Single cell genomics, transcriptional regulation, computational biology
使用账号密码登录
Welcome Back
使用表单注册
Welcome Back
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.
2010 D.Phil. (Statistics), Oxford University
2006 B.Sc (Biology), Duke University
Single cell genomics, transcriptional regulation, computational biology
Associate Faculty, Institute for Systems Genetics, NYU Langone Medical Center
Core Member, New York Genome Center
2006 Rhodes Scholarship
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
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
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
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
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
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
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
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
Integrative single-cell analysis.
Nat Rev Genet (2019 May) PMID: 30696980
Stuart T, Satija R
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
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
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
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
Erratum: Strength in numbers from integrated single-cell neuroscience.
Nat Biotechnol (2018 Sep 6) PMID: 30188549
Satija R
Transition Path Times in Non-Markovian Activated Rate Processes.
J Phys Chem B (2018 Dec 13) PMID: 30179506
Medina E, Satija R, Makarov DE
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
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
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
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
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
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
Strength in numbers from integrated single-cell neuroscience.
Nat Biotechnol (2018 Jan 10) PMID: 29319686
Satija R
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
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
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
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
Single-cell RNA sequencing to explore immune cell heterogeneity.
Nat Rev Immunol (2018 Jan) PMID: 28787399
Papalexi E, Satija R
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
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
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