Single Cell Analysis Program (SCAP)
Single Cell Analysis Program (SCAP)
Program Publications
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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 |
|---|---|---|---|---|---|
| Normalization and noise reduction for single cell RNA-seq experiments. | Ding B, Zheng L, Zhu Y, Li N, Jia H, Ai R, Wildberg A, Wang W | Bioinformatics (Oxford, England) | 25717193 | Bioinformatics | 2015 Jul 1 |
| Tools for the analysis of high-dimensional single-cell RNA sequencing data. | Wu Y, Zhang K | Nature reviews. Nephrology | 32221477 | Nat Rev Nephrol | 2020 Jul |
| Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain. | Lake BB, Chen S, Sos BC, Fan J, Kaeser GE, Yung YC, Duong TE, Gao D, Chun J, Kharchenko PV, Zhang K | Nature biotechnology | 29227469 | Nat Biotechnol | 2018 Jan |
| Mapping Human Tissues with Highly Multiplexed RNA in situ Hybridization. | Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer C, Yuan Y, Zhang Y, Song J, Knoten A, Lake BB, Gaut JP, Keene D, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K | bioRxiv : the preprint server for biology | 37645998 | bioRxiv | 2023 Aug 19 |
| Neuronal subtypes and diversity revealed by single-nucleus RNA sequencing of the human brain. | Lake BB, Ai R, Kaeser GE, Salathia NS, Yung YC, Liu R, Wildberg A, Gao D, Fung HL, Chen S, Vijayaraghavan R, Wong J, Chen A, Sheng X, Kaper F, Shen R, Ronaghi M, Fan JB, Wang W, Chun J, Zhang K | Science (New York, N.Y.) | 27339989 | Science | 2016 Jun 24 |
| Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis. | Fan J, Salathia N, Liu R, Kaeser GE, Yung YC, Herman JL, Kaper F, Fan JB, Zhang K, Chun J, Kharchenko PV | Nature methods | 26780092 | Nat Methods | 2016 Mar |
| A comparative strategy for single-nucleus and single-cell transcriptomes confirms accuracy in predicted cell-type expression from nuclear RNA. | Lake BB, Codeluppi S, Yung YC, Gao D, Chun J, Kharchenko PV, Linnarsson S, Zhang K | Scientific reports | 28729663 | Sci Rep | 2017 Jul 20 |
| Assessment of Single Cell RNA-Seq Normalization Methods. | Ding B, Zheng L, Wang W | G3 (Bethesda, Md.) | 28468817 | G3 (Bethesda) | 2017 Jul 5 |
| Mapping human tissues with highly multiplexed RNA in situ hybridization. | Kalhor K, Chen CJ, Lee HS, Cai M, Nafisi M, Que R, Palmer CR, Yuan Y, Zhang Y, Li X, Song J, Knoten A, Lake BB, Gaut JP, Keene CD, Lein E, Kharchenko PV, Chun J, Jain S, Fan JB, Zhang K | Nature communications | 38509069 | Nat Commun | 2024 Mar 20 |
| Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues. | Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Ferrante TC, Terry R, Turczyk BM, Yang JL, Lee HS, Aach J, Zhang K, Church GM | Nature protocols | 25675209 | Nat Protoc | 2015 Mar |
| Visualizing and Interpreting Single-Cell Gene Expression Datasets with Similarity Weighted Nonnegative Embedding. | Wu Y, Tamayo P, Zhang K | Cell systems | 30528274 | Cell Syst | 2018 Dec 26 |
| Single-nucleus analysis of accessible chromatin in developing mouse forebrain reveals cell-type-specific transcriptional regulation. | Preissl S, Fang R, Huang H, Zhao Y, Raviram R, Gorkin DU, Zhang Y, Sos BC, Afzal V, Dickel DE, Kuan S, Visel A, Pennacchio LA, Zhang K, Ren B | Nature neuroscience | 29434377 | Nat Neurosci | 2018 Mar |
| Assessing characteristics of RNA amplification methods for single cell RNA sequencing. | Dueck HR, Ai R, Camarena A, Ding B, Dominguez R, Evgrafov OV, Fan JB, Fisher SA, Herstein JS, Kim TK, Kim JM, Lin MY, Liu R, Mack WJ, McGroty S, Nguyen JD, Salathia N, Shallcross J, Souaiaia T, Spaethling JM, Walker CP, Wang J, Wang K, Wang W, Wildberg A, Zheng L, Chow RH, Eberwine J, Knowles JA, Zhang K, Kim J | BMC genomics | 27881084 | BMC Genomics | 2016 Nov 24 |
| Highly multiplexed subcellular RNA sequencing in situ. | Lee JH, Daugharthy ER, Scheiman J, Kalhor R, Yang JL, Ferrante TC, Terry R, Jeanty SS, Li C, Amamoto R, Peters DT, Turczyk BM, Marblestone AH, Inverso SA, Bernard A, Mali P, Rios X, Aach J, Church GM | Science (New York, N.Y.) | 24578530 | Science | 2014 Mar 21 |
| Massively parallel polymerase cloning and genome sequencing of single cells using nanoliter microwells. | Gole J, Gore A, Richards A, Chiu YJ, Fung HL, Bushman D, Chiang HI, Chun J, Lo YH, Zhang K | Nature biotechnology | 24213699 | Nat Biotechnol | 2013 Dec |
| High-throughput sequencing of the transcriptome and chromatin accessibility in the same cell. | Chen S, Lake BB, Zhang K | Nature biotechnology | 31611697 | Nat Biotechnol | 2019 Dec |
| Scalable dual-omics profiling with single-nucleus chromatin accessibility and mRNA expression sequencing 2 (SNARE-seq2). | Plongthongkum N, Diep D, Chen S, Lake BB, Zhang K | Nature protocols | 34650278 | Nat Protoc | 2021 Nov |
| DynaMorph: self-supervised learning of morphodynamic states of live cells. | Wu Z, Chhun BB, Popova G, Guo SM, Kim CN, Yeh LH, Nowakowski T, Zou J, Mehta SB | Molecular biology of the cell | 35138913 | Mol Biol Cell | 2022 May 15 |
| BABEL enables cross-modality translation between multiomic profiles at single-cell resolution. | Wu KE, Yost KE, Chang HY, Zou J | Proceedings of the National Academy of Sciences of the United States of America | 33827925 | Proc Natl Acad Sci U S A | 2021 Apr 13 |
| Muscling up the heart: a preadolescent cardiomyocyte proliferation contributes to heart growth. | Zhang CH, Kühn B | Circulation research | 25258401 | Circ Res | 2014 Sep 26 |
| Cardiac regeneration based on mechanisms of cardiomyocyte proliferation and differentiation. | Senyo SE, Lee RT, Kühn B | Stem cell research | 25306390 | Stem Cell Res | 2014 Nov |
| Transcriptome in vivo analysis (TIVA) of spatially defined single cells in live tissue. | Lovatt D, Ruble BK, Lee J, Dueck H, Kim TK, Fisher S, Francis C, Spaethling JM, Wolf JA, Grady MS, Ulyanova AV, Yeldell SB, Griepenburg JC, Buckley PT, Kim J, Sul JY, Dmochowski IJ, Eberwine J | Nature methods | 24412976 | Nat Methods | 2014 Feb |
| Single cell transcriptomics of noncoding RNAs and their cell-specificity. | Gawronski KAB, Kim J | Wiley interdisciplinary reviews. RNA | 28762653 | Wiley Interdiscip Rev RNA | 2017 Nov |
| CHEX-seq detects single-cell genomic single-stranded DNA with catalytical potential. | Lu Y, Lee J, Li J, Allu SR, Wang J, Kim H, Bullaughey KL, Fisher SA, Nordgren CE, Rosario JG, Anderson SA, Ulyanova AV, Brem S, Chen HI, Wolf JA, Grady MS, Vinogradov SA, Kim J, Eberwine J | Nature communications | 37963886 | Nat Commun | 2023 Nov 14 |
| Cellular Deconstruction: Finding Meaning in Individual Cell Variation. | Eberwine J, Kim J | Trends in cell biology | 26410403 | Trends Cell Biol | 2015 Oct |
| Single-neuron isolation for RNA analysis using pipette capture and laser capture microdissection. | Lovatt D, Bell T, Eberwine J | Cold Spring Harbor protocols | 25561613 | Cold Spring Harb Protoc | 2015 Jan 5 |
| Mechanisms of Cardiomyocyte Proliferation and Differentiation in Development and Regeneration. | Yester JW, Kühn B | Current cardiology reports | 28185170 | Curr Cardiol Rep | 2017 Feb |
| Variation is function: Are single cell differences functionally important?: Testing the hypothesis that single cell variation is required for aggregate function. | Dueck H, Eberwine J, Kim J | BioEssays : news and reviews in molecular, cellular and developmental biology | 26625861 | Bioessays | 2016 Feb |
| High-resolution transcriptome analysis reveals neuropathic pain gene-expression signatures in spinal microglia after nerve injury. | Jeong H, Na YJ, Lee K, Kim YH, Lee Y, Kang M, Jiang BC, Yeom YI, Wu LJ, Gao YJ, Kim J, Oh SB | Pain | 26761385 | Pain | 2016 Apr |
| Comprehensive catalog of dendritically localized mRNA isoforms from sub-cellular sequencing of single mouse neurons. | Middleton SA, Eberwine J, Kim J | BMC biology | 30678683 | BMC Biol | 2019 Jan 24 |
| Pervasive within-Mitochondrion Single-Nucleotide Variant Heteroplasmy as Revealed by Single-Mitochondrion Sequencing. | Morris J, Na YJ, Zhu H, Lee JH, Giang H, Ulyanova AV, Baltuch GH, Brem S, Chen HI, Kung DK, Lucas TH, O'Rourke DM, Wolf JA, Grady MS, Sul JY, Kim J, Eberwine J | Cell reports | 29212019 | Cell Rep | 2017 Dec 5 |
| Comprehensive analysis of 2.4 million patent-to-research citations maps the biomedical innovation and translation landscape. | Manjunath A, Li H, Song S, Zhang Z, Liu S, Kahrobai N, Gowda A, Seffens A, Zou J, Kumar I | Nature biotechnology | 34113042 | Nat Biotechnol | 2021 Jun |
| How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals. | Wu E, Wu K, Daneshjou R, Ouyang D, Ho DE, Zou J | Nature medicine | 33820998 | Nat Med | 2021 Apr |
| Data valuation for medical imaging using Shapley value and application to a large-scale chest X-ray dataset. | Tang S, Ghorbani A, Yamashita R, Rehman S, Dunnmon JA, Zou J, Rubin DL | Scientific reports | 33863957 | Sci Rep | 2021 Apr 16 |
| Integrating spatial gene expression and breast tumour morphology via deep learning. | He B, Bergenstråhle L, Stenbeck L, Abid A, Andersson A, Borg Å, Maaskola J, Lundeberg J, Zou J | Nature biomedical engineering | 32572199 | Nat Biomed Eng | 2020 Aug |
| GenePT: A Simple But Effective Foundation Model for Genes and Cells Built From ChatGPT. | Chen Y, Zou J | bioRxiv : the preprint server for biology | 37905130 | bioRxiv | 2024 Mar 5 |
| GPT detectors are biased against non-native English writers. | Liang W, Yuksekgonul M, Mao Y, Wu E, Zou J | Patterns (New York, N.Y.) | 37521038 | Patterns (N Y) | 2023 Jul 14 |
| Lack of Transparency and Potential Bias in Artificial Intelligence Data Sets and Algorithms: A Scoping Review. | Daneshjou R, Smith MP, Sun MD, Rotemberg V, Zou J | JAMA dermatology | 34550305 | JAMA Dermatol | 2021 Nov 1 |
| Antisense RNA amplification for target assessment of total mRNA from a single cell. | Morris J, Bell TJ, Buckley PT, Eberwine JH | Cold Spring Harbor protocols | 25368303 | Cold Spring Harb Protoc | 2014 Nov 3 |
| Control of cytokinesis by β-adrenergic receptors indicates an approach for regulating cardiomyocyte endowment. | Liu H, Zhang CH, Ammanamanchi N, Suresh S, Lewarchik C, Rao K, Uys GM, Han L, Abrial M, Yimlamai D, Ganapathy B, Guillermier C, Chen N, Khaladkar M, Spaethling J, Eberwine JH, Kim J, Walsh S, Choudhury S, Little K, Francis K, Sharma M, Viegas M, Bais A, Kostka D, Ding J, Bar-Joseph Z, Wu Y, Yechoor V, Moulik M, Johnson J, Weinberg J, Reyes-Múgica M, Steinhauser ML, Kühn B | Science translational medicine | 31597755 | Sci Transl Med | 2019 Oct 9 |
| Disparity in the quality of COVID-19 data reporting across India. | Vasudevan V, Gnanasekaran A, Sankar V, Vasudevan SA, Zou J | BMC public health | 34167499 | BMC Public Health | 2021 Jun 24 |
| Ensuring that biomedical AI benefits diverse populations. | Zou J, Schiebinger L | EBioMedicine | 33962897 | EBioMedicine | 2021 May |
| Primary Cell Culture of Live Neurosurgically Resected Aged Adult Human Brain Cells and Single Cell Transcriptomics. | Spaethling JM, Na YJ, Lee J, Ulyanova AV, Baltuch GH, Bell TJ, Brem S, Chen HI, Dueck H, Fisher SA, Garcia MP, Khaladkar M, Kung DK, Lucas TH Jr, O'Rourke DM, Stefanik D, Wang J, Wolf JA, Bartfai T, Grady MS, Sul JY, Kim J, Eberwine JH | Cell reports | 28099855 | Cell Rep | 2017 Jan 17 |
| Leveraging physiology and artificial intelligence to deliver advancements in health care. | Zhang A, Wu Z, Wu E, Wu M, Snyder MP, Zou J, Wu JC | Physiological reviews | 37104717 | Physiol Rev | 2023 Oct 1 |
| RNA-GPS Predicts SARS-CoV-2 RNA Residency to Host Mitochondria and Nucleolus. | Wu KE, Fazal FM, Parker KR, Zou J, Chang HY | Cell systems | 32673562 | Cell Syst | 2020 Jul 22 |
| PIVOT: platform for interactive analysis and visualization of transcriptomics data. | Zhu Q, Fisher SA, Dueck H, Middleton S, Khaladkar M, Kim J | BMC bioinformatics | 29304726 | BMC Bioinformatics | 2018 Jan 5 |
| The successes and future prospects of the linear antisense RNA amplification methodology. | Li J, Eberwine J | Nature protocols | 29599441 | Nat Protoc | 2018 May |
| Deep sequencing reveals cell-type-specific patterns of single-cell transcriptome variation. | Dueck H, Khaladkar M, Kim TK, Spaethling JM, Francis C, Suresh S, Fisher SA, Seale P, Beck SG, Bartfai T, Kuhn B, Eberwine J, Kim J | Genome biology | 26056000 | Genome Biol | 2015 Jun 9 |
| Alveolar epithelial cell processing of nanoparticles activates autophagy and lysosomal exocytosis. | Sipos A, Kim KJ, Chow RH, Flodby P, Borok Z, Crandall ED | American journal of physiology. Lung cellular and molecular physiology | 29722567 | Am J Physiol Lung Cell Mol Physiol | 2018 Aug 1 |
| Direct measurement of bipolar cell responses to electrical stimulation in wholemount mouse retina. | Walston ST, Chow RH, Weiland JD | Journal of neural engineering | 29513646 | J Neural Eng | 2018 Aug |
| Zika Virus Infects Intermediate Progenitor Cells and Post-mitotic Committed Neurons in Human Fetal Brain Tissues. | Lin MY, Wang YL, Wu WL, Wolseley V, Tsai MT, Radic V, Thornton ME, Grubbs BH, Chow RH, Huang IC | Scientific reports | 29093521 | Sci Rep | 2017 Nov 1 |
| Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp. | Kim JMH, Camarena A, Walker C, Lin MY, Wolseley V, Souaiaia T, Thornton M, Grubbs B, Chow RH, Evgrafov OV, Knowles JA | Scientific reports | 32029778 | Sci Rep | 2020 Feb 6 |
| Altered adult neurogenesis and gliogenesis in patients with mesial temporal lobe epilepsy. | Ammothumkandy A, Ravina K, Wolseley V, Tartt AN, Yu PN, Corona L, Zhang N, Nune G, Kalayjian L, Mann JJ, Rosoklija GB, Arango V, Dwork AJ, Lee B, Smith JAD, Song D, Berger TW, Heck C, Chow RH, Boldrini M, Liu CY, Russin JJ, Bonaguidi MA | Nature neuroscience | 35383330 | Nat Neurosci | 2022 Apr |
| Human adult neurogenesis loss corresponds with cognitive decline during epilepsy progression. | Ammothumkandy A, Corona L, Ravina K, Wolseley V, Nelson J, Atai N, Abedi A, Jimenez N, Armacost M, D'Orazio LM, Zuverza-Chavarria V, Cayce A, McCleary C, Nune G, Kalayjian L, Lee DJ, Lee B, Chow RH, Heck C, Russin JJ, Liu CY, Smith JAD, Bonaguidi MA | Cell stem cell | 39642885 | Cell Stem Cell | 2025 Feb 6 |
| Global DNA methylation and transcriptional analyses of human ESC-derived cardiomyocytes. | Gu Y, Liu GH, Plongthongkum N, Benner C, Yi F, Qu J, Suzuki K, Yang J, Zhang W, Li M, Montserrat N, Crespo I, Del Sol A, Esteban CR, Zhang K, Izpisua Belmonte JC | Protein & cell | 24474197 | Protein Cell | 2014 Jan |
| The 3D genome in transcriptional regulation and pluripotency. | Gorkin DU, Leung D, Ren B | Cell stem cell | 24905166 | Cell Stem Cell | 2014 Jun 5 |
| Efficient delivery and functional expression of transfected modified mRNA in human embryonic stem cell-derived retinal pigmented epithelial cells. | Hansson ML, Albert S, González Somermeyer L, Peco R, Mejía-Ramírez E, Montserrat N, Izpisua Belmonte JC | The Journal of biological chemistry | 25555917 | J Biol Chem | 2015 Feb 27 |
| Establishment of human iPSC-based models for the study and targeting of glioma initiating cells. | Sancho-Martinez I, Nivet E, Xia Y, Hishida T, Aguirre A, Ocampo A, Ma L, Morey R, Krause MN, Zembrzycki A, Ansorge O, Vazquez-Ferrer E, Dubova I, Reddy P, Lam D, Hishida Y, Wu MZ, Esteban CR, O'Leary D, Wahl GM, Verma IM, Laurent LC, Izpisua Belmonte JC | Nature communications | 26899176 | Nat Commun | 2016 Feb 22 |
| Large-Scale Profiling Reveals the Influence of Genetic Variation on Gene Expression in Human Induced Pluripotent Stem Cells. | DeBoever C, Li H, Jakubosky D, Benaglio P, Reyna J, Olson KM, Huang H, Biggs W, Sandoval E, D'Antonio M, Jepsen K, Matsui H, Arias A, Ren B, Nariai N, Smith EN, D'Antonio-Chronowska A, Farley EK, Frazer KA | Cell stem cell | 28388430 | Cell Stem Cell | 2017 Apr 6 |
| Tissue specific requirements for WNT11 in developing outflow tract and dorsal mesenchymal protrusion. | van Vliet PP, Lin L, Boogerd CJ, Martin JF, Andelfinger G, Grossfeld PD, Evans SM | Developmental biology | 28669819 | Dev Biol | 2017 Sep 1 |
| Developmental biology. Enhancing pluripotency and lineage specification. | Xie W, Ren B | Science (New York, N.Y.) | 23869010 | Science | 2013 Jul 19 |
| Efficient generation of human iPSCs by a synthetic self-replicative RNA. | Yoshioka N, Gros E, Li HR, Kumar S, Deacon DC, Maron C, Muotri AR, Chi NC, Fu XD, Yu BD, Dowdy SF | Cell stem cell | 23910086 | Cell Stem Cell | 2013 Aug 1 |
| iPSCORE: A Resource of 222 iPSC Lines Enabling Functional Characterization of Genetic Variation across a Variety of Cell Types. | Panopoulos AD, D'Antonio M, Benaglio P, Williams R, Hashem SI, Schuldt BM, DeBoever C, Arias AD, Garcia M, Nelson BC, Harismendy O, Jakubosky DA, Donovan MKR, Greenwald WW, Farnam K, Cook M, Borja V, Miller CA, Grinstein JD, Drees F, Okubo J, Diffenderfer KE, Hishida Y, Modesto V, Dargitz CT, Feiring R, Zhao C, Aguirre A, McGarry TJ, Matsui H, Li H, Reyna J, Rao F, O'Connor DT, Yeo GW, Evans SM, Chi NC, Jepsen K, Nariai N, Müller FJ, Goldstein LSB, Izpisua Belmonte JC, Adler E, Loring JF, Berggren WT, D'Antonio-Chronowska A, Smith EN, Frazer KA | Stem cell reports | 28410642 | Stem Cell Reports | 2017 Apr 11 |
| Pgltools: a genomic arithmetic tool suite for manipulation of Hi-C peak and other chromatin interaction data. | Greenwald WW, Li H, Smith EN, Benaglio P, Nariai N, Frazer KA | BMC bioinformatics | 28388874 | BMC Bioinformatics | 2017 Apr 7 |
| Single-nucleotide variants within heart enhancers increase binding affinity and disrupt heart development. | Jindal GA, Bantle AT, Solvason JJ, Grudzien JL, D'Antonio-Chronowska A, Lim F, Le SH, Song BP, Ragsac MF, Klie A, Larsen RO, Frazer KA, Farley EK | Developmental cell | 37848026 | Dev Cell | 2023 Nov 6 |
| Human heart rate: heritability of resting and stress values in twin pairs, and influence of genetic variation in the adrenergic pathway at a microribonucleic acid (microrna) motif in the 3'-UTR of cytochrome b561 [corrected]. | Zhang K, Deacon DC, Rao F, Schork AJ, Fung MM, Waalen J, Schork NJ, Nievergelt CM, Chi NC, O'Connor DT | Journal of the American College of Cardiology | 24140660 | J Am Coll Cardiol | 2014 Feb 4 |
| Epigenomic analysis of multilineage differentiation of human embryonic stem cells. | Xie W, Schultz MD, Lister R, Hou Z, Rajagopal N, Ray P, Whitaker JW, Tian S, Hawkins RD, Leung D, Yang H, Wang T, Lee AY, Swanson SA, Zhang J, Zhu Y, Kim A, Nery JR, Urich MA, Kuan S, Yen CA, Klugman S, Yu P, Suknuntha K, Propson NE, Chen H, Edsall LE, Wagner U, Li Y, Ye Z, Kulkarni A, Xuan Z, Chung WY, Chi NC, Antosiewicz-Bourget JE, Slukvin I, Stewart R, Zhang MQ, Wang W, Thomson JA, Ecker JR, Ren B | Cell | 23664764 | Cell | 2013 May 23 |
| Sorting out where fibroblasts come from. | Moore-Morris T, Tallquist MD, Evans SM | Circulation research | 25214570 | Circ Res | 2014 Sep 12 |
| Brief Report: Oxidative Stress Mediates Cardiomyocyte Apoptosis in a Human Model of Danon Disease and Heart Failure. | Hashem SI, Perry CN, Bauer M, Han S, Clegg SD, Ouyang K, Deacon DC, Spinharney M, Panopoulos AD, Izpisua Belmonte JC, Frazer KA, Chen J, Gong Q, Zhou Z, Chi NC, Adler ED | Stem cells (Dayton, Ohio) | 25826782 | Stem Cells | 2015 Jul |
| Cut and paste: restoring cellular function by gene correction. | Liu GH, Sancho-Martinez I, Izpisua Belmonte JC | Cell research | 22143565 | Cell Res | 2012 Feb |
| Analysis of protein-coding mutations in hiPSCs and their possible role during somatic cell reprogramming. | Ruiz S, Gore A, Li Z, Panopoulos AD, Montserrat N, Fung HL, Giorgetti A, Bilic J, Batchelder EM, Zaehres H, Schöler HR, Zhang K, Izpisua Belmonte JC | Nature communications | 23340422 | Nat Commun | 2013 |
| Beating in a dish: new hopes for cardiomyocyte regeneration. | Gu Y, Yi F, Liu GH, Izpisua Belmonte JC | Cell research | 23184058 | Cell Res | 2013 Mar |
| Generation of a drug-inducible reporter system to study cell reprogramming in human cells. | Ruiz S, Panopoulos AD, Montserrat N, Multon MC, Daury A, Rocher C, Spanakis E, Batchelder EM, Orsini C, Deleuze JF, Izpisua Belmonte JC | The Journal of biological chemistry | 23019325 | J Biol Chem | 2012 Nov 23 |
| Mathematical approaches to modeling development and reprogramming. | Morris R, Sancho-Martinez I, Sharpee TO, Izpisua Belmonte JC | Proceedings of the National Academy of Sciences of the United States of America | 24706886 | Proc Natl Acad Sci U S A | 2014 Apr 8 |
| In vivo activation of a conserved microRNA program induces mammalian heart regeneration. | Aguirre A, Montserrat N, Zacchigna S, Nivet E, Hishida T, Krause MN, Kurian L, Ocampo A, Vazquez-Ferrer E, Rodriguez-Esteban C, Kumar S, Moresco JJ, Yates JR 3rd, Campistol JM, Sancho-Martinez I, Giacca M, Izpisua Belmonte JC | Cell stem cell | 25517466 | Cell Stem Cell | 2014 Nov 6 |
| Regeneration: making muscle from hPSCs. | Zhu X, Fu L, Yi F, Liu GH, Ocampo A, Qu J, Izpisua Belmonte JC | Cell research | 25001388 | Cell Res | 2014 Oct |
| Resident fibroblast lineages mediate pressure overload-induced cardiac fibrosis. | Moore-Morris T, Guimarães-Camboa N, Banerjee I, Zambon AC, Kisseleva T, Velayoudon A, Stallcup WB, Gu Y, Dalton ND, Cedenilla M, Gomez-Amaro R, Zhou B, Brenner DA, Peterson KL, Chen J, Evans SM | The Journal of clinical investigation | 24937432 | J Clin Invest | 2014 Jul |
| Insights into the Mutational Burden of Human Induced Pluripotent Stem Cells from an Integrative Multi-Omics Approach. | D'Antonio M, Benaglio P, Jakubosky D, Greenwald WW, Matsui H, Donovan MKR, Li H, Smith EN, D'Antonio-Chronowska A, Frazer KA | Cell reports | 30044985 | Cell Rep | 2018 Jul 24 |
| Aberrant DNA Methylation in Human iPSCs Associates with MYC-Binding Motifs in a Clone-Specific Manner Independent of Genetics. | Panopoulos AD, Smith EN, Arias AD, Shepard PJ, Hishida Y, Modesto V, Diffenderfer KE, Conner C, Biggs W, Sandoval E, D'Antonio-Chronowska A, Berggren WT, Izpisua Belmonte JC, Frazer KA | Cell stem cell | 28388429 | Cell Stem Cell | 2017 Apr 6 |
| Systematic genetic analysis of the MHC region reveals mechanistic underpinnings of HLA type associations with disease. | D'Antonio M, Reyna J, Jakubosky D, Donovan MK, Bonder MJ, Matsui H, Stegle O, Nariai N, D'Antonio-Chronowska A, Frazer KA | eLife | 31746734 | Elife | 2019 Nov 20 |
| In vitro Differentiation of Human iPSC-derived Retinal Pigment Epithelium Cells (iPSC-RPE). | D'Antonio-Chronowska A, D'Antonio M, Frazer KA | Bio-protocol | 33654959 | Bio Protoc | 2019 Dec 20 |
| 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 |
| Enhancer release and retargeting activates disease-susceptibility genes. | Oh S, Shao J, Mitra J, Xiong F, D'Antonio M, Wang R, Garcia-Bassets I, Ma Q, Zhu X, Lee JH, Nair SJ, Yang F, Ohgi K, Frazer KA, Zhang ZD, Li W, Rosenfeld MG | Nature | 34040254 | Nature | 2021 Jul |
| In vitro Differentiation of Human iPSC-derived Cardiovascular Progenitor Cells (iPSC-CVPCs). | D'Antonio-Chronowska A, D'Antonio M, Frazer KA | Bio-protocol | 33659414 | Bio Protoc | 2020 Sep 20 |
| Fine mapping spatiotemporal mechanisms of genetic variants underlying cardiac traits and disease. | D'Antonio M, Nguyen JP, Arthur TD, iPSCORE Consortium, Matsui H, D'Antonio-Chronowska A, Frazer KA | Nature communications | 36854752 | Nat Commun | 2023 Feb 28 |
| Evolutionary conservation of Nkx2.5 autoregulation in the second heart field. | Clark CD, Zhang B, Lee B, Evans SI, Lassar AB, Lee KH | Developmental biology | 23165293 | Dev Biol | 2013 Feb 1 |
| The metabolome of induced pluripotent stem cells reveals metabolic changes occurring in somatic cell reprogramming. | Panopoulos AD, Yanes O, Ruiz S, Kida YS, Diep D, Tautenhahn R, Herrerías A, Batchelder EM, Plongthongkum N, Lutz M, Berggren WT, Zhang K, Evans RM, Siuzdak G, Izpisua Belmonte JC | Cell research | 22064701 | Cell Res | 2012 Jan |
| Connexin defects underlie arrhythmogenic right ventricular cardiomyopathy in a novel mouse model. | Lyon RC, Mezzano V, Wright AT, Pfeiffer E, Chuang J, Banares K, Castaneda A, Ouyang K, Cui L, Contu R, Gu Y, Evans SM, Omens JH, Peterson KL, McCulloch AD, Sheikh F | Human molecular genetics | 24108106 | Hum Mol Genet | 2014 Mar 1 |
| In heart failure reactivation of RNA-binding proteins is associated with the expression of 1,523 fetal-specific isoforms. | D'Antonio M, Nguyen JP, Arthur TD, Matsui H, Donovan MKR, D'Antonio-Chronowska A, Frazer KA | PLoS computational biology | 35226669 | PLoS Comput Biol | 2022 Feb |
| Correction to: Unveiling Complexity and Multipotentiality of Early Heart Fields. | Circulation research | 35239406 | Circ Res | 2022 Mar 4 | |
| A cut above the rest: targeted genome editing technologies in human pluripotent stem cells. | Li M, Suzuki K, Kim NY, Liu GH, Izpisua Belmonte JC | The Journal of biological chemistry | 24362028 | J Biol Chem | 2014 Feb 21 |
| Loss of IP3R-dependent Ca2+ signalling in thymocytes leads to aberrant development and acute lymphoblastic leukemia. | Ouyang K, Leandro Gomez-Amaro R, Stachura DL, Tang H, Peng X, Fang X, Traver D, Evans SM, Chen J | Nature communications | 25215520 | Nat Commun | 2014 Sep 12 |
| Cell-Surface Marker Signature for Enrichment of Ventricular Cardiomyocytes Derived from Human Embryonic Stem Cells. | Veevers J, Farah EN, Corselli M, Witty AD, Palomares K, Vidal JG, Emre N, Carson CT, Ouyang K, Liu C, van Vliet P, Zhu M, Hegarty JM, Deacon DC, Grinstein JD, Dirschinger RJ, Frazer KA, Adler ED, Knowlton KU, Chi NC, Martin JC, Chen J, Evans SM | Stem cell reports | 30122443 | Stem Cell Reports | 2018 Sep 11 |
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| Acoustofluidic actuation of in situ fabricated microrotors. | Kaynak M, Ozcelik A, Nama N, Nourhani A, Lammert PE, Crespi VH, Huang TJ | Lab on a chip | 27466140 | Lab Chip | 2016 Sep 21 |
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| Spatial colocalization and functional link of purinosomes with mitochondria. | French JB, Jones SA, Deng H, Pedley AM, Kim D, Chan CY, Hu H, Pugh RJ, Zhao H, Zhang Y, Huang TJ, Fang Y, Zhuang X, Benkovic SJ | Science (New York, N.Y.) | 26912862 | Science | 2016 Feb 12 |
| Rapid formation of size-controllable multicellular spheroids via 3D acoustic tweezers. | Chen K, Wu M, Guo F, Li P, Chan CY, Mao Z, Li S, Ren L, Zhang R, Huang TJ | Lab on a chip | 27327102 | Lab Chip | 2016 Jul 5 |
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| Wave number-spiral acoustic tweezers for dynamic and reconfigurable manipulation of particles and cells. | Tian Z, Yang S, Huang PH, Wang Z, Zhang P, Gu Y, Bachman H, Chen C, Wu M, Xie Y, Huang TJ | Science advances | 31172021 | Sci Adv | 2019 May |
| Exploring bubble oscillation and mass transfer enhancement in acoustic-assisted liquid-liquid extraction with a microfluidic device. | Xie Y, Chindam C, Nama N, Yang S, Lu M, Zhao Y, Mai JD, Costanzo F, Huang TJ | Scientific reports | 26223474 | Sci Rep | 2015 Jul 30 |
| Standing surface acoustic wave (SSAW)-based cell washing. | Li S, Ding X, Mao Z, Chen Y, Nama N, Guo F, Li P, Wang L, Cameron CE, Huang TJ | Lab on a chip | 25372273 | Lab Chip | 2015 Jan 7 |
| Acoustofluidic chemical waveform generator and switch. | Ahmed D, Muddana HS, Lu M, French JB, Ozcelik A, Fang Y, Butler PJ, Benkovic SJ, Manz A, Huang TJ | Analytical chemistry | 25405550 | Anal Chem | 2014 Dec 2 |
| Single-Cell Virology: On-Chip Investigation of Viral Infection Dynamics. | Guo F, Li S, Caglar MU, Mao Z, Liu W, Woodman A, Arnold JJ, Wilke CO, Huang TJ, Cameron CE | Cell reports | 29117571 | Cell Rep | 2017 Nov 7 |
| Probing Cell Deformability via Acoustically Actuated Bubbles. | Xie Y, Nama N, Li P, Mao Z, Huang PH, Zhao C, Costanzo F, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 26715211 | Small | 2016 Feb 17 |
| Acoustofluidic bacteria separation. | Li S, Ma F, Bachman H, Cameron CE, Zeng X, Huang TJ | Journal of micromechanics and microengineering : structures, devices, and systems | 28798539 | J Micromech Microeng | 2017 Jan 1 |
| Experimental and numerical studies on standing surface acoustic wave microfluidics. | Mao Z, Xie Y, Guo F, Ren L, Huang PH, Chen Y, Rufo J, Costanzo F, Huang TJ | Lab on a chip | 26698361 | Lab Chip | 2016 Feb 7 |
| Standing Surface Acoustic Wave (SSAW)-Based Fluorescence-Activated Cell Sorter. | Ren L, Yang S, Zhang P, Qu Z, Mao Z, Huang PH, Chen Y, Wu M, Wang L, Li P, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 30168662 | Small | 2018 Oct |
| On-Chip Production of Size-Controllable Liquid Metal Microdroplets Using Acoustic Waves. | Tang SY, Ayan B, Nama N, Bian Y, Lata JP, Guo X, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 27309129 | Small | 2016 Jul |
| Acoustofluidic Fluorescence Activated Cell Sorter. | Nawaz AA, Chen Y, Nama N, Nissly RH, Ren L, Ozcelik A, Wang L, McCoy JP, Levine SJ, Huang TJ | Analytical chemistry | 26331909 | Anal Chem | 2015 Dec 15 |
| A spatiotemporally controllable chemical gradient generator via acoustically oscillating sharp-edge structures. | Huang PH, Chan CY, Li P, Nama N, Xie Y, Wei CH, Chen Y, Ahmed D, Huang TJ | Lab on a chip | 26338516 | Lab Chip | 2015 Nov 7 |
| Investigation of micromixing by acoustically oscillated sharp-edges. | Nama N, Huang PH, Huang TJ, Costanzo F | Biomicrofluidics | 27158292 | Biomicrofluidics | 2016 Mar |
| Surface Acoustic Waves Grant Superior Spatial Control of Cells Embedded in Hydrogel Fibers. | Lata JP, Guo F, Guo J, Huang PH, Yang J, Huang TJ | Advanced materials (Deerfield Beach, Fla.) | 27571239 | Adv Mater | 2016 Oct |
| Precise Manipulation and Patterning of Protein Crystals for Macromolecular Crystallography Using Surface Acoustic Waves. | Guo F, Zhou W, Li P, Mao Z, Yennawar NH, French JB, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 25641793 | Small | 2015 Jun |
| Acoustic Actuation of in situ Fabricated Artificial Cilia. | Orbay S, Ozcelik A, Bachman H, Huang TJ | Journal of micromechanics and microengineering : structures, devices, and systems | 30479458 | J Micromech Microeng | 2018 Feb |
| Circulating Tumor Cell Phenotyping via High-Throughput Acoustic Separation. | Wu M, Huang PH, Zhang R, Mao Z, Chen C, Kemeny G, Li P, Lee AV, Gyanchandani R, Armstrong AJ, Dao M, Suresh S, Huang TJ | Small (Weinheim an der Bergstrasse, Germany) | 29968402 | Small | 2018 Aug |
| A high-throughput acoustic cell sorter. | Ren L, Chen Y, Li P, Mao Z, Huang PH, Rufo J, Guo F, Wang L, McCoy JP, Levine SJ, Huang TJ | Lab on a chip | 26289231 | Lab Chip | 2015 Oct 7 |
| Mixing high-viscosity fluids via acoustically driven bubbles. | Orbay S, Ozcelik A, Lata J, Kaynak M, Wu M, Huang TJ | Journal of micromechanics and microengineering : structures, devices, and systems | 31588165 | J Micromech Microeng | 2017 |
| Acoustic streaming: an arbitrary Lagrangian-Eulerian perspective. | Nama N, Huang TJ, Costanzo F | Journal of fluid mechanics | 29051631 | J Fluid Mech | 2017 Aug 25 |
| Rotational manipulation of single cells and organisms using acoustic waves. | Ahmed D, Ozcelik A, Bojanala N, Nama N, Upadhyay A, Chen Y, Hanna-Rose W, Huang TJ | Nature communications | 27004764 | Nat Commun | 2016 Mar 23 |
| Acoustofluidic coating of particles and cells. | Ayan B, Ozcelik A, Bachman H, Tang SY, Xie Y, Wu M, Li P, Huang TJ | Lab on a chip | 27754503 | Lab Chip | 2016 Nov 1 |
| Acoustic separation of circulating tumor cells. | Li P, Mao Z, Peng Z, Zhou L, Chen Y, Huang PH, Truica CI, Drabick JJ, El-Deiry WS, Dao M, Suresh S, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 25848039 | Proc Natl Acad Sci U S A | 2015 Apr 21 |
| A sharp-edge-based acoustofluidic chemical signal generator. | Huang PH, Chan CY, Li P, Wang Y, Nama N, Bachman H, Huang TJ | Lab on a chip | 29668002 | Lab Chip | 2018 May 15 |
| Acoustic actuation of bioinspired microswimmers. | Kaynak M, Ozcelik A, Nourhani A, Lammert PE, Crespi VH, Huang TJ | Lab on a chip | 27991641 | Lab Chip | 2017 Jan 31 |
| Plasmofluidics: Merging Light and Fluids at the Micro-/Nanoscale. | Wang M, Zhao C, Miao X, Zhao Y, Rufo J, Liu YJ, Huang TJ, Zheng Y | Small (Weinheim an der Bergstrasse, Germany) | 26140612 | Small | 2015 Sep 16 |
| Three-dimensional manipulation of single cells using surface acoustic waves. | Guo F, Mao Z, Chen Y, Xie Z, Lata JP, Li P, Ren L, Liu J, Yang J, Dao M, Suresh S, Huang TJ | Proceedings of the National Academy of Sciences of the United States of America | 26811444 | Proc Natl Acad Sci U S A | 2016 Feb 9 |
| Numerical study of acoustophoretic motion of particles in a PDMS microchannel driven by surface acoustic waves. | Nama N, Barnkob R, Mao Z, Kähler CJ, Costanzo F, Huang TJ | Lab on a chip | 26001199 | Lab Chip | 2015 Jun 21 |
| Hybrid Dielectric-loaded Nanoridge Plasmonic Waveguide for Low-Loss Light Transmission at the Subwavelength Scale. | Zhang B, Bian Y, Ren L, Guo F, Tang SY, Mao Z, Liu X, Sun J, Gong J, Guo X, Huang TJ | Scientific reports | 28091583 | Sci Rep | 2017 Jan 16 |
| Efficient labeling and imaging of protein-coding genes in living cells using CRISPR-Tag. | Chen B, Zou W, Xu H, Liang Y, Huang B | Nature communications | 30498221 | Nat Commun | 2018 Nov 29 |
| Epi-illumination SPIM for volumetric imaging with high spatial-temporal resolution. | Yang B, Chen X, Wang Y, Feng S, Pessino V, Stuurman N, Cho NH, Cheng KW, Lord SJ, Xu L, Xie D, Mullins RD, Leonetti MD, Huang B | Nature methods | 31061492 | Nat Methods | 2019 Jun |
| Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci. | Chen B, Hu J, Almeida R, Liu H, Balakrishnan S, Covill-Cooke C, Lim WA, Huang B | Nucleic acids research | 26740581 | Nucleic Acids Res | 2016 May 5 |
| Imaging Specific Genomic DNA in Living Cells. | Chen B, Guan J, Huang B | Annual review of biophysics | 27145877 | Annu Rev Biophys | 2016 Jul 5 |
| Condensin DC loads and spreads from recruitment sites to create loop-anchored TADs in C. elegans. | Kim J, Jimenez DS, Ragipani B, Zhang B, Street LA, Kramer M, Albritton SE, Winterkorn LH, Morao AK, Ercan S | eLife | 36331876 | Elife | 2022 Nov 4 |
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