| Year |
Citation |
Score |
| 2024 |
Mowery CT, Freimer JW, Chen Z, Casaní-Galdón S, Umhoefer JM, Arce MM, Gjoni K, Daniel B, Sandor K, Gowen BG, Nguyen V, Simeonov DR, Garrido CM, Curie GL, Schmidt R, ... ... Bernstein BE, et al. Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells. Nature Genetics. PMID 38811842 DOI: 10.1038/s41588-024-01743-5 |
0.313 |
|
| 2023 |
Chen Z, Javed N, Moore M, Wu J, Sun G, Vinyard M, Collins A, Pinello L, Najm FJ, Bernstein BE. Integrative dissection of gene regulatory elements at base resolution. Cell Genomics. 3: 100318. PMID 37388913 DOI: 10.1016/j.xgen.2023.100318 |
0.557 |
|
| 2023 |
Schreiber J, Boix C, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, ... ... Bernstein B, et al. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biology. 24: 79. PMID 37072822 DOI: 10.1186/s13059-023-02915-y |
0.447 |
|
| 2023 |
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. Nature Communications. 14: 448. PMID 36707513 DOI: 10.1038/s41467-023-36150-7 |
0.67 |
|
| 2022 |
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. Nature Genetics. 54: 1504-1513. PMID 36195755 DOI: 10.1038/s41588-022-01188-8 |
0.59 |
|
| 2022 |
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, ... ... Bernstein BE, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3 |
0.502 |
|
| 2021 |
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. Nature Biotechnology. PMID 33958785 DOI: 10.1038/s41587-021-00910-x |
0.366 |
|
| 2021 |
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, ... ... Bernstein BE, et al. Epigenetic silencing by SETDB1 suppresses tumour intrinsic immunogenicity. Nature. PMID 33953401 DOI: 10.1038/s41586-021-03520-4 |
0.544 |
|
| 2021 |
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, ... ... Bernstein BE, et al. Genome-wide programmable transcriptional memory by CRISPR-based epigenome editing. Cell. PMID 33838111 DOI: 10.1016/j.cell.2021.03.025 |
0.418 |
|
| 2020 |
Yao Q, Epstein CB, Banskota S, Issner R, Kim Y, Bernstein BE, Pinello L, Asgari MM. Epigenetic alterations in keratinocyte carcinoma. The Journal of Investigative Dermatology. PMID 33212152 DOI: 10.1016/j.jid.2020.10.018 |
0.333 |
|
| 2020 |
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 Reports. 33: 108222. PMID 33027665 DOI: 10.1016/j.celrep.2020.108222 |
0.534 |
|
| 2020 |
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, ... ... Bernstein BE, et al. Large-Scale Topological Changes Restrain Malignant Progression in Colorectal Cancer. Cell. PMID 32841603 DOI: 10.1016/J.Cell.2020.07.030 |
0.407 |
|
| 2020 |
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, ... ... Bernstein BE, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4 |
0.625 |
|
| 2020 |
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, ... ... Bernstein BE, et al. Perspectives on ENCODE. Nature. 583: 693-698. PMID 32728248 DOI: 10.1038/S41586-020-2449-8 |
0.462 |
|
| 2020 |
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 Biology. 21: 174. PMID 32669109 DOI: 10.1186/S13059-020-02085-1 |
0.323 |
|
| 2020 |
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, ... ... Bernstein BE, et al. Gain-of-function genetic alterations of G9a drive oncogenesis. Cancer Discovery. PMID 32269030 DOI: 10.1158/2159-8290.Cd-19-0532 |
0.675 |
|
| 2020 |
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, et al. Chromatin accessibility promotes hematopoietic and leukemia stem cell activity. Nature Communications. 11: 1406. PMID 32179749 DOI: 10.1038/S41467-020-15221-Z |
0.483 |
|
| 2019 |
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. PMID 31666694 DOI: 10.1038/S41586-019-1668-3 |
0.433 |
|
| 2019 |
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, et al. Inducible histone K-to-M mutations are dynamic tools to probe the physiological role of site-specific histone methylation in vitro and in vivo. Nature Cell Biology. PMID 31659274 DOI: 10.1038/S41556-019-0403-5 |
0.44 |
|
| 2019 |
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, et al. Re-programing Chromatin with a Bifunctional LSD1/HDAC Inhibitor Induces Therapeutic Differentiation in DIPG. Cancer Cell. PMID 31631026 DOI: 10.1016/J.Ccell.2019.09.005 |
0.445 |
|
| 2019 |
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. PMID 31618758 DOI: 10.1038/s41586-019-1668-3 |
0.326 |
|
| 2019 |
Tarjan DR, Flavahan WA, Bernstein BE. Epigenome editing strategies for the functional annotation of CTCF insulators. Nature Communications. 10: 4258. PMID 31534142 DOI: 10.1038/S41467-019-12166-W |
0.484 |
|
| 2019 |
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, ... ... Bernstein BE, et al. Resolving medulloblastoma cellular architecture by single-cell genomics. Nature. PMID 31341285 DOI: 10.1038/S41586-019-1434-6 |
0.313 |
|
| 2019 |
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, ... ... Bernstein BE, et al. An Integrative Model of Cellular States, Plasticity, and Genetics for Glioblastoma. Cell. PMID 31327527 DOI: 10.1016/J.Cell.2019.06.024 |
0.342 |
|
| 2019 |
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, ... ... Bernstein BE, et al. Enhancer signatures stratify and predict outcomes of non-functional pancreatic neuroendocrine tumors. Nature Medicine. PMID 31263286 DOI: 10.1038/S41591-019-0493-4 |
0.318 |
|
| 2019 |
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, ... ... Bernstein BE, et al. Corrupted coordination of epigenetic modifications leads to diverging chromatin states and transcriptional heterogeneity in CLL. Nature Communications. 10: 1874. PMID 31015400 DOI: 10.1038/S41467-019-09645-5 |
0.508 |
|
| 2019 |
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, ... ... Bernstein BE, et al. Single-Cell RNA-Seq Reveals AML Hierarchies Relevant to Disease Progression and Immunity. Cell. PMID 30827681 DOI: 10.1016/J.Cell.2019.01.031 |
0.366 |
|
| 2019 |
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. PMID 30705411 DOI: 10.1038/S41375-019-0386-Z |
0.353 |
|
| 2019 |
Shema E, Bernstein BE, Buenrostro JD. Single-cell and single-molecule epigenomics to uncover genome regulation at unprecedented resolution. Nature Genetics. 51: 19-25. PMID 30559489 DOI: 10.1038/S41588-018-0290-X |
0.387 |
|
| 2019 |
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, et al. Epigenome-wide study uncovers large-scale changes in histone acetylation driven by tau pathology in aging and Alzheimer's human brains. Nature Neuroscience. 22: 37-46. PMID 30559478 DOI: 10.1038/S41593-018-0291-1 |
0.365 |
|
| 2019 |
Guillaumet-Adkins A, Anand P, Yun H, Drier Y, Rogers A, Ouseph MM, Nair MS, Potdar S, Isenhart R, Kloeber JA, Vijaykumar T, Guo G, Frede J, Harris MH, Silverman LB, ... ... Bernstein BE, et al. Single Cell RNA-Seq Reveals Deranged Developmental Hierarchy with Coexisting Oncogenic States and Immune Evasion Programs in ETP T-ALL Blood. 134: 3953-3953. DOI: 10.1182/Blood-2019-130482 |
0.32 |
|
| 2019 |
Bihannic L, Hovestadt V, Smith K, Filbin M, Shaw M, Baumgartner A, DeWitt J, Groves A, Mayr L, Weisman H, Richman A, Shore M, Goumnerova L, Rosencrance C, Carter R, ... ... Bernstein B, et al. PDTM-32. RESOLVING MEDULLOBLASTOMA CELLULAR ARCHITECTURE BY SINGLE-CELL GENOMICS Neuro-Oncology. 21: vi194-vi194. DOI: 10.1093/Neuonc/Noz175.808 |
0.307 |
|
| 2018 |
Rahme GJ, Gaskell E, Bernstein BE. GABPβ1L Wakes Up TERT. Cancer Cell. 34: 358-360. PMID 30205042 DOI: 10.1016/J.Ccell.2018.08.011 |
0.329 |
|
| 2018 |
Karaayvaz M, Cristea S, Gillespie SM, Patel AP, Mylvaganam R, Luo CC, Specht MC, Bernstein BE, Michor F, Ellisen LW. Unravelling subclonal heterogeneity and aggressive disease states in TNBC through single-cell RNA-seq. Nature Communications. 9: 3588. PMID 30181541 DOI: 10.1038/S41467-018-06052-0 |
0.377 |
|
| 2018 |
Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T. Methylation of Histone H3 K4 Mediates Association of the Isw1p ATPase with Chromatin. Molecular Cell. 70: 983. PMID 29883612 DOI: 10.1016/j.molcel.2018.05.012 |
0.448 |
|
| 2018 |
Filbin MG, Tirosh I, Hovestadt V, Shaw ML, Escalante LE, Mathewson ND, Neftel C, Frank N, Pelton K, Hebert CM, Haberler C, Yizhak K, Gojo J, Egervari K, Mount C, ... ... Bernstein BE, et al. Developmental and oncogenic programs in H3K27M gliomas dissected by single-cell RNA-seq. Science (New York, N.Y.). 360: 331-335. PMID 29674595 DOI: 10.1126/Science.Aao4750 |
0.349 |
|
| 2018 |
Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, ... ... Bernstein BE, et al. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. 33: 785-787. PMID 29634952 DOI: 10.1016/j.ccell.2018.03.024 |
0.388 |
|
| 2018 |
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, ... ... Bernstein BE, et al. Heritability enrichment of specifically expressed genes identifies disease-relevant tissues and cell types. Nature Genetics. 50: 621-629. PMID 29632380 DOI: 10.1038/S41588-018-0081-4 |
0.337 |
|
| 2018 |
Van Galen P, Hovestadt V, Wadsworth II M, Hughes T, Griffin GK, Verga JA, Stephansky J, Pastika TJ, Lombardi Story J, Pinkus GS, Pozdnyakova O, Galinsky I, Stone RM, Graubert TA, Shalek AK, ... ... Bernstein BE, et al. Single-Cell RNA-Seq Reveals AML Cellular Hierarchies Relevant to Clinical Outcomes and Immunity Blood. 132: 542-542. DOI: 10.1182/Blood-2018-99-113502 |
0.348 |
|
| 2018 |
Flavahan WA, Drier Y, Johnstone SE, Tarjan DR, Hegazi E, Sicinska ET, Hemming ML, Raut CP, Hornick JL, Demetri GD, Bernstein BE. Abstract 2996: Insulator dysfunction and epigenetic oncogene activation in SDH-deficient gastrointestinal stromal tumor Cancer Research. 78: 2996-2996. DOI: 10.1158/1538-7445.Am2018-2996 |
0.45 |
|
| 2017 |
Kleppe M, Koche R, Zou L, van Galen P, Hill CE, Dong L, De Groote S, Papalexi E, Hanasoge Somasundara AV, Cordner K, Keller M, Farnoud N, Medina J, McGovern E, Reyes J, ... ... Bernstein BE, et al. Dual Targeting of Oncogenic Activation and Inflammatory Signaling Increases Therapeutic Efficacy in Myeloproliferative Neoplasms. Cancer Cell. PMID 29249691 DOI: 10.1016/J.Ccell.2017.11.009 |
0.517 |
|
| 2017 |
Ryan RJH, Petrovic J, Rausch DM, Zhou Y, Lareau CA, Kluk MJ, Christie AL, Lee WY, Tarjan DR, Guo B, Donohue LKH, Gillespie SM, Nardi V, Hochberg EP, Blacklow SC, ... ... Bernstein BE, et al. A B Cell Regulome Links Notch to Downstream Oncogenic Pathways in Small B Cell Lymphomas. Cell Reports. 21: 784-797. PMID 29045844 DOI: 10.1016/J.Celrep.2017.09.066 |
0.382 |
|
| 2017 |
Rao SSP, Huang SC, Glenn St Hilaire B, Engreitz JM, Perez EM, Kieffer-Kwon KR, Sanborn AL, Johnstone SE, Bascom GD, Bochkov ID, Huang X, Shamim MS, Shin J, Turner D, Ye Z, ... ... Bernstein BE, et al. Cohesin Loss Eliminates All Loop Domains. Cell. 171: 305-320.e24. PMID 28985562 DOI: 10.1016/J.Cell.2017.09.026 |
0.526 |
|
| 2017 |
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, ... ... Bernstein BE, et al. A Genetic Variant Associated with Five Vascular Diseases Is a Distal Regulator of Endothelin-1 Gene Expression. Cell. 170: 522-533.e15. PMID 28753427 DOI: 10.1016/J.Cell.2017.06.049 |
0.35 |
|
| 2017 |
Flavahan WA, Gaskell E, Bernstein BE. Epigenetic plasticity and the hallmarks of cancer. Science (New York, N.Y.). 357. PMID 28729483 DOI: 10.1126/Science.Aal2380 |
0.404 |
|
| 2017 |
Miller TE, Liau BB, Wallace LC, Morton AR, Xie Q, Dixit D, Factor DC, Kim LJY, Morrow JJ, Wu Q, Mack SC, Hubert CG, Gillespie SM, Flavahan WA, Hoffmann T, ... ... Bernstein BE, et al. Transcription elongation factors represent in vivo cancer dependencies in glioblastoma. Nature. PMID 28678782 DOI: 10.1038/Nature23000 |
0.701 |
|
| 2017 |
Venteicher AS, Tirosh I, Hebert C, Yizhak K, Neftel C, Filbin MG, Hovestadt V, Escalante LE, Shaw ML, Rodman C, Gillespie SM, Dionne D, Luo CC, Ravichandran H, Mylvaganam R, ... ... Bernstein BE, et al. Decoupling genetics, lineages, and microenvironment in IDH-mutant gliomas by single-cell RNA-seq. Science (New York, N.Y.). 355. PMID 28360267 DOI: 10.1126/Science.Aai8478 |
0.302 |
|
| 2017 |
Grossman SR, Zhang X, Wang L, Engreitz J, Melnikov A, Rogov P, Tewhey R, Isakova A, Deplancke B, Bernstein BE, Mikkelsen TS, Lander ES. Systematic dissection of genomic features determining transcription factor binding and enhancer function. Proceedings of the National Academy of Sciences of the United States of America. PMID 28137873 DOI: 10.1073/Pnas.1621150114 |
0.549 |
|
| 2017 |
Wang X, Lee R, Alver B, Haswell J, Wang S, Troisi E, Bernstein B, Park P, Roberts C. Abstract LB-096: SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation Cancer Research. 77. DOI: 10.1158/1538-7445.Am2017-Lb-096 |
0.435 |
|
| 2017 |
Miller TE, Liau B, Wallace LC, Morton A, Xie Q, Dixit D, Factor D, Kim L, Morrow J, Wu Q, Mack S, Hubert C, Paddison PJ, Horbinski C, Bernstein B, et al. GENE-30. TRANSCRIPTION ELONGATION FACTORS REPRESENT IN VIVO CANCER DEPENDENCIES IN GLIOBLASTOMA Neuro-Oncology. 19: vi99-vi99. DOI: 10.1093/Neuonc/Nox168.404 |
0.689 |
|
| 2016 |
Liau BB, Sievers C, Donohue LK, Gillespie SM, Flavahan WA, Miller TE, Venteicher AS, Hebert CH, Carey CD, Rodig SJ, Shareef SJ, Najm FJ, van Galen P, Wakimoto H, Cahill DP, ... ... Bernstein BE, et al. Adaptive Chromatin Remodeling Drives Glioblastoma Stem Cell Plasticity and Drug Tolerance. Cell Stem Cell. PMID 27989769 DOI: 10.1016/J.Stem.2016.11.003 |
0.713 |
|
| 2016 |
Wang X, Lee RS, Alver BH, Haswell JR, Wang S, Mieczkowski J, Drier Y, Gillespie SM, Archer TC, Wu JN, Tzvetkov EP, Troisi EC, Pomeroy SL, Biegel JA, Tolstorukov MY, ... Bernstein BE, et al. SMARCB1-mediated SWI/SNF complex function is essential for enhancer regulation. Nature Genetics. PMID 27941797 DOI: 10.1038/Ng.3746 |
0.41 |
|
| 2016 |
Tirosh I, Venteicher AS, Hebert C, Escalante LE, Patel AP, Yizhak K, Fisher JM, Rodman C, Mount C, Filbin MG, Neftel C, Desai N, Nyman J, Izar B, Luo CC, ... ... Bernstein BE, et al. Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma. Nature. PMID 27806376 DOI: 10.1038/Nature20123 |
0.356 |
|
| 2016 |
Xie Q, Wu Q, Kim L, Miller TE, Liau BB, Mack SC, Yang K, Factor DC, Fang X, Huang Z, Zhou W, Alazem K, Wang X, Bernstein BE, Bao S, et al. RBPJ maintains brain tumor-initiating cells through CDK9-mediated transcriptional elongation. The Journal of Clinical Investigation. PMID 27322055 DOI: 10.1172/Jci86114 |
0.717 |
|
| 2016 |
Shema E, Jones D, Shoresh N, Donohue L, Ram O, Bernstein BE. Single-molecule decoding of combinatorially modified nucleosomes. Science (New York, N.Y.). 352: 717-21. PMID 27151869 DOI: 10.1126/Science.Aad7701 |
0.46 |
|
| 2016 |
G Hendrickson D, Kelley DR, Tenen D, Bernstein B, Rinn JL. Widespread RNA binding by chromatin-associated proteins. Genome Biology. 17: 28. PMID 26883116 DOI: 10.1186/S13059-016-0878-3 |
0.407 |
|
| 2016 |
Drier Y, Cotton MJ, Williamson KE, Gillespie SM, Ryan RJ, Kluk MJ, Carey CD, Rodig SJ, Sholl LM, Afrogheh AH, Faquin WC, Queimado L, Qi J, Wick MJ, El-Naggar AK, ... ... Bernstein BE, et al. An oncogenic MYB feedback loop drives alternate cell fates in adenoid cystic carcinoma. Nature Genetics. PMID 26829750 DOI: 10.1038/Ng.3502 |
0.593 |
|
| 2016 |
Ryan RJ, Petrovic J, Rausch D, Lareau C, Lee W, Donohue L, Christie AL, Gillespie S, Kluk MJ, Nardi V, Faryabi RB, Hochberg EP, Weinstock DM, Bernstein BE, Aster JC, et al. Notch-Regulated Enhancers in B-Cell Lymphoma Activate MYC and Potentiate B-Cell Receptor Signaling Blood. 128: 457-457. DOI: 10.1182/Blood.V128.22.457.457 |
0.398 |
|
| 2016 |
Bernstein BE. Abstract IA01: Epigenetic mechanisms of tumor initiation and evolution Cancer Research. 76. DOI: 10.1158/1538-7445.Chromepi15-Ia01 |
0.414 |
|
| 2016 |
Ryan RJ, Petrovic J, Rausch DM, Lee W, Kluk M, Donohue L, Gillespie S, Aster JC, Pear WS, Bernstein BE. Abstract 886: Notch signaling activates B-cell specific enhancers to drive oncogene targets in B-cell lymphoma Cancer Research. 76: 886-886. DOI: 10.1158/1538-7445.Am2016-886 |
0.372 |
|
| 2016 |
Flavahan W, Drier Y, Tarjan D, Liau B, Gillespie S, Venteicher A, Stemmer-Rachamimov A, Suva M, Bernstein B. GENT-19. INSULATOR DYSFUNCTION AS AN ONCOGENIC DRIVER IN GLIOMA Neuro-Oncology. 18: vi77-vi77. DOI: 10.1093/Neuonc/Now212.325 |
0.61 |
|
| 2015 |
Flavahan WA, Drier Y, Liau BB, Gillespie SM, Venteicher AS, Stemmer-Rachamimov AO, Suvà ML, Bernstein BE. Insulator dysfunction and oncogene activation in IDH mutant gliomas. Nature. PMID 26700815 DOI: 10.1038/Nature16490 |
0.704 |
|
| 2015 |
van Galen P, Viny AD, Ram O, Ryan RJ, Cotton MJ, Donohue L, Sievers C, Drier Y, Liau BB, Gillespie SM, Carroll KM, Cross MB, Levine RL, Bernstein BE. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes. Molecular Cell. PMID 26687680 DOI: 10.1016/J.Molcel.2015.11.003 |
0.747 |
|
| 2015 |
Rotem A, Ram O, Shoresh N, Sperling RA, Goren A, Weitz DA, Bernstein BE. Single-cell ChIP-seq reveals cell subpopulations defined by chromatin state. Nature Biotechnology. 33: 1165-72. PMID 26458175 DOI: 10.1038/Nbt.3383 |
0.45 |
|
| 2015 |
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. 126: 1930-9. PMID 26320100 DOI: 10.1182/Blood-2015-06-649087 |
0.456 |
|
| 2015 |
Ryan RJ, Drier Y, Whitton H, Cotton MJ, Kaur J, Issner R, Gillespie S, Epstein CB, Nardi V, Sohani AR, Hochberg EP, Bernstein BE. Detection of Enhancer-Associated Rearrangements Reveals Mechanisms of Oncogene Dysregulation in B-cell Lymphoma. Cancer Discovery. 5: 1058-71. PMID 26229090 DOI: 10.1158/2159-8290.Cd-15-0370 |
0.418 |
|
| 2015 |
Rotem A, Ram O, Shoresh N, Sperling RA, Schnall-Levin M, Zhang H, Basu A, Bernstein BE, Weitz DA. High-Throughput Single-Cell Labeling (Hi-SCL) for RNA-Seq Using Drop-Based Microfluidics. Plos One. 10: e0116328. PMID 26000628 DOI: 10.1371/Journal.Pone.0116328 |
0.321 |
|
| 2015 |
Gagliani N, Vesely MC, Iseppon A, Brockmann L, Xu H, Palm NW, de Zoete MR, Licona-Limón P, Paiva RS, Ching T, Weaver C, Zi X, Pan X, Fan R, Garmire LX, ... ... Bernstein B, et al. Th17 cells transdifferentiate into regulatory T cells during resolution of inflammation. Nature. 523: 221-5. PMID 25924064 DOI: 10.1038/Nature14452 |
0.308 |
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| 2015 |
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. PMID 25742749 DOI: 10.1038/Leu.2015.61 |
0.352 |
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| 2015 |
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, ... ... Bernstein BE, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248 |
0.648 |
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| 2015 |
Ziller MJ, Edri R, Yaffe Y, Donaghey J, Pop R, Mallard W, Issner R, Gifford CA, Goren A, Xing J, Gu H, Cacchiarelli D, Tsankov AM, Epstein C, Rinn JL, ... ... Bernstein BE, et al. Dissecting neural differentiation regulatory networks through epigenetic footprinting. Nature. 518: 355-9. PMID 25533951 DOI: 10.1038/Nature13990 |
0.378 |
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| 2015 |
Farh KK, Marson A, Zhu J, Kleinewietfeld M, Housley WJ, Beik S, Shoresh N, Whitton H, Ryan RJ, Shishkin AA, Hatan M, Carrasco-Alfonso MJ, Mayer D, Luckey CJ, Patsopoulos NA, ... ... Bernstein BE, et al. Genetic and epigenetic fine mapping of causal autoimmune disease variants. Nature. 518: 337-43. PMID 25363779 DOI: 10.1038/Nature13835 |
0.567 |
|
| 2015 |
Venteicher A, Tirosh I, Hebert C, Escalante L, Nahed B, Cahill D, Curry W, Martuza R, Bernstein B, Louis D, Regev A, Suva M. STEM-22LARGE-SCALE SINGLE-CELL RNA-seq REVEALS A DEVELOPMENTAL CELLULAR HIERARCHY IN HUMAN OLIGODENDROGLIOMA Neuro-Oncology. 17: v212.4-v213. DOI: 10.1093/Neuonc/Nov234.22 |
0.316 |
|
| 2015 |
van Galen P, Viny AD, Ram O, Ryan RJH, Cotton MJ, Donohue L, Sievers C, Drier Y, Liau BB, Gillespie SM, Carroll KM, Cross MB, Levine RL, Bernstein BE. A Multiplexed System for Quantitative Comparisons of Chromatin Landscapes Molecular Cell. DOI: 10.1016/j.molcel.2015.11.003 |
0.688 |
|
| 2015 |
van Galen P, Ram O, Ryan RJ, Cotton MJ, Donohue L, Drier Y, Sievers C, Gillespie SM, Bernstein BE. A low-input, multiplexed assay for quantitative comparison of chromatin landscapes Experimental Hematology. 43: S99. DOI: 10.1016/J.Exphem.2015.06.271 |
0.347 |
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| 2014 |
Riggi N, Knoechel B, Gillespie SM, Rheinbay E, Boulay G, Suvà ML, Rossetti NE, Boonseng WE, Oksuz O, Cook EB, Formey A, Patel A, Gymrek M, Thapar V, Deshpande V, ... ... Bernstein BE, et al. EWS-FLI1 utilizes divergent chromatin remodeling mechanisms to directly activate or repress enhancer elements in Ewing sarcoma. Cancer Cell. 26: 668-81. PMID 25453903 DOI: 10.1016/J.Ccell.2014.10.004 |
0.451 |
|
| 2014 |
Yashiro-Ohtani Y, Wang H, Zang C, Arnett KL, Bailis W, Ho Y, Knoechel B, Lanauze C, Louis L, Forsyth KS, Chen S, Chung Y, Schug J, Blobel GA, Liebhaber SA, ... Bernstein BE, et al. Long-range enhancer activity determines Myc sensitivity to Notch inhibitors in T cell leukemia. Proceedings of the National Academy of Sciences of the United States of America. 111: E4946-53. PMID 25369933 DOI: 10.1073/Pnas.1407079111 |
0.428 |
|
| 2014 |
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111 |
0.54 |
|
| 2014 |
Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, ... ... Bernstein BE, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415 |
0.638 |
|
| 2014 |
De Jager PL, Srivastava G, Lunnon K, Burgess J, Schalkwyk LC, Yu L, Eaton ML, Keenan BT, Ernst J, McCabe C, Tang A, Raj T, Replogle J, Brodeur W, Gabriel S, ... ... Bernstein BE, et al. Alzheimer's disease: early alterations in brain DNA methylation at ANK1, BIN1, RHBDF2 and other loci. Nature Neuroscience. 17: 1156-63. PMID 25129075 DOI: 10.1038/Nn.3786 |
0.549 |
|
| 2014 |
Patel AP, Tirosh I, Trombetta JJ, Shalek AK, Gillespie SM, Wakimoto H, Cahill DP, Nahed BV, Curry WT, Martuza RL, Louis DN, Rozenblatt-Rosen O, Suvà ML, Regev A, Bernstein BE. Single-cell RNA-seq highlights intratumoral heterogeneity in primary glioblastoma. Science (New York, N.Y.). 344: 1396-401. PMID 24925914 DOI: 10.1126/Science.1254257 |
0.37 |
|
| 2014 |
Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111 |
0.628 |
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| 2014 |
Attanasio C, Nord AS, Zhu Y, Blow MJ, Biddie SC, Mendenhall EM, Dixon J, Wright C, Hosseini R, Akiyama JA, Holt A, Plajzer-Frick I, Shoukry M, Afzal V, Ren B, ... Bernstein BE, et al. Tissue-specific SMARCA4 binding at active and repressed regulatory elements during embryogenesis. Genome Research. 24: 920-9. PMID 24752179 DOI: 10.1101/Gr.168930.113 |
0.44 |
|
| 2014 |
Suvà ML, Rheinbay E, Gillespie SM, Patel AP, Wakimoto H, Rabkin SD, Riggi N, Chi AS, Cahill DP, Nahed BV, Curry WT, Martuza RL, Rivera MN, Rossetti N, Kasif S, ... ... Bernstein BE, et al. Reconstructing and reprogramming the tumor-propagating potential of glioblastoma stem-like cells. Cell. 157: 580-94. PMID 24726434 DOI: 10.1016/J.Cell.2014.02.030 |
0.411 |
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| 2014 |
Knoechel B, Roderick JE, Williamson KE, Zhu J, Lohr JG, Cotton MJ, Gillespie SM, Fernandez D, Ku M, Wang H, Piccioni F, Silver SJ, Jain M, Pearson D, Kluk MJ, ... ... Bernstein BE, et al. An epigenetic mechanism of resistance to targeted therapy in T cell acute lymphoblastic leukemia. Nature Genetics. 46: 364-70. PMID 24584072 DOI: 10.1038/Ng.2913 |
0.568 |
|
| 2014 |
Wang H, Yashiro-Ohtani Y, Zang C, Wong YJ, Bailis W, Knoechel B, Bernstein B, Blacklow S, Liu XS, Pear WS, Aster JC. Alternative Super-Enhancer States Determine MYC Sensitivity to Notch and Brd4 Inhibitors in T Lymphoblastic Leukemia/Lymphoma Blood. 124: 863-863. DOI: 10.1182/Blood.V124.21.863.863 |
0.451 |
|
| 2014 |
Spitzer B, Guryanova OA, Abdel-Wahab O, Kucine N, Adli M, Berman JN, Meshinchi S, Bernstein B, Pelossof R, Leslie C, Levine RL. Characterizing Transcriptional and Epigenetic Signatures Induced By FLT3-ITD Activation Blood. 124: 2186-2186. DOI: 10.1182/Blood.V124.21.2186.2186 |
0.404 |
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| 2014 |
Knoechel B, Roderick J, Williamson K, Zhu J, Lohr J, Cotton M, Gillespie S, Fernandez D, Ku M, Wang H, Piccioni F, Silver S, Jain M, Pearson D, Kluk M, ... ... Bernstein B, et al. Abstract 4782: Epigenetic resistance to Notch inhibition in T cell acute lymphoblastic leukemia Cancer Research. 74: 4782-4782. DOI: 10.1158/1538-7445.Am2014-4782 |
0.586 |
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| 2013 |
Abdel-Wahab O, Gao J, Adli M, Dey A, Trimarchi T, Chung YR, Kuscu C, Hricik T, Ndiaye-Lobry D, Lafave LM, Koche R, Shih AH, Guryanova OA, Kim E, Li S, ... ... Bernstein BE, et al. Deletion of Asxl1 results in myelodysplasia and severe developmental defects in vivo. The Journal of Experimental Medicine. 210: 2641-59. PMID 24218140 DOI: 10.1084/Jem.20131141 |
0.346 |
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| 2013 |
Maeder ML, Angstman JF, Richardson ME, Linder SJ, Cascio VM, Tsai SQ, Ho QH, Sander JD, Reyon D, Bernstein BE, Costello JF, Wilkinson MF, Joung JK. Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins. Nature Biotechnology. 31: 1137-42. PMID 24108092 DOI: 10.1038/Nbt.2726 |
0.491 |
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| 2013 |
Isono K, Endo TA, Ku M, Yamada D, Suzuki R, Sharif J, Ishikura T, Toyoda T, Bernstein BE, Koseki H. SAM domain polymerization links subnuclear clustering of PRC1 to gene silencing. Developmental Cell. 26: 565-77. PMID 24091011 DOI: 10.1016/J.Devcel.2013.08.016 |
0.381 |
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| 2013 |
Mendenhall EM, Williamson KE, Reyon D, Zou JY, Ram O, Joung JK, Bernstein BE. Locus-specific editing of histone modifications at endogenous enhancers. Nature Biotechnology. 31: 1133-6. PMID 24013198 DOI: 10.1038/Nbt.2701 |
0.536 |
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| 2013 |
Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK. In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites. Nucleic Acids Research. 41: e181. PMID 23945932 DOI: 10.1093/Nar/Gkt716 |
0.349 |
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| 2013 |
Ziller MJ, Gu H, Müller F, Donaghey J, Tsai LT, Kohlbacher O, De Jager PL, Rosen ED, Bennett DA, Bernstein BE, Gnirke A, Meissner A. Charting a dynamic DNA methylation landscape of the human genome. Nature. 500: 477-81. PMID 23925113 DOI: 10.1038/Nature12433 |
0.491 |
|
| 2013 |
Rheinbay E, Suvà ML, Gillespie SM, Wakimoto H, Patel AP, Shahid M, Oksuz O, Rabkin SD, Martuza RL, Rivera MN, Louis DN, Kasif S, Chi AS, Bernstein BE. An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Reports. 3: 1567-79. PMID 23707066 DOI: 10.1016/J.Celrep.2013.04.021 |
0.412 |
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| 2013 |
Gifford CA, Ziller MJ, Gu H, Trapnell C, Donaghey J, Tsankov A, Shalek AK, Kelley DR, Shishkin AA, Issner R, Zhang X, Coyne M, Fostel JL, Holmes L, Meldrim J, ... ... Bernstein BE, et al. Transcriptional and epigenetic dynamics during specification of human embryonic stem cells. Cell. 153: 1149-63. PMID 23664763 DOI: 10.1016/J.Cell.2013.04.037 |
0.6 |
|
| 2013 |
Suvà ML, Riggi N, Bernstein BE. Epigenetic reprogramming in cancer. Science (New York, N.Y.). 339: 1567-70. PMID 23539597 DOI: 10.1126/Science.1230184 |
0.431 |
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| 2013 |
Zhu J, Adli M, Zou JY, Verstappen G, Coyne M, Zhang X, Durham T, Miri M, Deshpande V, De Jager PL, Bennett DA, Houmard JA, Muoio DM, Onder TT, Camahort R, ... ... Bernstein BE, et al. Genome-wide chromatin state transitions associated with developmental and environmental cues. Cell. 152: 642-54. PMID 23333102 DOI: 10.1016/J.Cell.2012.12.033 |
0.438 |
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| 2013 |
Mendenhall EM, Williamson K, Reyon D, Joung JK, Bernstein BE. Identification of promoter targets of enhancers by epigenetic knockdown using TAL DNA binding proteins Epigenetics & Chromatin. 6. DOI: 10.1186/1756-8935-6-S1-O12 |
0.523 |
|
| 2013 |
Bernstein BE. Abstract IA06: Epigenetic regulation and heterogeneity in cancer Cancer Research. 73. DOI: 10.1158/1538-7445.Cec13-Ia06 |
0.424 |
|
| 2012 |
Peterson KA, Nishi Y, Ma W, Vedenko A, Shokri L, Zhang X, McFarlane M, Baizabal JM, Junker JP, van Oudenaarden A, Mikkelsen T, Bernstein BE, Bailey TL, Bulyk ML, Wong WH, et al. Neural-specific Sox2 input and differential Gli-binding affinity provide context and positional information in Shh-directed neural patterning. Genes & Development. 26: 2802-16. PMID 23249739 DOI: 10.1101/Gad.207142.112 |
0.359 |
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| 2012 |
Sebastián C, Zwaans BM, Silberman DM, Gymrek M, Goren A, Zhong L, Ram O, Truelove J, Guimaraes AR, Toiber D, Cosentino C, Greenson JK, MacDonald AI, McGlynn L, Maxwell F, ... ... Bernstein BE, et al. The histone deacetylase SIRT6 is a tumor suppressor that controls cancer metabolism. Cell. 151: 1185-99. PMID 23217706 DOI: 10.1016/J.Cell.2012.10.047 |
0.319 |
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| 2012 |
Beck S, Bernstein BE, Campbell RM, Costello JF, Dhanak D, Ecker JR, Greally JM, Issa JP, Laird PW, Polyak K, Tycko B, Jones PA. A blueprint for an international cancer epigenome consortium. A report from the AACR Cancer Epigenome Task Force. Cancer Research. 72: 6319-24. PMID 23188507 DOI: 10.1158/0008-5472.Can-12-3658 |
0.313 |
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| 2012 |
Ku M, Jaffe JD, Koche RP, Rheinbay E, Endoh M, Koseki H, Carr SA, Bernstein BE. H2A.Z landscapes and dual modifications in pluripotent and multipotent stem cells underlie complex genome regulatory functions. Genome Biology. 13: R85. PMID 23034477 DOI: 10.1186/Gb-2012-13-10-R85 |
0.466 |
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| 2012 |
Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111 |
0.573 |
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| 2012 |
Garber M, Yosef N, Goren A, Raychowdhury R, Thielke A, Guttman M, Robinson J, Minie B, Chevrier N, Itzhaki Z, Blecher-Gonen R, Bornstein C, Amann-Zalcenstein D, Weiner A, Friedrich D, ... ... Bernstein BE, et al. A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals. Molecular Cell. 47: 810-22. PMID 22940246 DOI: 10.1016/J.Molcel.2012.07.030 |
0.442 |
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| 2012 |
Abdel-Wahab O, Adli M, LaFave LM, Gao J, Hricik T, Shih AH, Pandey S, Patel JP, Chung YR, Koche R, Perna F, Zhao X, Taylor JE, Park CY, Carroll M, ... ... Bernstein BE, et al. ASXL1 mutations promote myeloid transformation through loss of PRC2-mediated gene repression. Cancer Cell. 22: 180-93. PMID 22897849 DOI: 10.1016/J.Ccr.2012.06.032 |
0.383 |
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| 2012 |
Endoh M, Endo TA, Endoh T, Isono K, Sharif J, Ohara O, Toyoda T, Ito T, Eskeland R, Bickmore WA, Vidal M, Bernstein BE, Koseki H. Histone H2A mono-ubiquitination is a crucial step to mediate PRC1-dependent repression of developmental genes to maintain ES cell identity. Plos Genetics. 8: e1002774. PMID 22844243 DOI: 10.1371/Journal.Pgen.1002774 |
0.514 |
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| 2012 |
Koppikar P, Bhagwat N, Kilpivaara O, Manshouri T, Adli M, Hricik T, Liu F, Saunders LM, Mullally A, Abdel-Wahab O, Leung L, Weinstein A, Marubayashi S, Goel A, Gönen M, ... ... Bernstein BE, et al. Heterodimeric JAK-STAT activation as a mechanism of persistence to JAK2 inhibitor therapy. Nature. 489: 155-9. PMID 22820254 DOI: 10.1038/Nature11303 |
0.304 |
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| 2012 |
Zullo JM, Demarco IA, Piqué-Regi R, Gaffney DJ, Epstein CB, Spooner CJ, Luperchio TR, Bernstein BE, Pritchard JK, Reddy KL, Singh H. DNA sequence-dependent compartmentalization and silencing of chromatin at the nuclear lamina. Cell. 149: 1474-87. PMID 22726435 DOI: 10.1016/J.Cell.2012.04.035 |
0.49 |
|
| 2012 |
Ryan RJ, Bernstein BE. Molecular biology. Genetic events that shape the cancer epigenome. Science (New York, N.Y.). 336: 1513-4. PMID 22723401 DOI: 10.1126/Science.1223730 |
0.457 |
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| 2012 |
Rheinbay E, Louis DN, Bernstein BE, Suvà ML. A tell-tail sign of chromatin: histone mutations drive pediatric glioblastoma. Cancer Cell. 21: 329-31. PMID 22439930 DOI: 10.1016/J.Ccr.2012.03.001 |
0.418 |
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| 2012 |
Mendenhall EM, Bernstein BE. DNA-protein interactions in high definition. Genome Biology. 13: 139. PMID 22283870 DOI: 10.1186/Gb-2012-13-1-139 |
0.405 |
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| 2011 |
Ram O, Goren A, Amit I, Shoresh N, Yosef N, Ernst J, Kellis M, Gymrek M, Issner R, Coyne M, Durham T, Zhang X, Donaghey J, Epstein CB, Regev A, ... Bernstein BE, et al. Combinatorial patterning of chromatin regulators uncovered by genome-wide location analysis in human cells. Cell. 147: 1628-39. PMID 22196736 DOI: 10.1016/J.Cell.2011.09.057 |
0.609 |
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| 2011 |
Ziller MJ, Müller F, Liao J, Zhang Y, Gu H, Bock C, Boyle P, Epstein CB, Bernstein BE, Lengauer T, Gnirke A, Meissner A. Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. Plos Genetics. 7: e1002389. PMID 22174693 DOI: 10.1371/Journal.Pgen.1002389 |
0.416 |
|
| 2011 |
Adli M, Bernstein BE. Whole-genome chromatin profiling from limited numbers of cells using nano-ChIP-seq. Nature Protocols. 6: 1656-68. PMID 21959244 DOI: 10.1038/Nprot.2011.402 |
0.415 |
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| 2011 |
Zhao B, Zou J, Wang H, Johannsen E, Peng CW, Quackenbush J, Mar JC, Morton CC, Freedman ML, Blacklow SC, Aster JC, Bernstein BE, Kieff E. Epstein-Barr virus exploits intrinsic B-lymphocyte transcription programs to achieve immortal cell growth. Proceedings of the National Academy of Sciences of the United States of America. 108: 14902-7. PMID 21746931 DOI: 10.1073/Pnas.1108892108 |
0.415 |
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| 2011 |
Wang H, Zou J, Zhao B, Johannsen E, Ashworth T, Wong H, Pear WS, Schug J, Blacklow SC, Arnett KL, Bernstein BE, Kieff E, Aster JC. Genome-wide analysis reveals conserved and divergent features of Notch1/RBPJ binding in human and murine T-lymphoblastic leukemia cells. Proceedings of the National Academy of Sciences of the United States of America. 108: 14908-13. PMID 21737748 DOI: 10.1073/Pnas.1109023108 |
0.41 |
|
| 2011 |
Ernst J, Kheradpour P, Mikkelsen TS, Shoresh N, Ward LD, Epstein CB, Zhang X, Wang L, Issner R, Coyne M, Ku M, Durham T, Kellis M, Bernstein BE. Mapping and analysis of chromatin state dynamics in nine human cell types. Nature. 473: 43-9. PMID 21441907 DOI: 10.1038/Nature09906 |
0.641 |
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| 2011 |
Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, ... Bernstein BE, et al. Initial genome sequencing and analysis of multiple myeloma. Nature. 471: 467-72. PMID 21430775 DOI: 10.1038/Nature09837 |
0.551 |
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| 2011 |
Jiang H, Shukla A, Wang X, Chen WY, Bernstein BE, Roeder RG. Role for Dpy-30 in ES cell-fate specification by regulation of H3K4 methylation within bivalent domains. Cell. 144: 513-25. PMID 21335234 DOI: 10.1016/J.Cell.2011.01.020 |
0.481 |
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| 2011 |
Koche RP, Smith ZD, Adli M, Gu H, Ku M, Gnirke A, Bernstein BE, Meissner A. Reprogramming factor expression initiates widespread targeted chromatin remodeling. Cell Stem Cell. 8: 96-105. PMID 21211784 DOI: 10.1016/J.Stem.2010.12.001 |
0.505 |
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| 2011 |
Zhou VW, Goren A, Bernstein BE. Charting histone modifications and the functional organization of mammalian genomes. Nature Reviews. Genetics. 12: 7-18. PMID 21116306 DOI: 10.1038/Nrg2905 |
0.79 |
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| 2011 |
Li X, Isono K, Yamada D, Endo TA, Endoh M, Shinga J, Mizutani-Koseki Y, Otte AP, Casanova M, Kitamura H, Kamijo T, Sharif J, Ohara O, Toyada T, Bernstein BE, et al. Mammalian polycomb-like Pcl2/Mtf2 is a novel regulatory component of PRC2 that can differentially modulate polycomb activity both at the Hox gene cluster and at Cdkn2a genes. Molecular and Cellular Biology. 31: 351-64. PMID 21059868 DOI: 10.1128/Mcb.00259-10 |
0.424 |
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| 2011 |
Abdel-Wahab O, Adli M, Saunders L, Gao J, Shih AH, Pandey S, Jaffe J, Zhao X, Perna F, Carroll M, Melnick A, Nimer SD, Aifantis I, Bernstein B, Levine RL. ASXL1 Mutations Promote Myeloid Transformation Through Inhibition of PRC2-Mediated Gene Repression Blood. 118: 405-405. DOI: 10.1182/Blood.V118.21.405.405 |
0.423 |
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| 2010 |
Mendenhall EM, Koche RP, Truong T, Zhou VW, Issac B, Chi AS, Ku M, Bernstein BE. GC-rich sequence elements recruit PRC2 in mammalian ES cells. Plos Genetics. 6: e1001244. PMID 21170310 DOI: 10.1371/Journal.Pgen.1001244 |
0.799 |
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| 2010 |
Bernstein BE, Stamatoyannopoulos JA, Costello JF, Ren B, Milosavljevic A, Meissner A, Kellis M, Marra MA, Beaudet AL, Ecker JR, Farnham PJ, Hirst M, Lander ES, Mikkelsen TS, Thomson JA. The NIH Roadmap Epigenomics Mapping Consortium. Nature Biotechnology. 28: 1045-8. PMID 20944595 DOI: 10.1038/Nbt1010-1045 |
0.585 |
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| 2010 |
Harris RA, Wang T, Coarfa C, Nagarajan RP, Hong C, Downey SL, Johnson BE, Fouse SD, Delaney A, Zhao Y, Olshen A, Ballinger T, Zhou X, Forsberg KJ, Gu J, ... ... Bernstein BE, et al. Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nature Biotechnology. 28: 1097-105. PMID 20852635 DOI: 10.1038/Nbt.1682 |
0.439 |
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| 2010 |
Adli M, Zhu J, Bernstein BE. Genome-wide chromatin maps derived from limited numbers of hematopoietic progenitors. Nature Methods. 7: 615-8. PMID 20622861 DOI: 10.1038/Nmeth.1478 |
0.459 |
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| 2010 |
Aiden AP, Rivera MN, Rheinbay E, Ku M, Coffman EJ, Truong TT, Vargas SO, Lander ES, Haber DA, Bernstein BE. Wilms tumor chromatin profiles highlight stem cell properties and a renal developmental network. Cell Stem Cell. 6: 591-602. PMID 20569696 DOI: 10.1016/J.Stem.2010.03.016 |
0.559 |
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| 2010 |
Ozsolak F, Goren A, Gymrek M, Guttman M, Regev A, Bernstein BE, Milos PM. Digital transcriptome profiling from attomole-level RNA samples. Genome Research. 20: 519-25. PMID 20133332 DOI: 10.1101/Gr.102129.109 |
0.371 |
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| 2010 |
Li G, Margueron R, Ku M, Chambon P, Bernstein BE, Reinberg D. Jarid2 and PRC2, partners in regulating gene expression. Genes & Development. 24: 368-80. PMID 20123894 DOI: 10.1101/Gad.1886410 |
0.515 |
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| 2010 |
Goren A, Ozsolak F, Shoresh N, Ku M, Adli M, Hart C, Gymrek M, Zuk O, Regev A, Milos PM, Bernstein BE. Chromatin profiling by directly sequencing small quantities of immunoprecipitated DNA. Nature Methods. 7: 47-9. PMID 19946276 DOI: 10.1038/Nmeth.1404 |
0.458 |
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| 2009 |
Yu M, Riva L, Xie H, Schindler Y, Moran TB, Cheng Y, Yu D, Hardison R, Weiss MJ, Orkin SH, Bernstein BE, Fraenkel E, Cantor AB. Insights into GATA-1-mediated gene activation versus repression via genome-wide chromatin occupancy analysis. Molecular Cell. 36: 682-95. PMID 19941827 DOI: 10.1016/J.Molcel.2009.11.002 |
0.459 |
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| 2009 |
Lieberman-Aiden E, van Berkum NL, Williams L, Imakaev M, Ragoczy T, Telling A, Amit I, Lajoie BR, Sabo PJ, Dorschner MO, Sandstrom R, Bernstein B, Bender MA, Groudine M, Gnirke A, et al. Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (New York, N.Y.). 326: 289-93. PMID 19815776 DOI: 10.1126/Science.1181369 |
0.516 |
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| 2009 |
Amit I, Garber M, Chevrier N, Leite AP, Donner Y, Eisenhaure T, Guttman M, Grenier JK, Li W, Zuk O, Schubert LA, Birditt B, Shay T, Goren A, Zhang X, ... ... Bernstein BE, et al. Unbiased reconstruction of a mammalian transcriptional network mediating pathogen responses. Science (New York, N.Y.). 326: 257-63. PMID 19729616 DOI: 10.1126/Science.1179050 |
0.403 |
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| 2009 |
Khalil AM, Guttman M, Huarte M, Garber M, Raj A, Rivea Morales D, Thomas K, Presser A, Bernstein BE, van Oudenaarden A, Regev A, Lander ES, Rinn JL. Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America. 106: 11667-72. PMID 19571010 DOI: 10.1073/Pnas.0904715106 |
0.606 |
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| 2009 |
Guttman M, Amit I, Garber M, French C, Lin MF, Feldser D, Huarte M, Zuk O, Carey BW, Cassady JP, Cabili MN, Jaenisch R, Mikkelsen TS, Jacks T, Hacohen N, ... Bernstein BE, et al. Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature. 458: 223-7. PMID 19182780 DOI: 10.1038/Nature07672 |
0.684 |
|
| 2009 |
Chi AS, Bernstein BE. Developmental biology. Pluripotent chromatin state. Science (New York, N.Y.). 323: 220-1. PMID 19131621 DOI: 10.1126/Science.1166261 |
0.518 |
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| 2009 |
Chapman MA, Brunet J, Keats JJ, Baker A, Adli M, Schinzel AC, Ahmann G, Christina H, Moore A, Shanmugam V, Perkins LM, Auclair D, Hahn WC, Bernstein BE, Bergsagel L, et al. HOXA9 Is a Novel Therapeutic Target in Multiple Myeloma. Blood. 114: 832-832. DOI: 10.1182/Blood.V114.22.832.832 |
0.399 |
|
| 2008 |
Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): Overview. Csh Protocols. 2008: pdb.top42. PMID 21356838 DOI: 10.1101/Pdb.Top42 |
0.656 |
|
| 2008 |
Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): III. Sample Purification. Csh Protocols. 2008: pdb.prot5004. PMID 21356836 DOI: 10.1101/Pdb.Prot5004 |
0.644 |
|
| 2008 |
Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): II. Second-Strand Synthesis and In Vitro Transcription. Csh Protocols. 2008: pdb.prot5003. PMID 21356835 DOI: 10.1101/Pdb.Prot5003 |
0.644 |
|
| 2008 |
Liu CL, Bernstein BE, Schreiber SL. Whole Genome Amplification by T7-Based Linear Amplification of DNA (TLAD): I. CIP Treatment of Samples and Tailing Reaction with Terminal Transferase. Csh Protocols. 2008: pdb.prot5002. PMID 21356834 DOI: 10.1101/Pdb.Prot5002 |
0.661 |
|
| 2008 |
Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, ... ... Bernstein BE, et al. Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. Plos Genetics. 4: e1000242. PMID 18974828 DOI: 10.1371/Journal.Pgen.1000242 |
0.632 |
|
| 2008 |
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 Biology. 9: R137. PMID 18798982 DOI: 10.1186/Gb-2008-9-9-R137 |
0.324 |
|
| 2008 |
Meissner A, Mikkelsen TS, Gu H, Wernig M, Hanna J, Sivachenko A, Zhang X, Bernstein BE, Nusbaum C, Jaffe DB, Gnirke A, Jaenisch R, Lander ES. Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature. 454: 766-70. PMID 18600261 DOI: 10.1038/Nature07107 |
0.617 |
|
| 2008 |
Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis. Nature. 454: 49-55. PMID 18509334 DOI: 10.1038/Nature07056 |
0.605 |
|
| 2008 |
Mendenhall EM, Bernstein BE. Chromatin state maps: new technologies, new insights. Current Opinion in Genetics & Development. 18: 109-15. PMID 18339538 DOI: 10.1016/J.Gde.2008.01.010 |
0.482 |
|
| 2008 |
Liu CL, Bernstein BE, Schreiber SL. Whole genome ampification by T7-based linear amplification of DNA (TLAD): I. CIP treatment of sample and tailing reaction with terminal transferase Cold Spring Harbor Protocols. 3. DOI: 10.1101/pdb.prot5002 |
0.595 |
|
| 2008 |
Mikkelsen TS, Hanna J, Zhang X, Ku M, Wernig M, Schorderet P, Bernstein BE, Jaenisch R, Lander ES, Meissner A. Dissecting direct reprogramming through integrative genomic analysis (Nature (2008) 454, (49-55)) Nature. 454: 794. DOI: 10.1038/Nature07196 |
0.461 |
|
| 2007 |
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, ... ... Bernstein BE, et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature. 448: 553-60. PMID 17603471 DOI: 10.1038/Nature06008 |
0.625 |
|
| 2007 |
Wernig M, Meissner A, Foreman R, Brambrink T, Ku M, Hochedlinger K, Bernstein BE, Jaenisch R. In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature. 448: 318-24. PMID 17554336 DOI: 10.1038/Nature05944 |
0.395 |
|
| 2007 |
Bernstein BE, Meissner A, Lander ES. The mammalian epigenome. Cell. 128: 669-81. PMID 17320505 DOI: 10.1016/J.Cell.2007.01.033 |
0.579 |
|
| 2006 |
Huebert DJ, Kamal M, O'Donovan A, Bernstein BE. Genome-wide analysis of histone modifications by ChIP-on-chip. Methods (San Diego, Calif.). 40: 365-9. PMID 17101450 DOI: 10.1016/J.Ymeth.2006.07.032 |
0.514 |
|
| 2006 |
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. Nature Structural & Molecular Biology. 13: 852-4. PMID 16892064 DOI: 10.1038/Nsmb1131 |
0.364 |
|
| 2006 |
Bernstein BE, Mikkelsen TS, Xie X, Kamal M, Huebert DJ, Cuff J, Fry B, Meissner A, Wernig M, Plath K, Jaenisch R, Wagschal A, Feil R, Schreiber SL, Lander ES. A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell. 125: 315-26. PMID 16630819 DOI: 10.1016/J.Cell.2006.02.041 |
0.705 |
|
| 2005 |
Huebert DJ, Bernstein BE. Genomic views of chromatin. Current Opinion in Genetics & Development. 15: 476-81. PMID 16099159 DOI: 10.1016/J.Gde.2005.08.001 |
0.466 |
|
| 2005 |
Bernstein BE, Kellis M. Large-scale discovery and validation of functional elements in the human genome. Genome Biology. 6: 312. PMID 15774039 DOI: 10.1186/Gb-2005-6-3-312 |
0.541 |
|
| 2005 |
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, Gingeras TR, Schreiber SL, Lander ES. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 120: 169-81. PMID 15680324 DOI: 10.1016/J.Cell.2005.01.001 |
0.674 |
|
| 2004 |
Bernstein BE, Liu CL, Humphrey EL, Perlstein EO, Schreiber SL. Global nucleosome occupancy in yeast. Genome Biology. 5: R62. PMID 15345046 DOI: 10.1186/Gb-2004-5-9-R62 |
0.801 |
|
| 2004 |
Humphrey EL, Shamji AF, Bernstein BE, Schreiber SL. Rpd3p relocation mediates a transcriptional response to rapamycin in yeast. Chemistry & Biology. 11: 295-9. PMID 15123258 DOI: 10.1016/J.Chembiol.2004.03.001 |
0.793 |
|
| 2004 |
Bernstein BE, Humphrey EL, Liu CL, Schreiber SL. The use of chromatin immunoprecipitation assays in genome-wide analyses of histone modifications. Methods in Enzymology. 376: 349-60. PMID 14975317 DOI: 10.1016/S0076-6879(03)76023-6 |
0.819 |
|
| 2003 |
Santos-Rosa H, Schneider R, Bernstein BE, Karabetsou N, Morillon A, Weise C, Schreiber SL, Mellor J, Kouzarides T. Methylation of histone H3 K4 mediates association of the Isw1p ATPase with chromatin Molecular Cell. 12: 1325-1332. PMID 14636589 DOI: 10.1016/S1097-2765(03)00438-6 |
0.565 |
|
| 2003 |
Liu CL, Schreiber SL, Bernstein BE. Development and validation of a T7 based linear amplification for genomic DNA. Bmc Genomics. 4: 19. PMID 12740028 DOI: 10.1186/1471-2164-4-19 |
0.685 |
|
| 2002 |
Schreiber SL, Bernstein BE. Signaling network model of chromatin. Cell. 111: 771-8. PMID 12526804 DOI: 10.1016/S0092-8674(02)01196-0 |
0.531 |
|
| 2002 |
Bernstein BE, Schreiber SL. Global approaches to chromatin. Chemistry & Biology. 9: 1167-73. PMID 12445767 DOI: 10.1016/S1074-5521(02)00265-X |
0.595 |
|
| 2002 |
Santos-Rosa H, Schneider R, Bannister AJ, Sherriff J, Bernstein BE, Emre NC, Schreiber SL, Mellor J, Kouzarides T. Active genes are tri-methylated at K4 of histone H3. Nature. 419: 407-11. PMID 12353038 DOI: 10.1038/Nature01080 |
0.541 |
|
| 2002 |
Bernstein BE, Humphrey EL, Erlich RL, Schneider R, Bouman P, Liu JS, Kouzarides T, Schreiber SL. Methylation of histone H3 Lys 4 in coding regions of active genes. Proceedings of the National Academy of Sciences of the United States of America. 99: 8695-700. PMID 12060701 DOI: 10.1073/Pnas.082249499 |
0.808 |
|
| 2000 |
Bernstein BE, Tong JK, Schreiber SL. Genomewide studies of histone deacetylase function in yeast. Proceedings of the National Academy of Sciences of the United States of America. 97: 13708-13. PMID 11095743 DOI: 10.1073/Pnas.250477697 |
0.798 |
|
| 1998 |
Bernstein BE, Williams DM, Bressi JC, Kuhn P, Gelb MH, Blackburn GM, Hol WG. A bisubstrate analog induces unexpected conformational changes in phosphoglycerate kinase from Trypanosoma brucei. Journal of Molecular Biology. 279: 1137-48. PMID 9642090 DOI: 10.1006/Jmbi.1998.1835 |
0.501 |
|
| 1998 |
Chandra NR, Muirhead H, Holbrook JJ, Bernstein BE, Hol WG, Sessions RB. A general method of domain closure is applied to phosphoglycerate kinase and the result compared with the crystal structure of a closed conformation of the enzyme. Proteins. 30: 372-80. PMID 9533621 DOI: 10.1002/(Sici)1097-0134(19980301)30:4<372::Aid-Prot4>3.0.Co;2-L |
0.498 |
|
| 1998 |
Bernstein BE, Hol WG. Crystal structures of substrates and products bound to the phosphoglycerate kinase active site reveal the catalytic mechanism. Biochemistry. 37: 4429-36. PMID 9521762 DOI: 10.1021/Bi9724117 |
0.503 |
|
| 1998 |
Bernstein BE, Michels PA, Kim H, Petra PH, Hol WG. The importance of dynamic light scattering in obtaining multiple crystal forms of Trypanosoma brucei PGK. Protein Science : a Publication of the Protein Society. 7: 504-7. PMID 9521128 DOI: 10.1002/Pro.5560070232 |
0.474 |
|
| 1997 |
Bernstein BE, Hol WG. Probing the limits of the molecular replacement method: the case of Trypanosoma brucei phosphoglycerate kinase. Acta Crystallographica. Section D, Biological Crystallography. 53: 756-64. PMID 15299865 DOI: 10.1107/S0907444997010214 |
0.497 |
|
| 1997 |
Bernstein BE, Michels PA, Hol WG. Synergistic effects of substrate-induced conformational changes in phosphoglycerate kinase activation. Nature. 385: 275-8. PMID 9000079 DOI: 10.1038/385275A0 |
0.504 |
|
| 1994 |
Bernstein BE, Hoffman RC, Klevit RE. Sequence-specific DNA recognition by Cys2, His2 zinc fingers Annals of the New York Academy of Sciences. 726: 92-104. PMID 8092710 DOI: 10.1111/J.1749-6632.1994.Tb52800.X |
0.322 |
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