Rahul Satija’s lab studies the causes and consequences of cellular heterogeneity in complex biological systems. His group is particularly interested in single cell genomics, with active development in both the dry and wet lab. The lab integrates novel statistical and machine learning-based methods with experimental analysis in order to better understand how cells work together to drive biological processes and behaviors.
Rahul Satija, PhD, is a Core Member and Assistant Investigator at the New York Genome Center, with a joint appointment as Assistant Professor at Center for Genomics and Systems Biology at NYU.
Dr. Satija’s group focuses on developing computational and experimental methods to sequence and interpret the molecular contents of a single cell. His group applies single cell genomics to understand the causes and consequences of cell-to-cell variation, with a particular focus on immune regulation and early development.
Dr. Satija holds a BS in Biology and Music from Duke University, and obtained his PhD in Statistics from Oxford University as a Rhodes Scholar. Prior to joining NYGC, he was a postdoctoral researcher at the Broad Institute of Harvard and MIT, where he developed new methods for single cell analysis.
Satija R*, Farrell JA*, Gennert D, Schier AF, Regev A. Spatial reconstruction of single-cell gene expression data. Nature Biotechnology. 2015.
Satija R, Shalek AK. Heterogeneity in immune responses: from populations to single cells. Trends in Immunology. 2014.
Shalek AK*, Satija R*, Shuga J*, Trombetta JJ, Lu D, Gennert D, Chen P, Gertner RS, Gaublomme JT, Yosef N, Schwartz S, Fowler B, Weaver S, Wang J, Wang X, Ding R, Raychowdhury R, Friedman N, Hacohen N, Park H, May AP, and Regev A. Single-Cell RNA-Seq Reveals Dynamic Paracrine Control of Cellular Variation. Nature. 2014.
Trombetta JJ*, Gennert D*, Lu D*, Satija R, Shalek AK, and Regev A. Preparation of Single Cell RNA-Seq Libraries for Next Generation Sequencing. Current Protocols in Molecular Biology. 2014.
Shalek AK*, Satija R*, Adiconis X, Gertner RS, Gaublomme JT, Raychowdhury R, Schwartz S, Yosef N, Malboeuf C, Lu D, Trombetta JJ, Gennert D, Gnirke A, Goren A, Hacohen N, Levin JZ, Park H, Regev A. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells. Nature. 2013.
Kinetics of adult hematopoietic stem cell differentiation in vivo.
Upadhaya S, Sawai CM, Papalexi E, Rashidfarrokhi A, Jang G, Chattopadhyay P, Satija R, Reizis B.
J Exp Med. 2018 Oct 5.
Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features.
Konstantinides N, Kapuralin K, Fadil C, Barboza L, Satija R, Desplan C.
Cell. 2018 June 9.
Integrated analysis of single cell transcriptomic data across conditions, technologies, and species
, Hoffman P, Smibert P, Papalexi E,
Nature Biotechnology. 2018 Apr. 2.
Molecular transitions in early progenitors during human cord blood hematopoiesis.
Zheng S, Papalexi E, Butler A, Stephenson W, Satija R.
Molecular Systems Biology. 2018 Mar. 15.
Developmental diversification of cortical inhibitory interneurons.
Nature. 2018 Mar. 5.
Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.
Stephenson W, Donlin LT, Butler A, Rozo C, Bracken B, Rashidfarrokhi A, Goodman SM, Ivashkiv LB, Bykerk VP, Orange DE, Darnell RB, Swerdlow HP, Satija R.
Nature Communications. 2018 Feb. 23.
Cell “hashing” with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
Stoeckius M, Zheng S, Houck-Loomis, B, Hao S, Yeung B, Smibert P, Satija R.
bioRxiv. 2017 Dec. 21.
Strength in numbers from integrated single-cell neuroscience.
Nature Biotechnology. 2018 Jan. 10.
Science Forum: The Human Cell Atlas.
Regev A, Teichmann SA ,Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell PJ, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Göttgens B, Hacohen N, Haniffa M, Hemberg M, Kim SK, Klenerman P, Kriegstein A, Lein E, Linnarsson S, Lundberg E, Lundeberg J, Majumder P, Marioni JC, Merad M, Mhlanga M, Nawijn M, Netea M, Nolan G, Pe’er D, Phillipakis A, Ponting CP, Quake SR, Reik W, Rozenblatt-Rosen O, Sanes JR, Satija R, Schumacher TN, Shalek AK, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton MR, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt FM, Weissman JS, Wold BJ, Xavier RJ, Yosef N; Human Cell Atlas Meeting Participants.
Elife. 2017 Dec. 5.
Landscape of X chromosome inactivation across human tissues.
Tukiainen T, Villani AC, Yen A, Rivas MA, Marshall JL, Satija R, Aguirre M, Gauthier L, Fleharty M, Kirby A, Cummings BB, Castel SE, Karczewski KJ, Aguet F, Byrnes A; GTEx Consortium; Laboratory, Data Analysis &Coordinating Center (LDACC)—Analysis Working Group; Statistical Methods groups—Analysis Working Group; Enhancing GTEx (eGTEx) groups; NIH Common Fund; NIH/NCI; NIH/NHGRI; NIH/NIMH; NIH/NIDA; Biospecimen Collection Source Site—NDRI; Biospecimen Collection Source Site—RPCI; Biospecimen Core Resource—VARI; Brain Bank Repository—University of Miami Brain Endowment Bank; Leidos Biomedical—Project Management; ELSI Study; Genome Browser Data Integration &Visualization—EBI; Genome Browser Data Integration &Visualization—UCSC Genomics Institute, University of California Santa Cruz, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG.
Nature. 2017 Oct. 11.
Single-cell RNA sequencing to explore immune cell heterogeneity.
Papalexi E, Satija R.
Nature Reviews Immunology. 2017 August 7.
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
Villani AC, Satija, R, Reynolds, G, Sarkizova S, Shekhar K, Fletcher J, Griesbeck M, Butler A, Zheng S, Lazo S, Jardine L, Dixon D, Stephenson E, Nilsson E, Grundberg I, McDonald D, Filby A, Li W, De Jager PL, Rozenblatt-Rosen O, Lane AA, Haniffa M, Regev A, Hacohen N.
Science. 2017 Apr 21.
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput.
Gierahn TM, Wadsworth MH 2nd, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK.
Nature Methods. 2017 Apr. 14. [Epub 2017 Feb 13]
- Kinetics of adult hematopoietic stem cell differentiation in vivo.