Chromatin-state discovery and genome annotation with ChromHMM.
Chromatin-state discovery and genome annotation with ChromHMM.
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DOI:
10.1038/nprot.2017.124
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发表时间:
2017-12
期刊:
影响因子:
14.8
通讯作者:
Kellis M
中科院分区:
文献类型:
--
作者:
Ernst J;Kellis M
Non-coding DNA regions play central roles in human biology, evolution, and disease. ChromHMM helps annotate the non-coding genome using epigenomic information across one or multiple cell types. It combines multiple genome-wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer a complete annotation for each cell type. ChromHMM learns chromatin state signatures using a multivariate hidden Markov model that explicitly models the combinatorial presence or absence of each mark. ChromHMM uses these signatures to generate a genome-wide annotation for each cell type, by calculating the most probable state in each genomic segment. ChromHMM provides automated enrichment analysis of the resulting annotations to facilitate the functional interpretations of each chromatin state. ChromHMM is distinguished by its modeling emphasis on combinations of marks, its tight integration with downstream functional enrichment analyses, its speed, and its ease of use. Chromatin states are learned, annotations produced, and enrichments computed within one day.
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影响因子:
64.8
作者:
Ernst, Jason;Kheradpour, Pouya;Mikkelsen, Tarjei S.;Shoresh, Noam;Ward, Lucas D.;Epstein, Charles B.;Zhang, Xiaolan;Wang, Li;Issner, Robbyn;Coyne, Michael;Ku, Manching;Durham, Timothy;Kellis, Manolis;Bernstein, Bradley E.
通讯作者:
Bernstein, Bradley E.
影响因子:
46.9
作者:
Ernst J;Kellis M
通讯作者:
Kellis M
影响因子:
7
作者:
Boyle AP;Hong EL;Hariharan M;Cheng Y;Schaub MA;Kasowski M;Karczewski KJ;Park J;Hitz BC;Weng S;Cherry JM;Snyder M
通讯作者:
Snyder M
影响因子:
64.8
作者:
Hibar, Derrek P.;Stein, Jason L.;Renteria, Miguel E.;Arias-Vasquez, Alejandro;Desrivieres, Sylvane;Jahanshad, Neda;Toro, Roberto;Wittfeld, Katharina;Abramovic, Lucija;Andersson, Micael;Aribisala, Benjamin S.;Armstrong, Nicola J.;Bernard, Manon;Bohlken, Marc M.;Boks, Marco P.;Bralten, Janita;Brown, Andrew A.;Chakravarty, M. Mallar;Chen, Qiang;Ching, Christopher R. K.;Cuellar-Partida, Gabriel;den Braber, Anouk;Giddaluru, Sudheer;Goldman, Aaron L.;Grimm, Oliver;Guadalupe, Tulio;Hass, Johanna;Woldehawariat, Girma;Holmes, Avram J.;Hoogman, Martine;Janowitz, Deborah;Jia, Tianye;Kim, Sungeun;Klein, Marieke;Kraemer, Bernd;Lee, Phil H.;Loohuis, Loes M. Olde;Luciano, Michelle;Macare, Christine;Mather, Karen A.;Mattheisen, Manuel;Milaneschi, Yuri;Nho, Kwangsik;Papmeyer, Martina;Ramasamy, Adaikalavan;Risacher, Shannon L.;Roiz-Santianez, Roberto;Rose, Emma J.;Salami, Alireza;Saemann, Philipp G.;Schmaal, Lianne;Schork, Andrew J.;Shin, Jean;Strike, Lachlan T.;Teumer, Alexander;van Donkelaar, Marjolein M. J.;van Eijk, Kristel R.;Walters, Raymond K.;Westlye, Lars T.;Whelan, Christopher D.;Winkler, Anderson M.;Zwiers, Marcel P.;Alhusaini, Saud;Athanasiu, Lavinia;Ehrlich, Stefan;Hakobjan, Marina M. H.;Hartberg, Cecilie B.;Haukvik, Unn K.;Heister, Angelien J. G. A. M.;Hoehn, David;Kasperaviciute, Dalia;Liewald, David C. M.;Lopez, Lorna M.;Makkinje, Remco R. R.;Matarin, Mar;Naber, Marlies A. M.;McKay, D. Reese;Needham, Margaret;Nugent, Allison C.;Puetz, Benno;Royle, Natalie A.;Shen, Li;Sprooten, Emma;Trabzuni, Daniah;van der Marel, Saskia S. L.;van Hulzen, Kimm J. E.;Walton, Esther;Wolf, Christiane;Almasy, Laura;Ames, David;Arepalli, Sampath;Assareh, Amelia A.;Bastin, Mark E.;Brodaty, Henry;Bulayeva, Kazima B.;Carless, Melanie A.;Cichon, Sven;Corvin, Aiden;Curran, Joanne E.;Czisch, Michael;de Zubicaray, Greig I.;Dillman, Allissa;Duggirala, Ravi;Dyer, Thomas D.;Erk, Susanne;Fedko, Iryna O.;Ferrucci, Luigi;Foroud, Tatiana M.;Fox, Peter T.;Fukunaga, Masaki;Gibbs, J. Raphael;Goering, Harald H. H.;Green, Robert C.;Guelfi, Sebastian;Hansell, Narelle K.;Hartman, Catharina A.;Hegenscheid, Katrin;Heinz, Andreas;Hernandez, Dena G.;Heslenfeld, Dirk J.;Hoekstra, Pieter J.;Holsboer, Florian;Homuth, Georg;Hottenga, Jouke-Jan;Ikeda, Masashi;Jack, Clifford R., Jr.;Jenkinson, Mark;Johnson, Robert;Kanai, Ryota;Keil, Maria;Kent, Jack W., Jr.;Kochunov, Peter;Kwok, John B.;Lawrie, Stephen M.;Liu, Xinmin;Longo, Dan L.;McMahon, Katie L.;Meisenzah, Eva;Melle, Ingrid;Mahnke, Sebastian;Montgomery, Grant W.;Mostert, Jeanette C.;Muehleisen, Thomas W.;Nalls, Michael A.;Nichols, Thomas E.;Nilsson, Lars G.;Noethen, Markus M.;Ohi, Kazutaka;Olvera, Rene L.;Perez-Iglesias, Rocio;Pike, G. Bruce;Potkin, Steven G.;Reinvang, Ivar;Reppermund, Simone;Rietschel, Marcella;Romanczuk-Seiferth, Nina;Rosen, Glenn D.;Rujescu, Dan;Schnell, Knut;Schofield, Peter R.;Smith, Colin;Steen, Vidar M.;Sussmann, Jessika E.;Thalamuthu, Anbupalam;Toga, Arthur W.;Traynor, Bryan J.;Troncoso, Juan;Turner, Jessica A.;Valdes Hernandez, Maria C.;van't Ent, Dennis;van der Brug, Marcel;van der Wee, Nic J. A.;van Tol, Marie-Jose;Veltman, Dick J.;Wassink, Thomas H.;Westman, Eric;Zielke, Ronald H.;Zonderman, Alan B.;Ashbrook, David G.;Hager, Reinmar;Lu, Lu;McMahon, Francis J.;Morris, Derek W.;Williams, Robert W.;Brunner, Han G.;Buckner, Randy L.;Buitelaar, Jan K.;Cahn, Wiepke;Calhoun, Vince D.;Cavalleri, Gianpiero L.;Crespo-Facorro, Benedicto;Dale, Anders M.;Davies, Gareth E.;Delanty, Norman;Depondt, Chantal;Djurovic, Srdjan;Drevets, Wayne C.;Espeseth, Thomas;Gollub, Randy L.;Ho, Beng-Choon;Hoffman, Wolfgang;Hosten, Norbert;Kahn, Rene S.;Le Hellard, Stephanie;Meyer-Lindenberg, Andreas;Mueller-Myhsok, Bertram;Nauck, Matthias;Nyberg, Lars;Pandolfo, Massimo;Penninx, Brenda W. J. H.;Roffman, Joshua L.;Sisodiya, Sanjay M.;Smoller, Jordan W.;van Bokhoven, Hans;van Haren, Neeltje E. M.;Voelzke, Henry;Walter, Henrik;Weiner, Michael W.;Wen, Wei;White, Tonya;Agartz, Ingrid;Andreassen, Ole A.;Blangero, John;Boomsma, Dorret I.;Brouwer, Rachel M.;Cannon, Dara M.;Cookson, Mark R.;de Geus, Eco J. 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Arfan;Martin, Nicholas G.;Wright, Margaret J.;Schumann, Gunter;Franke, Barbara;Thompson, Paul M., Jr.;Medland, Sarah E.
通讯作者:
Medland, Sarah E.
影响因子:
7
作者:
Brown, Emily J.;Bachtrog, Doris
通讯作者:
Bachtrog, Doris