Bradley E Bernstein

Summary

Affiliation: Harvard University
Country: USA

Publications

  1. pmc DNA-protein interactions in high definition
    Eric M Mendenhall
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    Genome Biol 13:139. 2012
  2. pmc The NIH Roadmap Epigenomics Mapping Consortium
    Bradley E Bernstein
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1045-8. 2010
  3. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
  4. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
  5. pmc Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    Oren Ram
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 147:1628-39. 2011
  6. pmc Reprogramming factor expression initiates widespread targeted chromatin remodeling
    Richard P Koche
    Broad Institute, Cambridge, MA 02142, USA
    Cell Stem Cell 8:96-105. 2011
  7. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
  8. doi request reprint A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
  9. pmc Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    Casey A Gifford
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 153:1149-63. 2013
  10. pmc Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network
    Aviva Presser Aiden
    Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Cell Stem Cell 6:591-602. 2010

Collaborators

Detail Information

Publications34

  1. pmc DNA-protein interactions in high definition
    Eric M Mendenhall
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
    Genome Biol 13:139. 2012
    ..An elegant, genome-wide approach to define the precise DNA sequences bound by transcription factors has been developed by Rhee and Pugh...
  2. pmc The NIH Roadmap Epigenomics Mapping Consortium
    Bradley E Bernstein
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, USA
    Nat Biotechnol 28:1045-8. 2010
    ....
  3. pmc Genome-scale DNA methylation maps of pluripotent and differentiated cells
    Alexander Meissner
    Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:766-70. 2008
    ..More generally, the results establish reduced representation bisulphite sequencing as a powerful technology for epigenetic profiling of cell populations relevant to developmental biology, cancer and regenerative medicine...
  4. pmc Dissecting direct reprogramming through integrative genomic analysis
    Tarjei S Mikkelsen
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 454:49-55. 2008
    ..We demonstrate that RNA inhibition of transcription factors can facilitate reprogramming, and that treatment with DNA methyltransferase inhibitors can improve the overall efficiency of the reprogramming process...
  5. pmc Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells
    Oren Ram
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 147:1628-39. 2011
    ..Our work provides a multiplex method that substantially enhances the ability to monitor CR binding, presents a large resource of CR maps, and reveals common principles for combinatorial CR function...
  6. pmc Reprogramming factor expression initiates widespread targeted chromatin remodeling
    Richard P Koche
    Broad Institute, Cambridge, MA 02142, USA
    Cell Stem Cell 8:96-105. 2011
    ..Our data provide evidence for an early, organized, and population-wide epigenetic response to ectopic reprogramming factors that clarify the temporal order through which somatic identity is reset during reprogramming...
  7. pmc Digital transcriptome profiling from attomole-level RNA samples
    Fatih Ozsolak
    Helicos BioSciences Corporation, Cambridge, MA 02139, USA
    Genome Res 20:519-25. 2010
    ....
  8. doi request reprint A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals
    Manuel Garber
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Mol Cell 47:810-22. 2012
    ....
  9. pmc Transcriptional and epigenetic dynamics during specification of human embryonic stem cells
    Casey A Gifford
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 153:1149-63. 2013
    ....
  10. pmc Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network
    Aviva Presser Aiden
    Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
    Cell Stem Cell 6:591-602. 2010
    ..We suggest that Wilms cells share a transcriptional and epigenetic landscape with a normal renal stem cell, which is inherently susceptible to transformation and may represent a cell of origin for this disease...
  11. doi request reprint Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq
    Mazhar Adli
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
    Nat Protoc 6:1656-68. 2011
    ..In terms of the numbers of cells required, the method provides two to three orders of magnitude of improvement over the conventional ChIP-seq method and the entire procedure can be completed within 4 d...
  12. pmc Mapping and analysis of chromatin state dynamics in nine human cell types
    Jason Ernst
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 473:43-9. 2011
    ..Our study presents a general framework for deciphering cis-regulatory connections and their roles in disease...
  13. pmc Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses
    Ido Amit
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, MA 02142, USA
    Science 326:257-63. 2009
    ..This study establishes a broadly applicable, comprehensive, and unbiased approach to reveal the wiring and functions of a regulatory network controlling a major transcriptional response in primary mammalian cells...
  14. pmc Genome-wide chromatin state transitions associated with developmental and environmental cues
    Jiang Zhu
    Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
    Cell 152:642-54. 2013
    ..We describe how these global chromatin state transitions relate to chromosome and nuclear architecture, and discuss their implications for lineage fidelity, cellular senescence, and reprogramming...
  15. pmc Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA
    Alon Goren
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
    Nat Methods 7:47-9. 2010
    ..This method is compatible with just 50 pg of DNA and should thus facilitate charting chromatin maps from limited cell populations...
  16. pmc Genomic distribution and inter-sample variation of non-CpG methylation across human cell types
    Michael J Ziller
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
    PLoS Genet 7:e1002389. 2011
    ..In summary these results contribute further to our understanding of cytosine methylation patterns in human cells using a large representative sample set...
  17. ncbi request reprint In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state
    Marius Wernig
    Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, USA
    Nature 448:318-24. 2007
    ..Our results show that the biological potency and epigenetic state of in-vitro-reprogrammed induced pluripotent stem cells are indistinguishable from those of ES cells...
  18. pmc Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth
    Bo Zhao
    Department of Medicine, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:14902-7. 2011
    ..The primed RBL program likely supports antigen-induced proliferation...
  19. pmc Initial genome sequencing and analysis of multiple myeloma
    Michael A Chapman
    The Eli and Edythe L Broad Institute, 7 Cambridge Center, Cambridge, Massachusetts 02412, USA
    Nature 471:467-72. 2011
    ..These results indicate that cancer genome sequencing of large collections of samples will yield new insights into cancer not anticipated by existing knowledge...
  20. pmc GC-rich sequence elements recruit PRC2 in mammalian ES cells
    Eric M Mendenhall
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, United States of America
    PLoS Genet 6:e1001244. 2010
    ....
  21. pmc The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism
    Carlos Sebastian
    The Massachusetts General Hospital Cancer Center, Harvard Medical School, Boston, MA 02114, USA
    Cell 151:1185-99. 2012
    ..Our studies reveal SIRT6 to be a potent tumor suppressor acting to suppress cancer metabolism...
  22. pmc Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals
    Mitchell Guttman
    Broad Institute of MIT and Harvard, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA
    Nature 458:223-7. 2009
    ..Together, these results define a unique collection of functional lincRNAs that are highly conserved and implicated in diverse biological processes...
  23. doi request reprint Charting a dynamic DNA methylation landscape of the human genome
    Michael J Ziller
    Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
    Nature 500:477-81. 2013
    ..Therefore, our selected DMRs can serve as a starting point to guide new, more effective reduced representation approaches to capture the most informative fraction of CpGs, as well as further pinpoint putative regulatory elements. ..
  24. doi request reprint Charting histone modifications and the functional organization of mammalian genomes
    Vicky W Zhou
    Howard Hughes Medical Institute and Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts 02114, USA
    Nat Rev Genet 12:7-18. 2011
    ..Here we review a selection of recent studies that have probed histone modifications and successive layers of chromatin structure in mammalian genomes, the patterns that have been identified and future directions for research...
  25. pmc Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors
    Mazhar Adli
    Howard Hughes Medical Institute, Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
    Nat Methods 7:615-8. 2010
    ..We used the technique to characterize mouse hematopoietic progenitors and thereby gain insight into their developmental program...
  26. pmc Model-based analysis of ChIP-Seq (MACS)
    Yong Zhang
    Department of Biostatistics and Computational Biology, Dana Farber Cancer Institute and Harvard School of Public Health, Boston, MA 02115, USA
    Genome Biol 9:R137. 2008
    ..MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome, allowing for more robust predictions. MACS compares favorably to existing ChIP-Seq peak-finding algorithms, and is freely available...
  27. pmc Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression
    Ahmad M Khalil
    The Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142, USA
    Proc Natl Acad Sci U S A 106:11667-72. 2009
    ..We propose a model in which some lincRNAs guide chromatin-modifying complexes to specific genomic loci to regulate gene expression...
  28. pmc EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas
    Russell J H Ryan
    Department of Pathology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
    PLoS ONE 6:e28585. 2011
    ..Our work may be helpful in the selection of lymphoma patients for future trials of pharmacologic agents targeting EZH2 and EZH2-regulated pathways...
  29. pmc Genome-wide maps of chromatin state in pluripotent and lineage-committed cells
    Tarjei S Mikkelsen
    Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
    Nature 448:553-60. 2007
    ..This study provides a framework for the application of comprehensive chromatin profiling towards characterization of diverse mammalian cell populations...
  30. pmc Large-scale discovery and validation of functional elements in the human genome
    Bradley E Bernstein
    Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02139, USA
    Genome Biol 6:312. 2005
    ..A report on the genomics workshop 'Identification of Functional Elements in Mammalian Genomes', Cold Spring Harbor, New York, 11-13 November 2004...
  31. ncbi request reprint Genomic views of chromatin
    Dana J Huebert
    Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Curr Opin Genet Dev 15:476-81. 2005
    ..In parallel, state-of-the-art imaging techniques are being used to investigate higher-order chromatin organization, and are beginning to bridge our understanding of chromatin biology with that of chromosome structure...
  32. pmc Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning
    Kevin A Peterson
    Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, Massachusetts 02138, USA
    Genes Dev 26:2802-16. 2012
    ....
  33. pmc Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells
    Hongfang Wang
    Department of Pathology, Brigham and Women s Hospital, Boston, MA 02115, USA
    Proc Natl Acad Sci U S A 108:14908-13. 2011
    ..Thus, there is a conserved network of cis-regulatory factors that interacts with Notch1 to regulate gene expression in TLL cells, as well as unique classes of divergent RBPJ-only sites that also likely regulate transcription...
  34. pmc Global nucleosome occupancy in yeast
    Bradley E Bernstein
    Department of Chemistry and Chemical Biology, Bauer Center for Genomics Research, and Howard Hughes Medical Institute, Harvard University, 12 Oxford Street, Cambridge, MA 02138, USA
    Genome Biol 5:R62. 2004
    ..We systematically evaluated nucleosome occupancy in yeast promoters by immunoprecipitating nucleosomal DNA and quantifying enrichment by microarrays...