Publications by authors named "Aviv Regev"

100Publications

Chromatin Potential Identified by Shared Single-Cell Profiling of RNA and Chromatin.

Cell 2020 Nov 23;183(4):1103-1116.e20. Epub 2020 Oct 23.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.09.056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7669735PMC
November 2020

Integrated regulatory models for inference of subtype-specific susceptibilities in glioblastoma.

Mol Syst Biol 2020 Sep;16(9):e9506

Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.15252/msb.20209506DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7516378PMC
September 2020

The Human and Mouse Enteric Nervous System at Single-Cell Resolution.

Cell 2020 Sep 3;182(6):1606-1622.e23. Epub 2020 Sep 3.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Howard Hughes Medical Institute and Koch Institute for Integrative Cancer Research, Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2020.08.003DOI Listing
September 2020

Author Correction: Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

Nat Biotechnol 2020 Oct;38(10):1211

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41587-020-0665-2DOI Listing
October 2020

Massively parallel single-cell mitochondrial DNA genotyping and chromatin profiling.

Nat Biotechnol 2020 Aug 12. Epub 2020 Aug 12.

Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.

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http://dx.doi.org/10.1038/s41587-020-0645-6DOI Listing
August 2020

Purifying Selection against Pathogenic Mitochondrial DNA in Human T Cells.

N Engl J Med 2020 10 12;383(16):1556-1563. Epub 2020 Aug 12.

From the Departments of Molecular Biology (M.A.W., V.K.M.), Neurology (M.A.W.), and Medicine (V.K.M) and the Genetics Unit, Department of Pediatrics (A.K.), Massachusetts General Hospital, Howard Hughes Medical Institute (M.A.W., A.R., V.K.M.), the Division of Hematology-Oncology, Boston Children's Hospital (C.A.L., L.S.L., V.G.S.), the Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School (C.A.L., L.S.L., V.G.S.), the Department of Systems Biology, Harvard Medical School (V.K.M.), and Harvard Medical School (M.A.W., A.K.), Boston, and the Klarman Cell Observatory (L.S.L., A.R.), Broad Institute of MIT (Massachusetts Institute of Technology) and Harvard (M.A.W., C.A.L., V.G.S., V.K.M.), the Harvard Stem Cell Institute (V.G.S.), and the Department of Biology and Koch Institute of Integrative Cancer Research, Massachusetts Institute of Technology (A.R.), Cambridge - both in Massachusetts.

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http://dx.doi.org/10.1056/NEJMoa2001265DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7593775PMC
October 2020

A Switch in p53 Dynamics Marks Cells That Escape from DSB-Induced Cell Cycle Arrest.

Cell Rep 2020 Aug;32(5):107995

Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2020.107995DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7521664PMC
August 2020

A Distinct Transcriptional Program in Human CAR T Cells Bearing the 4-1BB Signaling Domain Revealed by scRNA-Seq.

Mol Ther 2020 Jul 25. Epub 2020 Jul 25.

Cellular Immunotherapy Program and Cancer Center, Massachusetts General Hospital, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Department of Medicine, Massachusetts General Hospital, Boston, MA 02114, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ymthe.2020.07.023DOI Listing
July 2020

Epigenomic State Transitions Characterize Tumor Progression in Mouse Lung Adenocarcinoma.

Cancer Cell 2020 Aug 23;38(2):212-228.e13. Epub 2020 Jul 23.

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.ccell.2020.06.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7641015PMC
August 2020

The network effect: studying COVID-19 pathology with the Human Cell Atlas.

Nat Rev Mol Cell Biol 2020 08;21(8):415-416

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41580-020-0267-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7325637PMC
August 2020

Cell Atlas of The Human Fovea and Peripheral Retina.

Sci Rep 2020 06 17;10(1):9802. Epub 2020 Jun 17.

Department of Molecular and Cellular Biology and Center for Brain Science, Harvard University, Cambridge, MA, 02138, USA.

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http://dx.doi.org/10.1038/s41598-020-66092-9DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7299956PMC
June 2020

MAUDE: inferring expression changes in sorting-based CRISPR screens.

Genome Biol 2020 06 3;21(1):134. Epub 2020 Jun 3.

Klarman Cell Observatory, Broad Institute of MIT and Harvard University, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1186/s13059-020-02046-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7268349PMC
June 2020

Disease-associated astrocytes in Alzheimer's disease and aging.

Nat Neurosci 2020 06 27;23(6):701-706. Epub 2020 Apr 27.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41593-020-0624-8DOI Listing
June 2020

Integrated scRNA-Seq Identifies Human Postnatal Thymus Seeding Progenitors and Regulatory Dynamics of Differentiating Immature Thymocytes.

Immunity 2020 Jun 17;52(6):1088-1104.e6. Epub 2020 Apr 17.

Faculty of Medicine and Health Sciences, Department of Diagnostic Sciences, Ghent University, C. Heymanslaan 10, MRB2, Entrance 38, 9000 Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2020.03.019DOI Listing
June 2020

A Synthesis Concerning Conservation and Divergence of Cell Types across Epithelia.

Cold Spring Harb Perspect Biol 2020 Nov 2;12(11). Epub 2020 Nov 2.

Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1101/cshperspect.a035733DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7605222PMC
November 2020

The Taste Receptor TAS1R3 Regulates Small Intestinal Tuft Cell Homeostasis.

Immunohorizons 2020 01 24;4(1):23-32. Epub 2020 Jan 24.

Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, MA 02115;

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http://dx.doi.org/10.4049/immunohorizons.1900099DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7197368PMC
January 2020

Hyperactivation of sympathetic nerves drives depletion of melanocyte stem cells.

Nature 2020 01 22;577(7792):676-681. Epub 2020 Jan 22.

Department of Stem Cell and Regenerative Biology, Harvard University and Harvard Stem Cell Institute, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41586-020-1935-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184936PMC
January 2020

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

IL-33 Signaling Alters Regulatory T Cell Diversity in Support of Tumor Development.

Cell Rep 2019 12;29(10):2998-3008.e8

David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA 02139, USA; Department of Biology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA; 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.celrep.2019.10.120DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6990979PMC
December 2019

Deciphering eukaryotic gene-regulatory logic with 100 million random promoters.

Nat Biotechnol 2020 01 2;38(1):56-65. Epub 2019 Dec 2.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, USA.

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http://dx.doi.org/10.1038/s41587-019-0315-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6954276PMC
January 2020

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses.

Immunity 2019 10;51(4):696-708.e9

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Molecular Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA; Center for Microbiome Informatics and Therapeutics, Massachusetts Institute of Technology, Cambridge, MA 02114, USA; Center for Computational and Integrative Biology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613193037
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http://dx.doi.org/10.1016/j.immuni.2019.09.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6991097PMC
October 2019

Calcitonin Gene-Related Peptide Negatively Regulates Alarmin-Driven Type 2 Innate Lymphoid Cell Responses.

Immunity 2019 10 8;51(4):709-723.e6. Epub 2019 Oct 8.

Evergrande Center for Immunologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA; Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.immuni.2019.09.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7076585PMC
October 2019

Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1.

J Immunol 2019 10 26;203(7):1820-1829. Epub 2019 Aug 26.

Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02114;

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http://dx.doi.org/10.4049/jimmunol.1800419DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6761021PMC
October 2019

Ketone Body Signaling Mediates Intestinal Stem Cell Homeostasis and Adaptation to Diet.

Cell 2019 08;178(5):1115-1131.e15

Koch Institute for Integrative Cancer Research at MIT, Cambridge, MA 02139, USA; Department of Biology, MIT, Cambridge, MA 02139, USA; Department of Pathology, Massachusetts General Hospital Boston and Harvard Medical School, Boston, MA 02114, USA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.07.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6732196PMC
August 2019

An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma.

Cell 2019 08 18;178(4):835-849.e21. Epub 2019 Jul 18.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA; Klarman Cell Observatory, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.06.024DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6703186PMC
August 2019

DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction.

Cell 2019 06 20;178(1):229-241.e16. Epub 2019 Jun 20.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, MIT, Cambridge, MA 02139, USA; McGovern Institute for Brain Research at MIT, Cambridge, MA 02139, USA; Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.05.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6697087PMC
June 2019

Transcriptional States and Chromatin Accessibility Underlying Human Erythropoiesis.

Cell Rep 2019 06;27(11):3228-3240.e7

Division of Hematology/Oncology, Boston Children's Hospital, and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA. Electronic address:

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http://dx.doi.org/10.1016/j.celrep.2019.05.046DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6579117PMC
June 2019

Single-Cell Analysis of the Normal Mouse Aorta Reveals Functionally Distinct Endothelial Cell Populations.

Circulation 2019 07 31;140(2):147-163. Epub 2019 May 31.

Broad Institute of MIT and Harvard University, Cambridge, MA (A.S.K., S.K.V., L.N., A.S., P.T.E., A.R., S.K., R.M.G.).

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http://dx.doi.org/10.1161/CIRCULATIONAHA.118.038362DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6693656PMC
July 2019

A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia.

Cell 2019 06 23;177(7):1915-1932.e16. Epub 2019 May 23.

Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA; Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193045
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http://dx.doi.org/10.1016/j.cell.2019.04.040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6570562PMC
June 2019

The Pediatric Cell Atlas: Defining the Growth Phase of Human Development at Single-Cell Resolution.

Dev Cell 2019 04 28;49(1):10-29. Epub 2019 Mar 28.

Department of Biomedical Informatics, University of Cincinnati College of Medicine, and Cincinnati Children's Hospital Medical Center, Division of Biomedical Informatics, Cincinnati, OH 45229, USA.

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http://dx.doi.org/10.1016/j.devcel.2019.03.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6616346PMC
April 2019

Inflammatory regulatory network mediated by the joint action of NF-kB, STAT3, and AP-1 factors is involved in many human cancers.

Proc Natl Acad Sci U S A 2019 05 25;116(19):9453-9462. Epub 2019 Mar 25.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;

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http://dx.doi.org/10.1073/pnas.1821068116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6511065PMC
May 2019

Lineage Tracing in Humans Enabled by Mitochondrial Mutations and Single-Cell Genomics.

Cell 2019 03 28;176(6):1325-1339.e22. Epub 2019 Feb 28.

Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Harvard Stem Cell Institute, Cambridge, MA 02138, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193005
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http://dx.doi.org/10.1016/j.cell.2019.01.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6408267PMC
March 2019

Molecular Classification and Comparative Taxonomics of Foveal and Peripheral Cells in Primate Retina.

Cell 2019 02 31;176(5):1222-1237.e22. Epub 2019 Jan 31.

Center for Brain Science and Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA. Electronic address:

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http://dx.doi.org/10.1016/j.cell.2019.01.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6424338PMC
February 2019

Optimal-Transport Analysis of Single-Cell Gene Expression Identifies Developmental Trajectories in Reprogramming.

Cell 2019 02 31;176(4):928-943.e22. Epub 2019 Jan 31.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Department of Systems Biology Harvard Medical School, Boston, MA 02125, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674193003
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http://dx.doi.org/10.1016/j.cell.2019.01.006DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6402800PMC
February 2019

Checkpoint Blockade Immunotherapy Induces Dynamic Changes in PD-1CD8 Tumor-Infiltrating T Cells.

Immunity 2019 01 8;50(1):181-194.e6. Epub 2019 Jan 8.

Evergrande Center for Immunologic Diseases and Ann Romney Center for Neurologic Diseases, Harvard Medical School and Brigham and Women's Hospital, Boston, MA 02115, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S10747613183052
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http://dx.doi.org/10.1016/j.immuni.2018.11.014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6336113PMC
January 2019

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

Cell 2018 11 1;175(5):1307-1320.e22. Epub 2018 Nov 1.

Department of Molecular Biology, Massachusetts General Hospital, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Gastrointestinal Unit and Center for the Study of Inflammatory Bowel Disease, Massachusetts General Hospital, Boston, MA 02114, USA; Center for Microbiome informatics and Therapeutics, MIT, Cambridge, MA 02139, USA. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00928674183131
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http://dx.doi.org/10.1016/j.cell.2018.10.008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6239889PMC
November 2018

Regulation of Cellular Heterogeneity and Rates of Symmetric and Asymmetric Divisions in Triple-Negative Breast Cancer.

Cell Rep 2018 09;24(12):3237-3250

Department of Developmental Biology and Cancer Research, Institute for Medical Research-Israel-Canada, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S22111247183133
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http://dx.doi.org/10.1016/j.celrep.2018.08.053DOI Listing
September 2018

BROCKMAN: deciphering variance in epigenomic regulators by k-mer factorization.

BMC Bioinformatics 2018 07 3;19(1):253. Epub 2018 Jul 3.

Klarman Cell Observatory, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.

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http://dx.doi.org/10.1186/s12859-018-2255-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6029352PMC
July 2018

Genome-scale identification of transcription factors that mediate an inflammatory network during breast cellular transformation.

Nat Commun 2018 05 25;9(1):2068. Epub 2018 May 25.

Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA.

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http://www.nature.com/articles/s41467-018-04406-2
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http://dx.doi.org/10.1038/s41467-018-04406-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5970197PMC
May 2018