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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
Metabolic plasticity drives development during mammalian embryogenesis. Sharpley MS, Chi F, Hoeve JT, Banerjee U Developmental cell 34428399 Dev Cell 2021 Aug 23
Glycolysis-Independent Glucose Metabolism Distinguishes TE from ICM Fate during Mammalian Embryogenesis. Chi F, Sharpley MS, Nagaraj R, Roy SS, Banerjee U Developmental cell 32197068 Dev Cell 2020 Apr 6
Regulated noise in the epigenetic landscape of development and disease. Pujadas E, Feinberg AP Cell 22424224 Cell 2012 Mar 16
Reversible switching between epigenetic states in honeybee behavioral subcastes. Herb BR, Wolschin F, Hansen KD, Aryee MJ, Langmead B, Irizarry R, Amdam GV, Feinberg AP Nature neuroscience 22983211 Nat Neurosci 2012 Oct
The evolution of bacterial mechanosensitive channels. Booth IR, Miller S, Müller A, Lehtovirta-Morley L Cell calcium 25591932 Cell Calcium 2015 Mar
The glove-like structure of the conserved membrane protein TatC provides insight into signal sequence recognition in twin-arginine translocation. Ramasamy S, Abrol R, Suloway CJ, Clemons WM Jr Structure (London, England : 1993) 23583035 Structure 2013 May 7
Minimal requirements for inhibition of MraY by lysis protein E from bacteriophage ΦX174. Tanaka S, Clemons WM Jr Molecular microbiology 22742425 Mol Microbiol 2012 Sep
Pupil fluctuations track rapid changes in adrenergic and cholinergic activity in cortex. Reimer J, McGinley MJ, Liu Y, Rodenkirch C, Wang Q, McCormick DA, Tolias AS Nature communications 27824036 Nat Commun 2016 Nov 8
Benchmarking Spike Rate Inference in Population Calcium Imaging. Theis L, Berens P, Froudarakis E, Reimer J, Román Rosón M, Baden T, Euler T, Tolias AS, Bethge M Neuron 27151639 Neuron 2016 May 4
Pupil fluctuations track fast switching of cortical states during quiet wakefulness. Reimer J, Froudarakis E, Cadwell CR, Yatsenko D, Denfield GH, Tolias AS Neuron 25374359 Neuron 2014 Oct 22
Deep convolutional models improve predictions of macaque V1 responses to natural images. Cadena SA, Denfield GH, Walker EY, Gatys LA, Tolias AS, Bethge M, Ecker AS PLoS computational biology 31013278 PLoS Comput Biol 2019 Apr
Principles of connectivity among morphologically defined cell types in adult neocortex. Jiang X, Shen S, Cadwell CR, Berens P, Sinz F, Ecker AS, Patel S, Tolias AS Science (New York, N.Y.) 26612957 Science 2015 Nov 27
Electrophysiological, transcriptomic and morphologic profiling of single neurons using Patch-seq. Cadwell CR, Palasantza A, Jiang X, Berens P, Deng Q, Yilmaz M, Reimer J, Shen S, Bethge M, Tolias KF, Sandberg R, Tolias AS Nature biotechnology 26689543 Nat Biotechnol 2016 Feb
Waking State: Rapid Variations Modulate Neural and Behavioral Responses. McGinley MJ, Vinck M, Reimer J, Batista-Brito R, Zagha E, Cadwell CR, Tolias AS, Cardin JA, McCormick DA Neuron 26402600 Neuron 2015 Sep 23
Improved estimation and interpretation of correlations in neural circuits. Yatsenko D, Josić K, Ecker AS, Froudarakis E, Cotton RJ, Tolias AS PLoS computational biology 25826696 PLoS Comput Biol 2015 Mar
Attentional fluctuations induce shared variability in macaque primary visual cortex. Denfield GH, Ecker AS, Shinn TJ, Bethge M, Tolias AS Nature communications 29985411 Nat Commun 2018 Jul 9
Learning divisive normalization in primary visual cortex. Burg MF, Cadena SA, Denfield GH, Walker EY, Tolias AS, Bethge M, Ecker AS PLoS computational biology 34097695 PLoS Comput Biol 2021 Jun
Population code in mouse V1 facilitates readout of natural scenes through increased sparseness. Froudarakis E, Berens P, Ecker AS, Cotton RJ, Sinz FH, Yatsenko D, Saggau P, Bethge M, Tolias AS Nature neuroscience 24747577 Nat Neurosci 2014 Jun
On the Structure of Neuronal Population Activity under Fluctuations in Attentional State. Ecker AS, Denfield GH, Bethge M, Tolias AS The Journal of neuroscience : the official journal of the Society for Neuroscience 26843656 J Neurosci 2016 Feb 3
Multimodal profiling of single-cell morphology, electrophysiology, and gene expression using Patch-seq. Cadwell CR, Scala F, Li S, Livrizzi G, Shen S, Sandberg R, Jiang X, Tolias AS Nature protocols 29189773 Nat Protoc 2017 Dec
Cell type composition and circuit organization of clonally related excitatory neurons in the juvenile mouse neocortex. Cadwell CR, Scala F, Fahey PG, Kobak D, Mulherkar S, Sinz FH, Papadopoulos S, Tan ZH, Johnsson P, Hartmanis L, Li S, Cotton RJ, Tolias KF, Sandberg R, Berens P, Jiang X, Tolias AS eLife 32134385 Elife 2020 Mar 5
Gene delivery to the retina: from mouse to man. Bennett J, Chung DC, Maguire A Methods in enzymology 22365778 Methods Enzymol 2012
A synthetic AAV vector enables safe and efficient gene transfer to the mammalian inner ear. Landegger LD, Pan B, Askew C, Wassmer SJ, Gluck SD, Galvin A, Taylor R, Forge A, Stankovic KM, Holt JR, Vandenberghe LH Nature biotechnology 28165475 Nat Biotechnol 2017 Mar
Basal exon skipping and genetic pleiotropy: A predictive model of disease pathogenesis. Drivas TG, Wojno AP, Tucker BA, Stone EM, Bennett J Science translational medicine 26062849 Sci Transl Med 2015 Jun 10
Promising and delivering gene therapies for vision loss. Carvalho LS, Vandenberghe LH Vision research 25094052 Vision Res 2015 Jun
What Is Next for Retinal Gene Therapy? Vandenberghe LH Cold Spring Harbor perspectives in medicine 25877395 Cold Spring Harb Perspect Med 2015 Apr 15
Efficient transduction and optogenetic stimulation of retinal bipolar cells by a synthetic adeno-associated virus capsid and promoter. Cronin T, Vandenberghe LH, Hantz P, Juttner J, Reimann A, Kacsó AE, Huckfeldt RM, Busskamp V, Kohler H, Lagali PS, Roska B, Bennett J EMBO molecular medicine 25092770 EMBO Mol Med 2014 Sep
Perspectives on best practices for gene therapy programs. Cheever TR, Berkley D, Braun S, Brown RH, Byrne BJ, Chamberlain JS, Cwik V, Duan D, Federoff HJ, High KA, Kaspar BK, Klinger KW, Larkindale J, Lincecum J, Mavilio F, McDonald CL, McLaughlin J, Weiss McLeod B, Mendell JR, Nuckolls G, Stedman HH, Tagle DA, Vandenberghe LH, Wang H, Wernett PJ, Wilson JM, Porter JD, Gubitz AK Human gene therapy 25654329 Hum Gene Ther 2015 Mar
In vitro and in vivo rescue of aberrant splicing in CEP290-associated LCA by antisense oligonucleotide delivery. Garanto A, Chung DC, Duijkers L, Corral-Serrano JC, Messchaert M, Xiao R, Bennett J, Vandenberghe LH, Collin RW Human molecular genetics 27106101 Hum Mol Genet 2016 Jun 15
The Assembly-Activating Protein Promotes Stability and Interactions between AAV's Viral Proteins to Nucleate Capsid Assembly. Maurer AC, Pacouret S, Cepeda Diaz AK, Blake J, Andres-Mateos E, Vandenberghe LH Cell reports 29742436 Cell Rep 2018 May 8
Adeno-associated virus: fit to serve. Zinn E, Vandenberghe LH Current opinion in virology 25128609 Curr Opin Virol 2014 Oct
AAV9 targets cone photoreceptors in the nonhuman primate retina. Vandenberghe LH, Bell P, Maguire AM, Xiao R, Hopkins TB, Grant R, Bennett J, Wilson JM PloS one 23382846 PLoS One 2013
Retinal gene therapy coming of age. Cepko CL, Vandenberghe LH Human gene therapy 23458444 Hum Gene Ther 2013 Mar
Controlling AAV Tropism in the Nervous System with Natural and Engineered Capsids. Castle MJ, Turunen HT, Vandenberghe LH, Wolfe JH Methods in molecular biology (Clifton, N.J.) 26611584 Methods Mol Biol 2016
In Silico Reconstruction of the Viral Evolutionary Lineage Yields a Potent Gene Therapy Vector. Zinn E, Pacouret S, Khaychuk V, Turunen HT, Carvalho LS, Andres-Mateos E, Shah S, Shelke R, Maurer AC, Plovie E, Xiao R, Vandenberghe LH Cell reports 26235624 Cell Rep 2015 Aug 11
Restoration of Vision and Retinal Responses After Adeno-Associated Virus-Mediated Optogenetic Therapy in Blind Dogs. Nikonov S, Aravand P, Lyubarsky A, Nikonov R, Luo AJ, Wei Z, Maguire AM, Phelps NT, Shpylchak I, Willett K, Aleman TS, Huckfeldt RM, Ramachandran PS, Bennett J Translational vision science & technology 35604672 Transl Vis Sci Technol 2022 May 2
Membrane Potential Dynamics of CA1 Pyramidal Neurons during Hippocampal Ripples in Awake Mice. Hulse BK, Moreaux LC, Lubenov EV, Siapas AG Neuron 26889811 Neuron 2016 Feb 17
Structured Variability in Purkinje Cell Activity during Locomotion. Sauerbrei BA, Lubenov EV, Siapas AG Neuron 26291165 Neuron 2015 Aug 19
Model-based spike sorting with a mixture of drifting t-distributions. Shan KQ, Lubenov EV, Siapas AG Journal of neuroscience methods 28652008 J Neurosci Methods 2017 Aug 15
Brain State Dependence of Hippocampal Subthreshold Activity in Awake Mice. Hulse BK, Lubenov EV, Siapas AG Cell reports 28052244 Cell Rep 2017 Jan 3
Spatial tuning and brain state account for dorsal hippocampal CA1 activity in a non-spatial learning task. Shan KQ, Lubenov EV, Papadopoulou M, Siapas AG eLife 27487561 Elife 2016 Aug 3
Nanofabricated Neural Probes for Dense 3-D Recordings of Brain Activity. Rios G, Lubenov EV, Chi D, Roukes ML, Siapas AG Nano letters 27766885 Nano Lett 2016 Nov 9
Endogenous Retroviral Envelope Syncytin Induces HIV-1 Spreading and Establishes HIV Reservoirs in Placenta. Tang Y, Woodward BO, Pastor L, George AM, Petrechko O, Nouvet FJ, Haas DW, Jiang G, Hildreth JEK Cell reports 32234485 Cell Rep 2020 Mar 31
Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina. Li YN, Tsujimura T, Kawamura S, Dowling JE The Journal of comparative neurology 22907678 J Comp Neurol 2012 Nov 1
Spinal projection neurons control turning behaviors in zebrafish. Huang KH, Ahrens MB, Dunn TW, Engert F Current biology : CB 23910662 Curr Biol 2013 Aug 19
Large-scale imaging in small brains. Ahrens MB, Engert F Current opinion in neurobiology 25636154 Curr Opin Neurobiol 2015 Jun
Navigational strategies underlying phototaxis in larval zebrafish. Chen X, Engert F Frontiers in systems neuroscience 24723859 Front Syst Neurosci 2014
Neural Circuits Underlying Visually Evoked Escapes in Larval Zebrafish. Dunn TW, Gebhardt C, Naumann EA, Riegler C, Ahrens MB, Engert F, Del Bene F Neuron 26804997 Neuron 2016 Feb 3
Pluripotency factors in embryonic stem cells regulate differentiation into germ layers. Thomson M, Liu SJ, Zou LN, Smith Z, Meissner A, Ramanathan S Cell 21663792 Cell 2011 Jun 10
A compressed sensing framework for efficient dissection of neural circuits. Lee JB, Yonar A, Hallacy T, Shen CH, Milloz J, Srinivasan J, Kocabas A, Ramanathan S Nature methods 30573831 Nat Methods 2019 Jan
Potential role for snoRNAs in PKR activation during metabolic stress. Youssef OA, Safran SA, Nakamura T, Nix DA, Hotamisligil GS, Bass BL Proceedings of the National Academy of Sciences of the United States of America 25848059 Proc Natl Acad Sci U S A 2015 Apr 21
Drosophila dicer-2 cleavage is mediated by helicase- and dsRNA termini-dependent states that are modulated by Loquacious-PD. Sinha NK, Trettin KD, Aruscavage PJ, Bass BL Molecular cell 25891075 Mol Cell 2015 May 7
Identification of the long, edited dsRNAome of LPS-stimulated immune cells. Blango MG, Bass BL Genome research 27197207 Genome Res 2016 Jun
Genome-wide profiling of the C. elegans dsRNAome. Whipple JM, Youssef OA, Aruscavage PJ, Nix DA, Hong C, Johnson WE, Bass BL RNA (New York, N.Y.) 25805852 RNA 2015 May
Genome-wide identification and quantitative analysis of cleaved tRNA fragments induced by cellular stress. Saikia M, Krokowski D, Guan BJ, Ivanov P, Parisien M, Hu GF, Anderson P, Pan T, Hatzoglou M The Journal of biological chemistry 23086926 J Biol Chem 2012 Dec 14
How the fly balances its ability to combat different pathogens. Chambers MC, Lightfield KL, Schneider DS PLoS pathogens 23271964 PLoS Pathog 2012
Disease tolerance as a defense strategy. Medzhitov R, Schneider DS, Soares MP Science (New York, N.Y.) 22363001 Science 2012 Feb 24
Tracing personalized health curves during infections. Schneider DS PLoS biology 21957398 PLoS Biol 2011 Sep
Tolerance of infections. Ayres JS, Schneider DS Annual review of immunology 22224770 Annu Rev Immunol 2012
Guided Homing of Cells in Multi-Photon Microfabricated Bioscaffolds. Skylar-Scott MA, Liu MC, Wu Y, Dixit A, Yanik MF Advanced healthcare materials 27059425 Adv Healthc Mater 2016 May
Cholinergic Signaling Controls Conditioned Fear Behaviors and Enhances Plasticity of Cortical-Amygdala Circuits. Jiang L, Kundu S, Lederman JD, López-Hernández GY, Ballinger EC, Wang S, Talmage DA, Role LW Neuron 27161525 Neuron 2016 Jun 1
Electrophysiological properties of basal forebrain cholinergic neurons identified by genetic and optogenetic tagging. López-Hernández GY, Ananth M, Jiang L, Ballinger EC, Talmage DA, Role LW Journal of neurochemistry 28791701 J Neurochem 2017 Aug
Targeted gene knockout by direct delivery of zinc-finger nuclease proteins. Gaj T, Guo J, Kato Y, Sirk SJ, Barbas CF 3rd Nature methods 22751204 Nat Methods 2012 Jul 1
Structural characterization of anti-inflammatory immunoglobulin G Fc proteins. Ahmed AA, Giddens J, Pincetic A, Lomino JV, Ravetch JV, Wang LX, Bjorkman PJ Journal of molecular biology 25036289 J Mol Biol 2014 Sep 9
Intra-spike crosslinking overcomes antibody evasion by HIV-1. Galimidi RP, Klein JS, Politzer MS, Bai S, Seaman MS, Nussenzweig MC, West AP Jr, Bjorkman PJ Cell 25635457 Cell 2015 Jan 29
Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues. West AP Jr, Scharf L, Horwitz J, Klein F, Nussenzweig MC, Bjorkman PJ Proceedings of the National Academy of Sciences of the United States of America 23754383 Proc Natl Acad Sci U S A 2013 Jun 25
Antibody engineering for increased potency, breadth and half-life. Sievers SA, Scharf L, West AP Jr, Bjorkman PJ Current opinion in HIV and AIDS 25760931 Curr Opin HIV AIDS 2015 May
Structural basis for germ-line gene usage of a potent class of antibodies targeting the CD4-binding site of HIV-1 gp120. West AP Jr, Diskin R, Nussenzweig MC, Bjorkman PJ Proceedings of the National Academy of Sciences of the United States of America 22745174 Proc Natl Acad Sci U S A 2012 Jul 24
Design and characterization of structured protein linkers with differing flexibilities. Klein JS, Jiang S, Galimidi RP, Keeffe JR, Bjorkman PJ Protein engineering, design & selection : PEDS 25301959 Protein Eng Des Sel 2014 Oct
Structural insights on the role of antibodies in HIV-1 vaccine and therapy. West AP Jr, Scharf L, Scheid JF, Klein F, Bjorkman PJ, Nussenzweig MC Cell 24529371 Cell 2014 Feb 13
Discovery of small molecules that bind to K-Ras and inhibit Sos-mediated activation. Sun Q, Burke JP, Phan J, Burns MC, Olejniczak ET, Waterson AG, Lee T, Rossanese OW, Fesik SW Angewandte Chemie (International ed. in English) 22566140 Angew Chem Int Ed Engl 2012 Jun 18
A high-throughput fluorescence polarization anisotropy assay for the 70N domain of replication protein A. Souza-Fagundes EM, Frank AO, Feldkamp MD, Dorset DC, Chazin WJ, Rossanese OW, Olejniczak ET, Fesik SW Analytical biochemistry 22197419 Anal Biochem 2012 Feb 15
Discovery of Quinazolines That Activate SOS1-Mediated Nucleotide Exchange on RAS. Abbott JR, Patel PA, Howes JE, Akan DT, Kennedy JP, Burns MC, Browning CF, Sun Q, Rossanese OW, Phan J, Waterson AG, Fesik SW ACS medicinal chemistry letters 30258545 ACS Med Chem Lett 2018 Sep 13
Discovery of tricyclic indoles that potently inhibit Mcl-1 using fragment-based methods and structure-based design. Burke JP, Bian Z, Shaw S, Zhao B, Goodwin CM, Belmar J, Browning CF, Vigil D, Friberg A, Camper DV, Rossanese OW, Lee T, Olejniczak ET, Fesik SW Journal of medicinal chemistry 25844895 J Med Chem 2015 May 14
Fragment-based screening of the bromodomain of ATAD2. Harner MJ, Chauder BA, Phan J, Fesik SW Journal of medicinal chemistry 25314628 J Med Chem 2014 Nov 26
Interaction with WDR5 promotes target gene recognition and tumorigenesis by MYC. Thomas LR, Wang Q, Grieb BC, Phan J, Foshage AM, Sun Q, Olejniczak ET, Clark T, Dey S, Lorey S, Alicie B, Howard GC, Cawthon B, Ess KC, Eischen CM, Zhao Z, Fesik SW, Tansey WP Molecular cell 25818646 Mol Cell 2015 May 7
Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach. Frank AO, Feldkamp MD, Kennedy JP, Waterson AG, Pelz NF, Patrone JD, Vangamudi B, Camper DV, Rossanese OW, Chazin WJ, Fesik SW Journal of medicinal chemistry 24147804 J Med Chem 2013 Nov 27
Surface reengineering of RPA70N enables cocrystallization with an inhibitor of the replication protein A interaction motif of ATR interacting protein. Feldkamp MD, Frank AO, Kennedy JP, Patrone JD, Vangamudi B, Waterson AG, Fesik SW, Chazin WJ Biochemistry 23962067 Biochemistry 2013 Sep 17
Discovery of potent myeloid cell leukemia 1 (Mcl-1) inhibitors using fragment-based methods and structure-based design. Friberg A, Vigil D, Zhao B, Daniels RN, Burke JP, Garcia-Barrantes PM, Camper D, Chauder BA, Lee T, Olejniczak ET, Fesik SW Journal of medicinal chemistry 23244564 J Med Chem 2013 Jan 10
A method for the second-site screening of K-Ras in the presence of a covalently attached first-site ligand. Sun Q, Phan J, Friberg AR, Camper DV, Olejniczak ET, Fesik SW Journal of biomolecular NMR 25087006 J Biomol NMR 2014 Sep
Fragment-based drug discovery using NMR spectroscopy. Harner MJ, Frank AO, Fesik SW Journal of biomolecular NMR 23686385 J Biomol NMR 2013 Jun
MYC and MCL1 Cooperatively Promote Chemotherapy-Resistant Breast Cancer Stem Cells via Regulation of Mitochondrial Oxidative Phosphorylation. Lee KM, Giltnane JM, Balko JM, Schwarz LJ, Guerrero-Zotano AL, Hutchinson KE, Nixon MJ, Estrada MV, Sánchez V, Sanders ME, Lee T, Gómez H, Lluch A, Pérez-Fidalgo JA, Wolf MM, Andrejeva G, Rathmell JC, Fesik SW, Arteaga CL Cell metabolism 28978427 Cell Metab 2017 Oct 3
Discovery of 2-Indole-acylsulfonamide Myeloid Cell Leukemia 1 (Mcl-1) Inhibitors Using Fragment-Based Methods. Pelz NF, Bian Z, Zhao B, Shaw S, Tarr JC, Belmar J, Gregg C, Camper DV, Goodwin CM, Arnold AL, Sensintaffar JL, Friberg A, Rossanese OW, Lee T, Olejniczak ET, Fesik SW Journal of medicinal chemistry 26878343 J Med Chem 2016 Mar 10
Discovery and Structure-Based Optimization of Benzimidazole-Derived Activators of SOS1-Mediated Nucleotide Exchange on RAS. Hodges TR, Abbott JR, Little AJ, Sarkar D, Salovich JM, Howes JE, Akan DT, Sai J, Arnold AL, Browning C, Burns MC, Sobolik T, Sun Q, Beesetty Y, Coker JA, Scharn D, Stadtmueller H, Rossanese OW, Phan J, Waterson AG, McConnell DB, Fesik SW Journal of medicinal chemistry 30205005 J Med Chem 2018 Oct 11
Drugging the undruggable RAS: Mission possible? Cox AD, Fesik SW, Kimmelman AC, Luo J, Der CJ Nature reviews. Drug discovery 25323927 Nat Rev Drug Discov 2014 Nov
Discovery and biological characterization of potent myeloid cell leukemia-1 inhibitors. Lee T, Bian Z, Zhao B, Hogdal LJ, Sensintaffar JL, Goodwin CM, Belmar J, Shaw S, Tarr JC, Veerasamy N, Matulis SM, Koss B, Fischer MA, Arnold AL, Camper DV, Browning CF, Rossanese OW, Budhraja A, Opferman J, Boise LH, Savona MR, Letai A, Olejniczak ET, Fesik SW FEBS letters 27878989 FEBS Lett 2017 Jan
Approach for targeting Ras with small molecules that activate SOS-mediated nucleotide exchange. Burns MC, Sun Q, Daniels RN, Camper D, Kennedy JP, Phan J, Olejniczak ET, Lee T, Waterson AG, Rossanese OW, Fesik SW Proceedings of the National Academy of Sciences of the United States of America 24550516 Proc Natl Acad Sci U S A 2014 Mar 4
Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A. Patrone JD, Kennedy JP, Frank AO, Feldkamp MD, Vangamudi B, Pelz NF, Rossanese OW, Waterson AG, Chazin WJ, Fesik SW ACS medicinal chemistry letters 23914285 ACS Med Chem Lett 2013 Jul 11
Identification and Optimization of Anthranilic Acid Based Inhibitors of Replication Protein A. Patrone JD, Pelz NF, Bates BS, Souza-Fagundes EM, Vangamudi B, Camper DV, Kuznetsov AG, Browning CF, Feldkamp MD, Frank AO, Gilston BA, Olejniczak ET, Rossanese OW, Waterson AG, Chazin WJ, Fesik SW ChemMedChem 26748787 ChemMedChem 2016 Apr 19
Discovery of Sulfonamide-Derived Agonists of SOS1-Mediated Nucleotide Exchange on RAS Using Fragment-Based Methods. Sarkar D, Olejniczak ET, Phan J, Coker JA, Sai J, Arnold A, Beesetty Y, Waterson AG, Fesik SW Journal of medicinal chemistry 32673492 J Med Chem 2020 Aug 13
Dynamic states of population activity in prefrontal cortical networks of freely-moving macaque. Milton R, Shahidi N, Dragoi V Nature communications 32327660 Nat Commun 2020 Apr 23
Surpassing fundamental limits of oscillators using nonlinear resonators. Villanueva LG, Kenig E, Karabalin RB, Matheny MH, Lifshitz R, Cross MC, Roukes ML Physical review letters 23679770 Phys Rev Lett 2013 Apr 26
Surface adsorbate fluctuations and noise in nanoelectromechanical systems. Yang YT, Callegari C, Feng XL, Roukes ML Nano letters 21388120 Nano Lett 2011 Apr 13
Passive phase noise cancellation scheme. Kenig E, Cross MC, Lifshitz R, Karabalin RB, Villanueva LG, Matheny MH, Roukes ML Physical review letters 23004985 Phys Rev Lett 2012 Jun 29
Large-scale integration of nanoelectromechanical systems for gas sensing applications. Bargatin I, Myers EB, Aldridge JS, Marcoux C, Brianceau P, Duraffourg L, Colinet E, Hentz S, Andreucci P, Roukes ML Nano letters 22280452 Nano Lett 2012 Mar 14
Stress-induced variations in the stiffness of micro- and nanocantilever beams. Karabalin RB, Villanueva LG, Matheny MH, Sader JE, Roukes ML Physical review letters 23003973 Phys Rev Lett 2012 Jun 8
Optimal operating points of oscillators using nonlinear resonators. Kenig E, Cross MC, Villanueva LG, Karabalin RB, Matheny MH, Lifshitz R, Roukes ML Physical review. E, Statistical, nonlinear, and soft matter physics 23214857 Phys Rev E Stat Nonlin Soft Matter Phys 2012 Nov
Nonlinear mode-coupling in nanomechanical systems. Matheny MH, Villanueva LG, Karabalin RB, Sader JE, Roukes ML Nano letters 23496001 Nano Lett 2013 Apr 10
Nanoelectromechanical resonator arrays for ultrafast, gas-phase chromatographic chemical analysis. Li M, Myers EB, Tang HX, Aldridge SJ, McCaig HC, Whiting JJ, Simonson RJ, Lewis NS, Roukes ML Nano letters 20795729 Nano Lett 2010 Oct 13
Comparative advantages of mechanical biosensors. Arlett JL, Myers EB, Roukes ML Nature nanotechnology 21441911 Nat Nanotechnol 2011 Apr
Maternal nutrition induces pervasive gene expression changes but no detectable DNA methylation differences in the liver of adult offspring. Cannon MV, Buchner DA, Hester J, Miller H, Sehayek E, Nadeau JH, Serre D PloS one 24594983 PLoS One 2014
CMV infection, TLR-2 and -4 expression, and cytokine profiles in early-onset preeclampsia with HELLP syndrome. Xie F, von Dadelszen P, Nadeau J American journal of reproductive immunology (New York, N.Y. : 1989) 24612145 Am J Reprod Immunol 2014 Apr
Report of the National Heart, Lung, and Blood Institute Working Group on epigenetics and hypertension. Cowley AW Jr, Nadeau JH, Baccarelli A, Berecek K, Fornage M, Gibbons GH, Harrison DG, Liang M, Nathanielsz PW, O'Connor DT, Ordovas J, Peng W, Soares MB, Szyf M, Tolunay HE, Wood KC, Zhao K, Galis ZS Hypertension (Dallas, Tex. : 1979) 22431584 Hypertension 2012 May
Transgenerational epigenetic effects of the Apobec1 cytidine deaminase deficiency on testicular germ cell tumor susceptibility and embryonic viability. Nelson VR, Heaney JD, Tesar PJ, Davidson NO, Nadeau JH Proceedings of the National Academy of Sciences of the United States of America 22923694 Proc Natl Acad Sci U S A 2012 Oct 9
Transgenerational genetic effects of the paternal Y chromosome on daughters' phenotypes. Nelson VR, Spiezio SH, Nadeau JH Epigenomics 22121971 Epigenomics 2010 Aug
Transgenerational genetic effects. Nelson VR, Nadeau JH Epigenomics 22122083 Epigenomics 2010 Dec
Genome-wide identification and functional analysis of Apobec-1-mediated C-to-U RNA editing in mouse small intestine and liver. Blanc V, Park E, Schaefer S, Miller M, Lin Y, Kennedy S, Billing AM, Ben Hamidane H, Graumann J, Mortazavi A, Nadeau JH, Davidson NO Genome biology 24946870 Genome Biol 2014 Jun 19
Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system. Joung JK Journal of cellular biochemistry. Supplement 11842428 J Cell Biochem Suppl 2001
Counter-selectable marker for bacterial-based interaction trap systems. Meng X, Smith RM, Giesecke AV, Joung JK, Wolfe SA BioTechniques 16526407 Biotechniques 2006 Feb
Engineering designer transcription activator-like effector nucleases (TALENs) by REAL or REAL-Fast assembly. Reyon D, Khayter C, Regan MR, Joung JK, Sander JD Current protocols in molecular biology 23026907 Curr Protoc Mol Biol 2012 Oct
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
The bacterial two-hybrid system as a reporter system for analyzing protein-protein interactions. Giesecke AV, Joung JK CSH protocols 21357036 CSH Protoc 2007 Mar 1
Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system. Thibodeau-Beganny S, Joung JK Methods in molecular biology (Clifton, N.J.) 18314590 Methods Mol Biol 2007
In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases. Sebastiano V, Maeder ML, Angstman JF, Haddad B, Khayter C, Yeo DT, Goodwin MJ, Hawkins JS, Ramirez CL, Batista LF, Artandi SE, Wernig M, Joung JK Stem cells (Dayton, Ohio) 21898685 Stem Cells 2011 Nov
A combined yeast/bacteria two-hybrid system: development and evaluation. Serebriiskii IG, Fang R, Latypova E, Hopkins R, Vinson C, Joung JK, Golemis EA Molecular & cellular proteomics : MCP 15781424 Mol Cell Proteomics 2005 Jun
Repression of phase-variable cup gene expression by H-NS-like proteins in Pseudomonas aeruginosa. Vallet-Gely I, Donovan KE, Fang R, Joung JK, Dove SL Proceedings of the National Academy of Sciences of the United States of America 16043713 Proc Natl Acad Sci U S A 2005 Aug 2
Gene targeting of a disease-related gene in human induced pluripotent stem and embryonic stem cells. Zou J, Maeder ML, Mali P, Pruett-Miller SM, Thibodeau-Beganny S, Chou BK, Chen G, Ye Z, Park IH, Daley GQ, Porteus MH, Joung JK, Cheng L Cell stem cell 19540188 Cell Stem Cell 2009 Jul 2
ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool. Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D Nucleic acids research 20435679 Nucleic Acids Res 2010 Jul
Synergistic activation of transcription by Escherichia coli cAMP receptor protein. Joung JK, Le LU, Hochschild A Proceedings of the National Academy of Sciences of the United States of America 7681995 Proc Natl Acad Sci U S A 1993 Apr 1
Genetic strategy for analyzing specificity of dimer formation: Escherichia coli cyclic AMP receptor protein mutant altered in its dimerization specificity. Joung JK, Chung EH, King G, Yu C, Hirsh AS, Hochschild A Genes & development 7498794 Genes Dev 1995 Dec 1
Structural and functional characterization of human immunodeficiency virus tat protein. Ruben S, Perkins A, Purcell R, Joung K, Sia R, Burghoff R, Haseltine WA, Rosen CA Journal of virology 2535718 J Virol 1989 Jan
ZFNGenome: a comprehensive resource for locating zinc finger nuclease target sites in model organisms. Reyon D, Kirkpatrick JR, Sander JD, Zhang F, Voytas DF, Joung JK, Dobbs D, Coffman CR BMC genomics 21276248 BMC Genomics 2011 Jan 28
Targeted mutagenesis in zebrafish using customized zinc-finger nucleases. Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR Nature protocols 20010934 Nat Protoc 2009
Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system. Thibodeau-Beganny S, Maeder ML, Joung JK Methods in molecular biology (Clifton, N.J.) 20680826 Methods Mol Biol 2010
Revealing off-target cleavage specificities of zinc-finger nucleases by in vitro selection. Pattanayak V, Ramirez CL, Joung JK, Liu DR Nature methods 21822273 Nat Methods 2011 Aug 7
Engineering zinc finger nucleases for targeted mutagenesis of zebrafish. Sander JD, Yeh JR, Peterson RT, Joung JK Methods in cell biology 21924156 Methods Cell Biol 2011
Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs. Cade L, Reyon D, Hwang WY, Tsai SQ, Patel S, Khayter C, Joung JK, Sander JD, Peterson RT, Yeh JR Nucleic acids research 22684503 Nucleic Acids Res 2012 Sep
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Rapamycin-inspired macrocycles with new target specificity. Guo Z, Hong SY, Wang J, Rehan S, Liu W, Peng H, Das M, Li W, Bhat S, Peiffer B, Ullman BR, Tse CM, Tarmakova Z, Schiene-Fischer C, Fischer G, Coe I, Paavilainen VO, Sun Z, Liu JO Nature chemistry 30532015 Nat Chem 2019 Mar
Verapamil, and its metabolite norverapamil, inhibit macrophage-induced, bacterial efflux pump-mediated tolerance to multiple anti-tubercular drugs. Adams KN, Szumowski JD, Ramakrishnan L The Journal of infectious diseases 24532601 J Infect Dis 2014 Aug 1
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Computer-Assisted Transgenesis of Caenorhabditis elegans for Deep Phenotyping. Gilleland CL, Falls AT, Noraky J, Heiman MG, Yanik MF Genetics 26163188 Genetics 2015 Sep
Strategic protein target analysis for developing drugs to stop dental caries. Horst JA, Pieper U, Sali A, Zhan L, Chopra G, Samudrala R, Featherstone JD Advances in dental research 22899687 Adv Dent Res 2012 Sep
LoCo: a novel main chain scoring function for protein structure prediction based on local coordinates. Moughon SE, Samudrala R BMC bioinformatics 21920038 BMC Bioinformatics 2011 Sep 15
Structure prediction of partial-length protein sequences. Laurenzi A, Hung LH, Samudrala R International journal of molecular sciences 23867606 Int J Mol Sci 2013 Jul 17
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials. Fine J, Konc J, Samudrala R, Chopra G Journal of chemical information and modeling 32069042 J Chem Inf Model 2020 Mar 23
Shotgun drug repurposing biotechnology to tackle epidemics and pandemics. Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R Drug discovery today 32405249 Drug Discov Today 2020 Jul
Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function. Palanikumar L, Karpauskaite L, Al-Sayegh M, Chehade I, Alam M, Hassan S, Maity D, Ali L, Kalmouni M, Hunashal Y, Ahmed J, Houhou T, Karapetyan S, Falls Z, Samudrala R, Pasricha R, Esposito G, Afzal AJ, Hamilton AD, Kumar S, Magzoub M Nature communications 34172723 Nat Commun 2021 Jun 25
A Systematic Review of Computational Drug Discovery, Development, and Repurposing for Ebola Virus Disease Treatment. Schuler J, Hudson ML, Schwartz D, Samudrala R Molecules (Basel, Switzerland) 29053626 Molecules 2017 Oct 20
Computational Grafting of Epitopes. Manish M, Mishra S, Pahuja M, Anand A, Subbarao N, Samudrala R Methods in molecular biology (Clifton, N.J.) 37258909 Methods Mol Biol 2023
A fluorescence-based, gain-of-signal, live cell system to evaluate SARS-CoV-2 main protease inhibition. Dey-Rao R, Smith GR, Timilsina U, Falls Z, Samudrala R, Stavrou S, Melendy T Antiviral research 34626674 Antiviral Res 2021 Nov
Antiviral Approaches against Influenza Virus. Kumari R, Sharma SD, Kumar A, Ende Z, Mishina M, Wang Y, Falls Z, Samudrala R, Pohl J, Knight PR, Sambhara S Clinical microbiology reviews 36645300 Clin Microbiol Rev 2023 Mar 23
Exploration of interaction scoring criteria in the CANDO platform. Falls Z, Mangione W, Schuler J, Samudrala R BMC research notes 31174591 BMC Res Notes 2019 Jun 7
A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex. Chatrikhi R, Feeney CF, Pulvino MJ, Alachouzos G, MacRae AJ, Falls Z, Rai S, Brennessel WW, Jenkins JL, Walter MJ, Graubert TA, Samudrala R, Jurica MS, Frontier AJ, Kielkopf CL Cell chemical biology 33689684 Cell Chem Biol 2021 Aug 19
Accelerated protein structure comparison using TM-score-GPU. Hung LH, Samudrala R Bioinformatics (Oxford, England) 22718788 Bioinformatics 2012 Aug 15
Multiscale modelling of relationships between protein classes and drug behavior across all diseases using the CANDO platform. Sethi G, Chopra G, Samudrala R Mini reviews in medicinal chemistry 25694071 Mini Rev Med Chem 2015
Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens. Afzal AJ, Srour A, Goil A, Vasudaven S, Liu T, Samudrala R, Dogra N, Kohli P, Malakar A, Lightfoot DA BMC plant biology 23497186 BMC Plant Biol 2013 Mar 15
Fingerprinting CANDO: Increased Accuracy with Structure- and Ligand-Based Shotgun Drug Repurposing. Schuler J, Samudrala R ACS omega 31656912 ACS Omega 2019 Oct 22
Identifying Protein Features Responsible for Improved Drug Repurposing Accuracies Using the CANDO Platform: Implications for Drug Design. Mangione W, Samudrala R Molecules (Basel, Switzerland) 30621144 Molecules 2019 Jan 4
CANDO and the infinite drug discovery frontier. Minie M, Chopra G, Sethi G, Horst J, White G, Roy A, Hatti K, Samudrala R Drug discovery today 24980786 Drug Discov Today 2014 Sep
Evaluating the performance of drug-repurposing technologies. Schuler J, Falls Z, Mangione W, Hudson ML, Bruggemann L, Samudrala R Drug discovery today 34400352 Drug Discov Today 2022 Jan
Optimal COVID-19 therapeutic candidate discovery using the CANDO platform. Mangione W, Falls Z, Samudrala R Frontiers in pharmacology 36091793 Front Pharmacol 2022
Identifying Protein Features and Pathways Responsible for Toxicity Using Machine Learning and Tox21: Implications for Predictive Toxicology. Moukheiber L, Mangione W, Moukheiber M, Maleki S, Falls Z, Gao M, Samudrala R Molecules (Basel, Switzerland) 35566372 Molecules 2022 May 8
Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms. Van Norden M, Mangione W, Falls Z, Samudrala R bioRxiv : the preprint server for biology 39764006 bioRxiv 2024 Dec 16
Exploring Polypharmacology in Drug Discovery and Repurposing Using the CANDO Platform. Chopra G, Samudrala R Current pharmaceutical design 27013226 Curr Pharm Des 2016
Shotgun drug repurposing biotechnology to tackle epidemics and pandemics. Mangione W, Falls Z, Melendy T, Chopra G, Samudrala R ChemRxiv : the preprint server for chemistry 32511286 ChemRxiv 2020 May 4
Linking Genome and Exposome: Computational Analysis of Human Variation in Chemical-Target Interactions. Bruggemann L, Hawthorne C, Samudrala R, Lopez-Campos GH Studies in health technology and informatics 32570644 Stud Health Technol Inform 2020 Jun 16
Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform. Hudson ML, Samudrala R Molecules (Basel, Switzerland) 33925237 Molecules 2021 Apr 28
Multiscale Analysis and Validation of Effective Drug Combinations Targeting Driver KRAS Mutations in Non-Small Cell Lung Cancer. Bruggemann L, Falls Z, Mangione W, Schwartz SA, Battaglia S, Aalinkeel R, Mahajan SD, Samudrala R International journal of molecular sciences 36674513 Int J Mol Sci 2023 Jan 5
The impact of nucleosome structure on CRISPR/Cas9 fidelity. Handelmann CR, Tsompana M, Samudrala R, Buck MJ Nucleic acids research 36727449 Nucleic Acids Res 2023 Mar 21
The Promise and Challenge of Digital Biology. Minie ME, Samudrala R Journal of bioengineering & biomedical science 30338132 J Bioeng Biomed Sci 2013
Computational chemoproteomics to understand the role of selected psychoactives in treating mental health indications. Fine J, Lackner R, Samudrala R, Chopra G Scientific reports 31511563 Sci Rep 2019 Sep 11
Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Corrigendum. Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Dementiev A, Abad-Zapatero C, Movahedzadeh F Acta crystallographica. Section F, Structural biology communications 32254053 Acta Crystallogr F Struct Biol Commun 2020 Apr 1
Proteomic Network Analysis of Bronchoalveolar Lavage Fluid in Ex-Smokers to Discover Implicated Protein Targets and Novel Drug Treatments for Chronic Obstructive Pulmonary Disease. Mammen MJ, Tu C, Morris MC, Richman S, Mangione W, Falls Z, Qu J, Broderick G, Sethi S, Samudrala R Pharmaceuticals (Basel, Switzerland) 35631392 Pharmaceuticals (Basel) 2022 May 1
A Deep-Learning Proteomic-Scale Approach for Drug Design. Overhoff B, Falls Z, Mangione W, Samudrala R Pharmaceuticals (Basel, Switzerland) 34959678 Pharmaceuticals (Basel) 2021 Dec 7
The enzymatic and metabolic capabilities of early life. Goldman AD, Baross JA, Samudrala R PloS one 22970111 PLoS One 2012
Rv0100, a proposed acyl carrier protein in Mycobacterium tuberculosis: expression, purification and crystallization. Bondoc JMG, Gutka HJ, Almutairi MM, Patwell R, Rutter MW, Wolf NM, Samudrala R, Mehboob S, Movahedzadeh F Acta crystallographica. Section F, Structural biology communications 31584013 Acta Crystallogr F Struct Biol Commun 2019 Oct 1
Combating Ebola with Repurposed Therapeutics Using the CANDO Platform. Chopra G, Kaushik S, Elkin PL, Samudrala R Molecules (Basel, Switzerland) 27898018 Molecules 2016 Nov 25
Self-assembly of filamentous amelogenin requires calcium and phosphate: from dimers via nanoribbons to fibrils. Martinez-Avila O, Wu S, Kim SJ, Cheng Y, Khan F, Samudrala R, Sali A, Horst JA, Habelitz S Biomacromolecules 22974364 Biomacromolecules 2012 Nov 12
cando.py: Open Source Software for Predictive Bioanalytics of Large Scale Drug-Protein-Disease Data. Mangione W, Falls Z, Chopra G, Samudrala R Journal of chemical information and modeling 32515949 J Chem Inf Model 2020 Sep 28
Association of C>U RNA Editing with Human Disease Variants. Mandloi S, Falls Z, Deng R, Samudrala R, Elkin PL Studies in health technology and informatics 32570581 Stud Health Technol Inform 2020 Jun 16
Accurate Prediction of Inhibitor Binding to HIV-1 Protease Using CANDOCK. Falls Z, Fine J, Chopra G, Samudrala R Frontiers in chemistry 35111726 Front Chem 2021
Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations. Ko WY, Kaercher KA, Giombini E, Marcatili P, Froment A, Ibrahim M, Lema G, Nyambo TB, Omar SA, Wambebe C, Ranciaro A, Hirbo JB, Tishkoff SA American journal of human genetics 21664997 Am J Hum Genet 2011 Jun 10
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The evolution of human genetic and phenotypic variation in Africa. Campbell MC, Tishkoff SA Current biology : CB 20178763 Curr Biol 2010 Feb 23
A founder mutation in LEPRE1 carried by 1.5% of West Africans and 0.4% of African Americans causes lethal recessive osteogenesis imperfecta. Cabral WA, Barnes AM, Adeyemo A, Cushing K, Chitayat D, Porter FD, Panny SR, Gulamali-Majid F, Tishkoff SA, Rebbeck TR, Gueye SM, Bailey-Wilson JE, Brody LC, Rotimi CN, Marini JC Genetics in medicine : official journal of the American College of Medical Genetics 22281939 Genet Med 2012 May
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Retinoic acid signaling regulates sonic hedgehog and bone morphogenetic protein signalings during genital tubercle development. Liu L, Suzuki K, Nakagata N, Mihara K, Matsumaru D, Ogino Y, Yashiro K, Hamada H, Liu Z, Evans SM, Mendelsohn C, Yamada G Birth defects research. Part B, Developmental and reproductive toxicology 22127979 Birth Defects Res B Dev Reprod Toxicol 2012 Feb
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Chapter 19: Mechanical response of cytoskeletal networks. Gardel ML, Kasza KE, Brangwynne CP, Liu J, Weitz DA Methods in cell biology 19118688 Methods Cell Biol 2008
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Stressing the limits of focal adhesion mechanosensitivity. Oakes PW, Gardel ML Current opinion in cell biology 24998185 Curr Opin Cell Biol 2014 Oct
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Identification and characterization of a small molecule inhibitor of formin-mediated actin assembly. Rizvi SA, Neidt EM, Cui J, Feiger Z, Skau CT, Gardel ML, Kozmin SA, Kovar DR Chemistry & biology 19942139 Chem Biol 2009 Nov 25
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Preparation of complaint matrices for quantifying cellular contraction. Aratyn-Schaus Y, Oakes PW, Stricker J, Winter SP, Gardel ML Journal of visualized experiments : JoVE 21178972 J Vis Exp 2010 Dec 14
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Reconstitution of contractile actomyosin arrays. Murrell M, Thoresen T, Gardel M Methods in enzymology 24630112 Methods Enzymol 2014
Optimization of traction force microscopy for micron-sized focal adhesions. Stricker J, Sabass B, Schwarz US, Gardel ML Journal of physics. Condensed matter : an Institute of Physics journal 20523913 J Phys Condens Matter 2010 May 19
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Cell-ECM traction force modulates endogenous tension at cell-cell contacts. Maruthamuthu V, Sabass B, Schwarz US, Gardel ML Proceedings of the National Academy of Sciences of the United States of America 21383129 Proc Natl Acad Sci U S A 2011 Mar 22
Cell-substrate interactions. Gardel M, Schwarz U Journal of physics. Condensed matter : an Institute of Physics journal 21386358 J Phys Condens Matter 2010 May 19
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Materials science: Synthetic polymers with biological rigidity. Gardel ML Nature 23354043 Nature 2013 Jan 31
The clinically available NMDA receptor antagonist, memantine, exhibits relative safety in the developing rat brain. Manning SM, Boll G, Fitzgerald E, Selip DB, Volpe JJ, Jensen FE International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience 21624454 Int J Dev Neurosci 2011 Nov
Does acquired epileptogenesis in the immature brain require neuronal death. Baram TZ, Jensen FE, Brooks-Kayal A Epilepsy currents 21461261 Epilepsy Curr 2011 Jan
Altered development of glutamatergic synapses in layer V pyramidal neurons in NR3A knockout mice. Zhou C, Jensen FE, Sucher NJ Molecular and cellular neurosciences 19782137 Mol Cell Neurosci 2009 Dec
Neonatal seizures: an update on mechanisms and management. Jensen FE Clinics in perinatology 19944840 Clin Perinatol 2009 Dec
A mouse model of tuberous sclerosis: neuronal loss of Tsc1 causes dysplastic and ectopic neurons, reduced myelination, seizure activity, and limited survival. Meikle L, Talos DM, Onda H, Pollizzi K, Rotenberg A, Sahin M, Jensen FE, Kwiatkowski DJ The Journal of neuroscience : the official journal of the Society for Neuroscience 17522300 J Neurosci 2007 May 23
Early-life seizures alter synaptic calcium-permeable AMPA receptor function and plasticity. Lippman-Bell JJ, Zhou C, Sun H, Feske JS, Jensen FE Molecular and cellular neurosciences 27521497 Mol Cell Neurosci 2016 Oct
Strain-specific differences in perinatal rodent oligodendrocyte lineage progression and its correlation with human. Dean JM, Moravec MD, Grafe M, Abend N, Ren J, Gong X, Volpe JJ, Jensen FE, Hohimer AR, Back SA Developmental neuroscience 21865655 Dev Neurosci 2011
Developmental expression of N-methyl-D-aspartate (NMDA) receptor subunits in human white and gray matter: potential mechanism of increased vulnerability in the immature brain. Jantzie LL, Talos DM, Jackson MC, Park HK, Graham DA, Lechpammer M, Folkerth RD, Volpe JJ, Jensen FE Cerebral cortex (New York, N.Y. : 1991) 24046081 Cereb Cortex 2015 Feb
Bumetanide enhances phenobarbital efficacy in a rat model of hypoxic neonatal seizures. Cleary RT, Sun H, Huynh T, Manning SM, Li Y, Rotenberg A, Talos DM, Kahle KT, Jackson M, Rakhade SN, Berry G, Jensen FE PloS one 23536761 PLoS One 2013
AMPA receptor antagonist NBQX attenuates later-life epileptic seizures and autistic-like social deficits following neonatal seizures. Lippman-Bell JJ, Rakhade SN, Klein PM, Obeid M, Jackson MC, Joseph A, Jensen FE Epilepsia 24117347 Epilepsia 2013 Nov
Lestaurtinib (CEP-701) attenuates "second hit" kainic acid-induced seizures following early life hypoxic seizures. Obeid M, Rosenberg EC, Klein PM, Jensen FE Epilepsy research 24582454 Epilepsy Res 2014 May
Blinders, phenotype, and fashionable genetic analysis: a critical examination of the current state of epilepsy genetic studies. Greenberg DA, Subaran R Epilepsia 21219301 Epilepsia 2011 Jan
Association of the small GTPase Rheb with the NMDA receptor subunit NR3A. Sucher NJ, Yu E, Chan SF, Miri M, Lee BJ, Xiao B, Worley PF, Jensen FE Neuro-Signals 21135540 Neurosignals 2010
Contribution of axonal orientation to pathway-dependent modulation of excitatory transmission by direct current stimulation in isolated rat hippocampus. Kabakov AY, Muller PA, Pascual-Leone A, Jensen FE, Rotenberg A Journal of neurophysiology 22219028 J Neurophysiol 2012 Apr
Mammalian target of rapamycin complex 1 activation negatively regulates Polo-like kinase 2-mediated homeostatic compensation following neonatal seizures. Sun H, Kosaras B, Klein PM, Jensen FE Proceedings of the National Academy of Sciences of the United States of America 23479645 Proc Natl Acad Sci U S A 2013 Mar 26
The interaction between early life epilepsy and autistic-like behavioral consequences: a role for the mammalian target of rapamycin (mTOR) pathway. Talos DM, Sun H, Zhou X, Fitzgerald EC, Jackson MC, Klein PM, Lan VJ, Joseph A, Jensen FE PloS one 22567115 PLoS One 2012
Chloride cotransporter NKCC1 inhibitor bumetanide protects against white matter injury in a rodent model of periventricular leukomalacia. Jantzie LL, Hu MY, Park HK, Jackson MC, Yu J, Maxwell JR, Jensen FE Pediatric research 25585037 Pediatr Res 2015 Apr
The tower of Babel: survey on concepts and terminology in electrical status epilepticus in sleep and continuous spikes and waves during sleep in North America. Fernández IS, Chapman KE, Peters JM, Kothare SV, Nordli DR Jr, Jensen FE, Berg AT, Loddenkemper T Epilepsia 23163318 Epilepsia 2013 Apr
Neonatal seizures alter NMDA glutamate receptor GluN2A and 3A subunit expression and function in hippocampal CA1 neurons. Zhou C, Sun H, Klein PM, Jensen FE Frontiers in cellular neuroscience 26441533 Front Cell Neurosci 2015
Altered hippocampal dendritic spine maturation after hypoxia-induced seizures in neonatal rats. Lippman-Bell JJ, Handy M, Nieder CG, Getzfread M, Jensen FE Molecular and cellular neurosciences 34015497 Mol Cell Neurosci 2021 Jun
Finding a better drug for epilepsy: antiepileptogenesis targets. Kobow K, Auvin S, Jensen F, Löscher W, Mody I, Potschka H, Prince D, Sierra A, Simonato M, Pitkänen A, Nehlig A, Rho JM Epilepsia 23061663 Epilepsia 2012 Nov
Glutamate receptor 1 phosphorylation at serine 831 and 845 modulates seizure susceptibility and hippocampal hyperexcitability after early life seizures. Rakhade SN, Fitzgerald EF, Klein PM, Zhou C, Sun H, Huganir RL, Jensen FE The Journal of neuroscience : the official journal of the Society for Neuroscience 23223299 J Neurosci 2012 Dec 5
Developmental factors in the pathogenesis of neonatal seizures. Jensen FE Journal of pediatric neurology : JPN 20191097 J Pediatr Neurol 2009 Jan 1
The developing oligodendrocyte: key cellular target in brain injury in the premature infant. Volpe JJ, Kinney HC, Jensen FE, Rosenberg PA International journal of developmental neuroscience : the official journal of the International Society for Developmental Neuroscience 21382469 Int J Dev Neurosci 2011 Jun
Benign rolandic epileptiform discharges are associated with mood and behavior problems. Sarco DP, Boyer K, Lundy-Krigbaum SM, Takeoka M, Jensen F, Gregas M, Waber DP Epilepsy & behavior : E&B 21862414 Epilepsy Behav 2011 Oct
Perfusion Imaging of Focal Cortical Dysplasia Using Arterial Spin Labeling: Correlation With Histopathological Vascular Density. Wintermark P, Lechpammer M, Warfield SK, Kosaras B, Takeoka M, Poduri A, Madsen JR, Bergin AM, Whalen S, Jensen FE Journal of child neurology 23696629 J Child Neurol 2013 Nov
Issues related to development of antiepileptogenic therapies. Pitkänen A, Nehlig A, Brooks-Kayal AR, Dudek FE, Friedman D, Galanopoulou AS, Jensen FE, Kaminski RM, Kapur J, Klitgaard H, Löscher W, Mody I, Schmidt D Epilepsia 23909852 Epilepsia 2013 Aug
Hypoxia-induced neonatal seizures diminish silent synapses and long-term potentiation in hippocampal CA1 neurons. Zhou C, Lippman JJ, Sun H, Jensen FE The Journal of neuroscience : the official journal of the Society for Neuroscience 22171027 J Neurosci 2011 Dec 14
Epileptogenesis in the immature brain: emerging mechanisms. Rakhade SN, Jensen FE Nature reviews. Neurology 19578345 Nat Rev Neurol 2009 Jul
An international effort towards developing standards for best practices in analysis, interpretation and reporting of clinical genome sequencing results in the CLARITY Challenge. Brownstein CA, Beggs AH, Homer N, Merriman B, Yu TW, Flannery KC, DeChene ET, Towne MC, Savage SK, Price EN, Holm IA, Luquette LJ, Lyon E, Majzoub J, Neupert P, McCallie D Jr, Szolovits P, Willard HF, Mendelsohn NJ, Temme R, Finkel RS, Yum SW, Medne L, Sunyaev SR, Adzhubey I, Cassa CA, de Bakker PI, Duzkale H, Dworzyński P, Fairbrother W, Francioli L, Funke BH, Giovanni MA, Handsaker RE, Lage K, Lebo MS, Lek M, Leshchiner I, MacArthur DG, McLaughlin HM, Murray MF, Pers TH, Polak PP, Raychaudhuri S, Rehm HL, Soemedi R, Stitziel NO, Vestecka S, Supper J, Gugenmus C, Klocke B, Hahn A, Schubach M, Menzel M, Biskup S, Freisinger P, Deng M, Braun M, Perner S, Smith RJ, Andorf JL, Huang J, Ryckman K, Sheffield VC, Stone EM, Bair T, Black-Ziegelbein EA, Braun TA, Darbro B, DeLuca AP, Kolbe DL, Scheetz TE, Shearer AE, Sompallae R, Wang K, Bassuk AG, Edens E, Mathews K, Moore SA, Shchelochkov OA, Trapane P, Bossler A, Campbell CA, Heusel JW, Kwitek A, Maga T, Panzer K, Wassink T, Van Daele D, Azaiez H, Booth K, Meyer N, Segal MM, Williams MS, Tromp G, White P, Corsmeier D, Fitzgerald-Butt S, Herman G, Lamb-Thrush D, McBride KL, Newsom D, Pierson CR, Rakowsky AT, Maver A, Lovrečić L, Palandačić A, Peterlin B, Torkamani A, Wedell A, Huss M, Alexeyenko A, Lindvall JM, Magnusson M, Nilsson D, Stranneheim H, Taylan F, Gilissen C, Hoischen A, van Bon B, Yntema H, Nelen M, Zhang W, Sager J, Zhang L, Blair K, Kural D, Cariaso M, Lennon GG, Javed A, Agrawal S, Ng PC, Sandhu KS, Krishna S, Veeramachaneni V, Isakov O, Halperin E, Friedman E, Shomron N, Glusman G, Roach JC, Caballero J, Cox HC, Mauldin D, Ament SA, Rowen L, Richards DR, San Lucas FA, Gonzalez-Garay ML, Caskey CT, Bai Y, Huang Y, Fang F, Zhang Y, Wang Z, Barrera J, Garcia-Lobo JM, González-Lamuño D, Llorca J, Rodriguez MC, Varela I, Reese MG, De La Vega FM, Kiruluta E, Cargill M, Hart RK, Sorenson JM, Lyon GJ, Stevenson DA, Bray BE, Moore BM, Eilbeck K, Yandell M, Zhao H, Hou L, Chen X, Yan X, Chen M, Li C, Yang C, Gunel M, Li P, Kong Y, Alexander AC, Albertyn ZI, Boycott KM, Bulman DE, Gordon PM, Innes AM, Knoppers BM, Majewski J, Marshall CR, Parboosingh JS, Sawyer SL, Samuels ME, Schwartzentruber J, Kohane IS, Margulies DM Genome biology 24667040 Genome Biol 2014 Mar 25
Subunit composition of glutamate and gamma-aminobutyric acid receptors in status epilepticus. Loddenkemper T, Talos DM, Cleary RT, Joseph A, Sánchez Fernández I, Alexopoulos A, Kotagal P, Najm I, Jensen FE Epilepsy research 24613745 Epilepsy Res 2014 May
Cannabidiol attenuates seizure susceptibility and behavioural deficits in adult CDKL5(R59X) knock-in mice. Li X, Yennawar M, Wiest A, O'Brien WT, Babrowicz B, White RS, Talos DM, Jensen FE The European journal of neuroscience 38654472 Eur J Neurosci 2024 Jun
Regional differences in susceptibility to hypoxic-ischemic injury in the preterm brain: exploring the spectrum from white matter loss to selective grey matter injury in a rat model. Selip DB, Jantzie LL, Chang M, Jackson MC, Fitzgerald EC, Boll G, Murphy A, Jensen FE Neurology research international 22530125 Neurol Res Int 2012
Epilepsy as a spectrum disorder: Implications from novel clinical and basic neuroscience. Jensen FE Epilepsia 21214533 Epilepsia 2011 Jan
Development of later life spontaneous seizures in a rodent model of hypoxia-induced neonatal seizures. Rakhade SN, Klein PM, Huynh T, Hilario-Gomez C, Kosaras B, Rotenberg A, Jensen FE Epilepsia 21366558 Epilepsia 2011 Apr
Altered inhibition in tuberous sclerosis and type IIb cortical dysplasia. Talos DM, Sun H, Kosaras B, Joseph A, Folkerth RD, Poduri A, Madsen JR, Black PM, Jensen FE Annals of neurology 22447678 Ann Neurol 2012 Apr
Antiepileptic effects of levetiracetam in a rodent neonatal seizure model. Talos DM, Chang M, Kosaras B, Fitzgerald E, Murphy A, Folkerth RD, Jensen FE Pediatric research 23138400 Pediatr Res 2013 Jan
Issues related to symptomatic and disease-modifying treatments affecting cognitive and neuropsychiatric comorbidities of epilepsy. Brooks-Kayal AR, Bath KG, Berg AT, Galanopoulou AS, Holmes GL, Jensen FE, Kanner AM, O'Brien TJ, Whittemore VH, Winawer MR, Patel M, Scharfman HE Epilepsia 23909853 Epilepsia 2013 Aug
Epilepsy biomarkers. Engel J Jr, Pitkänen A, Loeb JA, Dudek FE, Bertram EH 3rd, Cole AJ, Moshé SL, Wiebe S, Jensen FE, Mody I, Nehlig A, Vezzani A Epilepsia 23909854 Epilepsia 2013 Aug
Developmental regulation of group I metabotropic glutamate receptors in the premature brain and their protective role in a rodent model of periventricular leukomalacia. Jantzie LL, Talos DM, Selip DB, An L, Jackson MC, Folkerth RD, Deng W, Jensen FE Neuron glia biology 22169210 Neuron Glia Biol 2010 Nov
Early alterations of AMPA receptors mediate synaptic potentiation induced by neonatal seizures. Rakhade SN, Zhou C, Aujla PK, Fishman R, Sucher NJ, Jensen FE The Journal of neuroscience : the official journal of the Society for Neuroscience 18685023 J Neurosci 2008 Aug 6
Gene expression profiling of a hypoxic seizure model of epilepsy suggests a role for mTOR and Wnt signaling in epileptogenesis. Theilhaber J, Rakhade SN, Sudhalter J, Kothari N, Klein P, Pollard J, Jensen FE PloS one 24086344 PLoS One 2013
AMPA Receptor Dysregulation and Therapeutic Interventions in a Mouse Model of CDKL5 Deficiency Disorder. Yennawar M, White RS, Jensen FE The Journal of neuroscience : the official journal of the Society for Neuroscience 30952813 J Neurosci 2019 Jun 12
Regulation of seizure-induced MeCP2 Ser421 phosphorylation in the developing brain. Rosenberg EC, Lippman-Bell JJ, Handy M, Soldan SS, Rakhade S, Hilario-Gomez C, Folweiler K, Jacobs L, Jensen FE Neurobiology of disease 29738885 Neurobiol Dis 2018 Aug
Models of hypoxia and ischemia-induced seizures. Sun H, Juul HM, Jensen FE Journal of neuroscience methods 26434705 J Neurosci Methods 2016 Feb 15
Dysregulation of FMRP/mTOR Signaling Cascade in Hypoxic-Ischemic Injury of Premature Human Brain. Lechpammer M, Wintermark P, Merry KM, Jackson MC, Jantzie LL, Jensen FE Journal of child neurology 26239490 J Child Neurol 2016 Mar
Reading chimpanzee faces: evidence for the role of verbal labels in categorical perception of emotion. Fugate JM, Gouzoules H, Barrett LF Emotion (Washington, D.C.) 20677871 Emotion 2010 Aug
A reliable protocol for the manual segmentation of the human amygdala and its subregions using ultra-high resolution MRI. Entis JJ, Doerga P, Barrett LF, Dickerson BC NeuroImage 22245260 Neuroimage 2012 Apr 2
Emotion Generation and Emotion Regulation: One or Two Depends on Your Point of View. Gross JJ, Barrett LF Emotion review : journal of the International Society for Research on Emotion 21479078 Emot Rev 2011 Jan
Reconstructing the Past: A Century of Ideas About Emotion in Psychology. Gendron M, Barrett LF Emotion review : journal of the International Society for Research on Emotion 20221412 Emot Rev 2009 Oct 1
The Future of Psychology: Connecting Mind to Brain. Barrett LF Perspectives on psychological science : a journal of the Association for Psychological Science 19844601 Perspect Psychol Sci 2009 Jul
Novelty as a dimension in the affective brain. Weierich MR, Wright CI, Negreira A, Dickerson BC, Barrett LF NeuroImage 19796697 Neuroimage 2010 Feb 1
Emotions are real. Barrett LF Emotion (Washington, D.C.) 22642358 Emotion 2012 Jun
Intrinsic amygdala-cortical functional connectivity predicts social network size in humans. Bickart KC, Hollenbeck MC, Barrett LF, Dickerson BC The Journal of neuroscience : the official journal of the Society for Neuroscience 23077058 J Neurosci 2012 Oct 17
A functional architecture of the human brain: emerging insights from the science of emotion. Lindquist KA, Barrett LF Trends in cognitive sciences 23036719 Trends Cogn Sci 2012 Nov
Authors’ response: what are emotions and how are they created in the brain? Lindquist KA, Wager TD, Bliss-Moreau E, Kober H, Barret LF The Behavioral and brain sciences 22783560 Behav Brain Sci 2012 Jun
Affective value and associative processing share a cortical substrate. Shenhav A, Barrett LF, Bar M Cognitive, affective & behavioral neuroscience 23090717 Cogn Affect Behav Neurosci 2013 Mar
Emotional granularity and borderline personality disorder. Suvak MK, Litz BT, Sloan DM, Zanarini MC, Barrett LF, Hofmann SG Journal of abnormal psychology 21171723 J Abnorm Psychol 2011 May
Bridging Token Identity Theory and Supervenience Theory Through Psychological Construction. Barrett LF Psychological inquiry 21785534 Psychol Inq 2011 Jan 1
Emotion perception, but not affect perception, is impaired with semantic memory loss. Lindquist KA, Gendron M, Barrett LF, Dickerson BC Emotion (Washington, D.C.) 24512242 Emotion 2014 Apr
The Brain Basis of Positive and Negative Affect: Evidence from a Meta-Analysis of the Human Neuroimaging Literature. Lindquist KA, Satpute AB, Wager TD, Weber J, Barrett LF Cerebral cortex (New York, N.Y. : 1991) 25631056 Cereb Cortex 2016 May
Involvement of Sensory Regions in Affective Experience: A Meta-Analysis. Satpute AB, Kang J, Bickart KC, Yardley H, Wager TD, Barrett LF Frontiers in psychology 26696928 Front Psychol 2015
A Bayesian model of category-specific emotional brain responses. Wager TD, Kang J, Johnson TD, Nichols TE, Satpute AB, Barrett LF PLoS computational biology 25853490 PLoS Comput Biol 2015 Apr
The power of predictions: An emerging paradigm for psychological research. Hutchinson JB, Barrett LF Current directions in psychological science 31749520 Curr Dir Psychol Sci 2019 Jun
Valence focus and self-esteem lability: reacting to hedonic cues in the social environment. Pietromonaco PR, Barrett LF Emotion (Washington, D.C.) 19485618 Emotion 2009 Jun
Affective learning enhances activity and functional connectivity in early visual cortex. Damaraju E, Huang YM, Barrett LF, Pessoa L Neuropsychologia 19410587 Neuropsychologia 2009 Oct
Neural correlates of novelty and face-age effects in young and elderly adults. Wright CI, Negreira A, Gold AL, Britton JC, Williams D, Barrett LF NeuroImage 18586522 Neuroimage 2008 Aug 15
Conceptualizing and experiencing compassion. Condon P, Feldman Barrett L Emotion (Washington, D.C.) 23914766 Emotion 2013 Oct
Sex differences in the neural correlates of affective experience. Moriguchi Y, Touroutoglou A, Dickerson BC, Barrett LF Social cognitive and affective neuroscience 23596188 Soc Cogn Affect Neurosci 2014 May
Decision making from economic and signal detection perspectives: development of an integrated framework. Lynn SK, Wormwood JB, Barrett LF, Quigley KS Frontiers in psychology 26217275 Front Psychol 2015
Situating emotional experience. Wilson-Mendenhall CD, Barrett LF, Barsalou LW Frontiers in human neuroscience 24324420 Front Hum Neurosci 2013
Heightened sensitivity to emotional expressions in generalised anxiety disorder, compared to social anxiety disorder, and controls. Bui E, Anderson E, Goetter EM, Campbell AA, Fischer LE, Barrett LF, Simon NM Cognition & emotion 26395075 Cogn Emot 2017 Jan
The neural representation of typical and atypical experiences of negative images: comparing fear, disgust and morbid fascination. Oosterwijk S, Lindquist KA, Adebayo M, Barrett LF Social cognitive and affective neuroscience 26180088 Soc Cogn Affect Neurosci 2016 Jan
Brain network connectivity-behavioral relationships exhibit trait-like properties: Evidence from hippocampal connectivity and memory. Touroutoglou A, Andreano JM, Barrett LF, Dickerson BC Hippocampus 26105075 Hippocampus 2015 Dec
Older and wiser? An affective science perspective on age-related challenges in financial decision making. Weierich MR, Kensinger EA, Munnell AH, Sass SA, Dickerson BC, Wright CI, Barrett LF Social cognitive and affective neuroscience 20587596 Soc Cogn Affect Neurosci 2011 Apr
Out of sight but not out of mind: unseen affective faces influence evaluations and social impressions. Anderson E, Siegel E, White D, Barrett LF Emotion (Washington, D.C.) 22506501 Emotion 2012 Dec
Trends in ambulatory self-report: the role of momentary experience in psychosomatic medicine. Conner TS, Barrett LF Psychosomatic medicine 22582330 Psychosom Med 2012 May
The visual impact of gossip. Anderson E, Siegel EH, Bliss-Moreau E, Barrett LF Science (New York, N.Y.) 21596956 Science 2011 Jun 17
How does this make you feel? A comparison of four affect induction procedures. Zhang X, Yu HW, Barrett LF Frontiers in psychology 25071659 Front Psychol 2014
Is there consistency and specificity of autonomic changes during emotional episodes? Guidance from the Conceptual Act Theory and psychophysiology. Quigley KS, Barrett LF Biological psychology 24388802 Biol Psychol 2014 Apr
Variety in emotional life: within-category typicality of emotional experiences is associated with neural activity in large-scale brain networks. Wilson-Mendenhall CD, Barrett LF, Barsalou LW Social cognitive and affective neuroscience 24563528 Soc Cogn Affect Neurosci 2015 Jan
Unseen Affective Faces Influence Person Perception Judgments in Schizophrenia. Kring AM, Siegel EH, Barrett LF Clinical psychological science : a journal of the Association for Psychological Science 25664225 Clin Psychol Sci 2014 Jul
Gender differences in oxytocin-associated disruption of decision bias during emotion perception. Lynn SK, Hoge EA, Fischer LE, Barrett LF, Simon NM Psychiatry research 24814142 Psychiatry Res 2014 Sep 30
Functional connectivity dynamics during film viewing reveal common networks for different emotional experiences. Raz G, Touroutoglou A, Wilson-Mendenhall C, Gilam G, Lin T, Gonen T, Jacob Y, Atzil S, Admon R, Bleich-Cohen M, Maron-Katz A, Hendler T, Barrett LF Cognitive, affective & behavioral neuroscience 27142636 Cogn Affect Behav Neurosci 2016 Aug
Emotion words: Adding face value. Fugate JMB, Gendron M, Nakashima SF, Barrett LF Emotion (Washington, D.C.) 28604040 Emotion 2018 Aug
Risk Factors, Neuroanatomical Correlates, and Outcome of Neuropsychiatric Symptoms in Alzheimer's Disease. Poulin SP, Bergeron D, Dickerson BC, Alzheimer’s Disease Neuroimaging Initiative Journal of Alzheimer's disease : JAD 28869463 J Alzheimers Dis 2017
Internal valence modulates the speed of object recognition. Panichello MF, Kveraga K, Chaumon M, Bar M, Barrett LF Scientific reports 28336933 Sci Rep 2017 Mar 23
Emotion fingerprints or emotion populations? A meta-analytic investigation of autonomic features of emotion categories. Siegel EH, Sands MK, Van den Noortgate W, Condon P, Chang Y, Dy J, Quigley KS, Barrett LF Psychological bulletin 29389177 Psychol Bull 2018 Apr
Large-scale brain networks in affective and social neuroscience: towards an integrative functional architecture of the brain. Barrett LF, Satpute AB Current opinion in neurobiology 23352202 Curr Opin Neurobiol 2013 Jun
The hundred-year emotion war: are emotions natural kinds or psychological constructions? Comment on Lench, Flores, and Bench (2011). Lindquist KA, Siegel EH, Quigley KS, Barrett LF Psychological bulletin 23294094 Psychol Bull 2013 Jan
The relation between valence and arousal in subjective experience. Kuppens P, Tuerlinckx F, Russell JA, Barrett LF Psychological bulletin 23231533 Psychol Bull 2013 Jul
She's emotional. He's having a bad day: attributional explanations for emotion stereotypes. Barrett LF, Bliss-Moreau E Emotion (Washington, D.C.) 19803587 Emotion 2009 Oct
Constructing emotion: the experience of fear as a conceptual act. Lindquist KA, Barrett LF Psychological science 18947355 Psychol Sci 2008 Sep
Affect as a Psychological Primitive. Barrett LF, Bliss-Moreau E Advances in experimental social psychology 20552040 Adv Exp Soc Psychol 2009
I Like the Sound of Your Voice: Affective Learning about Vocal Signals. Bliss-Moreau E, Barrett LF, Owren MJ Journal of experimental social psychology 20495619 J Exp Soc Psychol 2010 May 1
Amygdala volume and social network size in humans. Bickart KC, Wright CI, Dautoff RJ, Dickerson BC, Barrett LF Nature neuroscience 21186358 Nat Neurosci 2011 Feb
Differential hemodynamic response in affective circuitry with aging: an FMRI study of novelty, valence, and arousal. Moriguchi Y, Negreira A, Weierich M, Dautoff R, Dickerson BC, Wright CI, Barrett LF Journal of cognitive neuroscience 20521849 J Cogn Neurosci 2011 May
The brain basis of emotion: a meta-analytic review. Lindquist KA, Wager TD, Kober H, Bliss-Moreau E, Barrett LF The Behavioral and brain sciences 22617651 Behav Brain Sci 2012 Jun
Identification of discrete functional subregions of the human periaqueductal gray. Satpute AB, Wager TD, Cohen-Adad J, Bianciardi M, Choi JK, Buhle JT, Wald LL, Barrett LF Proceedings of the National Academy of Sciences of the United States of America 24082116 Proc Natl Acad Sci U S A 2013 Oct 15
Atrophy in distinct corticolimbic networks in frontotemporal dementia relates to social impairments measured using the Social Impairment Rating Scale. Bickart KC, Brickhouse M, Negreira A, Sapolsky D, Barrett LF, Dickerson BC Journal of neurology, neurosurgery, and psychiatry 24133285 J Neurol Neurosurg Psychiatry 2014 Apr
Visual predictions in the orbitofrontal cortex rely on associative content. Chaumon M, Kveraga K, Barrett LF, Bar M Cerebral cortex (New York, N.Y. : 1991) 23771980 Cereb Cortex 2014 Nov
Individual differences in learning the affective value of others under minimal conditions. Bliss-Moreau E, Barrett LF, Wright CI Emotion (Washington, D.C.) 18729580 Emotion 2008 Aug
Amygdala and fusiform gyrus temporal dynamics: responses to negative facial expressions. Britton JC, Shin LM, Barrett LF, Rauch SL, Wright CI BMC neuroscience 18474111 BMC Neurosci 2008 May 12
What You Feel Influences What You See: The Role of Affective Feelings in Resolving Binocular Rivalry. Anderson E, Siegel EH, Barrett LF Journal of experimental social psychology 21789027 J Exp Soc Psychol 2011 Jul
Amygdala atrophy is prominent in early Alzheimer's disease and relates to symptom severity. Poulin SP, Dautoff R, Morris JC, Barrett LF, Dickerson BC, Alzheimer's Disease Neuroimaging Initiative Psychiatry research 21920712 Psychiatry Res 2011 Oct 31
Variety is the spice of life: A psychological construction approach to understanding variability in emotion. Barrett LF Cognition & emotion 20221411 Cogn Emot 2009 Nov 1
Establishing the situated features associated with perceived stress. Lebois LA, Hertzog C, Slavich GM, Barrett LF, Barsalou LW Acta psychologica 27288834 Acta Psychol (Amst) 2016 Sep
Threat perception after the Boston Marathon bombings: The effects of personal relevance and conceptual framing. Wormwood JB, Lynn SK, Feldman Barrett L, Quigley KS Cognition & emotion 25707419 Cogn Emot 2016
Amygdala task-evoked activity and task-free connectivity independently contribute to feelings of arousal. Touroutoglou A, Bickart KC, Barrett LF, Dickerson BC Human brain mapping 24862171 Hum Brain Mapp 2014 Oct
Emotion words, emotion concepts, and emotional development in children: A constructionist hypothesis. Hoemann K, Xu F, Barrett LF Developmental psychology 31464489 Dev Psychol 2019 Sep
Learning situated emotions. Lebois LAM, Wilson-Mendenhall CD, Simmons WK, Barrett LF, Barsalou LW Neuropsychologia 29330097 Neuropsychologia 2020 Aug
Primary Interoceptive Cortex Activity during Simulated Experiences of the Body. Wilson-Mendenhall CD, Henriques A, Barsalou LW, Barrett LF Journal of cognitive neuroscience 30277431 J Cogn Neurosci 2019 Feb
A shift in perspective: Decentering through mindful attention to imagined stressful events. Lebois LA, Papies EK, Gopinath K, Cabanban R, Quigley KS, Krishnamurthy V, Barrett LF, Barsalou LW Neuropsychologia 26111487 Neuropsychologia 2015 Aug
Methodological recommendations for a heartbeat detection-based measure of interoceptive sensitivity. Kleckner IR, Wormwood JB, Simmons WK, Barrett LF, Quigley KS Psychophysiology 26265009 Psychophysiology 2015 Nov
Does language do more than communicate emotion? Lindquist KA, Satpute AB, Gendron M Current directions in psychological science 25983400 Curr Dir Psychol Sci 2015 Apr 1
Semantic Clustering during Verbal Episodic Memory Encoding and Retrieval in Older Adults: One Cognitive Mechanism of Superaging. Shaffer C, Andreano JM, Touroutoglou A, Barrett LF, Dickerson BC, Wong B Brain sciences 38391745 Brain Sci 2024 Feb 8
See it with feeling: affective predictions during object perception. Barrett LF, Bar M Philosophical transactions of the Royal Society of London. Series B, Biological sciences 19528014 Philos Trans R Soc Lond B Biol Sci 2009 May 12
Considering PTSD from the perspective of brain processes: a psychological construction approach. Suvak MK, Barrett LF Journal of traumatic stress 21298725 J Trauma Stress 2011 Feb
Emotion words shape emotion percepts. Gendron M, Lindquist KA, Barsalou L, Barrett LF Emotion (Washington, D.C.) 22309717 Emotion 2012 Apr
States of mind: emotions, body feelings, and thoughts share distributed neural networks. Oosterwijk S, Lindquist KA, Anderson E, Dautoff R, Moriguchi Y, Barrett LF NeuroImage 22677148 Neuroimage 2012 Sep
Neural evidence that human emotions share core affective properties. Wilson-Mendenhall CD, Barrett LF, Barsalou LW Psychological science 23603916 Psychol Sci 2013 Jun
Dissociable large-scale networks anchored in the right anterior insula subserve affective experience and attention. Touroutoglou A, Hollenbeck M, Dickerson BC, Feldman Barrett L NeuroImage 22361166 Neuroimage 2012 May 1
Grounding emotion in situated conceptualization. Wilson-Mendenhall CD, Barrett LF, Simmons WK, Barsalou LW Neuropsychologia 21192959 Neuropsychologia 2011 Apr
Affective state influences perception by affecting decision parameters underlying bias and sensitivity. Lynn SK, Zhang X, Barrett LF Emotion (Washington, D.C.) 22251054 Emotion 2012 Aug
The role of affective experience in work motivation: Test of a conceptual model. Seo MG, Bartunek JM, Barrett LF Journal of organizational behavior 21785527 J Organ Behav 2010 Oct
Experience Sampling Methods: A Modern Idiographic Approach to Personality Research. Conner TS, Tennen H, Fleeson W, Barrett LF Social and personality psychology compass 19898679 Soc Personal Psychol Compass 2009 May 1
Functional grouping and cortical-subcortical interactions in emotion: a meta-analysis of neuroimaging studies. Kober H, Barrett LF, Joseph J, Bliss-Moreau E, Lindquist K, Wager TD NeuroImage 18579414 Neuroimage 2008 Aug 15
Understanding the Mind by Measuring the Brain: Lessons From Measuring Behavior (Commentary on Vul et al., 2009). Barrett LF Perspectives on psychological science : a journal of the Association for Psychological Science 19672318 Perspect Psychol Sci 2009 May
Context is routinely encoded during emotion perception. Barrett LF, Kensinger EA Psychological science 20424107 Psychol Sci 2010 Apr
Perceptions of emotion from facial expressions are not culturally universal: evidence from a remote culture. Gendron M, Roberson D, van der Vyver JM, Barrett LF Emotion (Washington, D.C.) 24708506 Emotion 2014 Apr
Cultural variation in emotion perception is real: a response to Sauter, Eisner, Ekman, and Scott (2015). Gendron M, Roberson D, Barrett LF Psychological science 25608863 Psychol Sci 2015 Mar
Stronger Functional Connectivity in the Default Mode and Salience Networks Is Associated With Youthful Memory in Superaging. Zhang J, Andreano JM, Dickerson BC, Touroutoglou A, Barrett LF Cerebral cortex (New York, N.Y. : 1991) 31058917 Cereb Cortex 2020 Jan 10
Conscious awareness is necessary for affective faces to influence social judgments. Kleckner IR, Anderson EC, Betz NJ, Wormwood JB, Eskew RT Jr, Barrett LF Journal of experimental social psychology 31097841 J Exp Soc Psychol 2018 Nov
Emotion Words' Effect on Visual Awareness and Attention of Emotional Faces. Fugate JMB, MacDonald C, O'Hare AJ Frontiers in psychology 32010012 Front Psychol 2019
Words are a context for mental inference. Betz N, Hoemann K, Barrett LF Emotion (Washington, D.C.) 30628815 Emotion 2019 Dec
Introducing a Face Sort Paradigm to Evaluate Age Differences in Emotion Perception. Hoemann K, Vicaria IM, Gendron M, Stanley JT The journals of gerontology. Series B, Psychological sciences and social sciences 32211791 J Gerontol B Psychol Sci Soc Sci 2021 Aug 13
Cultural relativity in perceiving emotion from vocalizations. Gendron M, Roberson D, van der Vyver JM, Barrett LF Psychological science 24501109 Psychol Sci 2014 Apr
"Utilizing" signal detection theory. Lynn SK, Barrett LF Psychological science 25097061 Psychol Sci 2014 Sep
Intrinsic connectivity in the human brain does not reveal networks for 'basic' emotions. Touroutoglou A, Lindquist KA, Dickerson BC, Barrett LF Social cognitive and affective neuroscience 25680990 Soc Cogn Affect Neurosci 2015 Sep
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Working memory capacity is associated with optimal adaptation of response bias to perceptual sensitivity in emotion perception. Lynn SK, Ibagon C, Bui E, Palitz SA, Simon NM, Barrett LF Emotion (Washington, D.C.) 26461251 Emotion 2016 Mar
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Microbiota-targeted therapies: an ecological perspective. Lemon KP, Armitage GC, Relman DA, Fischbach MA Science translational medicine 22674555 Sci Transl Med 2012 Jun 6
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Microbiota's 'little helpers': bacteriophages and antibiotic-associated responses in the gut microbiome. Sun CL, Relman DA Genome biology 23906048 Genome Biol 2013 Jul 30
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Microbial invasion of the amniotic cavity in pregnancies with small-for-gestational-age fetuses. DiGiulio DB, Gervasi MT, Romero R, Vaisbuch E, Mazaki-Tovi S, Kusanovic JP, Seok KS, Gómez R, Mittal P, Gotsch F, Chaiworapongsa T, Oyarzún E, Kim CJ, Relman DA Journal of perinatal medicine 20482466 J Perinat Med 2010 Sep
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The pervasive effects of an antibiotic on the human gut microbiota, as revealed by deep 16S rRNA sequencing. Dethlefsen L, Huse S, Sogin ML, Relman DA PLoS biology 19018661 PLoS Biol 2008 Nov 18
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In vitro mineralization by preosteoblasts in poly(DL-lactide-co-glycolide) inverse opal scaffolds reinforced with hydroxyapatite nanoparticles. Choi SW, Zhang Y, Thomopoulos S, Xia Y Langmuir : the ACS journal of surfaces and colloids 20450216 Langmuir 2010 Jul 20
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Measuring the surface-enhanced Raman scattering enhancement factors of hot spots formed between an individual Ag nanowire and a single Ag nanocube. Camargo PH, Cobley CM, Rycenga M, Xia Y Nanotechnology 19801754 Nanotechnology 2009 Oct 28
Fabrication of Microbeads with a Controllable Hollow Interior and Porous Wall Using a Capillary Fluidic Device. Choi SW, Zhang Y, Xia Y Advanced functional materials 20191106 Adv Funct Mater 2009 Sep 23
A bioreducible polymer for efficient delivery of Fas-silencing siRNA into stem cell spheroids and enhanced therapeutic angiogenesis. Shim MS, Bhang SH, Yoon K, Choi K, Xia Y Angewandte Chemie (International ed. in English) 23074025 Angew Chem Int Ed Engl 2012 Nov 19
Investigation of neovascularization in three-dimensional porous scaffolds in vivo by a combination of multiscale photoacoustic microscopy and optical coherence tomography. Cai X, Zhang Y, Li L, Choi SW, MacEwan MR, Yao J, Kim C, Xia Y, Wang LV Tissue engineering. Part C, Methods 22838500 Tissue Eng Part C Methods 2013 Mar
Immuno gold nanocages with tailored optical properties for targeted photothermal destruction of cancer cells. Chen J, Wang D, Xi J, Au L, Siekkinen A, Warsen A, Li ZY, Zhang H, Xia Y, Li X Nano letters 17430005 Nano Lett 2007 May
Gold nanocages for cancer detection and treatment. Skrabalak SE, Au L, Lu X, Li X, Xia Y Nanomedicine (London, England) 17976028 Nanomedicine (Lond) 2007 Oct
Chronic label-free volumetric photoacoustic microscopy of melanoma cells in three-dimensional porous scaffolds. Zhang Y, Cai X, Choi SW, Kim C, Wang LV, Xia Y Biomaterials 20727581 Biomaterials 2010 Nov
Phase-Change Materials for Controlled Release and Related Applications. Qiu J, Huo D, Xia Y Advanced materials (Deerfield Beach, Fla.) 32383215 Adv Mater 2020 Jun
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Inverse Opal Scaffolds and Their Biomedical Applications. Zhang YS, Zhu C, Xia Y Advanced materials (Deerfield Beach, Fla.) 28649794 Adv Mater 2017 Sep
Using well-defined Ag nanocubes as substrates to quantify the spatial resolution and penetration depth of surface-enhanced Raman scattering imaging. Moran CH, Rycenga M, Xia X, Cobley CM, Xia Y Nanotechnology 24334508 Nanotechnology 2014 Jan 10
Multiple facets for extracellular matrix mimicking in regenerative medicine. Zhang YS, Xia Y Nanomedicine (London, England) 25816873 Nanomedicine (Lond) 2015
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Correlated Rayleigh Scattering Spectroscopy and Scanning Electron Microscopy Studies of Au-Ag Bimetallic Nanoboxes and Nanocages. Hu M, Chen J, Marquez M, Xia Y, Hartland GV The journal of physical chemistry. C, Nanomaterials and interfaces 18629346 J Phys Chem C Nanomater Interfaces 2007
Dark-field microscopy studies of single metal nanoparticles: understanding the factors that influence the linewidth of the localized surface plasmon resonance. Hu M, Novo C, Funston A, Wang H, Staleva H, Zou S, Mulvaney P, Xia Y, Hartland GV Journal of materials chemistry 18846243 J Mater Chem 2008
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Nanomaterial-Enabled Photothermal Heating and Its Use for Cancer Therapy via Localized Hyperthermia. Shen S, Qiu J, Huo D, Xia Y Small (Weinheim an der Bergstrasse, Germany) 37803412 Small 2024 Feb
A facile synthesis of asymmetric hybrid colloidal particles. Ohnuma A, Cho EC, Camargo PH, Au L, Ohtani B, Xia Y Journal of the American Chemical Society 19140763 J Am Chem Soc 2009 Feb 4
Non-invasive and in situ characterization of the degradation of biomaterial scaffolds by volumetric photoacoustic microscopy. Zhang YS, Cai X, Yao J, Xing W, Wang LV, Xia Y Angewandte Chemie (International ed. in English) 24130155 Angew Chem Int Ed Engl 2014 Jan 3
The mechanics of PLGA nanofiber scaffolds with biomimetic gradients in mineral for tendon-to-bone repair. Lipner J, Liu W, Liu Y, Boyle J, Genin GM, Xia Y, Thomopoulos S Journal of the mechanical behavior of biomedical materials 25194525 J Mech Behav Biomed Mater 2014 Dec
Gold Nanomaterials at Work in Biomedicine. Yang X, Yang M, Pang B, Vara M, Xia Y Chemical reviews 26293344 Chem Rev 2015 Oct 14
In Vivo Evaluation of Adipose-Derived Stromal Cells Delivered with a Nanofiber Scaffold for Tendon-to-Bone Repair. Lipner J, Shen H, Cavinatto L, Liu W, Havlioglu N, Xia Y, Galatz LM, Thomopoulos S Tissue engineering. Part A 26414599 Tissue Eng Part A 2015 Nov
Dissolving Ag from Au-Ag Alloy Nanoboxes with H(2)O(2): A Method for Both Tailoring the Optical Properties and Measuring the H(2)O(2) Concentration. Zhang Q, Cobley CM, Zeng J, Wen LP, Chen J, Xia Y The journal of physical chemistry. C, Nanomaterials and interfaces 20495675 J Phys Chem C Nanomater Interfaces 2010 Mar 5
Facile synthesis of Ag nanocubes of 30 to 70 nm in edge length with CF(3)COOAg as a precursor. Zhang Q, Li W, Wen LP, Chen J, Xia Y Chemistry (Weinheim an der Bergstrasse, Germany) 20593441 Chemistry 2010 Sep 3
Electrospun nanofibers for neural tissue engineering. Xie J, MacEwan MR, Schwartz AG, Xia Y Nanoscale 20648362 Nanoscale 2010 Jan
Nanofiber membranes with controllable microwells and structural cues and their use in forming cell microarrays and neuronal networks. Xie J, Liu W, MacEwan MR, Yeh YC, Thomopoulos S, Xia Y Small (Weinheim an der Bergstrasse, Germany) 21294253 Small 2011 Feb 7
Quantifying the cellular uptake of antibody-conjugated Au nanocages by two-photon microscopy and inductively coupled plasma mass spectrometry. Au L, Zhang Q, Cobley CM, Gidding M, Schwartz AG, Chen J, Xia Y ACS nano 19954236 ACS Nano 2010 Jan 26
The effect of sedimentation and diffusion on cellular uptake of gold nanoparticles. Cho EC, Zhang Q, Xia Y Nature nanotechnology 21516092 Nat Nanotechnol 2011 Apr 24
Gold nanocages: from synthesis to theranostic applications. Xia Y, Li W, Cobley CM, Chen J, Xia X, Zhang Q, Yang M, Cho EC, Brown PK Accounts of chemical research 21528889 Acc Chem Res 2011 Oct 18
Improving biomedical imaging with gold nanocages. Xia Y, Skrabalak SE SPIE newsroom 19704778 SPIE Newsroom 2008 May 12
Production of Ag nanocubes on a scale of 0.1 g per batch by protecting the NaHS-mediated polyol synthesis with argon. Zhang Q, Cobley C, Au L, McKiernan M, Schwartz A, Wen LP, Chen J, Xia Y ACS applied materials & interfaces 20305725 ACS Appl Mater Interfaces 2009 Sep
Understanding the SERS Effects of Single Silver Nanoparticles and Their Dimers, One at a Time. Rycenga M, Camargo PH, Li W, Moran CH, Xia Y The journal of physical chemistry letters 20368749 J Phys Chem Lett 2010 Feb 18
Colloidal hollow spheres of conducting polymers with smooth surface and uniform, controllable sizes. Bai MY, Cheng YJ, Wickline SA, Xia Y Small (Weinheim an der Bergstrasse, Germany) 19384880 Small 2009 Aug 3
Three-dimensional scaffolds for tissue engineering: the importance of uniformity in pore size and structure. Choi SW, Zhang Y, Xia Y Langmuir : the ACS journal of surfaces and colloids 21090781 Langmuir 2010 Dec 21
Morphological Evolution of Single-Crystal Ag Nanospheres during the Galvanic Replacement Reaction with HAuCl(4). Kim MH, Lu X, Wiley B, Lee EP, Xia Y The journal of physical chemistry. C, Nanomaterials and interfaces 18787649 J Phys Chem C Nanomater Interfaces 2008
Photoacoustic tomography of a rat cerebral cortex in vivo with au nanocages as an optical contrast agent. Yang X, Skrabalak SE, Li ZY, Xia Y, Wang LV Nano letters 18020475 Nano Lett 2007 Dec
Facile synthesis of tadpole-like nanostructures consisting of Au heads and Pd tails. Camargo PH, Xiong Y, Ji L, Zuo JM, Xia Y Journal of the American Chemical Society 18027954 J Am Chem Soc 2007 Dec 19
In vivo quantitative evaluation of the transport kinetics of gold nanocages in a lymphatic system by noninvasive photoacoustic tomography. Cai X, Li W, Kim CH, Yuan Y, Wang LV, Xia Y ACS nano 22054348 ACS Nano 2011 Dec 27
Quantifying the coverage density of poly(ethylene glycol) chains on the surface of gold nanostructures. Xia X, Yang M, Wang Y, Zheng Y, Li Q, Chen J, Xia Y ACS nano 22148912 ACS Nano 2012 Jan 24
Radioluminescent gold nanocages with controlled radioactivity for real-time in vivo imaging. Wang Y, Liu Y, Luehmann H, Xia X, Wan D, Cutler C, Xia Y Nano letters 23360442 Nano Lett 2013 Feb 13
Comparison study of gold nanohexapods, nanorods, and nanocages for photothermal cancer treatment. Wang Y, Black KC, Luehmann H, Li W, Zhang Y, Cai X, Wan D, Liu SY, Li M, Kim P, Li ZY, Wang LV, Liu Y, Xia Y ACS nano 23383982 ACS Nano 2013 Mar 26
Neovascularization in biodegradable inverse opal scaffolds with uniform and precisely controlled pore sizes. Choi SW, Zhang Y, Macewan MR, Xia Y Advanced healthcare materials 23184495 Adv Healthc Mater 2013 Jan
A plasmon-assisted optofluidic (PAOF) system for measuring the photothermal conversion efficiencies of gold nanostructures and controlling an electrical switch. Zeng J, Goldfeld D, Xia Y Angewandte Chemie (International ed. in English) 23494970 Angew Chem Int Ed Engl 2013 Apr 8
Synthesis of Ag nanocubes 18-32 nm in edge length: the effects of polyol on reduction kinetics, size control, and reproducibility. Wang Y, Zheng Y, Huang CZ, Xia Y Journal of the American Chemical Society 23317148 J Am Chem Soc 2013 Feb 6
Protein capsules with cross-linked, semipermeable, and enzyme-degradable surface barriers for controlled release. Zhou J, Hyun DC, Liu H, Wu H, Xia Y Macromolecular rapid communications 24957975 Macromol Rapid Commun 2014 Aug
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
Emerging applications of phase-change materials (PCMs): teaching an old dog new tricks. Hyun DC, Levinson NS, Jeong U, Xia Y Angewandte Chemie (International ed. in English) 24470287 Angew Chem Int Ed Engl 2014 Apr 7
Fabrication of Cell Patches Using Biodegradable Scaffolds with a Hexagonal Array of Interconnected Pores (SHAIPs). Zhang YS, Yao J, Wang LV, Xia Y Polymer 24443593 Polymer (Guildf) 2014 Jan 14
Neurite outgrowth on electrospun nanofibers with uniaxial alignment: the effects of fiber density, surface coating, and supporting substrate. Xie J, Liu W, MacEwan MR, Bridgman PC, Xia Y ACS nano 24444076 ACS Nano 2014 Feb 25
Near-infrared gold nanocages as a new class of tracers for photoacoustic sentinel lymph node mapping on a rat model. Song KH, Kim C, Cobley CM, Xia Y, Wang LV Nano letters 19072058 Nano Lett 2009 Jan
A SERS study of the molecular structure of alkanethiol monolayers on Ag nanocubes in the presence of aqueous glucose. Rycenga M, McLellan JM, Xia Y Chemical physics letters 20160847 Chem Phys Lett 2009 Sep 22
Fine tuning the optical properties of Au-Ag nanocages by selectively etching Ag with oxygen and a water-soluble thiol. Cho EC, Cobley CM, Rycenga M, Xia Y Journal of materials chemistry 19829745 J Mater Chem 2009 Jan 1
Conductive Core-Sheath Nanofibers and Their Potential Application in Neural Tissue Engineering. Xie J, Macewan MR, Willerth SM, Li X, Moran DW, Sakiyama-Elbert SE, Xia Y Advanced functional materials 19830261 Adv Funct Mater 2009 Jul 24
Nerve guidance conduits based on double-layered scaffolds of electrospun nanofibers for repairing the peripheral nervous system. Xie J, MacEwan MR, Liu W, Jesuraj N, Li X, Hunter D, Xia Y ACS applied materials & interfaces 24806389 ACS Appl Mater Interfaces 2014 Jun 25
Enhancing the Tactile and Near-Infrared Sensing Capabilities of Electrospun PVDF Nanofibers with the Use of Gold Nanocages. Li H, Wu T, Xie M, Shi Y, Shen S, Zhao M, Yang X, Figueroa-Cosme LM, Ke Q, Xia Y Journal of materials chemistry. C 30911394 J Mater Chem C Mater 2018 Oct 14
Design and Fabrication of a Hierarchically Structured Scaffold for Tendon-to-Bone Repair. Zhu C, Pongkitwitoon S, Qiu J, Thomopoulos S, Xia Y Advanced materials (Deerfield Beach, Fla.) 29534316 Adv Mater 2018 Apr
Nanobottles for Controlled Release and Drug Delivery. Qiu J, Xu J, Xia Y Advanced healthcare materials 32543127 Adv Healthc Mater 2021 Feb
Electrospun nanofibers for regenerative medicine. Liu W, Thomopoulos S, Xia Y Advanced healthcare materials 23184683 Adv Healthc Mater 2012 Jan 11
Quantitative analysis of the fate of gold nanocages in vitro and in vivo after uptake by U87-MG tumor cells. Cho EC, Zhang Y, Cai X, Moran CM, Wang LV, Xia Y Angewandte Chemie (International ed. in English) 23225223 Angew Chem Int Ed Engl 2013 Jan 21
Protein-protected Au clusters as a new class of nanoscale biosensor for label-free fluorescence detection of proteases. Wang Y, Wang Y, Zhou F, Kim P, Xia Y Small (Weinheim an der Bergstrasse, Germany) 22969016 Small 2012 Dec 21
Gold nanocages: synthesis, properties, and applications. Skrabalak SE, Chen J, Sun Y, Lu X, Au L, Cobley CM, Xia Y Accounts of chemical research 18570442 Acc Chem Res 2008 Dec
Measuring the Optical Absorption Cross-sections of Au-Ag Nanocages and Au Nanorods by Photoacoustic Imaging. Cho EC, Kim C, Zhou F, Cobley CM, Song KH, Chen J, Li ZY, Wang LV, Xia Y The journal of physical chemistry. C, Nanomaterials and interfaces 19680423 J Phys Chem C Nanomater Interfaces 2009 May 28
Gold Nanocages for Biomedical Applications. Skrabalak SE, Chen J, Au L, Lu X, Li X, Xia Y Advanced materials (Deerfield Beach, Fla.) 18648528 Adv Mater 2007 Oct 17
Preparation of uniform microspheres using a simple fluidic device and their crystallization into close-packed lattices. Choi SW, Cheong IW, Kim JH, Xia Y Small (Weinheim an der Bergstrasse, Germany) 19189332 Small 2009 Apr
A temperature-sensitive drug release system based on phase-change materials. Choi SW, Zhang Y, Xia Y Angewandte Chemie (International ed. in English) 20839209 Angew Chem Int Ed Engl 2010 Oct 18
Au@Ag core-shell nanocubes with finely tuned and well-controlled sizes, shell thicknesses, and optical properties. Ma Y, Li W, Cho EC, Li Z, Yu T, Zeng J, Xie Z, Xia Y ACS nano 20964400 ACS Nano 2010 Nov 23
Radially aligned, electrospun nanofibers as dural substitutes for wound closure and tissue regeneration applications. Xie J, Macewan MR, Ray WZ, Liu W, Siewe DY, Xia Y ACS nano 20695478 ACS Nano 2010 Sep 28
Uniform beads with controllable pore sizes for biomedical applications. Choi SW, Yeh YC, Zhang Y, Sung HW, Xia Y Small (Weinheim an der Bergstrasse, Germany) 20578116 Small 2010 Jul 19
Total synthesis of the polycyclic fungal metabolite (+/-)-communesin F. Liu P, Seo JH, Weinreb SM Angewandte Chemie (International ed. in English) 20175174 Angew Chem Int Ed Engl 2010 Mar 8
Engineering the Properties of Metal Nanostructures via Galvanic Replacement Reactions. Cobley CM, Xia Y Materials science & engineering. R, Reports : a review journal 21180400 Mater Sci Eng R Rep 2010 Nov 22
An enzyme-sensitive probe for photoacoustic imaging and fluorescence detection of protease activity. Xia X, Yang M, Oetjen LK, Zhang Y, Li Q, Chen J, Xia Y Nanoscale 21225037 Nanoscale 2011 Mar
Etching and dimerization: a simple and versatile route to dimers of silver nanospheres with a range of sizes. Li W, Camargo PH, Au L, Zhang Q, Rycenga M, Xia Y Angewandte Chemie (International ed. in English) 19943304 Angew Chem Int Ed Engl 2010
Bright three-photon luminescence from gold/silver alloyed nanostructures for bioimaging with negligible photothermal toxicity. Tong L, Cobley CM, Chen J, Xia Y, Cheng JX Angewandte Chemie (International ed. in English) 20544899 Angew Chem Int Ed Engl 2010 May 3
In vivo molecular photoacoustic tomography of melanomas targeted by bioconjugated gold nanocages. Kim C, Cho EC, Chen J, Song KH, Au L, Favazza C, Zhang Q, Cobley CM, Gao F, Xia Y, Wang LV ACS nano 20731439 ACS Nano 2010 Aug 24
Fabrication of cubic nanocages and nanoframes by dealloying Au/Ag alloy nanoboxes with an aqueous etchant based on Fe(NO3)3 or NH4OH. Lu X, Au L, McLellan J, Li ZY, Marquez M, Xia Y Nano letters 17489641 Nano Lett 2007 Jun
Microscale polymer bottles corked with a phase-change material for temperature-controlled release. Hyun DC, Lu P, Choi SI, Jeong U, Xia Y Angewandte Chemie (International ed. in English) 23959631 Angew Chem Int Ed Engl 2013 Sep 27
A Comparative Study of Galvanic Replacement Reactions Involving Ag Nanocubes and AuCl(2) or AuCl(4). Au L, Lu X, Xia Y Advanced materials (Deerfield Beach, Fla.) 18725963 Adv Mater 2008
Fabrication of Density Gradients of Biodegradable Polymer Microparticles and Their Use in Guiding Neurite Outgrowth. Li X, Macewan MR, Xie J Dr, Siewe D, Yuan X, Xia Y Advanced functional materials 21687818 Adv Funct Mater 2010 May 25
Probing the surface-enhanced Raman scattering properties of Au-Ag nanocages at two different excitation wavelengths. Rycenga M, Hou KK, Cobley CM, Schwartz AG, Camargo PH, Xia Y Physical chemistry chemical physics : PCCP 19588011 Phys Chem Chem Phys 2009 Jul 28
Metal-polymer hybrid colloidal particles with an eccentric structure. Ohnuma A, Cho EC, Jiang M, Ohtani B, Xia Y Langmuir : the ACS journal of surfaces and colloids 19621917 Langmuir 2009 Dec 15
A new theranostic system based on gold nanocages and phase-change materials with unique features for photoacoustic imaging and controlled release. Moon GD, Choi SW, Cai X, Li W, Cho EC, Jeong U, Wang LV, Xia Y Journal of the American Chemical Society 21401092 J Am Chem Soc 2011 Apr 6
Synthesis of gold microplates using bovine serum albumin as a reductant and a stabilizer. Au L, Lim B, Colletti P, Jun YS, Xia Y Chemistry, an Asian journal 19967737 Chem Asian J 2010 Jan 4
Putting Electrospun Nanofibers to Work for Biomedical Research. Xie J, Li X, Xia Y Macromolecular rapid communications 20011452 Macromol Rapid Commun 2008 Nov 19
Synthesis and Optical Properties of Cubic Gold Nanoframes. Au L, Chen Y, Zhou F, Camargo PH, Lim B, Li ZY, Ginger DS, Xia Y Nano research 20200595 Nano Res 2008 Dec 1
Stimuli-Responsive Materials for Controlled Release of Theranostic Agents. Wang Y, Shim MS, Levinson NS, Sung HW, Xia Y Advanced functional materials 25477774 Adv Funct Mater 2014 Jul 16
Seeing Through the Surface: Non-invasive Characterization of Biomaterial-Tissue Interactions Using Photoacoustic Microscopy. Zhang YS, Wang LV, Xia Y Annals of biomedical engineering 26471785 Ann Biomed Eng 2016 Mar
Radiolabeling of Gold Nanocages for Potential Applications in Tracking, Diagnosis, and Image-Guided Therapy. Qiu J, Liu Y, Xia Y Advanced healthcare materials 33470560 Adv Healthc Mater 2021 Aug
Seed-mediated synthesis of truncated gold decahedrons with a AuCl/oleylamine complex as precursor. Ma Y, Zeng J, Li W, McKiernan M, Xie Z, Xia Y Advanced materials (Deerfield Beach, Fla.) 20301132 Adv Mater 2010 May 4
Targeting gold nanocages to cancer cells for photothermal destruction and drug delivery. Cobley CM, Au L, Chen J, Xia Y Expert opinion on drug delivery 20345327 Expert Opin Drug Deliv 2010 May
Chitosan-Based Inverse Opals: Three-Dimensional Scaffolds with Uniform Pore Structures for Cell Culture. Choi SW, Xie J, Xia Y Advanced materials (Deerfield Beach, Fla.) 19710950 Adv Mater 2009 Apr 15
The effects of size, shape, and surface functional group of gold nanostructures on their adsorption and internalization by cells. Cho EC, Au L, Zhang Q, Xia Y Small (Weinheim an der Bergstrasse, Germany) 20029850 Small 2010 Feb 22
Nanofiber scaffolds with gradations in mineral content for mimicking the tendon-to-bone insertion site. Li X, Xie J, Lipner J, Yuan X, Thomopoulos S, Xia Y Nano letters 19537737 Nano Lett 2009 Jul
Gold nanocages as photothermal transducers for cancer treatment. Chen J, Glaus C, Laforest R, Zhang Q, Yang M, Gidding M, Welch MJ, Xia Y Small (Weinheim an der Bergstrasse, Germany) 20225187 Small 2010 Apr 9
Neurite outgrowth on nanofiber scaffolds with different orders, structures, and surface properties. Xie J, MacEwan MR, Li X, Sakiyama-Elbert SE, Xia Y ACS nano 19397333 ACS Nano 2009 May 26
Noninvasive photoacoustic microscopy of living cells in two and three dimensions through enhancement by a metabolite dye. Zhang Y, Cai X, Wang Y, Zhang C, Li L, Choi SW, Wang LV, Xia Y Angewandte Chemie (International ed. in English) 21681876 Angew Chem Int Ed Engl 2011 Aug 1
Controlling the synthesis and assembly of silver nanostructures for plasmonic applications. Rycenga M, Cobley CM, Zeng J, Li W, Moran CH, Zhang Q, Qin D, Xia Y Chemical reviews 21395318 Chem Rev 2011 Jun 8
Recent Developments in Shape-Controlled Synthesis of Silver Nanocrystals. Xia X, Zeng J, Zhang Q, Moran CH, Xia Y The journal of physical chemistry. C, Nanomaterials and interfaces 23105955 J Phys Chem C Nanomater Interfaces 2012
Facile synthesis of Ag nanocubes and Au nanocages. Skrabalak SE, Au L, Li X, Xia Y Nature protocols 17853874 Nat Protoc 2007
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Tailoring the Optical and Catalytic Properties of Gold-Silver Nanoboxes and Nanocages by Introducing Palladium. Cobley CM, Campbell DJ, Xia Y Advanced materials (Deerfield Beach, Fla.) 18568091 Adv Mater 2008 Feb
Isolating and probing the hot spot formed between two silver nanocubes. Camargo PH, Rycenga M, Au L, Xia Y Angewandte Chemie (International ed. in English) 19199309 Angew Chem Int Ed Engl 2009
A reactive oxygen species (ROS)-responsive polymer for safe, efficient, and targeted gene delivery in cancer cells. Shim MS, Xia Y Angewandte Chemie (International ed. in English) 23716349 Angew Chem Int Ed Engl 2013 Jul 1
Photoacoustic Microscopy in Tissue Engineering. Cai X, Zhang YS, Xia Y, Wang LV Materials today (Kidlington, England) 23766667 Mater Today (Kidlington) 2013 Mar 1
Gold nanocages covered with thermally-responsive polymers for controlled release by high-intensity focused ultrasound. Li W, Cai X, Kim C, Sun G, Zhang Y, Deng R, Yang M, Chen J, Achilefu S, Wang LV, Xia Y Nanoscale 21321760 Nanoscale 2011 Apr
Modifying the pores of an inverse opal scaffold with chitosan microstructures for truly three-dimensional cell culture. Zhang Y, Choi SW, Xia Y Macromolecular rapid communications 22231861 Macromol Rapid Commun 2012 Feb 27
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SV119-gold nanocage conjugates: a new platform for targeting cancer cells via sigma-2 receptors. Wang Y, Xu J, Xia X, Yang M, Vangveravong S, Chen J, Mach RH, Xia Y Nanoscale 22113350 Nanoscale 2012 Jan 21
Generation of hot spots with silver nanocubes for single-molecule detection by surface-enhanced Raman scattering. Rycenga M, Xia X, Moran CH, Zhou F, Qin D, Li ZY, Xia Y Angewandte Chemie (International ed. in English) 21542081 Angew Chem Int Ed Engl 2011 Jun 6
Vibrational response of Au-Ag nanoboxes and nanocages to ultrafast laser-induced heating. Petrova H, Lin CH, Hu M, Chen J, Siekkinen AR, Xia Y, Sader JE, Hartland GV Nano letters 17358093 Nano Lett 2007 Apr
Facile synthesis of branched au nanostructures by templating against a self-destructive lattice of magnetic fe nanoparticles. Li Z, Li W, Camargo PH, Xia Y Angewandte Chemie (International ed. in English) 18988222 Angew Chem Int Ed Engl 2008
The differentiation of embryonic stem cells seeded on electrospun nanofibers into neural lineages. Xie J, Willerth SM, Li X, Macewan MR, Rader A, Sakiyama-Elbert SE, Xia Y Biomaterials 18930315 Biomaterials 2009 Jan
Measuring the SERS Enhancement Factors of Dimers with Different Structures Constructed from Silver Nanocubes. Camargo PH, Au L, Rycenga M, Li W, Xia Y Chemical physics letters 20209069 Chem Phys Lett 2010 Jan
Using SV119-gold nanocage conjugates to eradicate cancer stem cells through a combination of photothermal and chemo therapies. Sun T, Wang Y, Wang Y, Xu J, Zhao X, Vangveravong S, Mach RH, Xia Y Advanced healthcare materials 24677807 Adv Healthc Mater 2014 Aug
Silver nanocube on gold microplate as a well-defined and highly active substrate for SERS detection. Xia X, Rycenga M, Qin D, Xia Y Journal of materials chemistry. C 24187611 J Mater Chem C Mater 2013 Oct 14
25th anniversary article: galvanic replacement: a simple and versatile route to hollow nanostructures with tunable and well-controlled properties. Xia X, Wang Y, Ruditskiy A, Xia Y Advanced materials (Deerfield Beach, Fla.) 24027074 Adv Mater 2013 Nov 26
A Facile and General Method for the Encapsulation of Different Types of Imaging Contrast Agents Within Micrometer-Sized Polymer Beads. Bai MY, Moran CH, Zhang L, Liu C, Zhang Y, Wang LV, Xia Y Advanced functional materials 31866803 Adv Funct Mater 2012 Feb 22
Silica-coated dimers of silver nanospheres as surface-enhanced Raman scattering tags for imaging cancer cells. Xia X, Li W, Zhang Y, Xia Y Interface focus 24427538 Interface Focus 2013 Jun 6
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A "window of opportunity:" the reduction of coronary heart disease and total mortality with menopausal therapies is age- and time-dependent. Hodis HN, Mack WJ Brain research 20977895 Brain Res 2011 Mar 16
Versatile, fully automated, microfluidic cell culture system. Gómez-Sjöberg R, Leyrat AA, Pirone DM, Chen CS, Quake SR Analytical chemistry 17953452 Anal Chem 2007 Nov 15
Noninvasive prenatal diagnosis in a fetus at risk for methylmalonic acidemia. Gu W, Koh W, Blumenfeld YJ, El-Sayed YY, Hudgins L, Hintz SR, Quake SR Genetics in medicine : official journal of the American College of Medical Genetics 24406457 Genet Med 2014 Jul
Single-molecule sequencing of an individual human genome. Pushkarev D, Neff NF, Quake SR Nature biotechnology 19668243 Nat Biotechnol 2009 Sep
Statistical mechanics of Monod-Wyman-Changeux (MWC) models. Marzen S, Garcia HG, Phillips R Journal of molecular biology 23499654 J Mol Biol 2013 May 13
Comparison of the theoretical and real-world evolutionary potential of a genetic circuit. Razo-Mejia M, Boedicker JQ, Jones D, DeLuna A, Kinney JB, Phillips R Physical biology 24685590 Phys Biol 2014 Apr
Concentration and length dependence of DNA looping in transcriptional regulation. Han L, Garcia HG, Blumberg S, Towles KB, Beausang JF, Nelson PC, Phillips R PloS one 19479049 PLoS One 2009 May 25
Building enhancers from the ground up: a synthetic biology approach. Amit R, Garcia HG, Phillips R, Fraser SE Cell 21729783 Cell 2011 Jul 8
Ion-dependent dynamics of DNA ejections for bacteriophage lambda. Wu D, Van Valen D, Hu Q, Phillips R Biophysical journal 20712993 Biophys J 2010 Aug 9
Biochemistry on a leash: the roles of tether length and geometry in signal integration proteins. Van Valen D, Haataja M, Phillips R Biophysical journal 19217847 Biophys J 2009 Feb 18
Membrane mechanics as a probe of ion-channel gating mechanisms. Reeves D, Ursell T, Sens P, Kondev J, Phillips R Physical review. E, Statistical, nonlinear, and soft matter physics 18999449 Phys Rev E Stat Nonlin Soft Matter Phys 2008 Oct
A feeling for the numbers in biology. Phillips R, Milo R Proceedings of the National Academy of Sciences of the United States of America 20018695 Proc Natl Acad Sci U S A 2009 Dec 22
Trajectory approach to two-state kinetics of single particles on sculpted energy landscapes. Wu D, Ghosh K, Inamdar M, Lee HJ, Fraser S, Dill K, Phillips R Physical review letters 19792475 Phys Rev Lett 2009 Jul 31
Directional interactions and cooperativity between mechanosensitive membrane proteins. Haselwandter CA, Phillips R Europhysics letters 25309021 Europhys Lett 2013 Mar
Single-cell census of mechanosensitive channels in living bacteria. Bialecka-Fornal M, Lee HJ, DeBerg HA, Gandhi CS, Phillips R PloS one 22427953 PLoS One 2012
Entropic tension in crowded membranes. Lindén M, Sens P, Phillips R PLoS computational biology 22438801 PLoS Comput Biol 2012
Comparison and calibration of different reporters for quantitative analysis of gene expression. Garcia HG, Lee HJ, Boedicker JQ, Phillips R Biophysical journal 21806921 Biophys J 2011 Aug 3
Elastic energy of polyhedral bilayer vesicles. Haselwandter CA, Phillips R Physical review. E, Statistical, nonlinear, and soft matter physics 21797397 Phys Rev E Stat Nonlin Soft Matter Phys 2011 Jun
Effect of promoter architecture on the cell-to-cell variability in gene expression. Sanchez A, Garcia HG, Jones D, Phillips R, Kondev J PLoS computational biology 21390269 PLoS Comput Biol 2011 Mar
Connection between oligomeric state and gating characteristics of mechanosensitive ion channels. Haselwandter CA, Phillips R PLoS computational biology 23696720 PLoS Comput Biol 2013
Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping. Johnson S, Chen YJ, Phillips R PloS one 24146776 PLoS One 2013
Teaching the principles of statistical dynamics. Ghosh K, Dill KA, Inamdar MM, Seitaridou E, Phillips R American journal of physics 23585693 Am J Phys 2006 Feb 1
Monod-Wyman-Changeux Analysis of Ligand-Gated Ion Channel Mutants. Einav T, Phillips R The journal of physical chemistry. B 28134524 J Phys Chem B 2017 Apr 20
Theoretical analysis of inducer and operator binding for cyclic-AMP receptor protein mutants. Einav T, Duque J, Phillips R PloS one 30256816 PLoS One 2018
Musings on mechanism: quest for a quark theory of proteins? Phillips R FASEB journal : official publication of the Federation of American Societies for Experimental Biology 28963318 FASEB J 2017 Oct
Mapping DNA sequence to transcription factor binding energy in vivo. Barnes SL, Belliveau NM, Ireland WT, Kinney JB, Phillips R PLoS computational biology 30716072 PLoS Comput Biol 2019 Feb
Design Principles of Length Control of Cytoskeletal Structures. Mohapatra L, Goode BL, Jelenkovic P, Phillips R, Kondev J Annual review of biophysics 27145876 Annu Rev Biophys 2016 Jul 5
Interplay of Protein Binding Interactions, DNA Mechanics, and Entropy in DNA Looping Kinetics. Mulligan PJ, Chen YJ, Phillips R, Spakowitz AJ Biophysical journal 26244743 Biophys J 2015 Aug 4
Morphological phase diagram for lipid membrane domains with entropic tension. Rim JE, Ursell TS, Phillips R, Klug WS Physical review letters 21405437 Phys Rev Lett 2011 Feb 4
Sequence dependence of transcription factor-mediated DNA looping. Johnson S, Lindén M, Phillips R Nucleic acids research 22718983 Nucleic Acids Res 2012 Sep
Real-time observations of single bacteriophage lambda DNA ejections in vitro. Grayson P, Han L, Winther T, Phillips R Proceedings of the National Academy of Sciences of the United States of America 17804798 Proc Natl Acad Sci U S A 2007 Sep 11
Transcriptional regulation by the numbers: applications. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Kuhlman T, Phillips R Current opinion in genetics & development 15797195 Curr Opin Genet Dev 2005 Apr
The effect of genome length on ejection forces in bacteriophage lambda. Grayson P, Evilevitch A, Inamdar MM, Purohit PK, Gelbart WM, Knobler CM, Phillips R Virology 16469346 Virology 2006 May 10
Reduced amino acid alphabets exhibit an improved sensitivity and selectivity in fold assignment. Peterson EL, Kondev J, Theriot JA, Phillips R Bioinformatics (Oxford, England) 19351620 Bioinformatics 2009 Jun 1
Morphology and interaction between lipid domains. Ursell TS, Klug WS, Phillips R Proceedings of the National Academy of Sciences of the United States of America 19620730 Proc Natl Acad Sci U S A 2009 Aug 11
Emerging roles for lipids in shaping membrane-protein function. Phillips R, Ursell T, Wiggins P, Sens P Nature 19458714 Nature 2009 May 21
Cooperative gating and spatial organization of membrane proteins through elastic interactions. Ursell T, Huang KC, Peterson E, Phillips R PLoS computational biology 17480116 PLoS Comput Biol 2007 May
Thermodynamics of biological processes. Garcia HG, Kondev J, Orme N, Theriot JA, Phillips R Methods in enzymology 21333788 Methods Enzymol 2011
Transcription by the numbers redux: experiments and calculations that surprise. Garcia HG, Sanchez A, Kuhlman T, Kondev J, Phillips R Trends in cell biology 20801657 Trends Cell Biol 2010 Dec
Statistical Mechanics of Allosteric Enzymes. Einav T, Mazutis L, Phillips R The journal of physical chemistry. B 27070509 J Phys Chem B 2016 Jul 7
Tuning Transcriptional Regulation through Signaling: A Predictive Theory of Allosteric Induction. Razo-Mejia M, Barnes SL, Belliveau NM, Chure G, Einav T, Lewis M, Phillips R Cell systems 29574055 Cell Syst 2018 Apr 25
Promoter architecture dictates cell-to-cell variability in gene expression. Jones DL, Brewster RC, Phillips R Science (New York, N.Y.) 25525251 Science 2014 Dec 19
Distinct structural features of TFAM drive mitochondrial DNA packaging versus transcriptional activation. Ngo HB, Lovely GA, Phillips R, Chan DC Nature communications 24435062 Nat Commun 2014
DNA sequence-dependent mechanics and protein-assisted bending in repressor-mediated loop formation. Boedicker JQ, Garcia HG, Johnson S, Phillips R Physical biology 24231252 Phys Biol 2013 Dec
Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. Brewster RC, Jones DL, Phillips R PLoS computational biology 23271961 PLoS Comput Biol 2012
Theoretical and experimental dissection of DNA loop-mediated repression. Boedicker JQ, Garcia HG, Phillips R Physical review letters 23383841 Phys Rev Lett 2013 Jan 4
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
Figure 1 Theory Meets Figure 2 Experiments in the Study of Gene Expression. Phillips R, Belliveau NM, Chure G, Garcia HG, Razo-Mejia M, Scholes C Annual review of biophysics 31084583 Annu Rev Biophys 2019 May 6
Predictive shifts in free energy couple mutations to their phenotypic consequences. Chure G, Razo-Mejia M, Belliveau NM, Einav T, Kaczmarek ZA, Barnes SL, Lewis M, Phillips R Proceedings of the National Academy of Sciences of the United States of America 31451655 Proc Natl Acad Sci U S A 2019 Sep 10
Anionic Lipids Impact RAS-Binding Site Accessibility and Membrane Binding Affinity of CRAF RBD-CRD. Travers T, López CA, Agamasu C, Hettige JJ, Messing S, García AE, Stephen AG, Gnanakaran S Biophysical journal 32649863 Biophys J 2020 Aug 4
Statistical mechanical model of coupled transcription from multiple promoters due to transcription factor titration. Rydenfelt M, Cox RS 3rd, Garcia H, Phillips R Physical review. E, Statistical, nonlinear, and soft matter physics 24580252 Phys Rev E Stat Nonlin Soft Matter Phys 2014 Jan
The transcription factor titration effect dictates level of gene expression. Brewster RC, Weinert FM, Garcia HG, Song D, Rydenfelt M, Phillips R Cell 24612990 Cell 2014 Mar 13
Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity. Garcia HG, Grayson P, Han L, Inamdar M, Kondev J, Nelson PC, Phillips R, Widom J, Wiggins PA Biopolymers 17103419 Biopolymers 2007 Feb 5
Transcriptional regulation by the numbers: models. Bintu L, Buchler NE, Garcia HG, Gerland U, Hwa T, Kondev J, Phillips R Current opinion in genetics & development 15797194 Curr Opin Genet Dev 2005 Apr
A single-molecule Hershey-Chase experiment. Van Valen D, Wu D, Chen YJ, Tuson H, Wiggins P, Phillips R Current biology : CB 22727695 Curr Biol 2012 Jul 24
Measuring flux distributions for diffusion in the small-numbers limit. Seitaridou E, Inamdar MM, Phillips R, Ghosh K, Dill K The journal of physical chemistry. B 17295536 J Phys Chem B 2007 Mar 8
First-principles calculation of DNA looping in tethered particle experiments. Towles KB, Beausang JF, Garcia HG, Phillips R, Nelson PC Physical biology 19571369 Phys Biol 2009 Jul 1
Minimal bending energies of bilayer polyhedra. Haselwandter CA, Phillips R Physical review letters 21231425 Phys Rev Lett 2010 Nov 26
Using synthetic biology to make cells tomorrow's test tubes. Garcia HG, Brewster RC, Phillips R Integrative biology : quantitative biosciences from nano to macro 26952708 Integr Biol (Camb) 2016 Apr 18
Napoleon Is in Equilibrium. Phillips R Annual review of condensed matter physics 27429713 Annu Rev Condens Matter Phys 2015 Mar
The influence of promoter architectures and regulatory motifs on gene expression in Escherichia coli. Rydenfelt M, Garcia HG, Cox RS 3rd, Phillips R PloS one 25549361 PLoS One 2014
Schrödinger's What Is Life? at 75. Phillips R Cell systems 34139159 Cell Syst 2021 Jun 16
Combinatorial Control through Allostery. Galstyan V, Funk L, Einav T, Phillips R The journal of physical chemistry. B 30768906 J Phys Chem B 2019 Apr 4
Exact theory of kinkable elastic polymers. Wiggins PA, Phillips R, Nelson PC Physical review. E, Statistical, nonlinear, and soft matter physics 15783354 Phys Rev E Stat Nonlin Soft Matter Phys 2005 Feb
Volume-exclusion effects in tethered-particle experiments: bead size matters. Segall DE, Nelson PC, Phillips R Physical review letters 16606235 Phys Rev Lett 2006 Mar 3
Dynamics of DNA ejection from bacteriophage. Inamdar MM, Gelbart WM, Phillips R Biophysical journal 16679360 Biophys J 2006 Jul 15
The rate of osmotic downshock determines the survival probability of bacterial mechanosensitive channel mutants. Bialecka-Fornal M, Lee HJ, Phillips R Journal of bacteriology 25349158 J Bacteriol 2015 Jan 1
Scaling of gene expression with transcription-factor fugacity. Weinert FM, Brewster RC, Rydenfelt M, Phillips R, Kegel WK Physical review letters 25554908 Phys Rev Lett 2014 Dec 19
Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time. Ireland WT, Beeler SM, Flores-Bautista E, McCarty NS, Röschinger T, Belliveau NM, Sweredoski MJ, Moradian A, Kinney JB, Phillips R eLife 32955440 Elife 2020 Sep 21
Theory in Biology: Figure 1 or Figure 7? Phillips R Trends in cell biology 26584768 Trends Cell Biol 2015 Dec
Probing individual environmental bacteria for viruses by using microfluidic digital PCR. Tadmor AD, Ottesen EA, Leadbetter JR, Phillips R Science (New York, N.Y.) 21719670 Science 2011 Jul 1
Quantitative dissection of the simple repression input-output function. Garcia HG, Phillips R Proceedings of the National Academy of Sciences of the United States of America 21730194 Proc Natl Acad Sci U S A 2011 Jul 19
Connecting the Dots between Mechanosensitive Channel Abundance, Osmotic Shock, and Survival at Single-Cell Resolution. Chure G, Lee HJ, Rasmussen A, Phillips R Journal of bacteriology 30201782 J Bacteriol 2018 Dec 1
Systematic approach for dissecting the molecular mechanisms of transcriptional regulation in bacteria. Belliveau NM, Barnes SL, Ireland WT, Jones DL, Sweredoski MJ, Moradian A, Hess S, Kinney JB, Phillips R Proceedings of the National Academy of Sciences of the United States of America 29728462 Proc Natl Acad Sci U S A 2018 May 22
Operator sequence alters gene expression independently of transcription factor occupancy in bacteria. Garcia HG, Sanchez A, Boedicker JQ, Osborne M, Gelles J, Kondev J, Phillips R Cell reports 22840405 Cell Rep 2012 Jul 26
Self-consistent theory of transcriptional control in complex regulatory architectures. Landman J, Brewster RC, Weinert FM, Phillips R, Kegel WK PloS one 28686609 PLoS One 2017
Binding and signaling of surface-immobilized reagentless fluorescent biosensors derived from periplasmic binding proteins. de Lorimier RM, Tian Y, Hellinga HW Protein science : a publication of the Protein Society 16823040 Protein Sci 2006 Aug
A miniaturized technique for assessing protein thermodynamics and function using fast determination of quantitative cysteine reactivity. Isom DG, Marguet PR, Oas TG, Hellinga HW Proteins 21387407 Proteins 2011 Apr
The backbone structure of the thermophilic Thermoanaerobacter tengcongensis ribose binding protein is essentially identical to its mesophilic E. coli homolog. Cuneo MJ, Tian Y, Allert M, Hellinga HW BMC structural biology 18373848 BMC Struct Biol 2008 Mar 28
Structural adaptations that modulate monosaccharide, disaccharide, and trisaccharide specificities in periplasmic maltose-binding proteins. Cuneo MJ, Changela A, Beese LS, Hellinga HW Journal of molecular biology 19361522 J Mol Biol 2009 May 29
Local encoding of computationally designed enzyme activity. Allert M, Dwyer MA, Hellinga HW Journal of molecular biology 17196220 J Mol Biol 2007 Feb 23
Identification of cognate ligands for the Escherichia coli phnD protein product and engineering of a reagentless fluorescent biosensor for phosphonates. Rizk SS, Cuneo MJ, Hellinga HW Protein science : a publication of the Protein Society 16751609 Protein Sci 2006 Jul
Wharton's Jelly Mesenchymal Stromal Cells and Derived Extracellular Vesicles as Post-Myocardial Infarction Therapeutic Toolkit: An Experienced View. Muñoz-Domínguez N, Roura S, Prat-Vidal C, Vives J Pharmaceutics 34575412 Pharmaceutics 2021 Aug 26
The crystal structure of a thermophilic glucose binding protein reveals adaptations that interconvert mono and di-saccharide binding sites. Cuneo MJ, Changela A, Warren JJ, Beese LS, Hellinga HW Journal of molecular biology 16904687 J Mol Biol 2006 Sep 15
Protein fabrication automation. Cox JC, Lape J, Sayed MA, Hellinga HW Protein science : a publication of the Protein Society 17242375 Protein Sci 2007 Mar
Structure-based design of robust glucose biosensors using a Thermotoga maritima periplasmic glucose-binding protein. Tian Y, Cuneo MJ, Changela A, Höcker B, Beese LS, Hellinga HW Protein science : a publication of the Protein Society 17766373 Protein Sci 2007 Oct
Picomole-scale characterization of protein stability and function by quantitative cysteine reactivity. Isom DG, Vardy E, Oas TG, Hellinga HW Proceedings of the National Academy of Sciences of the United States of America 20194783 Proc Natl Acad Sci U S A 2010 Mar 16
Structural analysis of semi-specific oligosaccharide recognition by a cellulose-binding protein of thermotoga maritima reveals adaptations for functional diversification of the oligopeptide periplasmic binding protein fold. Cuneo MJ, Beese LS, Hellinga HW The Journal of biological chemistry 19801540 J Biol Chem 2009 Nov 27
Structural analysis of a periplasmic binding protein in the tripartite ATP-independent transporter family reveals a tetrameric assembly that may have a role in ligand transport. Cuneo MJ, Changela A, Miklos AE, Beese LS, Krueger JK, Hellinga HW The Journal of biological chemistry 18723845 J Biol Chem 2008 Nov 21
Visualization of synaptic inhibition with an optogenetic sensor developed by cell-free protein engineering automation. Grimley JS, Li L, Wang W, Wen L, Beese LS, Hellinga HW, Augustine GJ The Journal of neuroscience : the official journal of the Society for Neuroscience 24107961 J Neurosci 2013 Oct 9
Multifactorial determinants of protein expression in prokaryotic open reading frames. Allert M, Cox JC, Hellinga HW Journal of molecular biology 20727358 J Mol Biol 2010 Oct 8
Ligand-induced conformational changes in a thermophilic ribose-binding protein. Cuneo MJ, Beese LS, Hellinga HW BMC structural biology 19019243 BMC Struct Biol 2008 Nov 19
Thermodynamic analysis of ligand-induced changes in protein thermal unfolding applied to high-throughput determination of ligand affinities with extrinsic fluorescent dyes. Layton CJ, Hellinga HW Biochemistry 21050007 Biochemistry 2010 Dec 28
Integration of cell-free protein coexpression with an enzyme-linked immunosorbent assay enables rapid analysis of protein-protein interactions directly from DNA. Layton CJ, Hellinga HW Protein science : a publication of the Protein Society 21674663 Protein Sci 2011 Aug
Generating coherent patterns of activity from chaotic neural networks. Sussillo D, Abbott LF Neuron 19709635 Neuron 2009 Aug 27
HCN hyperpolarization-activated cation channels inhibit EPSPs by interactions with M-type K(+) channels. George MS, Abbott LF, Siegelbaum SA Nature neuroscience 19363490 Nat Neurosci 2009 May
Stimulus-dependent suppression of chaos in recurrent neural networks. Rajan K, Abbott LF, Sompolinsky H Physical review. E, Statistical, nonlinear, and soft matter physics 20866644 Phys Rev E Stat Nonlin Soft Matter Phys 2010 Jul
Modular realignment of entorhinal grid cell activity as a basis for hippocampal remapping. Monaco JD, Abbott LF The Journal of neuroscience : the official journal of the Society for Neuroscience 21697391 J Neurosci 2011 Jun 22
Gating multiple signals through detailed balance of excitation and inhibition in spiking networks. Vogels TP, Abbott LF Nature neuroscience 19305402 Nat Neurosci 2009 Apr
A brainstem map of orofacial rhythms. Kaku H, Liu LD, Gao R, West S, Liao SM, Finkelstein A, Kleinfeld D, Thomas A, Tipparaju SL, Svoboda K, Li N bioRxiv : the preprint server for biology 39975015 bioRxiv 2025 Jan 27
A frugal CRISPR kit for equitable and accessible education in gene editing and synthetic biology. Collins M, Lau MB, Ma W, Shen A, Wang B, Cai S, La Russa M, Jewett MC, Qi LS Nature communications 39095367 Nat Commun 2024 Aug 3
The realization of CRISPR gene therapy. Ma Y, Qi LS Nature chemical biology 38872012 Nat Chem Biol 2024 Jul
Cortical activity emerges in region-specific patterns during early brain development. Suárez R, Bluett T, McCullough MH, Avitan L, Black DA, Paolino A, Fenlon LR, Goodhill GJ, Richards LJ bioRxiv : the preprint server for biology 36824827 bioRxiv 2023 Apr 8
Diverse axonal morphologies of individual callosal projection neurons reveal new insights into brain connectivity. Pal S, Lim JWC, Richards LJ Current opinion in neurobiology 38271848 Curr Opin Neurobiol 2024 Feb
Cortical activity emerges in region-specific patterns during early brain development. Suárez R, Bluett T, McCullough MH, Avitan L, Black DA, Paolino A, Fenlon LR, Goodhill GJ, Richards LJ Proceedings of the National Academy of Sciences of the United States of America 37216522 Proc Natl Acad Sci U S A 2023 May 30
Low-field MRI: Clinical promise and challenges. Arnold TC, Freeman CW, Litt B, Stein JM Journal of magnetic resonance imaging : JMRI 36120962 J Magn Reson Imaging 2023 Jan
A framework For brain atlases: Lessons from seizure dynamics. Revell AY, Silva AB, Arnold TC, Stein JM, Das SR, Shinohara RT, Bassett DS, Litt B, Davis KA NeuroImage 35339683 Neuroimage 2022 Jul 1
Seizure Detection in Continuous Inpatient EEG: A Comparison of Human vs Automated Review. Ganguly TM, Ellis CA, Tu D, Shinohara RT, Davis KA, Litt B, Pathmanathan J Neurology 35410905 Neurology 2022 May 31
Development of a natural language processing algorithm to extract seizure types and frequencies from the electronic health record. Decker BM, Turco A, Xu J, Terman SW, Kosaraju N, Jamil A, Davis KA, Litt B, Ellis CA, Khankhanian P, Hill CE Seizure 35882104 Seizure 2022 Oct
Spike patterns surrounding sleep and seizures localize the seizure-onset zone in focal epilepsy. Conrad EC, Revell AY, Greenblatt AS, Gallagher RS, Pattnaik AR, Hartmann N, Gugger JJ, Shinohara RT, Litt B, Marsh ED, Davis KA Epilepsia 36484572 Epilepsia 2023 Mar
A pharmacokinetic model of antiseizure medication load to guide care in the epilepsy monitoring unit. Ghosn NJ, Xie K, Pattnaik AR, Gugger JJ, Ellis CA, Sweeney E, Fox E, Bernabei JM, Johnson J, Boccanfuso J, Litt B, Conrad EC Epilepsia 36815252 Epilepsia 2023 May
Quantitative approaches to guide epilepsy surgery from intracranial EEG. Bernabei JM, Li A, Revell AY, Smith RJ, Gunnarsdottir KM, Ong IZ, Davis KA, Sinha N, Sarma S, Litt B Brain : a journal of neurology 36623936 Brain 2023 Jun 1
iEEG-recon: A fast and scalable pipeline for accurate reconstruction of intracranial electrodes and implantable devices. Lucas A, Scheid BH, Pattnaik AR, Gallagher R, Mojena M, Tranquille A, Prager B, Gleichgerrcht E, Gong R, Litt B, Davis KA, Das S, Stein JM, Sinha N Epilepsia 38148517 Epilepsia 2024 Mar
Artificial intelligence in epilepsy phenotyping. Knight A, Gschwind T, Galer P, Worrell GA, Litt B, Soltesz I, Beniczky S Epilepsia 37983589 Epilepsia 2023 Nov 20
MXene-infused bioelectronic interfaces for multiscale electrophysiology and stimulation. Driscoll N, Erickson B, Murphy BB, Richardson AG, Robbins G, Apollo NV, Mentzelopoulos G, Mathis T, Hantanasirisakul K, Bagga P, Gullbrand SE, Sergison M, Reddy R, Wolf JA, Chen HI, Lucas TH, Dillingham TR, Davis KA, Gogotsi Y, Medaglia JD, Vitale F Science translational medicine 34550728 Sci Transl Med 2021 Sep 22
Fractional-order model predictive control as a framework for electrical neurostimulation in epilepsy. Chatterjee S, Romero O, Ashourvan A, Pequito S Journal of neural engineering 33142281 J Neural Eng 2020 Dec 16
Extracting seizure frequency from epilepsy clinic notes: a machine reading approach to natural language processing. Xie K, Gallagher RS, Conrad EC, Garrick CO, Baldassano SN, Bernabei JM, Galer PD, Ghosn NJ, Greenblatt AS, Jennings T, Kornspun A, Kulick-Soper CV, Panchal JM, Pattnaik AR, Scheid BH, Wei D, Weitzman M, Muthukrishnan R, Kim J, Litt B, Ellis CA, Roth D Journal of the American Medical Informatics Association : JAMIA 35190834 J Am Med Inform Assoc 2022 Apr 13
Intracranial electroencephalographic biomarker predicts effective responsive neurostimulation for epilepsy prior to treatment. Scheid BH, Bernabei JM, Khambhati AN, Mouchtaris S, Jeschke J, Bassett DS, Becker D, Davis KA, Lucas T, Doyle W, Chang EF, Friedman D, Rao VR, Litt B Epilepsia 34997577 Epilepsia 2022 Mar
Generalization of finetuned transformer language models to new clinical contexts. Xie K, Terman SW, Gallagher RS, Hill CE, Davis KA, Litt B, Roth D, Ellis CA JAMIA open 37600072 JAMIA Open 2023 Oct
Resting-state background features demonstrate multidien cycles in long-term EEG device recordings. Ojemann WKS, Scheid BH, Mouchtaris S, Lucas A, LaRocque JJ, Aguila C, Ashourvan A, Caciagli L, Davis KA, Conrad EC, Litt B medRxiv : the preprint server for health sciences 37461688 medRxiv 2023 Jul 7
Long-term epilepsy outcome dynamics revealed by natural language processing of clinic notes. Xie K, Gallagher RS, Shinohara RT, Xie SX, Hill CE, Conrad EC, Davis KA, Roth D, Litt B, Ellis CA Epilepsia 37114472 Epilepsia 2023 Jul
Characterizing the treatment gap in the United States among adult patients with a new diagnosis of epilepsy. Decker BM, Ellis CA, Schriver E, Fischbein K, Smith D, Moyer JT, Kulick-Soper CV, Mowery D, Litt B, Hill CE Epilepsia 37150944 Epilepsia 2023 Jul
iEEG-recon: A Fast and Scalable Pipeline for Accurate Reconstruction of Intracranial Electrodes and Implantable Devices. Lucas A, Scheid BH, Pattnaik AR, Gallagher R, Mojena M, Tranquille A, Prager B, Gleichgerrcht E, Gong R, Litt B, Davis KA, Das S, Stein JM, Sinha N medRxiv : the preprint server for health sciences 37398160 medRxiv 2023 Jun 13
Quantitative EEG Spectral Features Differentiate Genetic Epilepsies and Predict Neurologic Outcomes. Galer PD, McKee JL, Ruggiero SM, Kaufman MC, McSalley I, Ganesan S, Ojemann WKS, Gonzalez AK, Cao Q, Litt B, Helbig I, Conrad EC medRxiv : the preprint server for health sciences 39417111 medRxiv 2024 Oct 10
Quantifying interictal intracranial EEG to predict focal epilepsy. Gallagher RS, Sinha N, Pattnaik AR, Ojemann WKS, Lucas A, LaRocque JJ, Bernabei JM, Greenblatt AS, Sweeney EM, Chen HI, Davis KA, Conrad EC, Litt B ArXiv 37547655 ArXiv 2023 Jul 27
Multi-contrast high-field quality image synthesis for portable low-field MRI using generative adversarial networks and paired data. Lucas A, Campbell Arnold T, Okar SV, Vadali C, Kawatra KD, Ren Z, Cao Q, Shinohara RT, Schindler MK, Davis KA, Litt B, Reich DS, Stein JM medRxiv : the preprint server for health sciences 38234785 medRxiv 2023 Dec 29
The seizure severity score: a quantitative tool for comparing seizures and their response to therapy. Pattnaik AR, Ghosn NJ, Ong IZ, Revell AY, Ojemann WKS, Scheid BH, Georgostathi G, Bernabei JM, Conrad EC, Sinha SR, Davis KA, Sinha N, Litt B Journal of neural engineering 37531949 J Neural Eng 2023 Aug 10
Remote effects of temporal lobe epilepsy surgery: Long-term morphological changes after surgical resection. Arnold TC, Kini LG, Bernabei JM, Revell AY, Das SR, Stein JM, Lucas TH, Englot DJ, Morgan VL, Litt B, Davis KA Epilepsia open 36944585 Epilepsia Open 2023 Jun
Time-evolving controllability of effective connectivity networks during seizure progression. Scheid BH, Ashourvan A, Stiso J, Davis KA, Mikhail F, Pasqualetti F, Litt B, Bassett DS Proceedings of the National Academy of Sciences of the United States of America 33495341 Proc Natl Acad Sci U S A 2021 Feb 2
Implanting intracranial electrodes does not affect spikes or network connectivity in nearby or connected brain regions. Conrad EC, Shinohara RT, Gugger JJ, Revell AY, Das S, Stein JM, Marsh ED, Davis KA, Litt B Network neuroscience (Cambridge, Mass.) 36607198 Netw Neurosci 2022 Jul
Quantifying trial-by-trial variability during cortico-cortical evoked potential mapping of epileptogenic tissue. Cornblath EJ, Lucas A, Armstrong C, Greenblatt AS, Stein JM, Hadar PN, Raghupathi R, Marsh E, Litt B, Davis KA, Conrad EC Epilepsia 36728906 Epilepsia 2023 Apr
Addressing spatial bias in intracranial EEG functional connectivity analyses for epilepsy surgical planning. Conrad EC, Bernabei JM, Sinha N, Ghosn NJ, Stein JM, Shinohara RT, Litt B Journal of neural engineering 36084621 J Neural Eng 2022 Sep 23
A Full-Stack Application for Detecting Seizures and Reducing Data During Continuous Electroencephalogram Monitoring. Bernabei JM, Owoputi O, Small SD, Nyema NT, Dumenyo E, Kim J, Baldassano SN, Painter C, Conrad EC, Ganguly TM, Balu R, Davis KA, Levine JM, Pathmanathan J, Litt B Critical care explorations 34278312 Crit Care Explor 2021 Jul
Clinical signatures of genetic epilepsies precede diagnosis in electronic medical records of 32,000 individuals. Galer PD, Parthasarathy S, Xian J, McKee JL, Ruggiero SM, Ganesan S, Kaufman MC, Cohen SR, Haag S, Chen C, Ojemann WKS, Kim D, Wilmarth O, Vaidiswaran P, Sederman C, Ellis CA, Gonzalez AK, Boßelmann CM, Lal D, Sederman R, Lewis-Smith D, Litt B, Helbig I Genetics in medicine : official journal of the American College of Medical Genetics 39011766 Genet Med 2024 Nov
On-Demand Seizures Facilitate Rapid Screening of Therapeutics for Epilepsy. Chen Y, Litt B, Vitale F, Takano H bioRxiv : the preprint server for biology 39464023 bioRxiv 2024 Oct 15
Electrocorticography and stereo EEG provide distinct measures of brain connectivity: implications for network models. Bernabei JM, Arnold TC, Shah P, Revell A, Ong IZ, Kini LG, Stein JM, Shinohara RT, Lucas TH, Davis KA, Bassett DS, Litt B Brain communications 34396112 Brain Commun 2021
Normative intracranial EEG maps epileptogenic tissues in focal epilepsy. Bernabei JM, Sinha N, Arnold TC, Conrad E, Ong I, Pattnaik AR, Stein JM, Shinohara RT, Lucas TH, Bassett DS, Davis KA, Litt B Brain : a journal of neurology 35640886 Brain 2022 Jun 30
Sensitivity of portable low-field magnetic resonance imaging for multiple sclerosis lesions. Arnold TC, Tu D, Okar SV, Nair G, By S, Kawatra KD, Robert-Fitzgerald TE, Desiderio LM, Schindler MK, Shinohara RT, Reich DS, Stein JM NeuroImage. Clinical 35792417 Neuroimage Clin 2022
Model-based design for seizure control by stimulation. Ashourvan A, Pequito S, Khambhati AN, Mikhail F, Baldassano SN, Davis KA, Lucas TH, Vettel JM, Litt B, Pappas GJ, Bassett DS Journal of neural engineering 32103826 J Neural Eng 2020 Mar 26
Simulated diagnostic performance of low-field MRI: Harnessing open-access datasets to evaluate novel devices. Arnold TC, Baldassano SN, Litt B, Stein JM Magnetic resonance imaging 34968700 Magn Reson Imaging 2022 Apr
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Solving brain circuit function and dysfunction with computational modeling and optogenetic fMRI. Lee JH, Liu Q, Dadgar-Kiani E Science (New York, N.Y.) 36327349 Science 2022 Nov 4
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In patients with late-life depression and cognitive decline, adding tDCS to cognitive training does not significantly affect depressive symptoms but shows potential benefits on cognition as measured by fMRI. Ha J, Fang Y, Cron GO, Heo J, Jung E, Lee D, Kim H, Kim E, Park JY, Lee JH Brain stimulation 38367933 Brain Stimul 2024 Mar-Apr
Quantitative 3D histochemistry reveals region-specific amyloid-β reduction by the antidiabetic drug netoglitazone. Catto F, Dadgar-Kiani E, Kirschenbaum D, Economides A, Reuss AM, Trevisan C, Caredio D, Mirzet D, Frick L, Weber-Stadlbauer U, Litvinov S, Koumoutsakos P, Hyung Lee J, Aguzzi A bioRxiv : the preprint server for biology 39185170 bioRxiv 2024 Aug 17
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A genetically encoded tool for reconstituting synthetic modulatory neurotransmission and reconnect neural circuits in vivo. Hawk JD, Wisdom EM, Sengupta T, Kashlan ZD, Colón-Ramos DA Nature communications 34373460 Nat Commun 2021 Aug 9
Local and dynamic regulation of neuronal glycolysis in vivo. Wolfe AD, Koberstein JN, Smith CB, Stewart ML, Hammarlund M, Hyman A, Stork PJ, Goodman R, Colón-Ramos DA bioRxiv : the preprint server for biology 37662365 bioRxiv 2023 Aug 26
Transforming the development and dissemination of cutting-edge microscopy and computation. Colón-Ramos DA, La Riviere P, Shroff H, Oldenbourg R Nature methods 31363203 Nat Methods 2019 Aug
Structural and developmental principles of neuropil assembly in C. elegans. Moyle MW, Barnes KM, Kuchroo M, Gonopolskiy A, Duncan LH, Sengupta T, Shao L, Guo M, Santella A, Christensen R, Kumar A, Wu Y, Moon KR, Wolf G, Krishnaswamy S, Bao Z, Shroff H, Mohler WA, Colón-Ramos DA Nature 33627875 Nature 2021 Mar
The active zone protein Clarinet regulates synaptic sorting of ATG-9 and presynaptic autophagy. Xuan Z, Yang S, Clark B, Hill SE, Manning L, Colón-Ramos DA PLoS biology 37053235 PLoS Biol 2023 Apr
Programmed Cell Death Modifies Neural Circuits and Tunes Intrinsic Behavior. Kochersberger A, Torkashvand MM, Lee D, Baskoylu S, Sengupta T, Koonce N, Emerson CE, Patel NV, Colón-Ramos D, Flavell S, Horvitz HR, Venkatachalam V, Hammarlund M bioRxiv : the preprint server for biology 37745399 bioRxiv 2023 Sep 25
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Sleep Analysis in Adult C. elegans Reveals State-Dependent Alteration of Neural and Behavioral Responses. Lawler DE, Chew YL, Hawk JD, Aljobeh A, Schafer WR, Albrecht DR The Journal of neuroscience : the official journal of the Society for Neuroscience 33446520 J Neurosci 2021 Mar 3
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A muscle-epidermis-glia signaling axis sustains synaptic specificity during allometric growth in Caenorhabditis elegans. Fan J, Ji T, Wang K, Huang J, Wang M, Manning L, Dong X, Shi Y, Zhang X, Shao Z, Colón-Ramos DA eLife 32255430 Elife 2020 Apr 7
Deep learning-based aberration compensation improves contrast and resolution in fluorescence microscopy. Guo M, Wu Y, Hobson CM, Su Y, Qian S, Krueger E, Christensen R, Kroeschell G, Bui J, Chaw M, Zhang L, Liu J, Hou X, Han X, Lu Z, Ma X, Zhovmer A, Combs C, Moyle M, Yemini E, Liu H, Liu Z, Benedetto A, La Riviere P, Colón-Ramos D, Shroff H bioRxiv : the preprint server for biology 37986950 bioRxiv 2024 Jul 15
NeuroSCAN: Exploring Neurodevelopment via Spatiotemporal Collation of Anatomical Networks. Koonce NL, Emerson SE, Bhaskar D, Kuchroo M, Moyle MW, Arroyo-Morales P, Martínez NV, Krishnaswamy S, Mohler W, Colón-Ramos D bioRxiv : the preprint server for biology 39484462 bioRxiv 2024 Oct 24
Configuration of electrical synapses filters sensory information to drive behavioral choices. Almoril-Porras A, Calvo AC, Niu L, Beagan J, Díaz García M, Hawk JD, Aljobeh A, Wisdom EM, Ren I, Wang ZW, Colón-Ramos DA Cell 39742807 Cell 2025 Jan 9
Phosphofructokinase relocalizes into subcellular compartments with liquid-like properties in vivo. Jang S, Xuan Z, Lagoy RC, Jawerth LM, Gonzalez IJ, Singh M, Prashad S, Kim HS, Patel A, Albrecht DR, Hyman AA, Colón-Ramos DA Biophysical journal 32853565 Biophys J 2021 Apr 6
Presynaptic autophagy is coupled to the synaptic vesicle cycle via ATG-9. Yang S, Park D, Manning L, Hill SE, Cao M, Xuan Z, Gonzalez I, Dong Y, Clark B, Shao L, Okeke I, Almoril-Porras A, Bai J, De Camilli P, Colón-Ramos DA Neuron 35065714 Neuron 2022 Mar 2
Antagonism between neuropeptides and monoamines in a distributed circuit for pathogen avoidance. Marquina-Solis J, Feng L, Vandewyer E, Beets I, Hawk J, Colón-Ramos DA, Yu J, Fox BW, Schroeder FC, Bargmann CI Cell reports 38573858 Cell Rep 2024 Apr 23
The active zone protein CLA-1 (Clarinet) bridges two subsynaptic domains to regulate presynaptic sorting of ATG-9. Xuan Z, Colón-Ramos DA Autophagy 37389488 Autophagy 2023 Oct
Specific configurations of electrical synapses filter sensory information to drive choices in behavior. Almoril-Porras A, Calvo AC, Niu L, Beagan J, Hawk JD, Aljobeh A, Wisdom EM, Ren I, Díaz-García M, Wang ZW, Colón-Ramos DA bioRxiv : the preprint server for biology 37577611 bioRxiv 2023 Aug 3
Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics. Bedbrook CN, Yang KK, Robinson JE, Mackey ED, Gradinaru V, Arnold FH Nature methods 31611694 Nat Methods 2019 Nov
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates. Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan EE, Huang SF, Ravindra Kumar S, Arokiaraj CM, Plattner VM, Campos LJ, Mich JK, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore BB, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V Nature communications 37291094 Nat Commun 2023 Jun 8
Primate-conserved carbonic anhydrase IV and murine-restricted LY6C1 enable blood-brain barrier crossing by engineered viral vectors. Shay TF, Sullivan EE, Ding X, Chen X, Ravindra Kumar S, Goertsen D, Brown D, Crosby A, Vielmetter J, Borsos M, Wolfe DA, Lam AW, Gradinaru V Science advances 37075114 Sci Adv 2023 Apr 21
Engineered AAVs for non-invasive gene delivery to rodent and non-human primate nervous systems. Chen X, Ravindra Kumar S, Adams CD, Yang D, Wang T, Wolfe DA, Arokiaraj CM, Ngo V, Campos LJ, Griffiths JA, Ichiki T, Mazmanian SK, Osborne PB, Keast JR, Miller CT, Fox AS, Chiu IM, Gradinaru V Neuron 35643078 Neuron 2022 Jul 20
Spatial transcriptomics for profiling the tropism of viral vectors in tissues. Jang MJ, Coughlin GM, Jackson CR, Chen X, Chuapoco MR, Vendemiatti JL, Wang AZ, Gradinaru V Nature biotechnology 36702899 Nat Biotechnol 2023 Sep
Adeno-associated viral vectors for functional intravenous gene transfer throughout the non-human primate brain. Chuapoco MR, Flytzanis NC, Goeden N, Christopher Octeau J, Roxas KM, Chan KY, Scherrer J, Winchester J, Blackburn RJ, Campos LJ, Man KNM, Sun J, Chen X, Lefevre A, Singh VP, Arokiaraj CM, Shay TF, Vendemiatti J, Jang MJ, Mich JK, Bishaw Y, Gore BB, Omstead V, Taskin N, Weed N, Levi BP, Ting JT, Miller CT, Deverman BE, Pickel J, Tian L, Fox AS, Gradinaru V Nature nanotechnology 37430038 Nat Nanotechnol 2023 Oct
Multiplexed Cre-dependent selection yields systemic AAVs for targeting distinct brain cell types. Ravindra Kumar S, Miles TF, Chen X, Brown D, Dobreva T, Huang Q, Ding X, Luo Y, Einarsson PH, Greenbaum A, Jang MJ, Deverman BE, Gradinaru V Nature methods 32313222 Nat Methods 2020 May
Functional gene delivery to and across brain vasculature of systemic AAVs with endothelial-specific tropism in rodents and broad tropism in primates. Chen X, Wolfe DA, Bindu DS, Zhang M, Taskin N, Goertsen D, Shay TF, Sullivan E, Huang SF, Kumar SR, Arokiaraj CM, Plattner V, Campos LJ, Mich J, Monet D, Ngo V, Ding X, Omstead V, Weed N, Bishaw Y, Gore B, Lein ES, Akrami A, Miller C, Levi BP, Keller A, Ting JT, Fox AS, Eroglu C, Gradinaru V bioRxiv : the preprint server for biology 36711773 bioRxiv 2023 Jan 13
Human cell surface-AAV interactomes identify LRP6 as blood-brain barrier transcytosis receptor and immune cytokine IL3 as AAV9 binder. Shay TF, Jang S, Brittain TJ, Chen X, Walker B, Tebbutt C, Fan Y, Wolfe DA, Arokiaraj CM, Sullivan EE, Ding X, Wang TY, Lei Y, Chuapoco MR, Chou TF, Gradinaru V Nature communications 39245720 Nat Commun 2024 Sep 8
Synaptic Communication in Brain Cancer. Monje M Cancer research 32381657 Cancer Res 2020 Jul 15
Activity Shapes Neural Circuit Form and Function: A Historical Perspective. Pan Y, Monje M The Journal of neuroscience : the official journal of the Society for Neuroscience 31996470 J Neurosci 2020 Jan 29
Diffuse intrinsic pontine glioma: molecular landscape and emerging therapeutic targets. Aziz-Bose R, Monje M Current opinion in oncology 31464759 Curr Opin Oncol 2019 Nov
Electrical and synaptic integration of glioma into neural circuits. Venkatesh HS, Morishita W, Geraghty AC, Silverbush D, Gillespie SM, Arzt M, Tam LT, Espenel C, Ponnuswami A, Ni L, Woo PJ, Taylor KR, Agarwal A, Regev A, Brang D, Vogel H, Hervey-Jumper S, Bergles DE, Suvà ML, Malenka RC, Monje M Nature 31534222 Nature 2019 Sep
Mild respiratory COVID can cause multi-lineage neural cell and myelin dysregulation. Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, O'Dea MR, Dutton S, Shamardani K, Nwangwu K, Mancusi R, Yalçın B, Taylor KR, Acosta-Alvarez L, Malacon K, Keough MB, Ni L, Woo PJ, Contreras-Esquivel D, Toland AMS, Gehlhausen JR, Klein J, Takahashi T, Silva J, Israelow B, Lucas C, Mao T, Peña-Hernández MA, Tabachnikova A, Homer RJ, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Vogel H, Hefti MM, Perl DP, Liddelow S, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M Cell 35768006 Cell 2022 Jul 7
Neural Signaling in Cancer. Keough MB, Monje M Annual review of neuroscience 35259916 Annu Rev Neurosci 2022 Jul 8
Microenvironmental interactions of oligodendroglial cells. Yalçın B, Monje M Developmental cell 34192527 Dev Cell 2021 Jul 12
Glioblastoma remodelling of human neural circuits decreases survival. Krishna S, Choudhury A, Keough MB, Seo K, Ni L, Kakaizada S, Lee A, Aabedi A, Popova G, Lipkin B, Cao C, Nava Gonzales C, Sudharshan R, Egladyous A, Almeida N, Zhang Y, Molinaro AM, Venkatesh HS, Daniel AGS, Shamardani K, Hyer J, Chang EF, Findlay A, Phillips JJ, Nagarajan S, Raleigh DR, Brang D, Monje M, Hervey-Jumper SL Nature 37138086 Nature 2023 May
Loss of Adaptive Myelination Contributes to Methotrexate Chemotherapy-Related Cognitive Impairment. Geraghty AC, Gibson EM, Ghanem RA, Greene JJ, Ocampo A, Goldstein AK, Ni L, Yang T, Marton RM, Paşca SP, Greenberg ME, Longo FM, Monje M Neuron 31122677 Neuron 2019 Jul 17
Diffuse Intrinsic Pontine Glioma: From Diagnosis to Next-Generation Clinical Trials. Vitanza NA, Monje M Current treatment options in neurology 31290035 Curr Treat Options Neurol 2019 Jul 10
A prognostic neural epigenetic signature in high-grade glioma. Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann JE, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Göller PC, Sahm F, Menstel JA, Zimmer DN, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL Nature medicine 38760585 Nat Med 2024 Jun
Remote neuronal activity drives glioma infiltration via Sema4f. Huang-Hobbs E, Cheng YT, Ko Y, Luna-Figueroa E, Lozzi B, Taylor KR, McDonald M, He P, Chen HC, Yang Y, Maleki E, Lee ZF, Murali S, Williamson M, Choi D, Curry R, Bayley J, Woo J, Jalali A, Monje M, Noebels JL, Harmanci AS, Rao G, Deneen B bioRxiv : the preprint server for biology 36993539 bioRxiv 2023 Mar 16
Cancer hallmarks intersect with neuroscience in the tumor microenvironment. Hanahan D, Monje M Cancer cell 36917953 Cancer Cell 2023 Mar 13
Glioma synapses recruit mechanisms of adaptive plasticity. Taylor KR, Barron T, Hui A, Spitzer A, Yalçin B, Ivec AE, Geraghty AC, Hartmann GG, Arzt M, Gillespie SM, Kim YS, Maleki Jahan S, Zhang H, Shamardani K, Su M, Ni L, Du PP, Woo PJ, Silva-Torres A, Venkatesh HS, Mancusi R, Ponnuswami A, Mulinyawe S, Keough MB, Chau I, Aziz-Bose R, Tirosh I, Suvà ML, Monje M Nature 37914930 Nature 2023 Nov
Cholinergic Neuronal Activity Promotes Diffuse Midline Glioma Growth through Muscarinic Signaling. Drexler R, Drinnenberg A, Gavish A, Yalcin B, Shamardani K, Rogers A, Mancusi R, Taylor KR, Kim YS, Woo PJ, Ravel A, Tatlock E, Ramakrishnan C, Ayala-Sarmiento AE, Pacheco DRF, Siverts L, Daigle TL, Tasic B, Zeng H, Breunig JJ, Deisseroth K, Monje M bioRxiv : the preprint server for biology 39386427 bioRxiv 2024 Sep 24
Therapeutic strategies for diffuse midline glioma from high-throughput combination drug screening. Lin GL, Wilson KM, Ceribelli M, Stanton BZ, Woo PJ, Kreimer S, Qin EY, Zhang X, Lennon J, Nagaraja S, Morris PJ, Quezada M, Gillespie SM, Duveau DY, Michalowski AM, Shinn P, Guha R, Ferrer M, Klumpp-Thomas C, Michael S, McKnight C, Minhas P, Itkin Z, Raabe EH, Chen L, Ghanem R, Geraghty AC, Ni L, Andreasson KI, Vitanza NA, Warren KE, Thomas CJ, Monje M Science translational medicine 31748226 Sci Transl Med 2019 Nov 20
Histone Variant and Cell Context Determine H3K27M Reprogramming of the Enhancer Landscape and Oncogenic State. Nagaraja S, Quezada MA, Gillespie SM, Arzt M, Lennon JJ, Woo PJ, Hovestadt V, Kambhampati M, Filbin MG, Suva ML, Nazarian J, Monje M Molecular cell 31588023 Mol Cell 2019 Dec 19
The bright and the dark side of myelin plasticity: Neuron-glial interactions in health and disease. Monje M, Káradóttir RT Seminars in cell & developmental biology 33293232 Semin Cell Dev Biol 2021 Aug
Microglia in Cancer Therapy-Related Cognitive Impairment. Gibson EM, Monje M Trends in neurosciences 33674135 Trends Neurosci 2021 Jun
The neurobiology of long COVID. Monje M, Iwasaki A Neuron 36288726 Neuron 2022 Nov 2
Neuronal hyperexcitability drives central and peripheral nervous system tumor progression in models of neurofibromatosis-1. Anastasaki C, Mo J, Chen JK, Chatterjee J, Pan Y, Scheaffer SM, Cobb O, Monje M, Le LQ, Gutmann DH Nature communications 35589737 Nat Commun 2022 May 19
GD2-CAR T cell therapy for H3K27M-mutated diffuse midline gliomas. Majzner RG, Ramakrishna S, Yeom KW, Patel S, Chinnasamy H, Schultz LM, Richards RM, Jiang L, Barsan V, Mancusi R, Geraghty AC, Good Z, Mochizuki AY, Gillespie SM, Toland AMS, Mahdi J, Reschke A, Nie EH, Chau IJ, Rotiroti MC, Mount CW, Baggott C, Mavroukakis S, Egeler E, Moon J, Erickson C, Green S, Kunicki M, Fujimoto M, Ehlinger Z, Reynolds W, Kurra S, Warren KE, Prabhu S, Vogel H, Rasmussen L, Cornell TT, Partap S, Fisher PG, Campen CJ, Filbin MG, Grant G, Sahaf B, Davis KL, Feldman SA, Mackall CL, Monje M Nature 35130560 Nature 2022 Mar
Mild respiratory SARS-CoV-2 infection can cause multi-lineage cellular dysregulation and myelin loss in the brain. Fernández-Castañeda A, Lu P, Geraghty AC, Song E, Lee MH, Wood J, Yalçın B, Taylor KR, Dutton S, Acosta-Alvarez L, Ni L, Contreras-Esquivel D, Gehlhausen JR, Klein J, Lucas C, Mao T, Silva J, Peña-Hernández MA, Tabachnikova A, Takahashi T, Tabacof L, Tosto-Mancuso J, Breyman E, Kontorovich A, McCarthy D, Quezado M, Hefti M, Perl D, Folkerth R, Putrino D, Nath A, Iwasaki A, Monje M bioRxiv : the preprint server for biology 35043113 bioRxiv 2022 Jan 10
The landscape of tumor cell states and spatial organization in H3-K27M mutant diffuse midline glioma across age and location. Liu I, Jiang L, Samuelsson ER, Marco Salas S, Beck A, Hack OA, Jeong D, Shaw ML, Englinger B, LaBelle J, Mire HM, Madlener S, Mayr L, Quezada MA, Trissal M, Panditharatna E, Ernst KJ, Vogelzang J, Gatesman TA, Halbert ME, Palova H, Pokorna P, Sterba J, Slaby O, Geyeregger R, Diaz A, Findlay IJ, Dun MD, Resnick A, Suvà ML, Jones DTW, Agnihotri S, Svedlund J, Koschmann C, Haberler C, Czech T, Slavc I, Cotter JA, Ligon KL, Alexandrescu S, Yung WKA, Arrillaga-Romany I, Gojo J, Monje M, Nilsson M, Filbin MG Nature genetics 36471067 Nat Genet 2022 Dec
The neuroscience of cancer. Mancusi R, Monje M Nature 37316719 Nature 2023 Jun
Haploinsufficiency of NFKBIA reshapes the epigenome antipodal to the IDH mutation and imparts disease fate in diffuse gliomas. Bredel M, Espinosa L, Kim H, Scholtens DM, McElroy JP, Rajbhandari R, Meng W, Kollmeyer TM, Malta TM, Quezada MA, Harsh GR, Lobo-Jarne T, Solé L, Merati A, Nagaraja S, Nair S, White JJ, Thudi NK, Fleming JL, Webb A, Natsume A, Ogawa S, Weber RG, Bertran J, Haque SJ, Hentschel B, Miller CR, Furnari FB, Chan TA, Grosu AL, Weller M, Barnholtz-Sloan JS, Monje M, Noushmehr H, Jenkins RB, Rogers CL, MacDonald DR, Pugh SL, Chakravarti A Cell reports. Medicine 37343523 Cell Rep Med 2023 Jun 20
Tumor inflammation-associated neurotoxicity. Mahdi J, Dietrich J, Straathof K, Roddie C, Scott BJ, Davidson TB, Prolo LM, Batchelor TT, Campen CJ, Davis KL, Gust J, Lim M, Majzner RG, Park JR, Partap S, Ramakrishna S, Richards R, Schultz L, Vitanza NA, Wang LD, Mackall CL, Monje M Nature medicine 37024595 Nat Med 2023 Apr
Cancer neuroscience: State of the field, emerging directions. Winkler F, Venkatesh HS, Amit M, Batchelor T, Demir IE, Deneen B, Gutmann DH, Hervey-Jumper S, Kuner T, Mabbott D, Platten M, Rolls A, Sloan EK, Wang TC, Wick W, Venkataramani V, Monje M Cell 37059069 Cell 2023 Apr 13
Neuron-oligodendroglial interactions in health and malignant disease. Taylor KR, Monje M Nature reviews. Neuroscience 37857838 Nat Rev Neurosci 2023 Dec
NF1 mutation drives neuronal activity-dependent initiation of optic glioma. Pan Y, Hysinger JD, Barron T, Schindler NF, Cobb O, Guo X, Yalçın B, Anastasaki C, Mulinyawe SB, Ponnuswami A, Scheaffer S, Ma Y, Chang KC, Xia X, Toonen JA, Lennon JJ, Gibson EM, Huguenard JR, Liau LM, Goldberg JL, Monje M, Gutmann DH Nature 34040258 Nature 2021 Jun
Monosynaptic tracing maps brain-wide afferent oligodendrocyte precursor cell connectivity. Mount CW, Yalçın B, Cunliffe-Koehler K, Sundaresh S, Monje M eLife 31625910 Elife 2019 Oct 18
Epigenetic neural glioblastoma enhances synaptic integration and predicts therapeutic vulnerability. Drexler R, Khatri R, Sauvigny T, Mohme M, Maire CL, Ryba A, Zghaibeh Y, Dührsen L, Salviano-Silva A, Lamszus K, Westphal M, Gempt J, Wefers AK, Neumann J, Bode H, Hausmann F, Huber TB, Bonn S, Jütten K, Delev D, Weber KJ, Harter PN, Onken J, Vajkoczy P, Capper D, Wiestler B, Weller M, Snijder B, Buck A, Weiss T, Keough MB, Ni L, Monje M, Silverbush D, Hovestadt V, Suvà ML, Krishna S, Hervey-Jumper SL, Schüller U, Heiland DH, Hänzelmann S, Ricklefs FL bioRxiv : the preprint server for biology 37609137 bioRxiv 2023 Aug 7
Developmental origins and emerging therapeutic opportunities for childhood cancer. Filbin M, Monje M Nature medicine 30842674 Nat Med 2019 Mar
Maladaptive myelination promotes generalized epilepsy progression. Knowles JK, Xu H, Soane C, Batra A, Saucedo T, Frost E, Tam LT, Fraga D, Ni L, Villar K, Talmi S, Huguenard JR, Monje M Nature neuroscience 35501379 Nat Neurosci 2022 May
Immunotherapy-related cognitive impairment after CAR T cell therapy in mice. Geraghty AC, Acosta-Alvarez L, Rotiroti M, Dutton S, O'Dea MR, Woo PJ, Xu H, Shamardani K, Mancusi R, Ni L, Mulinyawe SB, Kim WJ, Liddelow SA, Majzner RG, Monje M bioRxiv : the preprint server for biology 38798554 bioRxiv 2024 May 14
Nf1 mutation disrupts activity-dependent oligodendroglial plasticity and motor learning in mice. Pan Y, Hysinger JD, Yalçın B, Lennon JJ, Byun YG, Raghavan P, Schindler NF, Anastasaki C, Chatterjee J, Ni L, Xu H, Malacon K, Jahan SM, Ivec AE, Aghoghovwia BE, Mount CW, Nagaraja S, Scheaffer S, Attardi LD, Gutmann DH, Monje M Nature neuroscience 38816530 Nat Neurosci 2024 Aug
Emerging mechanistic underpinnings and therapeutic targets for chemotherapy-related cognitive impairment. Gibson EM, Monje M Current opinion in oncology 31449084 Curr Opin Oncol 2019 Nov
Transition to a mesenchymal state in neuroblastoma confers resistance to anti-GD2 antibody via reduced expression of ST8SIA1. Mabe NW, Huang M, Dalton GN, Alexe G, Schaefer DA, Geraghty AC, Robichaud AL, Conway AS, Khalid D, Mader MM, Belk JA, Ross KN, Sheffer M, Linde MH, Ly N, Yao W, Rotiroti MC, Smith BAH, Wernig M, Bertozzi CR, Monje M, Mitsiades CS, Majeti R, Satpathy AT, Stegmaier K, Majzner RG Nature cancer 35817829 Nat Cancer 2022 Aug
Neuron-Glial Interactions in Health and Brain Cancer. Pan Y, Monje M Advanced biology 35957525 Adv Biol (Weinh) 2022 Sep
Roadmap for the Emerging Field of Cancer Neuroscience. Monje M, Borniger JC, D'Silva NJ, Deneen B, Dirks PB, Fattahi F, Frenette PS, Garzia L, Gutmann DH, Hanahan D, Hervey-Jumper SL, Hondermarck H, Hurov JB, Kepecs A, Knox SM, Lloyd AC, Magnon C, Saloman JL, Segal RA, Sloan EK, Sun X, Taylor MD, Tracey KJ, Trotman LC, Tuveson DA, Wang TC, White RA, Winkler F Cell 32302564 Cell 2020 Apr 16
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Bright quantum dots emitting at ∼1,600 nm in the NIR-IIb window for deep tissue fluorescence imaging. Zhang M, Yue J, Cui R, Ma Z, Wan H, Wang F, Zhu S, Zhou Y, Kuang Y, Zhong Y, Pang DW, Dai H Proceedings of the National Academy of Sciences of the United States of America 29891702 Proc Natl Acad Sci U S A 2018 Jun 26
Molecular Cancer Imaging in the Second Near-Infrared Window Using a Renal-Excreted NIR-II Fluorophore-Peptide Probe. Wang W, Ma Z, Zhu S, Wan H, Yue J, Ma H, Ma R, Yang Q, Wang Z, Li Q, Qian Y, Yue C, Wang Y, Fan L, Zhong Y, Zhou Y, Gao H, Ruan J, Hu Z, Liang Y, Dai H Advanced materials (Deerfield Beach, Fla.) 29682821 Adv Mater 2018 May
Developing a Bright NIR-II Fluorophore with Fast Renal Excretion and Its Application in Molecular Imaging of Immune Checkpoint PD-L1. Wan H, Ma H, Zhu S, Wang F, Tian Y, Ma R, Yang Q, Hu Z, Zhu T, Wang W, Ma Z, Zhang M, Zhong Y, Sun H, Liang Y, Dai H Advanced functional materials 31832053 Adv Funct Mater 2018 Dec 12
Near-Infrared IIb Fluorescence Imaging of Vascular Regeneration with Dynamic Tissue Perfusion Measurement and High Spatial Resolution. Ma Z, Zhang M, Yue J, Alcazar C, Zhong Y, Doyle TC, Dai H, Huang NF Advanced functional materials 31327961 Adv Funct Mater 2018 Sep 5
Phosphorylcholine-conjugated gold-molecular clusters improve signal for Lymph Node NIR-II fluorescence imaging in preclinical cancer models. Baghdasaryan A, Wang F, Ren F, Ma Z, Li J, Zhou X, Grigoryan L, Xu C, Dai H Nature communications 36153336 Nat Commun 2022 Sep 24
A SARS-CoV-2 vaccine on an NIR-II/SWIR emitting nanoparticle platform. Jiang Y, Sanyal M, Hussein NA, Baghdasaryan A, Zhang M, Wang F, Ren F, Li J, Zhu G, Meng Y, Adamska JZ, Mellins E, Dai H Science advances 39919189 Sci Adv 2025 Feb 7
Rational Design of Molecular Fluorophores for Biological Imaging in the NIR-II Window. Yang Q, Ma Z, Wang H, Zhou B, Zhu S, Zhong Y, Wang J, Wan H, Antaris A, Ma R, Zhang X, Yang J, Zhang X, Sun H, Liu W, Liang Y, Dai H Advanced materials (Deerfield Beach, Fla.) 28117499 Adv Mater 2017 Mar
A high quantum yield molecule-protein complex fluorophore for near-infrared II imaging. Antaris AL, Chen H, Diao S, Ma Z, Zhang Z, Zhu S, Wang J, Lozano AX, Fan Q, Chew L, Zhu M, Cheng K, Hong X, Dai H, Cheng Z Nature communications 28524850 Nat Commun 2017 May 19
A mini-review on rare-earth down-conversion nanoparticles for NIR-II imaging of biological systems. Zhong Y, Dai H Nano research 34336144 Nano Res 2020 May
High-precision tumor resection down to few-cell level guided by NIR-IIb molecular fluorescence imaging. Wang F, Qu L, Ren F, Baghdasaryan A, Jiang Y, Hsu R, Liang P, Li J, Zhu G, Ma Z, Dai H Proceedings of the National Academy of Sciences of the United States of America 35380898 Proc Natl Acad Sci U S A 2022 Apr 12
A theranostic agent for cancer therapy and imaging in the second near-infrared window. Ma Z, Wan H, Wang W, Zhang X, Uno T, Yang Q, Yue J, Gao H, Zhong Y, Tian Y, Sun Q, Liang Y, Dai H Nano research 31832124 Nano Res 2019 Feb
In vivo non-invasive confocal fluorescence imaging beyond 1,700 nm using superconducting nanowire single-photon detectors. Wang F, Ren F, Ma Z, Qu L, Gourgues R, Xu C, Baghdasaryan A, Li J, Zadeh IE, Los JWN, Fognini A, Qin-Dregely J, Dai H Nature nanotechnology 35606441 Nat Nanotechnol 2022 Jun
Deep learning for in vivo near-infrared imaging. Ma Z, Wang F, Wang W, Zhong Y, Dai H Proceedings of the National Academy of Sciences of the United States of America 33372162 Proc Natl Acad Sci U S A 2021 Jan 5
Live imaging of follicle stimulating hormone receptors in gonads and bones using near infrared II fluorophore. Feng Y, Zhu S, Antaris AL, Chen H, Xiao Y, Lu X, Jiang L, Diao S, Yu K, Wang Y, Herraiz S, Yue J, Hong X, Hong G, Cheng Z, Dai H, Hsueh AJ Chemical science 28626555 Chem Sci 2017 May 1
In vivo NIR-II structured-illumination light-sheet microscopy. Wang F, Ma Z, Zhong Y, Salazar F, Xu C, Ren F, Qu L, Wu AM, Dai H Proceedings of the National Academy of Sciences of the United States of America 33526701 Proc Natl Acad Sci U S A 2021 Feb 9
Near-Infrared-II Molecular Dyes for Cancer Imaging and Surgery. Zhu S, Tian R, Antaris AL, Chen X, Dai H Advanced materials (Deerfield Beach, Fla.) 31025403 Adv Mater 2019 Jun
Light-sheet microscopy in the near-infrared II window. Wang F, Wan H, Ma Z, Zhong Y, Sun Q, Tian Y, Qu L, Du H, Zhang M, Li L, Ma H, Luo J, Liang Y, Li WJ, Hong G, Liu L, Dai H Nature methods 31086342 Nat Methods 2019 Jun
A bright organic NIR-II nanofluorophore for three-dimensional imaging into biological tissues. Wan H, Yue J, Zhu S, Uno T, Zhang X, Yang Q, Yu K, Hong G, Wang J, Li L, Ma Z, Gao H, Zhong Y, Su J, Antaris AL, Xia Y, Luo J, Liang Y, Dai H Nature communications 29563581 Nat Commun 2018 Mar 21
Molecular imaging in the second near-infrared window. Wan H, Du H, Wang F, Dai H Advanced functional materials 31885529 Adv Funct Mater 2019 Jun 21
Intratumor injected gold molecular clusters for NIR-II imaging and cancer therapy. Baghdasaryan A, Liu H, Ren F, Hsu R, Jiang Y, Wang F, Zhang M, Grigoryan L, Dai H Proceedings of the National Academy of Sciences of the United States of America 38261618 Proc Natl Acad Sci U S A 2024 Jan 30
Structure-Specific Cleavage of an RNA Repeat Expansion with a Dimeric Small Molecule Is Advantageous over Sequence-Specific Recognition by an Oligonucleotide. Benhamou RI, Angelbello AJ, Andrews RJ, Wang ET, Moss WN, Disney MD ACS chemical biology 31927948 ACS Chem Biol 2020 Feb 21
Target-Directed Approaches for Screening Small Molecules against RNA Targets. Haniff HS, Knerr L, Chen JL, Disney MD, Lightfoot HL SLAS discovery : advancing life sciences R & D 32419578 SLAS Discov 2020 Sep
Using Genome Sequence to Enable the Design of Medicines and Chemical Probes. Angelbello AJ, Chen JL, Childs-Disney JL, Zhang P, Wang ZF, Disney MD Chemical reviews 29322778 Chem Rev 2018 Feb 28
Precise small-molecule cleavage of an r(CUG) repeat expansion in a myotonic dystrophy mouse model. Angelbello AJ, Rzuczek SG, Mckee KK, Chen JL, Olafson H, Cameron MD, Moss WN, Wang ET, Disney MD Proceedings of the National Academy of Sciences of the United States of America 30926669 Proc Natl Acad Sci U S A 2019 Apr 16
Targeted Degradation of a Hypoxia-Associated Non-coding RNA Enhances the Selectivity of a Small Molecule Interacting with RNA. Costales MG, Suresh B, Vishnu K, Disney MD Cell chemical biology 31130520 Cell Chem Biol 2019 Aug 15
A Small Molecule that Binds an RNA Repeat Expansion Stimulates Its Decay via the Exosome Complex. Angelbello AJ, Benhamou RI, Rzuczek SG, Choudhary S, Tang Z, Chen JL, Roy M, Wang KW, Yildirim I, Jun AS, Thornton CA, Disney MD Cell chemical biology 33157036 Cell Chem Biol 2021 Jan 21
Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD. Ursu A, Wang KW, Bush JA, Choudhary S, Chen JL, Baisden JT, Zhang YJ, Gendron TF, Petrucelli L, Yildirim I, Disney MD ACS chemical biology 33196168 ACS Chem Biol 2020 Dec 18
Targeting RNA with Small Molecules To Capture Opportunities at the Intersection of Chemistry, Biology, and Medicine. Disney MD Journal of the American Chemical Society 30896935 J Am Chem Soc 2019 May 1
Small molecule targeting of RNA structures in neurological disorders. Angelbello AJ, Chen JL, Disney MD Annals of the New York Academy of Sciences 30964958 Ann N Y Acad Sci 2020 Jul
Fragment-Based Approaches to Identify RNA Binders. Suresh BM, Taghavi A, Childs-Disney JL, Disney MD Journal of medicinal chemistry 37186875 J Med Chem 2023 May 25
Development of pharmacophore models for small molecules targeting RNA: Application to the RNA repeat expansion in myotonic dystrophy type 1. Angelbello AJ, González ÀL, Rzuczek SG, Disney MD Bioorganic & medicinal chemistry letters 27839685 Bioorg Med Chem Lett 2016 Dec 1
Rational Design of Small Molecules Targeting Oncogenic Noncoding RNAs from Sequence. Disney MD, Angelbello AJ Accounts of chemical research 27993012 Acc Chem Res 2016 Dec 20
Studying a Drug-like, RNA-Focused Small Molecule Library Identifies Compounds That Inhibit RNA Toxicity in Myotonic Dystrophy. Rzuczek SG, Southern MR, Disney MD ACS chemical biology 26414664 ACS Chem Biol 2015 Dec 18
Small Molecule Recognition and Tools to Study Modulation of r(CGG)(exp) in Fragile X-Associated Tremor Ataxia Syndrome. Yang WY, He F, Strack RL, Oh SY, Frazer M, Jaffrey SR, Todd PK, Disney MD ACS chemical biology 27276216 ACS Chem Biol 2016 Sep 16
The RNA encoding the microtubule-associated protein tau has extensive structure that affects its biology. Chen JL, Moss WN, Spencer A, Zhang P, Childs-Disney JL, Disney MD PloS one 31291322 PLoS One 2019
A Toxic RNA Catalyzes the Cellular Synthesis of Its Own Inhibitor, Shunting It to Endogenous Decay Pathways. Benhamou RI, Angelbello AJ, Wang ET, Disney MD Cell chemical biology 31981476 Cell Chem Biol 2020 Feb 20
A blood-brain penetrant RNA-targeted small molecule triggers elimination of r(G(4)C(2))(exp) in c9ALS/FTD via the nuclear RNA exosome. Bush JA, Meyer SM, Fuerst R, Tong Y, Li Y, Benhamou RI, Aikawa H, Zanon PRA, Gibaut QMR, Angelbello AJ, Gendron TF, Zhang YJ, Petrucelli L, Heick Jensen T, Childs-Disney JL, Disney MD Proceedings of the National Academy of Sciences of the United States of America 36409902 Proc Natl Acad Sci U S A 2022 Nov 29
Small molecule alteration of RNA sequence in cells and animals. Guan L, Luo Y, Ja WW, Disney MD Bioorganic & medicinal chemistry letters 29079470 Bioorg Med Chem Lett 2018 Sep 1
Precise small-molecule recognition of a toxic CUG RNA repeat expansion. Rzuczek SG, Colgan LA, Nakai Y, Cameron MD, Furling D, Yasuda R, Disney MD Nature chemical biology 27941760 Nat Chem Biol 2017 Feb
The Hairpin Form of r(G(4)C(2))(exp) in c9ALS/FTD Is Repeat-Associated Non-ATG Translated and a Target for Bioactive Small Molecules. Wang ZF, Ursu A, Childs-Disney JL, Guertler R, Yang WY, Bernat V, Rzuczek SG, Fuerst R, Zhang YJ, Gendron TF, Yildirim I, Dwyer BG, Rice JE, Petrucelli L, Disney MD Cell chemical biology 30503283 Cell Chem Biol 2019 Feb 21
Design, Optimization, and Study of Small Molecules That Target Tau Pre-mRNA and Affect Splicing. Chen JL, Zhang P, Abe M, Aikawa H, Zhang L, Frank AJ, Zembryski T, Hubbs C, Park H, Withka J, Steppan C, Rogers L, Cabral S, Pettersson M, Wager TT, Fountain MA, Rumbaugh G, Childs-Disney JL, Disney MD Journal of the American Chemical Society 32364710 J Am Chem Soc 2020 May 13
Macrocyclization of a Ligand Targeting a Toxic RNA Dramatically Improves Potency. Benhamou RI, Vezina-Dawod S, Choudhary S, Won Wang K, Meyer SM, Yildirim I, Disney MD Chembiochem : a European journal of chemical biology 32649032 Chembiochem 2020 Nov 16
A Toxic RNA Templates the Synthesis of Its Own Fluorogenic Inhibitor by Using a Bio-orthogonal Tetrazine Ligation in Cells and Tissues. Angelbello AJ, Disney MD ACS chemical biology 32551539 ACS Chem Biol 2020 Jul 17
Gini Coefficients as a Single Value Metric to Define Chemical Probe Selectivity. Ursu A, Childs-Disney JL, Angelbello AJ, Costales MG, Meyer SM, Disney MD ACS chemical biology 32568503 ACS Chem Biol 2020 Aug 21
Identifying and validating small molecules interacting with RNA (SMIRNAs). Disney MD, Velagapudi SP, Li Y, Costales MG, Childs-Disney JL Methods in enzymology 31239057 Methods Enzymol 2019
Optimization of the Linker Domain in a Dimeric Compound that Degrades an r(CUG) Repeat Expansion in Cells. Benhamou RI, Abe M, Choudhary S, Meyer SM, Angelbello AJ, Disney MD Journal of medicinal chemistry 32657583 J Med Chem 2020 Jul 23
Methods to identify and optimize small molecules interacting with RNA (SMIRNAs). Ursu A, Vézina-Dawod S, Disney MD Drug discovery today 31356880 Drug Discov Today 2019 Oct
Progress toward the development of the small molecule equivalent of small interfering RNA. Disney MD, Suresh BM, Benhamou RI, Childs-Disney JL Current opinion in chemical biology 32036231 Curr Opin Chem Biol 2020 Jun
Translation of the intrinsically disordered protein α-synuclein is inhibited by a small molecule targeting its structured mRNA. Zhang P, Park HJ, Zhang J, Junn E, Andrews RJ, Velagapudi SP, Abegg D, Vishnu K, Costales MG, Childs-Disney JL, Adibekian A, Moss WN, Mouradian MM, Disney MD Proceedings of the National Academy of Sciences of the United States of America 31900363 Proc Natl Acad Sci U S A 2020 Jan 21
Small molecule recognition of disease-relevant RNA structures. Meyer SM, Williams CC, Akahori Y, Tanaka T, Aikawa H, Tong Y, Childs-Disney JL, Disney MD Chemical Society reviews 32975549 Chem Soc Rev 2020 Oct 5
Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G(4)C(2)) repeat expansion in vitro and in vivo ALS models. Bush JA, Aikawa H, Fuerst R, Li Y, Ursu A, Meyer SM, Benhamou RI, Chen JL, Khan T, Wagner-Griffin S, Van Meter MJ, Tong Y, Olafson H, McKee KK, Childs-Disney JL, Gendron TF, Zhang Y, Coyne AN, Wang ET, Yildirim I, Wang KW, Petrucelli L, Rothstein JD, Disney MD Science translational medicine 34705518 Sci Transl Med 2021 Oct 27
Poly(GP) proteins are a useful pharmacodynamic marker for C9ORF72-associated amyotrophic lateral sclerosis. Gendron TF, Chew J, Stankowski JN, Hayes LR, Zhang YJ, Prudencio M, Carlomagno Y, Daughrity LM, Jansen-West K, Perkerson EA, O'Raw A, Cook C, Pregent L, Belzil V, van Blitterswijk M, Tabassian LJ, Lee CW, Yue M, Tong J, Song Y, Castanedes-Casey M, Rousseau L, Phillips V, Dickson DW, Rademakers R, Fryer JD, Rush BK, Pedraza O, Caputo AM, Desaro P, Palmucci C, Robertson A, Heckman MG, Diehl NN, Wiggs E, Tierney M, Braun L, Farren J, Lacomis D, Ladha S, Fournier CN, McCluskey LF, Elman LB, Toledo JB, McBride JD, Tiloca C, Morelli C, Poletti B, Solca F, Prelle A, Wuu J, Jockel-Balsarotti J, Rigo F, Ambrose C, Datta A, Yang W, Raitcheva D, Antognetti G, McCampbell A, Van Swieten JC, Miller BL, Boxer AL, Brown RH, Bowser R, Miller TM, Trojanowski JQ, Grossman M, Berry JD, Hu WT, Ratti A, Traynor BJ, Disney MD, Benatar M, Silani V, Glass JD, Floeter MK, Rothstein JD, Boylan KB, Petrucelli L Science translational medicine 28356511 Sci Transl Med 2017 Mar 29
Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1. Chen JL, VanEtten DM, Fountain MA, Yildirim I, Disney MD Biochemistry 28617590 Biochemistry 2017 Jul 11
Design of a bioactive small molecule that targets r(AUUCU) repeats in spinocerebellar ataxia 10. Yang WY, Gao R, Southern M, Sarkar PS, Disney MD Nature communications 27248057 Nat Commun 2016 Jun 1
How We Think about Targeting RNA with Small Molecules. Costales MG, Childs-Disney JL, Haniff HS, Disney MD Journal of medicinal chemistry 32212706 J Med Chem 2020 Sep 10
Small-molecule targeted recruitment of a nuclease to cleave an oncogenic RNA in a mouse model of metastatic cancer. Costales MG, Aikawa H, Li Y, Childs-Disney JL, Abegg D, Hoch DG, Pradeep Velagapudi S, Nakai Y, Khan T, Wang KW, Yildirim I, Adibekian A, Wang ET, Disney MD Proceedings of the National Academy of Sciences of the United States of America 31964809 Proc Natl Acad Sci U S A 2020 Feb 4
Drugging the RNA World. Disney MD, Dwyer BG, Childs-Disney JL Cold Spring Harbor perspectives in biology 30385607 Cold Spring Harb Perspect Biol 2018 Nov 1
Decreasing the intrinsically disordered protein α-synuclein levels by targeting its structured mRNA with a ribonuclease-targeting chimera. Tong Y, Zhang P, Yang X, Liu X, Zhang J, Grudniewska M, Jung I, Abegg D, Liu J, Childs-Disney JL, Gibaut QMR, Haniff HS, Adibekian A, Mouradian MM, Disney MD Proceedings of the National Academy of Sciences of the United States of America 38181056 Proc Natl Acad Sci U S A 2024 Jan 9
Simultaneous dual-color fluorescence lifetime imaging with novel red-shifted fluorescent proteins. Laviv T, Kim BB, Chu J, Lam AJ, Lin MZ, Yasuda R Nature methods 27798609 Nat Methods 2016 Dec
CaMKII Autophosphorylation Is Necessary for Optimal Integration of Ca(2+) Signals during LTP Induction, but Not Maintenance. Chang JY, Parra-Bueno P, Laviv T, Szatmari EM, Lee SR, Yasuda R Neuron 28521133 Neuron 2017 May 17
In Vivo Imaging of the Coupling between Neuronal and CREB Activity in the Mouse Brain. Laviv T, Scholl B, Parra-Bueno P, Foote B, Zhang C, Yan L, Hayano Y, Chu J, Yasuda R Neuron 31883788 Neuron 2020 Mar 4
The NMDA receptor subunit GluN3A regulates synaptic activity-induced and myocyte enhancer factor 2C (MEF2C)-dependent transcription. Chen LF, Lyons MR, Liu F, Green MV, Hedrick NG, Williams AB, Narayanan A, Yasuda R, West AE The Journal of biological chemistry 32393578 J Biol Chem 2020 Jun 19
Imaging ERK and PKA Activation in Single Dendritic Spines during Structural Plasticity. Tang S, Yasuda R Neuron 28285819 Neuron 2017 Mar 22
Kinetics of Endogenous CaMKII Required for Synaptic Plasticity Revealed by Optogenetic Kinase Inhibitor. Murakoshi H, Shin ME, Parra-Bueno P, Szatmari EM, Shibata ACE, Yasuda R Neuron 28318784 Neuron 2017 Apr 5
High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing. Mikuni T, Nishiyama J, Sun Y, Kamasawa N, Yasuda R Cell 27180908 Cell 2016 Jun 16
An open-source tool for analysis and automatic identification of dendritic spines using machine learning. Smirnov MS, Garrett TR, Yasuda R PloS one 29975722 PLoS One 2018
PKCα integrates spatiotemporally distinct Ca(2+) and autocrine BDNF signaling to facilitate synaptic plasticity. Colgan LA, Hu M, Misler JA, Parra-Bueno P, Moran CM, Leitges M, Yasuda R Nature neuroscience 30013171 Nat Neurosci 2018 Aug
Autocrine BDNF-TrkB signalling within a single dendritic spine. Harward SC, Hedrick NG, Hall CE, Parra-Bueno P, Milner TA, Pan E, Laviv T, Hempstead BL, Yasuda R, McNamara JO Nature 27680698 Nature 2016 Oct 6
RGS14 Restricts Plasticity in Hippocampal CA2 by Limiting Postsynaptic Calcium Signaling. Evans PR, Parra-Bueno P, Smirnov MS, Lustberg DJ, Dudek SM, Hepler JR, Yasuda R eNeuro 29911178 eNeuro 2018 May-Jun
Rapid Ultrastructural Changes in the PSD and Surrounding Membrane after Induction of Structural LTP in Single Dendritic Spines. Sun Y, Smirnov M, Kamasawa N, Yasuda R The Journal of neuroscience : the official journal of the Society for Neuroscience 34266899 J Neurosci 2021 Aug 18
Longitudinal Two-Photon Imaging of Dorsal Hippocampal CA1 in Live Mice. Ulivi AF, Castello-Waldow TP, Weston G, Yan L, Yasuda R, Chen A, Attardo A Journal of visualized experiments : JoVE 31282875 J Vis Exp 2019 Jun 19
FRET Imaging of Rho GTPase Activity with Red Fluorescent Protein-Based FRET Pairs. Bajar BT, Guan X, Lam A, Lin MZ, Yasuda R, Laviv T, Chu J Methods in molecular biology (Clifton, N.J.) 35147933 Methods Mol Biol 2022
Mechanisms of Ca(2+)/calmodulin-dependent kinase II activation in single dendritic spines. Chang JY, Nakahata Y, Hayano Y, Yasuda R Nature communications 31239443 Nat Commun 2019 Jun 25
Reciprocal Activation within a Kinase-Effector Complex Underlying Persistence of Structural LTP. Saneyoshi T, Matsuno H, Suzuki A, Murakoshi H, Hedrick NG, Agnello E, O'Connell R, Stratton MM, Yasuda R, Hayashi Y Neuron 31078368 Neuron 2019 Jun 19
Virus-Mediated Genome Editing via Homology-Directed Repair in Mitotic and Postmitotic Cells in Mammalian Brain. Nishiyama J, Mikuni T, Yasuda R Neuron 29056297 Neuron 2017 Nov 15
Automated Remote Focusing, Drift Correction, and Photostimulation to Evaluate Structural Plasticity in Dendritic Spines. Smirnov MS, Evans PR, Garrett TR, Yan L, Yasuda R PloS one 28114380 PLoS One 2017
Rho GTPase complementation underlies BDNF-dependent homo- and heterosynaptic plasticity. Hedrick NG, Harward SC, Hall CE, Murakoshi H, McNamara JO, Yasuda R Nature 27680697 Nature 2016 Oct 6
Structure and mechanism of blood-brain-barrier lipid transporter MFSD2A. Wood CAP, Zhang J, Aydin D, Xu Y, Andreone BJ, Langen UH, Dror RO, Gu C, Feng L Nature 34349262 Nature 2021 Aug
Pericyte-to-endothelial cell signaling via vitronectin-integrin regulates blood-CNS barrier. Ayloo S, Lazo CG, Sun S, Zhang W, Cui B, Gu C Neuron 35294899 Neuron 2022 May 18
Development and Cell Biology of the Blood-Brain Barrier. Langen UH, Ayloo S, Gu C Annual review of cell and developmental biology 31299172 Annu Rev Cell Dev Biol 2019 Oct 6
Bridging barriers: a comparative look at the blood-brain barrier across organisms. O'Brown NM, Pfau SJ, Gu C Genes & development 29692355 Genes Dev 2018 Apr 1
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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
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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
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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
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Computational models in cardiology. Niederer SA, Lumens J, Trayanova NA Nature reviews. Cardiology 30361497 Nat Rev Cardiol 2019 Feb
Virtual electrophysiological study as a tool for evaluating efficacy of MRI techniques in predicting adverse arrhythmic events in ischemic patients. Ukwatta E, Nikolov P, Zabihollahy F, Trayanova NA, Wright GA Physics in medicine and biology 30412472 Phys Med Biol 2018 Nov 9
Cardiac Optogenetics: 2018. Boyle PM, Karathanos TV, Trayanova NA JACC. Clinical electrophysiology 29749932 JACC Clin Electrophysiol 2018 Feb
Optimal contrast-enhanced MRI image thresholding for accurate prediction of ventricular tachycardia using ex-vivo high resolution models. Deng D, Nikolov P, Arevalo HJ, Trayanova NA Computers in biology and medicine 30301573 Comput Biol Med 2018 Nov 1
Association of regional myocardial conduction velocity with the distribution of hypoattenuation on contrast-enhanced perfusion computed tomography in patients with postinfarct ventricular tachycardia. Ustunkaya T, Desjardins B, Liu B, Zahid S, Park J, Saju N, Trayanova N, Zimmerman SL, Marchlinski FE, Nazarian S Heart rhythm 30935494 Heart Rhythm 2019 Apr
Computationally guided personalized targeted ablation of persistent atrial fibrillation. Boyle PM, Zghaib T, Zahid S, Ali RL, Deng D, Franceschi WH, Hakim JB, Murphy MJ, Prakosa A, Zimmerman SL, Ashikaga H, Marine JE, Kolandaivelu A, Nazarian S, Spragg DD, Calkins H, Trayanova NA Nature biomedical engineering 31427780 Nat Biomed Eng 2019 Nov
Spatial dispersion analysis of LGE-CMR for prediction of ventricular arrhythmias in patients with cardiac sarcoidosis. Aronis KN, Okada DR, Xie E, Daimee UA, Prakosa A, Gilotra NA, Wu KC, Trayanova N, Chrispin J Pacing and clinical electrophysiology : PACE 34766627 Pacing Clin Electrophysiol 2021 Dec
Computational modeling of aberrant electrical activity following remuscularization with intramyocardially injected pluripotent stem cell-derived cardiomyocytes. Yu JK, Liang JA, Weinberg SH, Trayanova NA Journal of molecular and cellular cardiology 34487753 J Mol Cell Cardiol 2022 Jan
Optogenetics-enabled dynamic modulation of action potential duration in atrial tissue: feasibility of a novel therapeutic approach. Karathanos TV, Boyle PM, Trayanova NA Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology 25362173 Europace 2014 Nov
Computational analysis of the effect of valvular regurgitation on ventricular mechanics using a 3D electromechanics model. Lim KM, Hong SB, Lee BK, Shim EB, Trayanova N The journal of physiological sciences : JPS 25644379 J Physiol Sci 2015 Mar
Optogenetics-enabled assessment of viral gene and cell therapy for restoration of cardiac excitability. Ambrosi CM, Boyle PM, Chen K, Trayanova NA, Entcheva E Scientific reports 26621212 Sci Rep 2015 Dec 1
Intermittent drivers anchoring to structural heterogeneities as a major pathophysiological mechanism of human persistent atrial fibrillation. Haissaguerre M, Shah AJ, Cochet H, Hocini M, Dubois R, Efimov I, Vigmond E, Bernus O, Trayanova N The Journal of physiology 26890861 J Physiol 2016 May 1
Arrhythmia risk stratification of patients after myocardial infarction using personalized heart models. Arevalo HJ, Vadakkumpadan F, Guallar E, Jebb A, Malamas P, Wu KC, Trayanova NA Nature communications 27164184 Nat Commun 2016 May 10
Computational rabbit models to investigate the initiation, perpetuation, and termination of ventricular arrhythmia. Arevalo HJ, Boyle PM, Trayanova NA Progress in biophysics and molecular biology 27334789 Prog Biophys Mol Biol 2016 Jul
Opsin spectral sensitivity determines the effectiveness of optogenetic termination of ventricular fibrillation in the human heart: a simulation study. Karathanos TV, Bayer JD, Wang D, Boyle PM, Trayanova NA The Journal of physiology 26941055 J Physiol 2016 Dec 1
A feasibility study of arrhythmia risk prediction in patients with myocardial infarction and preserved ejection fraction. Deng D, Arevalo HJ, Prakosa A, Callans DJ, Trayanova NA Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology 28011832 Europace 2016 Dec
Towards personalized computational modelling of the fibrotic substrate for atrial arrhythmia. Boyle PM, Zahid S, Trayanova NA Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology 28011841 Europace 2016 Dec
Plakophilin-2 is required for transcription of genes that control calcium cycling and cardiac rhythm. Cerrone M, Montnach J, Lin X, Zhao YT, Zhang M, Agullo-Pascual E, Leo-Macias A, Alvarado FJ, Dolgalev I, Karathanos TV, Malkani K, Van Opbergen CJM, van Bavel JJA, Yang HQ, Vasquez C, Tester D, Fowler S, Liang F, Rothenberg E, Heguy A, Morley GE, Coetzee WA, Trayanova NA, Ackerman MJ, van Veen TAB, Valdivia HH, Delmar M Nature communications 28740174 Nat Commun 2017 Jul 24
Efficient preloading of the ventricles by a properly timed atrial contraction underlies stroke work improvement in the acute response to cardiac resynchronization therapy. Hu Y, Gurev V, Constantino J, Trayanova N Heart rhythm 23928177 Heart Rhythm 2013 Dec
A New MRI-Based Model of Heart Function with Coupled Hemodynamics and Application to Normal and Diseased Canine Left Ventricles. Choi YJ, Constantino J, Vedula V, Trayanova N, Mittal R Frontiers in bioengineering and biotechnology 26442254 Front Bioeng Biotechnol 2015
Mathematical approaches to understanding and imaging atrial fibrillation: significance for mechanisms and management. Trayanova NA Circulation research 24763468 Circ Res 2014 Apr 25
"Beauty is a light in the heart": the transformative potential of optogenetics for clinical applications in cardiovascular medicine. Boyle PM, Karathanos TV, Trayanova NA Trends in cardiovascular medicine 25453984 Trends Cardiovasc Med 2015 Feb
Myocardial infarct segmentation and reconstruction from 2D late-gadolinium enhanced magnetic resonance images. Ukwatta E, Yuan J, Qiu W, Wu KC, Trayanova N, Vadakkumpadan F Medical image computing and computer-assisted intervention : MICCAI ... International Conference on Medical Image Computing and Computer-Assisted Intervention 25485423 Med Image Comput Comput Assist Interv 2014
Myocardial Infarct Segmentation From Magnetic Resonance Images for Personalized Modeling of Cardiac Electrophysiology. Ukwatta E, Arevalo H, Li K, Yuan J, Qiu W, Malamas P, Wu KC, Trayanova NA, Vadakkumpadan F IEEE transactions on medical imaging 26731693 IEEE Trans Med Imaging 2016 Jun
Precisely parameterized experimental and computational models of tissue organization. Molitoris JM, Paliwal S, Sekar RB, Blake R, Park J, Trayanova NA, Tung L, Levchenko A Integrative biology : quantitative biosciences from nano to macro 26822672 Integr Biol (Camb) 2016 Feb
Computational models of heart disease. Smith N, Trayanova N Drug discovery today. Disease models 26843884 Drug Discov Today Dis Models 2014 Winter
Accurate Conduction Velocity Maps and Their Association With Scar Distribution on Magnetic Resonance Imaging in Patients With Postinfarction Ventricular Tachycardias. Aronis KN, Ali RL, Prakosa A, Ashikaga H, Berger RD, Hakim JB, Liang J, Tandri H, Teng F, Chrispin J, Trayanova NA Circulation. Arrhythmia and electrophysiology 32191131 Circ Arrhythm Electrophysiol 2020 Apr
Ventricular arrhythmia risk prediction in repaired Tetralogy of Fallot using personalized computational cardiac models. Shade JK, Cartoski MJ, Nikolov P, Prakosa A, Doshi A, Binka E, Olivieri L, Boyle PM, Spevak PJ, Trayanova NA Heart rhythm 31589989 Heart Rhythm 2020 Mar
Epicardial Conduction Speed, Electrogram Abnormality, and Computed Tomography Attenuation Associations in Arrhythmogenic Right Ventricular Cardiomyopathy. Ustunkaya T, Desjardins B, Wedan R, Chahal CAA, Zimmerman SL, Saju N, Zahid S, Sharma A, Han Y, Trayanova N, Marchlinski FE, Calkins H, Tandri H, Nazarian S JACC. Clinical electrophysiology 31648740 JACC Clin Electrophysiol 2019 Oct
Tropomyosin dynamics during cardiac muscle contraction as governed by a multi-well energy landscape. Aboelkassem Y, Trayanova N Progress in biophysics and molecular biology 30145015 Prog Biophys Mol Biol 2019 Jul
From genetics to smart watches: developments in precision cardiology. Trayanova N Nature reviews. Cardiology 30568275 Nat Rev Cardiol 2019 Feb
Spatially Adaptive Multi-Scale Optimization for Local Parameter Estimation in Cardiac Electrophysiology. Dhamala J, Arevalo HJ, Sapp J, Horacek M, Wu KC, Trayanova NA, Wang L IEEE transactions on medical imaging 28459685 IEEE Trans Med Imaging 2017 Sep
Role of 3-Dimensional Architecture of Scar and Surviving Tissue in Ventricular Tachycardia: Insights From High-Resolution Ex Vivo Porcine Models. Pashakhanloo F, Herzka DA, Halperin H, McVeigh ER, Trayanova NA Circulation. Arrhythmia and electrophysiology 29880529 Circ Arrhythm Electrophysiol 2018 Jun
Exploring susceptibility to atrial and ventricular arrhythmias resulting from remodeling of the passive electrical properties in the heart: a simulation approach. Trayanova NA, Boyle PM, Arevalo HJ, Zahid S Frontiers in physiology 25429272 Front Physiol 2014
Virtual 3D heart models to aid pacemaker implantation in children. Trayanova NA Future cardiology 24344653 Future Cardiol 2014 Jan
Computational modeling of cardiac optogenetics: Methodology overview & review of findings from simulations. Boyle PM, Karathanos TV, Entcheva E, Trayanova NA Computers in biology and medicine 26002074 Comput Biol Med 2015 Oct 1
New insights into defibrillation of the heart from realistic simulation studies. Trayanova NA, Rantner LJ Europace : European pacing, arrhythmias, and cardiac electrophysiology : journal of the working groups on cardiac pacing, arrhythmias, and cardiac cellular electrophysiology of the European Society of Cardiology 24798960 Europace 2014 May
Myofiber Architecture of the Human Atria as Revealed by Submillimeter Diffusion Tensor Imaging. Pashakhanloo F, Herzka DA, Ashikaga H, Mori S, Gai N, Bluemke DA, Trayanova NA, McVeigh ER Circulation. Arrhythmia and electrophysiology 27071829 Circ Arrhythm Electrophysiol 2016 Apr
Mechanisms linking electrical alternans and clinical ventricular arrhythmia in human heart failure. Bayer JD, Lalani GG, Vigmond EJ, Narayan SM, Trayanova NA Heart rhythm 27215536 Heart Rhythm 2016 Sep
Computational Identification of Ventricular Arrhythmia Risk in Pediatric Myocarditis. Cartoski MJ, Nikolov PP, Prakosa A, Boyle PM, Spevak PJ, Trayanova NA Pediatric cardiology 30840104 Pediatr Cardiol 2019 Apr
Light-based Approaches to Cardiac Arrhythmia Research: From Basic Science to Translational Applications. Karathanos TV, Boyle PM, Trayanova NA Clinical Medicine Insights. Cardiology 27840581 Clin Med Insights Cardiol 2016
Feasibility of using patient-specific models and the "minimum cut" algorithm to predict optimal ablation targets for left atrial flutter. Zahid S, Whyte KN, Schwarz EL, Blake RC 3rd, Boyle PM, Chrispin J, Prakosa A, Ipek EG, Pashakhanloo F, Halperin HR, Calkins H, Berger RD, Nazarian S, Trayanova NA Heart rhythm 27108938 Heart Rhythm 2016 Aug
Initiation of a High-Frequency Jet Ventilation Strategy for Catheter Ablation for Atrial Fibrillation: Safety and Outcomes Data. Sivasambu B, Hakim JB, Barodka V, Chrispin J, Berger RD, Ashikaga H, Ciuffo L, Tao S, Calkins H, Marine JE, Trayanova N, Spragg DD JACC. Clinical electrophysiology 30573114 JACC Clin Electrophysiol 2018 Dec
Arrhythmogenic propensity of the fibrotic substrate after atrial fibrillation ablation: a longitudinal study using magnetic resonance imaging-based atrial models. Ali RL, Hakim JB, Boyle PM, Zahid S, Sivasambu B, Marine JE, Calkins H, Trayanova NA, Spragg DD Cardiovascular research 30977811 Cardiovasc Res 2019 Oct 1
Degradation of T-Tubular Microdomains and Altered cAMP Compartmentation Lead to Emergence of Arrhythmogenic Triggers in Heart Failure Myocytes: An in silico Study. Loucks AD, O'Hara T, Trayanova NA Frontiers in physiology 30564142 Front Physiol 2018
Association of left atrial epicardial adipose tissue with electrogram bipolar voltage and fractionation: Electrophysiologic substrates for atrial fibrillation. Zghaib T, Ipek EG, Zahid S, Balouch MA, Misra S, Ashikaga H, Berger RD, Marine JE, Spragg DD, Zimmerman SL, Zipunnikov V, Trayanova N, Calkins H, Nazarian S Heart rhythm 27546816 Heart Rhythm 2016 Dec
Effect of KCNQ1 G229D mutation on cardiac pumping efficacy and reentrant dynamics in ventricles: Computational study. Yuniarti AR, Setianto F, Marcellinus A, Hwang HJ, Choi SW, Trayanova N, Lim KM International journal for numerical methods in biomedical engineering 29488358 Int J Numer Method Biomed Eng 2018 Jun
Biological substrate modification suppresses ventricular arrhythmias in a porcine model of chronic ischaemic cardiomyopathy. Dawkins JF, Ehdaie A, Rogers R, Soetkamp D, Valle J, Holm K, Sanchez L, Tremmel I, Nawaz A, Shehata M, Wang X, Prakosa A, Yu J, Van Eyk JE, Trayanova N, Marbán E, Cingolani E European heart journal 35262692 Eur Heart J 2022 Jun 6
Substrate Spatial Complexity Analysis for the Prediction of Ventricular Arrhythmias in Patients With Ischemic Cardiomyopathy. Okada DR, Miller J, Chrispin J, Prakosa A, Trayanova N, Jones S, Maggioni M, Wu KC Circulation. Arrhythmia and electrophysiology 32188287 Circ Arrhythm Electrophysiol 2020 Apr
Characterization of the Electrophysiologic Remodeling of Patients With Ischemic Cardiomyopathy by Clinical Measurements and Computer Simulations Coupled With Machine Learning. Aronis KN, Prakosa A, Bergamaschi T, Berger RD, Boyle PM, Chrispin J, Ju S, Marine JE, Sinha S, Tandri H, Ashikaga H, Trayanova NA Frontiers in physiology 34335294 Front Physiol 2021
Optimizing cardiac resynchronization therapy to minimize ATP consumption heterogeneity throughout the left ventricle: a simulation analysis using a canine heart failure model. Hu Y, Gurev V, Constantino J, Trayanova N Heart rhythm 24657430 Heart Rhythm 2014 Jun
Early somatic mosaicism is a rare cause of long-QT syndrome. Priest JR, Gawad C, Kahlig KM, Yu JK, O'Hara T, Boyle PM, Rajamani S, Clark MJ, Garcia ST, Ceresnak S, Harris J, Boyle S, Dewey FE, Malloy-Walton L, Dunn K, Grove M, Perez MV, Neff NF, Chen R, Maeda K, Dubin A, Belardinelli L, West J, Antolik C, Macaya D, Quertermous T, Trayanova NA, Quake SR, Ashley EA Proceedings of the National Academy of Sciences of the United States of America 27681629 Proc Natl Acad Sci U S A 2016 Oct 11
Sodium current reduction unmasks a structure-dependent substrate for arrhythmogenesis in the normal ventricles. Boyle PM, Park CJ, Arevalo HJ, Vigmond EJ, Trayanova NA PloS one 24489810 PLoS One 2014
Advances in modeling ventricular arrhythmias: from mechanisms to the clinic. Trayanova NA, Boyle PM Wiley interdisciplinary reviews. Systems biology and medicine 24375958 Wiley Interdiscip Rev Syst Biol Med 2014 Mar-Apr
Methodology for image-based reconstruction of ventricular geometry for patient-specific modeling of cardiac electrophysiology. Prakosa A, Malamas P, Zhang S, Pashakhanloo F, Arevalo H, Herzka DA, Lardo A, Halperin H, McVeigh E, Trayanova N, Vadakkumpadan F Progress in biophysics and molecular biology 25148771 Prog Biophys Mol Biol 2014 Aug
Image-based left ventricular shape analysis for sudden cardiac death risk stratification. Vadakkumpadan F, Trayanova N, Wu KC Heart rhythm 24854217 Heart Rhythm 2014 Oct
Disrupted calcium release as a mechanism for atrial alternans associated with human atrial fibrillation. Chang KC, Bayer JD, Trayanova NA PLoS computational biology 25501557 PLoS Comput Biol 2014 Dec
Virtual electrophysiological study of atrial fibrillation in fibrotic remodeling. McDowell KS, Zahid S, Vadakkumpadan F, Blauer J, MacLeod RS, Trayanova NA PloS one 25692857 PLoS One 2015
Mechanisms of arrhythmogenesis related to calcium-driven alternans in a model of human atrial fibrillation. Chang KC, Trayanova NA Scientific reports 27812021 Sci Rep 2016 Nov 4
Sensitivity of Ablation Targets Prediction to Electrophysiological Parameter Variability in Image-Based Computational Models of Ventricular Tachycardia in Post-infarction Patients. Deng D, Prakosa A, Shade J, Nikolov P, Trayanova NA Frontiers in physiology 31178758 Front Physiol 2019
Personalized virtual-heart technology for guiding the ablation of infarct-related ventricular tachycardia. Prakosa A, Arevalo HJ, Deng D, Boyle PM, Nikolov PP, Ashikaga H, Blauer JJE, Ghafoori E, Park CJ, Blake RC 3rd, Han FT, MacLeod RS, Halperin HR, Callans DJ, Ranjan R, Chrispin J, Nazarian S, Trayanova NA Nature biomedical engineering 30847259 Nat Biomed Eng 2018 Oct
Quantifying the uncertainty in model parameters using Gaussian process-based Markov chain Monte Carlo in cardiac electrophysiology. Dhamala J, Arevalo HJ, Sapp J, Horácek BM, Wu KC, Trayanova NA, Wang L Medical image analysis 29843078 Med Image Anal 2018 Aug
Relationship Between Fibrosis Detected on Late Gadolinium-Enhanced Cardiac Magnetic Resonance and Re-Entrant Activity Assessed With Electrocardiographic Imaging in Human Persistent Atrial Fibrillation. Cochet H, Dubois R, Yamashita S, Al Jefairi N, Berte B, Sellal JM, Hooks D, Frontera A, Amraoui S, Zemoura A, Denis A, Derval N, Sacher F, Corneloup O, Latrabe V, Clément-Guinaudeau S, Relan J, Zahid S, Boyle PM, Trayanova NA, Bernus O, Montaudon M, Laurent F, Hocini M, Haïssaguerre M, Jaïs P JACC. Clinical electrophysiology 29479568 JACC Clin Electrophysiol 2018 Jan
Increased thin filament activation enhances alternans in human chronic atrial fibrillation. Zile MA, Trayanova NA American journal of physiology. Heart and circulatory physiology 30141984 Am J Physiol Heart Circ Physiol 2018 Nov 1
Modeling the aging heart: from local respiratory defects to global rhythm disturbances. Khrapko K, Trayanova N, Nattel S Cell metabolism 25955202 Cell Metab 2015 May 5
Personalized Imaging and Modeling Strategies for Arrhythmia Prevention and Therapy. Trayanova NA, Boyle PM, Nikolov PP Current opinion in biomedical engineering 29546250 Curr Opin Biomed Eng 2018 Mar
A comprehensive, multiscale framework for evaluation of arrhythmias arising from cell therapy in the whole post-myocardial infarcted heart. Yu JK, Franceschi W, Huang Q, Pashakhanloo F, Boyle PM, Trayanova NA Scientific reports 31239508 Sci Rep 2019 Jun 25
New insights on the cardiac safety factor: Unraveling the relationship between conduction velocity and robustness of propagation. Boyle PM, Franceschi WH, Constantin M, Hawks C, Desplantez T, Trayanova NA, Vigmond EJ Journal of molecular and cellular cardiology 30677394 J Mol Cell Cardiol 2019 Mar
The role of personalized atrial modeling in understanding atrial fibrillation mechanisms and improving treatment. Aronis KN, Ali R, Trayanova NA International journal of cardiology 30755334 Int J Cardiol 2019 Jul 15
β-adrenergic stimulation augments transmural dispersion of repolarization via modulation of delayed rectifier currents I(Ks) and I(Kr) in the human ventricle. Kang C, Badiceanu A, Brennan JA, Gloschat C, Qiao Y, Trayanova NA, Efimov IR Scientific reports 29162896 Sci Rep 2017 Nov 21
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Discovery of a ZIP7 inhibitor from a Notch pathway screen. Nolin E, Gans S, Llamas L, Bandyopadhyay S, Brittain SM, Bernasconi-Elias P, Carter KP, Loureiro JJ, Thomas JR, Schirle M, Yang Y, Guo N, Roma G, Schuierer S, Beibel M, Lindeman A, Sigoillot F, Chen A, Xie KX, Ho S, Reece-Hoyes J, Weihofen WA, Tyskiewicz K, Hoepfner D, McDonald RI, Guthrie N, Dogra A, Guo H, Shao J, Ding J, Canham SM, Boynton G, George EL, Kang ZB, Antczak C, Porter JA, Wallace O, Tallarico JA, Palmer AE, Jenkins JL, Jain RK, Bushell SM, Fryer CJ Nature chemical biology 30643281 Nat Chem Biol 2019 Feb
Intramolecular Fluorescent Protein Association in a Class of Zinc FRET Sensors Leads to Increased Dynamic Range. Slocum JD, Palmer AE, Jimenez R The journal of physical chemistry. B 30942588 J Phys Chem B 2019 Apr 11
Zinc transporters belonging to the Cation Diffusion Facilitator (CDF) family have complementary roles in transporting zinc out of the cytosol. Choi S, Hu YM, Corkins ME, Palmer AE, Bird AJ PLoS genetics 29529046 PLoS Genet 2018 Mar
Dissociated Hippocampal Neurons Exhibit Distinct Zn(2+) Dynamics in a Stimulation-Method-Dependent Manner. Sanford L, Palmer AE ACS chemical neuroscience 32013397 ACS Chem Neurosci 2020 Feb 19
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Zn(2+) influx activates ERK and Akt signaling pathways. Anson KJ, Corbet GA, Palmer AE Proceedings of the National Academy of Sciences of the United States of America 33712543 Proc Natl Acad Sci U S A 2021 Mar 16
Superiority of SpiroZin2 Versus FluoZin-3 for monitoring vesicular Zn(2+) allows tracking of lysosomal Zn(2+) pools. Han Y, Goldberg JM, Lippard SJ, Palmer AE Scientific reports 30302024 Sci Rep 2018 Oct 9
Remodeling of Zn(2+) homeostasis upon differentiation of mammary epithelial cells. Han Y, Sanford L, Simpson DM, Dowell RD, Palmer AE Metallomics : integrated biometal science 31950952 Metallomics 2020 Mar 25
Intracellular Zn(2+) transients modulate global gene expression in dissociated rat hippocampal neurons. Sanford L, Carpenter MC, Palmer AE Scientific reports 31253848 Sci Rep 2019 Jun 28
Tools and techniques for illuminating the cell biology of zinc. Pratt EPS, Damon LJ, Anson KJ, Palmer AE Biochimica et biophysica acta. Molecular cell research 32980354 Biochim Biophys Acta Mol Cell Res 2021 Jan
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Critical Comparison of FRET-Sensor Functionality in the Cytosol and Endoplasmic Reticulum and Implications for Quantification of Ions. Carter KP, Carpenter MC, Fiedler B, Jimenez R, Palmer AE Analytical chemistry 28758723 Anal Chem 2017 Sep 5
A Critical and Comparative Review of Fluorescent Tools for Live-Cell Imaging. Specht EA, Braselmann E, Palmer AE Annual review of physiology 27860833 Annu Rev Physiol 2017 Feb 10
Single cell analysis reveals multiple requirements for zinc in the mammalian cell cycle. Lo MN, Damon LJ, Wei Tay J, Jia S, Palmer AE eLife 32014109 Elife 2020 Feb 4
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The Antiviral Mechanism of an Influenza A Virus Nucleoprotein-Specific Single-Domain Antibody Fragment. Hanke L, Knockenhauer KE, Brewer RC, van Diest E, Schmidt FI, Schwartz TU, Ploegh HL mBio 27965447 mBio 2016 Dec 13
Tissue-specific emergence of regulatory and intraepithelial T cells from a clonal T cell precursor. Bilate AM, Bousbaine D, Mesin L, Agudelo M, Leube J, Kratzert A, Dougan SK, Victora GD, Ploegh HL Science immunology 28783695 Sci Immunol 2016 Aug 26
In vitro AMPylation Assays Using Purified, Recombinant Proteins. Truttmann MC, Ploegh HL Bio-protocol 29170749 Bio Protoc 2017 Jul 20
Production of unnaturally linked chimeric proteins using a combination of sortase-catalyzed transpeptidation and click chemistry. Witte MD, Theile CS, Wu T, Guimaraes CP, Blom AE, Ploegh HL Nature protocols 23989675 Nat Protoc 2013 Sep
Allosteric activation of apicomplexan calcium-dependent protein kinases. Ingram JR, Knockenhauer KE, Markus BM, Mandelbaum J, Ramek A, Shan Y, Shaw DE, Schwartz TU, Ploegh HL, Lourido S Proceedings of the National Academy of Sciences of the United States of America 26305940 Proc Natl Acad Sci U S A 2015 Sep 8
Enzyme-Mediated Modification of Single-Domain Antibodies for Imaging Modalities with Different Characteristics. Rashidian M, Wang L, Edens JG, Jacobsen JT, Hossain I, Wang Q, Victora GD, Vasdev N, Ploegh H, Liang SH Angewandte Chemie (International ed. in English) 26630549 Angew Chem Int Ed Engl 2016 Jan 11
Phenotypic lentivirus screens to identify functional single domain antibodies. Schmidt FI, Hanke L, Morin B, Brewer R, Brusic V, Whelan SP, Ploegh HL Nature microbiology 27573105 Nat Microbiol 2016 Jun 20
Engineered red blood cells as carriers for systemic delivery of a wide array of functional probes. Shi J, Kundrat L, Pishesha N, Bilate A, Theile C, Maruyama T, Dougan SK, Ploegh HL, Lodish HF Proceedings of the National Academy of Sciences of the United States of America 24982154 Proc Natl Acad Sci U S A 2014 Jul 15
Graphene Oxide Nanosheets Modified with Single-Domain Antibodies for Rapid and Efficient Capture of Cells. Chen GY, Li Z, Theile CS, Bardhan NM, Kumar PV, Duarte JN, Maruyama T, Rashidfarrokh A, Belcher AM, Ploegh HL Chemistry (Weinheim an der Bergstrasse, Germany) 26472062 Chemistry 2015 Nov 23
Fluorophore-Conjugated Holliday Junctions for Generating Super-Bright Antibodies and Antibody Fragments. Li Z, Theile CS, Chen GY, Bilate AM, Duarte JN, Avalos AM, Fang T, Barberena R, Sato S, Ploegh HL Angewandte Chemie (International ed. in English) 26252716 Angew Chem Int Ed Engl 2015 Sep 28
PD-L1 is an activation-independent marker of brown adipocytes. Ingram JR, Dougan M, Rashidian M, Knoll M, Keliher EJ, Garrett S, Garforth S, Blomberg OS, Espinosa C, Bhan A, Almo SC, Weissleder R, Lodish H, Dougan SK, Ploegh HL Nature communications 28935898 Nat Commun 2017 Sep 21
Targeted antigen delivery by an anti-class II MHC VHH elicits focused αMUC1(Tn) immunity. Fang T, Van Elssen CHMJ, Duarte JN, Guzman JS, Chahal JS, Ling J, Ploegh HL Chemical science 28970938 Chem Sci 2017 Aug 1
The use of (18)F-2-fluorodeoxyglucose (FDG) to label antibody fragments for immuno-PET of pancreatic cancer. Rashidian M, Keliher E, Dougan M, Juras PK, Cavallari M, Wojtkiewicz GR, Jacobsen J, Edens JG, Tas JM, Victora G, Weissleder R, Ploegh H ACS central science 26955657 ACS Cent Sci 2015 Jun 24
Epithelial-to-Mesenchymal Transition Contributes to Immunosuppression in Breast Carcinomas. Dongre A, Rashidian M, Reinhardt F, Bagnato A, Keckesova Z, Ploegh HL, Weinberg RA Cancer research 28428275 Cancer Res 2017 Aug 1
rAMPing Up Stress Signaling: Protein AMPylation in Metazoans. Truttmann MC, Ploegh HL Trends in cell biology 28433487 Trends Cell Biol 2017 Aug
Vesicular stomatitis virus N protein-specific single-domain antibody fragments inhibit replication. Hanke L, Schmidt FI, Knockenhauer KE, Morin B, Whelan SP, Schwartz TU, Ploegh HL EMBO reports 28396572 EMBO Rep 2017 Jun
Enhanced Cell Capture on Functionalized Graphene Oxide Nanosheets through Oxygen Clustering. Bardhan NM, Kumar PV, Li Z, Ploegh HL, Grossman JC, Belcher AM, Chen GY ACS nano 28085249 ACS Nano 2017 Feb 28
One-step enzymatic modification of the cell surface redirects cellular cytotoxicity and parasite tropism. Swee LK, Lourido S, Bell GW, Ingram JR, Ploegh HL ACS chemical biology 25360987 ACS Chem Biol 2015 Feb 20
Structural biology. Structural basis for chemokine recognition and activation of a viral G protein-coupled receptor. Burg JS, Ingram JR, Venkatakrishnan AJ, Jude KM, Dukkipati A, Feinberg EN, Angelini A, Waghray D, Dror RO, Ploegh HL, Garcia KC Science (New York, N.Y.) 25745166 Science 2015 Mar 6
Rapid and Direct VHH and Target Identification by Staphylococcal Surface Display Libraries. Cavallari M International journal of molecular sciences 28704956 Int J Mol Sci 2017 Jul 12
Generation of Immunity against Pathogens via Single-Domain Antibody-Antigen Constructs. Duarte JN, Cragnolini JJ, Swee LK, Bilate AM, Bader J, Ingram JR, Rashidfarrokhi A, Fang T, Schiepers A, Hanke L, Ploegh HL Journal of immunology (Baltimore, Md. : 1950) 27821668 J Immunol 2016 Dec 15
HypE-specific nanobodies as tools to modulate HypE-mediated target AMPylation. Truttmann MC, Wu Q, Stiegeler S, Duarte JN, Ingram J, Ploegh HL The Journal of biological chemistry 25678711 J Biol Chem 2015 Apr 3
Intracellular expression of camelid single-domain antibodies specific for influenza virus nucleoprotein uncovers distinct features of its nuclear localization. Ashour J, Schmidt FI, Hanke L, Cragnolini J, Cavallari M, Altenburg A, Brewer R, Ingram J, Shoemaker C, Ploegh HL Journal of virology 25540369 J Virol 2015 Mar
Durable antitumor responses to CD47 blockade require adaptive immune stimulation. Sockolosky JT, Dougan M, Ingram JR, Ho CC, Kauke MJ, Almo SC, Ploegh HL, Garcia KC Proceedings of the National Academy of Sciences of the United States of America 27091975 Proc Natl Acad Sci U S A 2016 May 10
Posttranscriptional Regulation of Glycoprotein Quality Control in the Endoplasmic Reticulum Is Controlled by the E2 Ub-Conjugating Enzyme UBC6e. Hagiwara M, Ling J, Koenig PA, Ploegh HL Molecular cell 27570074 Mol Cell 2016 Sep 1
A census of human soluble protein complexes. Havugimana PC, Hart GT, Nepusz T, Yang H, Turinsky AL, Li Z, Wang PI, Boutz DR, Fong V, Phanse S, Babu M, Craig SA, Hu P, Wan C, Vlasblom J, Dar VU, Bezginov A, Clark GW, Wu GC, Wodak SJ, Tillier ER, Paccanaro A, Marcotte EM, Emili A Cell 22939629 Cell 2012 Aug 31
Insights into the regulation of protein abundance from proteomic and transcriptomic analyses. Vogel C, Marcotte EM Nature reviews. Genetics 22411467 Nat Rev Genet 2012 Mar 13
Intrinsic Antimicrobial Resistance Determinants in the Superbug Pseudomonas aeruginosa. Murray JL, Kwon T, Marcotte EM, Whiteley M mBio 26507235 mBio 2015 Oct 27
Solution-phase and solid-phase sequential, selective modification of side chains in KDYWEC and KDYWE as models for usage in single-molecule protein sequencing. Hernandez ET, Swaminathan J, Marcotte EM, Anslyn EV New journal of chemistry = Nouveau journal de chimie 28983186 New J Chem 2017 Jan 21
Identifying direct contacts between protein complex subunits from their conditional dependence in proteomics datasets. Drew K, Müller CL, Bonneau R, Marcotte EM PLoS computational biology 29023445 PLoS Comput Biol 2017 Oct
The Many Nuanced Evolutionary Consequences of Duplicated Genes. Teufel AI, Johnson MM, Laurent JM, Kachroo AH, Marcotte EM, Wilke CO Molecular biology and evolution 30428072 Mol Biol Evol 2019 Feb 1
Photography Coupled with Self-Propagating Chemical Cascades: Differentiation and Quantitation of G- and V-Nerve Agent Mimics via Chromaticity. Sun X, Boulgakov AA, Smith LN, Metola P, Marcotte EM, Anslyn EV ACS central science 30062113 ACS Cent Sci 2018 Jul 25
Systematic Discovery of Endogenous Human Ribonucleoprotein Complexes. Mallam AL, Sae-Lee W, Schaub JM, Tu F, Battenhouse A, Jang YJ, Kim J, Wallingford JB, Finkelstein IJ, Marcotte EM, Drew K Cell reports 31665645 Cell Rep 2019 Oct 29
Bringing Microscopy-By-Sequencing into View. Boulgakov AA, Ellington AD, Marcotte EM Trends in biotechnology 31416630 Trends Biotechnol 2020 Feb
Proteomic identification of monoclonal antibodies from serum. Boutz DR, Horton AP, Wine Y, Lavinder JJ, Georgiou G, Marcotte EM Analytical chemistry 24684310 Anal Chem 2014 May 20
Lanthanide nano-drums: a new class of molecular nanoparticles for potential biomedical applications. Jones RA, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Yang X, Schipper D, Hall JW, DePue LJ, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, Brown KA Faraday discussions 25284181 Faraday Discuss 2014
Paternal chromosome loss and metabolic crisis contribute to hybrid inviability in Xenopus. Gibeaux R, Acker R, Kitaoka M, Georgiou G, van Kruijsbergen I, Ford B, Marcotte EM, Nomura DK, Kwon T, Veenstra GJC, Heald R Nature 29320479 Nature 2018 Jan 18
Integration of over 9,000 mass spectrometry experiments builds a global map of human protein complexes. Drew K, Lee C, Huizar RL, Tu F, Borgeson B, McWhite CD, Ma Y, Wallingford JB, Marcotte EM Molecular systems biology 28596423 Mol Syst Biol 2017 Jun 8
The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot. Sardana R, Liu X, Granneman S, Zhu J, Gill M, Papoulas O, Marcotte EM, Tollervey D, Correll CC, Johnson AW PLoS biology 25710520 PLoS Biol 2015 Feb
Long-term neural and physiological phenotyping of a single human. Poldrack RA, Laumann TO, Koyejo O, Gregory B, Hover A, Chen MY, Gorgolewski KJ, Luci J, Joo SJ, Boyd RL, Hunicke-Smith S, Simpson ZB, Caven T, Sochat V, Shine JM, Gordon E, Snyder AZ, Adeyemo B, Petersen SE, Glahn DC, Reese Mckay D, Curran JE, Göring HH, Carless MA, Blangero J, Dougherty R, Leemans A, Handwerker DA, Frick L, Marcotte EM, Mumford JA Nature communications 26648521 Nat Commun 2015 Dec 9
Panorama of ancient metazoan macromolecular complexes. Wan C, Borgeson B, Phanse S, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A Nature 26344197 Nature 2015 Sep 17
Efforts to make and apply humanized yeast. Laurent JM, Young JH, Kachroo AH, Marcotte EM Briefings in functional genomics 26462863 Brief Funct Genomics 2016 Mar
Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity. Kachroo AH, Laurent JM, Yellman CM, Meyer AG, Wilke CO, Marcotte EM Science (New York, N.Y.) 25999509 Science 2015 May 22
UVnovo: A de Novo Sequencing Algorithm Using Single Series of Fragment Ions via Chromophore Tagging and 351 nm Ultraviolet Photodissociation Mass Spectrometry. Robotham SA, Horton AP, Cannon JR, Cotham VC, Marcotte EM, Brodbelt JS Analytical chemistry 26938041 Anal Chem 2016 Apr 5
Systematic bacterialization of yeast genes identifies a near-universally swappable pathway. Kachroo AH, Laurent JM, Akhmetov A, Szilagyi-Jones M, McWhite CD, Zhao A, Marcotte EM eLife 28661399 Elife 2017 Jun 29
A liquid-like organelle at the root of motile ciliopathy. Huizar RL, Lee C, Boulgakov AA, Horani A, Tu F, Marcotte EM, Brody SL, Wallingford JB eLife 30561330 Elife 2018 Dec 18
The proteomic response to mutants of the Escherichia coli RNA degradosome. Zhou L, Zhang AB, Wang R, Marcotte EM, Vogel C Molecular bioSystems 23403814 Mol Biosyst 2013 Apr 5
Statistical approach to protein quantification. Gerster S, Kwon T, Ludwig C, Matondo M, Vogel C, Marcotte EM, Aebersold R, Bühlmann P Molecular & cellular proteomics : MCP 24255132 Mol Cell Proteomics 2014 Feb
Applications of comparative evolution to human disease genetics. McWhite CD, Liebeskind BJ, Marcotte EM Current opinion in genetics & development 26338499 Curr Opin Genet Dev 2015 Dec
Sperm is epigenetically programmed to regulate gene transcription in embryos. Teperek M, Simeone A, Gaggioli V, Miyamoto K, Allen GE, Erkek S, Kwon T, Marcotte EM, Zegerman P, Bradshaw CR, Peters AH, Gurdon JB, Jullien J Genome research 27034506 Genome Res 2016 Aug
Computational discovery of pathway-level genetic vulnerabilities in non-small-cell lung cancer. Young JH, Peyton M, Seok Kim H, McMillan E, Minna JD, White MA, Marcotte EM Bioinformatics (Oxford, England) 26755624 Bioinformatics 2016 May 1
A highly parallel strategy for storage of digital information in living cells. Akhmetov A, Ellington AD, Marcotte EM BMC biotechnology 30333005 BMC Biotechnol 2018 Oct 17
Highly parallel single-molecule identification of proteins in zeptomole-scale mixtures. Swaminathan J, Boulgakov AA, Hernandez ET, Bardo AM, Bachman JL, Marotta J, Johnson AM, Anslyn EV, Marcotte EM Nature biotechnology 30346938 Nat Biotechnol 2018 Oct 22
Protein localization screening in vivo reveals novel regulators of multiciliated cell development and function. Tu F, Sedzinski J, Ma Y, Marcotte EM, Wallingford JB Journal of cell science 29180514 J Cell Sci 2018 Jan 29
Modes of interaction between individuals dominate the topologies of real world networks. Lee I, Kim E, Marcotte EM PloS one 25793969 PLoS One 2015
Controlled Measurement and Comparative Analysis of Cellular Components in E. coli Reveals Broad Regulatory Changes in Response to Glucose Starvation. Houser JR, Barnhart C, Boutz DR, Carroll SM, Dasgupta A, Michener JK, Needham BD, Papoulas O, Sridhara V, Sydykova DK, Marx CJ, Trent MS, Barrick JE, Marcotte EM, Wilke CO PLoS computational biology 26275208 PLoS Comput Biol 2015 Aug
Protein-to-mRNA ratios are conserved between Pseudomonas aeruginosa strains. Kwon T, Huse HK, Vogel C, Whiteley M, Marcotte EM Journal of proteome research 24742327 J Proteome Res 2014 May 2
Synthesis of Carboxy ATTO 647N Using Redox Cycling for Xanthone Access. Bachman JL, Pavlich CI, Boley AJ, Marcotte EM, Anslyn EV Organic letters 31825225 Org Lett 2020 Jan 17
Systematic comparison of variant calling pipelines using gold standard personal exome variants. Hwang S, Kim E, Lee I, Marcotte EM Scientific reports 26639839 Sci Rep 2015 Dec 7
A self-assembling lanthanide molecular nanoparticle for optical imaging. Brown KA, Yang X, Schipper D, Hall JW, DePue LJ, Gnanam AJ, Arambula JF, Jones JN, Swaminathan J, Dieye Y, Vadivelu J, Chandler DJ, Marcotte EM, Sessler JL, Ehrlich LI, Jones RA Dalton transactions (Cambridge, England : 2003) 25512085 Dalton Trans 2015 Feb 14
An efficient methodology to introduce o-(aminomethyl)phenyl-boronic acids into peptides: alkylation of secondary amines. Hernandez ET, Kolesnichenko IV, Reuther JF, Anslyn EV New journal of chemistry = Nouveau journal de chimie 28649175 New J Chem 2017 Jan 7
Metabolic crosstalk regulates Porphyromonas gingivalis colonization and virulence during oral polymicrobial infection. Kuboniwa M, Houser JR, Hendrickson EL, Wang Q, Alghamdi SA, Sakanaka A, Miller DP, Hutcherson JA, Wang T, Beck DAC, Whiteley M, Amano A, Wang H, Marcotte EM, Hackett M, Lamont RJ Nature microbiology 28924191 Nat Microbiol 2017 Nov
Improved Xanthone Synthesis, Stepwise Chemical Redox Cycling. Bachman JL, Escamilla PR, Boley AJ, Pavlich CI, Anslyn EV Organic letters 30582707 Org Lett 2019 Jan 4
HumanNet v2: human gene networks for disease research. Hwang S, Kim CY, Yang S, Kim E, Hart T, Marcotte EM, Lee I Nucleic acids research 30418591 Nucleic Acids Res 2019 Jan 8
Classification of Single Particles from Human Cell Extract Reveals Distinct Structures. Verbeke EJ, Mallam AL, Drew K, Marcotte EM, Taylor DW Cell reports 29972786 Cell Rep 2018 Jul 3
2,2'-Bipyridine and hydrazide containing peptides for cyclization and complex quaternary structural control. Hernandez ET, Rogelio Escamilla P, Kwon SY, Partridge J, McVeigh M, Rivera S, Reuther JF, Anslyn EV New journal of chemistry = Nouveau journal de chimie 30386131 New J Chem 2018 Jun 7
Single-step Precision Genome Editing in Yeast Using CRISPR-Cas9. Akhmetov A, Laurent JM, Gollihar J, Gardner EC, Garge RK, Ellington AD, Kachroo AH, Marcotte EM Bio-protocol 29770349 Bio Protoc 2018 Mar 20
The ciliopathy-associated CPLANE proteins direct basal body recruitment of intraflagellar transport machinery. Toriyama M, Lee C, Taylor SP, Duran I, Cohn DH, Bruel AL, Tabler JM, Drew K, Kelly MR, Kim S, Park TJ, Braun DA, Pierquin G, Biver A, Wagner K, Malfroot A, Panigrahi I, Franco B, Al-Lami HA, Yeung Y, Choi YJ, University of Washington Center for Mendelian Genomics, Duffourd Y, Faivre L, Rivière JB, Chen J, Liu KJ, Marcotte EM, Hildebrandt F, Thauvin-Robinet C, Krakow D, Jackson PK, Wallingford JB Nature genetics 27158779 Nat Genet 2016 Jun
Systems-wide Studies Uncover Commander, a Multiprotein Complex Essential to Human Development. Mallam AL, Marcotte EM Cell systems 28544880 Cell Syst 2017 May 24
A proteomic survey of widespread protein aggregation in yeast. O'Connell JD, Tsechansky M, Royal A, Boutz DR, Ellington AD, Marcotte EM Molecular bioSystems 24488121 Mol Biosyst 2014 Apr
Bacteriophages use an expanded genetic code on evolutionary paths to higher fitness. Hammerling MJ, Ellefson JW, Boutz DR, Marcotte EM, Ellington AD, Barrick JE Nature chemical biology 24487692 Nat Chem Biol 2014 Mar
MouseNet v2: a database of gene networks for studying the laboratory mouse and eight other model vertebrates. Kim E, Hwang S, Kim H, Shim H, Kang B, Yang S, Shim JH, Shin SY, Marcotte EM, Lee I Nucleic acids research 26527726 Nucleic Acids Res 2016 Jan 4
Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Phanse S, Wan C, Borgeson B, Tu F, Drew K, Clark G, Xiong X, Kagan O, Kwan J, Bezginov A, Chessman K, Pal S, Cromar G, Papoulas O, Ni Z, Boutz DR, Stoilova S, Havugimana PC, Guo X, Malty RH, Sarov M, Greenblatt J, Babu M, Derry WB, Tillier ER, Wallingford JB, Parkinson J, Marcotte EM, Emili A Data in brief 26870755 Data Brief 2016 Mar
A theoretical justification for single molecule peptide sequencing. Swaminathan J, Boulgakov AA, Marcotte EM PLoS computational biology 25714988 PLoS Comput Biol 2015 Feb
Towards Consensus Gene Ages. Liebeskind BJ, McWhite CD, Marcotte EM Genome biology and evolution 27259914 Genome Biol Evol 2016 Jun 27
Global tRNA misacylation induced by anaerobiosis and antibiotic exposure broadly increases stress resistance in Escherichia coli. Schwartz MH, Waldbauer JR, Zhang L, Pan T Nucleic acids research 27672035 Nucleic Acids Res 2016 Dec 1
Methionine Mistranslation Bypasses the Restraint of the Genetic Code to Generate Mutant Proteins with Distinct Activities. Wang X, Pan T PLoS genetics 26709516 PLoS Genet 2015 Dec
Diversity of human tRNA genes from the 1000-genomes project. Parisien M, Wang X, Pan T RNA biology 24448271 RNA Biol 2013 Dec
My adventure in tRNA biology, so far. Pan T RNA (New York, N.Y.) 25780201 RNA 2015 Apr
Efficient and quantitative high-throughput tRNA sequencing. Zheng G, Qin Y, Clark WC, Dai Q, Yi C, He C, Lambowitz AM, Pan T Nature methods 26214130 Nat Methods 2015 Sep
tRNA base methylation identification and quantification via high-throughput sequencing. Clark WC, Evans ME, Dominissini D, Zheng G, Pan T RNA (New York, N.Y.) 27613580 RNA 2016 Nov
tRNA Misacylation with Methionine in the Mouse Gut Microbiome in Situ. Schwartz MH, Pan T Microbial ecology 28070678 Microb Ecol 2017 Jul
Codon optimality controls differential mRNA translation during amino acid starvation. Saikia M, Wang X, Mao Y, Wan J, Pan T, Qian SB RNA (New York, N.Y.) 27613579 RNA 2016 Nov
Evolutionary Gain of Alanine Mischarging to Noncognate tRNAs with a G4:U69 Base Pair. Sun L, Gomes AC, He W, Zhou H, Wang X, Pan DW, Schimmel P, Pan T, Yang XL Journal of the American Chemical Society 27622773 J Am Chem Soc 2016 Oct 5
Temperature dependent mistranslation in a hyperthermophile adapts proteins to lower temperatures. Schwartz MH, Pan T Nucleic acids research 26657639 Nucleic Acids Res 2016 Jan 8
Adaptive translation as a mechanism of stress response and adaptation. Pan T Annual review of genetics 23988117 Annu Rev Genet 2013
N(6)-Methyladenosine Modification in a Long Noncoding RNA Hairpin Predisposes Its Conformation to Protein Binding. Zhou KI, Parisien M, Dai Q, Liu N, Diatchenko L, Sachleben JR, Pan T Journal of molecular biology 26343757 J Mol Biol 2016 Feb 27
Interaction of tRNA with MEK2 in pancreatic cancer cells. Wang X, Chow CR, Ebine K, Lee J, Rosner MR, Pan T, Munshi HG Scientific reports 27301426 Sci Rep 2016 Jun 15
Determining the fidelity of tRNA aminoacylation via microarrays. Schwartz MH, Pan T Methods (San Diego, Calif.) 27639882 Methods 2017 Jan 15
Modifications and functional genomics of human transfer RNA. Pan T Cell research 29463900 Cell Res 2018 Apr
Misacylation of tRNA with methionine in Saccharomyces cerevisiae. Wiltrout E, Goodenbour JM, Fréchin M, Pan T Nucleic acids research 22941646 Nucleic Acids Res 2012 Nov 1
Function and origin of mistranslation in distinct cellular contexts. Schwartz MH, Pan T Critical reviews in biochemistry and molecular biology 28075177 Crit Rev Biochem Mol Biol 2017 Apr
A dual fluorescent reporter for the investigation of methionine mistranslation in live cells. Gomes AC, Kordala AJ, Strack R, Wang X, Geslain R, Delaney K, Clark WC, Keenan R, Pan T RNA (New York, N.Y.) 26729921 RNA 2016 Mar
Stress Response and Adaptation Mediated by Amino Acid Misincorporation during Protein Synthesis. Wang X, Pan T Advances in nutrition (Bethesda, Md.) 27422514 Adv Nutr 2016 Jul
Selective Enzymatic Demethylation of N(2) ,N(2) -Dimethylguanosine in RNA and Its Application in High-Throughput tRNA Sequencing. Dai Q, Zheng G, Schwartz MH, Clark WC, Pan T Angewandte Chemie (International ed. in English) 28371071 Angew Chem Int Ed Engl 2017 Apr 24
Improving membrane protein expression by optimizing integration efficiency. Niesen MJM, Marshall SS, Miller TF 3rd, Clemons WM Jr The Journal of biological chemistry 28918393 J Biol Chem 2017 Nov 24
Chemoenzymatic syntheses of water-soluble lipid I fluorescent probes. Mitachi K, Siricilla S, Klaic L, Clemons WM Jr, Kurosu M Tetrahedron letters 26190869 Tetrahedron Lett 2015 Jun 3
Structurally derived universal mechanism for the catalytic cycle of the tail-anchored targeting factor Get3. Fry MY, Najdrová V, Maggiolo AO, Saladi SM, Doležal P, Clemons WM Jr Nature structural & molecular biology 35851188 Nat Struct Mol Biol 2022 Aug
A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency. Marshall SS, Niesen MJM, Müller A, Tiemann K, Saladi SM, Galimidi RP, Zhang B, Clemons WM Jr, Miller TF 3rd Cell reports 27524616 Cell Rep 2016 Aug 23
Comprehensive proteomic profiling of outer membrane vesicles from Campylobacter jejuni. Jang KS, Sweredoski MJ, Graham RL, Hess S, Clemons WM Jr Journal of proteomics 24382552 J Proteomics 2014 Feb 26
A statistical model for improved membrane protein expression using sequence-derived features. Saladi SM, Javed N, Müller A, Clemons WM Jr The Journal of biological chemistry 29378850 J Biol Chem 2018 Mar 30
A cationic cysteine-hydrazide as an enrichment tool for the mass spectrometric characterization of bacterial free oligosaccharides. Jang KS, Nani RR, Kalli A, Levin S, Müller A, Hess S, Reisman SE, Clemons WM Jr Analytical and bioanalytical chemistry 26100547 Anal Bioanal Chem 2015 Aug
Sequence-based features that are determinant for tail-anchored membrane protein sorting in eukaryotes. Fry MY, Saladi SM, Cunha A, Clemons WM Jr Traffic (Copenhagen, Denmark) 34288289 Traffic 2021 Sep
Molecular basis of tail-anchored integral membrane protein recognition by the cochaperone Sgt2. Lin KF, Fry MY, Saladi SM, Clemons WM Jr The Journal of biological chemistry 33610544 J Biol Chem 2021 Jan-Jun
The STI1-domain is a flexible alpha-helical fold with a hydrophobic groove. Fry MY, Saladi SM, Clemons WM Jr Protein science : a publication of the Protein Society 33620121 Protein Sci 2021 Apr
Structures of Get3d reveal a distinct architecture associated with the emergence of photosynthesis. Barlow AN, Manu MS, Saladi SM, Tarr PT, Yadav Y, Thinn AMM, Zhu Y, Laganowsky AD, Clemons WM Jr, Ramasamy S The Journal of biological chemistry 37100288 J Biol Chem 2023 Jun
The checkpoint for agonist selection precedes conventional selection in human thymus. Verstichel G, Vermijlen D, Martens L, Goetgeluk G, Brouwer M, Thiault N, Van Caeneghem Y, De Munter S, Weening K, Bonte S, Leclercq G, Taghon T, Kerre T, Saeys Y, Van Dorpe J, Cheroutre H, Vandekerckhove B Science immunology 28783686 Sci Immunol 2017 Feb 24
Following the fate of one insulin-reactive CD4 T cell: conversion into Teffs and Tregs in the periphery controls diabetes in NOD mice. Fousteri G, Jasinski J, Dave A, Nakayama M, Pagni P, Lambolez F, Juntti T, Sarikonda G, Cheng Y, Croft M, Cheroutre H, Eisenbarth G, von Herrath M Diabetes 22403296 Diabetes 2012 May
Negative selection of self-reactive chicken B cells requires B cell receptor signaling and is independent of the bursal microenvironment. Davani D, Pancer Z, Cheroutre H, Ratcliffe MJ Journal of immunology (Baltimore, Md. : 1950) 24516196 J Immunol 2014 Apr 1
Controlling airborne cues to study small animal navigation. Gershow M, Berck M, Mathew D, Luo L, Kane EA, Carlson JR, Samuel AD Nature methods 22245808 Nat Methods 2012 Jan 15
Imaging whole nervous systems: insights into behavior from worms to fish. Calarco JA, Samuel ADT Nature methods 30573822 Nat Methods 2019 Jan
Functional diversity among sensory receptors in a Drosophila olfactory circuit. Mathew D, Martelli C, Kelley-Swift E, Brusalis C, Gershow M, Samuel AD, Emonet T, Carlson JR Proceedings of the National Academy of Sciences of the United States of America 23690583 Proc Natl Acad Sci U S A 2013 Jun 4
Pan-neuronal imaging in roaming Caenorhabditis elegans. Venkatachalam V, Ji N, Wang X, Clark C, Mitchell JK, Klein M, Tabone CJ, Florman J, Ji H, Greenwood J, Chisholm AD, Srinivasan J, Alkema M, Zhen M, Samuel AD Proceedings of the National Academy of Sciences of the United States of America 26711989 Proc Natl Acad Sci U S A 2016 Feb 23
The Ionotropic Receptors IR21a and IR25a mediate cool sensing in Drosophila. Ni L, Klein M, Svec KV, Budelli G, Chang EC, Ferrer AJ, Benton R, Samuel AD, Garrity PA eLife 27126188 Elife 2016 Apr 29
An extrasynaptic GABAergic signal modulates a pattern of forward movement in Caenorhabditis elegans. Shen Y, Wen Q, Liu H, Zhong C, Qin Y, Harris G, Kawano T, Wu M, Xu T, Samuel AD, Zhang Y eLife 27138642 Elife 2016 May 3
Integration of Plasticity Mechanisms within a Single Sensory Neuron of C. elegans Actuates a Memory. Hawk JD, Calvo AC, Liu P, Almoril-Porras A, Aljobeh A, Torruella-Suárez ML, Ren I, Cook N, Greenwood J, Luo L, Wang ZW, Samuel ADT, Colón-Ramos DA Neuron 29307713 Neuron 2018 Jan 17
Reverse-correlation analysis of navigation dynamics in Drosophila larva using optogenetics. Hernandez-Nunez L, Belina J, Klein M, Si G, Claus L, Carlson JR, Samuel AD eLife 25942453 Elife 2015 May 5
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Differential targeting of feline photoreceptors by recombinant adeno-associated viral vectors: implications for preclinical gene therapy trials. Minella AL, Mowat FM, Willett KL, Sledge D, Bartoe JT, Bennett J, Petersen-Jones SM Gene therapy 25056608 Gene Ther 2014 Oct
Synthetic Adeno-Associated Viral Vector Efficiently Targets Mouse and Nonhuman Primate Retina In Vivo. Carvalho LS, Xiao R, Wassmer SJ, Langsdorf A, Zinn E, Pacouret S, Shah S, Comander JI, Kim LA, Lim L, Vandenberghe LH Human gene therapy 29325457 Hum Gene Ther 2018 Jul
Amelioration of Neurosensory Structure and Function in Animal and Cellular Models of a Congenital Blindness. Song JY, Aravand P, Nikonov S, Leo L, Lyubarsky A, Bennicelli JL, Pan J, Wei Z, Shpylchak I, Herrera P, Bennett DJ, Commins N, Maguire AM, Pham J, den Hollander AI, Cremers FPM, Koenekoop RK, Roepman R, Nishina P, Zhou S, Pan W, Ying GS, Aleman TS, de Melo J, McNamara I, Sun J, Mills J, Bennett J Molecular therapy : the journal of the American Society of Gene Therapy 29673930 Mol Ther 2018 Jun 6
AAV8BP2 and AAV8 transduce the mammalian cochlear lateral wall and endolymphatic sac with high efficiency. Isgrig K, Ishibashi Y, Lee HJ, Zhu J, Grati M, Bennett J, Griffith AJ, Roux I, Chien WW Molecular therapy. Methods & clinical development 36034771 Mol Ther Methods Clin Dev 2022 Sep 8
Refining surgical techniques for efficient posterior semicircular canal gene delivery in the adult mammalian inner ear with minimal hearing loss. Zhu J, Choi JW, Ishibashi Y, Isgrig K, Grati M, Bennett J, Chien W Scientific reports 34552193 Sci Rep 2021 Sep 22
Disruption of CEP290 microtubule/membrane-binding domains causes retinal degeneration. Drivas TG, Holzbaur EL, Bennett J The Journal of clinical investigation 24051377 J Clin Invest 2013 Oct
Safety and durability of effect of contralateral-eye administration of AAV2 gene therapy in patients with childhood-onset blindness caused by RPE65 mutations: a follow-on phase 1 trial. Bennett J, Wellman J, Marshall KA, McCague S, Ashtari M, DiStefano-Pappas J, Elci OU, Chung DC, Sun J, Wright JF, Cross DR, Aravand P, Cyckowski LL, Bennicelli JL, Mingozzi F, Auricchio A, Pierce EA, Ruggiero J, Leroy BP, Simonelli F, High KA, Maguire AM Lancet (London, England) 27375040 Lancet 2016 Aug 13
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AAV2.7m8 is a powerful viral vector for inner ear gene therapy. Isgrig K, McDougald DS, Zhu J, Wang HJ, Bennett J, Chien WW Nature communications 30683875 Nat Commun 2019 Jan 25
Novel mobility test to assess functional vision in patients with inherited retinal dystrophies. Chung DC, McCague S, Yu ZF, Thill S, DiStefano-Pappas J, Bennett J, Cross D, Marshall K, Wellman J, High KA Clinical & experimental ophthalmology 28697537 Clin Exp Ophthalmol 2018 Apr
Taking Stock of Retinal Gene Therapy: Looking Back and Moving Forward. Bennett J Molecular therapy : the journal of the American Society of Gene Therapy 28391961 Mol Ther 2017 May 3
Evaluation of Dose and Safety of AAV7m8 and AAV8BP2 in the Non-Human Primate Retina. Ramachandran PS, Lee V, Wei Z, Song JY, Casal G, Cronin T, Willett K, Huckfeldt R, Morgan JI, Aleman TS, Maguire AM, Bennett J Human gene therapy 27750461 Hum Gene Ther 2017 Feb
Single stranded adeno-associated virus achieves efficient gene transfer to anterior segment in the mouse eye. Wang L, Xiao R, Andres-Mateos E, Vandenberghe LH PloS one 28763501 PLoS One 2017
fMRI of retina-originated phosphenes experienced by patients with Leber congenital amaurosis. Ashtari M, Cyckowski L, Yazdi A, Viands A, Marshall K, Bókkon I, Maguire A, Bennett J PloS one 24465873 PLoS One 2014
Plasticity of the human visual system after retinal gene therapy in patients with Leber's congenital amaurosis. Ashtari M, Zhang H, Cook PA, Cyckowski LL, Shindler KS, Marshall KA, Aravand P, Vossough A, Gee JC, Maguire AM, Baker CI, Bennett J Science translational medicine 26180100 Sci Transl Med 2015 Jul 15
An Autogenously Regulated Expression System for Gene Therapeutic Ocular Applications. Sochor MA, Vasireddy V, Drivas TG, Wojno A, Doung T, Shpylchak I, Bennicelli J, Chung D, Bennett J, Lewis M Scientific reports 26597678 Sci Rep 2015 Nov 24
Evaluating Efficiencies of Dual AAV Approaches for Retinal Targeting. Carvalho LS, Turunen HT, Wassmer SJ, Luna-Velez MV, Xiao R, Bennett J, Vandenberghe LH Frontiers in neuroscience 28943836 Front Neurosci 2017
Efficacy and safety of voretigene neparvovec (AAV2-hRPE65v2) in patients with RPE65-mediated inherited retinal dystrophy: a randomised, controlled, open-label, phase 3 trial. Russell S, Bennett J, Wellman JA, Chung DC, Yu ZF, Tillman A, Wittes J, Pappas J, Elci O, McCague S, Cross D, Marshall KA, Walshire J, Kehoe TL, Reichert H, Davis M, Raffini L, George LA, Hudson FP, Dingfield L, Zhu X, Haller JA, Sohn EH, Mahajan VB, Pfeifer W, Weckmann M, Johnson C, Gewaily D, Drack A, Stone E, Wachtel K, Simonelli F, Leroy BP, Wright JF, High KA, Maguire AM Lancet (London, England) 28712537 Lancet 2017 Aug 26
Exosome-associated AAV2 vector mediates robust gene delivery into the murine retina upon intravitreal injection. Wassmer SJ, Carvalho LS, György B, Vandenberghe LH, Maguire CA Scientific reports 28361998 Sci Rep 2017 Mar 31
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Evaluating Public Health Interventions: 4. The Nurses' Health Study and Methods for Eliminating Bias Attributable to Measurement Error and Misclassification. Spiegelman D American journal of public health 27509282 Am J Public Health 2016 Sep
There is no impact of exposure measurement error on latency estimation in linear models. Peskoe SB, Spiegelman D, Wang M Statistics in medicine 30515870 Stat Med 2019 Mar 30
Augmented pseudo-likelihood estimation for two-phase studies. Rivera-Rodriguez C, Haneuse S, Wang M, Spiegelman D Statistical methods in medical research 30834815 Stat Methods Med Res 2020 Feb
Impact of the Affordable Care Act on Colorectal Cancer Incidence and Mortality. Lee C, Kushi LH, Reed ME, Eldridge EH, Lee JK, Zhang J, Spiegelman D American journal of preventive medicine 34763959 Am J Prev Med 2022 Mar
Facilitators and barriers to healthy eating in a worksite cafeteria: a qualitative study. Stern D, Blanco I, Olmos LA, Valdivia JJ, Shrestha A, Mattei J, Spiegelman D BMC public health 34022846 BMC Public Health 2021 May 22
Evaluating Public Health Interventions: 2. Stepping Up to Routine Public Health Evaluation With the Stepped Wedge Design. Spiegelman D American journal of public health 26885961 Am J Public Health 2016 Mar
Service readiness of health facilities in Bangladesh, Haiti, Kenya, Malawi, Namibia, Nepal, Rwanda, Senegal, Uganda and the United Republic of Tanzania. Leslie HH, Spiegelman D, Zhou X, Kruk ME Bulletin of the World Health Organization 29147054 Bull World Health Organ 2017 Nov 1
Inverse probability weighted estimation of risk under representative interventions in observational studies. Young JG, Logan RW, Robins JM, Hernán MA Journal of the American Statistical Association 31564760 J Am Stat Assoc 2019
Interpretation of the Individual Effect Under Treatment Spillover. Crawford FW, Morozova O, Buchanan AL, Spiegelman D American journal of epidemiology 31094425 Am J Epidemiol 2019 Aug 1
Association of the US President's Emergency Plan for AIDS Relief's Funding With Prevention of Mother-to-Child Transmission of HIV in Kenya. Barnhart DA, Tsikhutsu I, Kirui D, Sawe F, Muli J, Sugut W, Abboud N, Birx D, Hamm T, Coakley P, Hickey PW, Wolfman V, Lee E, Spiegelman D JAMA network open 31517966 JAMA Netw Open 2019 Sep 4
On the Analysis of Case-Control Studies in Cluster-correlated Data Settings. Haneuse S, Rivera-Rodriguez C Epidemiology (Cambridge, Mass.) 29068840 Epidemiology 2018 Jan
Spiegelman Responds. Spiegelman D American journal of public health 27153027 Am J Public Health 2016 Jun
Assessing the quality of tuberculosis care using routine surveillance data: a process evaluation employing the Zero TB Indicator Framework in Mongolia. Saranjav A, Parisi C, Zhou X, Dorjnamjil K, Samdan T, Erdenebaatar S, Chuluun A, Dalkh T, Ganbaatar G, Brooks MB, Spiegelman D, Ganmaa D, Davis JL BMJ open 35973702 BMJ Open 2022 Aug 16
Assessing Direct and Spillover Effects of Intervention Packages in Network-Randomized Studies. Buchanan AL, Hernández-Ramírez RU, Lok JJ, Vermund SH, Friedman SR, Forastiere L, Spiegelman D medRxiv : the preprint server for health sciences 38352598 medRxiv 2024 Feb 1
Overall, Direct, Spillover, and Composite Effects of Components of a Peer-Driven Intervention Package on Injection Risk Behavior Among People Who Inject Drugs in the HPTN 037 Study. Hernández-Ramírez RU, Spiegelman D, Lok JJ, Forastiere L, Friedman SR, Latkin CA, Vermund SH, Buchanan AL AIDS and behavior 37932493 AIDS Behav 2024 Jan
A note on "Design and analysis of stepped wedge cluster randomized trials". Liao X, Zhou X, Spiegelman D Contemporary clinical trials 26394003 Contemp Clin Trials 2015 Nov
Evaluating Public Health Interventions: 1. Examples, Definitions, and a Personal Note. Spiegelman D American journal of public health 26562122 Am J Public Health 2016 Jan
Evaluating Public Health Interventions: 5. Causal Inference in Public Health Research-Do Sex, Race, and Biological Factors Cause Health Outcomes? Glymour MM, Spiegelman D American journal of public health 27854526 Am J Public Health 2017 Jan
Comparison of HPV-16 and HPV-18 Genotyping and Cytological Testing as Triage Testing Within Human Papillomavirus-Based Screening in Mexico. Torres-Ibarra L, Cuzick J, Lorincz AT, Spiegelman D, Lazcano-Ponce E, Franco EL, Moscicki AB, Mahmud SM, Wheeler CM, Rivera-Paredez B, Hernández-López R, León-Maldonado L, Salmerón J, FRIDA Study Group. JAMA network open 31747033 JAMA Netw Open 2019 Nov 1
Facilitators and barriers to healthy eating in a worksite cafeteria: a qualitative study from Nepal. Shrestha A, Pyakurel P, Shrestha A, Gautam R, Manandhar N, Rhodes E, Tamrakar D, Karmacharya BM, Malik V, Mattei J, Spiegelman D Heart Asia 29225703 Heart Asia 2017
A maximum likelihood approach to power calculations for stepped wedge designs of binary outcomes. Zhou X, Liao X, Kunz LM, Normand ST, Wang M, Spiegelman D Biostatistics (Oxford, England) 30084949 Biostatistics 2020 Jan 1
Coaching Intensity, Adherence to Essential Birth Practices, and Health Outcomes in the BetterBirth Trial in Uttar Pradesh, India. Barnhart DA, Spiegelman D, Zigler CM, Kara N, Delaney MM, Kalita T, Maji P, Hirschhorn LR, Semrau KEA Global health, science and practice 32127359 Glob Health Sci Pract 2020 Mar 30
swdpwr: A SAS macro and an R package for power calculations in stepped wedge cluster randomized trials. Chen J, Zhou X, Li F, Spiegelman D Computer methods and programs in biomedicine 34818620 Comput Methods Programs Biomed 2022 Jan
Partial Identification of the Average Treatment Effect Using Instrumental Variables: Review of Methods for Binary Instruments, Treatments, and Outcomes. Swanson SA, Hernán MA, Miller M, Robins JM, Richardson TS Journal of the American Statistical Association 31537952 J Am Stat Assoc 2018
The Association of Cooking Fuel Use, Dietary Intake, and Blood Pressure among Rural Women in China. Bellows AL, Spiegelman D, Du S, Jaacks LM International journal of environmental research and public health 32751678 Int J Environ Res Public Health 2020 Jul 30
Estimating the natural indirect effect and the mediation proportion via the product method. Cheng C, Spiegelman D, Li F BMC medical research methodology 34800985 BMC Med Res Methodol 2021 Nov 20
Mediation analysis in the presence of continuous exposure measurement error. Cheng C, Spiegelman D, Li F Statistics in medicine 36869626 Stat Med 2023 May 20
Evaluating Public Health Interventions: 3. The Two-Stage Design for Confounding Bias Reduction-Having Your Cake and Eating It Two. Spiegelman D, Rivera-Rodriguez CL, Haneuse S American journal of public health 27285260 Am J Public Health 2016 Jul
On the analysis of two-phase designs in cluster-correlated data settings. Rivera-Rodriguez C, Spiegelman D, Haneuse S Statistics in medicine 31359448 Stat Med 2019 Oct 15
Optimizing the development and evaluation of complex interventions: lessons learned from the BetterBirth Program and associated trial. Barnhart DA, Semrau KEA, Zigler CM, Molina RL, Delaney MM, Hirschhorn LR, Spiegelman D Implementation science communications 32885188 Implement Sci Commun 2020
Worksite intervention study to prevent diabetes in Nepal: a randomised trial protocol. Pyakurel P, Shrestha A, Karmacharya BM, Budhathoki SS, Chaudhari RK, Tamrakar D, Shrestha A, Karmacharya RM, Shrestha A, Sharma S, Sharma SK, Spiegelman D Open heart 32847993 Open Heart 2020 Aug
Survival analysis with functions of mismeasured covariate histories: the case of chronic air pollution exposure in relation to mortality in the nurses' health study. Liao X, Zhou X, Wang M, Hart JE, Laden F, Spiegelman D Journal of the Royal Statistical Society. Series C, Applied statistics 29430064 J R Stat Soc Ser C Appl Stat 2018 Feb
Multiple robust estimation of marginal structural mean models for unconstrained outcomes. Babino L, Rotnitzky A, Robins J Biometrics 30004573 Biometrics 2019 Mar
Access of choice-disabled young women in Botswana to government structural support programmes: a cross-sectional study. Cockcroft A, Marokoane N, Kgakole L, Tswetla N, Andersson N AIDS care 29848044 AIDS Care 2018 Jun
Evaluating Public Health Interventions: 7. Let the Subject Matter Choose the Effect Measure: Ratio, Difference, or Something Else Entirely. Spiegelman D, Khudyakov P, Wang M, Vanderweele TJ American journal of public health 29161073 Am J Public Health 2018 Jan
Exposure misclassification in propensity score-based time-to-event data analysis. Yang Y, Wang M Statistical methods in medical research 33826453 Stat Methods Med Res 2021 May
How are qualitative methods used in implementation science research? A scoping review protocol. Hagaman A, Rhodes EC, Nyhan K, Katague M, Schwartz A, Spiegelman D JBI evidence synthesis 33323772 JBI Evid Synth 2021 Jun
Evaluating Public Health Interventions: 6. Modeling Ratios or Differences? Let the Data Tell Us. Spiegelman D, VanderWeele TJ American journal of public health 28590865 Am J Public Health 2017 Jul
The fidelity of implementation of recommended care for children with malaria by community health workers in Nigeria. Adeoti O, Spiegelman D, Afonne C, Falade CO, Jegede AS, Oshiname FO, Gomes M, Ajayi IO Implementation science : IS 32131852 Implement Sci 2020 Mar 4
Structural, interpersonal, psychosocial, and behavioral risk factors for HIV acquisition among female bar workers in Dar es Salaam, Tanzania. Barnhart DA, Harling G, Muya A, Ortblad KF, Mashasi I, Dambach P, Ulenga N, Mboggo E, Oldenburg CE, Bärnighausen TW, Spiegelman D AIDS care 31079476 AIDS Care 2019 Sep
Drivers of healthy eating in a workplace in Nepal: a qualitative study. Tamrakar D, Shrestha A, Rai A, Karmacharya BM, Malik V, Mattei J, Spiegelman D BMJ open 32102804 BMJ Open 2020 Feb 25
"Cross-sectional" stepped wedge designs always reduce the required sample size when there is no time effect. Zhou X, Liao X, Spiegelman D Journal of clinical epidemiology 28093263 J Clin Epidemiol 2017 Mar
Nepal Pioneer Worksite Intervention Study to lower cardio-metabolic risk factors: design and protocol. Shrestha A, Tamrakar D, Karmacharya BM, Shrestha A, Shrestha R, Bhatta RD, Pyakurel P, Khudyakov P, Malik V, Mattei J, Spiegelman D BMC cardiovascular disorders 30819098 BMC Cardiovasc Disord 2019 Feb 28
Spiegelman and Zhou Respond. Spiegelman D, Zhou X American journal of public health 30726133 Am J Public Health 2019 Mar
Estimation and Inference for the Mediation Proportion. Nevo D, Liao X, Spiegelman D The international journal of biostatistics 28930628 Int J Biostat 2017 Sep 20
Dietary interventions to prevent and manage diabetes in worksite settings: a meta-analysis. Shrestha A, Karmacharya BM, Khudyakov P, Weber MB, Spiegelman D Journal of occupational health 29187673 J Occup Health 2018 Jan 25
Estimation in the Cox survival regression model with covariate measurement error and a changepoint. Agami S, Zucker DM, Spiegelman D Biometrical journal. Biometrische Zeitschrift 32003495 Biom J 2020 Sep
Impact of the Affordable Care Act on Colorectal Cancer Outcomes: A Systematic Review. Xu MR, Kelly AMB, Kushi LH, Reed ME, Koh HK, Spiegelman D American journal of preventive medicine 32008799 Am J Prev Med 2020 Apr
Evaluating Public Health Interventions: 8. Causal Inference for Time-Invariant Interventions. Spiegelman D, Zhou X American journal of public health 30024804 Am J Public Health 2018 Sep
Assessing Individual and Disseminated Effects in Network-Randomized Studies. Buchanan AL, Vermund SH, Friedman SR, Spiegelman D American journal of epidemiology 30052722 Am J Epidemiol 2018 Nov 1
Health system measurement: Harnessing machine learning to advance global health. Leslie HH, Zhou X, Spiegelman D, Kruk ME PloS one 30289935 PLoS One 2018
Diet and Health - What Should We Eat ? Shrestha A, Spiegelman D Kathmandu University medical journal (KUMJ) 30353891 Kathmandu Univ Med J (KUMJ) 2017 Jul-Sept.
The effect of risk factor misclassification on the partial population attributable risk. Wong BHW, Peskoe SB, Spiegelman D Statistics in medicine 29333614 Stat Med 2018 Apr 15
Prevalence estimation when disease status is verified only among test positives: Applications in HIV screening programs. G Thomas E, B Peskoe S, Spiegelman D Statistics in medicine 29230839 Stat Med 2018 Mar 30
ANALYSIS OF "LEARN-AS-YOU-GO" (LAGO) STUDIES. Nevo D, Lok JJ, Spiegelman D Annals of statistics 35510045 Ann Stat 2021 Apr
Intra-Cluster Correlation Estimates for HIV-related Outcomes from Care and Treatment Clinics in Dar es Salaam, Tanzania. Barnhart D, Hertzmark E, Liu E, Mungure E, Muya AN, Sando D, Chalamilla G, Ulenga N, Bärnighausen T, Fawzi W, Spiegelman D Contemporary clinical trials communications 27766318 Contemp Clin Trials Commun 2016 Dec 15
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Transcriptome-wide Analysis of Roles for tRNA Modifications in Translational Regulation. Chou HJ, Donnard E, Gustafsson HT, Garber M, Rando OJ Molecular cell 29198561 Mol Cell 2017 Dec 7
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SHMT inhibition is effective and synergizes with methotrexate in T-cell acute lymphoblastic leukemia. García-Cañaveras JC, Lancho O, Ducker GS, Ghergurovich JM, Xu X, da Silva-Diz V, Minuzzo S, Indraccolo S, Kim H, Herranz D, Rabinowitz JD Leukemia 32382081 Leukemia 2021 Feb
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The metabolites NADP(+) and NADPH are the targets of the circadian protein Nocturnin (Curled). Estrella MA, Du J, Chen L, Rath S, Prangley E, Chitrakar A, Aoki T, Schedl P, Rabinowitz J, Korennykh A Nature communications 31147539 Nat Commun 2019 May 30
The adverse metabolic effects of branched-chain amino acids are mediated by isoleucine and valine. Yu D, Richardson NE, Green CL, Spicer AB, Murphy ME, Flores V, Jang C, Kasza I, Nikodemova M, Wakai MH, Tomasiewicz JL, Yang SE, Miller BR, Pak HH, Brinkman JA, Rojas JM, Quinn WJ 3rd, Cheng EP, Konon EN, Haider LR, Finke M, Sonsalla M, Alexander CM, Rabinowitz JD, Baur JA, Malecki KC, Lamming DW Cell metabolism 33887198 Cell Metab 2021 May 4
Quantitative Analysis of the Whole-Body Metabolic Fate of Branched-Chain Amino Acids. Neinast MD, Jang C, Hui S, Murashige DS, Chu Q, Morscher RJ, Li X, Zhan L, White E, Anthony TG, Rabinowitz JD, Arany Z Cell metabolism 30449684 Cell Metab 2019 Feb 5
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Macrophage de novo NAD(+) synthesis specifies immune function in aging and inflammation. Minhas PS, Liu L, Moon PK, Joshi AU, Dove C, Mhatre S, Contrepois K, Wang Q, Lee BA, Coronado M, Bernstein D, Snyder MP, Migaud M, Majeti R, Mochly-Rosen D, Rabinowitz JD, Andreasson KI Nature immunology 30478397 Nat Immunol 2019 Jan
Perinatal high fat diet and early life methyl donor supplementation alter one carbon metabolism and DNA methylation in the brain. McKee SE, Zhang S, Chen L, Rabinowitz JD, Reyes TM Journal of neurochemistry 29423909 J Neurochem 2018 Jun
Myeloid-derived itaconate suppresses cytotoxic CD8(+) T cells and promotes tumour growth. Zhao H, Teng D, Yang L, Xu X, Chen J, Jiang T, Feng AY, Zhang Y, Frederick DT, Gu L, Cai L, Asara JM, Pasca di Magliano M, Boland GM, Flaherty KT, Swanson KD, Liu D, Rabinowitz JD, Zheng B Nature metabolism 36376563 Nat Metab 2022 Dec
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Lactate dehydrogenase inhibition synergizes with IL-21 to promote CD8(+) T cell stemness and antitumor immunity. Hermans D, Gautam S, García-Cañaveras JC, Gromer D, Mitra S, Spolski R, Li P, Christensen S, Nguyen R, Lin JX, Oh J, Du N, Veenbergen S, Fioravanti J, Ebina-Shibuya R, Bleck C, Neckers LM, Rabinowitz JD, Gattinoni L, Leonard WJ Proceedings of the National Academy of Sciences of the United States of America 32123114 Proc Natl Acad Sci U S A 2020 Mar 17
Serine catabolism generates liver NADPH and supports hepatic lipogenesis. Zhang Z, TeSlaa T, Xu X, Zeng X, Yang L, Xing G, Tesz GJ, Clasquin MF, Rabinowitz JD Nature metabolism 34845393 Nat Metab 2021 Dec
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Local production of lactate, ribose phosphate, and amino acids within human triple-negative breast cancer. Ghergurovich JM, Lang JD, Levin MK, Briones N, Facista SJ, Mueller C, Cowan AJ, McBride MJ, Rodriguez ESR, Killian A, Dao T, Lamont J, Barron A, Su X, Hendricks WPD, Espina V, Von Hoff DD, O'Shaughnessy J, Rabinowitz JD Med (New York, N.Y.) 34223403 Med 2021 Jun 11
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Comprehensive quantification of fuel use by the failing and nonfailing human heart. Murashige D, Jang C, Neinast M, Edwards JJ, Cowan A, Hyman MC, Rabinowitz JD, Frankel DS, Arany Z Science (New York, N.Y.) 33060364 Science 2020 Oct 16
Mitochondrial translation requires folate-dependent tRNA methylation. Morscher RJ, Ducker GS, Li SH, Mayer JA, Gitai Z, Sperl W, Rabinowitz JD Nature 29364879 Nature 2018 Feb 1
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Chemical Basis for Deuterium Labeling of Fat and NADPH. Zhang Z, Chen L, Liu L, Su X, Rabinowitz JD Journal of the American Chemical Society 28911221 J Am Chem Soc 2017 Oct 18
mTOR Inhibition Restores Amino Acid Balance in Cells Dependent on Catabolism of Extracellular Protein. Nofal M, Zhang K, Han S, Rabinowitz JD Molecular cell 28918901 Mol Cell 2017 Sep 21
Dietary fructose feeds hepatic lipogenesis via microbiota-derived acetate. Zhao S, Jang C, Liu J, Uehara K, Gilbert M, Izzo L, Zeng X, Trefely S, Fernandez S, Carrer A, Miller KD, Schug ZT, Snyder NW, Gade TP, Titchenell PM, Rabinowitz JD, Wellen KE Nature 32214246 Nature 2020 Mar
Serine Catabolism Feeds NADH when Respiration Is Impaired. Yang L, Garcia Canaveras JC, Chen Z, Wang L, Liang L, Jang C, Mayr JA, Zhang Z, Ghergurovich JM, Zhan L, Joshi S, Hu Z, McReynolds MR, Su X, White E, Morscher RJ, Rabinowitz JD Cell metabolism 32187526 Cell Metab 2020 Apr 7
Novel Pyrrolo[3,2-d]pyrimidine Compounds Target Mitochondrial and Cytosolic One-carbon Metabolism with Broad-spectrum Antitumor Efficacy. Dekhne AS, Shah K, Ducker GS, Katinas JM, Wong-Roushar J, Nayeen MJ, Doshi A, Ning C, Bao X, Frühauf J, Liu J, Wallace-Povirk A, O'Connor C, Dzinic SH, White K, Kushner J, Kim S, Hüttemann M, Polin L, Rabinowitz JD, Li J, Hou Z, Dann CE 3rd, Gangjee A, Matherly LH Molecular cancer therapeutics 31289137 Mol Cancer Ther 2019 Oct
Glucose feeds the TCA cycle via circulating lactate. Hui S, Ghergurovich JM, Morscher RJ, Jang C, Teng X, Lu W, Esparza LA, Reya T, Le Zhan, Yanxiang Guo J, White E, Rabinowitz JD Nature 29045397 Nature 2017 Nov 2
Metabolite Exchange between Mammalian Organs Quantified in Pigs. Jang C, Hui S, Zeng X, Cowan AJ, Wang L, Chen L, Morscher RJ, Reyes J, Frezza C, Hwang HY, Imai A, Saito Y, Okamoto K, Vaspoli C, Kasprenski L, Zsido GA 2nd, Gorman JH 3rd, Gorman RC, Rabinowitz JD Cell metabolism 36070684 Cell Metab 2022 Sep 6
Slow TCA flux and ATP production in primary solid tumours but not metastases. Bartman CR, Weilandt DR, Shen Y, Lee WD, Han Y, TeSlaa T, Jankowski CSR, Samarah L, Park NR, da Silva-Diz V, Aleksandrova M, Gultekin Y, Marishta A, Wang L, Yang L, Roichman A, Bhatt V, Lan T, Hu Z, Xing X, Lu W, Davidson S, Wühr M, Vander Heiden MG, Herranz D, Guo JY, Kang Y, Rabinowitz JD Nature 36725930 Nature 2023 Feb
mTORC1 promotes cell growth via m(6)A-dependent mRNA degradation. Cho S, Lee G, Pickering BF, Jang C, Park JH, He L, Mathur L, Kim SS, Jung S, Tang HW, Monette S, Rabinowitz JD, Perrimon N, Jaffrey SR, Blenis J Molecular cell 33756105 Mol Cell 2021 May 20
The small intestine shields the liver from fructose-induced steatosis. Jang C, Wada S, Yang S, Gosis B, Zeng X, Zhang Z, Shen Y, Lee G, Arany Z, Rabinowitz JD Nature metabolism 32694791 Nat Metab 2020 Jul
Lactate: the ugly duckling of energy metabolism. Rabinowitz JD, Enerbäck S Nature metabolism 32694798 Nat Metab 2020 Jul
Restoring metabolism of myeloid cells reverses cognitive decline in ageing. Minhas PS, Latif-Hernandez A, McReynolds MR, Durairaj AS, Wang Q, Rubin A, Joshi AU, He JQ, Gauba E, Liu L, Wang C, Linde M, Sugiura Y, Moon PK, Majeti R, Suematsu M, Mochly-Rosen D, Weissman IL, Longo FM, Rabinowitz JD, Andreasson KI Nature 33473210 Nature 2021 Feb
The Source of Glycolytic Intermediates in Mammalian Tissues. TeSlaa T, Bartman CR, Jankowski CSR, Zhang Z, Xu X, Xing X, Wang L, Lu W, Hui S, Rabinowitz JD Cell metabolism 33472024 Cell Metab 2021 Feb 2
NADPH production by the oxidative pentose-phosphate pathway supports folate metabolism. Chen L, Zhang Z, Hoshino A, Zheng HD, Morley M, Arany Z, Rabinowitz JD Nature metabolism 31058257 Nat Metab 2019 Mar
Metabolite Measurement: Pitfalls to Avoid and Practices to Follow. Lu W, Su X, Klein MS, Lewis IA, Fiehn O, Rabinowitz JD Annual review of biochemistry 28654323 Annu Rev Biochem 2017 Jun 20
Quantitative Fluxomics of Circulating Metabolites. Hui S, Cowan AJ, Zeng X, Yang L, TeSlaa T, Li X, Bartman C, Zhang Z, Jang C, Wang L, Lu W, Rojas J, Baur J, Rabinowitz JD Cell metabolism 32791100 Cell Metab 2020 Oct 6
5,10-methenyltetrahydrofolate synthetase deficiency causes a neurometabolic disorder associated with microcephaly, epilepsy, and cerebral hypomyelination. Rodan LH, Qi W, Ducker GS, Demirbas D, Laine R, Yang E, Walker MA, Eichler F, Rabinowitz JD, Anselm I, Berry GT, Undiagnosed Diseases Network (UDN) Molecular genetics and metabolism 30031689 Mol Genet Metab 2018 Sep
Peak Annotation and Verification Engine for Untargeted LC-MS Metabolomics. Wang L, Xing X, Chen L, Yang L, Su X, Rabitz H, Lu W, Rabinowitz JD Analytical chemistry 30586294 Anal Chem 2019 Feb 5
Quantitative Analysis of NAD Synthesis-Breakdown Fluxes. Liu L, Su X, Quinn WJ 3rd, Hui S, Krukenberg K, Frederick DW, Redpath P, Zhan L, Chellappa K, White E, Migaud M, Mitchison TJ, Baur JA, Rabinowitz JD Cell metabolism 29685734 Cell Metab 2018 May 1
A small molecule G6PD inhibitor reveals immune dependence on pentose phosphate pathway. Ghergurovich JM, García-Cañaveras JC, Wang J, Schmidt E, Zhang Z, TeSlaa T, Patel H, Chen L, Britt EC, Piqueras-Nebot M, Gomez-Cabrera MC, Lahoz A, Fan J, Beier UH, Kim H, Rabinowitz JD Nature chemical biology 32393898 Nat Chem Biol 2020 Jul
Improved Annotation of Untargeted Metabolomics Data through Buffer Modifications That Shift Adduct Mass and Intensity. Lu W, Xing X, Wang L, Chen L, Zhang S, McReynolds MR, Rabinowitz JD Analytical chemistry 32614575 Anal Chem 2020 Sep 1
Ketogenic diet and chemotherapy combine to disrupt pancreatic cancer metabolism and growth. Yang L, TeSlaa T, Ng S, Nofal M, Wang L, Lan T, Zeng X, Cowan A, McBride M, Lu W, Davidson S, Liang G, Oh TG, Downes M, Evans R, Von Hoff D, Guo JY, Han H, Rabinowitz JD Med (New York, N.Y.) 35425930 Med 2022 Feb 11
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Sex and genetic background define the metabolic, physiologic, and molecular response to protein restriction. Green CL, Pak HH, Richardson NE, Flores V, Yu D, Tomasiewicz JL, Dumas SN, Kredell K, Fan JW, Kirsh C, Chaiyakul K, Murphy ME, Babygirija R, Barrett-Wilt GA, Rabinowitz J, Ong IM, Jang C, Simcox J, Lamming DW Cell metabolism 35108511 Cell Metab 2022 Feb 1
NAD precursors cycle between host tissues and the gut microbiome. Chellappa K, McReynolds MR, Lu W, Zeng X, Makarov M, Hayat F, Mukherjee S, Bhat YR, Lingala SR, Shima RT, Descamps HC, Cox T, Ji L, Jankowski C, Chu Q, Davidson SM, Thaiss CA, Migaud ME, Rabinowitz JD, Baur JA Cell metabolism 36476934 Cell Metab 2022 Dec 6
Reprogramming neuroblastoma by diet-enhanced polyamine depletion. Cherkaoui S, Yang L, McBride M, Turn CS, Lu W, Eigenmann C, Allen GE, Panasenko OO, Zhang L, Vu A, Liu K, Li Y, Gandhi OH, Surrey L, Wierer M, White E, Rabinowitz JD, Hogarty MD, Morscher RJ bioRxiv : the preprint server for biology 38260457 bioRxiv 2024 Jan 8
One-carbon unit supplementation fuels tumor-infiltrating T cells and augments checkpoint blockade. Xu X, Chen Z, Bartman CR, Xing X, Olszewski K, Rabinowitz JD bioRxiv : the preprint server for biology 37961420 bioRxiv 2023 Nov 3
CRISPR-Cas9 mediated one-step disabling of pancreatogenesis in pigs. Wu J, Vilarino M, Suzuki K, Okamura D, Bogliotti YS, Park I, Rowe J, McNabb B, Ross PJ, Belmonte JCI Scientific reports 28874671 Sci Rep 2017 Sep 5
Precise in vivo genome editing via single homology arm donor mediated intron-targeting gene integration for genetic disease correction. Suzuki K, Yamamoto M, Hernandez-Benitez R, Li Z, Wei C, Soligalla RD, Aizawa E, Hatanaka F, Kurita M, Reddy P, Ocampo A, Hishida T, Sakurai M, Nemeth AN, Nuñez Delicado E, Campistol JM, Magistretti P, Guillen P, Rodriguez Esteban C, Gong J, Yuan Y, Gu Y, Liu GH, López-Otín C, Wu J, Zhang K, Izpisua Belmonte JC Cell research 31444470 Cell Res 2019 Oct
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Functional sensory circuits built from neurons of two species. Throesch BT, Bin Imtiaz MK, Muñoz-Castañeda R, Sakurai M, Hartzell AL, James KN, Rodriguez AR, Martin G, Lippi G, Kupriyanov S, Wu Z, Osten P, Izpisua Belmonte JC, Wu J, Baldwin KK Cell 38670072 Cell 2024 Apr 25
Generation of Blastocyst-like Structures from Mouse Embryonic and Adult Cell Cultures. Li R, Zhong C, Yu Y, Liu H, Sakurai M, Yu L, Min Z, Shi L, Wei Y, Takahashi Y, Liao HK, Qiao J, Deng H, Nuñez-Delicado E, Rodriguez Esteban C, Wu J, Izpisua Belmonte JC Cell 31626770 Cell 2019 Oct 17
Efficient derivation of stable primed pluripotent embryonic stem cells from bovine blastocysts. Bogliotti YS, Wu J, Vilarino M, Okamura D, Soto DA, Zhong C, Sakurai M, Sampaio RV, Suzuki K, Izpisua Belmonte JC, Ross PJ Proceedings of the National Academy of Sciences of the United States of America 29440377 Proc Natl Acad Sci U S A 2018 Feb 27
Bile acids profile, histopathological indices and genetic variants for non-alcoholic fatty liver disease progression. Nimer N, Choucair I, Wang Z, Nemet I, Li L, Gukasyan J, Weeks TL, Alkhouri N, Zein N, Tang WHW, Fischbach MA, Brown JM, Allayee H, Dasarathy S, Gogonea V, Hazen SL Metabolism: clinical and experimental 33275980 Metabolism 2021 Mar
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Myeloid cells pave the way for lymphatic system development and maintenance. Ivanov S, Randolph GJ Pflugers Archiv : European journal of physiology 28220247 Pflugers Arch 2017 Apr
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Lymphoid Aggregates Remodel Lymphatic Collecting Vessels that Serve Mesenteric Lymph Nodes in Crohn Disease. Randolph GJ, Bala S, Rahier JF, Johnson MW, Wang PL, Nalbantoglu I, Dubuquoy L, Chau A, Pariente B, Kartheuser A, Zinselmeyer BH, Colombel JF The American journal of pathology 27746181 Am J Pathol 2016 Dec
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Tissue-Resident Macrophages in Pancreatic Ductal Adenocarcinoma Originate from Embryonic Hematopoiesis and Promote Tumor Progression. Zhu Y, Herndon JM, Sojka DK, Kim KW, Knolhoff BL, Zuo C, Cullinan DR, Luo J, Bearden AR, Lavine KJ, Yokoyama WM, Hawkins WG, Fields RC, Randolph GJ, DeNardo DG Immunity 28813661 Immunity 2017 Aug 15
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Cholesterol Accumulation in Dendritic Cells Links the Inflammasome to Acquired Immunity. Westerterp M, Gautier EL, Ganda A, Molusky MM, Wang W, Fotakis P, Wang N, Randolph GJ, D'Agati VD, Yvan-Charvet L, Tall AR Cell metabolism 28479366 Cell Metab 2017 Jun 6
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Lymphatic network remodeling after small bowel resection. Onufer EJ, Czepielewski R, Seiler KM, Erlich E, Courtney CM, Bustos A, Randolph GJ, Warner BW Journal of pediatric surgery 30879758 J Pediatr Surg 2019 Jun
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Myeloid-specific Asxl2 deletion limits diet-induced obesity by regulating energy expenditure. Zou W, Rohatgi N, Brestoff JR, Moley JR, Li Y, Williams JW, Alippe Y, Pan H, Pietka TA, Mbalaviele G, Newberry EP, Davidson NO, Dey A, Shoghi KI, Head RD, Wickline SA, Randolph GJ, Abumrad NA, Teitelbaum SL The Journal of clinical investigation 32310225 J Clin Invest 2020 May 1
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Liver injury after small bowel resection is prevented in obesity-resistant 129S1/SvImJ mice. Onufer EJ, Han YH, Courtney C, Steinberger A, Tecos M, Sutton S, Sescleifer A, Ou J, Sanguinetti Czepielewski R, Randolph GJ, Warner BW American journal of physiology. Gastrointestinal and liver physiology 33729834 Am J Physiol Gastrointest Liver Physiol 2021 May 1
A Stromal Niche Defined by Expression of the Transcription Factor WT1 Mediates Programming and Homeostasis of Cavity-Resident Macrophages. Buechler MB, Kim KW, Onufer EJ, Williams JW, Little CC, Dominguez CX, Li Q, Sandoval W, Cooper JE, Harris CA, Junttila MR, Randolph GJ, Turley SJ Immunity 31231034 Immunity 2019 Jul 16
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The Lymphatic Vasculature in the 21(st) Century: Novel Functional Roles in Homeostasis and Disease. Oliver G, Kipnis J, Randolph GJ, Harvey NL Cell 32707093 Cell 2020 Jul 23
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Wastewater sequencing reveals early cryptic SARS-CoV-2 variant transmission. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, McHardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Schiabor Barrett KM, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R Nature 35798029 Nature 2022 Sep
Enhancing untargeted metabolomics using metadata-based source annotation. Gauglitz JM, West KA, Bittremieux W, Williams CL, Weldon KC, Panitchpakdi M, Di Ottavio F, Aceves CM, Brown E, Sikora NC, Jarmusch AK, Martino C, Tripathi A, Meehan MJ, Dorrestein K, Shaffer JP, Coras R, Vargas F, Goldasich LD, Schwartz T, Bryant M, Humphrey G, Johnson AJ, Spengler K, Belda-Ferre P, Diaz E, McDonald D, Zhu Q, Elijah EO, Wang M, Marotz C, Sprecher KE, Vargas-Robles D, Withrow D, Ackermann G, Herrera L, Bradford BJ, Marques LMM, Amaral JG, Silva RM, Veras FP, Cunha TM, Oliveira RDR, Louzada-Junior P, Mills RH, Piotrowski PK, Servetas SL, Da Silva SM, Jones CM, Lin NJ, Lippa KA, Jackson SA, Daouk RK, Galasko D, Dulai PS, Kalashnikova TI, Wittenberg C, Terkeltaub R, Doty MM, Kim JH, Rhee KE, Beauchamp-Walters J, Wright KP Jr, Dominguez-Bello MG, Manary M, Oliveira MF, Boland BS, Lopes NP, Guma M, Swafford AD, Dutton RJ, Knight R, Dorrestein PC Nature biotechnology 35798960 Nat Biotechnol 2022 Dec
Compositionally Aware Phylogenetic Beta-Diversity Measures Better Resolve Microbiomes Associated with Phenotype. Martino C, McDonald D, Cantrell K, Dilmore AH, Vázquez-Baeza Y, Shenhav L, Shaffer JP, Rahman G, Armstrong G, Allaband C, Song SJ, Knight R mSystems 35477286 mSystems 2022 Jun 28
Naturalization of the microbiota developmental trajectory of Cesarean-born neonates after vaginal seeding. Song SJ, Wang J, Martino C, Jiang L, Thompson WK, Shenhav L, McDonald D, Marotz C, Harris PR, Hernandez CD, Henderson N, Ackley E, Nardella D, Gillihan C, Montacuti V, Schweizer W, Jay M, Combellick J, Sun H, Garcia-Mantrana I, Gil Raga F, Collado MC, Rivera-Viñas JI, Campos-Rivera M, Ruiz-Calderon JF, Knight R, Dominguez-Bello MG Med (New York, N.Y.) 35590169 Med 2021 Aug 13
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data. Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R Research square 39502785 Res Sq 2024 Oct 23
Determination of Effect Sizes for Power Analysis for Microbiome Studies Using Large Microbiome Databases. Rahman G, McDonald D, Gonzalez A, Vázquez-Baeza Y, Jiang L, Casals-Pascual C, Hakim D, Dilmore AH, Nowinski B, Peddada S, Knight R Genes 37372419 Genes (Basel) 2023 Jun 9
Greengenes2 unifies microbial data in a single reference tree. McDonald D, Jiang Y, Balaban M, Cantrell K, Zhu Q, Gonzalez A, Morton JT, Nicolaou G, Parks DH, Karst SM, Albertsen M, Hugenholtz P, DeSantis T, Song SJ, Bartko A, Havulinna AS, Jousilahti P, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Lahti L, Mirarab S, Knight R Nature biotechnology 37500913 Nat Biotechnol 2024 May
microbeMASST: a taxonomically informed mass spectrometry search tool for microbial metabolomics data. Zuffa S, Schmid R, Bauermeister A, P Gomes PW, Caraballo-Rodriguez AM, El Abiead Y, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, Pessotti RC, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Silva Dos Santos M, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, Vera Ponce de León A, Pope PB, La Rosa SL, La Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC Nature microbiology 38316926 Nat Microbiol 2024 Feb
A comparison of DNA/RNA extraction protocols for high-throughput sequencing of microbial communities. Shaffer JP, Marotz C, Belda-Ferre P, Martino C, Wandro S, Estaki M, Salido RA, Carpenter CS, Zaramela LS, Minich JJ, Bryant M, Sanders K, Fraraccio S, Ackermann G, Humphrey G, Swafford AD, Miller-Montgomery S, Knight R BioTechniques 33512248 Biotechniques 2021 Mar
Host variables confound gut microbiota studies of human disease. Vujkovic-Cvijin I, Sklar J, Jiang L, Natarajan L, Knight R, Belkaid Y Nature 33149306 Nature 2020 Nov
Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome. Huang S, Jiang S, Huo D, Allaband C, Estaki M, Cantu V, Belda-Ferre P, Vázquez-Baeza Y, Zhu Q, Ma C, Li C, Zarrinpar A, Liu YY, Knight R, Zhang J Microbiome 34193290 Microbiome 2021 Jun 30
Microbial context predicts SARS-CoV-2 prevalence in patients and the hospital built environment. Marotz C, Belda-Ferre P, Ali F, Das P, Huang S, Cantrell K, Jiang L, Martino C, Diner RE, Rahman G, McDonald D, Armstrong G, Kodera S, Donato S, Ecklu-Mensah G, Gottel N, Garcia MCS, Chiang LY, Salido RA, Shaffer JP, Bryant M, Sanders K, Humphrey G, Ackermann G, Haiminen N, Beck KL, Kim HC, Carrieri AP, Parida L, Vázquez-Baeza Y, Torriani FJ, Knight R, Gilbert JA, Sweeney DA, Allard SM medRxiv : the preprint server for health sciences 33236030 medRxiv 2020 Nov 22
Paired microbiome and metabolome analyses associate bile acid changes with colorectal cancer progression. Fu T, Huan T, Rahman G, Zhi H, Xu Z, Oh TG, Guo J, Coulter S, Tripathi A, Martino C, McCarville JL, Zhu Q, Cayabyab F, Low B, He M, Xing S, Vargas F, Yu RT, Atkins A, Liddle C, Ayres J, Raffatellu M, Dorrestein PC, Downes M, Knight R, Evans RM Cell reports 37611587 Cell Rep 2023 Aug 29
Global chemical effects of the microbiome include new bile-acid conjugations. Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC Nature 32103176 Nature 2020 Mar
A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities. Shaffer JP, Carpenter CS, Martino C, Salido RA, Minich JJ, Bryant M, Sanders K, Schwartz T, Humphrey G, Swafford AD, Knight R BioTechniques 35713407 Biotechniques 2022 Jun
A Sensitive, Rapid, and Portable CasRx-based Diagnostic Assay for SARS-CoV-2. Brogan DJ, Chaverra-Rodriguez D, Lin CP, Smidler AL, Yang T, Alcantara LM, Antoshechkin I, Liu J, Raban RR, Belda-Ferre P, Knight R, Komives EA, Akbari OS medRxiv : the preprint server for health sciences 33106816 medRxiv 2020 Oct 20
Context-aware dimensionality reduction deconvolutes gut microbial community dynamics. Martino C, Shenhav L, Marotz CA, Armstrong G, McDonald D, Vázquez-Baeza Y, Morton JT, Jiang L, Dominguez-Bello MG, Swafford AD, Halperin E, Knight R Nature biotechnology 32868914 Nat Biotechnol 2021 Feb
SARS-CoV-2 Distribution in Residential Housing Suggests Contact Deposition and Correlates with Rothia sp. Cantú VJ, Salido RA, Huang S, Rahman G, Tsai R, Valentine H, Magallanes CG, Aigner S, Baer NA, Barber T, Belda-Ferre P, Betty M, Bryant M, Casas Maya M, Castro-Martínez A, Chacón M, Cheung W, Crescini ES, De Hoff P, Eisner E, Farmer S, Hakim A, Kohn L, Lastrella AL, Lawrence ES, Morgan SC, Ngo TT, Nouri A, Plascencia A, Ruiz CA, Sathe S, Seaver P, Shwartz T, Smoot EW, Ostrander RT, Valles T, Yeo GW, Laurent LC, Fielding-Miller R, Knight R mSystems 35575492 mSystems 2022 Jun 28
Robustness of cancer microbiome signals over a broad range of methodological variation. Sepich-Poore GD, McDonald D, Kopylova E, Guccione C, Zhu Q, Austin G, Carpenter C, Fraraccio S, Wandro S, Kosciolek T, Janssen S, Metcalf JL, Song SJ, Kanbar J, Miller-Montgomery S, Heaton R, Mckay R, Patel SP, Swafford AD, Korem T, Knight R Oncogene 38396294 Oncogene 2024 Apr
TEMPTED: time-informed dimensionality reduction for longitudinal microbiome studies. Shi P, Martino C, Han R, Janssen S, Buck G, Serrano M, Owzar K, Knight R, Shenhav L, Zhang AR Genome biology 39696594 Genome Biol 2024 Dec 19
Bacterial modification of the host glycosaminoglycan heparan sulfate modulates SARS-CoV-2 infectivity. Martino C, Kellman BP, Sandoval DR, Clausen TM, Marotz CA, Song SJ, Wandro S, Zaramela LS, Salido Benítez RA, Zhu Q, Armingol E, Vázquez-Baeza Y, McDonald D, Sorrentino JT, Taylor B, Belda-Ferre P, Liang C, Zhang Y, Schifanella L, Klatt NR, Havulinna AS, Jousilahti P, Huang S, Haiminen N, Parida L, Kim HC, Swafford AD, Zengler K, Cheng S, Inouye M, Niiranen T, Jain M, Salomaa V, Esko JD, Lewis NE, Knight R bioRxiv : the preprint server for biology 32839779 bioRxiv 2020 Aug 18
Optimizing UniFrac with OpenACC Yields Greater Than One Thousand Times Speed Increase. Sfiligoi I, Armstrong G, Gonzalez A, McDonald D, Knight R mSystems 35638356 mSystems 2022 Jun 28
Cancer's second genome: Microbial cancer diagnostics and redefining clonal evolution as a multispecies process: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution: Humans and their tumors are not aseptic, and the multispecies nature of cancer modulates clinical care and clonal evolution. Sepich-Poore GD, Guccione C, Laplane L, Pradeu T, Curtius K, Knight R BioEssays : news and reviews in molecular, cellular and developmental biology 35253252 Bioessays 2022 May
Chemically informed analyses of metabolomics mass spectrometry data with Qemistree. Tripathi A, Vázquez-Baeza Y, Gauglitz JM, Wang M, Dührkop K, Nothias-Esposito M, Acharya DD, Ernst M, van der Hooft JJJ, Zhu Q, McDonald D, Brejnrod AD, Gonzalez A, Handelsman J, Fleischauer M, Ludwig M, Böcker S, Nothias LF, Knight R, Dorrestein PC Nature chemical biology 33199911 Nat Chem Biol 2021 Feb
The Gut Microbial Bile Acid Modulation and Its Relevance to Digestive Health and Diseases. Fogelson KA, Dorrestein PC, Zarrinpar A, Knight R Gastroenterology 36841488 Gastroenterology 2023 Jun
Phylogeny-Aware Analysis of Metagenome Community Ecology Based on Matched Reference Genomes while Bypassing Taxonomy. Zhu Q, Huang S, Gonzalez A, McGrath I, McDonald D, Haiminen N, Armstrong G, Vázquez-Baeza Y, Yu J, Kuczynski J, Sepich-Poore GD, Swafford AD, Das P, Shaffer JP, Lejzerowicz F, Belda-Ferre P, Havulinna AS, Méric G, Niiranen T, Lahti L, Salomaa V, Kim HC, Jain M, Inouye M, Gilbert JA, Knight R mSystems 35369727 mSystems 2022 Apr 26
Wastewater sequencing uncovers early, cryptic SARS-CoV-2 variant transmission. Karthikeyan S, Levy JI, De Hoff P, Humphrey G, Birmingham A, Jepsen K, Farmer S, Tubb HM, Valles T, Tribelhorn CE, Tsai R, Aigner S, Sathe S, Moshiri N, Henson B, Mark AM, Hakim A, Baer NA, Barber T, Belda-Ferre P, Chacón M, Cheung W, Cresini ES, Eisner ER, Lastrella AL, Lawrence ES, Marotz CA, Ngo TT, Ostrander T, Plascencia A, Salido RA, Seaver P, Smoot EW, McDonald D, Neuhard RM, Scioscia AL, Satterlund AM, Simmons EH, Abelman DB, Brenner D, Bruner JC, Buckley A, Ellison M, Gattas J, Gonias SL, Hale M, Hawkins F, Ikeda L, Jhaveri H, Johnson T, Kellen V, Kremer B, Matthews G, McLawhon RW, Ouillet P, Park D, Pradenas A, Reed S, Riggs L, Sanders A, Sollenberger B, Song A, White B, Winbush T, Aceves CM, Anderson C, Gangavarapu K, Hufbauer E, Kurzban E, Lee J, Matteson NL, Parker E, Perkins SA, Ramesh KS, Robles-Sikisaka R, Schwab MA, Spencer E, Wohl S, Nicholson L, Mchardy IH, Dimmock DP, Hobbs CA, Bakhtar O, Harding A, Mendoza A, Bolze A, Becker D, Cirulli ET, Isaksson M, Barrett KMS, Washington NL, Malone JD, Schafer AM, Gurfield N, Stous S, Fielding-Miller R, Garfein RS, Gaines T, Anderson C, Martin NK, Schooley R, Austin B, MacCannell DR, Kingsmore SF, Lee W, Shah S, McDonald E, Yu AT, Zeller M, Fisch KM, Longhurst C, Maysent P, Pride D, Khosla PK, Laurent LC, Yeo GW, Andersen KG, Knight R medRxiv : the preprint server for health sciences 35411350 medRxiv 2022 Apr 4
Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References. Hakim D, Wandro S, Zengler K, Zaramela LS, Nowinski B, Swafford A, Zhu Q, Song SJ, Gonzalez A, McDonald D, Knight R mSystems 36073806 mSystems 2022 Oct 26
Improving microbial phylogeny with citizen science within a mass-market video game. Sarrazin-Gendron R, Ghasemloo Gheidari P, Butyaev A, Keding T, Cai E, Zheng J, Mutalova R, Mounthanyvong J, Zhu Y, Nazarova E, Drogaris C, Erhart K, Borderlands Science Development Team, Borderlands Science players, Brouillette A, Richard G, Pitchford R, Caisse S, Blanchette M, McDonald D, Knight R, Szantner A, Waldispühl J Nature biotechnology 38622344 Nat Biotechnol 2025 Jan
Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution. Brennan C, Salido RA, Belda-Ferre P, Bryant M, Cowart C, Tiu MD, González A, McDonald D, Tribelhorn C, Zarrinpar A, Knight R mSystems 37350611 mSystems 2023 Aug 31
Generation of accurate, expandable phylogenomic trees with uDance. Balaban M, Jiang Y, Zhu Q, McDonald D, Knight R, Mirarab S Nature biotechnology 37500914 Nat Biotechnol 2024 May
A Taxonomically-informed Mass Spectrometry Search Tool for Microbial Metabolomics Data. Zuffa S, Schmid R, Bauermeister A, Gomes PWP, Caraballo-Rodriguez AM, Abiead YE, Aron AT, Gentry EC, Zemlin J, Meehan MJ, Avalon NE, Cichewicz RH, Buzun E, Terrazas MC, Hsu CY, Oles R, Ayala AV, Zhao J, Chu H, Kuijpers MCM, Jackrel SL, Tugizimana F, Nephali LP, Dubery IA, Madala NE, Moreira EA, Costa-Lotufo LV, Lopes NP, Rezende-Teixeira P, Jimenez PC, Rimal B, Patterson AD, Traxler MF, de Cassia Pessotti R, Alvarado-Villalobos D, Tamayo-Castillo G, Chaverri P, Escudero-Leyva E, Quiros-Guerrero LM, Bory AJ, Joubert J, Rutz A, Wolfender JL, Allard PM, Sichert A, Pontrelli S, Pullman BS, Bandeira N, Gerwick WH, Gindro K, Massana-Codina J, Wagner BC, Forchhammer K, Petras D, Aiosa N, Garg N, Liebeke M, Bourceau P, Kang KB, Gadhavi H, de Carvalho LPS, Dos Santos MS, Pérez-Lorente AI, Molina-Santiago C, Romero D, Franke R, Brönstrup M, de León AVP, Pope PB, Rosa SL, Barbera G, Roager HM, Laursen MF, Hammerle F, Siewert B, Peintner U, Licona-Cassani C, Rodriguez-Orduña L, Rampler E, Hildebrand F, Koellensperger G, Schoeny H, Hohenwallner K, Panzenboeck L, Gregor R, O'Neill EC, Roxborough ET, Odoi J, Bale NJ, Ding S, Sinninghe Damsté JS, Guan XL, Cui JJ, Ju KS, Silva DB, Silva FMR, da Silva GF, Koolen HHF, Grundmann C, Clement JA, Mohimani H, Broders K, McPhail KL, Ober-Singleton SE, Rath CM, McDonald D, Knight R, Wang M, Dorrestein PC Research square 37577622 Res Sq 2023 Aug 3
Incomplete human reference genomes can drive false sex biases and expose patient-identifying information in metagenomic data. Guccione C, Patel L, Tomofuji Y, McDonald D, Gonzalez A, Sepich-Poore GD, Sonehara K, Zakeri M, Chen Y, Dilmore AH, Damle N, Baranzini SE, Hightower G, Nakatsuji T, Gallo RL, Langmead B, Okada Y, Curtius K, Knight R Nature communications 39827261 Nat Commun 2025 Jan 18
Annexin-V stabilizes membrane defects by inducing lipid phase transition. Lin YC, Chipot C, Scheuring S Nature communications 31932647 Nat Commun 2020 Jan 13
Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism. Jiao F, Dehez F, Ni T, Yu X, Dittman JS, Gilbert R, Chipot C, Scheuring S Nature communications 36028507 Nat Commun 2022 Aug 26
Forces and energetics of the canonical tetrameric cation channel gating. Scheuring S Proceedings of the National Academy of Sciences of the United States of America 37399394 Proc Natl Acad Sci U S A 2023 Jul 11
Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Pan Y, Pohjolainen E, Schmidpeter PAM, Vaiana AC, Nimigean CM, Grubmüller H, Scheuring S Nature structural & molecular biology 36973509 Nat Struct Mol Biol 2023 Apr
Structural dynamics of channels and transporters by high-speed atomic force microscopy. Heath GR, Lin YC, Matin TR, Scheuring S Methods in enzymology 34059280 Methods Enzymol 2021
Localization atomic force microscopy. Heath GR, Kots E, Robertson JL, Lansky S, Khelashvili G, Weinstein H, Scheuring S Nature 34135520 Nature 2021 Jun
High-speed atomic force microscopy to study pore-forming proteins. Jiao F, Ruan Y, Scheuring S Methods in enzymology 33712187 Methods Enzymol 2021
A pentameric TRPV3 channel with a dilated pore. Lansky S, Betancourt JM, Zhang J, Jiang Y, Kim ED, Paknejad N, Nimigean CM, Yuan P, Scheuring S Nature 37648856 Nature 2023 Sep
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A concerted ATPase cycle of the protein transporter AAA-ATPase Bcs1. Pan Y, Zhan J, Jiang Y, Xia D, Scheuring S Nature communications 37821516 Nat Commun 2023 Oct 11
High-speed atomic force microscopy tracks the dynamic parts of the ribosome. Scheuring S Proceedings of the National Academy of Sciences of the United States of America 33431655 Proc Natl Acad Sci U S A 2021 Jan 26
Nanoreporter of an Enzymatic Suicide Inactivation Pathway. Yaari Z, Cheung JM, Baker HA, Frederiksen RS, Jena PV, Horoszko CP, Jiao F, Scheuring S, Luo M, Heller DA Nano letters 33119310 Nano Lett 2020 Nov 11
Membrane-mediated protein interactions drive membrane protein organization. Jiang Y, Thienpont B, Sapuru V, Hite RK, Dittman JS, Sturgis JN, Scheuring S Nature communications 36450733 Nat Commun 2022 Nov 30
Nanodissected elastically loaded clathrin lattices relax to increased curvature. Tagiltsev G, Haselwandter CA, Scheuring S Science advances 34389539 Sci Adv 2021 Aug
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The cyanobacterial protein VIPP1 forms ESCRT-III-like structures on lipid bilayers. Pan S, Gries K, Engel BD, Schroda M, Haselwandter CA, Scheuring S Nature structural & molecular biology 39060677 Nat Struct Mol Biol 2024 Jul 26
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Meningeal γδ T cells regulate anxiety-like behavior via IL-17a signaling in neurons. Alves de Lima K, Rustenhoven J, Da Mesquita S, Wall M, Salvador AF, Smirnov I, Martelossi Cebinelli G, Mamuladze T, Baker W, Papadopoulos Z, Lopes MB, Cao WS, Xie XS, Herz J, Kipnis J Nature immunology 32929273 Nat Immunol 2020 Nov
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Emergence of the Stem Cell Secretome in Regenerative Engineering. Daneshmandi L, Shah S, Jafari T, Bhattacharjee M, Momah D, Saveh-Shemshaki N, Lo KW, Laurencin CT Trends in biotechnology 32622558 Trends Biotechnol 2020 Dec
Synthesis, Physicochemical Analysis, and Side Group Optimization of Degradable Dipeptide-Based Polyphosphazenes as Potential Regenerative Biomaterials. Ogueri KS, Escobar Ivirico JL, Li Z, Blumenfield RH, Allcock HR, Laurencin CT ACS applied polymer materials 32699835 ACS Appl Polym Mater 2019 Jun 14
Skeletal Muscle Regenerative Engineering. Tang X, Daneshmandi L, Awale G, Nair LS, Laurencin CT Regenerative engineering and translational medicine 33778155 Regen Eng Transl Med 2019 Sep
Control of mesenchymal cell fate via application of FGF-8b in vitro. Otsuka T, Mengsteab PY, Laurencin CT Stem cell research 33445073 Stem Cell Res 2021 Mar
Muscle degeneration in chronic massive rotator cuff tears of the shoulder: Addressing the real problem using a graphene matrix. Saveh Shemshaki N, Kan HM, Barajaa M, Otsuka T, Lebaschi A, Mishra N, Nair LS, Laurencin CT Proceedings of the National Academy of Sciences of the United States of America 35939692 Proc Natl Acad Sci U S A 2022 Aug 16
Regenerative engineering: a review of recent advances and future directions. Esdaille CJ, Washington KS, Laurencin CT Regenerative medicine 34030463 Regen Med 2021 May
Bioinspired Scaffold Designs for Regenerating Musculoskeletal Tissue Interfaces. Barajaa MA, Nair LS, Laurencin CT Regenerative engineering and translational medicine 33344758 Regen Eng Transl Med 2020 Dec
Mechanically superior matrices promote osteointegration and regeneration of anterior cruciate ligament tissue in rabbits. Mengsteab PY, Otsuka T, McClinton A, Shemshaki NS, Shah S, Kan HM, Obopilwe E, Vella AT, Nair LS, Laurencin CT Proceedings of the National Academy of Sciences of the United States of America 33144508 Proc Natl Acad Sci U S A 2020 Nov 17
The Mechanism of Metallosis After Total Hip Arthroplasty. Ude CC, Esdaille CJ, Ogueri KS, Ho-Man K, Laurencin SJ, Nair LS, Laurencin CT Regenerative engineering and translational medicine 35530571 Regen Eng Transl Med 2021 Sep
Injectable amnion hydrogel-mediated delivery of adipose-derived stem cells for osteoarthritis treatment. Bhattacharjee M, Escobar Ivirico JL, Kan HM, Shah S, Otsuka T, Bordett R, Barajaa M, Nagiah N, Pandey R, Nair LS, Laurencin CT Proceedings of the National Academy of Sciences of the United States of America 35046053 Proc Natl Acad Sci U S A 2022 Jan 25
Addressing Justified Vaccine Hesitancy in the Black Community. Laurencin CT Journal of racial and ethnic health disparities 33783755 J Racial Ethn Health Disparities 2021 Jun
Inductive Materials for Regenerative Engineering. Hosseini FS, Nair LS, Laurencin CT Journal of dental research 33906507 J Dent Res 2021 Sep
Hyaluronic acid-British anti-Lewisite as a safer chelation therapy for the treatment of arthroplasty-related metallosis. Ude CC, Schmidt SJ, Laurencin S, Shah S, Esdaille J, Kan HM, Holt BD, Arnold AM, Wolf ME, Nair LS, Sydlik SA, Laurencin CT Proceedings of the National Academy of Sciences of the United States of America 37903261 Proc Natl Acad Sci U S A 2023 Nov 7
The Quest toward limb regeneration: a regenerative engineering approach. Laurencin CT, Nair LS Regenerative biomaterials 27047679 Regen Biomater 2016 Jun
Harnessing cAMP signaling in musculoskeletal regenerative engineering. Ifegwu OC, Awale G, Rajpura K, Lo KW, Laurencin CT Drug discovery today 28359841 Drug Discov Today 2017 Jul
An American Crisis: the Lack of Black Men in Medicine. Laurencin CT, Murray M Journal of racial and ethnic health disparities 28534304 J Racial Ethn Health Disparities 2017 Jun
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Growth factor delivery strategies for rotator cuff repair and regeneration. Prabhath A, Vernekar VN, Sanchez E, Laurencin CT International journal of pharmaceutics 29317260 Int J Pharm 2018 Jun 15
Regenerative Engineering of the Rotator Cuff of the Shoulder. Narayanan G, Nair LS, Laurencin CT ACS biomaterials science & engineering 33418763 ACS Biomater Sci Eng 2018 Mar 12
Kinetic degradation and biocompatibility evaluation of polycaprolactone-based biologics delivery matrices for regenerative engineering of the rotator cuff. Prabhath A, Vernekar VN, Vasu V, Badon M, Avochinou JE, Asandei AD, Kumbar SG, Weber E, Laurencin CT Journal of biomedical materials research. Part A 33974735 J Biomed Mater Res A 2021 Nov
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A Regenerative Polymer Blend Composed of Glycylglycine ethyl ester-substituted Polyphosphazene and Poly (lactic-co-glycolic acid). Ogueri KS, Ogueri KS, Allcock HR, Laurencin CT ACS applied polymer materials 32699836 ACS Appl Polym Mater 2020 Mar 13
A Pandemic on a Pandemic: Racism and COVID-19 in Blacks. Laurencin CT, Walker JM Cell systems 32702320 Cell Syst 2020 Jul 22
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The Role of Nanomaterials and Biological Agents on Rotator Cuff Regeneration. Washington KS, Shemshaki NS, Laurencin CT Regenerative engineering and translational medicine 35005215 Regen Eng Transl Med 2021 Dec
Ligament Regenerative Engineering: Braiding Scalable and Tunable Bioengineered Ligaments Using a Bench-Top Braiding Machine. Mengsteab PY, Freeman J, Barajaa MA, Nair LS, Laurencin CT Regenerative engineering and translational medicine 35005216 Regen Eng Transl Med 2021 Dec
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Graphene-Based Biomaterials for Bone Regenerative Engineering: A Comprehensive Review of the Field and Considerations Regarding Biocompatibility and Biodegradation. Daneshmandi L, Barajaa M, Tahmasbi Rad A, Sydlik SA, Laurencin CT Advanced healthcare materials 33103370 Adv Healthc Mater 2021 Jan
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Regenerative Engineering Animal Models for Knee Osteoarthritis. Esdaille CJ, Ude CC, Laurencin CT Regenerative engineering and translational medicine 35958163 Regen Eng Transl Med 2022 Jun
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Enhancing the Surface Properties of a Bioengineered Anterior Cruciate Ligament Matrix for Use with Point-of-Care Stem Cell Therapy. Yu X, Mengsteab PY, Narayanan G, Nair LS, Laurencin CT Engineering (Beijing, China) 34136308 Engineering (Beijing) 2021 Feb
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Robust phenotypic maintenance of limb cells during heterogeneous culture in a physiologically relevant polymeric-based constructed graft system. Barajaa MA, Nair LS, Laurencin CT Scientific reports 32678185 Sci Rep 2020 Jul 16
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Lung Cancer in Ever- and Never-Smokers: Findings from Multi-Population GWAS Studies. Li Y, Xiao X, Li J, Han Y, Cheng C, Fernandes GF, Slewitzke SE, Rosenberg SM, Zhu M, Byun J, Bossé Y, McKay JD, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeböller H, Wichmann HE, Christiani DC, Rennert G, Arnold SM, Goodman GE, Field JK, Davies MPA, Shete S, Marchand LL, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Sun R, Zienolddiny S, Grankvist K, Johansson M, Caporaso NE, Cox A, Hong YC, Lazarus P, Schabath MB, Aldrich MC, Schwartz AG, Gorlov I, Purrington KS, Yang P, Liu Y, Bailey-Wilson JE, Pinney SM, Mandal D, Willey JC, Gaba C, Brennan P, Xia J, Shen H, Amos CI Cancer epidemiology, biomarkers & prevention : a publication of the American Association for Cancer Research, cosponsored by the American Society of Preventive Oncology 38180474 Cancer Epidemiol Biomarkers Prev 2024 Mar 1
Biology before the SOS Response-DNA Damage Mechanisms at Chromosome Fragile Sites. Fitzgerald DM, Rosenberg SM Cells 34571923 Cells 2021 Sep 1
Drugging evolution of antibiotic resistance at a regulatory network hub. Zhai Y, Pribis JP, Dooling SW, Garcia-Villada L, Minnick PJ, Xia J, Liu J, Mei Q, Fitzgerald DM, Herman C, Hastings PJ, Costa-Mattioli M, Rosenberg SM Science advances 37352342 Sci Adv 2023 Jun 23
Cross-ancestry genome-wide meta-analysis of 61,047 cases and 947,237 controls identifies new susceptibility loci contributing to lung cancer. Byun J, Han Y, Li Y, Xia J, Long E, Choi J, Xiao X, Zhu M, Zhou W, Sun R, Bossé Y, Song Z, Schwartz A, Lusk C, Rafnar T, Stefansson K, Zhang T, Zhao W, Pettit RW, Liu Y, Li X, Zhou H, Walsh KM, Gorlov I, Gorlova O, Zhu D, Rosenberg SM, Pinney S, Bailey-Wilson JE, Mandal D, de Andrade M, Gaba C, Willey JC, You M, Anderson M, Wiencke JK, Albanes D, Lam S, Tardon A, Chen C, Goodman G, Bojeson S, Brenner H, Landi MT, Chanock SJ, Johansson M, Muley T, Risch A, Wichmann HE, Bickeböller H, Christiani DC, Rennert G, Arnold S, Field JK, Shete S, Le Marchand L, Melander O, Brunnstrom H, Liu G, Andrew AS, Kiemeney LA, Shen H, Zienolddiny S, Grankvist K, Johansson M, Caporaso N, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Patel A, Lan Q, Rothman N, Taylor F, Kachuri L, Witte JS, Sakoda LC, Spitz M, Brennan P, Lin X, McKay J, Hung RJ, Amos CI Nature genetics 35915169 Nat Genet 2022 Aug
Stress-Induced Mutagenesis, Gambler Cells, and Stealth Targeting Antibiotic-Induced Evolution. Pribis JP, Zhai Y, Hastings PJ, Rosenberg SM mBio 35658528 mBio 2022 Jun 28
Hyperactivation of monocytes and macrophages in MCI patients contributes to the progression of Alzheimer's disease. Munawara U, Catanzaro M, Xu W, Tan C, Hirokawa K, Bosco N, Dumoulin D, Khalil A, Larbi A, Lévesque S, Ramassamy C, Barron AE, Cunnane S, Beauregard PB, Bellenger JP, Rodrigues S, Desroches M, Witkowski JM, Laurent B, Frost EH, Fulop T Immunity & ageing : I & A 34154615 Immun Ageing 2021 Jun 21
Real-Time Monitoring of Multitarget Antimicrobial Mechanisms of Peptoids Using Label-Free Imaging with Optical Diffraction Tomography. Kim M, Cheon Y, Shin D, Choi J, Nielsen JE, Jeong MS, Nam HY, Kim SH, Lund R, Jenssen H, Barron AE, Lee S, Seo J Advanced science (Weinheim, Baden-Wurttemberg, Germany) 37341246 Adv Sci (Weinh) 2023 Aug
The anti-inflammatory effects of photobiomodulation are mediated by cytokines: Evidence from a mouse model of inflammation. Shamloo S, Defensor E, Ciari P, Ogawa G, Vidano L, Lin JS, Fortkort JA, Shamloo M, Barron AE Frontiers in neuroscience 37090796 Front Neurosci 2023
The activity of antimicrobial peptoids against multidrug-resistant ocular pathogens. Sara M, Yasir M, Kalaiselvan P, Hui A, Kuppusamy R, Kumar N, Chakraborty S, Yu TT, Wong EHH, Molchanova N, Jenssen H, Lin JS, Barron AE, Willcox M Contact lens & anterior eye : the journal of the British Contact Lens Association 38341309 Cont Lens Anterior Eye 2024 Apr
Peptide-mimetic treatment of Pseudomonas aeruginosa in a mouse model of respiratory infection. Moule MG, Benjamin AB, Burger ML, Herlan C, Lebedev M, Lin JS, Koster KJ, Wavare N, Adams LG, Bräse S, Munoz-Medina R, Cannon CL, Barron AE, Cirillo JD Communications biology 39174819 Commun Biol 2024 Aug 22
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Self-Assembly of Antimicrobial Peptoids Impacts Their Biological Effects on ESKAPE Bacterial Pathogens. Nielsen JE, Alford MA, Yung DBY, Molchanova N, Fortkort JA, Lin JS, Diamond G, Hancock REW, Jenssen H, Pletzer D, Lund R, Barron AE ACS infectious diseases 35175731 ACS Infect Dis 2022 Mar 11
Efficacy of Cathelicidin-Mimetic Antimicrobial Peptoids against Staphylococcus aureus. Benjamin AB, Moule MG, Didwania MK, Hardy J, Saenkham-Huntsinger P, Sule P, Nielsen JE, Lin JS, Contag CH, Barron AE, Cirillo JD Microbiology spectrum 35467395 Microbiol Spectr 2022 Jun 29
Potent Antiviral Activity against HSV-1 and SARS-CoV-2 by Antimicrobial Peptoids. Diamond G, Molchanova N, Herlan C, Fortkort JA, Lin JS, Figgins E, Bopp N, Ryan LK, Chung D, Adcock RS, Sherman M, Barron AE Pharmaceuticals (Basel, Switzerland) 33807248 Pharmaceuticals (Basel) 2021 Mar 31
Membrane-acting biomimetic peptoids against visceral leishmaniasis. Kumar V, Lin JS, Molchanova N, Fortkort JA, Reckmann C, Bräse S, Jenssen H, Barron AE, Chugh A FEBS open bio 36683396 FEBS Open Bio 2023 Mar
Acid-degradable lipid nanoparticles enhance the delivery of mRNA. Zhao S, Gao K, Han H, Stenzel M, Yin B, Song H, Lawanprasert A, Nielsen JE, Sharma R, Arogundade OH, Pimcharoen S, Chen YJ, Paul A, Tuma J, Collins MG, Wyle Y, Cranick MG, Burgstone BW, Perez BS, Barron AE, Smith AM, Lee HY, Wang A, Murthy N Nature nanotechnology 39179796 Nat Nanotechnol 2024 Nov
Targeting Impaired Antimicrobial Immunity in the Brain for the Treatment of Alzheimer's Disease. Fulop T, Tripathi S, Rodrigues S, Desroches M, Bunt T, Eiser A, Bernier F, Beauregard PB, Barron AE, Khalil A, Plotka A, Hirokawa K, Larbi A, Bocti C, Laurent B, Frost EH, Witkowski JM Neuropsychiatric disease and treatment 33976546 Neuropsychiatr Dis Treat 2021
Targeting Infectious Agents as a Therapeutic Strategy in Alzheimer's Disease. Fülöp T, Munawara U, Larbi A, Desroches M, Rodrigues S, Catanzaro M, Guidolin A, Khalil A, Bernier F, Barron AE, Hirokawa K, Beauregard PB, Dumoulin D, Bellenger JP, Witkowski JM, Frost E CNS drugs 32458360 CNS Drugs 2020 Jul
Anti-persister and Anti-biofilm Activity of Self-Assembled Antimicrobial Peptoid Ellipsoidal Micelles. Lin JS, Bekale LA, Molchanova N, Nielsen JE, Wright M, Bacacao B, Diamond G, Jenssen H, Santa Maria PL, Barron AE ACS infectious diseases 36018039 ACS Infect Dis 2022 Sep 9
Pf bacteriophages hinder sputum antibiotic diffusion via electrostatic binding. Chen Q, Cai P, Chang THW, Burgener E, Kratochvil MJ, Gupta A, Hargil A, Secor PR, Nielsen JE, Barron AE, Milla C, Heilshorn SC, Spakowitz A, Bollyky PL bioRxiv : the preprint server for biology 38496625 bioRxiv 2024 Mar 10
Antiviral Effect of Antimicrobial Peptoid TM9 and Murine Model of Respiratory Coronavirus Infection. Lebedev M, Benjamin AB, Kumar S, Molchanova N, Lin JS, Koster KJ, Leibowitz JL, Barron AE, Cirillo JD Pharmaceutics 38675125 Pharmaceutics 2024 Mar 27
Antiviral effect of peptoids on hepatitis B virus infection in cell culture. Murayama A, Igarashi H, Yamada N, Aly HH, Molchanova N, Lin JS, Nishitsuji H, Shimotohno K, Muramatsu M, Barron AE, Kato T Antiviral research 38272318 Antiviral Res 2024 Mar
Supramolecular Peptoid Structure Strengthens Complexation with Polyacrylic Acid Microgels. Zhao W, Lin JS, Nielsen JE, Sørensen K, Wadurkar AS, Ji J, Barron AE, Nangia S, Libera MR Biomacromolecules 38240722 Biomacromolecules 2024 Feb 12
Ethylene oxide graft copolymers reduce the immunogenicity of lipid nanoparticles. Qi Y, Han H, Liu A, Zhao S, Lawanprasert A, Nielsen JE, Choudhary H, Liang D, Barron AE, Murthy N RSC advances 39309654 RSC Adv 2024 Sep 18
From Global to Nano: A Geographical Perspective of Aggregatibacter actinomycetemcomitans. Ryder MI, Fine DH, Barron AE Pathogens (Basel, Switzerland) 39452709 Pathogens 2024 Sep 27
From start to finish-a molecular link in wound repair. Yun S, Greco V Science (New York, N.Y.) 35143296 Science 2022 Feb 11
Live imaging reveals chromatin compaction transitions and dynamic transcriptional bursting during stem cell differentiation in vivo. May D, Yun S, Gonzalez DG, Park S, Chen Y, Lathrop E, Cai B, Xin T, Zhao H, Wang S, Gonzalez LE, Cockburn K, Greco V eLife 36880644 Elife 2023 Mar 7
Mechanisms of skin vascular maturation and maintenance captured by longitudinal imaging of live mice. Kam CY, Singh ID, Gonzalez DG, Matte-Martone C, Solá P, Solanas G, Bonjoch J, Marsh E, Hirschi KK, Greco V Cell 37167971 Cell 2023 May 25
Probing the rules of cell coordination in live tissues by interpretable machine learning based on graph neural networks. Yamamoto T, Cockburn K, Greco V, Kawaguchi K PLoS computational biology 36067226 PLoS Comput Biol 2022 Sep
Injury prevents Ras mutant cell expansion in mosaic skin. Gallini S, Annusver K, Rahman NT, Gonzalez DG, Yun S, Matte-Martone C, Xin T, Lathrop E, Suozzi KC, Kasper M, Greco V Nature 37344586 Nature 2023 Jul
Correction: Cell cycle controls long-range calcium signaling in the regenerating epidermis. Moore JL, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Sanz NC, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V The Journal of cell biology 38477880 J Cell Biol 2024 Apr 1
Metabolic rewiring in skin epidermis drives tolerance to oncogenic mutations. Hemalatha A, Li Z, Gonzalez DG, Matte-Martone C, Tai K, Lathrop E, Gil D, Ganesan S, Gonzalez LE, Skala M, Perry RJ, Greco V Nature cell biology 39762578 Nat Cell Biol 2025 Feb
Functional cell death, corneoptosis, requires temporally controlled intracellular acidification. Moore JL, Greco V Proceedings of the National Academy of Sciences of the United States of America 33986147 Proc Natl Acad Sci U S A 2021 Jun 1
Cell cycle controls long-range calcium signaling in the regenerating epidermis. Moore JL, Bhaskar D, Gao F, Matte-Martone C, Du S, Lathrop E, Ganesan S, Shao L, Norris R, Campamà Sanz N, Annusver K, Kasper M, Cox A, Hendry C, Rieck B, Krishnaswamy S, Greco V The Journal of cell biology 37102999 J Cell Biol 2023 Jul 3
Skin-resident immune cells actively coordinate their distribution with epidermal cells during homeostasis. Park S, Matte-Martone C, Gonzalez DG, Lathrop EA, May DP, Pineda CM, Moore JL, Boucher JD, Marsh E, Schmitter-Sánchez A, Cockburn K, Markova O, Bellaïche Y, Greco V Nature cell biology 33958758 Nat Cell Biol 2021 May
Gradual differentiation uncoupled from cell cycle exit generates heterogeneity in the epidermal stem cell layer. Cockburn K, Annusver K, Gonzalez DG, Ganesan S, May DP, Mesa KR, Kawaguchi K, Kasper M, Greco V Nature cell biology 36357619 Nat Cell Biol 2022 Dec
Organ function is preserved despite reorganization of niche architecture in the hair follicle. Wei H, Du S, Parksong J, Pasolli HA, Matte-Martone C, Regot S, Gonzalez LE, Xin T, Greco V Cell stem cell 37419106 Cell Stem Cell 2023 Jul 6
Oncogenic Kras induces spatiotemporally specific tissue deformation through converting pulsatile into sustained ERK activation. Xin T, Gallini S, Wei H, Gonzalez DG, Matte-Martone C, Machida H, Fujiwara H, Pasolli HA, Suozzi KC, Gonzalez LE, Regot S, Greco V Nature cell biology 38689013 Nat Cell Biol 2024 Jun
A Spatiotemporal Compartmentalization of Glucose Metabolism Guides Mammalian Gastrulation Progression. Cao D, Zhong L, Hemalatha A, Bergmann J, Cox AL, Greco V, Sozen B bioRxiv : the preprint server for biology 37333168 bioRxiv 2023 Jun 8
Selective utilization of glucose metabolism guides mammalian gastrulation. Cao D, Bergmann J, Zhong L, Hemalatha A, Dingare C, Jensen T, Cox AL, Greco V, Steventon B, Sozen B Nature 39415005 Nature 2024 Oct
Dissecting dual roles of MyoD during lineage conversion to mature myocytes and myogenic stem cells. Yagi M, Ji F, Charlton J, Cristea S, Messemer K, Horwitz N, Di Stefano B, Tsopoulidis N, Hoetker MS, Huebner AJ, Bar-Nur O, Almada AE, Yamamoto M, Patelunas A, Goldhamer DJ, Wagers AJ, Michor F, Meissner A, Sadreyev RI, Hochedlinger K Genes & development 34413137 Genes Dev 2021 Sep 1
Directed evolution of a family of AAV capsid variants enabling potent muscle-directed gene delivery across species. Tabebordbar M, Lagerborg KA, Stanton A, King EM, Ye S, Tellez L, Krunnfusz A, Tavakoli S, Widrick JJ, Messemer KA, Troiano EC, Moghadaszadeh B, Peacker BL, Leacock KA, Horwitz N, Beggs AH, Wagers AJ, Sabeti PC Cell 34506722 Cell 2021 Sep 16
In Situ Modification of Tissue Stem and Progenitor Cell Genomes. Goldstein JM, Tabebordbar M, Zhu K, Wang LD, Messemer KA, Peacker B, Ashrafi Kakhki S, Gonzalez-Celeiro M, Shwartz Y, Cheng JKW, Xiao R, Barungi T, Albright C, Hsu YC, Vandenberghe LH, Wagers AJ Cell reports 31018138 Cell Rep 2019 Apr 23
High-efficiency purification of divergent AAV serotypes using AAVX affinity chromatography. Florea M, Nicolaou F, Pacouret S, Zinn EM, Sanmiguel J, Andres-Mateos E, Unzu C, Wagers AJ, Vandenberghe LH Molecular therapy. Methods & clinical development 36654797 Mol Ther Methods Clin Dev 2023 Mar 9
Harvard HIV and Aging Workshop: Perspectives and Priorities from Claude D. Pepper Centers and Centers for AIDS Research. Montano M, Bhasin S, D'Aquila RT, Erlandson KM, Evans WJ, Funderburg NT, Justice A, Ndhlovu LC, Ojikutu B, Pahor M, Pahwa S, Ryan AS, Schrack J, Schultz MB, Sebastiani P, Sinclair DA, Tripp J, Walker B, Womack JA, Yung R, Reeves RK AIDS research and human retroviruses 31456412 AIDS Res Hum Retroviruses 2019 Nov-Dec
Skeletal muscle overexpression of nicotinamide phosphoribosyl transferase in mice coupled with voluntary exercise augments exercise endurance. Costford SR, Brouwers B, Hopf ME, Sparks LM, Dispagna M, Gomes AP, Cornnell HH, Petucci C, Phelan P, Xie H, Yi F, Walter GA, Osborne TF, Sinclair DA, Mynatt RL, Ayala JE, Gardell SJ, Smith SR Molecular metabolism 29146412 Mol Metab 2018 Jan
Impairment of an Endothelial NAD(+)-H(2)S Signaling Network Is a Reversible Cause of Vascular Aging. Das A, Huang GX, Bonkowski MS, Longchamp A, Li C, Schultz MB, Kim LJ, Osborne B, Joshi S, Lu Y, Treviño-Villarreal JH, Kang MJ, Hung TT, Lee B, Williams EO, Igarashi M, Mitchell JR, Wu LE, Turner N, Arany Z, Guarente L, Sinclair DA Cell 29570999 Cell 2018 Mar 22
Multigenerational obesity-induced perturbations in oocyte-secreted factor signalling can be ameliorated by exercise and nicotinamide mononucleotide. Bertoldo MJ, Uddin GM, Youngson NA, Agapiou D, Walters KA, Sinclair DA, Morris MJ, Gilchrist RB Human reproduction open 30895251 Hum Reprod Open 2018
Voluntary exercise normalizes the proteomic landscape in muscle and brain and improves the phenotype of progeroid mice. Ross JM, Coppotelli G, Branca RM, Kim KM, Lehtiö J, Sinclair DA, Olson L Aging cell 31489782 Aging Cell 2019 Dec
Dynamic Acetylation of Phosphoenolpyruvate Carboxykinase Toggles Enzyme Activity between Gluconeogenic and Anaplerotic Reactions. Latorre-Muro P, Baeza J, Armstrong EA, Hurtado-Guerrero R, Corzana F, Wu LE, Sinclair DA, López-Buesa P, Carrodeguas JA, Denu JM Molecular cell 30193097 Mol Cell 2018 Sep 6
Assays for NAD(+)-Dependent Reactions and NAD(+) Metabolites. Schultz MB, Lu Y, Braidy N, Sinclair DA Methods in molecular biology (Clifton, N.J.) 30097862 Methods Mol Biol 2018
Resveratrol Improves Vascular Function and Mitochondrial Number but Not Glucose Metabolism in Older Adults. Pollack RM, Barzilai N, Anghel V, Kulkarni AS, Golden A, O'Broin P, Sinclair DA, Bonkowski MS, Coleville AJ, Powell D, Kim S, Moaddel R, Stein D, Zhang K, Hawkins M, Crandall JP The journals of gerontology. Series A, Biological sciences and medical sciences 28329397 J Gerontol A Biol Sci Med Sci 2017 Nov 9
Sirtuins and NAD(+) in the Development and Treatment of Metabolic and Cardiovascular Diseases. Kane AE, Sinclair DA Circulation research 30355082 Circ Res 2018 Sep 14
Publisher Correction: Longitudinal analysis of biomarker data from a personalized nutrition platform in healthy subjects. Westerman K, Reaver A, Roy C, Ploch M, Sharoni E, Nogal B, Sinclair DA, Katz DL, Blumberg JB, Blander G Scientific reports 30405144 Sci Rep 2018 Nov 8
Barrier-to-autointegration factor 1 (Banf1) regulates poly [ADP-ribose] polymerase 1 (PARP1) activity following oxidative DNA damage. Bolderson E, Burgess JT, Li J, Gandhi NS, Boucher D, Croft LV, Beard S, Plowman JJ, Suraweera A, Adams MN, Naqi A, Zhang SD, Sinclair DA, O'Byrne KJ, Richard DJ Nature communications 31796734 Nat Commun 2019 Dec 3
Amino Acid Restriction Triggers Angiogenesis via GCN2/ATF4 Regulation of VEGF and H(2)S Production. Longchamp A, Mirabella T, Arduini A, MacArthur MR, Das A, Treviño-Villarreal JH, Hine C, Ben-Sahra I, Knudsen NH, Brace LE, Reynolds J, Mejia P, Tao M, Sharma G, Wang R, Corpataux JM, Haefliger JA, Ahn KH, Lee CH, Manning BD, Sinclair DA, Chen CS, Ozaki CK, Mitchell JR Cell 29570992 Cell 2018 Mar 22
Sirtuin activators and inhibitors: Promises, achievements, and challenges. Dai H, Sinclair DA, Ellis JL, Steegborn C Pharmacology & therapeutics 29577959 Pharmacol Ther 2018 Aug
Quantitative proteomic analysis of extracellular vesicle subgroups isolated by an optimized method combining polymer-based precipitation and size exclusion chromatography. Martínez-Greene JA, Hernández-Ortega K, Quiroz-Baez R, Resendis-Antonio O, Pichardo-Casas I, Sinclair DA, Budnik B, Hidalgo-Miranda A, Uribe-Querol E, Ramos-Godínez MDP, Martínez-Martínez E Journal of extracellular vesicles 33936570 J Extracell Vesicles 2021 Apr
NAD(+) Repletion Rescues Female Fertility during Reproductive Aging. Bertoldo MJ, Listijono DR, Ho WJ, Riepsamen AH, Goss DM, Richani D, Jin XL, Mahbub S, Campbell JM, Habibalahi A, Loh WN, Youngson NA, Maniam J, Wong ASA, Selesniemi K, Bustamante S, Li C, Zhao Y, Marinova MB, Kim LJ, Lau L, Wu RM, Mikolaizak AS, Araki T, Le Couteur DG, Turner N, Morris MJ, Walters KA, Goldys E, O'Neill C, Gilchrist RB, Sinclair DA, Homer HA, Wu LE Cell reports 32049001 Cell Rep 2020 Feb 11
Nicotinamide mononucleotide (NMN) supplementation rescues cerebromicrovascular endothelial function and neurovascular coupling responses and improves cognitive function in aged mice. Tarantini S, Valcarcel-Ares MN, Toth P, Yabluchanskiy A, Tucsek Z, Kiss T, Hertelendy P, Kinter M, Ballabh P, Süle Z, Farkas E, Baur JA, Sinclair DA, Csiszar A, Ungvari Z Redox biology 31015147 Redox Biol 2019 Jun
Impacts of obesity, maternal obesity and nicotinamide mononucleotide supplementation on sperm quality in mice. Youngson NA, Uddin GM, Das A, Martinez C, Connaughton HS, Whiting S, Yu J, Sinclair DA, Aitken RJ, Morris MJ Reproduction (Cambridge, England) 31226694 Reproduction 2019 Aug 1
Molecular and Cellular Characterization of SIRT1 Allosteric Activators. Schultz MB, Rinaldi C, Lu Y, Amorim JA, Sinclair DA Methods in molecular biology (Clifton, N.J.) 31087296 Methods Mol Biol 2019
Multiple basal cell carcinomas in a patient with myotonic dystrophy type 1. Feng J, LaChance A, Sinclair DA, Asgari MM BMJ case reports 30852496 BMJ Case Rep 2019 Mar 8
Nicotinamide Improves Aspects of Healthspan, but Not Lifespan, in Mice. Mitchell SJ, Bernier M, Aon MA, Cortassa S, Kim EY, Fang EF, Palacios HH, Ali A, Navas-Enamorado I, Di Francesco A, Kaiser TA, Waltz TB, Zhang N, Ellis JL, Elliott PJ, Frederick DW, Bohr VA, Schmidt MS, Brenner C, Sinclair DA, Sauve AA, Baur JA, de Cabo R Cell metabolism 29514072 Cell Metab 2018 Mar 6
Mitohormesis and metabolic health: The interplay between ROS, cAMP and sirtuins. Palmeira CM, Teodoro JS, Amorim JA, Steegborn C, Sinclair DA, Rolo AP Free radical biology & medicine 31349039 Free Radic Biol Med 2019 Sep
NAD(+) in Brain Aging and Neurodegenerative Disorders. Lautrup S, Sinclair DA, Mattson MP, Fang EF Cell metabolism 31577933 Cell Metab 2019 Oct 1
Epigenetic changes during aging and their reprogramming potential. Kane AE, Sinclair DA Critical reviews in biochemistry and molecular biology 30822165 Crit Rev Biochem Mol Biol 2019 Feb
Frailty biomarkers in humans and rodents: Current approaches and future advances. Kane AE, Sinclair DA Mechanisms of ageing and development 31002925 Mech Ageing Dev 2019 Jun
Telomere Dysfunction Induces Sirtuin Repression that Drives Telomere-Dependent Disease. Amano H, Chaudhury A, Rodriguez-Aguayo C, Lu L, Akhanov V, Catic A, Popov YV, Verdin E, Johnson H, Stossi F, Sinclair DA, Nakamaru-Ogiso E, Lopez-Berestein G, Chang JT, Neilson JR, Meeker A, Finegold M, Baur JA, Sahin E Cell metabolism 30930169 Cell Metab 2019 Jun 4
Longitudinal analysis of biomarker data from a personalized nutrition platform in healthy subjects. Westerman K, Reaver A, Roy C, Ploch M, Sharoni E, Nogal B, Sinclair DA, Katz DL, Blumberg JB, Blander G Scientific reports 30279436 Sci Rep 2018 Oct 2
Comparing the Effects of Low-Protein and High-Carbohydrate Diets and Caloric Restriction on Brain Aging in Mice. Wahl D, Solon-Biet SM, Wang QP, Wali JA, Pulpitel T, Clark X, Raubenheimer D, Senior AM, Sinclair DA, Cooney GJ, de Cabo R, Cogger VC, Simpson SJ, Le Couteur DG Cell reports 30463018 Cell Rep 2018 Nov 20
Nicotinamide mononucleotide (NMN) supplementation ameliorates the impact of maternal obesity in mice: comparison with exercise. Uddin GM, Youngson NA, Doyle BM, Sinclair DA, Morris MJ Scientific reports 29118320 Sci Rep 2017 Nov 8
Targeting mitochondria for cardiovascular disorders: therapeutic potential and obstacles. Bonora M, Wieckowski MR, Sinclair DA, Kroemer G, Pinton P, Galluzzi L Nature reviews. Cardiology 30177752 Nat Rev Cardiol 2019 Jan
Therapeutic Potential of NAD-Boosting Molecules: The In Vivo Evidence. Rajman L, Chwalek K, Sinclair DA Cell metabolism 29514064 Cell Metab 2018 Mar 6
Influence of donor age on induced pluripotent stem cells. Lo Sardo V, Ferguson W, Erikson GA, Topol EJ, Baldwin KK, Torkamani A Nature biotechnology 27941802 Nat Biotechnol 2017 Jan
Genomic integrity of human induced pluripotent stem cells across nine studies in the NHLBI NextGen program. Kanchan K, Iyer K, Yanek LR, Carcamo-Orive I, Taub MA, Malley C, Baldwin K, Becker LC, Broeckel U, Cheng L, Cowan C, D'Antonio M, Frazer KA, Quertermous T, Mostoslavsky G, Murphy G, Rabinovitch M, Rader DJ, Steinberg MH, Topol E, Yang W, Knowles JW, Jaquish CE, Ruczinski I, Mathias RA Stem cell research 32442913 Stem Cell Res 2020 Jul
Rates of contributory de novo mutation in high and low-risk autism families. Yoon S, Munoz A, Yamrom B, Lee YH, Andrews P, Marks S, Wang Z, Reeves C, Winterkorn L, Krieger AM, Buja A, Pradhan K, Ronemus M, Baldwin KK, Levy D, Wigler M, Iossifov I Communications biology 34471188 Commun Biol 2021 Sep 1
Transcriptional profiling of isogenic Friedreich ataxia neurons and effect of an HDAC inhibitor on disease signatures. Lai JI, Nachun D, Petrosyan L, Throesch B, Campau E, Gao F, Baldwin KK, Coppola G, Gottesfeld JM, Soragni E The Journal of biological chemistry 30552117 J Biol Chem 2019 Feb 8
Unveiling the Role of the Most Impactful Cardiovascular Risk Locus through Haplotype Editing. Lo Sardo V, Chubukov P, Ferguson W, Kumar A, Teng EL, Duran M, Zhang L, Cost G, Engler AJ, Urnov F, Topol EJ, Torkamani A, Baldwin KK Cell 30528432 Cell 2018 Dec 13
Diverse reprogramming codes for neuronal identity. Tsunemoto R, Lee S, Szűcs A, Chubukov P, Sokolova I, Blanchard JW, Eade KT, Bruggemann J, Wu C, Torkamani A, Sanna PP, Baldwin KK Nature 29743677 Nature 2018 May
Multiple Click-Selective tRNA Synthetases Expand Mammalian Cell-Specific Proteomics. Yang AC, du Bois H, Olsson N, Gate D, Lehallier B, Berdnik D, Brewer KD, Bertozzi CR, Elias JE, Wyss-Coray T Journal of the American Chemical Society 29775058 J Am Chem Soc 2018 Jun 13
CD22 blockade restores homeostatic microglial phagocytosis in ageing brains. Pluvinage JV, Haney MS, Smith BAH, Sun J, Iram T, Bonanno L, Li L, Lee DP, Morgens DW, Yang AC, Shuken SR, Gate D, Scott M, Khatri P, Luo J, Bertozzi CR, Bassik MC, Wyss-Coray T Nature 30944478 Nature 2019 Apr
A single-cell transcriptomic atlas characterizes ageing tissues in the mouse. Tabula Muris Consortium Nature 32669714 Nature 2020 Jul
Papain-based Single Cell Isolation of Primary Murine Brain Endothelial Cells Using Flow Cytometry. Yousef H, Czupalla CJ, Lee D, Butcher EC, Wyss-Coray T Bio-protocol 31032379 Bio Protoc 2018 Nov 20
Aged blood impairs hippocampal neural precursor activity and activates microglia via brain endothelial cell VCAM1. Yousef H, Czupalla CJ, Lee D, Chen MB, Burke AN, Zera KA, Zandstra J, Berber E, Lehallier B, Mathur V, Nair RV, Bonanno LN, Yang AC, Peterson T, Hadeiba H, Merkel T, Körbelin J, Schwaninger M, Buckwalter MS, Quake SR, Butcher EC, Wyss-Coray T Nature medicine 31086348 Nat Med 2019 Jun
A neuronal blood marker is associated with mortality in old age. Kaeser SA, Lehallier B, Thinggaard M, Häsler LM, Apel A, Bergmann C, Berdnik D, Jeune B, Christensen K, Grönke S, Partridge L, Wyss-Coray T, Mengel-From J, Jucker M Nature aging 37118632 Nat Aging 2021 Feb
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Intrinsic Versus Extrinsic Cancer Risk Factors and Aging. Podolskiy DI, Gladyshev VN Trends in molecular medicine 27544777 Trends Mol Med 2016 Oct
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