Harvard Catalyst Profiles

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Bradley E. Bernstein, M.D., Ph.D.

Title
Institution
Department
Address
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Research
The research activities and funding listed below are automatically derived from NIH ExPORTER and other sources, which might result in incorrect or missing items. Faculty can login to make corrections and additions.
  1. UM1HG009390 (BERNSTEIN, BRADLEY EVAN) Feb 1, 2017 - Jan 31, 2021
    NIH/NHGRI
    A Catalog of Cell Types and Genomic Elements in Tissues, Organoids and Disease
    Role: Principal Investigator
  2. R01HG009269 (BERNSTEIN, BRADLEY EVAN) Sep 28, 2016 - Jul 31, 2020
    NIH/NHGRI
    Single-molecule systems for decoding combinatorial chromatin modifications
    Role: Principal Investigator
  3. DP1CA216873 (BERNSTEIN, BRADLEY EVAN) Sep 21, 2016 - Jul 31, 2021
    NIH/NCI
    Epigenetic plasticity in tumor initiation and evolution
    Role: Principal Investigator
  4. U54HG006991 (BERNSTEIN, BRADLEY EVAN) Sep 21, 2012 - Jul 31, 2017
    NIH/NHGRI
    Expanding the catalog of chromatin regulatory elements in the human genome
    Role: Principal Investigator
  5. U01ES017155 (BERNSTEIN, BRADLEY EVAN) Sep 29, 2008 - Sep 30, 2013
    NIH/NIEHS
    Production sequencing of reference human epigenomes
    Role: Principal Investigator

Bibliographic
Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
  1. Pastore A, Gaiti F, Lu SX, Brand RM, Kulm S, Chaligne R, Gu H, Huang KY, Stamenova EK, Béguelin W, Jiang Y, Schulman RC, Kim KT, Alonso A, Allan JN, Furman RR, Gnirke A, Wu CJ, Melnick AM, Meissner A, Bernstein BE, Abdel-Wahab O, Landau DA. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nat Commun. 2019 04 23; 10(1):1874. PMID: 31015400.
    Citations:    
  2. van Galen P, Hovestadt V, Wadsworth Ii MH, Hughes TK, Griffin GK, Battaglia S, Verga JA, Stephansky J, Pastika TJ, Lombardi Story J, Pinkus GS, Pozdnyakova O, Galinsky I, Stone RM, Graubert TA, Shalek AK, Aster JC, Lane AA, Bernstein BE. Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. Cell. 2019 Mar 07; 176(6):1265-1281.e24. PMID: 30827681.
    Citations:    
  3. Yassin M, Aqaqe N, Yassin AA, van Galen P, Kugler E, Bernstein BE, Koren-Michowitz M, Canaani J, Nagler A, Lechman ER, Dick JE, Wienholds E, Izraeli S, Milyavsky M. 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 Jan 31. PMID: 30705411.
    Citations:    Fields:    
  4. Shema E, Bernstein BE, Buenrostro JD. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nat Genet. 2019 01; 51(1):19-25. PMID: 30559489.
    Citations:    Fields:    
  5. Klein HU, McCabe C, Gjoneska E, Sullivan SE, Kaskow BJ, Tang A, Smith RV, Xu J, Pfenning AR, Bernstein BE, Meissner A, Schneider JA, Mostafavi S, Tsai LH, Young-Pearse TL, Bennett DA, De Jager PL. 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. PMID: 30559478.
    Citations:    Fields:    
  6. 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, Islam M, Haigis MC, Looper RE, Ligon KL, Bernstein BE, Carrasco RD, Cahill DP, Asara JM, Metallo CM, Yennawar NH, Vander Heiden MG, Kaelin WG. Transaminase Inhibition by 2-Hydroxyglutarate Impairs Glutamate Biosynthesis and Redox Homeostasis in Glioma. Cell. 2018 09 20; 175(1):101-116.e25. PMID: 30220459.
    Citations:    
  7. Rahme GJ, Gaskell E, Bernstein BE. GABPß1L Wakes Up TERT. Cancer Cell. 2018 09 10; 34(3):358-360. PMID: 30205042.
    Citations:    Fields:    
  8. 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. Nat Commun. 2018 09 04; 9(1):3588. PMID: 30181541.
    Citations:    Fields:    Translation:HumansCells
  9. 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. Mol Cell. 2018 06 07; 70(5):983. PMID: 29883612.
    Citations:    Fields:    
  10. 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, van Galen P, Bonal DM, Nguyen QD, Beck A, Sinai C, Czech T, Dorfer C, Goumnerova L, Lavarino C, Carcaboso AM, Mora J, Mylvaganam R, Luo CC, Peyrl A, Popovic M, Azizi A, Batchelor TT, Frosch MP, Martinez-Lage M, Kieran MW, Bandopadhayay P, Beroukhim R, Fritsch G, Getz G, Rozenblatt-Rosen O, Wucherpfennig KW, Louis DN, Monje M, Slavc I, Ligon KL, Golub TR, Regev A, Bernstein BE, Suvà ML. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science. 2018 04 20; 360(6386):331-335. PMID: 29674595.
    Citations: 2     Fields:    Translation:HumansCells
  11. 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, Roberts J, Witkin M, Rapaport F, Teruya-Feldstein J, Qi J, Rampal R, Bernstein BE, Bradner JE, Levine RL. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 04 09; 33(4):785-787. PMID: 29634952.
    Citations: 1     Fields:    
  12. Finucane HK, Reshef YA, Anttila V, Slowikowski K, Gusev A, Byrnes A, Gazal S, Loh PR, Lareau C, Shoresh N, Genovese G, Saunders A, Macosko E, Pollack S, Perry JRB, Buenrostro JD, Bernstein BE, Raychaudhuri S, McCarroll S, Neale BM, Price AL. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nat Genet. 2018 04; 50(4):621-629. PMID: 29632380.
    Citations: 3     Fields:    
  13. Najm FJ, Strand C, Donovan KF, Hegde M, Sanson KR, Vaimberg EW, Sullender ME, Hartenian E, Kalani Z, Fusi N, Listgarten J, Younger ST, Bernstein BE, Root DE, Doench JG. Orthologous CRISPR-Cas9 enzymes for combinatorial genetic screens. Nat Biotechnol. 2018 02; 36(2):179-189. PMID: 29251726.
    Citations: 10     Fields:    Translation:HumansCells
  14. 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, Roberts J, Witkin M, Rapaport F, Teruya-Feldstein J, Qi J, Rampal R, Bernstein BE, Bradner JE, Levine RL. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 2018 01 08; 33(1):29-43.e7. PMID: 29249691.
    Citations: 3     Fields:    Translation:AnimalsCells
  15. Puram SV, Tirosh I, Parikh AS, Patel AP, Yizhak K, Gillespie S, Rodman C, Luo CL, Mroz EA, Emerick KS, Deschler DG, Varvares MA, Mylvaganam R, Rozenblatt-Rosen O, Rocco JW, Faquin WC, Lin DT, Regev A, Bernstein BE. Single-Cell Transcriptomic Analysis of Primary and Metastatic Tumor Ecosystems in Head and Neck Cancer. Cell. 2017 Dec 14; 171(7):1611-1624.e24. PMID: 29198524.
    Citations: 19     Fields:    Translation:HumansCells
  16. 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, Lockerman EL, Garcia A, Gillepsie S, Archibald HL, Gomez-Caraballo M, Nulton TJ, Windle BE, Piotrowska Z, Sahingur SE, Taylor SM, Dozmorov M, Sequist LV, Bernstein B, Ebi H, Engelman JA, Faber AC. 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. PMID: 29051323.
    Citations: 1     Fields:    
  17. 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, Weinstock DM, Faryabi RB, Bernstein BE, Aster JC, Pear WS. A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Rep. 2017 Oct 17; 21(3):784-797. PMID: 29045844.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  18. 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, Omer AD, Robinson JT, Schlick T, Bernstein BE, Casellas R, Lander ES, Aiden EL. Cohesin Loss Eliminates All Loop Domains. Cell. 2017 Oct 05; 171(2):305-320.e24. PMID: 28985562.
    Citations: 50     Fields:    Translation:HumansCells
  19. 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. 2017 09 11; 6. PMID: 28891793.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  20. Gupta RM, Hadaya J, Trehan A, Zekavat SM, Roselli C, Klarin D, Emdin CA, Hilvering CRE, Bianchi V, Mueller C, Khera AV, Ryan RJH, Engreitz JM, Issner R, Shoresh N, Epstein CB, de Laat W, Brown JD, Schnabel RB, Bernstein BE, Kathiresan S. 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. PMID: 28753427.
    Citations: 21     Fields:    Translation:HumansCells
  21. Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science. 2017 Jul 21; 357(6348). PMID: 28729483.
    Citations: 29     Fields:    Translation:HumansCells
  22. 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, Thummalapalli R, Hemann MT, Paddison PJ, Horbinski CM, Zuber J, Scacheri PC, Bernstein BE, Tesar PJ, Rich JN. Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature. 2017 07 20; 547(7663):355-359. PMID: 28678782.
    Citations: 17     Fields:    Translation:HumansAnimalsCells
  23. 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, Mount C, Onozato ML, Nahed BV, Wakimoto H, Curry WT, Iafrate AJ, Rivera MN, Frosch MP, Golub TR, Brastianos PK, Getz G, Patel AP, Monje M, Cahill DP, Rozenblatt-Rosen O, Louis DN, Bernstein BE, Regev A, Suvà ML. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science. 2017 03 31; 355(6332). PMID: 28360267.
    Citations: 38     Fields:    Translation:HumansCells
  24. 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. Proc Natl Acad Sci U S A. 2017 02 14; 114(7):E1291-E1300. PMID: 28137873.
    Citations: 10     Fields:    Translation:AnimalsCells
  25. 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, Rich JN, Aster JC, Suvà ML, Patel AP, Bernstein BE. Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell. 2017 02 02; 20(2):233-246.e7. PMID: 27989769.
    Citations: 18     Fields:    Translation:HumansCells
  26. 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, Park PJ, Roberts CW. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nat Genet. 2017 Feb; 49(2):289-295. PMID: 27941797.
    Citations: 15     Fields:    Translation:HumansCells
  27. 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, Francis JM, Patel AA, Onozato ML, Riggi N, Livak KJ, Gennert D, Satija R, Nahed BV, Curry WT, Martuza RL, Mylvaganam R, Iafrate AJ, Frosch MP, Golub TR, Rivera MN, Getz G, Rozenblatt-Rosen O, Cahill DP, Monje M, Bernstein BE, Louis DN, Regev A, Suvà ML. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. 2016 11 10; 539(7628):309-313. PMID: 27806376.
    Citations: 60     Fields:    Translation:HumansCells
  28. 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. 2016 Aug; 63 Suppl 1:158. PMID: 27399421.
    Citations:    
  29. 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, Rich JN. RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation. J Clin Invest. 2016 07 01; 126(7):2757-72. PMID: 27322055.
    Citations: 6     Fields:    Translation:HumansAnimalsCells
  30. Shema E, Jones D, Shoresh N, Donohue L, Ram O, Bernstein BE. Single-molecule decoding of combinatorially modified nucleosomes. Science. 2016 May 06; 352(6286):717-21. PMID: 27151869.
    Citations: 25     Fields:    Translation:HumansAnimalsCells
  31. G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biol. 2016 Feb 16; 17:28. PMID: 26883116.
    Citations: 43     Fields:    Translation:HumansCells
  32. 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, Bradner JE, Moskaluk CA, Aster JC, Knoechel B, Bernstein BE. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nat Genet. 2016 Mar; 48(3):265-72. PMID: 26829750.
    Citations: 29     Fields:    Translation:HumansCells
  33. 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. 2016 Jan 07; 529(7584):110-4. PMID: 26700815.
    Citations: 153     Fields:    Translation:HumansCells
  34. 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. Mol Cell. 2016 Jan 07; 61(1):170-80. PMID: 26687680.
    Citations: 9     Fields:    Translation:HumansCells
  35. 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. Nat Biotechnol. 2015 Nov; 33(11):1165-72. PMID: 26458175.
    Citations: 98     Fields:    Translation:HumansAnimalsCells
  36. Renneville A, Van Galen P, Canver MC, McConkey M, Krill-Burger JM, Dorfman DM, Holson EB, Bernstein BE, Orkin SH, Bauer DE, Ebert BL. EHMT1 and EHMT2 inhibition induces fetal hemoglobin expression. Blood. 2015 Oct 15; 126(16):1930-9. PMID: 26320100.
    Citations: 13     Fields:    Translation:HumansAnimalsCells
  37. 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 Discov. 2015 Oct; 5(10):1058-71. PMID: 26229090.
    Citations: 23     Fields:    Translation:HumansCells
  38. 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. 2015; 10(5):e0116328. PMID: 26000628.
    Citations: 18     Fields:    
  39. Gagliani N, Amezcua 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, Cotton MJ, Drier Y, Bernstein B, Geginat J, Stockinger B, Esplugues E, Huber S, Flavell RA. Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature. 2015 Jul 09; 523(7559):221-5. PMID: 25924064.
    Citations: 139     Fields:    Translation:AnimalsCells
  40. Dahlberg A, Woo S, Delaney C, Boyle P, Gnirke A, Bock C, Bernstein BE, Meissner A, Gottardo R, Bernstein ID. Notch-mediated expansion of cord blood progenitors: maintenance of transcriptional and epigenetic fidelity. Leukemia. 2015 Sep; 29(9):1948-51. PMID: 25742749.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  41. Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, Sarkar A, Quon G, Sandstrom RS, Eaton ML, Wu YC, Pfenning AR, Wang X, Claussnitzer M, Liu Y, Coarfa C, Harris RA, Shoresh N, Epstein CB, Gjoneska E, Leung D, Xie W, Hawkins RD, Lister R, Hong C, Gascard P, Mungall AJ, Moore R, Chuah E, Tam A, Canfield TK, Hansen RS, Kaul R, Sabo PJ, Bansal MS, Carles A, Dixon JR, Farh KH, Feizi S, Karlic R, Kim AR, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer TR, Neph SJ, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari RC, Siebenthall KT, Sinnott-Armstrong NA, Stevens M, Thurman RE, Wu J, Zhang B, Zhou X, Beaudet AE, Boyer LA, De Jager PL, Farnham PJ, Fisher SJ, Haussler D, Jones SJ, Li W, Marra MA, McManus MT, Sunyaev S, Thomson JA, Tlsty TD, Tsai LH, Wang W, Waterland RA, Zhang MQ, Chadwick LH, Bernstein BE, Costello JF, Ecker JR, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos JA, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature. 2015 Feb 19; 518(7539):317-30. PMID: 25693563.
    Citations: 964     Fields:    Translation:HumansCells
  42. Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cachiarelli D, Tsankov A, Epstein C, Rinn JR, Mikkelsen TS, Kohlbacher O, Gnirke A, Bernstein BE, Elkabetz Y, Meissner A. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 2015 Feb 19; 518(7539):355-359. PMID: 25533951.
    Citations: 48     Fields:    Translation:HumansCells
  43. 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, Blacklow SC, Liu XS, Aster JC, Pear WS. 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. PMID: 25369933.
    Citations: 45     Fields:    Translation:HumansAnimalsCells
  44. 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, Ting DT, Hornicek FJ, Nielsen GP, Stamenkovic I, Aryee MJ, Bernstein BE, Rivera MN. 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. PMID: 25453903.
    Citations: 52     Fields:    Translation:HumansAnimalsCells
  45. 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, De Jager PL, Kuchroo VK, Epstein CB, Daly MJ, Hafler DA, Bernstein BE. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 2015 Feb 19; 518(7539):337-43. PMID: 25363779.
    Citations: 324     Fields:    Translation:HumansCells
  46. 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, Egelhofer TA, Hu SS, Alekseyenko AA, Rechtsteiner A, Asker D, Belsky JA, Bowman SK, Chen QB, Chen RA, Day DS, Dong Y, Dose AC, Duan X, Epstein CB, Ercan S, Feingold EA, Ferrari F, Garrigues JM, Gehlenborg N, Good PJ, Haseley P, He D, Herrmann M, Hoffman MM, Jeffers TE, Kharchenko PV, Kolasinska-Zwierz P, Kotwaliwale CV, Kumar N, Langley SA, Larschan EN, Latorre I, Libbrecht MW, Lin X, Park R, Pazin MJ, Pham HN, Plachetka A, Qin B, Schwartz YB, Shoresh N, Stempor P, Vielle A, Wang C, Whittle CM, Xue H, Kingston RE, Kim JH, Bernstein BE, Dernburg AF, Pirrotta V, Kuroda MI, Noble WS, Tullius TD, Kellis M, MacAlpine DM, Strome S, Elgin SC, Liu XS, Lieb JD, Ahringer J, Karpen GH, Park PJ. Comparative analysis of metazoan chromatin organization. Nature. 2014 Aug 28; 512(7515):449-52. PMID: 25164756.
    Citations: 86     Fields:    Translation:HumansAnimalsCells
  47. 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, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos J, Weng Z, White KP, Hardison RC. 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. PMID: 25275169.
    Citations: 1     Fields:    Translation:Humans
  48. 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, Chai HS, Younkin C, Younkin SG, Zou F, Szyf M, Epstein CB, Schneider JA, Bernstein BE, Meissner A, Ertekin-Taner N, Chibnik LB, Kellis M, Mill J, Bennett DA. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nat Neurosci. 2014 Sep; 17(9):1156-63. PMID: 25129075.
    Citations: 126     Fields:    Translation:HumansCells
  49. 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, Fawell S, Gilliland G, Zhang T, Kremer BE, Knoechel B, Bernstein BE, Pear WS, Liu XS, Aster JC, Sathyanarayanan S. Discovery of biomarkers predictive of GSI response in triple-negative breast cancer and adenoid cystic carcinoma. Cancer Discov. 2014 Oct; 4(10):1154-67. PMID: 25104330.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  50. 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, Brockdorff N, Koseki H. 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. PMID: 24951669.
    Citations:    
  51. 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. 2014 Jun 20; 344(6190):1396-401. PMID: 24925914.
    Citations: 519     Fields:    Translation:Humans
  52. 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, Rubin EM, Visel A, Pennacchio LA. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Res. 2014 Jun; 24(6):920-9. PMID: 24752179.
    Citations: 22     Fields:    Translation:AnimalsCells
  53. 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, Giddings MC, Gilbert DM, Gingeras TR, Green ED, Guigo R, Hubbard T, Kent J, Lieb JD, Myers RM, Pazin MJ, Ren B, Stamatoyannopoulos JA, Weng Z, White KP, Hardison RC. Defining functional DNA elements in the human genome. Proc Natl Acad Sci U S A. 2014 Apr 29; 111(17):6131-8. PMID: 24753594.
    Citations: 164     Fields:    Translation:HumansCells
  54. 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, Beik S, Kadri S, Tirosh I, Wortman I, Shalek AK, Rozenblatt-Rosen O, Regev A, Louis DN, Bernstein BE. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 2014 Apr 24; 157(3):580-94. PMID: 24726434.
    Citations: 186     Fields:    Translation:HumansCells
  55. 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, Ott CJ, Shultz LD, Brehm MA, Greiner DL, Gutierrez A, Stegmaier K, Kung AL, Root DE, Bradner JE, Aster JC, Kelliher MA, Bernstein BE. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nat Genet. 2014 Apr; 46(4):364-70. PMID: 24584072.
    Citations: 78     Fields:    Translation:HumansAnimalsCells
  56. 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, Pandey S, Shin JY, Telis L, Liu J, Bhatt PK, Monette S, Zhao X, Mason CE, Park CY, Bernstein BE, Aifantis I, Levine RL. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. J Exp Med. 2013 Nov 18; 210(12):2641-59. PMID: 24218140.
    Citations: 69     Fields:    Translation:HumansAnimalsCells
  57. 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. Nat Biotechnol. 2013 Dec; 31(12):1137-42. PMID: 24108092.
    Citations: 145     Fields:    Translation:HumansCells
  58. 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. Dev Cell. 2013 Sep 30; 26(6):565-77. PMID: 24091011.
    Citations: 41     Fields:    Translation:AnimalsCells
  59. Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. Locus-specific editing of histone modifications at endogenous enhancers. Nat Biotechnol. 2013 Dec; 31(12):1133-6. PMID: 24013198.
    Citations: 127     Fields:    Translation:Cells
  60. 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 Res. 2013 Oct; 41(19):e181. PMID: 23945932.
    Citations: 23     Fields:    Translation:HumansCells
  61. 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. 2013 Aug 22; 500(7463):477-81. PMID: 23925113.
    Citations: 389     Fields:    Translation:HumansCells
  62. 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 Rep. 2013 May 30; 3(5):1567-79. PMID: 23707066.
    Citations: 59     Fields:    Translation:HumansCells
  63. 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, Guttman M, Epstein C, Park H, Kohlbacher O, Rinn J, Gnirke A, Lander ES, Bernstein BE, Meissner A. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 2013 May 23; 153(5):1149-63. PMID: 23664763.
    Citations: 148     Fields:    Translation:HumansCells
  64. Suvà ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science. 2013 Mar 29; 339(6127):1567-70. PMID: 23539597.
    Citations: 214     Fields:    Translation:HumansAnimalsCells
  65. 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, Cowan CA, Meissner A, Epstein CB, Shoresh N, Bernstein BE. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 2013 Jan 31; 152(3):642-54. PMID: 23333102.
    Citations: 202     Fields:    Translation:HumansCells
  66. 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, McMahon AP. 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. PMID: 23249739.
    Citations: 52     Fields:    Translation:AnimalsCells
  67. 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, Edwards J, Giacosa S, Guccione E, Weissleder R, Bernstein BE, Regev A, Shiels PG, Lombard DB, Mostoslavsky R. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 2012 Dec 07; 151(6):1185-99. PMID: 23217706.
    Citations: 170     Fields:    Translation:HumansAnimalsCells
  68. 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 Res. 2012 Dec 15; 72(24):6319-24. PMID: 23188507.
    Citations: 8     Fields:    Translation:Humans
  69. 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 Biol. 2012 Oct 03; 13(10):R85. PMID: 23034477.
    Citations: 50     Fields:    Translation:HumansAnimalsCells
  70. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
    Citations: 3893     Fields:    Translation:HumansAnimalsCells
  71. 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, Estrov Z, Ebert BL, Chiosis G, Nimer SD, Bernstein BE, Verstovsek S, Levine RL. Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature. 2012 Sep 06; 489(7414):155-9. PMID: 22820254.
    Citations: 80     Fields:    Translation:HumansAnimalsCells
  72. 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, Gerstein M, Gertz J, Hartemink AJ, Hoffman MM, Iyer VR, Jung YL, Karmakar S, Kellis M, Kharchenko PV, Li Q, Liu T, Liu XS, Ma L, Milosavljevic A, Myers RM, Park PJ, Pazin MJ, Perry MD, Raha D, Reddy TE, Rozowsky J, Shoresh N, Sidow A, Slattery M, Stamatoyannopoulos JA, Tolstorukov MY, White KP, Xi S, Farnham PJ, Lieb JD, Wold BJ, Snyder M. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res. 2012 Sep; 22(9):1813-31. PMID: 22955991.
    Citations: 436     Fields:    Translation:HumansAnimals
  73. 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, Meldrim J, Ram O, Cheng C, Gnirke A, Fisher S, Friedman N, Wong B, Bernstein BE, Nusbaum C, Hacohen N, Regev A, Amit I. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Mol Cell. 2012 Sep 14; 47(5):810-22. PMID: 22940246.
    Citations: 148     Fields:    Translation:AnimalsCells
  74. 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, Melnick A, Nimer SD, Jaffe JD, Aifantis I, Bernstein BE, Levine RL. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 2012 Aug 14; 22(2):180-93. PMID: 22897849.
    Citations: 129     Fields:    Translation:HumansAnimalsCells
  75. 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 Genet. 2012; 8(7):e1002774. PMID: 22844243.
    Citations: 65     Fields:    Translation:AnimalsCells
  76. Ryan RJ, Bernstein BE. Molecular biology. Genetic events that shape the cancer epigenome. Science. 2012 Jun 22; 336(6088):1513-4. PMID: 22723401.
    Citations: 30     Fields:    Translation:HumansCells
  77. 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. 2012 Jun 22; 149(7):1474-87. PMID: 22726435.
    Citations: 137     Fields:    Translation:AnimalsCells
  78. Rheinbay E, Louis DN, Bernstein BE, Suvà ML. A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma. Cancer Cell. 2012 Mar 20; 21(3):329-31. PMID: 22439930.
    Citations: 7     Fields:    
  79. Mendenhall EM, Bernstein BE. DNA-protein interactions in high definition. Genome Biol. 2012 Jan 27; 13(1):139. PMID: 22283870.
    Citations: 1     Fields:    Translation:HumansCells
  80. 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. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 2011 Dec 23; 147(7):1628-39. PMID: 22196736.
    Citations: 155     Fields:    Translation:HumansCells
  81. Ryan RJ, Nitta M, Borger D, Zukerberg LR, Ferry JA, Harris NL, Iafrate AJ, Bernstein BE, Sohani AR, Le LP. EZH2 codon 641 mutations are common in BCL2-rearranged germinal center B cell lymphomas. PLoS One. 2011; 6(12):e28585. PMID: 22194861.
    Citations: 34     Fields:    Translation:HumansAnimalsCells
  82. 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 Genet. 2011 Dec; 7(12):e1002389. PMID: 22174693.
    Citations: 135     Fields:    Translation:HumansAnimalsCells
  83. Adli M, Bernstein BE. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nat Protoc. 2011 Sep 29; 6(10):1656-68. PMID: 21959244.
    Citations: 74     Fields:    Translation:AnimalsCells
  84. 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. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14902-7. PMID: 21746931.
    Citations: 71     Fields:    Translation:HumansCells
  85. 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. Proc Natl Acad Sci U S A. 2011 Sep 06; 108(36):14908-13. PMID: 21737748.
    Citations: 100     Fields:    Translation:HumansAnimalsCells
  86. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
    Citations: 591     Fields:    Translation:HumansCells
  87. 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, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, Onofrio R, Pugh TJ, Rajkumar SV, Ramos AH, Siegel DS, Sivachenko A, Stewart AK, Trudel S, Vij R, Voet D, Winckler W, Zimmerman T, Carpten J, Trent J, Hahn WC, Garraway LA, Meyerson M, Lander ES, Getz G, Golub TR. Initial genome sequencing and analysis of multiple myeloma. Nature. 2011 Mar 24; 471(7339):467-72. PMID: 21430775.
    Citations: 491     Fields:    Translation:HumansCells
  88. 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. 2011 May 05; 473(7345):43-9. PMID: 21441907.
    Citations: 1137     Fields:    Translation:HumansCells
  89. 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. 2011 Feb 18; 144(4):513-25. PMID: 21335234.
    Citations: 108     Fields:    Translation:AnimalsCells
  90. 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. 2011 Jan 07; 8(1):96-105. PMID: 21211784.
    Citations: 139     Fields:    Translation:AnimalsCells
  91. 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 Genet. 2010 Dec 09; 6(12):e1001244. PMID: 21170310.
    Citations: 141     Fields:    Translation:HumansAnimalsCells
  92. Zhou VW, Goren A, Bernstein BE. Charting histone modifications and the functional organization of mammalian genomes. Nat Rev Genet. 2011 Jan; 12(1):7-18. PMID: 21116306.
    Citations: 409     Fields:    Translation:HumansAnimalsCells
  93. 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, Brockdorff N, Koseki H. 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. PMID: 21059868.
    Citations: 20     Fields:    Translation:HumansAnimalsCells
  94. 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. Nat Biotechnol. 2010 Oct; 28(10):1045-8. PMID: 20944595.
    Citations: 547     Fields:    Translation:HumansCells
  95. 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, Echipare L, O'Geen H, Lister R, Pelizzola M, Xi Y, Epstein CB, Bernstein BE, Hawkins RD, Ren B, Chung WY, Gu H, Bock C, Gnirke A, Zhang MQ, Haussler D, Ecker JR, Li W, Farnham PJ, Waterland RA, Meissner A, Marra MA, Hirst M, Milosavljevic A, Costello JF. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol. 2010 Oct; 28(10):1097-105. PMID: 20852635.
    Citations: 258     Fields:    Translation:HumansCells
  96. Adli M, Zhu J, Bernstein BE. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nat Methods. 2010 Aug; 7(8):615-8. PMID: 20622861.
    Citations: 84     Fields:    Translation:AnimalsCells
  97. 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. 2010 Jun 04; 6(6):591-602. PMID: 20569696.
    Citations: 32     Fields:    Translation:HumansCells
  98. Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Digital transcriptome profiling from attomole-level RNA samples. Genome Res. 2010 Apr; 20(4):519-25. PMID: 20133332.
    Citations: 31     Fields:    Translation:AnimalsCells
  99. Li G, Margueron R, Ku M, Chambon P, Bernstein BE, Reinberg D. Jarid2 and PRC2, partners in regulating gene expression. Genes Dev. 2010 Feb 15; 24(4):368-80. PMID: 20123894.
    Citations: 189     Fields:    Translation:AnimalsCells
  100. 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. Nat Methods. 2010 Jan; 7(1):47-9. PMID: 19946276.
    Citations: 58     Fields:    Translation:HumansAnimalsCells
  101. 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. Mol Cell. 2009 Nov 25; 36(4):682-95. PMID: 19941827.
    Citations: 150     Fields:    Translation:AnimalsCells
  102. 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, Stamatoyannopoulos J, Mirny LA, Lander ES, Dekker J. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science. 2009 Oct 09; 326(5950):289-93. PMID: 19815776.
    Citations: 1430     Fields:    Translation:HumansCells
  103. 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, Smith Z, Deering R, McDonald RC, Cabili M, Bernstein BE, Rinn JL, Meissner A, Root DE, Hacohen N, Regev A. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science. 2009 Oct 09; 326(5950):257-63. PMID: 19729616.
    Citations: 240     Fields:    Translation:AnimalsCells
  104. 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. Proc Natl Acad Sci U S A. 2009 Jul 14; 106(28):11667-72. PMID: 19571010.
    Citations: 1045     Fields:    Translation:HumansCells
  105. 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, Kellis M, Regev A, Rinn JL, Lander ES. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 2009 Mar 12; 458(7235):223-7. PMID: 19182780.
    Citations: 1385     Fields:    Translation:AnimalsCells
  106. Chi AS, Bernstein BE. Developmental biology. Pluripotent chromatin state. Science. 2009 Jan 09; 323(5911):220-1. PMID: 19131621.
    Citations: 24     Fields:    Translation:AnimalsCells
  107. 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, Koseki H, Bernstein BE. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet. 2008 Oct; 4(10):e1000242. PMID: 18974828.
    Citations: 456     Fields:    Translation:HumansAnimalsCells
  108. Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Model-based analysis of ChIP-Seq (MACS). Genome Biol. 2008; 9(9):R137. PMID: 18798982.
    Citations: 2870     Fields:    Translation:HumansCells
  109. 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. 2008 Aug 07; 454(7205):766-70. PMID: 18600261.
    Citations: 1022     Fields:    Translation:AnimalsCells
  110. 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. 2008 Jul 03; 454(7200):49-55. PMID: 18509334.
    Citations: 549     Fields:    Translation:AnimalsCells
  111. Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview. CSH Protoc. 2008 May 01; 2008:pdb.top42. PMID: 21356838.
    Citations: 3     
  112. Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification. CSH Protoc. 2008 May 01; 2008:pdb.prot5004. PMID: 21356836.
    Citations:    
  113. 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 Protoc. 2008 May 01; 2008:pdb.prot5003. PMID: 21356835.
    Citations: 3     
  114. 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 Protoc. 2008 May 01; 2008:pdb.prot5002. PMID: 21356834.
    Citations:    
  115. Mendenhall EM, Bernstein BE. Chromatin state maps: new technologies, new insights. Curr Opin Genet Dev. 2008 Apr; 18(2):109-15. PMID: 18339538.
    Citations: 33     Fields:    Translation:HumansAnimalsCells
  116. 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, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 2007 Aug 02; 448(7153):553-60. PMID: 17603471.
    Citations: 1746     Fields:    Translation:AnimalsCells
  117. 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. 2007 Jul 19; 448(7151):318-24. PMID: 17554336.
    Citations: 880     Fields:    Translation:AnimalsCells
  118. Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 2007 Feb 23; 128(4):669-81. PMID: 17320505.
    Citations: 663     Fields:    Translation:HumansAnimalsCells
  119. Huebert DJ, Kamal M, O'Donovan A, Bernstein BE. Genome-wide analysis of histone modifications by ChIP-on-chip. Methods. 2006 Dec; 40(4):365-9. PMID: 17101450.
    Citations: 17     Fields:    Translation:AnimalsCells
  120. Steward MM, Lee JS, O'Donovan A, Wyatt M, Bernstein BE, Shilatifard A. Molecular regulation of H3K4 trimethylation by ASH2L, a shared subunit of MLL complexes. Nat Struct Mol Biol. 2006 Sep; 13(9):852-4. PMID: 16892064.
    Citations: 137     Fields:    Translation:HumansCells
  121. 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. 2006 Apr 21; 125(2):315-26. PMID: 16630819.
    Citations: 1897     Fields:    Translation:AnimalsCells
  122. Huebert DJ, Bernstein BE. Genomic views of chromatin. Curr Opin Genet Dev. 2005 Oct; 15(5):476-81. PMID: 16099159.
    Citations: 12     Fields:    Translation:Cells
  123. Bernstein BE, Kellis M. Large-scale discovery and validation of functional elements in the human genome. Genome Biol. 2005; 6(3):312. PMID: 15774039.
    Citations: 1     Fields:    Translation:Humans
  124. 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. 2005 Jan 28; 120(2):169-81. PMID: 15680324.
    Citations: 590     Fields:    Translation:HumansAnimalsCells
  125. Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. Global nucleosome occupancy in yeast. Genome Biol. 2004; 5(9):R62. PMID: 15345046.
    Citations: 161     Fields:    Translation:Cells
  126. Humphrey EL, Shamji AF, Bernstein BE, Schreiber SL. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chem Biol. 2004 Mar; 11(3):295-9. PMID: 15123258.
    Citations: 24     Fields:    Translation:AnimalsCells
  127. Bernstein BE, Humphrey EL, Liu CL, Schreiber SL. The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods Enzymol. 2004; 376:349-60. PMID: 14975317.
    Citations: 14     Fields:    Translation:AnimalsCells
  128. 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. Mol Cell. 2003 Nov; 12(5):1325-32. PMID: 14636589.
    Citations: 95     Fields:    Translation:HumansAnimalsCells
  129. Liu CL, Schreiber SL, Bernstein BE. Development and validation of a T7 based linear amplification for genomic DNA. BMC Genomics. 2003 May 09; 4(1):19. PMID: 12740028.
    Citations: 50     Fields:    Translation:AnimalsCells
  130. Schreiber SL, Bernstein BE. Signaling network model of chromatin. Cell. 2002 Dec 13; 111(6):771-8. PMID: 12526804.
    Citations: 123     Fields:    Translation:AnimalsCells
  131. Bernstein BE, Schreiber SL. Global approaches to chromatin. Chem Biol. 2002 Nov; 9(11):1167-73. PMID: 12445767.
    Citations: 5     Fields:    Translation:Cells
  132. 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. 2002 Sep 26; 419(6905):407-11. PMID: 12353038.
    Citations: 675     Fields:    Translation:AnimalsCells
  133. 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. Proc Natl Acad Sci U S A. 2002 Jun 25; 99(13):8695-700. PMID: 12060701.
    Citations: 273     Fields:    Translation:AnimalsCells
  134. Scanlon MJ, Henderson DC, Bernstein B. SEMAPHORE1 functions during the regulation of ancestrally duplicated knox genes and polar auxin transport in maize. Development. 2002 Jun; 129(11):2663-73. PMID: 12015294.
    Citations: 26     Fields:    Translation:AnimalsCells
  135. Bernstein BE, Tong JK, Schreiber SL. Genomewide studies of histone deacetylase function in yeast. Proc Natl Acad Sci U S A. 2000 Dec 05; 97(25):13708-13. PMID: 11095743.
    Citations: 129     Fields:    Translation:AnimalsCells
  136. Strauss EA, Rao BK, Bernstein B, Scott RA. A bullous eruption in an acutely ill child. J Cutan Med Surg. 1999 Jul; 3(5):242-6. PMID: 10381949.
    Citations:    Fields:    Translation:Humans
  137. 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. J Mol Biol. 1998 Jun 26; 279(5):1137-48. PMID: 9642090.
    Citations: 5     Fields:    Translation:AnimalsCells
  138. Bernstein BE, Hol WG. Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism. Biochemistry. 1998 Mar 31; 37(13):4429-36. PMID: 9521762.
    Citations: 5     Fields:    Translation:AnimalsCells
  139. 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. 1998 Mar 01; 30(4):372-80. PMID: 9533621.
    Citations:    Fields:    Translation:AnimalsCells
  140. 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 Sci. 1998 Feb; 7(2):504-7. PMID: 9521128.
    Citations: 1     Fields:    Translation:AnimalsCells
  141. Bernstein BE, Hol WG. Probing the limits of the molecular replacement method: the case of Trypanosoma brucei phosphoglycerate kinase. Acta Crystallogr D Biol Crystallogr. 1997 Nov 01; 53(Pt 6):756-64. PMID: 15299865.
    Citations: 1     Fields:    
  142. Bernstein BE, Michels PA, Hol WG. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Nature. 1997 Jan 16; 385(6613):275-8. PMID: 9000079.
    Citations: 26     Fields:    Translation:AnimalsCells
  143. Miller ML, Szer I, Yogev R, Bernstein B. Fever of unknown origin. Pediatr Clin North Am. 1995 Oct; 42(5):999-1015. PMID: 7567198.
    Citations:    Fields:    Translation:Humans
  144. Bernstein BE, Hoffman RC, Klevit RE. Sequence-specific DNA recognition by Cys2, His2 zinc fingers. Ann N Y Acad Sci. 1994 Jul 29; 726:92-102; discussion 102-4. PMID: 8092710.
    Citations:    Fields:    Translation:HumansAnimalsCells
  145. Bernstein BE, Hoffman RC, Horvath S, Herriott JR, Klevit RE. Structure of a histidine-X4-histidine zinc finger domain: insights into ADR1-UAS1 protein-DNA recognition. Biochemistry. 1994 Apr 19; 33(15):4460-70. PMID: 8161501.
    Citations: 3     Fields:    Translation:Cells
  146. Giannini EH, Brewer EJ, Miller ML, Gibbas D, Passo MH, Hoyeraal HM, Bernstein B, Person DA, Fink CW, Sawyer LA, et al. Ibuprofen suspension in the treatment of juvenile rheumatoid arthritis. Pediatric Rheumatology Collaborative Study Group. J Pediatr. 1990 Oct; 117(4):645-52. PMID: 2213396.
    Citations: 11     Fields:    Translation:HumansCTClinical Trials
  147. Schichor A, Beck A, Bernstein B, Crabtree B. Seat belt use and stress in adolescents. Adolescence. 1990; 25(100):773-9. PMID: 2275431.
    Citations:    Fields:    Translation:Humans
  148. WILLIAMS RH, JAFFE H, BERNSTEIN B. Comparisons of the distribution of radioactive iodine in serum and urine in different levels of thyroid function. J Clin Invest. 1949 Sep; 28(5 Pt. 2):1222-7. PMID: 18139299.
    Citations:    
  149. Williams RH, Jaffe H, Bernstein B. COMPARISONS OF THE DISTRIBUTION OF RADIOACTIVE IODINE IN SERUM AND URINE IN DIFFERENT LEVELS OF THYROID FUNCTION. J Clin Invest. 1949 Sep; 28(5 Pt 2):1222-7. PMID: 16695794.
    Citations: 5     Fields:    Translation:Humans
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Funded by the NIH/NCATS Clinical and Translational Science Award (CTSA) program, grant number UL1TR001102, and through institutional support from Harvard University, Harvard Medical School, Harvard T.H. Chan School of Public Health, Beth Israel Deaconess Medical Center, Boston Children's Hospital, Brigham and Women's Hospital, Massachusetts General Hospital and the Dana Farber Cancer Institute.