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An integrated encyclopedia of DNA elements in the human genome

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dc.contributor.author Altshuler, Robert Charles
dc.contributor.author Ernst, Jason
dc.contributor.author Kellis, Manolis
dc.contributor.author Kheradpour, Pouya
dc.contributor.author Ward, Lucas D.
dc.contributor.author Eaton, Matthew Lucas
dc.contributor.author Hendrix, David A.
dc.contributor.author Jungreis, Irwin
dc.contributor.author Lin, Michael F.
dc.contributor.author Washietl, Stefan
dc.date.accessioned 2014-05-15T19:00:46Z
dc.date.available 2014-05-15T19:00:46Z
dc.date.issued 2012-09
dc.date.submitted 2011-11
dc.identifier.issn 0028-0836
dc.identifier.issn 1476-4687
dc.identifier.uri http://hdl.handle.net/1721.1/87013
dc.description.abstract The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research. en_US
dc.language.iso en_US
dc.publisher Nature Publishing Group en_US
dc.relation.isversionof http://dx.doi.org/10.1038/nature11247 en_US
dc.rights Creative Commons Attribution-Noncommercial-Share Alike en_US
dc.rights.uri http://creativecommons.org/licenses/by-nc-sa/4.0/ en_US
dc.source PMC en_US
dc.title An integrated encyclopedia of DNA elements in the human genome en_US
dc.type Article en_US
dc.identifier.citation Dunham, Ian, Anshul Kundaje, Shelley F. Aldred, Patrick J. Collins, Carrie A. Davis, Francis Doyle, Charles B. Epstein, et al. “An Integrated Encyclopedia of DNA Elements in the Human Genome.” Nature 489, no. 7414 (September 5, 2012): 57–74. en_US
dc.contributor.department Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science en_US
dc.contributor.department Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory en_US
dc.contributor.mitauthor Altshuler, Robert Charles en_US
dc.contributor.mitauthor Ernst, Jason en_US
dc.contributor.mitauthor Kellis, Manolis en_US
dc.contributor.mitauthor Kheradpour, Pouya en_US
dc.contributor.mitauthor Ward, Lucas D. en_US
dc.contributor.mitauthor Eaton, Matthew Lucas en_US
dc.contributor.mitauthor Hendrix, David A. en_US
dc.contributor.mitauthor Jungreis, Irwin en_US
dc.contributor.mitauthor Lin, Michael F. en_US
dc.contributor.mitauthor Washietl, Stefan en_US
dc.relation.journal Nature en_US
dc.identifier.mitlicense OPEN_ACCESS_POLICY en_US
dc.eprint.version Author's final manuscript en_US
dc.type.uri http://purl.org/eprint/type/JournalArticle en_US
eprint.status http://purl.org/eprint/status/PeerReviewed en_US
dspace.orderedauthors Dunham, Ian; Kundaje, Anshul; Aldred, Shelley F.; Collins, Patrick J.; Davis, Carrie A.; Doyle, Francis; Epstein, Charles B.; Frietze, Seth; Harrow, Jennifer; Kaul, Rajinder; Khatun, Jainab; Lajoie, Bryan R.; Landt, Stephen G.; Lee, Bum-Kyu; Pauli, Florencia; Rosenbloom, Kate R.; Sabo, Peter; Safi, Alexias; Sanyal, Amartya; Shoresh, Noam; Simon, Jeremy M.; Song, Lingyun; Trinklein, Nathan D.; Altshuler, Robert C.; Birney, Ewan; Brown, James B.; Cheng, Chao; Djebali, Sarah; Dong, Xianjun; Dunham, Ian; Ernst, Jason; Furey, Terrence S.; Gerstein, Mark; Giardine, Belinda; Greven, Melissa; Hardison, Ross C.; Harris, Robert S.; Herrero, Javier; Hoffman, Michael M.; Iyer, Sowmya; Kellis, Manolis; Khatun, Jainab; Kheradpour, Pouya; Kundaje, Anshul; Lassmann, Timo; Li, Qunhua; Lin, Xinying; Marinov, Georgi K.; Merkel, Angelika; Mortazavi, Ali; Parker, Stephen C. J.; Reddy, Timothy E.; Rozowsky, Joel; Schlesinger, Felix; Thurman, Robert E.; Wang, Jie; Ward, Lucas D.; Whitfield, Troy W.; Wilder, Steven P.; Wu, Weisheng; Xi, Hualin S.; Yip, Kevin Y.; Zhuang, Jiali; Bernstein, Bradley E.; Birney, Ewan; Dunham, Ian; Green, Eric D.; Gunter, Chris; Snyder, Michael; Pazin, Michael J.; Lowdon, Rebecca F.; Dillon, Laura A. L.; Adams, Leslie B.; Kelly, Caroline J.; Zhang, Julia; Wexler, Judith R.; Green, Eric D.; Good, Peter J.; Feingold, Elise A.; Bernstein, Bradley E.; Birney, Ewan; Crawford, Gregory E.; Dekker, Job; Elnitski, Laura; Farnham, Peggy J.; Gerstein, Mark; Giddings, Morgan C.; Gingeras, Thomas R.; Green, Eric D.; Guigó, Roderic; Hardison, Ross C.; Hubbard, Timothy J.; Kellis, Manolis; Kent, W. James; Lieb, Jason D.; Margulies, Elliott H.; Myers, Richard M.; Snyder, Michael; Stamatoyannopoulos, John A.; Tenenbaum, Scott A.; Weng, Zhiping; White, Kevin P.; Wold, Barbara; Khatun, Jainab; Yu, Yanbao; Wrobel, John; Risk, Brian A.; Gunawardena, Harsha P.; Kuiper, Heather C.; Maier, Christopher W.; Xie, Ling; Chen, Xian; Giddings, Morgan C.; Bernstein, Bradley E.; Epstein, Charles B.; Shoresh, Noam; Ernst, Jason; Kheradpour, Pouya; Mikkelsen, Tarjei S.; Gillespie, Shawn; Goren, Alon; Ram, Oren; Zhang, Xiaolan; Wang, Li; Issner, Robbyn; Coyne, Michael J.; Durham, Timothy; Ku, Manching; Truong, Thanh; Ward, Lucas D.; Altshuler, Robert C.; Eaton, Matthew L.; Kellis, Manolis; Djebali, Sarah; Davis, Carrie A.; Merkel, Angelika; Dobin, Alex; Lassmann, Timo; Mortazavi, Ali; Tanzer, Andrea; Lagarde, Julien; Lin, Wei; Schlesinger, Felix; Xue, Chenghai; Marinov, Georgi K.; Khatun, Jainab; Williams, Brian A.; Zaleski, Chris; Rozowsky, Joel; Röder, Maik; Kokocinski, Felix; Abdelhamid, Rehab F.; Alioto, Tyler; Antoshechkin, Igor; Baer, Michael T.; Batut, Philippe; Bell, Ian; Bell, Kimberly; Chakrabortty, Sudipto; Chen, Xian; Chrast, Jacqueline; Curado, Joao; Derrien, Thomas; Drenkow, Jorg; Dumais, Erica; Dumais, Jackie; Duttagupta, Radha; Fastuca, Megan; Fejes-Toth, Kata; Ferreira, Pedro; Foissac, Sylvain; Fullwood, Melissa J.; Gao, Hui; Gonzalez, David; Gordon, Assaf; Gunawardena, Harsha P.; Howald, Cédric; Jha, Sonali; Johnson, Rory; Kapranov, Philipp; King, Brandon; Kingswood, Colin; Li, Guoliang; Luo, Oscar J.; Park, Eddie; Preall, Jonathan B.; Presaud, Kimberly; Ribeca, Paolo; Risk, Brian A.; Robyr, Daniel; Ruan, Xiaoan; Sammeth, Michael; Sandhu, Kuljeet Singh; Schaeffer, Lorain; See, Lei-Hoon; Shahab, Atif; Skancke, Jorgen; Suzuki, Ana Maria; Takahashi, Hazuki; Tilgner, Hagen; Trout, Diane; Walters, Nathalie; Wang, Huaien; Wrobel, John; Yu, Yanbao; Hayashizaki, Yoshihide; Harrow, Jennifer; Gerstein, Mark; Hubbard, Timothy J.; Reymond, Alexandre; Antonarakis, Stylianos E.; Hannon, Gregory J.; Giddings, Morgan C.; Ruan, Yijun; Wold, Barbara; Carninci, Piero; Guigó, Roderic; Gingeras, Thomas R.; Rosenbloom, Kate R.; Sloan, Cricket A.; Learned, Katrina; Malladi, Venkat S.; Wong, Matthew C.; Barber, Galt P.; Cline, Melissa S.; Dreszer, Timothy R.; Heitner, Steven G.; Karolchik, Donna; Kent, W. James; Kirkup, Vanessa M.; Meyer, Laurence R.; Long, Jeffrey C.; Maddren, Morgan; Raney, Brian J.; Furey, Terrence S.; Song, Lingyun; Grasfeder, Linda L.; Giresi, Paul G.; Lee, Bum-Kyu; Battenhouse, Anna; Sheffield, Nathan C.; Simon, Jeremy M.; Showers, Kimberly A.; Safi, Alexias; London, Darin; Bhinge, Akshay A.; Shestak, Christopher; Schaner, Matthew R.; Ki Kim, Seul; Zhang, Zhuzhu Z.; Mieczkowski, Piotr A.; Mieczkowska, Joanna O.; Liu, Zheng; McDaniell, Ryan M.; Ni, Yunyun; Rashid, Naim U.; Kim, Min Jae; Adar, Sheera; Zhang, Zhancheng; Wang, Tianyuan; Winter, Deborah; Keefe, Damian; Birney, Ewan; Iyer, Vishwanath R.; Lieb, Jason D.; Crawford, Gregory E.; Li, Guoliang; Sandhu, Kuljeet Singh; Zheng, Meizhen; Wang, Ping; Luo, Oscar J.; Shahab, Atif; Fullwood, Melissa J.; Ruan, Xiaoan; Ruan, Yijun; Myers, Richard M.; Pauli, Florencia; Williams, Brian A.; Gertz, Jason; Marinov, Georgi K.; Reddy, Timothy E.; Vielmetter, Jost; Partridge, E.; Trout, Diane; Varley, Katherine E.; Gasper, Clarke; Bansal, Anita; Pepke, Shirley; Jain, Preti; Amrhein, Henry; Bowling, Kevin M.; Anaya, Michael; Cross, Marie K.; King, Brandon; Muratet, Michael A.; Antoshechkin, Igor; Newberry, Kimberly M.; McCue, Kenneth; Nesmith, Amy S.; Fisher-Aylor, Katherine I.; Pusey, Barbara; DeSalvo, Gilberto; Parker, Stephanie L.; Balasubramanian, Sreeram; Davis, Nicholas S.; Meadows, Sarah K.; Eggleston, Tracy; Gunter, Chris; Newberry, J. Scott; Levy, Shawn E.; Absher, Devin M.; Mortazavi, Ali; Wong, Wing H.; Wold, Barbara; Blow, Matthew J.; Visel, Axel; Pennachio, Len A.; Elnitski, Laura; Margulies, Elliott H.; Parker, Stephen C. J.; Petrykowska, Hanna M.; Abyzov, Alexej; Aken, Bronwen; Barrell, Daniel; Barson, Gemma; Berry, Andrew; Bignell, Alexandra; Boychenko, Veronika; Bussotti, Giovanni; Chrast, Jacqueline; Davidson, Claire; Derrien, Thomas; Despacio-Reyes, Gloria; Diekhans, Mark; Ezkurdia, Iakes; Frankish, Adam; Gilbert, James; Gonzalez, Jose Manuel; Griffiths, Ed; Harte, Rachel; Hendrix, David A.; Howald, Cédric; Hunt, Toby; Jungreis, Irwin; Kay, Mike; Khurana, Ekta; Kokocinski, Felix; Leng, Jing; Lin, Michael F.; Loveland, Jane; Lu, Zhi; Manthravadi, Deepa; Mariotti, Marco; Mudge, Jonathan; Mukherjee, Gaurab; Notredame, Cedric; Pei, Baikang; Rodriguez, Jose Manuel; Saunders, Gary; Sboner, Andrea; Searle, Stephen; Sisu, Cristina; Snow, Catherine; Steward, Charlie; Tanzer, Andrea; Tapanari, Electra; Tress, Michael L.; van Baren, Marijke J.; Walters, Nathalie; Washietl, Stefan; Wilming, Laurens; Zadissa, Amonida; Zhang, Zhengdong; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Gerstein, Mark; Reymond, Alexandre; Guigó, Roderic; Harrow, Jennifer; Hubbard, Timothy J.; Landt, Stephen G.; Frietze, Seth; Abyzov, Alexej; Addleman, Nick; Alexander, Roger P.; Auerbach, Raymond K.; Balasubramanian, Suganthi; Bettinger, Keith; Bhardwaj, Nitin; Boyle, Alan P.; Cao, Alina R.; Cayting, Philip; Charos, Alexandra; Cheng, Yong; Cheng, Chao; Eastman, Catharine; Euskirchen, Ghia; Fleming, Joseph D.; Grubert, Fabian; Habegger, Lukas; Hariharan, Manoj; Harmanci, Arif; Iyengar, Sushma; Jin, Victor X.; Karczewski, Konrad J.; Kasowski, Maya; Lacroute, Phil; Lam, Hugo; Lamarre-Vincent, Nathan; Leng, Jing; Lian, Jin; Lindahl-Allen, Marianne; Min, Renqiang; Miotto, Benoit; Monahan, Hannah; Moqtaderi, Zarmik; Mu, Xinmeng J.; O’Geen, Henriette; Ouyang, Zhengqing; Patacsil, Dorrelyn; Pei, Baikang; Raha, Debasish; Ramirez, Lucia; Reed, Brian; Rozowsky, Joel; Sboner, Andrea; Shi, Minyi; Sisu, Cristina; Slifer, Teri; Witt, Heather; Wu, Linfeng; Xu, Xiaoqin; Yan, Koon-Kiu; Yang, Xinqiong; Yip, Kevin Y.; Zhang, Zhengdong; Struhl, Kevin; Weissman, Sherman M.; Gerstein, Mark; Farnham, Peggy J.; Snyder, Michael; Tenenbaum, Scott A.; Penalva, Luiz O.; Doyle, Francis; Karmakar, Subhradip; Landt, Stephen G.; Bhanvadia, Raj R.; Choudhury, Alina; Domanus, Marc; Ma, Lijia; Moran, Jennifer; Patacsil, Dorrelyn; Slifer, Teri; Victorsen, Alec; Yang, Xinqiong; Snyder, Michael; White, Kevin P.; Auer, Thomas; Centanin, Lazaro; Eichenlaub, Michael; Gruhl, Franziska; Heermann, Stephan; Hoeckendorf, Burkhard; Inoue, Daigo; Kellner, Tanja; Kirchmaier, Stephan; Mueller, Claudia; Reinhardt, Robert; Schertel, Lea; Schneider, Stephanie; Sinn, Rebecca; Wittbrodt, Beate; Wittbrodt, Jochen; Weng, Zhiping; Whitfield, Troy W.; Wang, Jie; Collins, Patrick J.; Aldred, Shelley F.; Trinklein, Nathan D.; Partridge, E. Christopher; Myers, Richard M.; Dekker, Job; Jain, Gaurav; Lajoie, Bryan R.; Sanyal, Amartya; Balasundaram, Gayathri; Bates, Daniel L.; Byron, Rachel; Canfield, Theresa K.; Diegel, Morgan J.; Dunn, Douglas; Ebersol, Abigail K.; Frum, Tristan; Garg, Kavita; Gist, Erica; Hansen, R. Scott; Boatman, Lisa; Haugen, Eric; Humbert, Richard; Jain, Gaurav; Johnson, Audra K.; Johnson, Ericka M.; Kutyavin, Tattyana V.; Lajoie, Bryan R.; Lee, Kristen; Lotakis, Dimitra; Maurano, Matthew T.; Neph, Shane J.; Neri, Fiedencio V.; Nguyen, Eric D.; Qu, Hongzhu; Reynolds, Alex P.; Roach, Vaughn; Rynes, Eric; Sabo, Peter; Sanchez, Minerva E.; Sandstrom, Richard S.; Sanyal, Amartya; Shafer, Anthony O.; Stergachis, Andrew B.; Thomas, Sean; Thurman, Robert E.; Vernot, Benjamin; Vierstra, Jeff; Vong, Shinny; Wang, Hao; Weaver, Molly A.; Yan, Yongqi; Zhang, Miaohua; Akey, Joshua M.; Bender, Michael; Dorschner, Michael O.; Groudine, Mark; MacCoss, Michael J.; Navas, Patrick; Stamatoyannopoulos, George; Kaul, Rajinder; Dekker, Job; Stamatoyannopoulos, John A.; Dunham, Ian; Beal, Kathryn; Brazma, Alvis; Flicek, Paul; Herrero, Javier; Johnson, Nathan; Keefe, Damian; Lukk, Margus; Luscombe, Nicholas M.; Sobral, Daniel; Vaquerizas, Juan M.; Wilder, Steven P.; Batzoglou, Serafim; Sidow, Arend; Hussami, Nadine; Kyriazopoulou-Panagiotopoulou, Sofia; Libbrecht, Max W.; Schaub, Marc A.; Kundaje, Anshul; Hardison, Ross C.; Miller, Webb; Giardine, Belinda; Harris, Robert S.; Wu, Weisheng; Bickel, Peter J.; Banfai, Balazs; Boley, Nathan P.; Brown, James B.; Huang, Haiyan; Li, Qunhua; Li, Jingyi Jessica; Noble, William Stafford; Bilmes, Jeffrey A.; Buske, Orion J.; Hoffman, Michael M.; Sahu, Avinash D.; Kharchenko, Peter V.; Park, Peter J.; Baker, Dannon; Taylor, James; Weng, Zhiping; Iyer, Sowmya; Dong, Xianjun; Greven, Melissa; Lin, Xinying; Wang, Jie; Xi, Hualin S.; Zhuang, Jiali; Gerstein, Mark; Alexander, Roger P.; Balasubramanian, Suganthi; Cheng, Chao; Harmanci, Arif; Lochovsky, Lucas; Min, Renqiang; Mu, Xinmeng J.; Rozowsky, Joel; Yan, Koon-Kiu; Yip, Kevin Y.; Birney, Ewan en_US
dc.identifier.orcid https://orcid.org/0000-0001-5096-1932
dc.identifier.orcid https://orcid.org/0000-0002-8305-9125
dc.identifier.orcid https://orcid.org/0000-0002-8017-809X


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