Bradley E. Bernstein - Publications

Affiliations: 
Biology: Medical Sciences, Division of Harvard University, Cambridge, MA, United States 
Area:
Genetics, Molecular Biology, Bioinformatics Biology

118 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any innacuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 McBrayer SK, Mayers JR, DiNatale GJ, Shi DD, Khanal J, Chakraborty AA, Sarosiek KA, Briggs KJ, Robbins AK, Sewastianik T, Shareef SJ, Olenchock BA, Parker SJ, Tateishi K, Spinelli JB, ... ... Bernstein BE, et al. Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. Cell. PMID 30220459 DOI: 10.1016/j.cell.2018.08.038  1
2018 Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nature Communications. 9: 3588. PMID 30181541 DOI: 10.1038/s41467-018-06052-0  1
2018 Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T. Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin. Molecular Cell. 70: 983. PMID 29883612 DOI: 10.1016/j.molcel.2018.05.012  1
2018 Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, ... ... Bernstein BE, et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science (New York, N.Y.). 360: 331-335. PMID 29674595 DOI: 10.1126/science.aao4750  1
2018 Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, ... ... Bernstein BE, et al. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 33: 785-787. PMID 29634952 DOI: 10.1016/j.ccell.2018.03.024  1
2017 Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, ... ... Bernstein BE, et al. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. PMID 29249691 DOI: 10.1016/j.ccell.2017.11.009  1
2017 Faber AC, Song KA, Niederst MJ, Lochmann TL, Hata AN, Kitai H, Ham J, Floros KV, Hicks MA, Hu H, Mulvey HE, Drier Y, Heisey DAR, Hughes MT, Patel NU, ... ... Bernstein BE, et al. Epithelial-to-mesenchymal transition antagonizes response to targeted therapies in lung cancer by suppressing BIM. Clinical Cancer Research : An Official Journal of the American Association For Cancer Research. PMID 29051323 DOI: 10.1158/1078-0432.CCR-17-1577  1
2017 Ryan RJH, Petrovic J, Rausch DM, Zhou Y, Lareau CA, Kluk MJ, Christie AL, Lee WY, Tarjan DR, Guo B, Donohue LKH, Gillespie SM, Nardi V, Hochberg EP, Blacklow SC, ... ... Bernstein BE, et al. A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Reports. 21: 784-797. PMID 29045844 DOI: 10.1016/j.celrep.2017.09.066  1
2017 Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, ... ... Bernstein BE, et al. Cohesin Loss Eliminates All Loop Domains. Cell. 171: 305-320.e24. PMID 28985562 DOI: 10.1016/j.cell.2017.09.026  1
2017 Shah N, Wang P, Wongvipat J, Karthaus WR, Abida W, Armenia J, Rockowitz S, Drier Y, Bernstein BE, Long HW, Freedman ML, Arora VK, Zheng D, Sawyers CL. Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer. Elife. 6. PMID 28891793 DOI: 10.7554/eLife.27861  1
2017 Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science (New York, N.Y.). 357. PMID 28729483 DOI: 10.1126/science.aal2380  1
2017 Miller TE, Liau BB, Wallace LC, Morton AR, Xie Q, Dixit D, Factor DC, Kim LJY, Morrow JJ, Wu Q, Mack SC, Hubert CG, Gillespie SM, Flavahan WA, Hoffmann T, ... ... Bernstein BE, et al. Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature. PMID 28678782 DOI: 10.1038/nature23000  1
2017 Venteicher AS, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin MG, Hovestadt V, Escalante LE, Shaw ML, Rodman C, Gillespie SM, Dionne D, Luo CC, Ravichandran H, Mylvaganam R, ... ... Bernstein BE, et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science (New York, N.Y.). 355. PMID 28360267 DOI: 10.1126/science.aai8478  1
2017 Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proceedings of the National Academy of Sciences of the United States of America. PMID 28137873 DOI: 10.1073/pnas.1621150114  1
2016 Venteicher AS, Tirosh I, Hebert C, Escalante L, Martuza RL, Nahed BV, Curry WT, Cahill DP, Bernstein B, Louis DN, Regev A, Suva M. 142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. Neurosurgery. 63: 158. PMID 28175463 DOI: 10.1227/01.neu.0000489712.44702.0d  1
2016 Liau BB, Sievers C, Donohue LK, Gillespie SM, Flavahan WA, Miller TE, Venteicher AS, Hebert CH, Carey CD, Rodig SJ, Shareef SJ, Najm FJ, van Galen P, Wakimoto H, Cahill DP, ... ... Bernstein BE, et al. Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell. PMID 27989769 DOI: 10.1016/j.stem.2016.11.003  1
2016 Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, ... Bernstein BE, et al. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nature Genetics. PMID 27941797 DOI: 10.1038/ng.3746  1
2016 Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, ... ... Bernstein BE, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. PMID 27806376 DOI: 10.1038/nature20123  1
2016 Venteicher AS, Tirosh I, Hebert C, Escalante L, Martuza RL, Nahed BV, Curry WT, Cahill DP, Bernstein B, Louis DN, Regev A, Suva M. 142 Genetic and Nongenetic Determinants of Cellular Architecture in IDH1-Mutant Oligodendrogliomas and Astrocytomas Using Single-Cell Transcriptome Analysis. Neurosurgery. 63: 158. PMID 27399421 DOI: 10.1227/01.neu.0000489712.44702.0d  1
2016 Xie Q, Wu Q, Kim L, Miller TE, Liau BB, Mack SC, Yang K, Factor DC, Fang X, Huang Z, Zhou W, Alazem K, Wang X, Bernstein BE, Bao S, et al. RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation. The Journal of Clinical Investigation. PMID 27322055 DOI: 10.1172/JCI86114  1
2016 Shema E, Jones D, Shoresh N, Donohue L, Ram O, Bernstein BE. Single-molecule decoding of combinatorially modified nucleosomes. Science (New York, N.Y.). 352: 717-21. PMID 27151869 DOI: 10.1126/science.aad7701  1
2016 G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biology. 17: 28. PMID 26883116 DOI: 10.1186/s13059-016-0878-3  1
2016 Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, ... ... Bernstein BE, et al. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nature Genetics. PMID 26829750 DOI: 10.1038/ng.3502  1
2015 Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. PMID 26700815 DOI: 10.1038/nature16490  1
2015 van Galen P, Viny AD, Ram O, Ryan RJ, Cotton MJ, Donohue L, Sievers C, Drier Y, Liau BB, Gillespie SM, Carroll KM, Cross MB, Levine RL, Bernstein BE. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Molecular Cell. PMID 26687680 DOI: 10.1016/j.molcel.2015.11.003  1
2015 Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nature Biotechnology. 33: 1165-72. PMID 26458175 DOI: 10.1038/nbt.3383  1
2015 Ryan RJ, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discovery. 5: 1058-71. PMID 26229090 DOI: 10.1158/2159-8290.CD-15-0370  1
2015 Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, Basu A, Bernstein BE, Weitz DA. High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. Plos One. 10: e0116328. PMID 26000628 DOI: 10.1371/journal.pone.0116328  1
2015 Gagliani N, Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR, Licona-Limón P, Paiva RS, Ching T, Weaver C, Zi X, Pan X, Fan R, Garmire LX, ... ... Bernstein B, et al. Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature. 523: 221-5. PMID 25924064 DOI: 10.1038/nature14452  1
2015 Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, ... ... Bernstein BE, et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 518: 355-9. PMID 25533951 DOI: 10.1038/nature13990  1
2015 Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, ... ... Bernstein BE, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 518: 337-43. PMID 25363779 DOI: 10.1038/nature13835  1
2014 Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, ... ... Bernstein BE, et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell. 26: 668-81. PMID 25453903 DOI: 10.1016/j.ccell.2014.10.004  1
2014 Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, ... Bernstein BE, et al. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proceedings of the National Academy of Sciences of the United States of America. 111: E4946-53. PMID 25369933 DOI: 10.1073/pnas.1407079111  1
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/pnas.1410434111  1
2014 Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Bernstein BE, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/nature13415  1
2014 De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, ... ... Bernstein BE, et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nature Neuroscience. 17: 1156-63. PMID 25129075 DOI: 10.1038/nn.3786  1
2014 Stoeck A, Lejnine S, Truong A, Pan L, Wang H, Zang C, Yuan J, Ware C, MacLean J, Garrett-Engele PW, Kluk M, Laskey J, Haines BB, Moskaluk C, Zawel L, ... ... Bernstein BE, et al. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discovery. 4: 1154-67. PMID 25104330 DOI: 10.1158/2159-8290.CD-13-0830  1
2014 Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science (New York, N.Y.). 344: 1396-401. PMID 24925914 DOI: 10.1126/science.1254257  1
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/pnas.1318948111  1
2014 Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, ... Bernstein BE, et al. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research. 24: 920-9. PMID 24752179 DOI: 10.1101/gr.168930.113  1
2014 Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, ... ... Bernstein BE, et al. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 157: 580-94. PMID 24726434 DOI: 10.1016/j.cell.2014.02.030  1
2014 Knoechel B, Roderick JE, Williamson KE, Zhu J, Lohr JG, Cotton MJ, Gillespie SM, Fernandez D, Ku M, Wang H, Piccioni F, Silver SJ, Jain M, Pearson D, Kluk MJ, ... ... Bernstein BE, et al. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nature Genetics. 46: 364-70. PMID 24584072 DOI: 10.1038/ng.2913  1
2013 Abdel-Wahab O, Gao J, Adli M, Dey A, Trimarchi T, Chung YR, Kuscu C, Hricik T, Ndiaye-Lobry D, Lafave LM, Koche R, Shih AH, Guryanova OA, Kim E, Li S, ... ... Bernstein BE, et al. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. The Journal of Experimental Medicine. 210: 2641-59. PMID 24218140 DOI: 10.1084/jem.20131141  1
2013 Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nature Biotechnology. 31: 1137-42. PMID 24108092 DOI: 10.1038/nbt.2726  1
2013 Isono K, Endo TA, Ku M, Yamada D, Suzuki R, Sharif J, Ishikura T, Toyoda T, Bernstein BE, Koseki H. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Developmental Cell. 26: 565-77. PMID 24091011 DOI: 10.1016/j.devcel.2013.08.016  1
2013 Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. Locus-specific editing of histone modifications at endogenous enhancers. Nature Biotechnology. 31: 1133-6. PMID 24013198 DOI: 10.1038/nbt.2701  1
2013 Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK. In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Research. 41: e181. PMID 23945932 DOI: 10.1093/nar/gkt716  1
2013 Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature. 500: 477-81. PMID 23925113 DOI: 10.1038/nature12433  1
2013 Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Reports. 3: 1567-79. PMID 23707066 DOI: 10.1016/j.celrep.2013.04.021  1
2013 Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, ... ... Bernstein BE, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/j.cell.2013.04.037  1
2013 Suvà ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science (New York, N.Y.). 339: 1567-70. PMID 23539597 DOI: 10.1126/science.1230184  1
2013 Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, ... ... Bernstein BE, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 152: 642-54. PMID 23333102 DOI: 10.1016/j.cell.2012.12.033  1
2012 Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, et al. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes & Development. 26: 2802-16. PMID 23249739 DOI: 10.1101/gad.207142.112  1
2012 Sebastián C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, MacDonald AI, McGlynn L, Maxwell F, ... ... Bernstein BE, et al. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 151: 1185-99. PMID 23217706 DOI: 10.1016/j.cell.2012.10.047  1
2012 Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Research. 72: 6319-24. PMID 23188507 DOI: 10.1158/0008-5472.CAN-12-3658  1
2012 Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biology. 13: R85. PMID 23034477 DOI: 10.1186/gb-2012-13-10-r85  1
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/gr.136184.111  1
2012 Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, ... ... Bernstein BE, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular Cell. 47: 810-22. PMID 22940246 DOI: 10.1016/j.molcel.2012.07.030  1
2012 Abdel-Wahab O, Adli M, LaFave LM, Gao J, Hricik T, Shih AH, Pandey S, Patel JP, Chung YR, Koche R, Perna F, Zhao X, Taylor JE, Park CY, Carroll M, ... ... Bernstein BE, et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 22: 180-93. PMID 22897849 DOI: 10.1016/j.ccr.2012.06.032  1
2012 Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, Toyoda T, Ito T, Eskeland R, Bickmore WA, Vidal M, Bernstein BE, Koseki H. Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. Plos Genetics. 8: e1002774. PMID 22844243 DOI: 10.1371/journal.pgen.1002774  1
2012 Koppikar P, Bhagwat N, Kilpivaara O, Manshouri T, Adli M, Hricik T, Liu F, Saunders LM, Mullally A, Abdel-Wahab O, Leung L, Weinstein A, Marubayashi S, Goel A, Gönen M, ... ... Bernstein BE, et al. Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature. 489: 155-9. PMID 22820254 DOI: 10.1038/nature11303  1
2012 Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 149: 1474-87. PMID 22726435 DOI: 10.1016/j.cell.2012.04.035  1
2012 Rheinbay E, Louis DN, Bernstein BE, Suvà ML. A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma. Cancer Cell. 21: 329-31. PMID 22439930 DOI: 10.1016/j.ccr.2012.03.001  1
2012 Mendenhall EM, Bernstein BE. DNA-protein interactions in high definition. Genome Biology. 13: 139. PMID 22283870 DOI: 10.1186/gb-2012-13-1-139  1
2011 Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, ... Bernstein BE, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 147: 1628-39. PMID 22196736 DOI: 10.1016/j.cell.2011.09.057  1
2011 Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. Plos Genetics. 7: e1002389. PMID 22174693 DOI: 10.1371/journal.pgen.1002389  1
2011 Zhao B, Zou J, Wang H, Johannsen E, Peng CW, Quackenbush J, Mar JC, Morton CC, Freedman ML, Blacklow SC, Aster JC, Bernstein BE, Kieff E. Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proceedings of the National Academy of Sciences of the United States of America. 108: 14902-7. PMID 21746931 DOI: 10.1073/pnas.1108892108  1
2011 Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL, Bernstein BE, Kieff E, Aster JC. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proceedings of the National Academy of Sciences of the United States of America. 108: 14908-13. PMID 21737748 DOI: 10.1073/pnas.1109023108  1
2011 Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 473: 43-9. PMID 21441907 DOI: 10.1038/nature09906  1
2011 Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, ... Bernstein BE, et al. Initial genome sequencing and analysis of multiple myeloma. Nature. 471: 467-72. PMID 21430775 DOI: 10.1038/nature09837  1
2011 Jiang H, Shukla A, Wang X, Chen WY, Bernstein BE, Roeder RG. Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell. 144: 513-25. PMID 21335234 DOI: 10.1016/j.cell.2011.01.020  1
2011 Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell. 8: 96-105. PMID 21211784 DOI: 10.1016/j.stem.2010.12.001  1
2011 Zhou VW, Goren A, Bernstein BE. Charting histone modifications and the functional organization of mammalian genomes. Nature Reviews. Genetics. 12: 7-18. PMID 21116306 DOI: 10.1038/nrg2905  1
2011 Li X, Isono K, Yamada D, Endo TA, Endoh M, Shinga J, Mizutani-Koseki Y, Otte AP, Casanova M, Kitamura H, Kamijo T, Sharif J, Ohara O, Toyada T, Bernstein BE, et al. 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. Molecular and Cellular Biology. 31: 351-64. PMID 21059868 DOI: 10.1128/MCB.00259-10  1
2010 Mendenhall EM, Koche RP, Truong T, Zhou VW, Issac B, Chi AS, Ku M, Bernstein BE. GC-rich sequence elements recruit PRC2 in mammalian ES cells. Plos Genetics. 6: e1001244. PMID 21170310 DOI: 10.1371/journal.pgen.1001244  1
2010 Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/nbt1010-1045  1
2010 Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Bernstein BE, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/nbt.1682  1
2010 Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE. Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 6: 591-602. PMID 20569696 DOI: 10.1016/j.stem.2010.03.016  1
2010 Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Digital transcriptome profiling from attomole-level RNA samples. Genome Research. 20: 519-25. PMID 20133332 DOI: 10.1101/gr.102129.109  1
2010 Li G, Margueron R, Ku M, Chambon P, Bernstein BE, Reinberg D. Jarid2 and PRC2, partners in regulating gene expression. Genes & Development. 24: 368-80. PMID 20123894 DOI: 10.1101/gad.1886410  1
2010 Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nature Methods. 7: 47-9. PMID 19946276 DOI: 10.1038/nmeth.1404  1
2009 Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Molecular Cell. 36: 682-95. PMID 19941827 DOI: 10.1016/j.molcel.2009.11.002  1
2009 Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.). 326: 289-93. PMID 19815776 DOI: 10.1126/science.1181369  1
2009 Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, ... ... Bernstein BE, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (New York, N.Y.). 326: 257-63. PMID 19729616 DOI: 10.1126/science.1179050  1
2009 Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America. 106: 11667-72. PMID 19571010 DOI: 10.1073/pnas.0904715106  1
2009 Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, ... Bernstein BE, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458: 223-7. PMID 19182780 DOI: 10.1038/nature07672  1
2009 Chi AS, Bernstein BE. Developmental biology. Pluripotent chromatin state. Science (New York, N.Y.). 323: 220-1. PMID 19131621 DOI: 10.1126/science.1166261  1
2008 Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview. Csh Protocols. 2008: pdb.top42. PMID 21356838 DOI: 10.1101/pdb.top42  1
2008 Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification. Csh Protocols. 2008: pdb.prot5004. PMID 21356836 DOI: 10.1101/pdb.prot5004  1
2008 Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription. Csh Protocols. 2008: pdb.prot5003. PMID 21356835 DOI: 10.1101/pdb.prot5003  1
2008 Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase. Csh Protocols. 2008: pdb.prot5002. PMID 21356834  1
2008 Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, ... ... Bernstein BE, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. Plos Genetics. 4: e1000242. PMID 18974828 DOI: 10.1371/journal.pgen.1000242  1
2008 Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 454: 766-70. PMID 18600261 DOI: 10.1038/nature07107  1
2008 Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature. 454: 49-55. PMID 18509334 DOI: 10.1038/nature07056  1
2008 Mendenhall EM, Bernstein BE. Chromatin state maps: new technologies, new insights. Current Opinion in Genetics & Development. 18: 109-15. PMID 18339538 DOI: 10.1016/j.gde.2008.01.010  1
2007 Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, ... ... Bernstein BE, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 448: 553-60. PMID 17603471 DOI: 10.1038/nature06008  1
2007 Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 448: 318-24. PMID 17554336 DOI: 10.1038/nature05944  1
2007 Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 128: 669-81. PMID 17320505 DOI: 10.1016/j.cell.2007.01.033  1
2006 Huebert DJ, Kamal M, O'Donovan A, Bernstein BE. Genome-wide analysis of histone modifications by ChIP-on-chip. Methods (San Diego, Calif.). 40: 365-9. PMID 17101450 DOI: 10.1016/j.ymeth.2006.07.032  1
2006 Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 125: 315-26. PMID 16630819 DOI: 10.1016/j.cell.2006.02.041  1
2005 Bernstein BE, Kellis M. Large-scale discovery and validation of functional elements in the human genome. Genome Biology. 6: 312. PMID 15774039 DOI: 10.1186/gb-2005-6-3-312  0.8
2005 Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, Schreiber SL, Lander ES. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 120: 169-81. PMID 15680324 DOI: 10.1016/j.cell.2005.01.001  1
2004 Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. Global nucleosome occupancy in yeast. Genome Biology. 5: R62. PMID 15345046 DOI: 10.1186/gb-2004-5-9-r62  1
2004 Humphrey EL, Shamji AF, Bernstein BE, Schreiber SL. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chemistry & Biology. 11: 295-9. PMID 15123258 DOI: 10.1016/j.chembiol.2004.03.001  1
2004 Bernstein BE, Humphrey EL, Liu CL, Schreiber SL. The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods in Enzymology. 376: 349-60. PMID 14975317 DOI: 10.1016/S0076-6879(03)76023-6  1
2003 Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin Molecular Cell. 12: 1325-1332. PMID 14636589 DOI: 10.1016/S1097-2765(03)00438-6  1
2003 Liu CL, Schreiber SL, Bernstein BE. Development and validation of a T7 based linear amplification for genomic DNA. Bmc Genomics. 4: 19. PMID 12740028 DOI: 10.1186/1471-2164-4-19  1
2002 Schreiber SL, Bernstein BE. Signaling network model of chromatin. Cell. 111: 771-8. PMID 12526804  1
2002 Bernstein BE, Schreiber SL. Global approaches to chromatin. Chemistry & Biology. 9: 1167-73. PMID 12445767  1
2002 Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature. 419: 407-11. PMID 12353038 DOI: 10.1038/nature01080  1
2002 Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, Schreiber SL. 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. 99: 8695-700. PMID 12060701 DOI: 10.1073/pnas.082249499  1
2000 Bernstein BE, Tong JK, Schreiber SL. Genomewide studies of histone deacetylase function in yeast. Proceedings of the National Academy of Sciences of the United States of America. 97: 13708-13. PMID 11095743 DOI: 10.1073/pnas.250477697  1
1998 Bernstein BE, Williams DM, Bressi JC, Kuhn P, Gelb MH, Blackburn GM, Hol WG. A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei. Journal of Molecular Biology. 279: 1137-48. PMID 9642090 DOI: 10.1006/jmbi.1998.1835  1
1998 Chandra NR, Muirhead H, Holbrook JJ, Bernstein BE, Hol WG, Sessions RB. A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. Proteins. 30: 372-80. PMID 9533621 DOI: 10.1002/(SICI)1097-0134(19980301)30:4<372::AID-PROT4>3.0.CO;2-L  1
1998 Bernstein BE, Hol WG. Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism. Biochemistry. 37: 4429-36. PMID 9521762 DOI: 10.1021/bi9724117  1
1998 Bernstein BE, Michels PA, Kim H, Petra PH, Hol WG. The importance of dynamic light scattering in obtaining multiple crystal forms of Trypanosoma brucei PGK. Protein Science : a Publication of the Protein Society. 7: 504-7. PMID 9521128 DOI: 10.1002/pro.5560070232  1
1997 Bernstein BE, Hol WG. Probing the limits of the molecular replacement method: the case of Trypanosoma brucei phosphoglycerate kinase. Acta Crystallographica. Section D, Biological Crystallography. 53: 756-64. PMID 15299865 DOI: 10.1107/S0907444997010214  1
1997 Bernstein BE, Michels PA, Hol WG. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Nature. 385: 275-8. PMID 9000079 DOI: 10.1038/385275a0  1
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