Stuart T, Srivastava A, Lareau C, Satija R
Multimodal single-cell chromatin analysis with Signac
bioRxiv. 2020

Hao Y*, Hao S*, Andersen-Nissen E, Mauck WM, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zagar M, Hoffman P, Stoeckius M, Papalexi E, Mimitou EP, Jain J, Srivastava A, Stuart T, Fleming LB, Yeung B, Rogers AJ, McElrath JM, Blish CA, Gottardo R, Smibert P*, Satija R*
Integrated analysis of multimodal single-cell data
bioRxiv. 2020

Papalexi E, Mimitou E, Butler A, Foster S, Bracken B, Mauck WM, Wessels H, Yeung BZ, Smibert P, Satija R
Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens
Nature Genetics (In press). 2020

Wu L, Hollinshead KER, Hao Y, Au C, Kroehling L, Ng, C, Woan-Yu L, Li D, Silva HM, Shin J, Lafaille JJ, Possemato R, Pacold ME, Papagiannakopoulos TY, Kimmelman AC, Satija R, Littman DR
Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy
Cell. 2020

Groen SC, Calic I, Joly-Lopez Z, Platts AE, Choi JY, Natividad M, Dorph K, Mauck WM, Bracken B, Cabral C, Kumar A, Torres RO, Satija R, Vergara G, Henry A, Franks SJ, Purugganan MD
The strength and pattern of natural selection on gene expression in rice
Nature. 2020

Stuart T*, Butler A*, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, Hao Y, Stoeckius M, Smibert P, Satija R
Comprehensive Integration of Single-Cell Data
Cell. 2019

Wang W*, Niu X*, Stuart T, Estelle J, Mauck WM, Kelly R, Satija R*, Christiaen L*
A single cell transcriptional roadmap for cardiopharyngeal fate diversification
Nature Cell Biology. 2019

Hafemeister C, Satija R
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression
Genome Biology. 2019

Rood J, Stuart T*, Ghazanfar S*, Biancalini T*, Fisher E, Butler A, Hupalowska A, Gaffney L, Mauck WM, Eraslan G, Marioni JC*, Regev A*, Satija R*
Toward a Common Coordinate Framework for the Human Body
Cell. 2019

Stuart T, Satija R
Integrative single-cell analysis
Nature Reviews Genetics. 2019

HuBMAP consortium
The human body at cellular resolution: the NIH Human Biomolecular Atlas Program
Nature. 2019

Tikhonova A, Dolgalev I, Ku H, Sivaraj K, Hoxha E, Cuesta-Dominguez A, Pinho S, Akhmetzyanova I, Gao J, Witkowski M, Guillamot MR, Gutkin M, Zhang Y, Marier C, Diefenbach C, Kousteni S, Heguy A, Zhong H, Fooksman D, Butler J, Economides A, Frenette PS, Adams R, Satija R, Tsirigos A, Aifantis I
The bone marrow microenvironment at single-cell resolution.
Nature. 2019

Mimitou E, Cheng A, Montalbano A, Hao S, Stoeckius M, Legut M, Roush T, Herrera A, Papalexi E, Ouyang Z, Satija R, Sanjana N, Koralov S, Smibert P
Multiplexed detection of proteins, transcriptomes, clonotypes, and CRISPR perturbations in single cells.
Nature Methods. 2019

Mayer C*, Hafemeister C*, Bandler RC*, Machold R, Allaway K, Jaglin X, Brito R, Butler A, Fishell G*, Satija R*
Developmental diversification of cortical inhibitory interneurons
Nature. 2018

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R
Integrating single-cell transcriptomic data across different conditions, technologies, and species
Nature Biotechnology. 2018

Stoeckius M*, Zheng S*, Houck-Loomis B, Hao S, Yeung B, Smibert P*, Satija R*
Cell 'hashing' with barcoded antibodies enables multiplexing and doublet detection for single cell genomics
Genome Biology. 2018

Konstantinides N, Kapuralin K, Barboza L, Satija R, Desplan C
Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features
Cell. 2018

Zheng S, Papalexi E, Butler A, Stephenson W, Satija R
Molecular transitions in early progenitors during human cord blood hematopoiesis
Molecular Systems Biology. 2018

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*
Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic Instrumentation
Nature Communications. 2018

Upadhaya S*, Sawai C*, Papalexi E, Rashidfarrokhi A, Jang G, Chattopadhyay P, Satija R, Reizis B
Kinetics of adult hematopoietic stem cell differentiation in vivo
Journal of Experimental Medicine. 2018

Papalexi E, Satija R
Single-cell RNA sequencing to explore immune cell heterogeneity
Nature Reviews Immunology. 2017

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Swerdlow H, Satija R, Smibert P
Simultaneous measurement of epitopes and transcriptomes in single cells.
Nature Methods. 2017

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
Single-cell RNA-seq reveals new types of human blood dendritic cells, monocytes, and progenitors
Science. 2017

Regev A, Teichmann SA, Lander ES, ... , Human Cell Atlas Meeting Participants
The Human Cell Atlas
eLife. 2017

Gierahn TM, Wadsworth II MH, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK
Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput
Nature Methods. 2017

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, GTEx Consortium
Landscape of X chromosome inactivation across human tissues
Nature. 2017

Breton G, Zheng S, Valieris R, da Silva IT, Satija R, Nussenzweig MC
Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs
Journal of Experimental Medicine. 2016

Velasco S, Ibrahim MM, Kakumanu A, Garipler G, Aydin, B, Al-Sayegh MA, Hirsekorn A, Abdul-Rahman F, Satija R, Ohler U, Mahony S, Mazzoni EO
A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells
Cell Stem Cell. 2016

Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, Francis JM, Patel AA, Onozato ML, Riggi N, Livak KJ, Gennert D, Satija R, Nahed BV, Curry WT, Martuza RL, Mylvaganam R, lafrate JA, Frosch MP, Golub TR, Rivera MN, Getz G, Rozenblatt-Rosen O, Cahill DP, Monje M, Bernstein BE, Louis DN, Regev A, Suvà ML
Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma
Nature. 2016

Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD.
Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions.
Cell. 2016

Wurtzel O, Cote LE, Poirier A, Satija R, Regev A, Reddien PW.
A Generic and Cell-Type-Specific Wound Response Precedes Regeneration.
Developmental Cell. 2015

Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, Pandolfi PP, Mak T, Satija R, Shalek AK, Kuchroo VK.
Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.
Cell. 2015

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT.
Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses
Cell. 2015

Satija R, Shalek AK.
MERFISHing for spatial context.
Trends in Immunology. 2015

Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A.
A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.
Cell. 2015

Parnas O, Jovanovic M, Eisenhaure TM, Herbst RH, Dixit A, Ye CJ, Przybylski D, Platt RJ, Tirosh I, Sanjana NE, Shalem O, Satija R, Raychowdhury R, Mertins P, Carr SA, Zhang F, Hacohen N, Regev A.
The Regulatory Factor ZFHX3 Modifies Circadian Function in SCN via an AT Motif-Driven Axis.
Cell. 2015

Powers A, Satija R.
Single-cell analysis reveals key roles for Bcl11a in regulating stem cell fate decisions.
Genome Biology. 2015

Satija R*, Farrell JA*, Gennert D, Schier AF, Regev A.
Spatial reconstruction of single-cell gene expression data.
Nature Biotechnology. 2015

Macosko EZ, Basu A, Satija R, Nemesh J, Shekhar K, Goldman M, Tirosh I, Bialas A, Kamitaki N, Martersteck E, Trombetta JT, Weitz DA, Sanes JR, Shalek AK, Regev A, McCaroll SA.
Highly Parallel Genome-wide Expression Profiling of Individual Cells using nanoliter droplets.
Cell. 2015

Jovanovic M*, Rooney MA*, Mertins P, Przybylski D, Chevrier N, Satija R,Rodriguez EH, Fields AP, Schwartz S, Raychowdhury R, Mumbach MR, Eisenhaure T, Rabani M, Gennert D, Lu D, Delorey T, Weissman JS, Carr SA, Hacohen N, and Regev A.
Dynamic profiling of the protein life cycle in response to pathogens.
Science. 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

Kumar RM, Cahan P, Shalek AK, Satija R, DaleyKeyser AJ, Li H, Zhang J, Pardee K, Gennert D, Trombetta JJ, Ferrante TC, Regev A, Daley GQ & Collins JJ.
Deconstructing transcriptional heterogeneity in pluripotent stem cells.
Nature. 2014

Schwartz S, Bernstein DA, Mumbach MR, Jovanovic M, Herbst RH, León-Ricardo BX, Engreitz JM, Guttman M, Satija R, Lander ES, Fink G, & Regev A.
Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA.
Cell. 2014

Lohr JG, Adalsteinsson VA, Cibulskis K, ChoudhurD, Rosenberg M, Cruz-Gordillo P, Francis JM, Zhang CZ, Shalek AK, Satija R, Trombetta JJ, Lu D, Tallapragada N, Tahirova N, Kim S, Blumenstiel B, Sougnez C, Lowe A, Wong B, Auclair D, Van Allen EM, Nakabayashi M, Lis RT, Lee GSM, Li T, Chabot ME, Ly A, Taplin ME, Clancy TE, Loda M, Regev A, Meyerson M, Hahn WC, Kantoff PW, Golub TR, Getz G, Boehm JS & Love JC.
Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer
Nature Biotechnology. 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

Adiconis X, Borges-Rivera D, Satija R, DeLuca DS, Busby MA, Berlin AM, Sivachenko A, Thompson DA, Wysoker A, Fennell T, Gnirke A, Pochet N, Regev A, Levin JZ.
Comparative analysis of RNA sequencing methods for degraded or low-input samples.
Nature Methods. 2013

Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, & Regev A.
High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis
Cell. 2013

Yosef N, Shalek AK, Gaublomme JT, Jin H, Lee Y, Awasthi A, Wu C, Karwacz K, Xiao S, Jorgolli M, Gennert D, Satija R, ShakyaA, Lu DY, Trombetta JJ, Pillai MR, Ratcliffe PJ, Coleman ML, Bix M, Tantin D, Park H, Kuchroo VK & Regev A.
Dynamic regulatory network controlling TH17 cell differentiation
Nature. 2013

Satija R, Bradley RK.
The TAGteam motif facilitates binding of 21 sequence-specific transcription factors in the Drosophila embryo.
Genome Research. 2012

Joyce PI, Satija R, Chen M, Kuwabara PE
The Atypical Calpains: Evolutionary Analyses and Roles in Caenorhabditis elegans Cellular Degeneration
PLoS Genetics. 2012

Satija R, Hein J, Lunter GA.
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.
Bioinformatics. 2010