu H, Wallingford MC, Wang N, Wilkinson GS, Williams RW, Yan Q, Yao M, Young BG, Zhang B, Zhang Z, Zhao Y, Zhao P, Zhou W, Zoller JA, Ernst J, Seluanov A, Gorbunova V, Yang XW, Raj K, Horvath S | Science (New York, N.Y.) | 37561875 | Science | 2023 Aug 11 |
| Applying deductive reasoning and the principles of particle physics to aging research. | Moldakozhayev A, Tskhay A, Gladyshev VN | Aging | 34543232 | Aging (Albany NY) | 2021 Sep 20 |
| COVID-19 mortality rate in children is U-shaped. | Khera N, Santesmasses D, Kerepesi C, Gladyshev VN | Aging | 34411000 | Aging (Albany NY) | 2021 Aug 18 |
| Rapamycin treatment during development extends life span and health span of male mice and Daphnia magna. | Shindyapina AV, Cho Y, Kaya A, Tyshkovskiy A, Castro JP, Deik A, Gordevicius J, Poganik JR, Clish CB, Horvath S, Peshkin L, Gladyshev VN | Science advances | 36112674 | Sci Adv | 2022 Sep 16 |
| Metabolism, homeostasis, and aging. | Moldakozhayev A, Gladyshev VN | Trends in endocrinology and metabolism: TEM | 36681595 | Trends Endocrinol Metab | 2023 Mar |
| Profiling epigenetic age in single cells. | Trapp A, Kerepesi C, Gladyshev VN | Nature aging | 36211119 | Nat Aging | 2021 Dec |
| Emerging rejuvenation strategies-Reducing the biological age. | Zhang B, Trapp A, Kerepesi C, Gladyshev VN | Aging cell | 34972247 | Aging Cell | 2022 Jan |
| Cap-independent translation of GPLD1 enhances markers of brain health in long-lived mutant and drug-treated mice. | Li X, Shi X, McPherson M, Hager M, Garcia GG, Miller RA | Aging cell | 35930768 | Aging Cell | 2022 Sep |
| Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging. | Kerepesi C, Zhang B, Lee SG, Trapp A, Gladyshev VN | Science advances | 34172448 | Sci Adv | 2021 Jun |
| Evolution of natural lifespan variation and molecular strategies of extended lifespan in yeast. | Kaya A, Phua CZJ, Lee M, Wang L, Tyshkovskiy A, Ma S, Barre B, Liu W, Harrison BR, Zhao X, Zhou X, Wasko BM, Bammler TK, Promislow DE, Kaeberlein M, Gladyshev VN | eLife | 34751131 | Elife | 2021 Nov 9 |
| Reprogramming to recover youthful epigenetic information and restore vision. | Lu Y, Brommer B, Tian X, Krishnan A, Meer M, Wang C, Vera DL, Zeng Q, Yu D, Bonkowski MS, Yang JH, Zhou S, Hoffmann EM, Karg MM, Schultz MB, Kane AE, Davidsohn N, Korobkina E, Chwalek K, Rajman LA, Church GM, Hochedlinger K, Gladyshev VN, Horvath S, Levine ME, Gregory-Ksander MS, Ksander BR, He Z, Sinclair DA | Nature | 33268865 | Nature | 2020 Dec |
| Four anti-aging drugs and calorie-restricted diet produce parallel effects in fat, brain, muscle, macrophages, and plasma of young mice. | Li X, McPherson M, Hager M, Lee M, Chang P, Miller RA | GeroScience | 36920743 | Geroscience | 2023 Aug |
| Validation of biomarkers of aging. | Moqri M, Herzog C, Poganik JR, Ying K, Justice JN, Belsky DW, Higgins-Chen AT, Chen BH, Cohen AA, Fuellen G, Hägg S, Marioni RE, Widschwendter M, Fortney K, Fedichev PO, Zhavoronkov A, Barzilai N, Lasky-Su J, Kiel DP, Kennedy BK, Cummings S, Slagboom PE, Verdin E, Maier AB, Sebastiano V, Snyder MP, Gladyshev VN, Horvath S, Ferrucci L | Nature medicine | 38355974 | Nat Med | 2024 Feb |
| Biomarkers of aging for the identification and evaluation of longevity interventions. | Moqri M, Herzog C, Poganik JR, Biomarkers of Aging Consortium, Justice J, Belsky DW, Higgins-Chen A, Moskalev A, Fuellen G, Cohen AA, Bautmans I, Widschwendter M, Ding J, Fleming A, Mannick J, Han JJ, Zhavoronkov A, Barzilai N, Kaeberlein M, Cummings S, Kennedy BK, Ferrucci L, Horvath S, Verdin E, Maier AB, Snyder MP, Sebastiano V, Gladyshev VN | Cell | 37657418 | Cell | 2023 Aug 31 |
| Defining the condensate landscape of fusion oncoproteins. | Tripathi S, Shirnekhi HK, Gorman SD, Chandra B, Baggett DW, Park CG, Somjee R, Lang B, Hosseini SMH, Pioso BJ, Li Y, Iacobucci I, Gao Q, Edmonson MN, Rice SV, Zhou X, Bollinger J, Mitrea DM, White MR, McGrail DJ, Jarosz DF, Yi SS, Babu MM, Mullighan CG, Zhang J, Sahni N, Kriwacki RW | Nature communications | 37770423 | Nat Commun | 2023 Sep 28 |
| Identification of protein aggregates in the aging vertebrate brain with prion-like and phase-separation properties. | Harel I, Chen YR, Ziv I, Singh PP, Heinzer D, Navarro Negredo P, Goshtchevsky U, Wang W, Astre G, Moses E, McKay A, Machado BE, Hebestreit K, Yin S, Sánchez Alvarado A, Jarosz DF, Brunet A | Cell reports | 38810650 | Cell Rep | 2024 Jun 25 |
| A Non-amyloid Prion Particle that Activates a Heritable Gene Expression Program. | Chakravarty AK, Smejkal T, Itakura AK, Garcia DM, Jarosz DF | Molecular cell | 31757755 | Mol Cell | 2020 Jan 16 |
| Biomolecular Condensation: A New Phase in Cancer Research. | Chakravarty AK, McGrail DJ, Lozanoski TM, Dunn BS, Shih DJH, Cirillo KM, Cetinkaya SH, Zheng WJ, Mills GB, Yi SS, Jarosz DF, Sahni N | Cancer discovery | 35852417 | Cancer Discov | 2022 Sep 2 |
| Tissue-specific landscape of protein aggregation and quality control in an aging vertebrate. | Chen YR, Harel I, Singh PP, Ziv I, Moses E, Goshtchevsky U, Machado BE, Brunet A, Jarosz DF | Developmental cell | 38810654 | Dev Cell | 2024 Jul 22 |
| A prion accelerates proliferation at the expense of lifespan. | Garcia DM, Campbell EA, Jakobson CM, Tsuchiya M, Shaw EA, DiNardo AL, Kaeberlein M, Jarosz DF | eLife | 34545808 | Elife | 2021 Sep 15 |
| An automated feeding system for the African killifish reveals the impact of diet on lifespan and allows scalable assessment of associative learning. | McKay A, Costa EK, Chen J, Hu CK, Chen X, Bedbrook CN, Khondker RC, Thielvoldt M, Priya Singh P, Wyss-Coray T, Brunet A | eLife | 36354233 | Elife | 2022 Nov 10 |
| Widespread Prion-Based Control of Growth and Differentiation Strategies in Saccharomyces cerevisiae. | Itakura AK, Chakravarty AK, Jakobson CM, Jarosz DF | Molecular cell | 31757756 | Mol Cell | 2020 Jan 16 |
| Old and new models for the study of human ageing. | Brunet A | Nature reviews. Molecular cell biology | 32572179 | Nat Rev Mol Cell Biol | 2020 Sep |
| Rapid and precise genome engineering in a naturally short-lived vertebrate. | Bedbrook CN, Nath RD, Nagvekar R, Deisseroth K, Brunet A | eLife | 37191291 | Elife | 2023 May 9 |
| Transcription-wide mapping of dihydrouridine reveals that mRNA dihydrouridylation is required for meiotic chromosome segregation. | Finet O, Yague-Sanz C, Krüger LK, Tran P, Migeot V, Louski M, Nevers A, Rougemaille M, Sun J, Ernst FGM, Wacheul L, Wery M, Morillon A, Dedon P, Lafontaine DLJ, Hermand D | Molecular cell | 34798057 | Mol Cell | 2022 Jan 20 |
| Phenoxy Radical Reactivity of Nucleic Acids: Practical Implications for Biotinylation. | Wilbanks B, Garcia B, Byrne S, Dedon P, Maher LJ 3rd | Chembiochem : a European journal of chemical biology | 33368926 | Chembiochem | 2021 Apr 16 |
| Discovery adductomics provides a comprehensive portrait of tissue-, age- and sex-specific DNA modifications in rodents and humans. | Guilbaud A, Ghanegolmohammadi F, Wang Y, Leng J, Kreymerman A, Gamboa Varela J, Garbern J, Elwell H, Cao F, Ricci-Blair EM, Liang C, Balamkundu S, Vidoudez C, DeMott MS, Bedi K, Margulies KB, Bennett DA, Palmer AA, Barkley-Levenson A, Lee RT, Dedon PC | Nucleic acids research | 37843128 | Nucleic Acids Res | 2023 Nov 10 |
| Exercise plasma boosts memory and dampens brain inflammation via clusterin. | De Miguel Z, Khoury N, Betley MJ, Lehallier B, Willoughby D, Olsson N, Yang AC, Hahn O, Lu N, Vest RT, Bonanno LN, Yerra L, Zhang L, Saw NL, Fairchild JK, Lee D, Zhang H, McAlpine PL, Contrepois K, Shamloo M, Elias JE, Rando TA, Wyss-Coray T | Nature | 34880498 | Nature | 2021 Dec |
| Interaction between epigenetic and metabolism in aging stem cells. | Brunet A, Rando TA | Current opinion in cell biology | 28129586 | Curr Opin Cell Biol | 2017 Apr |
| Fleeting factors, turning back time. | Rando TA | Nature biotechnology | 28267729 | Nat Biotechnol | 2017 Mar 7 |
| Deltex2 represses MyoD expression and inhibits myogenic differentiation by acting as a negative regulator of Jmjd1c. | Luo D, de Morree A, Boutet S, Quach N, Natu V, Rustagi A, Rando TA | Proceedings of the National Academy of Sciences of the United States of America | 28351977 | Proc Natl Acad Sci U S A | 2017 Apr 11 |
| Stem Cell Quiescence: Dynamism, Restraint, and Cellular Idling. | van Velthoven CTJ, Rando TA | Cell stem cell | 30735649 | Cell Stem Cell | 2019 Feb 7 |
| Impaired Notch Signaling Leads to a Decrease in p53 Activity and Mitotic Catastrophe in Aged Muscle Stem Cells. | Liu L, Charville GW, Cheung TH, Yoo B, Santos PJ, Schroeder M, Rando TA | Cell stem cell | 30244867 | Cell Stem Cell | 2018 Oct 4 |
| Mesenchymal Stromal Cells Are Required for Regeneration and Homeostatic Maintenance of Skeletal Muscle. | Wosczyna MN, Konishi CT, Perez Carbajal EE, Wang TT, Walsh RA, Gan Q, Wagner MW, Rando TA | Cell reports | 31091443 | Cell Rep | 2019 May 14 |
| Stem cells and healthy aging. | Goodell MA, Rando TA | Science (New York, N.Y.) | 26785478 | Science | 2015 Dec 4 |
| Translational strategies and challenges in regenerative medicine. | Dimmeler S, Ding S, Rando TA, Trounson A | Nature medicine | 25100527 | Nat Med | 2014 Aug |
| UTX in muscle regeneration--the right dose and the right time. | Liu L, Rando TA | The Journal of clinical investigation | 26999609 | J Clin Invest | 2016 Apr 1 |
| Transient non-integrative expression of nuclear reprogramming factors promotes multifaceted amelioration of aging in human cells. | Sarkar TJ, Quarta M, Mukherjee S, Colville A, Paine P, Doan L, Tran CM, Chu CR, Horvath S, Qi LS, Bhutani N, Rando TA, Sebastiano V | Nature communications | 32210226 | Nat Commun | 2020 Mar 24 |
| Hairless regulates heterochromatin maintenance and muscle stem cell function as a histone demethylase antagonist. | Liu L, Rodriguez-Mateo C, Huang P, Huang A, Lieu A, Mao M, Chung M, Yang S, Yu K, Charville GW, Gan Q, Rando TA | Proceedings of the National Academy of Sciences of the United States of America | 34493660 | Proc Natl Acad Sci U S A | 2021 Sep 14 |
| Quantifying and correcting bias due to outcome dependent self-reported weights in longitudinal study of weight loss interventions. | Tong J, Duan R, Li R, Luo C, Moore JH, Zhu J, Foster GD, Volpp KG, Yancy WS Jr, Shaw PA, Chen Y | Scientific reports | 37925516 | Sci Rep | 2023 Nov 4 |
| Regenerative medicine: Of fish and men. | Rando TA | Nature chemical biology | 24441638 | Nat Chem Biol | 2014 Feb |
| Chromatin modifications as determinants of muscle stem cell quiescence and chronological aging. | Liu L, Cheung TH, Charville GW, Hurgo BM, Leavitt T, Shih J, Brunet A, Rando TA | Cell reports | 23810552 | Cell Rep | 2013 Jul 11 |
| A Muscle Stem Cell Support Group: Coordinated Cellular Responses in Muscle Regeneration. | Wosczyna MN, Rando TA | Developmental cell | 30016618 | Dev Cell | 2018 Jul 16 |
| Alive and well? Exploring disease by studying lifespan. | Brett JO, Rando TA | Current opinion in genetics & development | 25005743 | Curr Opin Genet Dev | 2014 Jun |
| mTORC1 controls the adaptive transition of quiescent stem cells from G0 to G(Alert). | Rodgers JT, King KY, Brett JO, Cromie MJ, Charville GW, Maguire KK, Brunson C, Mastey N, Liu L, Tsai CR, Goodell MA, Rando TA | Nature | 24870234 | Nature | 2014 Jun 19 |
| An artificial niche preserves the quiescence of muscle stem cells and enhances their therapeutic efficacy. | Quarta M, Brett JO, DiMarco R, De Morree A, Boutet SC, Chacon R, Gibbons MC, Garcia VA, Su J, Shrager JB, Heilshorn S, Rando TA | Nature biotechnology | 27240197 | Nat Biotechnol | 2016 Jul |
| Mimicking the niche: cytokines expand muscle stem cells. | Quarta M, Rando TA | Cell research | 26113258 | Cell Res | 2015 Jul |
| Stem cells as vehicles for youthful regeneration of aged tissues. | Rando TA, Wyss-Coray T | The journals of gerontology. Series A, Biological sciences and medical sciences | 24833585 | J Gerontol A Biol Sci Med Sci | 2014 Jun |
| Cardiac aging and rejuvenation--a sense of humors? | Rando TA, Finkel T | The New England journal of medicine | 23924010 | N Engl J Med | 2013 Aug 8 |
| Targeting microRNA-mediated gene repression limits adipogenic conversion of skeletal muscle mesenchymal stromal cells. | Wosczyna MN, Perez Carbajal EE, Wagner MW, Paredes S, Konishi CT, Liu L, Wang TT, Walsh RA, Gan Q, Morrissey CS, Rando TA | Cell stem cell | 33945794 | Cell Stem Cell | 2021 Jul 1 |
| Biomechanics show stem cell necessity for effective treatment of volumetric muscle loss using bioengineered constructs. | Quarta M, Cromie Lear MJ, Blonigan J, Paine P, Chacon R, Rando TA | NPJ Regenerative medicine | 30323949 | NPJ Regen Med | 2018 |
| Induction of autophagy supports the bioenergetic demands of quiescent muscle stem cell activation. | Tang AH, Rando TA | The EMBO journal | 25316028 | EMBO J | 2014 Dec 1 |
| The JAK-STAT pathway is critical in ventilator-induced diaphragm dysfunction. | Tang H, Smith IJ, Hussain SN, Goldberg P, Lee M, Sugiarto S, Godinez GL, Singh BK, Payan DG, Rando TA, Kinsella TM, Shrager JB | Molecular medicine (Cambridge, Mass.) | 25286450 | Mol Med | 2015 Feb 19 |
| Aging of the skeletal muscle extracellular matrix drives a stem cell fibrogenic conversion. | Stearns-Reider KM, D'Amore A, Beezhold K, Rothrauff B, Cavalli L, Wagner WR, Vorp DA, Tsamis A, Shinde S, Zhang C, Barchowsky A, Rando TA, Tuan RS, Ambrosio F | Aging cell | 28371268 | Aging Cell | 2017 Jun |
| Exercise reprograms the inflammatory landscape of multiple stem cell compartments during mammalian aging. | Liu L, Kim S, Buckley MT, Reyes JM, Kang J, Tian L, Wang M, Lieu A, Mao M, Rodriguez-Mateo C, Ishak HD, Jeong M, Wu JC, Goodell MA, Brunet A, Rando TA | Cell stem cell | 37080206 | Cell Stem Cell | 2023 May 4 |
| Isolation of skeletal muscle stem cells by fluorescence-activated cell sorting. | Liu L, Cheung TH, Charville GW, Rando TA | Nature protocols | 26401916 | Nat Protoc | 2015 Oct |
| Bioengineered constructs combined with exercise enhance stem cell-mediated treatment of volumetric muscle loss. | Quarta M, Cromie M, Chacon R, Blonigan J, Garcia V, Akimenko I, Hamer M, Paine P, Stok M, Shrager JB, Rando TA | Nature communications | 28631758 | Nat Commun | 2017 Jun 20 |
| Intronic polyadenylation of PDGFRα in resident stem cells attenuates muscle fibrosis. | Mueller AA, van Velthoven CT, Fukumoto KD, Cheung TH, Rando TA | Nature | 27894125 | Nature | 2016 Dec 8 |
| Smad3 initiates oxidative stress and proteolysis that underlies diaphragm dysfunction during mechanical ventilation. | Tang H, L Kennedy C, Lee M, Gao Y, Xia H, Olguin F, Fraga DA, Ayers K, Choi S, Kim M, Tehrani A, Sowb YA, Rando TA, Shrager JB | Scientific reports | 29109401 | Sci Rep | 2017 Nov 6 |
| Transcriptional Profiling of Quiescent Muscle Stem Cells In Vivo. | van Velthoven CTJ, de Morree A, Egner IM, Brett JO, Rando TA | Cell reports | 29141228 | Cell Rep | 2017 Nov 14 |
| Exercise rejuvenates quiescent skeletal muscle stem cells in old mice through restoration of Cyclin D1. | Brett JO, Arjona M, Ikeda M, Quarta M, de Morrée A, Egner IM, Perandini LA, Ishak HD, Goshayeshi A, Benjamin DI, Both P, Rodríguez-Mateo C, Betley MJ, Wyss-Coray T, Rando TA | Nature metabolism | 32601609 | Nat Metab | 2020 Apr |
| mTORC1 Activation during Repeated Regeneration Impairs Somatic Stem Cell Maintenance. | Haller S, Kapuria S, Riley RR, O'Leary MN, Schreiber KH, Andersen JK, Melov S, Que J, Rando TA, Rock J, Kennedy BK, Rodgers JT, Jasper H | Cell stem cell | 29220665 | Cell Stem Cell | 2017 Dec 7 |
| Identification and characterization of latency-associated peptide-expressing γδ T cells. | Rezende RM, da Cunha AP, Kuhn C, Rubino S, M'Hamdi H, Gabriely G, Vandeventer T, Liu S, Cialic R, Pinheiro-Rosa N, Oliveira RP, Gaublomme JT, Obholzer N, Kozubek J, Pochet N, Faria AMC, Weiner HL | Nature communications | 26644347 | Nat Commun | 2015 Dec 8 |
| Regulation of astrocyte activation by glycolipids drives chronic CNS inflammation. | Mayo L, Trauger SA, Blain M, Nadeau M, Patel B, Alvarez JI, Mascanfroni ID, Yeste A, Kivisäkk P, Kallas K, Ellezam B, Bakshi R, Prat A, Antel JP, Weiner HL, Quintana FJ | Nature medicine | 25216636 | Nat Med | 2014 Oct |
| Impaired glutamate recycling and GluN2B-mediated neuronal calcium overload in mice lacking TGF-β1 in the CNS. | Koeglsperger T, Li S, Brenneis C, Saulnier JL, Mayo L, Carrier Y, Selkoe DJ, Weiner HL | Glia | 23536313 | Glia | 2013 Jun |
| Age and the association of dementia-related pathology with trajectories of cognitive decline. | Jansen WJ, Wilson RS, Visser PJ, Nag S, Schneider JA, James BD, Leurgans SE, Capuano AW, Bennett DA, Boyle PA | Neurobiology of aging | 29078129 | Neurobiol Aging | 2018 Jan |
| Microglial signatures and their role in health and disease. | Butovsky O, Weiner HL | Nature reviews. Neuroscience | 30206328 | Nat Rev Neurosci | 2018 Oct |
| Identification of a unique TGF-β-dependent molecular and functional signature in microglia. | Butovsky O, Jedrychowski MP, Moore CS, Cialic R, Lanser AJ, Gabriely G, Koeglsperger T, Dake B, Wu PM, Doykan CE, Fanek Z, Liu L, Chen Z, Rothstein JD, Ransohoff RM, Gygi SP, Antel JP, Weiner HL | Nature neuroscience | 24316888 | Nat Neurosci | 2014 Jan |
| Environmental Enrichment Potently Prevents Microglia-Mediated Neuroinflammation by Human Amyloid β-Protein Oligomers. | Xu H, Gelyana E, Rajsombath M, Yang T, Li S, Selkoe D | The Journal of neuroscience : the official journal of the Society for Neuroscience | 27581448 | J Neurosci | 2016 Aug 31 |
| Targeting miR-155 restores abnormal microglia and attenuates disease in SOD1 mice. | Butovsky O, Jedrychowski MP, Cialic R, Krasemann S, Murugaiyan G, Fanek Z, Greco DJ, Wu PM, Doykan CE, Kiner O, Lawson RJ, Frosch MP, Pochet N, Fatimy RE, Krichevsky AM, Gygi SP, Lassmann H, Berry J, Cudkowicz ME, Weiner HL | Annals of neurology | 25381879 | Ann Neurol | 2015 Jan |
| The TREM2-APOE Pathway Drives the Transcriptional Phenotype of Dysfunctional Microglia in Neurodegenerative Diseases. | Krasemann S, Madore C, Cialic R, Baufeld C, Calcagno N, El Fatimy R, Beckers L, O'Loughlin E, Xu Y, Fanek Z, Greco DJ, Smith ST, Tweet G, Humulock Z, Zrzavy T, Conde-Sanroman P, Gacias M, Weng Z, Chen H, Tjon E, Mazaheri F, Hartmann K, Madi A, Ulrich JD, Glatzel M, Worthmann A, Heeren J, Budnik B, Lemere C, Ikezu T, Heppner FL, Litvak V, Holtzman DM, Lassmann H, Weiner HL, Ochando J, Haass C, Butovsky O | Immunity | 28930663 | Immunity | 2017 Sep 19 |
| Scara1 deficiency impairs clearance of soluble amyloid-β by mononuclear phagocytes and accelerates Alzheimer's-like disease progression. | Frenkel D, Wilkinson K, Zhao L, Hickman SE, Means TK, Puckett L, Farfara D, Kingery ND, Weiner HL, El Khoury J | Nature communications | 23799536 | Nat Commun | 2013 |
| Acute microglia ablation induces neurodegeneration in the somatosensory system. | Rubino SJ, Mayo L, Wimmer I, Siedler V, Brunner F, Hametner S, Madi A, Lanser A, Moreira T, Donnelly D, Cox L, Rezende RM, Butovsky O, Lassmann H, Weiner HL | Nature communications | 30385785 | Nat Commun | 2018 Nov 1 |
| Bacteroidota inhibit microglia clearance of amyloid-beta and promote plaque deposition in Alzheimer's disease mouse models. | Wasén C, Beauchamp LC, Vincentini J, Li S, LeServe DS, Gauthier C, Lopes JR, Moreira TG, Ekwudo MN, Yin Z, da Silva P, Krishnan RK, Butovsky O, Cox LM, Weiner HL | Nature communications | 38719797 | Nat Commun | 2024 May 8 |
| The multiple roles of life stress in metabolic disorders. | Kivimäki M, Bartolomucci A, Kawachi I | Nature reviews. Endocrinology | 36224493 | Nat Rev Endocrinol | 2023 Jan |
| A computational approach to studying ageing at the individual level. | Harvanek ZM, Mourão MA, Schnell S, Pletcher SD | Proceedings. Biological sciences | 26865300 | Proc Biol Sci | 2016 Feb 10 |
| No Significant Effect of Maternal Perception of the Food Environment on Reproductive Success or Pup Outcomes in C57BL/6J Mice. | Gibbs VK, Schwartz TS, Johnson MS, Patki A, Nagy TR, George BJ, Allison DB | Obesity (Silver Spring, Md.) | 29476611 | Obesity (Silver Spring) | 2018 Apr |
| Longevity is impacted by growth hormone action during early postnatal period. | Sun LY, Fang Y, Patki A, Koopman JJ, Allison DB, Hill CM, Masternak MM, Darcy J, Wang J, McFadden S, Bartke A | eLife | 28675141 | Elife | 2017 Jul 4 |
| Circadian disruption of hippocampus in an early senescence male mouse model. | Davis JA, Paul JR, Mokashi MV, Yates SA, Mount DJ, Munir HA, Goode LK, Young ME, Allison DB, Gamble KL | Pharmacology, biochemistry, and behavior | 35447158 | Pharmacol Biochem Behav | 2022 Jun |
| Diurnal, metabolic and thermogenic alterations in a murine model of accelerated aging. | Allison DB, Ren G, Peliciari-Garcia RA, Mia S, McGinnis GR, Davis J, Gamble KL, Kim JA, Young ME | Chronobiology international | 32819176 | Chronobiol Int | 2020 Aug |
| Positive and negative gustatory inputs affect Drosophila lifespan partly in parallel to dFOXO signaling. | Ostojic I, Boll W, Waterson MJ, Chan T, Chandra R, Pletcher SD, Alcedo J | Proceedings of the National Academy of Sciences of the United States of America | 24847072 | Proc Natl Acad Sci U S A | 2014 Jun 3 |
| Social stress shortens lifespan in mice. | Razzoli M, Nyuyki-Dufe K, Gurney A, Erickson C, McCallum J, Spielman N, Marzullo M, Patricelli J, Kurata M, Pope EA, Touma C, Palme R, Largaespada DA, Allison DB, Bartolomucci A | Aging cell | 29806171 | Aging Cell | 2018 Aug |
| Chronic subordination stress induces hyperphagia and disrupts eating behavior in mice modeling binge-eating-like disorder. | Razzoli M, Sanghez V, Bartolomucci A | Frontiers in nutrition | 25621284 | Front Nutr | 2015 |
| Second-hand eating? Maternal perception of the food environment affects reproductive investment in mice. | Schwartz TS, Gainer R, Dohm ED, Johnson MS, Wyss JM, Allison DB | Obesity (Silver Spring, Md.) | 25864567 | Obesity (Silver Spring) | 2015 May |
| FLIC: high-throughput, continuous analysis of feeding behaviors in Drosophila. | Ro J, Harvanek ZM, Pletcher SD | PloS one | 24978054 | PLoS One | 2014 |
| Stress-induced activation of brown adipose tissue prevents obesity in conditions of low adaptive thermogenesis. | Razzoli M, Frontini A, Gurney A, Mondini E, Cubuk C, Katz LS, Cero C, Bolan PJ, Dopazo J, Vidal-Puig A, Cinti S, Bartolomucci A | Molecular metabolism | 26844204 | Mol Metab | 2016 Jan |
| Contextual modifiers of healthspan, lifespan, and epigenome in mice under chronic social stress. | Razzoli M, Nyuyki-Dufe K, Chen BH, Bartolomucci A | Proceedings of the National Academy of Sciences of the United States of America | 37043532 | Proc Natl Acad Sci U S A | 2023 Apr 18 |
| Water sensor ppk28 modulates Drosophila lifespan and physiology through AKH signaling. | Waterson MJ, Chung BY, Harvanek ZM, Ostojic I, Alcedo J, Pletcher SD | Proceedings of the National Academy of Sciences of the United States of America | 24821805 | Proc Natl Acad Sci U S A | 2014 Jun 3 |
| Oxidative costs of reproduction in mouse strains selected for different levels of food intake and which differ in reproductive performance. | Jothery AH, Vaanholt LM, Mody N, Arnous A, Lykkesfeldt J, Bünger L, Hill WG, Mitchell SE, Allison DB, Speakman JR | Scientific reports | 27841266 | Sci Rep | 2016 Nov 14 |
| Stress, overeating, and obesity: Insights from human studies and preclinical models. | Razzoli M, Pearson C, Crow S, Bartolomucci A | Neuroscience and biobehavioral reviews | 28292531 | Neurosci Biobehav Rev | 2017 May |
| Targeting glucose metabolism for healthy aging. | Brewer RA, Gibbs VK, Smith DL Jr | Nutrition and healthy aging | 28035340 | Nutr Healthy Aging | 2016 Oct 27 |
| Effects of fluctuating temperature and food availability on reproduction and lifespan. | Schwartz TS, Pearson P, Dawson J, Allison DB, Gohlke JM | Experimental gerontology | 27364192 | Exp Gerontol | 2016 Dec 15 |
| Sex Differences in Lifespan. | Austad SN, Fischer KE | Cell metabolism | 27304504 | Cell Metab | 2016 Jun 14 |
| Innovative approaches in cognitive aging. | Austad SN, Wood MA, Villeda SA, Voss JL, Sahay A, Albert M | Neurobiology of aging | 31277894 | Neurobiol Aging | 2019 Nov |
| The Dichotomous Effect of Chronic Stress on Obesity. | Razzoli M, Bartolomucci A | Trends in endocrinology and metabolism: TEM | 27162125 | Trends Endocrinol Metab | 2016 Jul |
| Body Mass Index and Subjective Social Status: The Coronary Artery Risk Development in Young Adults Study. | Dhurandhar EJ, Pavela G, Kaiser KA, Dutton GR, Fontaine KR, Kim D, Shikany JM, Allison DB, Lewis CE | Obesity (Silver Spring, Md.) | 29280341 | Obesity (Silver Spring) | 2018 Feb |
| The effect of a pharmaceutical ghrelin agonist on lifespan in C57BL/6J male mice: A controlled experiment. | Kaiser KA, Kadish I, van Groen T, Smith DL Jr, Dickinson S, Henschel B, Parker ES, Brown AW, Allison DB | Aging cell | 36734122 | Aging Cell | 2023 Apr |
| Drosophila life span and physiology are modulated by sexual perception and reward. | Gendron CM, Kuo TH, Harvanek ZM, Chung BY, Yew JY, Dierick HA, Pletcher SD | Science (New York, N.Y.) | 24292624 | Science | 2014 Jan 31 |
| Oxidative costs of reproduction: Oxidative stress in mice fed standard and low antioxidant diets. | Vaanholt LM, Milne A, Zheng Y, Hambly C, Mitchell SE, Valencak TG, Allison DB, Speakman JR | Physiology & behavior | 26569452 | Physiol Behav | 2016 Feb 1 |
| Adaptive Physiological Response to Perceived Scarcity as a Mechanism of Sensory Modulation of Life Span. | Waterson MJ, Chan TP, Pletcher SD | The journals of gerontology. Series A, Biological sciences and medical sciences | 25878032 | J Gerontol A Biol Sci Med Sci | 2015 Sep |
| Calories or protein? The effect of dietary restriction on lifespan in rodents is explained by calories alone. | Speakman JR, Mitchell SE, Mazidi M | Experimental gerontology | 27006163 | Exp Gerontol | 2016 Dec 15 |
| Effect of Food Predictability on Life Span in Male Mice. | Rowland NE, Robertson KL, Minaya D, Minervini V, Cervantez M, Kaiser KA, Allison DB | The journals of gerontology. Series A, Biological sciences and medical sciences | 30289438 | J Gerontol A Biol Sci Med Sci | 2019 Jul 12 |
| Nutrition and energetics in rodent longevity research. | Gibbs VK, Smith DL Jr | Experimental gerontology | 27073168 | Exp Gerontol | 2016 Dec 15 |
| Ghrelin agonist does not foster insulin resistance but improves cognition in an Alzheimer's disease mouse model. | Kunath N, van Groen T, Allison DB, Kumar A, Dozier-Sharpe M, Kadish I | Scientific reports | 26090621 | Sci Rep | 2015 Jun 19 |
| Serotonin signaling mediates protein valuation and aging. | Ro J, Pak G, Malec PA, Lyu Y, Allison DB, Kennedy RT, Pletcher SD | eLife | 27572262 | Elife | 2016 Aug 23 |
| Sex-dependent Differences in Liver and Gut Metabolomic Profiles With Acarbose and Calorie Restriction in C57BL/6 Mice. | Gibbs VK, Brewer RA, Miyasaki ND, Patki A, Smith DL Jr | The journals of gerontology. Series A, Biological sciences and medical sciences | 28651373 | J Gerontol A Biol Sci Med Sci | 2018 Jan 16 |
| Acute Dietary Restriction Acts via TOR, PP2A, and Myc Signaling to Boost Innate Immunity in Drosophila. | Lee JE, Rayyan M, Liao A, Edery I, Pletcher SD | Cell reports | 28700947 | Cell Rep | 2017 Jul 11 |
| Not feeling the heat? Effects of dietary protein on satiation and satiety in mice are not due to its impact on body temperature. | Osorio M J, Mitchell SE, Hambly C, Allison DB, Speakman JR | Appetite | 38759755 | Appetite | 2024 Sep 1 |
| Reproduction has immediate effects on female mortality, but no discernible lasting physiological impacts: A test of the disposable soma theory. | Mitchell SE, Simpson M, Coulet L, Gouedard S, Hambly C, Morimoto J, Allison DB, Speakman JR | Proceedings of the National Academy of Sciences of the United States of America | 39374394 | Proc Natl Acad Sci U S A | 2024 Oct 15 |
| Femtosecond laser nanoaxotomy lab-on-a-chip for in vivo nerve regeneration studies. | Guo SX, Bourgeois F, Chokshi T, Durr NJ, Hilliard MA, Chronis N, Ben-Yakar A | Nature methods | 18408725 | Nat Methods | 2008 Jun |
| Femtosecond laser nanoaxotomy properties and their effect on axonal recovery in C. elegans. | Bourgeois F, Ben-Yakar A | Optics express | 18725955 | Opt Express | 2008 Apr 14 |
| Microfluidics for the analysis of behavior, nerve regeneration, and neural cell biology in C. elegans. | Ben-Yakar A, Chronis N, Lu H | Current opinion in neurobiology | 19896831 | Curr Opin Neurobiol | 2009 Oct |
| High-Content Microfluidic Screening Platform Used To Identify σ2R/Tmem97 Binding Ligands that Reduce Age-Dependent Neurodegeneration in C. elegans SC_APP Model. | Mondal S, Hegarty E, Sahn JJ, Scott LL, Gökçe SK, Martin C, Ghorashian N, Satarasinghe PN, Iyer S, Sae-Lee W, Hodges TR, Pierce JT, Martin SF, Ben-Yakar A | ACS chemical neuroscience | 29426225 | ACS Chem Neurosci | 2018 May 16 |
| An automated microfluidic multiplexer for fast delivery of C. elegans populations from multiwells. | Ghorashian N, Gökçe SK, Guo SX, Everett WN, Ben-Yakar A | PloS one | 24069313 | PLoS One | 2013 |
| An automated microfluidic device for time-lapse imaging of mouse embryonic stem cells. | Laing AF, Tirumala V, Hegarty E, Mondal S, Zhao P, Hamilton WB, Brickman JM, Ben-Yakar A | Biomicrofluidics | 31558920 | Biomicrofluidics | 2019 Sep |
| Activity-Dependent Regulation of the Proapoptotic BH3-Only Gene egl-1 in a Living Neuron Pair in Caenorhabditis elegans. | Cohn J, Dwivedi V, Valperga G, Zarate N, de Bono M, Horvitz HR, Pierce JT | G3 (Bethesda, Md.) | 31519744 | G3 (Bethesda) | 2019 Nov 5 |
| Ultrasound measurements of cavitation bubble radius for femtosecond laser-induced breakdown in water. | Aglyamov SR, Karpiouk AB, Bourgeois F, Ben-Yakar A, Emelianov SY | Optics letters | 18552957 | Opt Lett | 2008 Jun 15 |
| Axonal regeneration proceeds through specific axonal fusion in transected C. elegans neurons. | Neumann B, Nguyen KC, Hall DH, Ben-Yakar A, Hilliard MA | Developmental dynamics : an official publication of the American Association of Anatomists | 21416556 | Dev Dyn | 2011 Jun |
| Small molecule modulator of sigma 2 receptor is neuroprotective and reduces cognitive deficits and neuroinflammation in experimental models of Alzheimer's disease. | Yi B, Sahn JJ, Ardestani PM, Evans AK, Scott LL, Chan JZ, Iyer S, Crisp A, Zuniga G, Pierce JT, Martin SF, Shamloo M | Journal of neurochemistry | 27926996 | J Neurochem | 2017 Feb |
| Long-term activity drives dendritic branch elaboration of a C. elegans sensory neuron. | Cohn JA, Cebul ER, Valperga G, Brose L, de Bono M, Heiman MG, Pierce JT | Developmental biology | 31945343 | Dev Biol | 2020 May 1 |
| A fully automated microfluidic femtosecond laser axotomy platform for nerve regeneration studies in C. elegans. | Gokce SK, Guo SX, Ghorashian N, Everett WN, Jarrell T, Kottek A, Bovik AC, Ben-Yakar A | PloS one | 25470130 | PLoS One | 2014 |
| Small-molecule-mediated axonal branching in Caenorhabditis elegans. | Zlotkowski K, Pierce-Shimomura J, Siegel D | Chembiochem : a European journal of chemical biology | 23362121 | Chembiochem | 2013 Feb 11 |
| A multi-trap microfluidic chip enabling longitudinal studies of nerve regeneration in Caenorhabditis elegans. | Gokce SK, Hegarty EM, Mondal S, Zhao P, Ghorashian N, Hilliard MA, Ben-Yakar A | Scientific reports | 28852096 | Sci Rep | 2017 Aug 29 |
| Magnetosensitive neurons mediate geomagnetic orientation in Caenorhabditis elegans. | Vidal-Gadea A, Ward K, Beron C, Ghorashian N, Gokce S, Russell J, Truong N, Parikh A, Gadea O, Ben-Yakar A, Pierce-Shimomura J | eLife | 26083711 | Elife | 2015 Jun 17 |
| APP-Induced Patterned Neurodegeneration Is Exacerbated by APOE4 in Caenorhabditis elegans. | Sae-Lee W, Scott LL, Brose L, Encarnacion AJ, Shi T, Kore P, Oyibo LO, Ye C, Rozmiarek SK, Pierce JT | G3 (Bethesda, Md.) | 32580938 | G3 (Bethesda) | 2020 Aug 5 |
| Large-scale microfluidics providing high-resolution and high-throughput screening of Caenorhabditis elegans poly-glutamine aggregation model. | Mondal S, Hegarty E, Martin C, Gökçe SK, Ghorashian N, Ben-Yakar A | Nature communications | 27725672 | Nat Commun | 2016 Oct 11 |
| Worming our way to Alzheimer's disease drug discovery. | Iyer S, Pierce-Shimomura JT | Biological psychiatry | 23399470 | Biol Psychiatry | 2013 Mar 1 |
| Quantitative ultrasound method to detect and monitor laser-induced cavitation bubbles. | Karpiouk AB, Aglyamov SR, Bourgeois F, Ben-Yakar A, Emelianov SY | Journal of biomedical optics | 18601556 | J Biomed Opt | 2008 May-Jun |
| Ultrafast laser nanosurgery in microfluidics for genome-wide screenings. | Ben-Yakar A, Bourgeois F | Current opinion in biotechnology | 19278850 | Curr Opin Biotechnol | 2009 Feb |
| Line excitation array detection fluorescence microscopy at 0.8 million frames per second. | Martin C, Li T, Hegarty E, Zhao P, Mondal S, Ben-Yakar A | Nature communications | 30374138 | Nat Commun | 2018 Oct 29 |
| Systematic Functional Characterization of Human 21st Chromosome Orthologs in Caenorhabditis elegans. | Nordquist SK, Smith SR, Pierce JT | G3 (Bethesda, Md.) | 29367452 | G3 (Bethesda) | 2018 Mar 2 |
| Planar Laser Activated Neuronal Scanning (PLANS) System for in vivo Flow Cytometry. | Watson N, Mondal S, DuPlissis A, Kim KH, Ben-Yakar A | Frontiers in optics. Annual Meeting of the Optical Society of America | 35350105 | Front Opt | 2020 Sep |
