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Rahul Satija

Associate Professor of Biology  

rahul.satija@nyu.edu

Junior Investigator and Core Member, New York Genome Center

Brief Introduction

Assistant Professor at the NYU Center for Genomics and Systems Biology Rahul Satija joined the New York Genome Center in December 2014 as a Junior Investigator and Core Member, with a joint appointment as an Assistant Professor at the NYU Center for Genomics and Systems Biology. Rahul’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.

Rahul 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 the New York Genome Center, he was a postdoctoral researcher at the Broad Institute of Harvard and MIT, where he developed new methods for single cell analysis.


  • EDUCATION

  • 2010    D.Phil. (Statistics), Oxford University

  • 2006    B.Sc (Biology), Duke University

  • AREAS OF RESEARCH/INTEREST

    Single cell genomics, transcriptional regulation, computational biology

  • ASSOCIATED WITH OTHER DEPARTMENTS OR PROGRAMS

  • EXTERNAL AFFILIATIONS

  • FELLOWSHIPS/HONORS

  • 2006    Rhodes Scholarship

  • PUBLICATIONS

    Date of these PubMed search results: March 24 2020  Get the current Pubmed search results

  1. The strength and pattern of natural selection on gene expression in rice.
    Nature (2020 Feb) PMID: 32051590
    Groen SC, Calic I, Joly‑Lopez Z, Platts AE, Choi JY, Natividad M, Dorph K, Mauck WM 3rd, Bracken B, Cabral CLU, Kumar A, Torres RO, Satija R, Vergara G, Henry A, Franks SJ, Purugganan MD

  2. Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.
    Genome Biol (2019 Dec 23) PMC6927181 free full-text archive
    Hafemeister C, Satija R

  3. Toward a Common Coordinate Framework for the Human Body.
    Cell (2019 Dec 12) PMC6934046 free full-text archive
    Rood JE, Stuart T, Ghazanfar S, Biancalani T, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck W, Eraslan G, Marioni JC, Regev A, Satija R

  4. Author Correction: The bone marrow microenvironment at single-cell resolution.
    Nature (2019 Aug) PMID: 31296938
    Tikhonova AN, Dolgalev I, Hu H, Sivaraj KK, Hoxha E, Cuesta‑Dominguez A, Pinho S, Akhmetzyanova I, Gao J, Witkowski M, Guillamot M, Gutkin MC, Zhang Y, Marier C, Diefenbach C, Kousteni S, Heguy A, Zhong H, Fooksman DR, Butler JM, Economides A, Frenette PS, Adams RH, Satija R, Tsirigos A, Aifantis I

  5. Comprehensive Integration of Single-Cell Data.
    Cell (2019 Jun 13) PMC6687398 free full-text archive
    Stuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM 3rd, Hao Y, Stoeckius M, Smibert P, Satija R

  6. A single-cell transcriptional roadmap for cardiopharyngeal fate diversification.
    Nat Cell Biol (2019 Jun) PMID: 31160712
    Wang W, Niu X, Stuart T, Jullian E, Mauck WM 3rd, Kelly RG, Satija R, Christiaen L

  7. Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells.
    Nat Methods (2019 May) PMC6557128 free full-text archive
    Mimitou EP, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana NE, Koralov SB, Smibert P

  8. The bone marrow microenvironment at single-cell resolution.
    Nature (2019 May) PMC6607432 free full-text archive
    Tikhonova AN, Dolgalev I, Hu H, Sivaraj KK, Hoxha E, Cuesta‑Dominguez A, Pinho S, Akhmetzyanova I, Gao J, Witkowski M, Guillamot M, Gutkin MC, Zhang Y, Marier C, Diefenbach C, Kousteni S, Heguy A, Zhong H, Fooksman DR, Butler JM, Economides A, Frenette PS, Adams RH, Satija R, Tsirigos A, Aifantis I

  9. Integrative single-cell analysis.
    Nat Rev Genet (2019 May) PMID: 30696980
    Stuart T, Satija R

  10. Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding.
    J Phys Chem B (2019 Jan 31) PMID: 30648875
    Satija R, Makarov DE

  11. Generalized Langevin Equation as a Model for Barrier Crossing Dynamics in Biomolecular Folding.
    J Phys Chem A (2019 Jan 3) PMID: 30605332
    Satija R, Makarov DE

  12. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics.
    Genome Biol (2018 Dec 19) PMC6300015 free full-text archive
    Stoeckius M, Zheng S, Houck‑Loomis B, Hao S, Yeung BZ, Mauck WM 3rd, Smibert P, Satija R

  13. Kinetics of adult hematopoietic stem cell differentiation in vivo.
    J Exp Med (2018 Nov 5) PMC6219744 free full-text archive
    Upadhaya S, Sawai CM, Papalexi E, Rashidfarrokhi A, Jang G, Chattopadhyay P, Satija R, Reizis B

  14. Erratum: Strength in numbers from integrated single-cell neuroscience.
    Nat Biotechnol (2018 Sep 6) PMID: 30188549
    Satija R

  15. Transition Path Times in Non-Markovian Activated Rate Processes.
    J Phys Chem B (2018 Dec 13) PMID: 30179506
    Medina E, Satija R, Makarov DE

  16. Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features.
    Cell (2018 Jul 26) PMC6082168 free full-text archive
    Konstantinides N, Kapuralin K, Fadil C, Barboza L, Satija R, Desplan C

  17. Integrating single-cell transcriptomic data across different conditions, technologies, and species.
    Nat Biotechnol (2018 Jun) PMC6700744 free full-text archive
    Butler A, Hoffman P, Smibert P, Papalexi E, Satija R

  18. Molecular transitions in early progenitors during human cord blood hematopoiesis.
    Mol Syst Biol (2018 Mar 15) PMC5852373 free full-text archive
    Zheng S, Papalexi E, Butler A, Stephenson W, Satija R

  19. Corrigendum: Landscape of X chromosome inactivation across human tissues.
    Nature (2018 Mar 7) PMID: 29517003
    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, Consortium G, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG

  20. Developmental diversification of cortical inhibitory interneurons.
    Nature (2018 Mar 22) PMC6052457 free full-text archive
    Mayer C, Hafemeister C, Bandler RC, Machold R, Batista Brito R, Jaglin X, Allaway K, Butler A, Fishell G, Satija R

  21. Single-cell RNA-seq of rheumatoid arthritis synovial tissue using low-cost microfluidic instrumentation.
    Nat Commun (2018 Feb 23) PMC5824814 free full-text archive
    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

  22. Strength in numbers from integrated single-cell neuroscience.
    Nat Biotechnol (2018 Jan 10) PMID: 29319686
    Satija R

  23. Insights into the role of ribonuclease 4 polymorphisms in amyotrophic lateral sclerosis.
    J Biomol Struct Dyn (2019 Jan) PMID: 29279004
    Padhi AK, Narain P, Dave U, Satija R, Patir A, Gomes J

  24. The Human Cell Atlas.
    Elife (2017 Dec 5) PMC5762154 free full-text archive
    Regev A, Teichmann SA, Lander ES, Amit I, Benoist C, Birney E, Bodenmiller B, Campbell P, Carninci P, Clatworthy M, Clevers H, Deplancke B, Dunham I, Eberwine J, Eils R, Enard W, Farmer A, Fugger L, Gottgens B, Hacohen N, Haniffa M, Hemberg M, Kim S, 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 S, Reik W, Rozenblatt‑Rosen O, Sanes J, Satija R, Schumacher TN, Shalek A, Shapiro E, Sharma P, Shin JW, Stegle O, Stratton M, Stubbington MJT, Theis FJ, Uhlen M, van Oudenaarden A, Wagner A, Watt F, Weissman J, Wold B, Xavier R, Yosef N

  25. Transition path times reveal memory effects and anomalous diffusion in the dynamics of protein folding.
    J Chem Phys (2017 Oct 21) PMID: 29055292
    Satija R, Das A, Makarov DE

  26. Landscape of X chromosome inactivation across human tissues.
    Nature (2017 Oct 11) PMC5685192 free full-text archive
    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, Lappalainen T, Regev A, Ardlie KG, Hacohen N, MacArthur DG

  27. Single-cell RNA sequencing to explore immune cell heterogeneity.
    Nat Rev Immunol (2018 Jan) PMID: 28787399
    Papalexi E, Satija R

  28. Simultaneous epitope and transcriptome measurement in single cells.
    Nat Methods (2017 Sep) PMC5669064 free full-text archive
    Stoeckius M, Hafemeister C, Stephenson W, Houck‑Loomis B, Chattopadhyay PK, Swerdlow H, Satija R, Smibert P

  29. Design of a Toolbox of RNA Thermometers.
    ACS Synth Biol (2017 Aug 18) PMID: 28437108
    Sen S, Apurva D, Satija R, Siegal D, Murray RM

  30. Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors.
    Science (2017 Apr 21) PMC5775029 free full-text archive
    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

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