2015
Integrative analysis of 111 reference human epigenomes
Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller M, Amin V, Whitaker J, Schultz M, Ward L, Sarkar A, Quon G, Sandstrom R, Eaton M, Wu Y, Pfenning A, Wang X, ClaussnitzerYaping Liu M, Coarfa C, Alan Harris R, Shoresh N, Epstein C, Gjoneska E, Leung D, Xie W, David Hawkins R, Lister R, Hong C, Gascard P, Mungall A, Moore R, Chuah E, Tam A, Canfield T, Scott Hansen R, Kaul R, Sabo P, Bansal M, Carles A, Dixon J, Farh K, Feizi S, Karlic R, Kim A, Kulkarni A, Li D, Lowdon R, Elliott G, Mercer T, Neph S, Onuchic V, Polak P, Rajagopal N, Ray P, Sallari R, Siebenthall K, Sinnott-Armstrong N, Stevens M, Thurman R, Wu J, Zhang B, Zhou X, Abdennur N, Adli M, Akerman M, Barrera L, Antosiewicz-Bourget J, Ballinger T, Barnes M, Bates D, Bell R, Bennett D, Bianco K, Bock C, Boyle P, Brinchmann J, Caballero-Campo P, Camahort R, Carrasco-Alfonso M, Charnecki T, Chen H, Chen Z, Cheng J, Cho S, Chu A, Chung W, Cowan C, Athena Deng Q, Deshpande V, Diegel M, Ding B, Durham T, Echipare L, Edsall L, Flowers D, Genbacev-Krtolica O, Gifford C, Gillespie S, Giste E, Glass I, Gnirke A, Gormley M, Gu H, Gu J, Hafler D, Hangauer M, Hariharan M, Hatan M, Haugen E, He Y, Heimfeld S, Herlofsen S, Hou Z, Humbert R, Issner R, Jackson A, Jia H, Jiang P, Johnson A, Kadlecek T, Kamoh B, Kapidzic M, Kent J, Kim A, Kleinewietfeld M, Klugman S, Krishnan J, Kuan S, Kutyavin T, Lee A, Lee K, Li J, Li N, Li Y, Ligon K, Lin S, Lin Y, Liu J, Liu Y, Luckey C, Ma Y, Maire C, Marson A, Mattick J, Mayo M, McMaster M, Metsky H, Mikkelsen T, Miller D, Miri M, Mukame E, Nagarajan R, Neri F, Nery J, Nguyen T, O’Geen H, Paithankar S, Papayannopoulou T, Pelizzola M, Plettner P, Propson N, Raghuraman S, Raney B, Raubitschek A, Reynolds A, Richards H, Riehle K, Rinaudo P, Robinson J, Rockweiler N, Rosen E, Rynes E, Schein J, Sears R, Sejnowski T, Shafer A, Shen L, Shoemaker R, Sigaroudinia M, Slukvin I, Stehling-Sun S, Stewart R, Subramanian S, Suknuntha K, Swanson S, Tian S, Tilden H, Tsai L, Urich M, Vaughn I, Vierstra J, Vong S, Wagner U, Wang H, Wang T, Wang Y, Weiss A, Whitton H, Wildberg A, Witt H, Won K, Xie M, Xing X, Xu I, Xuan Z, Ye Z, Yen C, Yu P, Zhang X, Zhang X, Zhao J, Zhou Y, Zhu J, Zhu Y, Ziegler S, Beaudet A, Boyer L, De Jager P, Farnham P, Fisher S, Haussler D, Jones S, Li W, Marra M, McManus M, Sunyaev S, Thomson J, Tlsty T, Tsai L, Wang W, Waterland R, Zhang M, Chadwick L, Bernstein B, Costello J, Ecker J, Hirst M, Meissner A, Milosavljevic A, Ren B, Stamatoyannopoulos J, Wang T, Kellis M. Integrative analysis of 111 reference human epigenomes. Nature 2015, 518: 317-330. PMID: 25693563, PMCID: PMC4530010, DOI: 10.1038/nature14248.Peer-Reviewed Original ResearchConceptsHuman epigenomeHuman diseasesIntegrative analysisReference human genome sequenceDiverse human traitsRoadmap Epigenomics ConsortiumHuman genome sequenceHistone modification patternsRelevant cell typesEpigenomic informationEpigenomic marksDNA accessibilityRegulatory modulesGene regulationEpigenomic studiesGenome sequenceDNA methylationGenetic variationRegulatory elementsCellular differentiationMolecular basisModification patternsEpigenomeHuman traitsCell types
2014
Genetic and epigenetic fine mapping of causal autoimmune disease variants
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 2014, 518: 337-343. PMID: 25363779, PMCID: PMC4336207, DOI: 10.1038/nature13835.Peer-Reviewed Original ResearchConceptsCausal variantsAutoimmune diseasesT cellsRegulatory T cellsNon-coding risk variantsT cell subsetsEnhancer-associated RNAsGenome-wide association studiesPrimary immune cellsCandidate causal variantsGene regulatory modelsImmune cellsImmune stimulationB cellsGene activationFine mappingTranscription factorsMaster regulatorHistone acetylationImmune differentiationSequence determinantsGene expressionAssociation studiesDiseaseHuman diseases
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