Publications by authors named "Bradley E Bernstein"

100Publications

Epigenetic alterations in keratinocyte carcinoma.

J Invest Dermatol 2020 Nov 16. Epub 2020 Nov 16.

Department of Dermatology, Massachusetts General Hospital, Boston, MA, USA; Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, MA, USA.

View Article and Find Full Text PDF
November 2020

Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization.

Biophys J 2020 Nov 22;119(9):1905-1916. Epub 2020 Sep 22.

Departments of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts. Electronic address:

View Article and Find Full Text PDF
November 2020

Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies.

Cell Rep 2020 Oct;33(1):108222

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

View Article and Find Full Text PDF
October 2020

Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer.

Cell 2020 Sep 24;182(6):1474-1489.e23. Epub 2020 Aug 24.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02129, USA. Electronic address:

View Article and Find Full Text PDF
September 2020

Detecting sample swaps in diverse NGS data types using linkage disequilibrium.

Nat Commun 2020 07 29;11(1):3697. Epub 2020 Jul 29.

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

View Article and Find Full Text PDF
July 2020

Immunohistochemical quantification of partial-EMT in oral cavity squamous cell carcinoma primary tumors is associated with nodal metastasis.

Oral Oncol 2019 12 6;99:104458. Epub 2019 Nov 6.

Department of Otolaryngology, Massachusetts Eye and Ear Infirmary, Boston, MA, USA; Department of Otolaryngology, Harvard Medical School, Boston, MA, USA. Electronic address:

View Article and Find Full Text PDF
December 2019

Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG.

Cancer Cell 2019 11 17;36(5):528-544.e10. Epub 2019 Oct 17.

Division of Newborn Medicine and Epigenetics Program, Department of Medicine, Boston Children's Hospital, Boston, MA 02115, USA; Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. Electronic address:

View Article and Find Full Text PDF
November 2019

Epigenome editing strategies for the functional annotation of CTCF insulators.

Nat Commun 2019 09 18;10(1):4258. Epub 2019 Sep 18.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA.

View Article and Find Full Text PDF
September 2019

Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity.

Cell 2019 03 28;176(6):1265-1281.e24. Epub 2019 Feb 28.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Ludwig Center at Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Electronic address:

View Article and Find Full Text PDF
March 2019

Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution.

Nat Genet 2019 01 17;51(1):19-25. Epub 2018 Dec 17.

Broad Institute of MIT and Harvard, Cambridge, MA, USA.

View Article and Find Full Text PDF
January 2019

GABPβ1L Wakes Up TERT.

Cancer Cell 2018 09;34(3):358-360

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

View Article and Find Full Text PDF
September 2018

Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms.

Cancer Cell 2018 01 14;33(1):29-43.e7. Epub 2017 Dec 14.

Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, Box 20, New York, NY 10065, USA; Center for Epigenetics Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA. Electronic address:

View Article and Find Full Text PDF
January 2018

Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer.

Cell 2017 Dec 30;171(7):1611-1624.e24. Epub 2017 Nov 30.

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

View Article and Find Full Text PDF
December 2017

Cohesin Loss Eliminates All Loop Domains.

Cell 2017 Oct;171(2):305-320.e24

The Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA; Departments of Computer Science and Computational and Applied Mathematics, Rice University, Houston, TX 77030, USA. Electronic address:

View Article and Find Full Text PDF
October 2017

A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression.

Cell 2017 Jul;170(3):522-533.e15

Broad Institute of MIT and Harvard University, Cambridge, MA, USA; Cardiology Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA USA; Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA. Electronic address:

View Article and Find Full Text PDF
July 2017

Epigenetic plasticity and the hallmarks of cancer.

Science 2017 Jul;357(6348)

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA, and Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.

View Article and Find Full Text PDF
July 2017

Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance.

Cell Stem Cell 2017 02 15;20(2):233-246.e7. Epub 2016 Dec 15.

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

View Article and Find Full Text PDF
February 2017

Single-molecule decoding of combinatorially modified nucleosomes.

Science 2016 May;352(6286):717-21

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.

View Article and Find Full Text PDF
May 2016

Insulator dysfunction and oncogene activation in IDH mutant gliomas.

Nature 2016 Jan 23;529(7584):110-4. Epub 2015 Dec 23.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA.

View Article and Find Full Text PDF
January 2016

A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes.

Mol Cell 2016 Jan 10;61(1):170-80. Epub 2015 Dec 10.

Department of Pathology, Massachusetts General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Center for Cancer Research, Massachusetts General Hospital, Boston, MA 02114, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA. Electronic address:

View Article and Find Full Text PDF
January 2016

Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state.

Nat Biotechnol 2015 Nov 12;33(11):1165-72. Epub 2015 Oct 12.

Epigenomics Program, The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

View Article and Find Full Text PDF
November 2015

EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression.

Blood 2015 Oct 28;126(16):1930-9. Epub 2015 Aug 28.

Division of Hematology, Department of Medicine, Brigham and Women's Hospital, Boston, MA; Harvard Medical School, Boston, MA; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA;

View Article and Find Full Text PDF
October 2015

Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma.

Cancer Discov 2015 Oct 30;5(10):1058-71. Epub 2015 Jul 30.

Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts. Broad Institute of Harvard University and MIT, Cambridge, Massachusetts.

View Article and Find Full Text PDF
October 2015

High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics.

PLoS One 2015 22;10(5):e0116328. Epub 2015 May 22.

Department of Physics and School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts, United States of America.

View Article and Find Full Text PDF
March 2016

Integrative analysis of 111 reference human epigenomes.

Nature 2015 Feb;518(7539):317-30

1] Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, 32 Vassar St, Cambridge, Massachusetts 02139, USA. [2] The Broad Institute of Harvard and MIT, 415 Main Street, Cambridge, Massachusetts 02142, USA.

View Article and Find Full Text PDF
February 2015

Genetic and epigenetic fine mapping of causal autoimmune disease variants.

Nature 2015 Feb 29;518(7539):337-43. Epub 2014 Oct 29.

1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Howard Hughes Medical Institute, Chevy Chase, Maryland 20815, USA [3] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA [4] Center for Systems Biology and Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts 02114, USA.

View Article and Find Full Text PDF
February 2015

Comparative analysis of metazoan chromatin organization.

Nature 2014 Aug;512(7515):449-52

1] Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA [2] Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Informatics Program, Children's Hospital, Boston, Massachusetts 02215, USA.

View Article and Find Full Text PDF
August 2014

Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma.

Science 2014 Jun 12;344(6190):1396-401. Epub 2014 Jun 12.

Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA. Broad Institute of Harvard and Massachusetts Institute of Techonology (MIT), Cambridge, MA 02142, USA. Howard Hughes Medical Institute Chevy Chase, MD 20815, USA.

View Article and Find Full Text PDF
June 2014

Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis.

Genome Res 2014 Jun 21;24(6):920-9. Epub 2014 Apr 21.

Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA; US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA;

View Article and Find Full Text PDF
June 2014

Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells.

Cell 2014 Apr 10;157(3):580-94. Epub 2014 Apr 10.

Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:

View Article and Find Full Text PDF
April 2014

An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia.

Nat Genet 2014 Apr 2;46(4):364-70. Epub 2014 Mar 2.

1] Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [2] Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. [3] Center for Cancer Research, Massachusetts General Hospital, Boston, Massachusetts, USA. [4] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA.

View Article and Find Full Text PDF
April 2014

Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo.

J Exp Med 2013 Nov 11;210(12):2641-59. Epub 2013 Nov 11.

Human Oncology and Pathogenesis Program, 2 Leukemia Service, 3 Gerstner Sloan-Kettering Graduate School of Biomedical Sciences, and 4 Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, NY 10065.

View Article and Find Full Text PDF
November 2013

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

Nat Biotechnol 2013 Dec 9;31(12):1137-42. Epub 2013 Oct 9.

1] Department of Pathology and Center for Cancer Research, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [2] Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, Massachusetts, USA. [3] Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, Massachusetts, USA. [4].

View Article and Find Full Text PDF
December 2013

SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing.

Dev Cell 2013 Sep;26(6):565-77

Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Sciences (IMS-RCAI), 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; CREST, Japan Science and Technology Agency, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan; PREST, Japan Science and Technology Agency, 1-7-22 Suehiro, Tsurumi-ku, Yokohama 230-0045, Japan. Electronic address:

View Article and Find Full Text PDF
September 2013

Locus-specific editing of histone modifications at endogenous enhancers.

Nat Biotechnol 2013 Dec 8;31(12):1133-6. Epub 2013 Sep 8.

1] Howard Hughes Medical Institute, Chevy Chase, Maryland, USA. [2] Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA. [3] Broad Institute of Harvard and MIT, Cambridge Massachusetts, USA. [4] Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, USA. [5].

View Article and Find Full Text PDF
December 2013

In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.

Nucleic Acids Res 2013 Oct 14;41(19):e181. Epub 2013 Aug 14.

Molecular Pathology Unit, Center for Cancer Research, Massachusetts General Hospital, Charlestown, MA 02129, USA, Center for Computational and Integrative Biology, Massachusetts General Hospital, Charlestown, MA 02129, USA, Department of Pathology, Harvard Medical School, Boston, MA 02115, USA, Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA 02115, USA, Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 01238, USA, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA and Howard Hughes Medical Institute, Chevy Chase, MD 02815, USA.

View Article and Find Full Text PDF
October 2013

Epigenetic reprogramming in cancer.

Science 2013 Mar;339(6127):1567-70

Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.

View Article and Find Full Text PDF
March 2013

A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force.

Cancer Res 2012 Dec 27;72(24):6319-24. Epub 2012 Nov 27.

Research Department of Cancer Biology, University College London Cancer Institute, University College London, London, United Kingdom.

View Article and Find Full Text PDF
December 2012

Molecular biology. Genetic events that shape the cancer epigenome.

Science 2012 Jun;336(6088):1513-4

Howard Hughes Medical Institute, Department of Pathology and Center for Cancer Research, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

View Article and Find Full Text PDF
June 2012

A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma.

Cancer Cell 2012 Mar;21(3):329-31

Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA.

View Article and Find Full Text PDF
March 2012

DNA-protein interactions in high definition.

Genome Biol 2012 Jan 27;13(1):139. Epub 2012 Jan 27.

Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA.

View Article and Find Full Text PDF
January 2012

EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas.

PLoS One 2011 14;6(12):e28585. Epub 2011 Dec 14.

Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America.

View Article and Find Full Text PDF
August 2012

Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq.

Nat Protoc 2011 Sep 29;6(10):1656-68. Epub 2011 Sep 29.

Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

View Article and Find Full Text PDF
September 2011