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The EN-TEx resource of multi-tissue personal epigenomes & variant-impact models.
Rozowsky J, Gao J, Borsari B, Yang YT, Galeev T, Gürsoy G, Epstein CB, Xiong K, Xu J, Li T, Liu J, Yu K, Berthel A, Chen Z, Navarro F, Sun MS, Wright J, Chang J, Cameron CJF, Shoresh N, Gaskell E, Drenkow J, Adrian J, Aganezov S, Aguet F, Balderrama-Gutierrez G, Banskota S, Corona GB, Chee S, Chhetri SB, Cortez Martins GC, Danyko C, Davis CA, Farid D, Farrell NP, Gabdank I, Gofin Y, Gorkin DU, Gu M, Hecht V, Hitz BC, Issner R, Jiang Y, Kirsche M, Kong X, Lam BR, Li S, Li B, Li X, Lin KZ, Luo R, Mackiewicz M, Meng R, Moore JE, Mudge J, Nelson N, Nusbaum C, Popov I, Pratt HE, Qiu Y, Ramakrishnan S, Raymond J, Salichos L, Scavelli A, Schreiber JM, Sedlazeck FJ, See LH, Sherman RM, Shi X, Shi M, Sloan CA, Strattan JS, Tan Z, Tanaka FY, Vlasova A, Wang J, Werner J, Williams B, Xu M, Yan C, Yu L, Zaleski C, Zhang J, Ardlie K, Cherry JM, Mendenhall EM, Noble WS, Weng Z, Levine ME, Dobin A, Wold B, Mortazavi A, Ren B, Gillis J, Myers RM, Snyder MP, Choudhary J, Milosavljevic A, Schatz MC, Bernstein BE, Guigó R, Gingeras TR, Gerstein M. Rozowsky J, et al. Among authors: bernstein be. Cell. 2023 Mar 30;186(7):1493-1511.e40. doi: 10.1016/j.cell.2023.02.018. Cell. 2023. PMID: 37001506 Free PMC article.
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells.
Mikkelsen TS, Ku M, Jaffe DB, Issac B, Lieberman E, Giannoukos G, Alvarez P, Brockman W, Kim TK, Koche RP, Lee W, Mendenhall E, O'Donovan A, Presser A, Russ C, Xie X, Meissner A, Wernig M, Jaenisch R, Nusbaum C, Lander ES, Bernstein BE. Mikkelsen TS, et al. Among authors: bernstein be. Nature. 2007 Aug 2;448(7153):553-60. doi: 10.1038/nature06008. Epub 2007 Jul 1. Nature. 2007. PMID: 17603471 Free PMC article.
Chromatin state maps: new technologies, new insights.
Mendenhall EM, Bernstein BE. Mendenhall EM, et al. Among authors: bernstein be. Curr Opin Genet Dev. 2008 Apr;18(2):109-15. doi: 10.1016/j.gde.2008.01.010. Epub 2008 Mar 12. Curr Opin Genet Dev. 2008. PMID: 18339538 Free PMC article. Review.
Model-based analysis of ChIP-Seq (MACS).
Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W, Liu XS. Zhang Y, et al. Among authors: bernstein be. Genome Biol. 2008;9(9):R137. doi: 10.1186/gb-2008-9-9-r137. Epub 2008 Sep 17. Genome Biol. 2008. PMID: 18798982 Free PMC article.
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains.
Ku M, Koche RP, Rheinbay E, Mendenhall EM, Endoh M, Mikkelsen TS, Presser A, Nusbaum C, Xie X, Chi AS, Adli M, Kasif S, Ptaszek LM, Cowan CA, Lander ES, Koseki H, Bernstein BE. Ku M, et al. Among authors: bernstein be. PLoS Genet. 2008 Oct;4(10):e1000242. doi: 10.1371/journal.pgen.1000242. Epub 2008 Oct 31. PLoS Genet. 2008. PMID: 18974828 Free PMC article.
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications.
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. Harris RA, et al. Among authors: bernstein be. Nat Biotechnol. 2010 Oct;28(10):1097-105. doi: 10.1038/nbt.1682. Epub 2010 Sep 19. Nat Biotechnol. 2010. PMID: 20852635 Free PMC article.
The NIH Roadmap Epigenomics Mapping Consortium.
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. Bernstein BE, et al. Nat Biotechnol. 2010 Oct;28(10):1045-8. doi: 10.1038/nbt1010-1045. Nat Biotechnol. 2010. PMID: 20944595 Free PMC article.
GC-rich sequence elements recruit PRC2 in mammalian ES cells.
Mendenhall EM, Koche RP, Truong T, Zhou VW, Issac B, Chi AS, Ku M, Bernstein BE. Mendenhall EM, et al. Among authors: bernstein be. PLoS Genet. 2010 Dec 9;6(12):e1001244. doi: 10.1371/journal.pgen.1001244. PLoS Genet. 2010. PMID: 21170310 Free PMC article.
202 results