2022
Zhang B*, Srivastava A*, Mimitou E, Stuart T, Raimondi I, Hao Y, Smibert P, Satija R
Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-proNature Biotechnology. 2022
Choudhary S, Satija R
Comparison and evaluation of statistical error models for scRNA-seqGenome Biology. 2022
Stuart T, Hao S, Zhang B, Mekerishvili L, Landau D, Maniatis S, Satija R, Raimondi I
Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolutionbioRxiv. 2022
Hao Y, Stuart T, Kowalski M, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R
Dictionary learning for integrative, multimodal, and scalable single-cell analysisbioRxiv. 2022
Wessels H*, Mendez-Mancilla A*, Papalexi E, Mauck W, Lu L, Morris J, Mimitou E, Smibert P, Sanjana N*, Satija R*
Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seqbioRxiv. 2022
2021
Stuart T, Srivastava A, Madad S, Lareau C, Satija R
Single-cell chromatin state analysis with SignacNature Methods. 2021
Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R*, Marioni J*
geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seqbioRxiv. 2021
Mimitou E, Lareau C, Chen K, Zorzetto-Fernandes A, Hao Y, Takeshima Y, Luo W, Huang T, Yeung B, Papalexi E, Thakore P, Kibayashi T, Wing J, Hata M, Satija R, Nazor K, Sakaguchi S, Ludwig L, Sankaran V, Regev A, Smibert P
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cellsNature Biotechnology. 2021
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 dataCell. 2021
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 screensNature Genetics. 2021
Kaufmann KB, Zeng AGX, Coyaud E, Garcia-Prat L, Papalexi E, Murison A, Laurent EMN, Chan-Seng-Yue M, Gan OI, Pan K, McLeod J, Boutzen H, Zandi S, Takayanagi S, Satija R, Raught B, Xie SZ, Dick J
A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemnessNature Immunology. 2021
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 RedundancyCell. 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 riceNature. 2020
2019
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 DataCell. 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 diversificationNature Cell Biology. 2019
Hafemeister C, Satija R
Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regressionGenome 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 BodyCell. 2019
HuBMAP consortium
The human body at cellular resolution: the NIH Human Biomolecular Atlas ProgramNature. 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
2018
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 interneuronsNature. 2018
Butler A, Hoffman P, Smibert P, Papalexi E, Satija R
Integrating single-cell transcriptomic data across different conditions, technologies, and speciesNature Biotechnology. 2018
Stoeckius M*, Zheng S*, Houck-Loomis B, Hao S, Yeung B, Mauck WM, Smibert P*, Satija R*
Cell 'hashing' with barcoded antibodies enables multiplexing and doublet detection for single cell genomicsGenome Biology. 2018
Konstantinides N, Kapuralin K, Barboza L, Satija R, Desplan C
Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal FeaturesCell. 2018
Zheng S, Papalexi E, Butler A, Stephenson W, Satija R
Molecular transitions in early progenitors during human cord blood hematopoiesisMolecular 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 InstrumentationNature 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 vivoJournal of Experimental Medicine. 2018
2017
Papalexi E, Satija R
Single-cell RNA sequencing to explore immune cell heterogeneityNature 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 progenitorsScience. 2017
Regev A, Teichmann SA, Lander ES, ... , Human Cell Atlas Meeting Participants
The Human Cell AtlaseLife. 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 throughputNature 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 tissuesNature. 2017
2016
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+ DCsJournal 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 cellsCell 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 oligodendrogliomaNature. 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
2015
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 ResponsesCell. 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
2014
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 cancerNature Biotechnology. 2014
2013
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 MeiosisCell. 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 differentiationNature. 2013
2012
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 DegenerationPLoS Genetics. 2012
2010
Satija R, Hein J, Lunter GA.
Genome-wide functional element detection using pairwise statistical alignment outperforms multiple genome footprinting techniques.Bioinformatics. 2010
