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
2008
Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines
Choy E, Yelensky R, Bonakdar S, Plenge RM, Saxena R, De Jager PL, Shaw SY, Wolfish CS, Slavik JM, Cotsapas C, Rivas M, Dermitzakis ET, Cahir-McFarland E, Kieff E, Hafler D, Daly MJ, Altshuler D. Genetic Analysis of Human Traits In Vitro: Drug Response and Gene Expression in Lymphoblastoid Cell Lines. PLOS Genetics 2008, 4: e1000287. PMID: 19043577, PMCID: PMC2583954, DOI: 10.1371/journal.pgen.1000287.Peer-Reviewed Original ResearchConceptsLymphoblastoid cell linesBiological noiseGenome-wide significanceInternational HapMap ProjectDrug responseCell linesGenotype-phenotype relationshipsIndividual mRNAsEQTL SNPsGenetic analysisGene expressionHapMap projectHuman cellsHuman traitsNon-genetic factorsQTLMetabolic stateModel systemGenesMRNA levelsBaseline growth ratesSpurious associationsGrowth ratePharmacogenetic experimentsEQTLs
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