An integrated encyclopedia of DNA elements in the human genome

Ian Correction Dunham, Anshul Kundaje, Shelley F. Aldred, Patrick J. Collins, Carrie A. Davis, Francis Doyle, Charles B. Epstein, Seth Frietze, Jennifer Harrow, Rajinder Kaul, Jainab Khatun, Bryan R. Lajoie, Stephen G. Landt, Bum Kyu Lee, Florencia Pauli, Kate R. Rosenbloom, Peter Sabo, Alexias Safi, Amartya Sanyal, Noam ShoreshJeremy M. Simon, Lingyun Song, Nathan D. Trinklein, Robert C. Altshuler, Ewan Birney, James B. Brown, Chao Cheng, Sarah Djebali, Xianjun Dong, Jason Ernst, Terrence S. Furey, Mark Gerstein, Belinda Giardine, Melissa Greven, Ross C. Hardison, Robert S. Harris, Javier Herrero, Michael M. Hoffman, Sowmya Iyer, Manolis Kellis, Pouya Kheradpour, Timo Lassmann, Qunhua Li, Xinying Lin, Georgi K. Marinov, Angelika Merkel, Ali Mortazavi, Stephen C J Parker, Timothy E. Reddy, Joel Rozowsky, Felix Schlesinger, Robert E. Thurman, Jie Wang, Lucas D. Ward, Troy W. Whitfield, Steven P. Wilder, Weisheng Wu, Hualin S. Xi, Kevin Y. Yip, Jiali Zhuang, Bradley E. Bernstein, Eric D. Green, Chris Gunter, Michael Snyder, Michael J. Pazin, Rebecca F. Lowdon, Laura A L Dillon, Leslie B. Adams, Caroline J. Kelly, Julia Zhang, Judith R. Wexler, Peter J. Good, Elise A. Feingold, Gregory E. Crawford, Job Dekker, Laura Elnitski, Peggy J. Farnham, Morgan C. Giddings, Thomas R. Gingeras, Roderic Guigó, Timothy J. Hubbard, W. James Kent, Jason D. Lieb, Elliott H. Margulies, Richard M. Myers, John A. Stamatoyannopoulos, Scott A. Tenenbaum, Zhiping Weng, Kevin P. White, Barbara Wold, Yanbao Yu, John Wrobel, Brian A. Risk, Harsha P. Gunawardena, Heather C. Kuiper, Christopher W. Maier, Ling Xie, Xian Chen, Tarjei S. Mikkelsen, Shawn Gillespie, Alon Goren, Oren Ram, Xiaolan Zhang, Li Wang, Robbyn Issner, Michael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Matthew L. Eaton, Alex Dobin, Andrea Tanzer, Julien Lagarde, Wei Lin, Chenghai Xue, Brian A. Williams, Chris Zaleski, Maik Röder, Felix Kokocinski, Rehab F. Abdelhamid, Tyler Alioto, Igor Antoshechkin, Michael T. Baer, Philippe Batut, Ian Bell, Kimberly Bell, Sudipto Chakrabortty, Jacqueline Chrast, Joao Curado, Thomas Derrien, Jorg Drenkow, Erica Dumais, Jackie Dumais, Radha Duttagupta, Megan Fastuca, Kata Fejes-Toth, Pedro Ferreira, Sylvain Foissac, Melissa J. Fullwood, Hui Gao, David Gonzalez, Assaf Gordon, Cédric Howald, Sonali Jha, Rory Johnson, Philipp Kapranov, Brandon King, Colin Kingswood, Guoliang Li, Oscar J. Luo, Eddie Park, Jonathan B. Preall, Kimberly Presaud, Paolo Ribeca, Daniel Robyr, Xiaoan Ruan, Michael Sammeth, Kuljeet Singh Sandhu, Lorain Schaeffer, Lei Hoon See, Atif Shahab, Jorgen Skancke, Ana Maria Suzuki, Hazuki Takahashi, Hagen Tilgner, Diane Trout, Nathalie Walters, Huaien Wang, Yoshihide Hayashizaki, Alexandre Reymond, Stylianos E. Antonarakis, Gregory J. Hannon, Yijun Ruan, Piero Carninci, Cricket A. Sloan, Katrina Learned, Venkat S. Malladi, Matthew C. Wong, Galt P. Barber, Melissa S. Cline, Timothy R. Dreszer, Steven G. Heitner, Donna Karolchik, Vanessa M. Kirkup, Laurence R. Meyer, Jeffrey C. Long, Morgan Maddren, Brian J. Raney, Linda L. Grasfeder, Paul G. Giresi, Anna Battenhouse, Nathan C. Sheffield, Kimberly A. Showers, Darin London, Akshay A. Bhinge, Christopher Shestak, Matthew R. Schaner, Seul Ki Kim, Zhuzhu Z. Zhang, Piotr A. Mieczkowski, Joanna O. Mieczkowska, Zheng Liu, Ryan M. McDaniell, Yunyun Ni, Naim U. Rashid, Min Jae Kim, Sheera Adar, Zhancheng Zhang, Tianyuan Wang, Deborah Winter, Damian Keefe, Vishwanath R. Iyer, Meizhen Zheng, Ping Wang, Jason Gertz, Jost Vielmetter, E. Christopher Partridge, Katherine E. Varley, Clarke Gasper, Anita Bansal, Shirley Pepke, Preti Jain, Henry Amrhein, Kevin M. Bowling, Michael Anaya, Marie K. Cross, Michael A. Muratet, Kimberly M. Newberry, Kenneth McCue, Amy S. Nesmith, Katherine I. Fisher-Aylor, Barbara Pusey, Gilberto DeSalvo, Stephanie L. Parker, Sreeram Balasubramanian, Nicholas S. Davis, Sarah K. Meadows, Tracy Eggleston, J. Scott Newberry, Shawn E. Levy, Devin M. Absher, Wing H. Wong, Matthew J. Blow, Axel Visel, Len A. Pennachio, Hanna M. Petrykowska, Alexej Abyzov, Bronwen Aken, Daniel Barrell, Gemma Barson, Andrew Berry, Alexandra Bignell, Veronika Boychenko, Giovanni Bussotti, Claire Davidson, Gloria Despacio-Reyes, Mark Diekhans, Iakes Ezkurdia, Adam Frankish, James Gilbert, Jose Manuel Gonzalez, Ed Griffiths, Rachel Harte, David A. Hendrix, Toby Hunt, Irwin Jungreis, Mike Kay, Ekta Khurana, Jing Leng, Michael F. Lin, Jane Loveland, Zhi Lu, Deepa Manthravadi, Marco Mariotti, Jonathan Mudge, Gaurab Mukherjee, Cedric Notredame, Baikang Pei, Jose Manuel Rodriguez, Gary Saunders, Andrea Sboner, Stephen Searle, Cristina Sisu, Catherine Snow, Charlie Steward, Electra Tapanari, Michael L. Tress, Marijke J. Van Baren, Stefan Washietl, Laurens Wilming, Amonida Zadissa, Zhengdong Zhang, Michael Brent, David Haussler, Alfonso Valencia, Nick Addleman, Roger P. Alexander, Raymond K. Auerbach, Suganthi Balasubramanian, Keith Bettinger, Nitin Bhardwaj, Alan P. Boyle, Alina R. Cao, Philip Cayting, Alexandra Charos, Yong Cheng, Catharine Eastman, Ghia Euskirchen, Joseph D. Fleming, Fabian Grubert, Lukas Habegger, Manoj Hariharan, Arif Harmanci, Sushma Iyengar, Victor X. Jin, Konrad J. Karczewski, Maya Kasowski, Phil Lacroute, Hugo Lam, Nathan Lamarre-Vincent, Jin Lian, Marianne Lindahl-Allen, Renqiang Min, Benoit Miotto, Hannah Monahan, Zarmik Moqtaderi, Xinmeng J. Mu, Henriette O'Geen, Zhengqing Ouyang, Dorrelyn Patacsil, Debasish Raha, Lucia Ramirez, Brian Reed, Minyi Shi, Teri Slifer, Heather Witt, Linfeng Wu, Xiaoqin Xu, Koon Kiu Yan, Xinqiong Yang, Kevin Struhl, Sherman M. Weissman, Luiz O. Penalva, Subhradip Karmakar, Raj R. Bhanvadia, Alina Choudhury, Marc Domanus, Lijia Ma, Jennifer Moran, Alec Victorsen, Thomas Auer, Lazaro Centanin, Michael Eichenlaub, Franziska Gruhl, Stephan Heermann, Burkhard Hoeckendorf, Daigo Inoue, Tanja Kellner, Stephan Kirchmaier, Claudia Mueller, Robert Reinhardt, Lea Schertel, Stephanie Schneider, Rebecca Sinn, Beate Wittbrodt, Jochen Wittbrodt, Gaurav Jain, Gayathri Balasundaram, Daniel L. Bates, Rachel Byron, Theresa K. Canfield, Morgan J. Diegel, Douglas Dunn, Abigail K. Ebersol, Tristan Frum, Kavita Garg, Erica Gist, R. Scott Hansen, Lisa Boatman, Eric Haugen, Richard Humbert, Audra K. Johnson, Ericka M. Johnson, Tattyana V. Kutyavin, Kristen Lee, Dimitra Lotakis, Matthew T. Maurano, Shane J. Neph, Fiedencio V. Neri, Eric D. Nguyen, Hongzhu Qu, Alex P. Reynolds, Vaughn Roach, Eric Rynes, Minerva E. Sanchez, Richard S. Sandstrom, Anthony O. Shafer, Andrew B. Stergachis, Sean Thomas, Benjamin Vernot, Jeff Vierstra, Shinny Vong, Hao Wang, Molly A. Weaver, Yongqi Yan, Miaohua Zhang, Joshua M. Akey, Michael Bender, Michael O. Dorschner, Mark Groudine, Michael J. MacCoss, Patrick Navas, George Stamatoyannopoulos, Kathryn Beal, Alvis Brazma, Paul Flicek, Nathan Johnson, Margus Lukk, Nicholas M. Luscombe, Daniel Sobral, Juan M. Vaquerizas, Serafim Batzoglou, Arend Sidow, Nadine Hussami, Sofia Kyriazopoulou-Panagiotopoulou, Max W. Libbrecht, Marc A. Schaub, Webb Miller, Peter J. Bickel, Balazs Banfai, Nathan P. Boley, Haiyan Huang, Jingyi Jessica Li, William Stafford Noble, Jeffrey A. Bilmes, Orion J. Buske, Avinash D. Sahu, Peter V. Kharchenko, Peter J. Park, Dannon Baker, James Taylor, Lucas Lochovsky

Research output: Contribution to journalArticle

7488 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)57-74
Number of pages18
JournalNature
Volume489
Issue number7414
DOIs
StatePublished - Sep 6 2012
Externally publishedYes

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Encyclopedias
Human Genome
DNA
Histone Code
Genome
Genes
Open Reading Frames
Chromatin
Biomedical Research
Transcription Factors

ASJC Scopus subject areas

  • General

Cite this

Correction Dunham, I., Kundaje, A., Aldred, S. F., Collins, P. J., Davis, C. A., Doyle, F., ... Lochovsky, L. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57-74. https://doi.org/10.1038/nature11247

An integrated encyclopedia of DNA elements in the human genome. / Correction 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; 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; Kheradpour, Pouya; 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.; 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.; Good, Peter J.; Feingold, Elise A.; Crawford, Gregory E.; Dekker, Job; Elnitski, Laura; Farnham, Peggy J.; Giddings, Morgan C.; Gingeras, Thomas R.; Guigó, Roderic; Hubbard, Timothy J.; Kent, W. James; Lieb, Jason D.; Margulies, Elliott H.; Myers, Richard M.; Stamatoyannopoulos, John A.; Tenenbaum, Scott A.; Weng, Zhiping; White, Kevin P.; Wold, Barbara; Yu, Yanbao; Wrobel, John; Risk, Brian A.; Gunawardena, Harsha P.; Kuiper, Heather C.; Maier, Christopher W.; Xie, Ling; Chen, Xian; Mikkelsen, Tarjei S.; Gillespie, Shawn; Goren, Alon; Ram, Oren; Zhang, Xiaolan; Wang, Li; Issner, Robbyn; Coyne, Michael J.; Durham, Timothy; Ku, Manching; Truong, Thanh; Eaton, Matthew L.; Dobin, Alex; Tanzer, Andrea; Lagarde, Julien; Lin, Wei; Xue, Chenghai; Williams, Brian A.; Zaleski, Chris; Röder, Maik; Kokocinski, Felix; Abdelhamid, Rehab F.; Alioto, Tyler; Antoshechkin, Igor; Baer, Michael T.; Batut, Philippe; Bell, Ian; Bell, Kimberly; Chakrabortty, Sudipto; 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; 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; 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; Hayashizaki, Yoshihide; Reymond, Alexandre; Antonarakis, Stylianos E.; Hannon, Gregory J.; Ruan, Yijun; Carninci, Piero; 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; Kirkup, Vanessa M.; Meyer, Laurence R.; Long, Jeffrey C.; Maddren, Morgan; Raney, Brian J.; Grasfeder, Linda L.; Giresi, Paul G.; Battenhouse, Anna; Sheffield, Nathan C.; Showers, Kimberly A.; London, Darin; Bhinge, Akshay A.; Shestak, Christopher; Schaner, Matthew R.; Kim, Seul Ki; 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; Iyer, Vishwanath R.; Zheng, Meizhen; Wang, Ping; Gertz, Jason; Vielmetter, Jost; Partridge, E. Christopher; Varley, Katherine E.; Gasper, Clarke; Bansal, Anita; Pepke, Shirley; Jain, Preti; Amrhein, Henry; Bowling, Kevin M.; Anaya, Michael; Cross, Marie K.; Muratet, Michael A.; 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; Newberry, J. Scott; Levy, Shawn E.; Absher, Devin M.; Wong, Wing H.; Blow, Matthew J.; Visel, Axel; Pennachio, Len A.; Petrykowska, Hanna M.; Abyzov, Alexej; Aken, Bronwen; Barrell, Daniel; Barson, Gemma; Berry, Andrew; Bignell, Alexandra; Boychenko, Veronika; Bussotti, Giovanni; Davidson, Claire; Despacio-Reyes, Gloria; Diekhans, Mark; Ezkurdia, Iakes; Frankish, Adam; Gilbert, James; Gonzalez, Jose Manuel; Griffiths, Ed; Harte, Rachel; Hendrix, David A.; Hunt, Toby; Jungreis, Irwin; Kay, Mike; Khurana, Ekta; 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; Tapanari, Electra; Tress, Michael L.; Van Baren, Marijke J.; Washietl, Stefan; Wilming, Laurens; Zadissa, Amonida; Zhang, Zhengdong; Brent, Michael; Haussler, David; Valencia, Alfonso; 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; 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; Lian, Jin; Lindahl-Allen, Marianne; Min, Renqiang; Miotto, Benoit; Monahan, Hannah; Moqtaderi, Zarmik; Mu, Xinmeng J.; O'Geen, Henriette; Ouyang, Zhengqing; Patacsil, Dorrelyn; Raha, Debasish; Ramirez, Lucia; Reed, Brian; Shi, Minyi; Slifer, Teri; Witt, Heather; Wu, Linfeng; Xu, Xiaoqin; Yan, Koon Kiu; Yang, Xinqiong; Struhl, Kevin; Weissman, Sherman M.; Penalva, Luiz O.; Karmakar, Subhradip; Bhanvadia, Raj R.; Choudhury, Alina; Domanus, Marc; Ma, Lijia; Moran, Jennifer; Victorsen, Alec; 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; Jain, Gaurav; 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; Johnson, Audra K.; Johnson, Ericka M.; Kutyavin, Tattyana V.; 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; Sanchez, Minerva E.; Sandstrom, Richard S.; Shafer, Anthony O.; Stergachis, Andrew B.; Thomas, Sean; 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; Beal, Kathryn; Brazma, Alvis; Flicek, Paul; Johnson, Nathan; Lukk, Margus; Luscombe, Nicholas M.; Sobral, Daniel; Vaquerizas, Juan M.; Batzoglou, Serafim; Sidow, Arend; Hussami, Nadine; Kyriazopoulou-Panagiotopoulou, Sofia; Libbrecht, Max W.; Schaub, Marc A.; Miller, Webb; Bickel, Peter J.; Banfai, Balazs; Boley, Nathan P.; Huang, Haiyan; Li, Jingyi Jessica; Noble, William Stafford; Bilmes, Jeffrey A.; Buske, Orion J.; Sahu, Avinash D.; Kharchenko, Peter V.; Park, Peter J.; Baker, Dannon; Taylor, James; Lochovsky, Lucas.

In: Nature, Vol. 489, No. 7414, 06.09.2012, p. 57-74.

Research output: Contribution to journalArticle

Correction Dunham, I, Kundaje, A, Aldred, SF, Collins, PJ, Davis, CA, Doyle, F, Epstein, CB, Frietze, S, Harrow, J, Kaul, R, Khatun, J, Lajoie, BR, Landt, SG, Lee, BK, Pauli, F, Rosenbloom, KR, Sabo, P, Safi, A, Sanyal, A, Shoresh, N, Simon, JM, Song, L, Trinklein, ND, Altshuler, RC, Birney, E, Brown, JB, Cheng, C, Djebali, S, Dong, X, Ernst, J, Furey, TS, Gerstein, M, Giardine, B, Greven, M, Hardison, RC, Harris, RS, Herrero, J, Hoffman, MM, Iyer, S, Kellis, M, Kheradpour, P, Lassmann, T, Li, Q, Lin, X, Marinov, GK, Merkel, A, Mortazavi, A, Parker, SCJ, Reddy, TE, Rozowsky, J, Schlesinger, F, Thurman, RE, Wang, J, Ward, LD, Whitfield, TW, Wilder, SP, Wu, W, Xi, HS, Yip, KY, Zhuang, J, Bernstein, BE, Green, ED, Gunter, C, Snyder, M, Pazin, MJ, Lowdon, RF, Dillon, LAL, Adams, LB, Kelly, CJ, Zhang, J, Wexler, JR, Good, PJ, Feingold, EA, Crawford, GE, Dekker, J, Elnitski, L, Farnham, PJ, Giddings, MC, Gingeras, TR, Guigó, R, Hubbard, TJ, Kent, WJ, Lieb, JD, Margulies, EH, Myers, RM, Stamatoyannopoulos, JA, Tenenbaum, SA, Weng, Z, White, KP, Wold, B, Yu, Y, Wrobel, J, Risk, BA, Gunawardena, HP, Kuiper, HC, Maier, CW, Xie, L, Chen, X, Mikkelsen, TS, Gillespie, S, Goren, A, Ram, O, Zhang, X, Wang, L, Issner, R, Coyne, MJ, Durham, T, Ku, M, Truong, T, Eaton, ML, Dobin, A, Tanzer, A, Lagarde, J, Lin, W, Xue, C, Williams, BA, Zaleski, C, Röder, M, Kokocinski, F, Abdelhamid, RF, Alioto, T, Antoshechkin, I, Baer, MT, Batut, P, Bell, I, Bell, K, Chakrabortty, S, Chrast, J, Curado, J, Derrien, T, Drenkow, J, Dumais, E, Dumais, J, Duttagupta, R, Fastuca, M, Fejes-Toth, K, Ferreira, P, Foissac, S, Fullwood, MJ, Gao, H, Gonzalez, D, Gordon, A, Howald, C, Jha, S, Johnson, R, Kapranov, P, King, B, Kingswood, C, Li, G, Luo, OJ, Park, E, Preall, JB, Presaud, K, Ribeca, P, Robyr, D, Ruan, X, Sammeth, M, Sandhu, KS, Schaeffer, L, See, LH, Shahab, A, Skancke, J, Suzuki, AM, Takahashi, H, Tilgner, H, Trout, D, Walters, N, Wang, H, Hayashizaki, Y, Reymond, A, Antonarakis, SE, Hannon, GJ, Ruan, Y, Carninci, P, Sloan, CA, Learned, K, Malladi, VS, Wong, MC, Barber, GP, Cline, MS, Dreszer, TR, Heitner, SG, Karolchik, D, Kirkup, VM, Meyer, LR, Long, JC, Maddren, M, Raney, BJ, Grasfeder, LL, Giresi, PG, Battenhouse, A, Sheffield, NC, Showers, KA, London, D, Bhinge, AA, Shestak, C, Schaner, MR, Kim, SK, Zhang, ZZ, Mieczkowski, PA, Mieczkowska, JO, Liu, Z, McDaniell, RM, Ni, Y, Rashid, NU, Kim, MJ, Adar, S, Zhang, Z, Wang, T, Winter, D, Keefe, D, Iyer, VR, Zheng, M, Wang, P, Gertz, J, Vielmetter, J, Partridge, EC, Varley, KE, Gasper, C, Bansal, A, Pepke, S, Jain, P, Amrhein, H, Bowling, KM, Anaya, M, Cross, MK, Muratet, MA, Newberry, KM, McCue, K, Nesmith, AS, Fisher-Aylor, KI, Pusey, B, DeSalvo, G, Parker, SL, Balasubramanian, S, Davis, NS, Meadows, SK, Eggleston, T, Newberry, JS, Levy, SE, Absher, DM, Wong, WH, Blow, MJ, Visel, A, Pennachio, LA, Petrykowska, HM, Abyzov, A, Aken, B, Barrell, D, Barson, G, Berry, A, Bignell, A, Boychenko, V, Bussotti, G, Davidson, C, Despacio-Reyes, G, Diekhans, M, Ezkurdia, I, Frankish, A, Gilbert, J, Gonzalez, JM, Griffiths, E, Harte, R, Hendrix, DA, Hunt, T, Jungreis, I, Kay, M, Khurana, E, Leng, J, Lin, MF, Loveland, J, Lu, Z, Manthravadi, D, Mariotti, M, Mudge, J, Mukherjee, G, Notredame, C, Pei, B, Rodriguez, JM, Saunders, G, Sboner, A, Searle, S, Sisu, C, Snow, C, Steward, C, Tapanari, E, Tress, ML, Van Baren, MJ, Washietl, S, Wilming, L, Zadissa, A, Zhang, Z, Brent, M, Haussler, D, Valencia, A, Addleman, N, Alexander, RP, Auerbach, RK, Balasubramanian, S, Bettinger, K, Bhardwaj, N, Boyle, AP, Cao, AR, Cayting, P, Charos, A, Cheng, Y, Eastman, C, Euskirchen, G, Fleming, JD, Grubert, F, Habegger, L, Hariharan, M, Harmanci, A, Iyengar, S, Jin, VX, Karczewski, KJ, Kasowski, M, Lacroute, P, Lam, H, Lamarre-Vincent, N, Lian, J, Lindahl-Allen, M, Min, R, Miotto, B, Monahan, H, Moqtaderi, Z, Mu, XJ, O'Geen, H, Ouyang, Z, Patacsil, D, Raha, D, Ramirez, L, Reed, B, Shi, M, Slifer, T, Witt, H, Wu, L, Xu, X, Yan, KK, Yang, X, Struhl, K, Weissman, SM, Penalva, LO, Karmakar, S, Bhanvadia, RR, Choudhury, A, Domanus, M, Ma, L, Moran, J, Victorsen, A, Auer, T, Centanin, L, Eichenlaub, M, Gruhl, F, Heermann, S, Hoeckendorf, B, Inoue, D, Kellner, T, Kirchmaier, S, Mueller, C, Reinhardt, R, Schertel, L, Schneider, S, Sinn, R, Wittbrodt, B, Wittbrodt, J, Jain, G, Balasundaram, G, Bates, DL, Byron, R, Canfield, TK, Diegel, MJ, Dunn, D, Ebersol, AK, Frum, T, Garg, K, Gist, E, Hansen, RS, Boatman, L, Haugen, E, Humbert, R, Johnson, AK, Johnson, EM, Kutyavin, TV, Lee, K, Lotakis, D, Maurano, MT, Neph, SJ, Neri, FV, Nguyen, ED, Qu, H, Reynolds, AP, Roach, V, Rynes, E, Sanchez, ME, Sandstrom, RS, Shafer, AO, Stergachis, AB, Thomas, S, Vernot, B, Vierstra, J, Vong, S, Wang, H, Weaver, MA, Yan, Y, Zhang, M, Akey, JM, Bender, M, Dorschner, MO, Groudine, M, MacCoss, MJ, Navas, P, Stamatoyannopoulos, G, Beal, K, Brazma, A, Flicek, P, Johnson, N, Lukk, M, Luscombe, NM, Sobral, D, Vaquerizas, JM, Batzoglou, S, Sidow, A, Hussami, N, Kyriazopoulou-Panagiotopoulou, S, Libbrecht, MW, Schaub, MA, Miller, W, Bickel, PJ, Banfai, B, Boley, NP, Huang, H, Li, JJ, Noble, WS, Bilmes, JA, Buske, OJ, Sahu, AD, Kharchenko, PV, Park, PJ, Baker, D, Taylor, J & Lochovsky, L 2012, 'An integrated encyclopedia of DNA elements in the human genome', Nature, vol. 489, no. 7414, pp. 57-74. https://doi.org/10.1038/nature11247
Correction Dunham I, Kundaje A, Aldred SF, Collins PJ, Davis CA, Doyle F et al. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6;489(7414):57-74. https://doi.org/10.1038/nature11247
Correction 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 ; 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 ; Kheradpour, Pouya ; 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. ; 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. ; Good, Peter J. ; Feingold, Elise A. ; Crawford, Gregory E. ; Dekker, Job ; Elnitski, Laura ; Farnham, Peggy J. ; Giddings, Morgan C. ; Gingeras, Thomas R. ; Guigó, Roderic ; Hubbard, Timothy J. ; Kent, W. James ; Lieb, Jason D. ; Margulies, Elliott H. ; Myers, Richard M. ; Stamatoyannopoulos, John A. ; Tenenbaum, Scott A. ; Weng, Zhiping ; White, Kevin P. ; Wold, Barbara ; Yu, Yanbao ; Wrobel, John ; Risk, Brian A. ; Gunawardena, Harsha P. ; Kuiper, Heather C. ; Maier, Christopher W. ; Xie, Ling ; Chen, Xian ; Mikkelsen, Tarjei S. ; Gillespie, Shawn ; Goren, Alon ; Ram, Oren ; Zhang, Xiaolan ; Wang, Li ; Issner, Robbyn ; Coyne, Michael J. ; Durham, Timothy ; Ku, Manching ; Truong, Thanh ; Eaton, Matthew L. ; Dobin, Alex ; Tanzer, Andrea ; Lagarde, Julien ; Lin, Wei ; Xue, Chenghai ; Williams, Brian A. ; Zaleski, Chris ; Röder, Maik ; Kokocinski, Felix ; Abdelhamid, Rehab F. ; Alioto, Tyler ; Antoshechkin, Igor ; Baer, Michael T. ; Batut, Philippe ; Bell, Ian ; Bell, Kimberly ; Chakrabortty, Sudipto ; 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 ; 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 ; 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 ; Hayashizaki, Yoshihide ; Reymond, Alexandre ; Antonarakis, Stylianos E. ; Hannon, Gregory J. ; Ruan, Yijun ; Carninci, Piero ; 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 ; Kirkup, Vanessa M. ; Meyer, Laurence R. ; Long, Jeffrey C. ; Maddren, Morgan ; Raney, Brian J. ; Grasfeder, Linda L. ; Giresi, Paul G. ; Battenhouse, Anna ; Sheffield, Nathan C. ; Showers, Kimberly A. ; London, Darin ; Bhinge, Akshay A. ; Shestak, Christopher ; Schaner, Matthew R. ; Kim, Seul Ki ; 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 ; Iyer, Vishwanath R. ; Zheng, Meizhen ; Wang, Ping ; Gertz, Jason ; Vielmetter, Jost ; Partridge, E. Christopher ; Varley, Katherine E. ; Gasper, Clarke ; Bansal, Anita ; Pepke, Shirley ; Jain, Preti ; Amrhein, Henry ; Bowling, Kevin M. ; Anaya, Michael ; Cross, Marie K. ; Muratet, Michael A. ; 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 ; Newberry, J. Scott ; Levy, Shawn E. ; Absher, Devin M. ; Wong, Wing H. ; Blow, Matthew J. ; Visel, Axel ; Pennachio, Len A. ; Petrykowska, Hanna M. ; Abyzov, Alexej ; Aken, Bronwen ; Barrell, Daniel ; Barson, Gemma ; Berry, Andrew ; Bignell, Alexandra ; Boychenko, Veronika ; Bussotti, Giovanni ; Davidson, Claire ; Despacio-Reyes, Gloria ; Diekhans, Mark ; Ezkurdia, Iakes ; Frankish, Adam ; Gilbert, James ; Gonzalez, Jose Manuel ; Griffiths, Ed ; Harte, Rachel ; Hendrix, David A. ; Hunt, Toby ; Jungreis, Irwin ; Kay, Mike ; Khurana, Ekta ; 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 ; Tapanari, Electra ; Tress, Michael L. ; Van Baren, Marijke J. ; Washietl, Stefan ; Wilming, Laurens ; Zadissa, Amonida ; Zhang, Zhengdong ; Brent, Michael ; Haussler, David ; Valencia, Alfonso ; 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 ; 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 ; Lian, Jin ; Lindahl-Allen, Marianne ; Min, Renqiang ; Miotto, Benoit ; Monahan, Hannah ; Moqtaderi, Zarmik ; Mu, Xinmeng J. ; O'Geen, Henriette ; Ouyang, Zhengqing ; Patacsil, Dorrelyn ; Raha, Debasish ; Ramirez, Lucia ; Reed, Brian ; Shi, Minyi ; Slifer, Teri ; Witt, Heather ; Wu, Linfeng ; Xu, Xiaoqin ; Yan, Koon Kiu ; Yang, Xinqiong ; Struhl, Kevin ; Weissman, Sherman M. ; Penalva, Luiz O. ; Karmakar, Subhradip ; Bhanvadia, Raj R. ; Choudhury, Alina ; Domanus, Marc ; Ma, Lijia ; Moran, Jennifer ; Victorsen, Alec ; 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 ; Jain, Gaurav ; 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 ; Johnson, Audra K. ; Johnson, Ericka M. ; Kutyavin, Tattyana V. ; 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 ; Sanchez, Minerva E. ; Sandstrom, Richard S. ; Shafer, Anthony O. ; Stergachis, Andrew B. ; Thomas, Sean ; 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 ; Beal, Kathryn ; Brazma, Alvis ; Flicek, Paul ; Johnson, Nathan ; Lukk, Margus ; Luscombe, Nicholas M. ; Sobral, Daniel ; Vaquerizas, Juan M. ; Batzoglou, Serafim ; Sidow, Arend ; Hussami, Nadine ; Kyriazopoulou-Panagiotopoulou, Sofia ; Libbrecht, Max W. ; Schaub, Marc A. ; Miller, Webb ; Bickel, Peter J. ; Banfai, Balazs ; Boley, Nathan P. ; Huang, Haiyan ; Li, Jingyi Jessica ; Noble, William Stafford ; Bilmes, Jeffrey A. ; Buske, Orion J. ; Sahu, Avinash D. ; Kharchenko, Peter V. ; Park, Peter J. ; Baker, Dannon ; Taylor, James ; Lochovsky, Lucas. / An integrated encyclopedia of DNA elements in the human genome. In: Nature. 2012 ; Vol. 489, No. 7414. pp. 57-74.
@article{e9c50d6ca67441f4aba1b80bf1a5ef1d,
title = "An integrated encyclopedia of DNA elements in the human genome",
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.",
author = "{Correction Dunham}, Ian and Anshul Kundaje and Aldred, {Shelley F.} and Collins, {Patrick J.} and Davis, {Carrie A.} and Francis Doyle and Epstein, {Charles B.} and Seth Frietze and Jennifer Harrow and Rajinder Kaul and Jainab Khatun and Lajoie, {Bryan R.} and Landt, {Stephen G.} and Lee, {Bum Kyu} and Florencia Pauli and Rosenbloom, {Kate R.} and Peter Sabo and Alexias Safi and Amartya Sanyal and Noam Shoresh and Simon, {Jeremy M.} and Lingyun Song and Trinklein, {Nathan D.} and Altshuler, {Robert C.} and Ewan Birney and Brown, {James B.} and Chao Cheng and Sarah Djebali and Xianjun Dong and Jason Ernst and Furey, {Terrence S.} and Mark Gerstein and Belinda Giardine and Melissa Greven and Hardison, {Ross C.} and Harris, {Robert S.} and Javier Herrero and Hoffman, {Michael M.} and Sowmya Iyer and Manolis Kellis and Pouya Kheradpour and Timo Lassmann and Qunhua Li and Xinying Lin and Marinov, {Georgi K.} and Angelika Merkel and Ali Mortazavi and Parker, {Stephen C J} and Reddy, {Timothy E.} and Joel Rozowsky and Felix Schlesinger and Thurman, {Robert E.} and Jie Wang and Ward, {Lucas D.} and Whitfield, {Troy W.} and Wilder, {Steven P.} and Weisheng Wu and Xi, {Hualin S.} and Yip, {Kevin Y.} and Jiali Zhuang and Bernstein, {Bradley E.} and Green, {Eric D.} and Chris Gunter and Michael Snyder and Pazin, {Michael J.} and Lowdon, {Rebecca F.} and Dillon, {Laura A L} and Adams, {Leslie B.} and Kelly, {Caroline J.} and Julia Zhang and Wexler, {Judith R.} and Good, {Peter J.} and Feingold, {Elise A.} and Crawford, {Gregory E.} and Job Dekker and Laura Elnitski and Farnham, {Peggy J.} and Giddings, {Morgan C.} and Gingeras, {Thomas R.} and Roderic Guig{\'o} and Hubbard, {Timothy J.} and Kent, {W. James} and Lieb, {Jason D.} and Margulies, {Elliott H.} and Myers, {Richard M.} and Stamatoyannopoulos, {John A.} and Tenenbaum, {Scott A.} and Zhiping Weng and White, {Kevin P.} and Barbara Wold and Yanbao Yu and John Wrobel and Risk, {Brian A.} and Gunawardena, {Harsha P.} and Kuiper, {Heather C.} and Maier, {Christopher W.} and Ling Xie and Xian Chen and Mikkelsen, {Tarjei S.} and Shawn Gillespie and Alon Goren and Oren Ram and Xiaolan Zhang and Li Wang and Robbyn Issner and Coyne, {Michael J.} and Timothy Durham and Manching Ku and Thanh Truong and Eaton, {Matthew L.} and Alex Dobin and Andrea Tanzer and Julien Lagarde and Wei Lin and Chenghai Xue and Williams, {Brian A.} and Chris Zaleski and Maik R{\"o}der and Felix Kokocinski and Abdelhamid, {Rehab F.} and Tyler Alioto and Igor Antoshechkin and Baer, {Michael T.} and Philippe Batut and Ian Bell and Kimberly Bell and Sudipto Chakrabortty and Jacqueline Chrast and Joao Curado and Thomas Derrien and Jorg Drenkow and Erica Dumais and Jackie Dumais and Radha Duttagupta and Megan Fastuca and Kata Fejes-Toth and Pedro Ferreira and Sylvain Foissac and Fullwood, {Melissa J.} and Hui Gao and David Gonzalez and Assaf Gordon and C{\'e}dric Howald and Sonali Jha and Rory Johnson and Philipp Kapranov and Brandon King and Colin Kingswood and Guoliang Li and Luo, {Oscar J.} and Eddie Park and Preall, {Jonathan B.} and Kimberly Presaud and Paolo Ribeca and Daniel Robyr and Xiaoan Ruan and Michael Sammeth and Sandhu, {Kuljeet Singh} and Lorain Schaeffer and See, {Lei Hoon} and Atif Shahab and Jorgen Skancke and Suzuki, {Ana Maria} and Hazuki Takahashi and Hagen Tilgner and Diane Trout and Nathalie Walters and Huaien Wang and Yoshihide Hayashizaki and Alexandre Reymond and Antonarakis, {Stylianos E.} and Hannon, {Gregory J.} and Yijun Ruan and Piero Carninci and Sloan, {Cricket A.} and Katrina Learned and Malladi, {Venkat S.} and Wong, {Matthew C.} and Barber, {Galt P.} and Cline, {Melissa S.} and Dreszer, {Timothy R.} and Heitner, {Steven G.} and Donna Karolchik and Kirkup, {Vanessa M.} and Meyer, {Laurence R.} and Long, {Jeffrey C.} and Morgan Maddren and Raney, {Brian J.} and Grasfeder, {Linda L.} and Giresi, {Paul G.} and Anna Battenhouse and Sheffield, {Nathan C.} and Showers, {Kimberly A.} and Darin London and Bhinge, {Akshay A.} and Christopher Shestak and Schaner, {Matthew R.} and Kim, {Seul Ki} and Zhang, {Zhuzhu Z.} and Mieczkowski, {Piotr A.} and Mieczkowska, {Joanna O.} and Zheng Liu and McDaniell, {Ryan M.} and Yunyun Ni and Rashid, {Naim U.} and Kim, {Min Jae} and Sheera Adar and Zhancheng Zhang and Tianyuan Wang and Deborah Winter and Damian Keefe and Iyer, {Vishwanath R.} and Meizhen Zheng and Ping Wang and Jason Gertz and Jost Vielmetter and Partridge, {E. Christopher} and Varley, {Katherine E.} and Clarke Gasper and Anita Bansal and Shirley Pepke and Preti Jain and Henry Amrhein and Bowling, {Kevin M.} and Michael Anaya and Cross, {Marie K.} and Muratet, {Michael A.} and Newberry, {Kimberly M.} and Kenneth McCue and Nesmith, {Amy S.} and Fisher-Aylor, {Katherine I.} and Barbara Pusey and Gilberto DeSalvo and Parker, {Stephanie L.} and Sreeram Balasubramanian and Davis, {Nicholas S.} and Meadows, {Sarah K.} and Tracy Eggleston and Newberry, {J. Scott} and Levy, {Shawn E.} and Absher, {Devin M.} and Wong, {Wing H.} and Blow, {Matthew J.} and Axel Visel and Pennachio, {Len A.} and Petrykowska, {Hanna M.} and Alexej Abyzov and Bronwen Aken and Daniel Barrell and Gemma Barson and Andrew Berry and Alexandra Bignell and Veronika Boychenko and Giovanni Bussotti and Claire Davidson and Gloria Despacio-Reyes and Mark Diekhans and Iakes Ezkurdia and Adam Frankish and James Gilbert and Gonzalez, {Jose Manuel} and Ed Griffiths and Rachel Harte and Hendrix, {David A.} and Toby Hunt and Irwin Jungreis and Mike Kay and Ekta Khurana and Jing Leng and Lin, {Michael F.} and Jane Loveland and Zhi Lu and Deepa Manthravadi and Marco Mariotti and Jonathan Mudge and Gaurab Mukherjee and Cedric Notredame and Baikang Pei and Rodriguez, {Jose Manuel} and Gary Saunders and Andrea Sboner and Stephen Searle and Cristina Sisu and Catherine Snow and Charlie Steward and Electra Tapanari and Tress, {Michael L.} and {Van Baren}, {Marijke J.} and Stefan Washietl and Laurens Wilming and Amonida Zadissa and Zhengdong Zhang and Michael Brent and David Haussler and Alfonso Valencia and Nick Addleman and Alexander, {Roger P.} and Auerbach, {Raymond K.} and Suganthi Balasubramanian and Keith Bettinger and Nitin Bhardwaj and Boyle, {Alan P.} and Cao, {Alina R.} and Philip Cayting and Alexandra Charos and Yong Cheng and Catharine Eastman and Ghia Euskirchen and Fleming, {Joseph D.} and Fabian Grubert and Lukas Habegger and Manoj Hariharan and Arif Harmanci and Sushma Iyengar and Jin, {Victor X.} and Karczewski, {Konrad J.} and Maya Kasowski and Phil Lacroute and Hugo Lam and Nathan Lamarre-Vincent and Jin Lian and Marianne Lindahl-Allen and Renqiang Min and Benoit Miotto and Hannah Monahan and Zarmik Moqtaderi and Mu, {Xinmeng J.} and Henriette O'Geen and Zhengqing Ouyang and Dorrelyn Patacsil and Debasish Raha and Lucia Ramirez and Brian Reed and Minyi Shi and Teri Slifer and Heather Witt and Linfeng Wu and Xiaoqin Xu and Yan, {Koon Kiu} and Xinqiong Yang and Kevin Struhl and Weissman, {Sherman M.} and Penalva, {Luiz O.} and Subhradip Karmakar and Bhanvadia, {Raj R.} and Alina Choudhury and Marc Domanus and Lijia Ma and Jennifer Moran and Alec Victorsen and Thomas Auer and Lazaro Centanin and Michael Eichenlaub and Franziska Gruhl and Stephan Heermann and Burkhard Hoeckendorf and Daigo Inoue and Tanja Kellner and Stephan Kirchmaier and Claudia Mueller and Robert Reinhardt and Lea Schertel and Stephanie Schneider and Rebecca Sinn and Beate Wittbrodt and Jochen Wittbrodt and Gaurav Jain and Gayathri Balasundaram and Bates, {Daniel L.} and Rachel Byron and Canfield, {Theresa K.} and Diegel, {Morgan J.} and Douglas Dunn and Ebersol, {Abigail K.} and Tristan Frum and Kavita Garg and Erica Gist and Hansen, {R. Scott} and Lisa Boatman and Eric Haugen and Richard Humbert and Johnson, {Audra K.} and Johnson, {Ericka M.} and Kutyavin, {Tattyana V.} and Kristen Lee and Dimitra Lotakis and Maurano, {Matthew T.} and Neph, {Shane J.} and Neri, {Fiedencio V.} and Nguyen, {Eric D.} and Hongzhu Qu and Reynolds, {Alex P.} and Vaughn Roach and Eric Rynes and Sanchez, {Minerva E.} and Sandstrom, {Richard S.} and Shafer, {Anthony O.} and Stergachis, {Andrew B.} and Sean Thomas and Benjamin Vernot and Jeff Vierstra and Shinny Vong and Hao Wang and Weaver, {Molly A.} and Yongqi Yan and Miaohua Zhang and Akey, {Joshua M.} and Michael Bender and Dorschner, {Michael O.} and Mark Groudine and MacCoss, {Michael J.} and Patrick Navas and George Stamatoyannopoulos and Kathryn Beal and Alvis Brazma and Paul Flicek and Nathan Johnson and Margus Lukk and Luscombe, {Nicholas M.} and Daniel Sobral and Vaquerizas, {Juan M.} and Serafim Batzoglou and Arend Sidow and Nadine Hussami and Sofia Kyriazopoulou-Panagiotopoulou and Libbrecht, {Max W.} and Schaub, {Marc A.} and Webb Miller and Bickel, {Peter J.} and Balazs Banfai and Boley, {Nathan P.} and Haiyan Huang and Li, {Jingyi Jessica} and Noble, {William Stafford} and Bilmes, {Jeffrey A.} and Buske, {Orion J.} and Sahu, {Avinash D.} and Kharchenko, {Peter V.} and Park, {Peter J.} and Dannon Baker and James Taylor and Lucas Lochovsky",
year = "2012",
month = "9",
day = "6",
doi = "10.1038/nature11247",
language = "English (US)",
volume = "489",
pages = "57--74",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7414",

}

TY - JOUR

T1 - An integrated encyclopedia of DNA elements in the human genome

AU - Correction Dunham, Ian

AU - Kundaje, Anshul

AU - Aldred, Shelley F.

AU - Collins, Patrick J.

AU - Davis, Carrie A.

AU - Doyle, Francis

AU - Epstein, Charles B.

AU - Frietze, Seth

AU - Harrow, Jennifer

AU - Kaul, Rajinder

AU - Khatun, Jainab

AU - Lajoie, Bryan R.

AU - Landt, Stephen G.

AU - Lee, Bum Kyu

AU - Pauli, Florencia

AU - Rosenbloom, Kate R.

AU - Sabo, Peter

AU - Safi, Alexias

AU - Sanyal, Amartya

AU - Shoresh, Noam

AU - Simon, Jeremy M.

AU - Song, Lingyun

AU - Trinklein, Nathan D.

AU - Altshuler, Robert C.

AU - Birney, Ewan

AU - Brown, James B.

AU - Cheng, Chao

AU - Djebali, Sarah

AU - Dong, Xianjun

AU - Ernst, Jason

AU - Furey, Terrence S.

AU - Gerstein, Mark

AU - Giardine, Belinda

AU - Greven, Melissa

AU - Hardison, Ross C.

AU - Harris, Robert S.

AU - Herrero, Javier

AU - Hoffman, Michael M.

AU - Iyer, Sowmya

AU - Kellis, Manolis

AU - Kheradpour, Pouya

AU - Lassmann, Timo

AU - Li, Qunhua

AU - Lin, Xinying

AU - Marinov, Georgi K.

AU - Merkel, Angelika

AU - Mortazavi, Ali

AU - Parker, Stephen C J

AU - Reddy, Timothy E.

AU - Rozowsky, Joel

AU - Schlesinger, Felix

AU - Thurman, Robert E.

AU - Wang, Jie

AU - Ward, Lucas D.

AU - Whitfield, Troy W.

AU - Wilder, Steven P.

AU - Wu, Weisheng

AU - Xi, Hualin S.

AU - Yip, Kevin Y.

AU - Zhuang, Jiali

AU - Bernstein, Bradley E.

AU - Green, Eric D.

AU - Gunter, Chris

AU - Snyder, Michael

AU - Pazin, Michael J.

AU - Lowdon, Rebecca F.

AU - Dillon, Laura A L

AU - Adams, Leslie B.

AU - Kelly, Caroline J.

AU - Zhang, Julia

AU - Wexler, Judith R.

AU - Good, Peter J.

AU - Feingold, Elise A.

AU - Crawford, Gregory E.

AU - Dekker, Job

AU - Elnitski, Laura

AU - Farnham, Peggy J.

AU - Giddings, Morgan C.

AU - Gingeras, Thomas R.

AU - Guigó, Roderic

AU - Hubbard, Timothy J.

AU - Kent, W. James

AU - Lieb, Jason D.

AU - Margulies, Elliott H.

AU - Myers, Richard M.

AU - Stamatoyannopoulos, John A.

AU - Tenenbaum, Scott A.

AU - Weng, Zhiping

AU - White, Kevin P.

AU - Wold, Barbara

AU - Yu, Yanbao

AU - Wrobel, John

AU - Risk, Brian A.

AU - Gunawardena, Harsha P.

AU - Kuiper, Heather C.

AU - Maier, Christopher W.

AU - Xie, Ling

AU - Chen, Xian

AU - Mikkelsen, Tarjei S.

AU - Gillespie, Shawn

AU - Goren, Alon

AU - Ram, Oren

AU - Zhang, Xiaolan

AU - Wang, Li

AU - Issner, Robbyn

AU - Coyne, Michael J.

AU - Durham, Timothy

AU - Ku, Manching

AU - Truong, Thanh

AU - Eaton, Matthew L.

AU - Dobin, Alex

AU - Tanzer, Andrea

AU - Lagarde, Julien

AU - Lin, Wei

AU - Xue, Chenghai

AU - Williams, Brian A.

AU - Zaleski, Chris

AU - Röder, Maik

AU - Kokocinski, Felix

AU - Abdelhamid, Rehab F.

AU - Alioto, Tyler

AU - Antoshechkin, Igor

AU - Baer, Michael T.

AU - Batut, Philippe

AU - Bell, Ian

AU - Bell, Kimberly

AU - Chakrabortty, Sudipto

AU - Chrast, Jacqueline

AU - Curado, Joao

AU - Derrien, Thomas

AU - Drenkow, Jorg

AU - Dumais, Erica

AU - Dumais, Jackie

AU - Duttagupta, Radha

AU - Fastuca, Megan

AU - Fejes-Toth, Kata

AU - Ferreira, Pedro

AU - Foissac, Sylvain

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PY - 2012/9/6

Y1 - 2012/9/6

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=84865790047&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84865790047&partnerID=8YFLogxK

U2 - 10.1038/nature11247

DO - 10.1038/nature11247

M3 - Article

C2 - 22955616

AN - SCOPUS:84865790047

VL - 489

SP - 57

EP - 74

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7414

ER -