Stewart, Ron

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

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

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

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

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

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

A statistical approach for identifying differential distributions in single-cell RNA-seq experiments

Korthauer, K. D., Chu, L.-F., Newton, M. A., Li, Y., Thomson, J., Stewart, R., & Kendziorski, C. (2016) · Genome Biology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 273

Network inference with Granger causality ensembles on single-cell transcriptomics

Deshpande, A., Chu, L.-F., Stewart, R., & Gitter, A. (2022) · Cell Reports

Gene Regulatory Network AnalysisSingle-cell and spatial transcriptomics

Cited by 130

Rapid changes in chromatin structure during dedifferentiation of primary hepatocytes in vitro

Seirup, M., Sengupta, S., Swanson, S., McIntosh, B. E., Collins, M., Chu, L.-F., Cheng, Z., Gorkin, D. U., Duffin, B., Bolin, J. M., et al. (2022) · Genomics

Liver physiology and pathologyDrug-Induced Hepatotoxicity and Protection

Cited by 13

Co-culture with mouse embryonic fibroblasts improves maintenance of metabolic function of human small hepatocyte progenitor cells

Sengupta, S., Johnson, B., Seirup, M., Ardalani, H., Duffin, B., Barrett-Wilt, G. A., Stewart, R., & Thomson, J. A. (2020) · Current Research in Toxicology

Liver physiology and pathologyDrug-Induced Hepatotoxicity and Protection

Cited by 9

Serial KinderMiner (SKiM) discovers and annotates biomedical knowledge using co-occurrence and transformer models

Millikin, R. J., Raja, K., Steill, J., Lock, C., Tu, X., Ross, I., Tsoi, L. C., Kuusisto, F., Ni, Z., Livny, M., et al. (2023) · BMC Bioinformatics

Biomedical Text Mining and OntologiesBioinformatics and Genomic Networks

Cited by 9

SKiM-GPT: combining biomedical literature-based discovery with large language model hypothesis evaluation

Freeman, J., Millikin, R. J., Xu, L., Sharma, I., Moore, B., Lock, C., Shine George, K., Bal, A., Mohanty, C., & Stewart, R. (2025) · BMC Bioinformatics

Biomedical Text Mining and OntologiesTopic Modeling

Cited by 4