Thomson, James A.

Induced Pluripotent Stem Cell Lines Derived from Human Somatic Cells

Yu, J., Vodyanik, M. A., Smuga-Otto, K., Antosiewicz-Bourget, J., Frane, J. L., Tian, S., Nie, J., Jonsdottir, G. A., Ruotti, V., Stewart, R., et al. (2007) · Science

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 10,310

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 6,368

Human DNA methylomes at base resolution show widespread epigenomic differences

Lister, R., Pelizzola, M., Dowen, R. H., Hawkins, R. D., Hon, G., Tonti-Filippini, J., Nery, J. R., Lee, L., Ye, Z., Ngo, Q.-M., et al. (2009) · Nature

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 4,673

Histone modifications at human enhancers reflect global cell-type-specific gene expression

Heintzman, N. D., Hon, G. C., Hawkins, R. D., Kheradpour, P., Stark, A., Harp, L. F., Ye, Z., Lee, L. K., Stuart, R. K., Ching, C. W., et al. (2009) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 2,533

Human induced pluripotent stem cells free of vector and transgene sequences

Yu, J., Hu, K., Smuga-Otto, K., Tian, S., Stewart, R., Slukvin, I. I., & Thomson, J. A. (2009) · Science

Pluripotent Stem Cells ResearchCRISPR and Genetic Engineering

Cited by 2,386

The NIH Roadmap Epigenomics Mapping Consortium

Bernstein, B. E., Stamatoyannopoulos, J. A., Costello, J. F., Ren, B., Milosavljevic, A., Meissner, A., Kellis, M., Marra, M. A., Beaudet, A. L., Ecker, J. R., et al. (2010) · Nature Biotechnology

Epigenetics and DNA MethylationGenomics and Chromatin Dynamics

Cited by 1,892

Chromatin architecture reorganization during stem cell differentiation

Dixon, J. R., Jung, I., Selvaraj, S., Shen, Y., Antosiewicz-Bourget, J. E., Lee, A. Y., Ye, Z., Kim, A., Rajagopal, N., Xie, W., et al. (2015) · Nature

Genomics and Chromatin DynamicsEpigenetics and DNA Methylation

Cited by 1,646

Chemically defined conditions for human iPSC derivation and culture

Chen, G., Gulbranson, D. R., Hou, Z., Bolin, J. M., Ruotti, V., Probasco, M. D., Smuga-Otto, K., Howden, S. E., Diol, N. R., Propson, N. E., et al. (2011) · Nature Methods

Pluripotent Stem Cells ResearchMesenchymal stem cell research

Cited by 1,447

Induced pluripotent stem cells from a spinal muscular atrophy patient

Ebert, A. D., Yu, J., Rose, F. F., Mattis, V. B., Lorson, C. L., Thomson, J. A., & Svendsen, C. N. (2009) · Nature

Pluripotent Stem Cells ResearchNeurogenetic and Muscular Disorders Research

Cited by 1,441

Somatic coding mutations in human induced pluripotent stem cells

Gore, A., Li, Z., Fung, H.-L., Young, J. E., Agarwal, S., Antosiewicz-Bourget, J., Canto, I., Giorgetti, A., Israel, M. A., Kiskinis, E., et al. (2011) · Nature

Pluripotent Stem Cells ResearchCRISPR and Genetic Engineering

Cited by 1,273

RNA-Seq gene expression estimation with read mapping uncertainty

Li, B., Ruotti, V., Stewart, R. M., Thomson, J. A., & Dewey, C. N. (2010) · Bioinformatics

Genomics and Phylogenetic StudiesGene expression and cancer classification

Cited by 1,198

Derivation of human embryonic stem cells in defined conditions

Ludwig, T. E., Levenstein, M. E., Jones, J. M., Berggren, W. T., Mitchen, E. R., Frane, J. L., Crandall, L. J., Daigh, C. A., Conard, K. R., Piekarczyk, M. S., et al. (2006) · Nature Biotechnology

Pluripotent Stem Cells ResearchAnimal Genetics and Reproduction

Cited by 1,114

Multilineage differentiation from human embryonic stem cell lines

Odorico, J. S., Kaufman, D. S., & Thomson, J. A. (2001) · Stem Cells

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 969

Distinct epigenomic landscapes of pluripotent and lineage-committed human cells

Hawkins, R. D., Hon, G. C., Lee, L. K., Ngo, Q., Lister, R., Pelizzola, M., Edsall, L. E., Kuan, S., Luu, Y., Klugman, S., et al. (2010) · Cell stem cell

Epigenetics and DNA MethylationPluripotent Stem Cells Research

Cited by 806

Human Embryonic Stem Cells Develop Into Multiple Types of Cardiac Myocytes: Action Potential Characterization

He, J.-Q., Ma, Y., Lee, Y., Thomson, J. A., & Kamp, T. J. (2003) · Circulation Research

Pluripotent Stem Cells ResearchCardiac electrophysiology and arrhythmias

Cited by 800

Whole-Genome Analysis of Histone H3 Lysine 4 and Lysine 27 Methylation in Human Embryonic Stem Cells

Pan, G., Tian, S., Nie, J., Yang, C., Ruotti, V., Wei, H., Jonsdottir, G. A., Stewart, R., & Thomson, J. A. (2007) · Cell Stem Cell

Epigenetics and DNA MethylationPluripotent Stem Cells Research

Cited by 711

Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis

Hou, Z., Zhang, Y., Propson, N. E., Howden, S. E., Chu, L.-F., Sontheimer, E. J., & Thomson, J. A. (2013) · Proceedings of the National Academy of Sciences

CRISPR and Genetic EngineeringPluripotent Stem Cells Research

Cited by 681

Feeder-independent culture of human embryonic stem cells

Ludwig, T. E., Bergendahl, V., Levenstein, M. E., Yu, J., Probasco, M. D., & Thomson, J. A. (2006) · Nature Methods

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 681

Single-cell RNA-seq reveals novel regulators of human embryonic stem cell differentiation to definitive endoderm

Chu, L.-F., Leng, N., Zhang, J., Hou, Z., Mamott, D., Vereide, D. T., Choi, J., Kendziorski, C., Stewart, R., & Thomson, J. A. (2016) · Genome Biology

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 477

Human pluripotent stem cell-derived neural constructs for predicting neural toxicity

Schwartz, M. P., Hou, Z., Propson, N. E., Zhang, J., Engstrom, C. J., Costa, V. S., Jiang, P., Nguyen, B. K., Bolin, J. M., Daly, W., et al. (2015) · Proceedings of the National Academy of Sciences

Pluripotent Stem Cells ResearchAnimal testing and alternatives

Cited by 325

SCnorm: robust normalization of single-cell RNA-seq data

Bacher, R., Chu, L.-F., Leng, N., Gasch, A. P., Thomson, J. A., Stewart, R. M., Newton, M., & Kendziorski, C. (2017) · Nature Methods

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 282

Functional cardiac fibroblasts derived from human pluripotent stem cells via second heart field progenitors

Zhang, J., Tao, R., Campbell, K. F., Carvalho, J. L., Ruiz, E. C., Kim, G. C., Schmuck, E. G., Raval, A. N., da Rocha, A. M., Herron, T. J., et al. (2019) · Nature Communications

Pluripotent Stem Cells ResearchCongenital heart defects research

Cited by 201

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Phanstiel, D., Brumbaugh, J., Berggren, W. T., Conard, K., Feng, X., Levenstein, M. E., McAlister, G. C., Thomson, J. A., & Coon, J. J. (2008) · Proceedings of the National Academy of Sciences

Genomics and Chromatin DynamicsAdvanced Proteomics Techniques and Applications

Cited by 166

Human Vascular Tissue Models Formed from Human Induced Pluripotent Stem Cell Derived Endothelial Cells

Belair, D. G., Whisler, J. A., Valdez, J., Velazquez, J., Molenda, J. A., Vickerman, V., Lewis, R., Daigh, C., Hansen, T. D., Mann, D. A., et al. (2015) · Stem Cell Reviews and Reports

Angiogenesis and VEGF in CancerPluripotent Stem Cells Research

Cited by 120