2023

Dictionary learning for integrative, multimodal, and scalable single-cell analysis

Hao Y, Stuart T, Kowalski M, Choudhary S, Hoffman P, Hartman A, Srivastava A, Molla G, Madad S, Fernandez-Granda C, Satija R

Nature Biotechnology. 2023

Watch Yuhan Hao's CEGS Virtual Series talk on this work

CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators

Kowalski M*, Wessels H*, Linder J*, Choudhary S, Hartman A, Hao Y, Mascio I, Dalgarno C, Kundaje A, Satija R

bioRxiv. 2023

Watch Madeline Kowalski and Harm Wessels's CEGS Virtual Series talk on this work

Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection

Zhang B*, Upadhyay R*, Hao Y, Samanovic M, Herati R, Blair J, Axelrad J, Mulligan M, Littman D*, Satija R*

bioRxiv. 2023

Watch Bingjie Zhang's CEGS Virtual Series talk on this work

2022

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

Wessels H*, Mendez-Mancilla A*, Hao Y, Papalexi E, Mauck W, Lu L, Morris J, Mimitou E, Smibert P, Sanjana N*, Satija R*

Nature Methods. 2022

Watch Harm Wessels's CEGS Virtual Series talk on this work

Nanobody-tethered transposition allows for multifactorial chromatin profiling at single-cell resolution

Stuart T, Hao S, Zhang B, Mekerishvili L, Landau D, Maniatis S, Satija R, Raimondi I

Nature Biotechnology. 2022

Watch Tim Stuart's CEGS Virtual Series talk on this work

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

Zhang B*, Srivastava A*, Mimitou E, Stuart T, Raimondi I, Hao Y, Smibert P, Satija R

Nature Biotechnology. 2022

Watch Bingjie Zhang and Avi Srivastava's CEGS Virtual Series talk on this work

2021

Single-cell chromatin state analysis with Signac

Stuart T, Srivastava A, Madad S, Lareau C, Satija R

Nature Methods. 2021

geneBasis: an iterative approach for unsupervised selection of targeted gene panels from scRNA-seq

Missarova A, Jain J, Butler A, Ghazanfar S, Stuart T, Brusko M, Wasserfall C, Nick H, Brusko T, Atkinson M, Satija R*, Marioni J*

bioRxiv. 2021

Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells

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

Nature Biotechnology. 2021

Integrated analysis of multimodal single-cell data

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*

Cell. 2021

Characterizing the molecular regulation of inhibitory immune checkpoints with multi-modal single-cell screens

Papalexi E, Mimitou E, Butler A, Foster S, Bracken B, Mauck WM, Wessels H, Yeung BZ, Smibert P, Satija R

Nature Genetics. 2021

A latent subset of human hematopoietic stem cells resists regenerative stress to preserve stemness

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

Nature Immunology. 2021

2020

Niche-Selective Inhibition of Pathogenic Th17 Cells by Targeting Metabolic Redundancy

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

Cell. 2020

The strength and pattern of natural selection on gene expression in rice

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

Nature. 2020

2019

Comprehensive Integration of Single-Cell Data

Stuart T*, Butler A*, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, Hao Y, Stoeckius M, Smibert P, Satija R

Cell. 2019

A single cell transcriptional roadmap for cardiopharyngeal fate diversification

Wang W*, Niu X*, Stuart T, Estelle J, Mauck WM, Kelly R, Satija R*, Christiaen L*

Nature Cell Biology. 2019

Toward a Common Coordinate Framework for the Human Body

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*

Cell. 2019

Integrative single-cell analysis

Stuart T, Satija R

Nature Reviews Genetics. 2019

The bone marrow microenvironment at single-cell resolution.

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

Nature. 2019

Multiplexed detection of proteins, transcriptomes, clonotypes, and CRISPR perturbations in single cells.

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

Nature Methods. 2019

2018

Developmental diversification of cortical inhibitory interneurons

Mayer C*, Hafemeister C*, Bandler RC*, Machold R, Allaway K, Jaglin X, Brito R, Butler A, Fishell G*, Satija R*

Nature. 2018

Integrating single-cell transcriptomic data across different conditions, technologies, and species

Butler A, Hoffman P, Smibert P, Papalexi E, Satija R

Nature Biotechnology. 2018

Cell 'hashing' with barcoded antibodies enables multiplexing and doublet detection for single cell genomics

Stoeckius M*, Zheng S*, Houck-Loomis B, Hao S, Yeung B, Mauck WM, Smibert P*, Satija R*

Genome Biology. 2018

Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features

Konstantinides N, Kapuralin K, Barboza L, Satija R, Desplan C

Cell. 2018

Molecular transitions in early progenitors during human cord blood hematopoiesis

Zheng S, Papalexi E, Butler A, Stephenson W, Satija R

Molecular Systems Biology. 2018

Single-Cell RNA-Seq Of Rheumatoid Arthritis Synovial Tissue Using Low Cost Microfluidic Instrumentation

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*

Nature Communications. 2018

Kinetics of adult hematopoietic stem cell differentiation in vivo

Upadhaya S*, Sawai C*, Papalexi E, Rashidfarrokhi A, Jang G, Chattopadhyay P, Satija R, Reizis B

Journal of Experimental Medicine. 2018

2017

Single-cell RNA sequencing to explore immune cell heterogeneity

Papalexi E, Satija R

Nature Reviews Immunology. 2017

Simultaneous measurement of epitopes and transcriptomes in single cells.

Stoeckius M, Hafemeister C, Stephenson W, Houck-Loomis B, Swerdlow H, Satija R, Smibert P

Nature Methods. 2017

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

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

Science. 2017

The Human Cell Atlas

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

eLife. 2017

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput

Gierahn TM, Wadsworth II MH, Hughes TK, Bryson BD, Butler A, Satija R, Fortune S, Love JC, Shalek AK

Nature Methods. 2017

Landscape of X chromosome inactivation across human tissues

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

Nature. 2017

2016

Human dendritic cells (DCs) are derived from distinct circulating precursors that are precommitted to become CD1c+ or CD141+ DCs

Breton G, Zheng S, Valieris R, da Silva IT, Satija R, Nussenzweig MC

Journal of Experimental Medicine. 2016

A multi-step transcriptional and chromatin state cascade underlies motor neuron programming from embryonic stem cells

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

Cell Stem Cell. 2016

Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma

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

Nature. 2016

Root Regeneration Triggers an Embryo-like Sequence Guided by Hormonal Interactions.

Efroni I, Mello A, Nawy T, Ip PL, Rahni R, DelRose N, Powers A, Satija R, Birnbaum KD.

Cell. 2016

2015

A Generic and Cell-Type-Specific Wound Response Precedes Regeneration.

Wurtzel O, Cote LE, Poirier A, Satija R, Regev A, Reddien PW.

Developmental Cell. 2015

Single-Cell Genomics Unveils Critical Regulators of Th17 Cell Pathogenicity.

Gaublomme JT, Yosef N, Lee Y, Gertner RS, Yang LV, Wu C, Pandolfi PP, Mak T, Satija R, Shalek AK, Kuchroo VK.

Cell. 2015

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

MERFISHing for spatial context.

Satija R, Shalek AK.

Trends in Immunology. 2015

A Genome-wide CRISPR Screen in Primary Immune Cells to Dissect Regulatory Networks.

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.

Cell. 2015

The Regulatory Factor ZFHX3 Modifies Circadian Function in SCN via an AT Motif-Driven Axis.

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.

Cell. 2015

Spatial reconstruction of single-cell gene expression data.

Satija R*, Farrell JA*, Gennert D, Schier AF, Regev A.

Nature Biotechnology. 2015

Highly Parallel Genome-wide Expression Profiling of Individual Cells using nanoliter droplets.

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.

Cell. 2015

Dynamic profiling of the protein life cycle in response to pathogens.

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.

Science. 2015

2014

Heterogeneity in immune responses: from populations to single cells.

Satija R, Shalek AK.

Trends in Immunology. 2014

Single-Cell RNA-Seq Reveals Dynamic Paracrine Control of Cellular Variation.

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.

Nature. 2014

Preparation of Single Cell RNA-Seq Libraries for Next Generation Sequencing.

Trombetta JJ*, Gennert D*, Lu D *, Satija R, Shalek AK, and Regev A.

Current Protocols in Molecular Biology. 2014

Deconstructing transcriptional heterogeneity in pluripotent stem cells.

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.

Nature. 2014

Transcriptome-wide Mapping Reveals Widespread Dynamic-Regulated Pseudouridylation of ncRNA and mRNA.

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.

Cell. 2014

Whole-exome sequencing of circulating tumor cells provides a window into metastatic prostate cancer

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.

Nature Biotechnology. 2014

2013

Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells.

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.

Nature. 2013

Comparative analysis of RNA sequencing methods for degraded or low-input samples.

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.

Nature Methods. 2013

High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis

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.

Cell. 2013

Dynamic regulatory network controlling TH17 cell differentiation

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.

Nature. 2013

2012

2010