Bradley Bernstein, MD, PhD

Bradley Bernstein, MD, PhD

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Bradley Bernstein, MD, PhD

Dr. Bernstein received his B.S. from Yale University in 1992 and his M.D. and Ph.D. from the University of Washington in 1999, before completing a residency in clinical pathology at Brigham and Women’s Hospital and postdoctoral research at Harvard University. He served on the faculty at Massachusetts General Hospital from 2005 to 2021. He is currently Chair of Cancer Biology at the Dana-Farber Cancer Institute, where he holds the Richard and Nancy Lubin Family Chair. He is also the Director of the Gene Regulation Observatory at the Broad Institute, a Professor of Cell Biology and Pathology at Harvard Medical School, and an Investigator in Harvard’s Ludwig Institute.



Chair of Cancer Biology, Dana-Farber Cancer Institute
Richard and Nancy Lubin Family Chair
Professor of Cell Biology and Pathology, Harvard Medical School

Clinical Interests

Brain tumors, Glioblastoma, Sarcomas

Board Certification

  • Clinical Pathology


  • Brigham and Women's Hospital

Medical School

  • University of Washington

Recent Awards

  • Early Career Scientist Award from the Howard Hughes Medical Institute
  • Elizabeth and Michael Ruane Endowed Scholar Award in Endocrine Pathology
  • Career Award in the Biomedical Sciences from the Burroughs Wellcome Fund
  • NIH Director’s Pioneer Award
  • American Cancer Society Professorship
  • Paul Marks Prize for Cancer Research


    Dr. Bernstein’s research focuses on epigenetic gene regulation. His lab studies how gene activity is controlled by regulatory sequences, and by the way the genes are packaged into chromatin. His work is notable for the characterization of chromatin structures that underlie stem cell pluripotency, the identification of regulatory sequences that impact autoimmunity and other diseases, and the characterization of epigenetic aberrations that turn on oncogenes and drive tumors.

    Research Departments


      • Exposure of iPSC-derived human microglia to brain substrates enables the generation and manipulation of diverse transcriptional states in vitro. Nat Immunol. 2023 08; 24(8):1382-1390. View in: Pubmed

      • Modeling epigenetic lesions that cause gliomas. Cell. 2023 08 17; 186(17):3674-3685.e14. View in: Pubmed

      • Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin. Nature. 2023 Jun; 618(7966):834-841. View in: Pubmed

      • Impact of supraphysiologic MDM2 expression on chromatin networks and therapeutic responses in sarcoma. Cell Genom. 2023 Jul 12; 3(7):100321. View in: Pubmed

      • Integrative dissection of gene regulatory elements at base resolution. Cell Genom. 2023 Jun 14; 3(6):100318. View in: Pubmed

      • The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biol. 2023 04 18; 24(1):79. View in: Pubmed

      • The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models. Cell. 2023 03 30; 186(7):1493-1511.e40. View in: Pubmed

      • Chromatin complex dependencies reveal targeting opportunities in leukemia. Nat Commun. 2023 01 27; 14(1):448. View in: Pubmed

      • Epigenetic clocks, aging, and cancer. Science. 2022 Dec 23; 378(6626):1276-1277. View in: Pubmed

      • Single-cell RNA sequencing identifies a paracrine interaction that may drive oncogenic notch signaling in human adenoid cystic carcinoma. Cell Rep. 2022 Nov 29; 41(9):111743. View in: Pubmed

      • Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements. Nat Genet. 2022 10; 54(10):1504-1513. View in: Pubmed

      • Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3. View in: Pubmed

      • Author Correction: Perspectives on ENCODE. Nature. 2022 May; 605(7909):E4. View in: Pubmed

      • Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol. 2022 07; 40(7):1030-1034. View in: Pubmed

      • Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution. Cell Rep Methods. 2021 09 27; 1(5). View in: Pubmed

      • Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nat Biotechnol. 2021 09; 39(9):1086-1094. View in: Pubmed

      • Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL. Blood. 2021 05 06; 137(18):2463-2480. View in: Pubmed

      • Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. 2021 07; 595(7866):309-314. View in: Pubmed

      • Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. 2021 04 29; 184(9):2503-2519.e17. View in: Pubmed

      • Serving on the Navy's Hospital Ships During the Response to COVID-19: Perspective from Two Deployed Missouri Physicians. Mo Med. 2021 Mar-Apr; 118(2):110-112. View in: Pubmed

      • Epigenetic Alterations in Keratinocyte Carcinoma. J Invest Dermatol. 2021 05; 141(5):1207-1218. View in: Pubmed

      • High Seroprevalence of Anti-SARS-CoV-2 Antibodies in Chelsea, Massachusetts. J Infect Dis. 2020 11 13; 222(12):1955-1959. View in: Pubmed

      • Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies. Cell Rep. 2020 10 06; 33(1):108222. View in: Pubmed

      • Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization. Biophys J. 2020 11 03; 119(9):1905-1916. View in: Pubmed

      • Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J. 2020 10; 34(10):13877-13884. View in: Pubmed

      • Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 10; 38(10):1174-1183. View in: Pubmed

      • Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23. View in: Pubmed

      • Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. View in: Pubmed

      • Perspectives on ENCODE. Nature. 2020 07; 583(7818):693-698. View in: Pubmed

      • Detecting sample swaps in diverse NGS data types using linkage disequilibrium. Nat Commun. 2020 07 29; 11(1):3697. View in: Pubmed

      • Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol. 2020 07 15; 21(1):174. View in: Pubmed

      • Test performance evaluation of SARS-CoV-2 serological assays. medRxiv. 2020 May 17. View in: Pubmed

      • Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis. Cancer Discov. 2020 07; 10(7):980-997. View in: Pubmed

      • Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun. 2020 03 16; 11(1):1406. View in: Pubmed

      • Immunohistochemical quantification of partial-EMT in oral cavity squamous cell carcinoma primary tumors is associated with nodal metastasis. Oral Oncol. 2019 12; 99:104458. View in: Pubmed

      • Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nat Cell Biol. 2019 11; 21(11):1449-1461. View in: Pubmed

      • Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG. Cancer Cell. 2019 11 11; 36(5):528-544.e10. View in: Pubmed

      • Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature. 2019 11; 575(7781):229-233. View in: Pubmed

      • Altered chromosomal topology drives oncogenic programs in SDH-deficient GIST. Nature. 2019 Oct 16. View in: Pubmed

      • Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019 Oct; 25(10):1627. View in: Pubmed

      • Epigenome editing strategies for the functional annotation of CTCF insulators. Nat Commun. 2019 09 18; 10(1):4258. View in: Pubmed

      • Resolving medulloblastoma cellular architecture by single-cell genomics. Nature. 2019 08; 572(7767):74-79. View in: Pubmed

      • An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell. 2019 08 08; 178(4):835-849.e21. View in: Pubmed

      • Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019 08; 25(8):1260-1265. View in: Pubmed

      • Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat Commun. 2019 04 23; 10(1):1874. View in: Pubmed

      • Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. Cell. 2019 03 07; 176(6):1265-1281.e24. View in: Pubmed

      • A novel method for detecting the cellular stemness state in normal and leukemic human hematopoietic cells can predict disease outcome and drug sensitivity. Leukemia. 2019 08; 33(8):2061-2077. View in: Pubmed

      • Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. Nat Neurosci. 2019 01; 22(1):37-46. View in: Pubmed

      • Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nat Genet. 2019 01; 51(1):19-25. View in: Pubmed

      • Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. Cell. 2018 09 20; 175(1):101-116.e25. View in: Pubmed

      • GABPß1L Wakes Up TERT. Cancer Cell. 2018 09 10; 34(3):358-360. View in: Pubmed

      • Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nat Commun. 2018 09 04; 9(1):3588. View in: Pubmed

      • Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin. Mol Cell. 2018 06 07; 70(5):983. View in: Pubmed

      • Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018 04 20; 360(6386):331-335. View in: Pubmed

      • Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 04 09; 33(4):785-787. View in: Pubmed

      • Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet. 2018 04; 50(4):621-629. View in: Pubmed

      • Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol. 2018 02; 36(2):179-189. View in: Pubmed

      • Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 01 08; 33(1):29-43.e7. View in: Pubmed

      • Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. Cell. 2017 Dec 14; 171(7):1611-1624.e24. View in: Pubmed

      • Epithelial-to-Mesenchymal Transition Antagonizes Response to Targeted Therapies in Lung Cancer by Suppressing BIM. Clin Cancer Res. 2018 01 01; 24(1):197-208. View in: Pubmed

      • A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Rep. 2017 Oct 17; 21(3):784-797. View in: Pubmed

      • Cohesin Loss Eliminates All Loop Domains. Cell. 2017 Oct 05; 171(2):305-320.e24. View in: Pubmed

      • Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer. Elife. 2017 09 11; 6. View in: Pubmed

      • A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression. Cell. 2017 Jul 27; 170(3):522-533.e15. View in: Pubmed

      • Epigenetic plasticity and the hallmarks of cancer. Science. 2017 Jul 21; 357(6348). View in: Pubmed

      • Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature. 2017 07 20; 547(7663):355-359. View in: Pubmed

      • Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017 03 31; 355(6332). View in: Pubmed

      • Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proc Natl Acad Sci U S A. 2017 02 14; 114(7):E1291-E1300. View in: Pubmed

      • Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell. 2017 02 02; 20(2):233-246.e7. View in: Pubmed

      • SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017 Feb; 49(2):289-295. View in: Pubmed

      • Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016 11 10; 539(7628):309-313. View in: Pubmed

      • 142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. Neurosurgery. 2016 Aug; 63 Suppl 1:158. View in: Pubmed

      • RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation. J Clin Invest. 2016 07 01; 126(7):2757-72. View in: Pubmed

      • Single-molecule decoding of combinatorially modified nucleosomes. Science. 2016 May 06; 352(6286):717-21. View in: Pubmed

      • Widespread RNA binding by chromatin-associated proteins. Genome Biol. 2016 Feb 16; 17:28. View in: Pubmed

      • An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016 Mar; 48(3):265-72. View in: Pubmed

      • Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. 2016 Jan 07; 529(7584):110-4. View in: Pubmed

      • A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Mol Cell. 2016 Jan 07; 61(1):170-80. View in: Pubmed

      • Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nat Biotechnol. 2015 Nov; 33(11):1165-72. View in: Pubmed

      • EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression. Blood. 2015 Oct 15; 126(16):1930-9. View in: Pubmed

      • Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discov. 2015 Oct; 5(10):1058-71. View in: Pubmed

      • High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. PLoS One. 2015; 10(5):e0116328. View in: Pubmed

      • Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature. 2015 Jul 09; 523(7559):221-5. View in: Pubmed

      • Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity. Leukemia. 2015 Sep; 29(9):1948-51. View in: Pubmed

      • Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. View in: Pubmed

      • Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19; 518(7539):355-359. View in: Pubmed

      • Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proc Natl Acad Sci U S A. 2014 Nov 18; 111(46):E4946-53. View in: Pubmed

      • EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell. 2014 Nov 10; 26(5):668-681. View in: Pubmed

      • Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015 Feb 19; 518(7539):337-43. View in: Pubmed

      • Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. View in: Pubmed

      • Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proc Natl Acad Sci U S A. 2014 Aug 19; 111(33):E3366. View in: Pubmed

      • Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014 Sep; 17(9):1156-63. View in: Pubmed

      • Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov. 2014 Oct; 4(10):1154-67. View in: Pubmed

      • Mammalian Polycomb-Like Pcl2/Mtf2 Is a Novel Regulatory Component of PRC2 That Can Differentially Modulate Polycomb Activity both at the Hox Gene Cluster and at Cdkn2a Genes. Mol Cell Biol. 2014 Jul 15; 34(14):2773. View in: Pubmed

      • Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science. 2014 Jun 20; 344(6190):1396-401. View in: Pubmed

      • Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun; 24(6):920-9. View in: Pubmed

      • Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. View in: Pubmed

      • Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 2014 Apr 24; 157(3):580-94. View in: Pubmed

      • An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat Genet. 2014 Apr; 46(4):364-70. View in: Pubmed

      • Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J Exp Med. 2013 Nov 18; 210(12):2641-59. View in: Pubmed

      • Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nat Biotechnol. 2013 Dec; 31(12):1137-42. View in: Pubmed

      • SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Dev Cell. 2013 Sep 30; 26(6):565-77. View in: Pubmed

      • Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol. 2013 Dec; 31(12):1133-6. View in: Pubmed

      • In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Res. 2013 Oct; 41(19):e181. View in: Pubmed

      • Charting a dynamic DNA methylation landscape of the human genome. Nature. 2013 Aug 22; 500(7463):477-81. View in: Pubmed

      • An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Rep. 2013 May 30; 3(5):1567-79. View in: Pubmed

      • Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. View in: Pubmed

      • Epigenetic reprogramming in cancer. Science. 2013 Mar 29; 339(6127):1567-70. View in: Pubmed

      • Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31; 152(3):642-54. View in: Pubmed

      • Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes Dev. 2012 Dec 15; 26(24):2802-16. View in: Pubmed

      • The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012 Dec 07; 151(6):1185-99. View in: Pubmed

      • A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Res. 2012 Dec 15; 72(24):6319-24. View in: Pubmed

      • H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biol. 2012 Oct 03; 13(10):R85. View in: Pubmed

      • An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. View in: Pubmed

      • Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature. 2012 Sep 06; 489(7414):155-9. View in: Pubmed

      • ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. View in: Pubmed

      • A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell. 2012 Sep 14; 47(5):810-22. View in: Pubmed

      • ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012 Aug 14; 22(2):180-93. View in: Pubmed

      • Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. PLoS Genet. 2012; 8(7):e1002774. View in: Pubmed

      • Molecular biology. Genetic events that shape the cancer epigenome. Science. 2012 Jun 22; 336(6088):1513-4. View in: Pubmed

      • DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 2012 Jun 22; 149(7):1474-87. View in: Pubmed

      • A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma. Cancer Cell. 2012 Mar 20; 21(3):329-31. View in: Pubmed

      • DNA-protein interactions in high definition. Genome Biol. 2012 Jan 27; 13(1):139. View in: Pubmed

      • Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23; 147(7):1628-39. View in: Pubmed

      • EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas. PLoS One. 2011; 6(12):e28585. View in: Pubmed

      • Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet. 2011 Dec; 7(12):e1002389. View in: Pubmed

      • Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc. 2011 Sep 29; 6(10):1656-68. View in: Pubmed

      • Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14902-7. View in: Pubmed

      • Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14908-13. View in: Pubmed

      • A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. View in: Pubmed

      • Initial genome sequencing and analysis of multiple myeloma. Nature. 2011 Mar 24; 471(7339):467-72. View in: Pubmed

      • Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 2011 May 05; 473(7345):43-9. View in: Pubmed

      • Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell. 2011 Feb 18; 144(4):513-25. View in: Pubmed

      • Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell. 2011 Jan 07; 8(1):96-105. View in: Pubmed

      • GC-rich sequence elements recruit PRC2 in mammalian ES cells. PLoS Genet. 2010 Dec 09; 6(12):e1001244. View in: Pubmed

      • Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet. 2011 Jan; 12(1):7-18. View in: Pubmed

      • Mammalian polycomb-like Pcl2/Mtf2 is a novel regulatory component of PRC2 that can differentially modulate polycomb activity both at the Hox gene cluster and at Cdkn2a genes. Mol Cell Biol. 2011 Jan; 31(2):351-64. View in: Pubmed

      • The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol. 2010 Oct; 28(10):1045-8. View in: Pubmed

      • Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. View in: Pubmed

      • Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug; 7(8):615-8. View in: Pubmed

      • Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 2010 Jun 04; 6(6):591-602. View in: Pubmed

      • Digital transcriptome profiling from attomole-level RNA samples. Genome Res. 2010 Apr; 20(4):519-25. View in: Pubmed

      • Jarid2 and PRC2, partners in regulating gene expression. Genes Dev. 2010 Feb 15; 24(4):368-80. View in: Pubmed

      • Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nat Methods. 2010 Jan; 7(1):47-9. View in: Pubmed

      • Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Mol Cell. 2009 Nov 25; 36(4):682-95. View in: Pubmed

      • Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 09; 326(5950):289-93. View in: Pubmed

      • Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009 Oct 09; 326(5950):257-63. View in: Pubmed

      • Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A. 2009 Jul 14; 106(28):11667-72. View in: Pubmed

      • Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009 Mar 12; 458(7235):223-7. View in: Pubmed

      • Developmental biology. Pluripotent chromatin state. Science. 2009 Jan 09; 323(5911):220-1. View in: Pubmed

      • Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008 Oct; 4(10):e1000242. View in: Pubmed

      • Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. View in: Pubmed

      • Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 2008 Aug 07; 454(7205):766-70. View in: Pubmed

      • Dissecting direct reprogramming through integrative genomic analysis. Nature. 2008 Jul 03; 454(7200):49-55. View in: Pubmed

      • Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview. CSH Protoc. 2008 May 01; 2008:pdb.top42. View in: Pubmed

      • Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription. CSH Protoc. 2008 May 01; 2008:pdb.prot5003. View in: Pubmed

      • Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification. CSH Protoc. 2008 May 01; 2008:pdb.prot5004. View in: Pubmed

      • Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase. CSH Protoc. 2008 May 01; 2008:pdb.prot5002. View in: Pubmed

      • Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev. 2008 Apr; 18(2):109-15. View in: Pubmed

      • Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 02; 448(7153):553-60. View in: Pubmed

      • In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 2007 Jul 19; 448(7151):318-24. View in: Pubmed

      • The mammalian epigenome. Cell. 2007 Feb 23; 128(4):669-81. View in: Pubmed

      • Genome-wide analysis of histone modifications by ChIP-on-chip. Methods. 2006 Dec; 40(4):365-9. View in: Pubmed

      • Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes. Nat Struct Mol Biol. 2006 Sep; 13(9):852-4. View in: Pubmed

      • A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 2006 Apr 21; 125(2):315-26. View in: Pubmed

      • Genomic views of chromatin. Curr Opin Genet Dev. 2005 Oct; 15(5):476-81. View in: Pubmed

      • Large-scale discovery and validation of functional elements in the human genome. Genome Biol. 2005; 6(3):312. View in: Pubmed

      • Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005 Jan 28; 120(2):169-81. View in: Pubmed

      • Global nucleosome occupancy in yeast. Genome Biol. 2004; 5(9):R62. View in: Pubmed

      • Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem Biol. 2004 Mar; 11(3):295-9. View in: Pubmed

      • The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol. 2004; 376:349-60. View in: Pubmed

      • Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin. Mol Cell. 2003 Nov; 12(5):1325-32. View in: Pubmed

      • Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics. 2003 May 09; 4(1):19. View in: Pubmed

      • Signaling network model of chromatin. Cell. 2002 Dec 13; 111(6):771-8. View in: Pubmed

      • Global approaches to chromatin. Chem Biol. 2002 Nov; 9(11):1167-73. View in: Pubmed

      • Active genes are tri-methylated at K4 of histone H3. Nature. 2002 Sep 26; 419(6905):407-11. View in: Pubmed

      • Methylation of histone H3 Lys 4 in coding regions of active genes. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8695-700. View in: Pubmed

      • SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize. Development. 2002 Jun; 129(11):2663-73. View in: Pubmed

      • Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci U S A. 2000 Dec 05; 97(25):13708-13. View in: Pubmed

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      Dana-Farber Cancer Institute

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      Dana-Farber Cancer Institute

      450 Brookline Avenue LC 8313 Boston, MA 02215
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      42.3374, -71.1082