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Bradley Bernstein

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Mouse

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Oligonucleotide Array Sequence Analysis

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TOP 3
Jiang Zhu; James Y Zou; Mazhar Adli; David A Bennett; Ray Camahort; Chad A Cowan; Michael Coyne; Philip L De Jager; Vikram Deshpande; Timothy Durham; Charles B Epstein; Joseph A Houmard; Alexander Meissner; Mohammad Miri; Deborah M Muoio; Tamer T Onder; Noam Shoresh; Griet Verstappen; Xiaolan Zhang; Bradley E Bernstein
Genome-wide chromatin state transitions associated with developmental and environmental cues.
Kevin A Peterson; Leila Shokri; Alexander van Oudenaarden; Anastasia Vedenko; Wing H Wong; Xiaoxiao Zhang; Tarjei Mikkelsen; Yuichi Nishi; Timothy Lawrence Bailey; José-Manuel Baizabal; Bradley E Bernstein; Martha L Bulyk; Jan Philipp Junker; Wenxiu Ma; Matthew McFarlane; Andrew P McMahon
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.
Manuel Garber; Andreas Gnirke; Alon Goren; Mitchell Guttman; Nir Hacohen; Zohar Itzhaki; James Meldrim; Brian Minie; Chad Nusbaum; Oren Ram; Raktima Raychowdhury; Aviv Regev; James Robinson; Anne Thielke; Assaf Weiner; Bang Wong; Nir Yosef; Bradley E Bernstein; Ronnie Blecher-Gonen; Chamutal Bornstein; Christine Cheng; Nicolas Chevrier; Sheila Fisher; Nir Friedman; Dennis Friedrich; Daniela Amann-Zalcenstein; Ido Amit
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.

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All Publications

2013: Jiang Zhu; James Y Zou; Mazhar Adli; David A Bennett; Ray Camahort; Chad A Cowan; Michael Coyne; Philip L De Jager; Vikram Deshpande; Timothy Durham; Charles B Epstein; Joseph A Houmard; Alexander Meissner; Mohammad Miri; Deborah M Muoio; Tamer T Onder; Noam Shoresh; Griet Verstappen; Xiaolan Zhang; Bradley E Bernstein
Genome-wide chromatin state transitions associated with developmental and environmental cues.
Cell 2013;152(3):642-54.
2012: Kevin A Peterson; Leila Shokri; Alexander van Oudenaarden; Anastasia Vedenko; Wing H Wong; Xiaoxiao Zhang; Tarjei Mikkelsen; Yuichi Nishi; Timothy Lawrence Bailey; José-Manuel Baizabal; Bradley E Bernstein; Martha L Bulyk; Jan Philipp Junker; Wenxiu Ma; Matthew McFarlane; Andrew P McMahon
Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning.
Genes & development 2012;26(24):2802-16.
2012: Manuel Garber; Andreas Gnirke; Alon Goren; Mitchell Guttman; Nir Hacohen; Zohar Itzhaki; James Meldrim; Brian Minie; Chad Nusbaum; Oren Ram; Raktima Raychowdhury; Aviv Regev; James Robinson; Anne Thielke; Assaf Weiner; Bang Wong; Nir Yosef; Bradley E Bernstein; Ronnie Blecher-Gonen; Chamutal Bornstein; Christine Cheng; Nicolas Chevrier; Sheila Fisher; Nir Friedman; Dennis Friedrich; Daniela Amann-Zalcenstein; Ido Amit
A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals.
Molecular cell 2012;47(5):810-22.
2012: Russell J H Ryan; Bradley E Bernstein
Molecular biology. Genetic events that shape the cancer epigenome.
Science (New York, N.Y.) 2012;336(6088):1513-4.
2011: Jason Ernst; Pouya Kheradpour; Tarjei S Mikkelsen; Noam Shoresh; Lucas D Ward; Charles B Epstein; Xiaolan Zhang; Li Wang; Robbyn Issner; Michael Coyne; Manching Ku; Timothy Durham; Manolis Kellis; Bradley E Bernstein
Mapping and analysis of chromatin state dynamics in nine human cell types.
Nature 2011;473(7345):43-9.
2011: Richard P Koche; Zachary D Smith; Mazhar Adli; Hongcang Gu; Manching Ku; Andreas Gnirke; Bradley E Bernstein; Alexander Meissner
Reprogramming factor expression initiates widespread targeted chromatin remodeling.
Cell stem cell 2011;8(1):96-105.
2010: Aviva Presser Aiden; Miguel N Rivera; Esther Rheinbay; Manching Ku; Erik J Coffman; Thanh T Truong; Sara O Vargas; Eric S Lander; Daniel A Haber; Bradley E Bernstein
Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network.
Cell stem cell 2010;6(6):591-602.
2010: Fatih Ozsolak; Alon Goren; Melissa Gymrek; Mitchell Guttman; Aviv Regev; Bradley E Bernstein; Patrice M Milos
Digital transcriptome profiling from attomole-level RNA samples.
Genome research 2010;20(4):519-25.
2010: Alon Goren; Fatih Ozsolak; Noam Shoresh; Manching Ku; Mazhar Adli; Chris Hart; Melissa Gymrek; Or Zuk; Aviv Regev; Patrice M Milos; Bradley E Bernstein
Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA.
Nature methods 2010;7(1):47-9.
2009: Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley E Bernstein; MA Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
Science (New York, N.Y.) 2009;326(5950):289-93.
2009: Ido Amit; manuel garber; Nicolas Chevrier; Ana Paula Leite; Yoni Donner; Thomas Eisenhaure; Mitchell Guttman; Jennifer K Grenier; Weibo Li; Or Zuk; Lisa A Schubert; Brian Birditt; Tal Shay; Alon Goren; Xiaolan Zhang; Zachary Smith; Raquel Deering; Rebecca C McDonald; Moran Cabili; Bradley E Bernstein; John L Rinn; Alex Meissner; David E Root; Nir Hacohen; Aviv Regev
Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses.
Science (New York, N.Y.) 2009;326(5950):257-63.
2009: Mitchell Guttman; Ido Amit; manuel garber; Courtney French; Michael F Lin; David M. Feldser; Maite Huarte; Or Zuk; Bryce W Carey; John P Cassady; Moran N Cabili; Rudolf Jaenisch; Tarjei S Mikkelsen; Tyler Jacks; Nir Hacohen; Bradley E Bernstein; Manolis Kellis; Aviv Regev; John L Rinn; Eric S Lander
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.
Nature 2009;458(7235):223-7.
2009: Andrew S Chi; Bradley E Bernstein
Developmental biology. Pluripotent chromatin state.
Science (New York, N.Y.) 2009;323(5911):220-1.
2008: Manching Ku; Richard P Koche; Esther Rheinbay; Eric M Mendenhall; Mitsuhiro Endoh; Tarjei S Mikkelsen; Aviva Presser; Chad Nusbaum; Xiaohui Xie; Andrew S Chi; Mazhar Adli; Simon Kasif; Leon M Ptaszek; Chad A Cowan; Eric S Lander; Haruhiko Koseki; Bradley E Bernstein
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
PLoS genetics 2008;4(10):e1000242.
2008: Alexander Meissner; Tarjei S Mikkelsen; Hongcang Gu; Marius Wernig; Jacob Hanna; Andrey Sivachenko; Xiaolan Zhang; Bradley E Bernstein; Chad Nusbaum; David B Jaffe; Andreas Gnirke; Rudolf Jaenisch; Eric S Lander
Genome-scale DNA methylation maps of pluripotent and differentiated cells.
Nature 2008;454(7205):766-70.
2008: Tarjei S Mikkelsen; Jacob Hanna; Xiaolan Zhang; Manching Ku; Marius Wernig; Patrick Schorderet; Bradley E Bernstein; Rudolf Jaenisch; Eric S Lander; Alexander Meissner
Dissecting direct reprogramming through integrative genomic analysis.
Nature 2008;454(7200):49-55.
2008: Eric M Mendenhall; Bradley E Bernstein
Chromatin state maps: new technologies, new insights.
Current opinion in genetics & development 2008;18(2):109-15.
2007: Tarjei S Mikkelsen; Manching Ku; David B Jaffe; Biju Issac; Erez Lieberman; Georgia Giannoukos; Pablo Alvarez; William Brockman; Tae Kyoung Kim; Richard P Koche; William Lee; Eric Mendenhall; Aisling O'Donovan; Aviva Presser; Carsten Russ; Xiaohui Xie; Alexander Meissner; Marius Wernig; Rudolf Jaenisch; Chad Nusbaum; Eric S Lander; Bradley E Bernstein
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Nature 2007;448(7153):553-60.
2007: Marius Wernig; Alexander Meissner; Ruth Foreman; Tobias Brambrink; Manching Ku; Konrad Hochedlinger; Bradley E Bernstein; Rudolf Jaenisch
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state.
Nature 2007;448(7151):318-24.
2007: Bradley E Bernstein; Alexander Meissner; Eric S Lander
The mammalian epigenome.
Cell 2007;128(4):669-81.
2006: Dana J Huebert; Michael Kamal; Aisling O'Donovan; Bradley E Bernstein
Genome-wide analysis of histone modifications by ChIP-on-chip.
Methods (San Diego, Calif.) 2006;40(4):365-9.
2006: Melissa M Steward; Jung-Shin Lee; Aisling O'Donovan; Matt Wyatt; Bradley E Bernstein; Ali Shilatifard
Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes.
Nature structural & molecular biology 2006;13(9):852-4.
2006: Bradley E Bernstein; Tarjei S Mikkelsen; Xiaohui Xie; Michael Kamal; Dana J Huebert; James Cuff; Ben Fry; Alexander Meissner; Marius Wernig; Kathrin Plath; Rudolf Jaenisch; Alexandre Wagschal; Robert Feil; Stuart L Schreiber; Eric S Lander
A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Cell 2006;125(2):315-26.
2005: Dana J Huebert; Bradley E Bernstein
Genomic views of chromatin.
Current opinion in genetics & development 2005;15(5):476-81.
2005: Bradley E Bernstein; Michael Kamal; Kerstin Lindblad-Toh; Stefan Bekiranov; Dione K Bailey; Dana J Huebert; Scott McMahon; Elinor K. Karlsson; Edward J Kulbokas; Thomas Gingeras; Stuart L Schreiber; Eric S Lander
Genomic maps and comparative analysis of histone modifications in human and mouse.
Cell 2005;120(2):169-81.
2005: Bradley E Bernstein; Manolis Kellis
Large-scale discovery and validation of functional elements in the human genome.
Genome biology 2005;6(3):312.
2004: Emily Humphrey-Dixon; Alykhan F Shamji; Bradley E Bernstein; Stuart L Schreiber
Rpd3p relocation mediates a transcriptional response to rapamycin in yeast.
Chemistry & biology 2004;11(3):295-9.
2004: Bradley E Bernstein; Chih Long Liu; Emily Humphrey-Dixon; Ethan O Perlstein; Stuart L Schreiber
Global nucleosome occupancy in yeast.
Genome biology 2004;5(9):R62.
2004: Bradley E Bernstein; Emily Humphrey-Dixon; Chih Long Liu; Stuart L Schreiber
The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications.
Methods in enzymology 2004;376():349-60.
2003: Chih Long Liu; Stuart L Schreiber; Bradley E Bernstein
Development and validation of a T7 based linear amplification for genomic DNA.
BMC genomics 2003;4(1):19.
2002: Stuart L Schreiber; Bradley E Bernstein
Signaling network model of chromatin.
Cell 2002;111(6):771-8.
2002: Bradley E Bernstein; Stuart L Schreiber
Global approaches to chromatin.
Chemistry & biology 2002;9(11):1167-73.
2002: Bradley E Bernstein; Emily Humphrey-Dixon; Rachel L Erlich; Robert Schneider; Peter Bouman; Jun Liu; Tony Kouzarides; Stuart L Schreiber
Methylation of histone H3 Lys 4 in coding regions of active genes.
Proceedings of the National Academy of Sciences of the United States of America 2002;99(13):8695-700.
2000: Bradley E Bernstein; JK Tong; Stuart L Schreiber
Genomewide studies of histone deacetylase function in yeast.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(25):13708-13.