Harvard Catalyst Profiles

Contact, publication, and social network information about Harvard faculty and fellows.

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

Title
Institution
Department
Address
Phone
Other Positions
Title
Institution
Department

Research
research activities and funding
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.
Most Recent  |  List All
  1. U24HG012090 (ARDLIE, KRISTIN) Sep 22, 2021 - Jun 30, 2026
    NIH
    Developmental GTEx Laboratory, Data Analysis and Coordination Center
    Role: Co-Principal Investigator
  2. UM1HG011986 (BUENROSTRO, JASON DANIEL) Sep 9, 2021 - May 31, 2026
    NIH
    A Foundational Resource of Functional Elements, TF footprints and Gene Regulatory Interactions
    Role: Co-Principal Investigator
  3. UM1HG009390 (BERNSTEIN, BRADLEY EVAN) Feb 1, 2017 - Jan 31, 2022
    NIH
    A Catalog of Cell Types and Genomic Elements in Tissues, Organoids and Disease
    Role: Principal Investigator
  4. R01HG009269 (BERNSTEIN, BRADLEY EVAN) Sep 28, 2016 - Jan 31, 2021
    NIH
    Single-molecule systems for decoding combinatorial chromatin modifications
    Role: Principal Investigator
  5. DP1CA216873 (BERNSTEIN, BRADLEY EVAN) Sep 21, 2016 - Jul 31, 2022
    NIH
    Epigenetic plasticity in tumor initiation and evolution
    Role: Principal Investigator

Bibliographic
selected publications
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.
Newest   |   Oldest   |   Most Cited   |   Most Discussed   |   Timeline   |   Field Summary   |   Plain Text
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. Najm FJ, DeWeirdt P, Moore MM, Bevill SM, El Farran CA, Macias KA, Hegde M, Waterbury AL, Liau BB, van Galen P, Doench JG, Bernstein BE. Chromatin complex dependencies reveal targeting opportunities in leukemia. Nat Commun. 2023 Jan 27; 14(1):448. PMID: 36707513; PMCID: PMC9883437.
    Citations:    Fields:    Translation:HumansCells
  2. Johnstone SE, Gladyshev VN, Aryee MJ, Bernstein BE. Epigenetic clocks, aging, and cancer. Science. 2022 12 23; 378(6626):1276-1277. PMID: 36548410.
    Citations:    Fields:    Translation:HumansCells
  3. Parikh AS, Wizel A, Davis D, Lefranc-Torres A, Rodarte-Rascon AI, Miller LE, Emerick KS, Varvares MA, Deschler DG, Faquin WC, Aster JC, Lin DT, Bernstein BE, Drier Y, Puram SV. Single-cell RNA sequencing identifies a paracrine interaction that may drive oncogenic notch signaling in human adenoid cystic carcinoma. Cell Rep. 2022 11 29; 41(9):111743. PMID: 36450256; PMCID: PMC9760094.
    Citations:    Fields:    Translation:Humans
  4. Battaglia S, Dong K, Wu J, Chen Z, Najm FJ, Zhang Y, Moore MM, Hecht V, Shoresh N, Bernstein BE. Long-range phasing of dynamic, tissue-specific and allele-specific regulatory elements. Nat Genet. 2022 10; 54(10):1504-1513. PMID: 36195755.
    Citations: 2     Fields:    Translation:HumansAnimalsCells
  5. Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2022 May; 605(7909):E3. PMID: 35474001; PMCID: PMC9095460.
    Citations:    Fields:    
  6. Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Author Correction: Perspectives on ENCODE. Nature. 2022 May; 605(7909):E4. PMID: 35474002; PMCID: PMC9095462.
    Citations:    Fields:    
  7. Miller TE, Lareau CA, Verga JA, DePasquale EAK, Liu V, Ssozi D, Sandor K, Yin Y, Ludwig LS, El Farran CA, Morgan DM, Satpathy AT, Griffin GK, Lane AA, Love JC, Bernstein BE, Sankaran VG, van Galen P. Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol. 2022 07; 40(7):1030-1034. PMID: 35210612; PMCID: PMC9288977.
    Citations: 4     Fields:    Translation:HumansCells
  8. Kim KL, van Galen P, Hovestadt V, Rahme GJ, Andreishcheva EN, Shinde A, Gaskell E, Jones DR, Shema E, Bernstein BE. Systematic detection of m6A-modified transcripts at single-molecule and single-cell resolution. Cell Rep Methods. 2021 Sep 27; 1(5). PMID: 34734208.
    Citations:    
  9. Shareef SJ, Bevill SM, Raman AT, Aryee MJ, van Galen P, Hovestadt V, Bernstein BE. Extended-representation bisulfite sequencing of gene regulatory elements in multiplexed samples and single cells. Nat Biotechnol. 2021 09; 39(9):1086-1094. PMID: 33958785; PMCID: PMC8434949.
    Citations: 6     Fields:    Translation:HumansCells
  10. Anand P, Guillaumet-Adkins A, Dimitrova V, Yun H, Drier Y, Sotudeh N, Rogers A, Ouseph MM, Nair M, Potdar S, Isenhart R, Kloeber JA, Vijaykumar T, Niu L, Vincent T, Guo G, Frede J, Harris MH, Place AE, Silverman LB, Teachey DT, Lane AA, DeAngelo DJ, Aster JC, Bernstein BE, Lohr JG, Knoechel B. Single-cell RNA-seq reveals developmental plasticity with coexisting oncogenic states and immune evasion programs in ETP-ALL. Blood. 2021 05 06; 137(18):2463-2480. PMID: 33227818; PMCID: PMC8109012.
    Citations: 13     Fields:    Translation:HumansCells
  11. Griffin GK, Wu J, Iracheta-Vellve A, Patti JC, Hsu J, Davis T, Dele-Oni D, Du PP, Halawi AG, Ishizuka JJ, Kim SY, Klaeger S, Knudsen NH, Miller BC, Nguyen TH, Olander KE, Papanastasiou M, Rachimi S, Robitschek EJ, Schneider EM, Yeary MD, Zimmer MD, Jaffe JD, Carr SA, Doench JG, Haining WN, Yates KB, Manguso RT, Bernstein BE. Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. 2021 07; 595(7866):309-314. PMID: 33953401; PMCID: PMC9166167.
    Citations: 31     Fields:    Translation:HumansAnimalsCells
  12. Nuñez JK, Chen J, Pommier GC, Cogan JZ, Replogle JM, Adriaens C, Ramadoss GN, Shi Q, Hung KL, Samelson AJ, Pogson AN, Kim JYS, Chung A, Leonetti MD, Chang HY, Kampmann M, Bernstein BE, Hovestadt V, Gilbert LA, Weissman JS. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. 2021 04 29; 184(9):2503-2519.e17. PMID: 33838111; PMCID: PMC8376083.
    Citations: 52     Fields:    Translation:HumansCells
  13. Dunn GP, Bernstein B. Serving on the Navy's Hospital Ships During the Response to COVID-19: Perspective from Two Deployed Missouri Physicians. Mo Med. 2021 Mar-Apr; 118(2):110-112. PMID: 33840845.
    Citations:    Fields:    Translation:HumansCells
  14. Yao Q, Epstein CB, Banskota S, Issner R, Kim Y, Bernstein BE, Pinello L, Asgari MM. Epigenetic Alterations in Keratinocyte Carcinoma. J Invest Dermatol. 2021 05; 141(5):1207-1218. PMID: 33212152; PMCID: PMC8068579.
    Citations: 3     Fields:    Translation:HumansCells
  15. Naranbhai V, Chang CC, Beltran WFG, Miller TE, Astudillo MG, Villalba JA, Yang D, Gelfand J, Bernstein BE, Feldman J, Hauser BM, Caradonna TM, Alter G, Murali MR, Jasrasaria R, Quinlan J, Xerras DC, Betancourt JR, Louis DN, Schmidt AG, Lennerz J, Poznansky MC, Iafrate AJ. High Seroprevalence of Anti-SARS-CoV-2 Antibodies in Chelsea, Massachusetts. J Infect Dis. 2020 11 13; 222(12):1955-1959. PMID: 32906151; PMCID: PMC7499676.
    Citations: 31     Fields:    Translation:Humans
  16. Kim IS, Wu J, Rahme GJ, Battaglia S, Dixit A, Gaskell E, Chen H, Pinello L, Bernstein BE. Parallel Single-Cell RNA-Seq and Genetic Recording Reveals Lineage Decisions in Developing Embryoid Bodies. Cell Rep. 2020 10 06; 33(1):108222. PMID: 33027665.
    Citations: 5     Fields:    Translation:HumansCells
  17. Qi Y, Reyes A, Johnstone SE, Aryee MJ, Bernstein BE, Zhang B. Data-Driven Polymer Model for Mechanistic Exploration of Diploid Genome Organization. Biophys J. 2020 11 03; 119(9):1905-1916. PMID: 33086041.
    Citations: 16     Fields:    Translation:HumansCells
  18. Miller TE, Garcia Beltran WF, Bard AZ, Gogakos T, Anahtar MN, Astudillo MG, Yang D, Thierauf J, Fisch AS, Mahowald GK, Fitzpatrick MJ, Nardi V, Feldman J, Hauser BM, Caradonna TM, Marble HD, Ritterhouse LL, Turbett SE, Batten J, Georgantas NZ, Alter G, Schmidt AG, Harris JB, Gelfand JA, Poznansky MC, Bernstein BE, Louis DN, Dighe A, Charles RC, Ryan ET, Branda JA, Pierce VM, Murali MR, Iafrate AJ, Rosenberg ES, Lennerz JK. Clinical sensitivity and interpretation of PCR and serological COVID-19 diagnostics for patients presenting to the hospital. FASEB J. 2020 10; 34(10):13877-13884. PMID: 32856766; PMCID: PMC7461169.
    Citations: 43     Fields:    Translation:HumansCellsCTClinical Trials
  19. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk RP, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Evaluation of SARS-CoV-2 serology assays reveals a range of test performance. Nat Biotechnol. 2020 10; 38(10):1174-1183. PMID: 32855547; PMCID: PMC7740072.
    Citations: 125     Fields:    Translation:HumansCellsPHPublic Health
  20. Johnstone SE, Reyes A, Qi Y, Adriaens C, Hegazi E, Pelka K, Chen JH, Zou LS, Drier Y, Hecht V, Shoresh N, Selig MK, Lareau CA, Iyer S, Nguyen SC, Joyce EF, Hacohen N, Irizarry RA, Zhang B, Aryee MJ, Bernstein BE. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. 2020 09 17; 182(6):1474-1489.e23. PMID: 32841603.
    Citations: 25     Fields:    Translation:HumansCells
  21. Javed N, Farjoun Y, Fennell TJ, Epstein CB, Bernstein BE, Shoresh N. Detecting sample swaps in diverse NGS data types using linkage disequilibrium. Nat Commun. 2020 07 29; 11(1):3697. PMID: 32728101.
    Citations: 1     Fields:    Translation:HumansCells
  22. Snyder MP, Gingeras TR, Moore JE, Weng Z, Gerstein MB, Ren B, Hardison RC, Stamatoyannopoulos JA, Graveley BR, Feingold EA, Pazin MJ, Pagan M, Gilchrist DA, Hitz BC, Cherry JM, Bernstein BE, Mendenhall EM, Zerbino DR, Frankish A, Flicek P, Myers RM. Perspectives on ENCODE. Nature. 2020 07; 583(7818):693-698. PMID: 32728248; PMCID: PMC7410827.
    Citations: 39     Fields:    Translation:HumansAnimalsCells
  23. Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, Shen Y, He Y, Mackiewicz M, Pauli-Behn F, Williams BA, Mortazavi A, Keller CA, Zhang XO, Elhajjajy SI, Huey J, Dickel DE, Snetkova V, Wei X, Wang X, Rivera-Mulia JC, Rozowsky J, Zhang J, Chhetri SB, Zhang J, Victorsen A, White KP, Visel A, Yeo GW, Burge CB, Lécuyer E, Gilbert DM, Dekker J, Rinn J, Mendenhall EM, Ecker JR, Kellis M, Klein RJ, Noble WS, Kundaje A, Guigó R, Farnham PJ, Cherry JM, Myers RM, Ren B, Graveley BR, Gerstein MB, Pennacchio LA, Snyder MP, Bernstein BE, Wold B, Hardison RC, Gingeras TR, Stamatoyannopoulos JA, Weng Z. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 2020 07; 583(7818):699-710. PMID: 32728249; PMCID: PMC7410828.
    Citations: 275     Fields:    Translation:HumansAnimalsCells
  24. Eyler CE, Matsunaga H, Hovestadt V, Vantine SJ, van Galen P, Bernstein BE. Single-cell lineage analysis reveals genetic and epigenetic interplay in glioblastoma drug resistance. Genome Biol. 2020 07 15; 21(1):174. PMID: 32669109.
    Citations: 21     Fields:    Translation:Humans
  25. Whitman JD, Hiatt J, Mowery CT, Shy BR, Yu R, Yamamoto TN, Rathore U, Goldgof GM, Whitty C, Woo JM, Gallman AE, Miller TE, Levine AG, Nguyen DN, Bapat SP, Balcerek J, Bylsma SA, Lyons AM, Li S, Wong AW, Gillis-Buck EM, Steinhart ZB, Lee Y, Apathy R, Lipke MJ, Smith JA, Zheng T, Boothby IC, Isaza E, Chan J, Acenas DD, Lee J, Macrae TA, Kyaw TS, Wu D, Ng DL, Gu W, York VA, Eskandarian HA, Callaway PC, Warrier L, Moreno ME, Levan J, Torres L, Farrington LA, Loudermilk R, Koshal K, Zorn KC, Garcia-Beltran WF, Yang D, Astudillo MG, Bernstein BE, Gelfand JA, Ryan ET, Charles RC, Iafrate AJ, Lennerz JK, Miller S, Chiu CY, Stramer SL, Wilson MR, Manglik A, Ye CJ, Krogan NJ, Anderson MS, Cyster JG, Ernst JD, Wu AHB, Lynch KL, Bern C, Hsu PD, Marson A. Test performance evaluation of SARS-CoV-2 serological assays. medRxiv. 2020 May 17. PMID: 32511497; PMCID: PMC7273265.
    Citations: 11     
  26. Kato S, Weng QY, Insco ML, Chen KY, Muralidhar S, Pozniak J, Diaz JMS, Drier Y, Nguyen N, Lo JA, van Rooijen E, Kemeny LV, Zhan Y, Feng Y, Silkworth W, Powell CT, Liau BB, Xiong Y, Jin J, Newton-Bishop J, Zon LI, Bernstein BE, Fisher DE. Gain-of-Function Genetic Alterations of G9a Drive Oncogenesis. Cancer Discov. 2020 07; 10(7):980-997. PMID: 32269030; PMCID: PMC7334057.
    Citations: 16     Fields:    Translation:HumansCells
  27. Cabal-Hierro L, van Galen P, Prado MA, Higby KJ, Togami K, Mowery CT, Paulo JA, Xie Y, Cejas P, Furusawa T, Bustin M, Long HW, Sykes DB, Gygi SP, Finley D, Bernstein BE, Lane AA. Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nat Commun. 2020 03 16; 11(1):1406. PMID: 32179749.
    Citations: 10     Fields:    Translation:HumansAnimalsCells
  28. Parikh AS, Puram SV, Faquin WC, Richmon JD, Emerick KS, Deschler DG, Varvares MA, Tirosh I, Bernstein BE, Lin DT. Immunohistochemical quantification of partial-EMT in oral cavity squamous cell carcinoma primary tumors is associated with nodal metastasis. Oral Oncol. 2019 12; 99:104458. PMID: 31704557.
    Citations: 20     Fields:    Translation:Humans
  29. Brumbaugh J, Kim IS, Ji F, Huebner AJ, Di Stefano B, Schwarz BA, Charlton J, Coffey A, Choi J, Walsh RM, Schindler JW, Anselmo A, Meissner A, Sadreyev RI, Bernstein BE, Hock H, Hochedlinger K. Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nat Cell Biol. 2019 11; 21(11):1449-1461. PMID: 31659274; PMCID: PMC6858577.
    Citations: 17     Fields:    Translation:AnimalsCells
  30. Anastas JN, Zee BM, Kalin JH, Kim M, Guo R, Alexandrescu S, Blanco MA, Giera S, Gillespie SM, Das J, Wu M, Nocco S, Bonal DM, Nguyen QD, Suva ML, Bernstein BE, Alani R, Golub TR, Cole PA, Filbin MG, Shi Y. Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG. Cancer Cell. 2019 11 11; 36(5):528-544.e10. PMID: 31631026.
    Citations: 43     Fields:    Translation:HumansAnimalsCells
  31. Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE. Altered chromosomal topology drives oncogenic programs in SDH-deficient GISTs. Nature. 2019 11; 575(7781):229-233. PMID: 31666694.
    Citations: 61     Fields:    Translation:HumansAnimalsCells
  32. Flavahan WA, Drier Y, Johnstone SE, Hemming ML, Tarjan DR, Hegazi E, Shareef SJ, Javed NM, Raut CP, Eschle BK, Gokhale PC, Hornick JL, Sicinska ET, Demetri GD, Bernstein BE. Altered chromosomal topology drives oncogenic programs in SDH-deficient GIST. Nature. 2019 Oct 16. PMID: 31618758.
    Citations:    
  33. Cejas P, Drier Y, Dreijerink KMA, Brosens LAA, Deshpande V, Epstein CB, Conemans EB, Morsink FHM, Graham MK, Valk GD, Vriens MR, Castillo CF, Ferrone CR, Adar T, Bowden M, Whitton HJ, Da Silva A, Font-Tello A, Long HW, Gaskell E, Shoresh N, Heaphy CM, Sicinska E, Kulke MH, Chung DC, Bernstein BE, Shivdasani RA. Publisher Correction: Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019 Oct; 25(10):1627. PMID: 31501535.
    Citations:    Fields:    
  34. Tarjan DR, Flavahan WA, Bernstein BE. Epigenome editing strategies for the functional annotation of CTCF insulators. Nat Commun. 2019 09 18; 10(1):4258. PMID: 31534142; PMCID: PMC6751197.
    Citations: 19     Fields:    Translation:HumansCells
  35. Hovestadt V, Smith KS, Bihannic L, Filbin MG, Shaw ML, Baumgartner A, DeWitt JC, Groves A, Mayr L, Weisman HR, Richman AR, Shore ME, Goumnerova L, Rosencrance C, Carter RA, Phoenix TN, Hadley JL, Tong Y, Houston J, Ashmun RA, DeCuypere M, Sharma T, Flasch D, Silkov A, Ligon KL, Pomeroy SL, Rivera MN, Rozenblatt-Rosen O, Rusert JM, Wechsler-Reya RJ, Li XN, Peyrl A, Gojo J, Kirchhofer D, Lötsch D, Czech T, Dorfer C, Haberler C, Geyeregger R, Halfmann A, Gawad C, Easton J, Pfister SM, Regev A, Gajjar A, Orr BA, Slavc I, Robinson GW, Bernstein BE, Suvà ML, Northcott PA. Resolving medulloblastoma cellular architecture by single-cell genomics. Nature. 2019 08; 572(7767):74-79. PMID: 31341285.
    Citations: 93     Fields:    Translation:HumansAnimalsCells
  36. Neftel C, Laffy J, Filbin MG, Hara T, Shore ME, Rahme GJ, Richman AR, Silverbush D, Shaw ML, Hebert CM, Dewitt J, Gritsch S, Perez EM, Gonzalez Castro LN, Lan X, Druck N, Rodman C, Dionne D, Kaplan A, Bertalan MS, Small J, Pelton K, Becker S, Bonal D, Nguyen QD, Servis RL, Fung JM, Mylvaganam R, Mayr L, Gojo J, Haberler C, Geyeregger R, Czech T, Slavc I, Nahed BV, Curry WT, Carter BS, Wakimoto H, Brastianos PK, Batchelor TT, Stemmer-Rachamimov A, Martinez-Lage M, Frosch MP, Stamenkovic I, Riggi N, Rheinbay E, Monje M, Rozenblatt-Rosen O, Cahill DP, Patel AP, Hunter T, Verma IM, Ligon KL, Louis DN, Regev A, Bernstein BE, Tirosh I, Suvà ML. An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell. 2019 08 08; 178(4):835-849.e21. PMID: 31327527; PMCID: PMC6703186.
    Citations: 428     Fields:    Translation:HumansAnimalsCells
  37. Cejas P, Drier Y, Dreijerink KMA, Brosens LAA, Deshpande V, Epstein CB, Conemans EB, Morsink FHM, Graham MK, Valk GD, Vriens MR, Castillo CF, Ferrone CR, Adar T, Bowden M, Whitton HJ, Da Silva A, Font-Tello A, Long HW, Gaskell E, Shoresh N, Heaphy CM, Sicinska E, Kulke MH, Chung DC, Bernstein BE, Shivdasani RA. Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nat Med. 2019 08; 25(8):1260-1265. PMID: 31263286; PMCID: PMC6919319.
    Citations: 51     Fields:    Translation:HumansCells
  38. 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: 26     Fields:    Translation:HumansCells
  39. 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 03 07; 176(6):1265-1281.e24. PMID: 30827681.
    Citations: 214     Fields:    Translation:HumansCells
  40. 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 08; 33(8):2061-2077. PMID: 30705411.
    Citations: 4     Fields:    Translation:HumansCells
  41. 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; PMCID: PMC6516529.
    Citations: 64     Fields:    Translation:HumansCells
  42. 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: 57     Fields:    Translation:HumansAnimalsCells
  43. 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; PMCID: PMC6219629.
    Citations: 110     Fields:    Translation:HumansCells
  44. Rahme GJ, Gaskell E, Bernstein BE. GABPß1L Wakes Up TERT. Cancer Cell. 2018 09 10; 34(3):358-360. PMID: 30205042.
    Citations:    Fields:    Translation:HumansCells
  45. 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; PMCID: PMC6123496.
    Citations: 148     Fields:    Translation:HumansCells
  46. 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: 1     Fields:    
  47. 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: 179     Fields:    Translation:HumansCells
  48. 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: 23     Fields:    
  49. 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: 281     Fields:    Translation:HumansCells
  50. 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; PMCID: PMC5800952.
    Citations: 92     Fields:    Translation:HumansCells
  51. 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: 70     Fields:    Translation:AnimalsCells
  52. 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; PMCID: PMC5878932.
    Citations: 626     Fields:    Translation:HumansCells
  53. 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; PMCID: PMC5959009.
    Citations: 37     Fields:    Translation:HumansAnimalsCells
  54. 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: 30     Fields:    Translation:HumansAnimalsCells
  55. 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: 568     Fields:    Translation:HumansCells
  56. 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; PMCID: PMC5593504.
    Citations: 80     Fields:    Translation:HumansAnimalsCells
  57. 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: 137     Fields:    Translation:HumansCells
  58. Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science. 2017 Jul 21; 357(6348). PMID: 28729483; PMCID: PMC5940341.
    Citations: 388     Fields:    Translation:HumansCells
  59. 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: 77     Fields:    Translation:HumansAnimalsCells
  60. 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: 312     Fields:    Translation:HumansCells
  61. 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; PMCID: PMC5321001.
    Citations: 64     Fields:    Translation:AnimalsCells
  62. 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: 161     Fields:    Translation:HumansCells
  63. 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; PMCID: PMC5285474.
    Citations: 124     Fields:    Translation:HumansCells
  64. 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; PMCID: PMC5465819.
    Citations: 366     Fields:    Translation:HumansCells
  65. 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:    
  66. 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; PMCID: PMC4922685.
    Citations: 26     Fields:    Translation:HumansAnimalsCells
  67. 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: 52     Fields:    Translation:HumansAnimalsCells
  68. 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; PMCID: PMC4756407.
    Citations: 98     Fields:    Translation:HumansCells
  69. 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; PMCID: PMC4767593.
    Citations: 100     Fields:    Translation:HumansCells
  70. 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; PMCID: PMC4831574.
    Citations: 489     Fields:    Translation:HumansCells
  71. 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; PMCID: PMC4707994.
    Citations: 49     Fields:    Translation:HumansCells
  72. 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; PMCID: PMC4636926.
    Citations: 324     Fields:    Translation:HumansAnimalsCells
  73. 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; PMCID: PMC4608240.
    Citations: 44     Fields:    Translation:HumansAnimalsCells
  74. 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: 49     Fields:    Translation:HumansCells
  75. 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: 31     Fields:    
  76. 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; PMCID: PMC4498984.
    Citations: 333     Fields:    Translation:AnimalsCells
  77. 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: 3     Fields:    Translation:HumansAnimalsCells
  78. 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; PMCID: PMC4530010.
    Citations: 2568     Fields:    Translation:HumansCells
  79. 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; PMCID: PMC4336237.
    Citations: 99     Fields:    Translation:HumansCells
  80. 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: 96     Fields:    Translation:HumansAnimalsCells
  81. 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; PMCID: PMC4492343.
    Citations: 165     Fields:    Translation:HumansAnimalsCells
  82. 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; PMCID: PMC4336207.
    Citations: 771     Fields:    Translation:HumansCells
  83. 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: 182     Fields:    Translation:HumansAnimalsCells
  84. 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: 2     Fields:    Translation:Humans
  85. 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; PMCID: PMC4292795.
    Citations: 358     Fields:    Translation:HumansCells
  86. 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; PMCID: PMC4184927.
    Citations: 71     Fields:    Translation:HumansAnimalsCells
  87. 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:    
  88. 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: 1650     Fields:    Translation:Humans
  89. 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; PMCID: PMC4035993.
    Citations: 295     Fields:    Translation:HumansCells
  90. 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: 36     Fields:    Translation:AnimalsCells
  91. 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: 390     Fields:    Translation:HumansCells
  92. 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: 174     Fields:    Translation:HumansAnimalsCells
  93. 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; PMCID: PMC3832937.
    Citations: 158     Fields:    Translation:HumansAnimalsCells
  94. 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: 218     Fields:    Translation:HumansCells
  95. 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: 114     Fields:    Translation:AnimalsCells
  96. 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: 179     Fields:    Translation:Cells
  97. 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: 29     Fields:    Translation:HumansCells
  98. 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; PMCID: PMC3821869.
    Citations: 610     Fields:    Translation:HumansCells
  99. 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; PMCID: PMC3774301.
    Citations: 123     Fields:    Translation:HumansCells
  100. 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: 236     Fields:    Translation:HumansCells
  101. Suvà ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science. 2013 Mar 29; 339(6127):1567-70. PMID: 23539597.
    Citations: 332     Fields:    Translation:HumansAnimalsCells
  102. 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; PMCID: PMC3563935.
    Citations: 283     Fields:    Translation:HumansCells
  103. 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: 83     Fields:    Translation:AnimalsCells
  104. 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: 301     Fields:    Translation:HumansAnimalsCells
  105. 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: 12     Fields:    Translation:Humans
  106. 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: 94     Fields:    Translation:HumansAnimalsCells
  107. 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: 149     Fields:    Translation:HumansAnimalsCells
  108. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616; PMCID: PMC3439153.
    Citations: 7176     Fields:    Translation:HumansAnimalsCells
  109. 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: 881     Fields:    Translation:HumansAnimals
  110. 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: 200     Fields:    Translation:AnimalsCells
  111. 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; PMCID: PMC3422511.
    Citations: 266     Fields:    Translation:HumansAnimalsCells
  112. 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: 118     Fields:    Translation:AnimalsCells
  113. 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: 222     Fields:    Translation:AnimalsCells
  114. Ryan RJ, Bernstein BE. Molecular biology. Genetic events that shape the cancer epigenome. Science. 2012 Jun 22; 336(6088):1513-4. PMID: 22723401.
    Citations: 37     Fields:    Translation:HumansCells
  115. 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: 12     Fields:    
  116. 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
  117. 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: 193     Fields:    Translation:HumansCells
  118. 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: 53     Fields:    Translation:HumansAnimalsCells
  119. 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; PMCID: PMC3234221.
    Citations: 188     Fields:    Translation:HumansAnimalsCells
  120. 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: 101     Fields:    Translation:AnimalsCells
  121. 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: 114     Fields:    Translation:HumansCells
  122. 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: 142     Fields:    Translation:HumansAnimalsCells
  123. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
    Citations: 732     Fields:    Translation:HumansCells
  124. 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: 728     Fields:    Translation:HumansCells
  125. 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: 1595     Fields:    Translation:HumansCells
  126. 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: 141     Fields:    Translation:AnimalsCells
  127. 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: 185     Fields:    Translation:AnimalsCells
  128. 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: 226     Fields:    Translation:HumansAnimalsCells
  129. 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: 569     Fields:    Translation:HumansAnimalsCells
  130. 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: 34     Fields:    Translation:HumansAnimalsCells
  131. 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: 900     Fields:    Translation:HumansCells
  132. 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: 326     Fields:    Translation:HumansCells
  133. 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: 94     Fields:    Translation:AnimalsCells
  134. 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: 42     Fields:    Translation:HumansCells
  135. 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: 36     Fields:    Translation:AnimalsCells
  136. 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: 256     Fields:    Translation:AnimalsCells
  137. 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: 64     Fields:    Translation:HumansAnimalsCells
  138. 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: 185     Fields:    Translation: