Publications by authors named "Rahul Satija"

57Publications

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

Cell 2020 Aug 1;182(3):641-654.e20. Epub 2020 Jul 1.

The Kimmel Center for Biology and Medicine of the Skirball Institute, New York University School of Medicine, New York, NY, USA; Howard Hughes Medical Institute, New York, NY, USA; Department of Pathology, New York University School of Medicine, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.06.014DOI Listing
August 2020

Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression.

Genome Biol 2019 12 23;20(1):296. Epub 2019 Dec 23.

New York Genome Center, 101 6th Ave, New York, 10013, NY, USA.

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http://dx.doi.org/10.1186/s13059-019-1874-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6927181PMC
December 2019

Toward a Common Coordinate Framework for the Human Body.

Cell 2019 12;179(7):1455-1467

New York Genome Center, New York, NY 10013, USA; New York University, Center for Genomics and Systems Biology, New York, NY 10012, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6934046PMC
December 2019

Comprehensive Integration of Single-Cell Data.

Cell 2019 06 6;177(7):1888-1902.e21. Epub 2019 Jun 6.

New York Genome Center, New York, NY, USA; Center for Genomics and Systems Biology, New York University, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.05.031DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6687398PMC
June 2019

A single-cell transcriptional roadmap for cardiopharyngeal fate diversification.

Nat Cell Biol 2019 06 3;21(6):674-686. Epub 2019 Jun 3.

Center for Developmental Genetics, Department of Biology, New York University, New York, NY, USA.

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http://dx.doi.org/10.1038/s41556-019-0336-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7491489PMC
June 2019

Integrative single-cell analysis.

Nat Rev Genet 2019 05;20(5):257-272

New York Genome Center, New York, NY, USA.

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http://dx.doi.org/10.1038/s41576-019-0093-7DOI Listing
May 2019

Kinetics of adult hematopoietic stem cell differentiation in vivo.

J Exp Med 2018 11 5;215(11):2815-2832. Epub 2018 Oct 5.

Department of Pathology, New York University School of Medicine, New York, NY

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http://dx.doi.org/10.1084/jem.20180136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6219744PMC
November 2018

Erratum: Strength in numbers from integrated single-cell neuroscience.

Authors:
Rahul Satija

Nat Biotechnol 2018 09;36(9):899

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http://dx.doi.org/10.1038/nbt0918-899dDOI Listing
September 2018

Phenotypic Convergence: Distinct Transcription Factors Regulate Common Terminal Features.

Cell 2018 07 18;174(3):622-635.e13. Epub 2018 Jun 18.

Department of Biology, New York University, New York, NY 10003, USA; New York University Abu Dhabi, Saadiyat Island, Abu Dhabi, United Arab Emirates. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2018.05.021DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6082168PMC
July 2018

Strength in numbers from integrated single-cell neuroscience.

Authors:
Rahul Satija

Nat Biotechnol 2018 01;36(1):41-42

New York Genome Center, New York, New York, USA, and New York University, Center for Genomics and Systems Biology, New York, New York, USA.

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http://dx.doi.org/10.1038/nbt.4055DOI Listing
January 2018

Single-cell RNA sequencing to explore immune cell heterogeneity.

Nat Rev Immunol 2018 01 7;18(1):35-45. Epub 2017 Aug 7.

Center for Genomics and Systems Biology, New York University, New York, NY 10003-6688, USA.

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http://dx.doi.org/10.1038/nri.2017.76DOI Listing
January 2018

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

Nat Methods 2017 Apr 13;14(4):395-398. Epub 2017 Feb 13.

Institute for Medical Engineering &Science (IMES) and Department of Chemistry, MIT, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nmeth.4179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5376227PMC
April 2017

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

J Exp Med 2016 12 18;213(13):2861-2870. Epub 2016 Nov 18.

Laboratory of Molecular Immunology, The Rockefeller University, New York, NY 10065.

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http://dx.doi.org/10.1084/jem.20161135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5154947PMC
December 2016

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

Cell 2016 Jun 19;165(7):1721-1733. Epub 2016 May 19.

Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2016.04.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4912400PMC
June 2016

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

Dev Cell 2015 Dec;35(5):632-645

Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.devcel.2015.11.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4817857PMC
December 2015

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

Cell 2015 Dec 19;163(6):1400-12. Epub 2015 Nov 19.

Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA; Howard Hughes Medical Institute and David H. Koch Institute of Integrative Cancer Biology, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.11.009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4671824PMC
December 2015

Single-cell analysis reveals key roles for Bcl11a in regulating stem cell fate decisions.

Genome Biol 2015 Sep 21;16:199. Epub 2015 Sep 21.

New York Genome Center, New York, NY, 10012, USA.

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http://dx.doi.org/10.1186/s13059-015-0778-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4576375PMC
September 2015

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Cell 2015 Sep 3;162(6):1309-21. Epub 2015 Sep 3.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://www.cell.com/cms/attachment/2035742002/2051265527/mmc
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http://linkinghub.elsevier.com/retrieve/pii/S009286741501041
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http://dx.doi.org/10.1016/j.cell.2015.08.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4578813PMC
September 2015

MERFISHing for spatial context.

Trends Immunol 2015 Jul 23;36(7):390-1. Epub 2015 May 23.

New York Genome Center, New York, NY, USA; New York University, Center for Genomics and Systems Biology, New York, NY, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2015.05.002DOI Listing
July 2015

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets.

Cell 2015 May;161(5):1202-1214

Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2015.05.002DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4481139PMC
May 2015

Spatial reconstruction of single-cell gene expression data.

Nat Biotechnol 2015 May 13;33(5):495-502. Epub 2015 Apr 13.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

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http://dx.doi.org/10.1038/nbt.3192DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4430369PMC
May 2015

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

Science 2015 Mar 12;347(6226):1259038. Epub 2015 Feb 12.

The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA. HHMI, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02140, USA.

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http://dx.doi.org/10.1126/science.1259038DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4506746PMC
March 2015

Transcriptome-wide mapping reveals widespread dynamic-regulated pseudouridylation of ncRNA and mRNA.

Cell 2014 Sep 11;159(1):148-162. Epub 2014 Sep 11.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA. Electronic address:

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http://authors.library.caltech.edu/50054/10/mmc4.pdf
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http://linkinghub.elsevier.com/retrieve/pii/S009286741401098
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http://dx.doi.org/10.1016/j.cell.2014.08.028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4180118PMC
September 2014

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

Curr Protoc Mol Biol 2014 Jul 1;107:4.22.1-17. Epub 2014 Jul 1.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts.

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http://doi.wiley.com/10.1002/0471142727.mb0422s107
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http://dx.doi.org/10.1002/0471142727.mb0422s107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4338574PMC
July 2014

Perturbation of m6A writers reveals two distinct classes of mRNA methylation at internal and 5' sites.

Cell Rep 2014 Jul 26;8(1):284-96. Epub 2014 Jun 26.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2014.05.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4142486PMC
July 2014

Single-cell RNA-seq reveals dynamic paracrine control of cellular variation.

Nature 2014 Jun 11;510(7505):363-9. Epub 2014 Jun 11.

1] Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA.

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http://dx.doi.org/10.1038/nature13437DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4193940PMC
June 2014

Heterogeneity in immune responses: from populations to single cells.

Trends Immunol 2014 May 16;35(5):219-29. Epub 2014 Apr 16.

Department of Chemistry and Chemical Biology and Department of Physics, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.it.2014.03.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035247PMC
May 2014

The atypical calpains: evolutionary analyses and roles in Caenorhabditis elegans cellular degeneration.

PLoS Genet 2012 29;8(3):e1002602. Epub 2012 Mar 29.

School of Biochemistry, University of Bristol, Bristol, United Kingdom.

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http://dx.doi.org/10.1371/journal.pgen.1002602DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3315469PMC
September 2012

BigFoot: Bayesian alignment and phylogenetic footprinting with MCMC.

BMC Evol Biol 2009 Aug 28;9:217. Epub 2009 Aug 28.

Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford, UK.

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http://dx.doi.org/10.1186/1471-2148-9-217DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2744684PMC
August 2009

Stochastic models of sequence evolution including insertion-deletion events.

Stat Methods Med Res 2009 Oct 16;18(5):453-85. Epub 2009 Feb 16.

Bioinformatics Group, Alfréd Rényi Institute of Mathematics, Hungarian Academy of Sciences, 1053 Budapest, Reáltanoda u. 13-15, Hungary.

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http://dx.doi.org/10.1177/0962280208099500DOI Listing
October 2009

Combining statistical alignment and phylogenetic footprinting to detect regulatory elements.

Bioinformatics 2008 May 18;24(10):1236-42. Epub 2008 Mar 18.

Department of Statistics, Oxford University, Oxford, UK.

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http://dx.doi.org/10.1093/bioinformatics/btn104DOI Listing
May 2008

The genome of the sea urchin Strongylocentrotus purpuratus.

Authors:
Erica Sodergren George M Weinstock Eric H Davidson R Andrew Cameron Richard A Gibbs Robert C Angerer Lynne M Angerer Maria Ina Arnone David R Burgess Robert D Burke James A Coffman Michael Dean Maurice R Elphick Charles A Ettensohn Kathy R Foltz Amro Hamdoun Richard O Hynes William H Klein William Marzluff David R McClay Robert L Morris Arcady Mushegian Jonathan P Rast L Courtney Smith Michael C Thorndyke Victor D Vacquier Gary M Wessel Greg Wray Lan Zhang Christine G Elsik Olga Ermolaeva Wratko Hlavina Gretchen Hofmann Paul Kitts Melissa J Landrum Aaron J Mackey Donna Maglott Georgia Panopoulou Albert J Poustka Kim Pruitt Victor Sapojnikov Xingzhi Song Alexandre Souvorov Victor Solovyev Zheng Wei Charles A Whittaker Kim Worley K James Durbin Yufeng Shen Olivier Fedrigo David Garfield Ralph Haygood Alexander Primus Rahul Satija Tonya Severson Manuel L Gonzalez-Garay Andrew R Jackson Aleksandar Milosavljevic Mark Tong Christopher E Killian Brian T Livingston Fred H Wilt Nikki Adams Robert Bellé Seth Carbonneau Rocky Cheung Patrick Cormier Bertrand Cosson Jenifer Croce Antonio Fernandez-Guerra Anne-Marie Genevière Manisha Goel Hemant Kelkar Julia Morales Odile Mulner-Lorillon Anthony J Robertson Jared V Goldstone Bryan Cole David Epel Bert Gold Mark E Hahn Meredith Howard-Ashby Mark Scally John J Stegeman Erin L Allgood Jonah Cool Kyle M Judkins Shawn S McCafferty Ashlan M Musante Robert A Obar Amanda P Rawson Blair J Rossetti Ian R Gibbons Matthew P Hoffman Andrew Leone Sorin Istrail Stefan C Materna Manoj P Samanta Viktor Stolc Waraporn Tongprasit Qiang Tu Karl-Frederik Bergeron Bruce P Brandhorst James Whittle Kevin Berney David J Bottjer Cristina Calestani Kevin Peterson Elly Chow Qiu Autumn Yuan Eran Elhaik Dan Graur Justin T Reese Ian Bosdet Shin Heesun Marco A Marra Jacqueline Schein Michele K Anderson Virginia Brockton Katherine M Buckley Avis H Cohen Sebastian D Fugmann Taku Hibino Mariano Loza-Coll Audrey J Majeske Cynthia Messier Sham V Nair Zeev Pancer David P Terwilliger Cavit Agca Enrique Arboleda Nansheng Chen Allison M Churcher F Hallböök Glen W Humphrey Mohammed M Idris Takae Kiyama Shuguang Liang Dan Mellott Xiuqian Mu Greg Murray Robert P Olinski Florian Raible Matthew Rowe John S Taylor Kristin Tessmar-Raible D Wang Karen H Wilson Shunsuke Yaguchi Terry Gaasterland Blanca E Galindo Herath J Gunaratne Celina Juliano Masashi Kinukawa Gary W Moy Anna T Neill Mamoru Nomura Michael Raisch Anna Reade Michelle M Roux Jia L Song Yi-Hsien Su Ian K Townley Ekaterina Voronina Julian L Wong Gabriele Amore Margherita Branno Euan R Brown Vincenzo Cavalieri Véronique Duboc Louise Duloquin Constantin Flytzanis Christian Gache François Lapraz Thierry Lepage Annamaria Locascio Pedro Martinez Giorgio Matassi Valeria Matranga Ryan Range Francesca Rizzo Eric Röttinger Wendy Beane Cynthia Bradham Christine Byrum Tom Glenn Sofia Hussain Gerard Manning Esther Miranda Rebecca Thomason Katherine Walton Athula Wikramanayke Shu-Yu Wu Ronghui Xu C Titus Brown Lili Chen Rachel F Gray Pei Yun Lee Jongmin Nam Paola Oliveri Joel Smith Donna Muzny Stephanie Bell Joseph Chacko Andrew Cree Stacey Curry Clay Davis Huyen Dinh Shannon Dugan-Rocha Jerry Fowler Rachel Gill Cerrissa Hamilton Judith Hernandez Sandra Hines Jennifer Hume Laronda Jackson Angela Jolivet Christie Kovar Sandra Lee Lora Lewis George Miner Margaret Morgan Lynne V Nazareth Geoffrey Okwuonu David Parker Ling-Ling Pu Rachel Thorn Rita Wright

Science 2006 Nov;314(5801):941-52

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http://dx.doi.org/10.1126/science.1133609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159423PMC
November 2006