Satija, Rahul

Integrated analysis of multimodal single-cell data

Hao, Y., Hao, S., Andersen-Nissen, E., Mauck, W. M., Zheng, S., Butler, A., Lee, M. J., Wilk, A. J., Darby, C., Zagar, M., et al. (2020) · Cell

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 15,508

Comprehensive Integration of Single-Cell Data

Stuart, T., Butler, A., Hoffman, P., Hafemeister, C., Papalexi, E., Mauck, W. M., Hao, Y., Stoeckius, M., Smibert, P., & Satija, R. (2019) · Cell

Single-cell and spatial transcriptomicsBioinformatics and Genomic Networks

Cited by 15,453

Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets.

Macosko, E. Z., Basu, A., Satija, R., Nemesh, J., Shekhar, K., Goldman, M., Tirosh, I., Bialas, A. R., Kamitaki, N., Martersteck, E. M., et al. (2015) · Cell

Single-cell and spatial transcriptomicsInnovative Microfluidic and Catalytic Techniques Innovation

Cited by 7,110

Spatial reconstruction of single-cell gene expression data

Satija, R., Farrell, J. A., Gennert, D., Schier, A. F., & Regev, A. (2015) · Nature Biotechnology

Single-cell and spatial transcriptomicsGene expression and cancer classification

Cited by 7,055

Single-cell RNA sequencing to explore immune cell heterogeneity

Papalexi, E., & Satija, R. (2018) · Nature Reviews Immunology

Single-cell and spatial transcriptomicsGenomics and Phylogenetic Studies

Cited by 1,806

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells

Shalek, A. K., Satija, R., Adiconis, X., Gertner, R. S., Gaublomme, J. T., Raychowdhury, R., Schwartz, S., Yosef, N., Malboeuf, C., Lu, D., et al. (2013) · Nature

Single-cell and spatial transcriptomicsRNA Research and Splicing

Cited by 1,190

Landscape of X chromosome inactivation across human tissues

GTEx Consortium, Tukiainen, T., Villani, A.-C., Yen, A., Rivas, M. A., Marshall, J. L., Satija, R., Aguirre, M., Gauthier, L., Fleharty, M., et al. (2017) · Nature

Genetic and Clinical Aspects of Sex Determination and Chromosomal AbnormalitiesGenomics and Chromatin Dynamics

Cited by 1,138

The Genome of the Sea Urchin Strongylocentrotus purpuratus

Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science

Genomics and Phylogenetic StudiesDevelopmental Biology and Gene Regulation

Cited by 1,132

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation

Shalek, A. K., Satija, R., Shuga, J., Trombetta, J. J., Gennert, D., Lu, D., Chen, P., Gertner, R. S., Gaublomme, J. T., Yosef, N., et al. (2014) · Nature

Single-cell and spatial transcriptomicsGene Regulatory Network Analysis

Cited by 1,000

The bone marrow microenvironment at single-cell resolution

Tikhonova, A. N., Dolgalev, I., Hu, H., Sivaraj, K. K., Hoxha, E., Cuesta-Domínguez, Á., Pinho, S., Akhmetzyanova, I., Gao, J., Witkowski, M., et al. (2019) · Nature

Hematopoietic Stem Cell TransplantationSingle-cell and spatial transcriptomics

Cited by 936

Dynamic regulatory network controlling TH17 cell differentiation

Yosef, N., Shalek, A. K., Gaublomme, J. T., Jin, H., Lee, Y., Awasthi, A., Wu, C., Karwacz, K., Xiao, S., Jorgolli, M., et al. (2013) · Nature

Gene Regulatory Network AnalysisPsoriasis: Treatment and Pathogenesis

Cited by 682

Single-cell genomics unveils critical regulators of Th17 cell pathogenicity

Gaublomme, J. T., Yosef, N., Lee, Y., Gertner, R. S., Yang, L. V., Wu, C., Pandolfi, P. P., Mak, T., Satija, R., Shalek, A. K., et al. (2015) · Cell

Psoriasis: Treatment and PathogenesisT-cell and B-cell Immunology

Cited by 575

Developmental diversification of cortical inhibitory interneurons

Mayer, C., Hafemeister, C., Bandler, R. C., Machold, R., Batista Brito, R., Jaglin, X., Allaway, K., Butler, A., Fishell, G., & Satija, R. (2018) · Nature

Neurogenesis and neuroplasticity mechanismsSingle-cell and spatial transcriptomics

Cited by 492

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science

Advanced Proteomics Techniques and ApplicationsGene Regulatory Network Analysis

Cited by 460

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks

Parnas, O., Jovanovic, M., Eisenhaure, T. M., Herbst, R. H., Dixit, A., Ye, C. J., Przybylski, D., Platt, R. J., Tirosh, I., Sanjana, N. E., et al. (2015) · Cell

Immune Response and InflammationCRISPR and Genetic Engineering

Cited by 440

Deconstructing transcriptional heterogeneity in pluripotent stem cells

Kumar, R. M., Cahan, P., Shalek, A. K., Satija, R., Jay DaleyKeyser, A., Li, H., Zhang, J., Pardee, K., Gennert, D., Trombetta, J. J., et al. (2014) · Nature

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 356

Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens

Papalexi, E., Mimitou, E. P., Butler, A. W., Foster, S., Bracken, B., Mauck, W. M., Wessels, H.-H., Hao, Y., Yeung, B. Z., Smibert, P., et al. (2021) · Nature Genetics

Cancer Immunotherapy and BiomarkersSingle-cell and spatial transcriptomics

Cited by 237

Phenotypic convergence: distinct transcription factors regulate common terminal features

Konstantinides, N., Kapuralin, K., Fadil, C., Barboza, L., Satija, R., & Desplan, C. (2018) · Cell

Single-cell and spatial transcriptomicsDevelopmental Biology and Gene Regulation

Cited by 226

NIH SenNet Consortium to map senescent cells throughout the human lifespan to understand physiological health.

SenNet Consortium, Writing Group, Lee, P. J., Benz, C. C., Blood, P., Börner, K., Campisi, J., Chen, F., Daldrup-Link, H., De Jager, P., et al. (2022) · Nature Aging

Telomeres, Telomerase, and SenescenceGenetics, Aging, and Longevity in Model Organisms

Cited by 122

A Multi-step Transcriptional and Chromatin State Cascade Underlies Motor Neuron Programming from Embryonic Stem Cells

Velasco, S., Ibrahim, M. M., Kakumanu, A., Garipler, G., Aydin, B., Al-Sayegh, M. A., Hirsekorn, A., Abdul-Rahman, F., Satija, R., Ohler, U., et al. (2017) · Cell Stem Cell

Pluripotent Stem Cells ResearchDevelopmental Biology and Gene Regulation

Cited by 111

A panoramic view of cell population dynamics in mammalian aging

Zhang, Z., Schaefer, C., Jiang, W., Lu, Z., Lee, J., Sziraki, A., Abdulraouf, A., Wick, B., Haeussler, M., Li, Z., et al. (2025) · Science

Single-cell and spatial transcriptomicsGenetics, Aging, and Longevity in Model Organisms

Cited by 95