RAHUL SATIJA
`Curriculum Vitae
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`
`Phone: (917)-753-4257 101 Avenue of the Americas, 4th Floor
`E-mail: rsatija@nygenome.org New York, NY 10013
`
`EDUCATION
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`December 1, 2014 – Present
`Core Member, New York Genome Center
`Associate Professor, New York University, Center for Genomics and Systems Biology
`Affiliate Faculty, NYU Langone Medical Center, Institute for Systems Genetics
`Disciplines : Statistical learning, computational biology, single cell genomics
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`2011-2014 – Broad Institute of Harvard and MIT, Cambridge, MA
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`Ruth L. Kirchstein Postdoctoral Fellow
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`Advisor: Dr. Aviv Regev
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`2010-2011 – Medical Research Council, Mammalian Genetics Unit, Harwell UK
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`Medical Research Council Training Fellow in Biomedical Informatics
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`Advisor: Dr. Pat Nolan
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`2006-2010 - Oxford University, Balliol College, Oxford UK
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`Rhodes Scholar
`Degree Course: D.Phil (Oxon) in Statistics, Advisor: Dr. Jotun Hein
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`2002-2006 - Duke University, Durham NC
`Degree Course: B.Sc. in Biology, Music, Mathematics, Summa Cum Laude
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`HONORS AND AWARDS
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` 2020
`2016
`2016
`2012
`2006
`2006
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` Director, NIH Center for Excellence in Genomic Science (CEGS)
`NIH ‘New Innovator’ Award
`Kavli Fellow, National Academy of Sciences
`Ruth L. Kirchstein National Research Service Award Postdoctoral Fellowship
`Rhodes Scholarship
`Hertz Foundation Graduate Fellowship Award
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`PUBLICATIONS (* - equal contribution, † - corresponding author)
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`Dictionary learning for integrative, multimodal, and scalable single-cell analysis
`Y Hao, T Stuart, M Kowalski, S Choudhary, P Hoffman, A Hartman, A Srivastava, G Molla, S Madad,
`C Fernandez-Granda, R Satija†
`Nature Biotechnology (In Press)
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`Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq
`HH Wessels*, A Mendez-Mancilla*, E Papalexi, WM Mauck, L Lu, JA Morris, E Mimitou, P Smibert,
`NE Sanjana†, R Satija†
`Nature Methods (2022)
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`TwinStrand EX1101
`TwinStrand Biosciences v. Guardant Health
`IPR2022-01400
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`Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution
`T Stuart, S Hao, B Zhang, L Mekerishvili, DA Landau, S Maniatis, R Satija, I Raimondi
`Nature Biotechnology (2022)
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`Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro
`B Zhang*, A Stivastava*, E Mimitou, T Stuart, I Raimondi, Y Hao, P Smibert, R Satija†
`Nature Biotechnology (2022)
`
`Comparison and evaluation of statistical error models for scRNA-seq
`S Choudhary, R Satija†
`Genome Biology (2022)
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`Single nucleus multi-omics identifies human cortical cell regulatory genome diversity
`C Luo, H Lui, F Xie, E Armand, K Siletti, T Bakken, R Fang, W Doyle, T Stuart, R Hodge, L Hu, B
`Wang, Z Zhang, S Preissl, DS Lee, J Zhou, SY Niu, DA Davis, DC Mash, R Satija, JR Dixon, S
`Linnarsson, E Lein, MM Behrens, B Ren, E Mukamel, J Ecker
`Cell Genomics (2022)
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`Integrated analysis of multimodal single-cell data
`Y Hao*, S Hao*, E Andersen-Nissen, WM Mauck, S Zheng, A Butler, MJ Lee, AJ Wilk, C Darby, M
`Zager, P Hoffman, M Stoeckius, E Papalexi, EP Mimitou, J Jain, A Srivastava, T Stuart, LB Fleming, B
`Yeung, AJ Rogers, JM McElarth, CA Blish, R Gottardo, P Smibert†, R Satija†
`Cell (2021)
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`Scalable, multimodal profiling of chromatin accessibility, gene expression, and protein levels in single
`cells
`EP Mimitou*, CA Lareau*, KY Chen*, AL Zorzetto-Fernandes, Y Hao, Y Takeshima, W Luo, T Huang,
`BZ Yeung, EP Papalexi, PI Thaoke, T Kibayashi, HB Wing, M Hata, R Satija, KL Nazor, S Sakaguchi,
`LS Ludwin, VG Sankaran, A Regev, P Smibert
`Nature Biotechnology (2021)
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`Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell
`screens
`E Papalexi, E Mimitou, A Butler, S Foster, B Bracken, WM Mauck, H Wessels, BZ Yeung, P Smibert,
`R Satija†
`Nature Genetics (2021)
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`Multimodal single-cell chromatin analysis with Signac
`T Stuart†, A Srivastava, C Lareau, R Satija†
`Nature Methods (2021)
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`A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness
`KB Kaufmann, AGX Zeng, E Coyaud, L Garcia-Prat, E Papalexi, A Murison, EMN Laurent, OI Gan, K
`Pan, J McLeod, H Boutzen, S Zandi, S Takayanagi, R Satija, B Raught, SZ Xie, J Dick
`Nature Immunology (2021)
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`geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq
`A Missarova, J Jain, A Butler, S Ghazanfar, T Stuart, M Brusko, C Wasserfall, H Nick, T Brusko, M
`Atksinson, R Satija*†, J Marioni*†
`Genome Biology (2021)
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`Selective metabolic redundancy of Gpi1 allows for specific inhibition of inflammatory Th17 cells.
`L Wu, KER Hollinshead, Y Hao, C Au, L Kroehling, C Ng, L Woan-Yu, D Li, HM Silva, J Shin, JJ
`Lafaille, R Possemato, ME Pacold, TY Papagiannakopoulos, AC Kimmelman, R Satija, DR Littman
`Cell (2020)
`
`The strength and pattern of natural selection on gene expression in rice.
`SC Groen, I Calic, Z Joly-Lopez, AE Platts, JY Choi, M Natividad, K Dorph, WM Mauck, B Bracken,
`CLU Cabral, A Kumar, RO Torres, R Satija, G Vergara, A Henry, SJ Franks, MD Purugannan
`Nature (2020)
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`Comprehensive integration of single cell data
`T Stuart*, A Butler*, P Hoffman, C Hafemeister, E Papalexi, WM Mauck, M Stoeckius, P Smibert,
`R Satija†
`Cell (2019)
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`The bone marrow micro-environment at single cell resolution
`A Tikhonova, I Dolgalev, H Ku, K Sivaraj, E Hoxha, A Cuesta-Dominguez, S Pinho, I Akhmetzyanova ,
`J Gao , M Witkowski , MR Guillamot , M Gutkin , Y Zhang , C Marier , C Diefenbach , S Kousteni , A
`Heguy , H Zhong , D Fooksman , J Butler , A Economides , PS Frenette , R Adams , R Satija, A
`Tsirigos, I Aifantis
`Nature (2019)
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`A single cell transcriptional roadmap for cardiopharyngeal fate diversification
`W Wang*, X Niu*, T Stuart, J Estelle, R Kelly, R Satija*†, L Christiaen*†
`Nature Cell Biology (2019).
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`Normalization and variance stabilization of single-cell RNA-seq data using regularized negative
`binomial regression
`C Hafemeister†, R Satija†
`Genome Biology (2019)
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`Toward a Common Coordinate Framework for the Human Body
`J Rood, T Stuart*, S Ghazanfar*, T Biancalini*, E Fisher, A Butler, A Hupalowska, L Gaffney, WM
`Mauck, G Eraslan, JC Marioni†, A Regev†, R Satija†
`Cell (2019)
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`The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
`HuBMAP Consortium
`Nature (2019)
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`Integrative single-cell analysis
`T Stuart, R Satija†
`Nature Reviews Genetics (2019)
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`Multiplexed detection of proteins, transcriptomes, clonotypes, and CRISPR perturbations in single cells.
`E Mimitou, A Cheng, A Montalbano, S Hao, M Stoeckius, M Legut, T Roush, A Herrera, E Papalexi, Z
`Ouyang, R Satija, NE Sanjana, S Koralov, P Smibert
`Nature Methods (2019)
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`Inhibitory neuron diversity originates from cardinal classes shared across germinal zones.
`C Mayer*, C Hafemeister*, RC Bandler*, R Machold, G Fishell *†, R Satija*†
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`Nature (2018)
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`Integrated analysis of single cell transcriptomic data across conditions, technologies, and species
`A Butler, P Hoffman, P Smibert, E Papalexi, R Satija†
`Nature Biotechnology (2018)
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`Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic
`Instrumentation
`W Stephenson*, LT Donlin*, A Butler*, C Rozo, A Rashidfarrokhi, SM Goodman, LB Ivashkiv, VP
`Bykerk, DE Orange, RB Darnell, HP Swerdlow*†, R Satija*†
`Nature Communications (2018)
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`Molecular transitions in early progenitors during human cord blood hematopoiesis
`S Zheng, E Papalexi, A Butler, W Stephenson, R Satija†
`Molecular Systems Biology (2018)
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`Phenotypic convergence in the brain: distinct transcription factors regulate common terminal neuronal
`characters
`N Konstantinides, K Kapuralin, C Fadil, L Barboza, R Satija, C Desplan
`Cell (2018)
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`Cell 'hashing' with barcoded antibodies enables multiplexing and doublet detection for single cell
`genomics
`M Stoeckius*, S Zheng*, B Houck-Loomis, S Hao, B Yeung, WM Mauck, P Smibert*†, R Satija*†
`Genome Biology (2018)
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`Kinetics of adult hematopoietic stem cell differentiation in vivo
`S Upadhaya, CM Sawai, E Papalexi, A Rashidfarrokhi, G Jang, P Chattopadhyay, R Satija, B Reizis
`Journal of Experimental Medicine (2018)
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`Large-scale simultaneous measurement of epitopes and transcriptomes in single cells.
`M Stoeckius, C Hafemeister, W Stephenson, B Houck-Loomis, H Swerdlow, R Satija, P Smibert
`Nature Methods (2017).
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`Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes and progenitors
`AC Villani*, R Satija*, G Reynolds, K Shekhar, S Sarikova, A Butler, S Zheng, W Li, P Jager, O
`Rosenblatt-Rosen, M Hannifa, A Regev, N Hacohen.
`Science (2017)
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`Single cell RNA-sequencing to explore immune cell heterogeneity
`E Papalexi, R Satija†
`Nature Reviews Immunology (2017).
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`Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
`TM Gierahn, MH Wadsworth, TK Hughes, BD Bryson, A Butler, R Satija, S Fortune, JC Love, AK
`Shalek
`Nature Methods (2017)
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`The Human Cell Atlas
`A Regev, SA Teichmann, ES Lander, 56 named authors (including R Satija), Human Cell Atlas Meeting
`Participants
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`eLife (2017)
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`Landscape of X chromosome inactivation across human tissues
`T Tukiainen, AC Villani, A Yen, MA Rivas, JL Marshall, R Satija, M Aguirre, L Gauthier, M Fleharty,
`A Kirby, BB Cummings, SE Castel, KJ Karczewski, F Aguet, A Byrnes, T Lappalainen, A Regev, KG
`Ardlie, N Hacohen, DG MacArthur, GTEx Consortium
`Nature (2017).
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` A
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` multi-step transcriptional and chromatin state cascade underlies motor neuron programming from
`embryonic stem cells
`S Velasco, MM Ibrahim, A Kakumanu, G Garipler, B Aydin, MA Al-Sayegh, A Hirsekorn, F Abdul-
`Rahman, R Satija, U Ohler, S Mahony, EO Mazzoni
`Cell Stem Cell (2016)
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`Human dendritic cells (DCs) are derived from distinct circulating precursors that are pre-committed to
`become CD1c+ or CD141+ DCs.
`G Breton, S Zheng, R Valieris, I Silva, R Satija, M Nussenzweig.
`Journal of Experimental Medicine (2016)
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`Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions
`I Efroni, A Mello, T Nawy, PL Ip, R Rahni, N Delrose, A Powers, R Satija, K Birnbaum.
`Cell (2016)
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`Single-cell analysis reveals key roles for Bcl11a in regulating stem cell fate decisions.
`Powers AN, Satija R†.
`Genome Biology (2015)
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`Spatial reconstruction of single-cell gene expression.
`R Satija*, JA Farrell*, D Gennert, AF Schier, A Regev.
`Nature Biotechnology (2015).
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`Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets
`EZ Macosko, A Basu, R Satija, J Nemesh, K Shekhar, M Goldman, I Tirosh, A Bialas, N Kamitaki, E
`Martersteck, JT Trombetta, DA Weitz, JR Sanes, AK Shalek, A Regev, SA McCaroll.
`Cell (2015).
`
`MERFishing for spatial context.
`AK Shalek, R. Satija†. Trends in Immunology (2015).
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`The Regulatory Factor ZFHX3 Modifies Circadian Function in SCN via an AT Motif-Driven Axis.
`Parsons MJ, Brancaccio M, Sethi S, Maywood ES, Satija R, Edwards JK, et al. Cell (2015)
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`Pathogen cell-to-cell variability drives heterogeneity in host immune responses.
`Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier
`RJ, Regev A, Hung DT. Cell (2015)
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`Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
`Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang L V, Wu C, Pandolfi P, Mak T, Satija R, Shalek
`AK, Kuchrkoo VK, Park H, Regev A. Cell (2015)
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` Generic and Cell-Type-Specific Wound Response Precedes Regeneration in Planarians.
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`Wurtzel O, Cote LE, Poirier A, Satija R, Regev A, Reddien PW. Dev Cell (2015)
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`Heterogeneity in immune responses- from populations to single cells.
`R. Satija†, A.K. Shalek†. Trends in Immunology (2014).
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`Large-scale single cell RNA-Seq reveals dynamic paracrine control of cellular varaition.
`A.K. Shalek*, R. Satija*†, J. Shuga*, J.J. Trombetta, D. Lu, D. Gennert, P. Chen, R.S. Gertner, J.T.
`Gaublomme, N. Yosef, S. Schwartz, B. Fowler, S. Weaver, J. Wang, X. Wang, R. Ding, R.
`Raychowdhury, N. Hacohen, H. Park, A.P. May†, A. Regev†. Nature (2014).
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`Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.
`A.K. Shalek*, R. Satija*, X. Adiconis, R.S. Gertner, J.T. Gaublomme, R. Raychowdhury, S. Schwartz,
`N. Yosef, C. Malboeuf, D. Lu, J.J. Trombetta, D. Gennert, A. Gnirke, A. Goren, N. Hacohen, J.L. Levin,
`H. Park, Regev, A. (2013). Single-cell transcriptomics reveals bimodality in expression and splicing in
`immune cells. Nature (2013).
`
`Comparative analysis of RNA sequencing methods for degraded or low-input samples.
`X. Adiconis*, D. Borges-Rivera*, R. Satija, D.S. DeLuca, M.A. Busby, A. Berlin, A. Sivachenko, D. A.
`Thompson, A. Wysocker, T. Fennell, A. Gnirke, N. Pochet, A. Regev, J.Z. Levin. Comparative analysis
`of RNA sequencing methods for degraded or low-input samples. Nature Methods (2013).
`
`Dynamic regulatory network controlling TH17 cell differentiation. N. Yosef, A.K. Shalek, J.
`Gaublomme, Y. Lee, A. Awasthi, H. Jin, C. Wu, K. Karwacz, S. Xiao, M. Jorgolli, D. Gennert, R.
`Satija, A. Shakya, D.Y. Lu, J.J. Trombetta, M. Pillai, P.J. Ratcliffe, M.L. Coleman, M. Bix, D. Tantin,
`H. Park, V.K Kuchroo, A. Regev. Nature (2013).
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`High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in
`Yeast Meiosis. S. Schwartz*, S. Agarwala*, M.R. Mumbach, M. Jovanovic, P. Mertins, A. Shishkin, Y.
`Tabach, T.S. Mikkelsen, R. Satija, G. Ruvkun, S. Carr, E.S. Lander, G.R. Fink, A. Regev. Cell (2013).
`
`The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila
`embryo. R. Satija, R.K. Bradley. Genome Research (2012)
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`The atypical calpains: evolutionary analyses and roles in Caenorhabditis elegans cellular degeneration.
`P.I. Joyce, R. Satija, M. Chen, P.E. Kuwabara. PLoS Genetics (2012).
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`Genome-wide functional element detection using pairwise statistical alignment outperforms multiple
`genome footprinting techniques. R. Satija†, J. Hein, G. A. Lunter. Bioinformatics (2010).
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`BigFoot: Bayesian alignment and footprinting of large datasets. R. Satija†, I. Miklos, A. Novak, R.
`Lyngsoe, J. Hein. BMC Evol. Biol (2009).
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`Stochastic models of sequence evolution including insertion-seletion events. I. Miklós, A. Novák, R.
`Satija, R. Lyngsoe, J. Hein. Statistical Methods in Medical Research (2009).
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`Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.
`R. Satija†, L. Pachter, and J. Hein. Bioinformatics (2008).
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`The Genome of the Sea Urchin Strongylocentrotus purpuratus. Sea Urchin Genome Sequencing
`Consortium. Science (2006).
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`In situ neutron imaging technique for evaluation of water management systems in operating PEM fuel
`cells. R. Satija, D.L. Jacobson, M. Arif, S.A. Werner. Journal of Power Sources (2004).
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`PROFESSIONAL ACTIVITIES
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`Reviewer for: Science, Nature, Cell, Nature Biotechnology, Nature Immunology, Nature Methods,
`Science Signalling, Cell Stem Cell, Molecular Systems Biology, Trends in Immunology, Molecular
`Biology and Evolution, Genome Biology, Genome Research, PLoS Computational Biology,
`Bioinformatics, BMC Bioinformatics
`
` I
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` am a member of the Analysis working Group for the Human Cell Atlas, a group of eight scientists who
`recommend optimal experimental design and best computational practices for the broader consortium.
`
` I
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` have led the creation of two yearly symposia. Each year (2016-present), we host Single Cell Genomics
`Day, a practical workshop to teach others how to apply new techniques in the field. All talks are free for
`in-person attendees, and are openly live-streamed online. In 2019, we additionally launched the NYU-
`Nature conference “Next-generation genomics”, aiming to highlight new research in sequencing
`technology and analysis. We excusively included junior faculty as invited speakers, to promote
`discoveries made by new investigators.
`
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`SOFTWARE PACKAGES
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`Seurat: R-toolkit for single cell genomics
`http://www.satijalab.org/seurat
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`Azimuth: Automated mapping of single-cell sequencing datasets to reference atlases
`http://azimuth.hubmapconsortium.org
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`GRAPeFoot: Simultanous Bayesian pairwise genomic alignment and functional element annotation
`http://sourceforge.net/projects/grapefoot/
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` BigFoot: Bayesian multiple alignment and phylogenetic footprinting with MCMC
` http://sourceforge.net/projects/bigfoot/
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`TEACHING AT NYU
`
`Instructor of Record
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`Fall 2020
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`Fall 2019
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`Fall 2017
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`Fall 2016
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`Contributing lecturer
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`BIOL-GA 2025 : Statistical learning for large-scale biological data
`15 students; 15/15 classes
`BIOL-GA 2025 : Statistical learning for large-scale biological data
`15 students; 15/15 classes
`BIOL-GA 2025 : Statistical learning for large-scale biological data
`14 students; 15/15 classes
`BIOL-GA 2025 : Statistical learning for large-scale biological data
`15 students; 15/15 classes
`
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`Spring 2017 BIOL-GA 2020. Biocore IV; 1 class
`Spring 2017 BIOL-GA 2019. Biocore IV; 1 class
`Spring 2017 BIOL-GA 2004. Biocore IV; 1 class
`Spring 2016 BIOL-GA 2004. Biocore IV; 1 class
`Spring 2016 BIOL-GA 2131. Developmental and Stem Cell Systems II; 1 class
`Spring 2015 BIOL-GA 2004. Biocore IV; 1 class
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`STUDENT AND TRAINEE SUPERVISION
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`Postdoctoral
`
`Christian Mayer (2014-2018), joint w/Gord Fishell
`Current position: Group Leader at Max Planck Institute for Neurobiology
`Lin Wu (2015-2021), joint w/Dan Littman
`Current position: Group Leader at Shenzhen Bay Laboratory
`Hans-Hermann Wessels (2018-Present)
`Tim Stuart (2018-Present)
`Bingjie Zhang (2018-Present)
`Saket Choudhary (2020-Present)
`John Blair (2020-Present)
`Kristof Torkenczy (2020-Present)
`Avi Srivastava (2020-Present)
`Longda Jiang (2021-Present)
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`Ph.D. students
`
`Shiwei Zheng (2015-2019)
`Current Position: Postdoctoral Fellow, Harvard Medical School
`Andrew Butler (2016-2021)
`Current Position: Postdoctoral Fellow, Fred Hutchinson Cancer Research Institute
`Efi Papalexi (2016-Present)
`Current Position: Senior Research Scientist, Parse Biosciences
`Yuhan Hao (2018-Present)
`Madeline Kowalksi (2020-Present)
`
`M.S. students
`
`Xiang Niu (2015-2017)
`Bernadette Bracken (2016-2019)
`Ashley Powers (2015-2016)
`Shaista Madad (2020-2021)
`
`Thesis Committees Kristen Gulino (2016-2019)
`Chang Wang (2017-2019)
`Geraldine Cayanan (2019-present)
`Dalia Barkley (2018-2021)
`Soobeom Lee (2020-present)
`Daniel Obaji (2020-present
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`0008
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