A user's guide to the Encyclopedia of DNA elements (ENCODE)

Richard M. Myers, John Stamatoyannopoulos, Michael Snyder, Ian Dunham, Ross C. Hardison, Bradley E. Bernstein, Thomas R. Gingeras, W. James Kent, Ewan Birney, Barbara Wold, Gregory E. Crawford, Bradley E. Bernstein, Charles B. Epstein, Noam Shoresh, Jason Ernst, Tarjei S. Mikkelsen, Pouya Kheradpour, Xiaolan Zhang, Li Wang, Robbyn IssnerMichael J. Coyne, Timothy Durham, Manching Ku, Thanh Truong, Lucas D. Ward, Robert C. Altshuler, Michael F. Lin, Manolis Kellis, Thomas R. Gingeras, Carrie A. Davis, Philipp Kapranov, Alexander Dobin, Christopher Zaleski, Felix Schlesinger, Philippe Batut, Sudipto Chakrabortty, Sonali Jha, Wei Lin, Jorg Drenkow, Huaien Wang, Kim Bell, Hui Gao, Ian Bell, Erica Dumais, Jacqueline Dumais, Stylianos E. Antonarakis, Catherine Ucla, Christelle Borel, Roderic Guigo, Sarah Djebali, Julien Lagarde, Colin Kingswood, Paolo Ribeca, Micha Sammeth, Tyler Alioto, Angelika Merkel, Hagen Tilgner, Piero Carninci, Yoshihide Hayashizaki, Timo Lassmann, Hazuki Takahashi, Rehab F. Abdelhamid, Gregory Hannon, Katalin Toth Fejes, Jonathan Preall, Assaf Gordon, Vihra Sotirova, Alexandre Reymond, Cedric Howald, Emilie Aït Yahya Graison, Jacqueline Chrast, Yijun Ruan, Xiaoan Ruan, Atif Shahab, Wan Ting Poh, Chia Lin Wei, Gregory E. Crawford, Terrence S. Furey, Alan P. Boyle, Nathan C. Sheffield, Lingyun Song, Yoichiro Shibata, Teresa Vales, Deborah Winter, Zhancheng Zhang, Darin London, Tianyuan Wang, Ewan Birney, Damian Keefe, Vishwanath R. Iyer, Bum Kyu Lee, Ryan M. McDaniell, Zheng Liu, Anna Battenhouse, Akshay A. Bhinge, Jason D. Lieb, Linda L. Grasfeder, Kimberly A. Showers, Paul G. Giresi, Seul K C Kim, Christopher Shestak, Richard M. Myers, Florencia Pauli, Timothy E. Reddy, Jason Gertz, E. Christopher Partridge, Preti Jain, Rebekka O. Sprouse, Anita Bansal, Barbara Pusey, Michael A. Muratet, Katherine E. Varley, Kevin M. Bowling, Kimberly M. Newberry, Amy S. Nesmith, Jason A. Dilocker, Stephanie L. Parker, Lindsay L. Waite, Krista Thibeault, Kevin Roberts, Devin M. Absher, Barbara Wold, Ali Mortazavi, Brian Williams, Georgi Marinov, Diane Trout, Shirley Pepke, Brandon King, Kenneth McCue, Anthony Kirilusha, Gilberto DeSalvo, Katherine Aylor Fisher, Henry Amrhein, Jost Vielmetter, Gavin Sherlock, Arend Sidow, Serafim Batzoglou, Rami Rauch, Anshul Kundaje, Max Libbrecht, Elliott H. Margulies, Stephen C J Parker, Laura Elnitski, Eric D. Green, Tim Hubbard, Jennifer Harrow, Stephen Searle, Felix Kokocinski, Browen Aken, Adam Frankish, Toby Hunt, Gloria Despacio-Reyes, Mike Kay, Gaurab Mukherjee, Alexandra Bignell, Gary Saunders, Veronika Boychenko, Michael Brent, M. J. van Baren, Randall H. Brown, Mark Gerstein, Ekta Khurana, Suganthi Balasubramanian, Zhengdong Zhang, Hugo Lam, Philip Cayting, Rebecca Robilotto, Zhi Lu, Roderic Guigo, Thomas Derrien, Andrea Tanzer, David G. Knowles, Marco Mariotti, W. James Kent, David Haussler, Rachel Harte, Mark Diekhans, Manolis Kellis, Mike Lin, Pouya Kheradpour, Jason Ernst, Alexandre Reymond, Cedric Howald, Emilie Aït Yahya Graison, Jacqueline Chrast, Alfonso Valencia, Michael Tress, Jose Manuel Rodriguez, Michael Snyder, Stephen G. Landt, Debasish Raha, Minyi Shi, Ghia Euskirchen, Fabian Grubert, Maya Kasowski, Jin Lian, Philip Cayting, Phil Lacroute, Youhan Xu, Hannah Monahan, Dorrelyn Patacsil, Teri Slifer, Xinqiong Yang, Alexandra Charos, Brian Reed, Linfeng Wu, Raymond K. Auerbach, Lukas Habegger, Manoj Hariharan, Joel Rozowsky, Alexej Abyzov, Sherman M. Weissman, Mark Gerstein, Kevin Struhl, Nathan Vincent Lamarre, Marianne Allen Lindahl, Benoit Miotto, Zarmik Moqtaderi, Joseph D. Fleming, Peter Newburger, Peggy J. Farnham, Seth Frietze, Henriette O'Geen, Xiaoqin Xu, Kim R. Blahnik, Alina R. Cao, Sushma Iyengar, John A. Stamatoyannopoulos, Rajinder Kaul, Robert E. Thurman, Hao Wang, Patrick A. Navas, Richard Sandstrom, Peter J. Sabo, Molly Weaver, Theresa Canfield, Kristen Lee, Shane Neph, Vaughan Roach, Alex Reynolds, Audra Johnson, Eric Rynes, Erika Giste, Shinny Vong, Jun Neri, Tristan Frum, Ericka M. Johnson, Eric D. Nguyen, Abigail K. Ebersol, Minerva E. Sanchez, Hadar H. Sheffer, Dimitra Lotakis, Eric Haugen, Richard Humbert, Tanya Kutyavin, Tony Shafer, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, W. James Kent, Kate R. Rosenbloom, Timothy R. Dreszer, Brian J. Raney, Galt P. Barber, Laurence R. Meyer, Cricket A. Sloan, Venkat S. Malladi, Melissa S. Cline, Katrina Learned, Vanessa K. Swing, Ann S. Zweig, Brooke Rhead, Pauline A. Fujita, Krishna Roskin, Donna Karolchik, Robert M. Kuhn, David Haussler, Ewan Birney, Ian Dunham, Steven P. Wilder, Damian Keefe, Daniel Sobral, Javier Herrero, Kathryn Beal, Margus Lukk, Alvis Brazma, Juan M. Vaquerizas, Nicholas M. Luscombe, Peter J. Bickel, Nathan Boley, James B. Brown, Qunhua Li, Haiyan Huang, Mark Gerstein, Lukas Habegger, Andrea Sboner, Joel Rozowsky, Raymond K. Auerbach, Kevin Y. Yip, Chao Cheng, Koon Kiu Yan, Nitin Bhardwaj, Jing Wang, Lucas Lochovsky, Justin Jee, Theodore Gibson, Jing Leng, Jiang Du, Ross C. Hardison, Robert S. Harris, Giltae Song, Webb Miller, David Haussler, Krishna Roskin, Bernard Suh, Ting Wang, Benedict Paten, William S. Noble, Michael M. Hoffman, Orion J. Buske, Zhiping Weng, Xianjun Dong, Jie Wang, Hualin Xi, Scott A. Tenenbaum, Frank Doyle, Luiz O. Penalva, Sridar Chittur, Thomas D. Tullius, Stephen C J Parker, Kevin P. White, Subhradip Karmakar, Alec Victorsen, Nader Jameel, Nick Bild, Robert L. Grossman, Michael Snyder, Stephen G. Landt, Xinqiong Yang, Dorrelyn Patacsil, Teri Slifer, Job Dekker, Bryan R. Lajoie, Amartya Sanyal, Zhiping Weng, Troy W. Whitfield, Jie Wang, Patrick J. Collins, Nathan D. Trinklein, E. Christopher Partridge, Richard M. Myers, Morgan C. Giddings, Xian Chen, Jainab Khatun, Chris Maier, Yanbao Yu, Harsha Gunawardena, Brian Risk, Elise A. Feingold, Rebecca F. Lowdon, Laura A L Dillon, Peter J. Good

Research output: Contribution to journalArticle

921 Citations (Scopus)

Abstract

The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

Original languageEnglish (US)
Article numbere1001046
JournalPLoS Biology
Volume9
Issue number4
DOIs
StatePublished - Apr 2011

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Encyclopedias
Human Genome
Genes
DNA
genome
Nucleic Acid Regulatory Sequences
DNA Methylation
Chromatin
DNA methylation
Databases
Technology
chromatin
Health
Biological Sciences
genes

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Immunology and Microbiology(all)
  • Neuroscience(all)

Cite this

Myers, R. M., Stamatoyannopoulos, J., Snyder, M., Dunham, I., Hardison, R. C., Bernstein, B. E., ... Good, P. J. (2011). A user's guide to the Encyclopedia of DNA elements (ENCODE). PLoS Biology, 9(4), [e1001046]. https://doi.org/10.1371/journal.pbio.1001046

A user's guide to the Encyclopedia of DNA elements (ENCODE). / Myers, Richard M.; Stamatoyannopoulos, John; Snyder, Michael; Dunham, Ian; Hardison, Ross C.; Bernstein, Bradley E.; Gingeras, Thomas R.; Kent, W. James; Birney, Ewan; Wold, Barbara; Crawford, Gregory E.; Bernstein, Bradley E.; Epstein, Charles B.; Shoresh, Noam; Ernst, Jason; Mikkelsen, Tarjei S.; Kheradpour, Pouya; Zhang, Xiaolan; Wang, Li; Issner, Robbyn; Coyne, Michael J.; Durham, Timothy; Ku, Manching; Truong, Thanh; Ward, Lucas D.; Altshuler, Robert C.; Lin, Michael F.; Kellis, Manolis; Gingeras, Thomas R.; Davis, Carrie A.; Kapranov, Philipp; Dobin, Alexander; Zaleski, Christopher; Schlesinger, Felix; Batut, Philippe; Chakrabortty, Sudipto; Jha, Sonali; Lin, Wei; Drenkow, Jorg; Wang, Huaien; Bell, Kim; Gao, Hui; Bell, Ian; Dumais, Erica; Dumais, Jacqueline; Antonarakis, Stylianos E.; Ucla, Catherine; Borel, Christelle; Guigo, Roderic; Djebali, Sarah; Lagarde, Julien; Kingswood, Colin; Ribeca, Paolo; Sammeth, Micha; Alioto, Tyler; Merkel, Angelika; Tilgner, Hagen; Carninci, Piero; Hayashizaki, Yoshihide; Lassmann, Timo; Takahashi, Hazuki; Abdelhamid, Rehab F.; Hannon, Gregory; Fejes, Katalin Toth; Preall, Jonathan; Gordon, Assaf; Sotirova, Vihra; Reymond, Alexandre; Howald, Cedric; Graison, Emilie Aït Yahya; Chrast, Jacqueline; Ruan, Yijun; Ruan, Xiaoan; Shahab, Atif; Poh, Wan Ting; Wei, Chia Lin; Crawford, Gregory E.; Furey, Terrence S.; Boyle, Alan P.; Sheffield, Nathan C.; Song, Lingyun; Shibata, Yoichiro; Vales, Teresa; Winter, Deborah; Zhang, Zhancheng; London, Darin; Wang, Tianyuan; Birney, Ewan; Keefe, Damian; Iyer, Vishwanath R.; Lee, Bum Kyu; McDaniell, Ryan M.; Liu, Zheng; Battenhouse, Anna; Bhinge, Akshay A.; Lieb, Jason D.; Grasfeder, Linda L.; Showers, Kimberly A.; Giresi, Paul G.; Kim, Seul K C; Shestak, Christopher; Myers, Richard M.; Pauli, Florencia; Reddy, Timothy E.; Gertz, Jason; Partridge, E. Christopher; Jain, Preti; Sprouse, Rebekka O.; Bansal, Anita; Pusey, Barbara; Muratet, Michael A.; Varley, Katherine E.; Bowling, Kevin M.; Newberry, Kimberly M.; Nesmith, Amy S.; Dilocker, Jason A.; Parker, Stephanie L.; Waite, Lindsay L.; Thibeault, Krista; Roberts, Kevin; Absher, Devin M.; Wold, Barbara; Mortazavi, Ali; Williams, Brian; Marinov, Georgi; Trout, Diane; Pepke, Shirley; King, Brandon; McCue, Kenneth; Kirilusha, Anthony; DeSalvo, Gilberto; Fisher, Katherine Aylor; Amrhein, Henry; Vielmetter, Jost; Sherlock, Gavin; Sidow, Arend; Batzoglou, Serafim; Rauch, Rami; Kundaje, Anshul; Libbrecht, Max; Margulies, Elliott H.; Parker, Stephen C J; Elnitski, Laura; Green, Eric D.; Hubbard, Tim; Harrow, Jennifer; Searle, Stephen; Kokocinski, Felix; Aken, Browen; Frankish, Adam; Hunt, Toby; Despacio-Reyes, Gloria; Kay, Mike; Mukherjee, Gaurab; Bignell, Alexandra; Saunders, Gary; Boychenko, Veronika; Brent, Michael; van Baren, M. J.; Brown, Randall H.; Gerstein, Mark; Khurana, Ekta; Balasubramanian, Suganthi; Zhang, Zhengdong; Lam, Hugo; Cayting, Philip; Robilotto, Rebecca; Lu, Zhi; Guigo, Roderic; Derrien, Thomas; Tanzer, Andrea; Knowles, David G.; Mariotti, Marco; Kent, W. James; Haussler, David; Harte, Rachel; Diekhans, Mark; Kellis, Manolis; Lin, Mike; Kheradpour, Pouya; Ernst, Jason; Reymond, Alexandre; Howald, Cedric; Graison, Emilie Aït Yahya; Chrast, Jacqueline; Valencia, Alfonso; Tress, Michael; Rodriguez, Jose Manuel; Snyder, Michael; Landt, Stephen G.; Raha, Debasish; Shi, Minyi; Euskirchen, Ghia; Grubert, Fabian; Kasowski, Maya; Lian, Jin; Cayting, Philip; Lacroute, Phil; Xu, Youhan; Monahan, Hannah; Patacsil, Dorrelyn; Slifer, Teri; Yang, Xinqiong; Charos, Alexandra; Reed, Brian; Wu, Linfeng; Auerbach, Raymond K.; Habegger, Lukas; Hariharan, Manoj; Rozowsky, Joel; Abyzov, Alexej; Weissman, Sherman M.; Gerstein, Mark; Struhl, Kevin; Lamarre, Nathan Vincent; Lindahl, Marianne Allen; Miotto, Benoit; Moqtaderi, Zarmik; Fleming, Joseph D.; Newburger, Peter; Farnham, Peggy J.; Frietze, Seth; O'Geen, Henriette; Xu, Xiaoqin; Blahnik, Kim R.; Cao, Alina R.; Iyengar, Sushma; Stamatoyannopoulos, John A.; Kaul, Rajinder; Thurman, Robert E.; Wang, Hao; Navas, Patrick A.; Sandstrom, Richard; Sabo, Peter J.; Weaver, Molly; Canfield, Theresa; Lee, Kristen; Neph, Shane; Roach, Vaughan; Reynolds, Alex; Johnson, Audra; Rynes, Eric; Giste, Erika; Vong, Shinny; Neri, Jun; Frum, Tristan; Johnson, Ericka M.; Nguyen, Eric D.; Ebersol, Abigail K.; Sanchez, Minerva E.; Sheffer, Hadar H.; Lotakis, Dimitra; Haugen, Eric; Humbert, Richard; Kutyavin, Tanya; Shafer, Tony; Dekker, Job; Lajoie, Bryan R.; Sanyal, Amartya; Kent, W. James; Rosenbloom, Kate R.; Dreszer, Timothy R.; Raney, Brian J.; Barber, Galt P.; Meyer, Laurence R.; Sloan, Cricket A.; Malladi, Venkat S.; Cline, Melissa S.; Learned, Katrina; Swing, Vanessa K.; Zweig, Ann S.; Rhead, Brooke; Fujita, Pauline A.; Roskin, Krishna; Karolchik, Donna; Kuhn, Robert M.; Haussler, David; Birney, Ewan; Dunham, Ian; Wilder, Steven P.; Keefe, Damian; Sobral, Daniel; Herrero, Javier; Beal, Kathryn; Lukk, Margus; Brazma, Alvis; Vaquerizas, Juan M.; Luscombe, Nicholas M.; Bickel, Peter J.; Boley, Nathan; Brown, James B.; Li, Qunhua; Huang, Haiyan; Gerstein, Mark; Habegger, Lukas; Sboner, Andrea; Rozowsky, Joel; Auerbach, Raymond K.; Yip, Kevin Y.; Cheng, Chao; Yan, Koon Kiu; Bhardwaj, Nitin; Wang, Jing; Lochovsky, Lucas; Jee, Justin; Gibson, Theodore; Leng, Jing; Du, Jiang; Hardison, Ross C.; Harris, Robert S.; Song, Giltae; Miller, Webb; Haussler, David; Roskin, Krishna; Suh, Bernard; Wang, Ting; Paten, Benedict; Noble, William S.; Hoffman, Michael M.; Buske, Orion J.; Weng, Zhiping; Dong, Xianjun; Wang, Jie; Xi, Hualin; Tenenbaum, Scott A.; Doyle, Frank; Penalva, Luiz O.; Chittur, Sridar; Tullius, Thomas D.; Parker, Stephen C J; White, Kevin P.; Karmakar, Subhradip; Victorsen, Alec; Jameel, Nader; Bild, Nick; Grossman, Robert L.; Snyder, Michael; Landt, Stephen G.; Yang, Xinqiong; Patacsil, Dorrelyn; Slifer, Teri; Dekker, Job; Lajoie, Bryan R.; Sanyal, Amartya; Weng, Zhiping; Whitfield, Troy W.; Wang, Jie; Collins, Patrick J.; Trinklein, Nathan D.; Partridge, E. Christopher; Myers, Richard M.; Giddings, Morgan C.; Chen, Xian; Khatun, Jainab; Maier, Chris; Yu, Yanbao; Gunawardena, Harsha; Risk, Brian; Feingold, Elise A.; Lowdon, Rebecca F.; Dillon, Laura A L; Good, Peter J.

In: PLoS Biology, Vol. 9, No. 4, e1001046, 04.2011.

Research output: Contribution to journalArticle

Myers, RM, Stamatoyannopoulos, J, Snyder, M, Dunham, I, Hardison, RC, Bernstein, BE, Gingeras, TR, Kent, WJ, Birney, E, Wold, B, Crawford, GE, Bernstein, BE, Epstein, CB, Shoresh, N, Ernst, J, Mikkelsen, TS, Kheradpour, P, Zhang, X, Wang, L, Issner, R, Coyne, MJ, Durham, T, Ku, M, Truong, T, Ward, LD, Altshuler, RC, Lin, MF, Kellis, M, Gingeras, TR, Davis, CA, Kapranov, P, Dobin, A, Zaleski, C, Schlesinger, F, Batut, P, Chakrabortty, S, Jha, S, Lin, W, Drenkow, J, Wang, H, Bell, K, Gao, H, Bell, I, Dumais, E, Dumais, J, Antonarakis, SE, Ucla, C, Borel, C, Guigo, R, Djebali, S, Lagarde, J, Kingswood, C, Ribeca, P, Sammeth, M, Alioto, T, Merkel, A, Tilgner, H, Carninci, P, Hayashizaki, Y, Lassmann, T, Takahashi, H, Abdelhamid, RF, Hannon, G, Fejes, KT, Preall, J, Gordon, A, Sotirova, V, Reymond, A, Howald, C, Graison, EAY, Chrast, J, Ruan, Y, Ruan, X, Shahab, A, Poh, WT, Wei, CL, Crawford, GE, Furey, TS, Boyle, AP, Sheffield, NC, Song, L, Shibata, Y, Vales, T, Winter, D, Zhang, Z, London, D, Wang, T, Birney, E, Keefe, D, Iyer, VR, Lee, BK, McDaniell, RM, Liu, Z, Battenhouse, A, Bhinge, AA, Lieb, JD, Grasfeder, LL, Showers, KA, Giresi, PG, Kim, SKC, Shestak, C, Myers, RM, Pauli, F, Reddy, TE, Gertz, J, Partridge, EC, Jain, P, Sprouse, RO, Bansal, A, Pusey, B, Muratet, MA, Varley, KE, Bowling, KM, Newberry, KM, Nesmith, AS, Dilocker, JA, Parker, SL, Waite, LL, Thibeault, K, Roberts, K, Absher, DM, Wold, B, Mortazavi, A, Williams, B, Marinov, G, Trout, D, Pepke, S, King, B, McCue, K, Kirilusha, A, DeSalvo, G, Fisher, KA, Amrhein, H, Vielmetter, J, Sherlock, G, Sidow, A, Batzoglou, S, Rauch, R, Kundaje, A, Libbrecht, M, Margulies, EH, Parker, SCJ, Elnitski, L, Green, ED, Hubbard, T, Harrow, J, Searle, S, Kokocinski, F, Aken, B, Frankish, A, Hunt, T, Despacio-Reyes, G, Kay, M, Mukherjee, G, Bignell, A, Saunders, G, Boychenko, V, Brent, M, van Baren, MJ, Brown, RH, Gerstein, M, Khurana, E, Balasubramanian, S, Zhang, Z, Lam, H, Cayting, P, Robilotto, R, Lu, Z, Guigo, R, Derrien, T, Tanzer, A, Knowles, DG, Mariotti, M, Kent, WJ, Haussler, D, Harte, R, Diekhans, M, Kellis, M, Lin, M, Kheradpour, P, Ernst, J, Reymond, A, Howald, C, Graison, EAY, Chrast, J, Valencia, A, Tress, M, Rodriguez, JM, Snyder, M, Landt, SG, Raha, D, Shi, M, Euskirchen, G, Grubert, F, Kasowski, M, Lian, J, Cayting, P, Lacroute, P, Xu, Y, Monahan, H, Patacsil, D, Slifer, T, Yang, X, Charos, A, Reed, B, Wu, L, Auerbach, RK, Habegger, L, Hariharan, M, Rozowsky, J, Abyzov, A, Weissman, SM, Gerstein, M, Struhl, K, Lamarre, NV, Lindahl, MA, Miotto, B, Moqtaderi, Z, Fleming, JD, Newburger, P, Farnham, PJ, Frietze, S, O'Geen, H, Xu, X, Blahnik, KR, Cao, AR, Iyengar, S, Stamatoyannopoulos, JA, Kaul, R, Thurman, RE, Wang, H, Navas, PA, Sandstrom, R, Sabo, PJ, Weaver, M, Canfield, T, Lee, K, Neph, S, Roach, V, Reynolds, A, Johnson, A, Rynes, E, Giste, E, Vong, S, Neri, J, Frum, T, Johnson, EM, Nguyen, ED, Ebersol, AK, Sanchez, ME, Sheffer, HH, Lotakis, D, Haugen, E, Humbert, R, Kutyavin, T, Shafer, T, Dekker, J, Lajoie, BR, Sanyal, A, Kent, WJ, Rosenbloom, KR, Dreszer, TR, Raney, BJ, Barber, GP, Meyer, LR, Sloan, CA, Malladi, VS, Cline, MS, Learned, K, Swing, VK, Zweig, AS, Rhead, B, Fujita, PA, Roskin, K, Karolchik, D, Kuhn, RM, Haussler, D, Birney, E, Dunham, I, Wilder, SP, Keefe, D, Sobral, D, Herrero, J, Beal, K, Lukk, M, Brazma, A, Vaquerizas, JM, Luscombe, NM, Bickel, PJ, Boley, N, Brown, JB, Li, Q, Huang, H, Gerstein, M, Habegger, L, Sboner, A, Rozowsky, J, Auerbach, RK, Yip, KY, Cheng, C, Yan, KK, Bhardwaj, N, Wang, J, Lochovsky, L, Jee, J, Gibson, T, Leng, J, Du, J, Hardison, RC, Harris, RS, Song, G, Miller, W, Haussler, D, Roskin, K, Suh, B, Wang, T, Paten, B, Noble, WS, Hoffman, MM, Buske, OJ, Weng, Z, Dong, X, Wang, J, Xi, H, Tenenbaum, SA, Doyle, F, Penalva, LO, Chittur, S, Tullius, TD, Parker, SCJ, White, KP, Karmakar, S, Victorsen, A, Jameel, N, Bild, N, Grossman, RL, Snyder, M, Landt, SG, Yang, X, Patacsil, D, Slifer, T, Dekker, J, Lajoie, BR, Sanyal, A, Weng, Z, Whitfield, TW, Wang, J, Collins, PJ, Trinklein, ND, Partridge, EC, Myers, RM, Giddings, MC, Chen, X, Khatun, J, Maier, C, Yu, Y, Gunawardena, H, Risk, B, Feingold, EA, Lowdon, RF, Dillon, LAL & Good, PJ 2011, 'A user's guide to the Encyclopedia of DNA elements (ENCODE)', PLoS Biology, vol. 9, no. 4, e1001046. https://doi.org/10.1371/journal.pbio.1001046
Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE et al. A user's guide to the Encyclopedia of DNA elements (ENCODE). PLoS Biology. 2011 Apr;9(4). e1001046. https://doi.org/10.1371/journal.pbio.1001046
Myers, Richard M. ; Stamatoyannopoulos, John ; Snyder, Michael ; Dunham, Ian ; Hardison, Ross C. ; Bernstein, Bradley E. ; Gingeras, Thomas R. ; Kent, W. James ; Birney, Ewan ; Wold, Barbara ; Crawford, Gregory E. ; Bernstein, Bradley E. ; Epstein, Charles B. ; Shoresh, Noam ; Ernst, Jason ; Mikkelsen, Tarjei S. ; Kheradpour, Pouya ; Zhang, Xiaolan ; Wang, Li ; Issner, Robbyn ; Coyne, Michael J. ; Durham, Timothy ; Ku, Manching ; Truong, Thanh ; Ward, Lucas D. ; Altshuler, Robert C. ; Lin, Michael F. ; Kellis, Manolis ; Gingeras, Thomas R. ; Davis, Carrie A. ; Kapranov, Philipp ; Dobin, Alexander ; Zaleski, Christopher ; Schlesinger, Felix ; Batut, Philippe ; Chakrabortty, Sudipto ; Jha, Sonali ; Lin, Wei ; Drenkow, Jorg ; Wang, Huaien ; Bell, Kim ; Gao, Hui ; Bell, Ian ; Dumais, Erica ; Dumais, Jacqueline ; Antonarakis, Stylianos E. ; Ucla, Catherine ; Borel, Christelle ; Guigo, Roderic ; Djebali, Sarah ; Lagarde, Julien ; Kingswood, Colin ; Ribeca, Paolo ; Sammeth, Micha ; Alioto, Tyler ; Merkel, Angelika ; Tilgner, Hagen ; Carninci, Piero ; Hayashizaki, Yoshihide ; Lassmann, Timo ; Takahashi, Hazuki ; Abdelhamid, Rehab F. ; Hannon, Gregory ; Fejes, Katalin Toth ; Preall, Jonathan ; Gordon, Assaf ; Sotirova, Vihra ; Reymond, Alexandre ; Howald, Cedric ; Graison, Emilie Aït Yahya ; Chrast, Jacqueline ; Ruan, Yijun ; Ruan, Xiaoan ; Shahab, Atif ; Poh, Wan Ting ; Wei, Chia Lin ; Crawford, Gregory E. ; Furey, Terrence S. ; Boyle, Alan P. ; Sheffield, Nathan C. ; Song, Lingyun ; Shibata, Yoichiro ; Vales, Teresa ; Winter, Deborah ; Zhang, Zhancheng ; London, Darin ; Wang, Tianyuan ; Birney, Ewan ; Keefe, Damian ; Iyer, Vishwanath R. ; Lee, Bum Kyu ; McDaniell, Ryan M. ; Liu, Zheng ; Battenhouse, Anna ; Bhinge, Akshay A. ; Lieb, Jason D. ; Grasfeder, Linda L. ; Showers, Kimberly A. ; Giresi, Paul G. ; Kim, Seul K C ; Shestak, Christopher ; Myers, Richard M. ; Pauli, Florencia ; Reddy, Timothy E. ; Gertz, Jason ; Partridge, E. Christopher ; Jain, Preti ; Sprouse, Rebekka O. ; Bansal, Anita ; Pusey, Barbara ; Muratet, Michael A. ; Varley, Katherine E. ; Bowling, Kevin M. ; Newberry, Kimberly M. ; Nesmith, Amy S. ; Dilocker, Jason A. ; Parker, Stephanie L. ; Waite, Lindsay L. ; Thibeault, Krista ; Roberts, Kevin ; Absher, Devin M. ; Wold, Barbara ; Mortazavi, Ali ; Williams, Brian ; Marinov, Georgi ; Trout, Diane ; Pepke, Shirley ; King, Brandon ; McCue, Kenneth ; Kirilusha, Anthony ; DeSalvo, Gilberto ; Fisher, Katherine Aylor ; Amrhein, Henry ; Vielmetter, Jost ; Sherlock, Gavin ; Sidow, Arend ; Batzoglou, Serafim ; Rauch, Rami ; Kundaje, Anshul ; Libbrecht, Max ; Margulies, Elliott H. ; Parker, Stephen C J ; Elnitski, Laura ; Green, Eric D. ; Hubbard, Tim ; Harrow, Jennifer ; Searle, Stephen ; Kokocinski, Felix ; Aken, Browen ; Frankish, Adam ; Hunt, Toby ; Despacio-Reyes, Gloria ; Kay, Mike ; Mukherjee, Gaurab ; Bignell, Alexandra ; Saunders, Gary ; Boychenko, Veronika ; Brent, Michael ; van Baren, M. J. ; Brown, Randall H. ; Gerstein, Mark ; Khurana, Ekta ; Balasubramanian, Suganthi ; Zhang, Zhengdong ; Lam, Hugo ; Cayting, Philip ; Robilotto, Rebecca ; Lu, Zhi ; Guigo, Roderic ; Derrien, Thomas ; Tanzer, Andrea ; Knowles, David G. ; Mariotti, Marco ; Kent, W. James ; Haussler, David ; Harte, Rachel ; Diekhans, Mark ; Kellis, Manolis ; Lin, Mike ; Kheradpour, Pouya ; Ernst, Jason ; Reymond, Alexandre ; Howald, Cedric ; Graison, Emilie Aït Yahya ; Chrast, Jacqueline ; Valencia, Alfonso ; Tress, Michael ; Rodriguez, Jose Manuel ; Snyder, Michael ; Landt, Stephen G. ; Raha, Debasish ; Shi, Minyi ; Euskirchen, Ghia ; Grubert, Fabian ; Kasowski, Maya ; Lian, Jin ; Cayting, Philip ; Lacroute, Phil ; Xu, Youhan ; Monahan, Hannah ; Patacsil, Dorrelyn ; Slifer, Teri ; Yang, Xinqiong ; Charos, Alexandra ; Reed, Brian ; Wu, Linfeng ; Auerbach, Raymond K. ; Habegger, Lukas ; Hariharan, Manoj ; Rozowsky, Joel ; Abyzov, Alexej ; Weissman, Sherman M. ; Gerstein, Mark ; Struhl, Kevin ; Lamarre, Nathan Vincent ; Lindahl, Marianne Allen ; Miotto, Benoit ; Moqtaderi, Zarmik ; Fleming, Joseph D. ; Newburger, Peter ; Farnham, Peggy J. ; Frietze, Seth ; O'Geen, Henriette ; Xu, Xiaoqin ; Blahnik, Kim R. ; Cao, Alina R. ; Iyengar, Sushma ; Stamatoyannopoulos, John A. ; Kaul, Rajinder ; Thurman, Robert E. ; Wang, Hao ; Navas, Patrick A. ; Sandstrom, Richard ; Sabo, Peter J. ; Weaver, Molly ; Canfield, Theresa ; Lee, Kristen ; Neph, Shane ; Roach, Vaughan ; Reynolds, Alex ; Johnson, Audra ; Rynes, Eric ; Giste, Erika ; Vong, Shinny ; Neri, Jun ; Frum, Tristan ; Johnson, Ericka M. ; Nguyen, Eric D. ; Ebersol, Abigail K. ; Sanchez, Minerva E. ; Sheffer, Hadar H. ; Lotakis, Dimitra ; Haugen, Eric ; Humbert, Richard ; Kutyavin, Tanya ; Shafer, Tony ; Dekker, Job ; Lajoie, Bryan R. ; Sanyal, Amartya ; Kent, W. James ; Rosenbloom, Kate R. ; Dreszer, Timothy R. ; Raney, Brian J. ; Barber, Galt P. ; Meyer, Laurence R. ; Sloan, Cricket A. ; Malladi, Venkat S. ; Cline, Melissa S. ; Learned, Katrina ; Swing, Vanessa K. ; Zweig, Ann S. ; Rhead, Brooke ; Fujita, Pauline A. ; Roskin, Krishna ; Karolchik, Donna ; Kuhn, Robert M. ; Haussler, David ; Birney, Ewan ; Dunham, Ian ; Wilder, Steven P. ; Keefe, Damian ; Sobral, Daniel ; Herrero, Javier ; Beal, Kathryn ; Lukk, Margus ; Brazma, Alvis ; Vaquerizas, Juan M. ; Luscombe, Nicholas M. ; Bickel, Peter J. ; Boley, Nathan ; Brown, James B. ; Li, Qunhua ; Huang, Haiyan ; Gerstein, Mark ; Habegger, Lukas ; Sboner, Andrea ; Rozowsky, Joel ; Auerbach, Raymond K. ; Yip, Kevin Y. ; Cheng, Chao ; Yan, Koon Kiu ; Bhardwaj, Nitin ; Wang, Jing ; Lochovsky, Lucas ; Jee, Justin ; Gibson, Theodore ; Leng, Jing ; Du, Jiang ; Hardison, Ross C. ; Harris, Robert S. ; Song, Giltae ; Miller, Webb ; Haussler, David ; Roskin, Krishna ; Suh, Bernard ; Wang, Ting ; Paten, Benedict ; Noble, William S. ; Hoffman, Michael M. ; Buske, Orion J. ; Weng, Zhiping ; Dong, Xianjun ; Wang, Jie ; Xi, Hualin ; Tenenbaum, Scott A. ; Doyle, Frank ; Penalva, Luiz O. ; Chittur, Sridar ; Tullius, Thomas D. ; Parker, Stephen C J ; White, Kevin P. ; Karmakar, Subhradip ; Victorsen, Alec ; Jameel, Nader ; Bild, Nick ; Grossman, Robert L. ; Snyder, Michael ; Landt, Stephen G. ; Yang, Xinqiong ; Patacsil, Dorrelyn ; Slifer, Teri ; Dekker, Job ; Lajoie, Bryan R. ; Sanyal, Amartya ; Weng, Zhiping ; Whitfield, Troy W. ; Wang, Jie ; Collins, Patrick J. ; Trinklein, Nathan D. ; Partridge, E. Christopher ; Myers, Richard M. ; Giddings, Morgan C. ; Chen, Xian ; Khatun, Jainab ; Maier, Chris ; Yu, Yanbao ; Gunawardena, Harsha ; Risk, Brian ; Feingold, Elise A. ; Lowdon, Rebecca F. ; Dillon, Laura A L ; Good, Peter J. / A user's guide to the Encyclopedia of DNA elements (ENCODE). In: PLoS Biology. 2011 ; Vol. 9, No. 4.
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title = "A user's guide to the Encyclopedia of DNA elements (ENCODE)",
abstract = "The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.",
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Christopher} and Preti Jain and Sprouse, {Rebekka O.} and Anita Bansal and Barbara Pusey and Muratet, {Michael A.} and Varley, {Katherine E.} and Bowling, {Kevin M.} and Newberry, {Kimberly M.} and Nesmith, {Amy S.} and Dilocker, {Jason A.} and Parker, {Stephanie L.} and Waite, {Lindsay L.} and Krista Thibeault and Kevin Roberts and Absher, {Devin M.} and Barbara Wold and Ali Mortazavi and Brian Williams and Georgi Marinov and Diane Trout and Shirley Pepke and Brandon King and Kenneth McCue and Anthony Kirilusha and Gilberto DeSalvo and Fisher, {Katherine Aylor} and Henry Amrhein and Jost Vielmetter and Gavin Sherlock and Arend Sidow and Serafim Batzoglou and Rami Rauch and Anshul Kundaje and Max Libbrecht and Margulies, {Elliott H.} and Parker, {Stephen C J} and Laura Elnitski and Green, {Eric D.} and Tim Hubbard and Jennifer Harrow and Stephen Searle and Felix Kokocinski and Browen Aken and Adam Frankish and Toby Hunt and Gloria Despacio-Reyes and Mike Kay and Gaurab Mukherjee and Alexandra Bignell and Gary Saunders and Veronika Boychenko and Michael Brent and {van Baren}, {M. J.} and Brown, {Randall H.} and Mark Gerstein and Ekta Khurana and Suganthi Balasubramanian and Zhengdong Zhang and Hugo Lam and Philip Cayting and Rebecca Robilotto and Zhi Lu and Roderic Guigo and Thomas Derrien and Andrea Tanzer and Knowles, {David G.} and Marco Mariotti and Kent, {W. James} and David Haussler and Rachel Harte and Mark Diekhans and Manolis Kellis and Mike Lin and Pouya Kheradpour and Jason Ernst and Alexandre Reymond and Cedric Howald and Graison, {Emilie A{\"i}t Yahya} and Jacqueline Chrast and Alfonso Valencia and Michael Tress and Rodriguez, {Jose Manuel} and Michael Snyder and Landt, {Stephen G.} and Debasish Raha and Minyi Shi and Ghia Euskirchen and Fabian Grubert and Maya Kasowski and Jin Lian and Philip Cayting and Phil Lacroute and Youhan Xu and Hannah Monahan and Dorrelyn Patacsil and Teri Slifer and Xinqiong Yang and Alexandra Charos and Brian Reed and Linfeng Wu and Auerbach, {Raymond K.} and Lukas Habegger and Manoj Hariharan and Joel Rozowsky and Alexej Abyzov and Weissman, {Sherman M.} and Mark Gerstein and Kevin Struhl and Lamarre, {Nathan Vincent} and Lindahl, {Marianne Allen} and Benoit Miotto and Zarmik Moqtaderi and Fleming, {Joseph D.} and Peter Newburger and Farnham, {Peggy J.} and Seth Frietze and Henriette O'Geen and Xiaoqin Xu and Blahnik, {Kim R.} and Cao, {Alina R.} and Sushma Iyengar and Stamatoyannopoulos, {John A.} and Rajinder Kaul and Thurman, {Robert E.} and Hao Wang and Navas, {Patrick A.} and Richard Sandstrom and Sabo, {Peter J.} and Molly Weaver and Theresa Canfield and Kristen Lee and Shane Neph and Vaughan Roach and Alex Reynolds and Audra Johnson and Eric Rynes and Erika Giste and Shinny Vong and Jun Neri and Tristan Frum and Johnson, {Ericka M.} and Nguyen, {Eric D.} and Ebersol, {Abigail K.} and Sanchez, {Minerva E.} and Sheffer, {Hadar H.} and Dimitra Lotakis and Eric Haugen and Richard Humbert and Tanya Kutyavin and Tony Shafer and Job Dekker and Lajoie, {Bryan R.} and Amartya Sanyal and Kent, {W. James} and Rosenbloom, {Kate R.} and Dreszer, {Timothy R.} and Raney, {Brian J.} and Barber, {Galt P.} and Meyer, {Laurence R.} and Sloan, {Cricket A.} and Malladi, {Venkat S.} and Cline, {Melissa S.} and Katrina Learned and Swing, {Vanessa K.} and Zweig, {Ann S.} and Brooke Rhead and Fujita, {Pauline A.} and Krishna Roskin and Donna Karolchik and Kuhn, {Robert M.} and David Haussler and Ewan Birney and Ian Dunham and Wilder, {Steven P.} and Damian Keefe and Daniel Sobral and Javier Herrero and Kathryn Beal and Margus Lukk and Alvis Brazma and Vaquerizas, {Juan M.} and Luscombe, {Nicholas M.} and Bickel, {Peter J.} and Nathan Boley and Brown, {James B.} and Qunhua Li and Haiyan Huang and Mark Gerstein and Lukas Habegger and Andrea Sboner and Joel Rozowsky and Auerbach, {Raymond K.} and Yip, {Kevin Y.} and Chao Cheng and Yan, {Koon Kiu} and Nitin Bhardwaj and Jing Wang and Lucas Lochovsky and Justin Jee and Theodore Gibson and Jing Leng and Jiang Du and Hardison, {Ross C.} and Harris, {Robert S.} and Giltae Song and Webb Miller and David Haussler and Krishna Roskin and Bernard Suh and Ting Wang and Benedict Paten and Noble, {William S.} and Hoffman, {Michael M.} and Buske, {Orion J.} and Zhiping Weng and Xianjun Dong and Jie Wang and Hualin Xi and Tenenbaum, {Scott A.} and Frank Doyle and Penalva, {Luiz O.} and Sridar Chittur and Tullius, {Thomas D.} and Parker, {Stephen C J} and White, {Kevin P.} and Subhradip Karmakar and Alec Victorsen and Nader Jameel and Nick Bild and Grossman, {Robert L.} and Michael Snyder and Landt, {Stephen G.} and Xinqiong Yang and Dorrelyn Patacsil and Teri Slifer and Job Dekker and Lajoie, {Bryan R.} and Amartya Sanyal and Zhiping Weng and Whitfield, {Troy W.} and Jie Wang and Collins, {Patrick J.} and Trinklein, {Nathan D.} and Partridge, {E. Christopher} and Myers, {Richard M.} and Giddings, {Morgan C.} and Xian Chen and Jainab Khatun and Chris Maier and Yanbao Yu and Harsha Gunawardena and Brian Risk and Feingold, {Elise A.} and Lowdon, {Rebecca F.} and Dillon, {Laura A L} and Good, {Peter J.}",
year = "2011",
month = "4",
doi = "10.1371/journal.pbio.1001046",
language = "English (US)",
volume = "9",
journal = "PLoS Biology",
issn = "1544-9173",
publisher = "Public Library of Science",
number = "4",

}

TY - JOUR

T1 - A user's guide to the Encyclopedia of DNA elements (ENCODE)

AU - Myers, Richard M.

AU - Stamatoyannopoulos, John

AU - Snyder, Michael

AU - Dunham, Ian

AU - Hardison, Ross C.

AU - Bernstein, Bradley E.

AU - Gingeras, Thomas R.

AU - Kent, W. James

AU - Birney, Ewan

AU - Wold, Barbara

AU - Crawford, Gregory E.

AU - Bernstein, Bradley E.

AU - Epstein, Charles B.

AU - Shoresh, Noam

AU - Ernst, Jason

AU - Mikkelsen, Tarjei S.

AU - Kheradpour, Pouya

AU - Zhang, Xiaolan

AU - Wang, Li

AU - Issner, Robbyn

AU - Coyne, Michael J.

AU - Durham, Timothy

AU - Ku, Manching

AU - Truong, Thanh

AU - Ward, Lucas D.

AU - Altshuler, Robert C.

AU - Lin, Michael F.

AU - Kellis, Manolis

AU - Gingeras, Thomas R.

AU - Davis, Carrie A.

AU - Kapranov, Philipp

AU - Dobin, Alexander

AU - Zaleski, Christopher

AU - Schlesinger, Felix

AU - Batut, Philippe

AU - Chakrabortty, Sudipto

AU - Jha, Sonali

AU - Lin, Wei

AU - Drenkow, Jorg

AU - Wang, Huaien

AU - Bell, Kim

AU - Gao, Hui

AU - Bell, Ian

AU - Dumais, Erica

AU - Dumais, Jacqueline

AU - Antonarakis, Stylianos E.

AU - Ucla, Catherine

AU - Borel, Christelle

AU - Guigo, Roderic

AU - Djebali, Sarah

AU - Lagarde, Julien

AU - Kingswood, Colin

AU - Ribeca, Paolo

AU - Sammeth, Micha

AU - Alioto, Tyler

AU - Merkel, Angelika

AU - Tilgner, Hagen

AU - Carninci, Piero

AU - Hayashizaki, Yoshihide

AU - Lassmann, Timo

AU - Takahashi, Hazuki

AU - Abdelhamid, Rehab F.

AU - Hannon, Gregory

AU - Fejes, Katalin Toth

AU - Preall, Jonathan

AU - Gordon, Assaf

AU - Sotirova, Vihra

AU - Reymond, Alexandre

AU - Howald, Cedric

AU - Graison, Emilie Aït Yahya

AU - Chrast, Jacqueline

AU - Ruan, Yijun

AU - Ruan, Xiaoan

AU - Shahab, Atif

AU - Poh, Wan Ting

AU - Wei, Chia Lin

AU - Crawford, Gregory E.

AU - Furey, Terrence S.

AU - Boyle, Alan P.

AU - Sheffield, Nathan C.

AU - Song, Lingyun

AU - Shibata, Yoichiro

AU - Vales, Teresa

AU - Winter, Deborah

AU - Zhang, Zhancheng

AU - London, Darin

AU - Wang, Tianyuan

AU - Birney, Ewan

AU - Keefe, Damian

AU - Iyer, Vishwanath R.

AU - Lee, Bum Kyu

AU - McDaniell, Ryan M.

AU - Liu, Zheng

AU - Battenhouse, Anna

AU - Bhinge, Akshay A.

AU - Lieb, Jason D.

AU - Grasfeder, Linda L.

AU - Showers, Kimberly A.

AU - Giresi, Paul G.

AU - Kim, Seul K C

AU - Shestak, Christopher

AU - Myers, Richard M.

AU - Pauli, Florencia

AU - Reddy, Timothy E.

AU - Gertz, Jason

AU - Partridge, E. Christopher

AU - Jain, Preti

AU - Sprouse, Rebekka O.

AU - Bansal, Anita

AU - Pusey, Barbara

AU - Muratet, Michael A.

AU - Varley, Katherine E.

AU - Bowling, Kevin M.

AU - Newberry, Kimberly M.

AU - Nesmith, Amy S.

AU - Dilocker, Jason A.

AU - Parker, Stephanie L.

AU - Waite, Lindsay L.

AU - Thibeault, Krista

AU - Roberts, Kevin

AU - Absher, Devin M.

AU - Wold, Barbara

AU - Mortazavi, Ali

AU - Williams, Brian

AU - Marinov, Georgi

AU - Trout, Diane

AU - Pepke, Shirley

AU - King, Brandon

AU - McCue, Kenneth

AU - Kirilusha, Anthony

AU - DeSalvo, Gilberto

AU - Fisher, Katherine Aylor

AU - Amrhein, Henry

AU - Vielmetter, Jost

AU - Sherlock, Gavin

AU - Sidow, Arend

AU - Batzoglou, Serafim

AU - Rauch, Rami

AU - Kundaje, Anshul

AU - Libbrecht, Max

AU - Margulies, Elliott H.

AU - Parker, Stephen C J

AU - Elnitski, Laura

AU - Green, Eric D.

AU - Hubbard, Tim

AU - Harrow, Jennifer

AU - Searle, Stephen

AU - Kokocinski, Felix

AU - Aken, Browen

AU - Frankish, Adam

AU - Hunt, Toby

AU - Despacio-Reyes, Gloria

AU - Kay, Mike

AU - Mukherjee, Gaurab

AU - Bignell, Alexandra

AU - Saunders, Gary

AU - Boychenko, Veronika

AU - Brent, Michael

AU - van Baren, M. J.

AU - Brown, Randall H.

AU - Gerstein, Mark

AU - Khurana, Ekta

AU - Balasubramanian, Suganthi

AU - Zhang, Zhengdong

AU - Lam, Hugo

AU - Cayting, Philip

AU - Robilotto, Rebecca

AU - Lu, Zhi

AU - Guigo, Roderic

AU - Derrien, Thomas

AU - Tanzer, Andrea

AU - Knowles, David G.

AU - Mariotti, Marco

AU - Kent, W. James

AU - Haussler, David

AU - Harte, Rachel

AU - Diekhans, Mark

AU - Kellis, Manolis

AU - Lin, Mike

AU - Kheradpour, Pouya

AU - Ernst, Jason

AU - Reymond, Alexandre

AU - Howald, Cedric

AU - Graison, Emilie Aït Yahya

AU - Chrast, Jacqueline

AU - Valencia, Alfonso

AU - Tress, Michael

AU - Rodriguez, Jose Manuel

AU - Snyder, Michael

AU - Landt, Stephen G.

AU - Raha, Debasish

AU - Shi, Minyi

AU - Euskirchen, Ghia

AU - Grubert, Fabian

AU - Kasowski, Maya

AU - Lian, Jin

AU - Cayting, Philip

AU - Lacroute, Phil

AU - Xu, Youhan

AU - Monahan, Hannah

AU - Patacsil, Dorrelyn

AU - Slifer, Teri

AU - Yang, Xinqiong

AU - Charos, Alexandra

AU - Reed, Brian

AU - Wu, Linfeng

AU - Auerbach, Raymond K.

AU - Habegger, Lukas

AU - Hariharan, Manoj

AU - Rozowsky, Joel

AU - Abyzov, Alexej

AU - Weissman, Sherman M.

AU - Gerstein, Mark

AU - Struhl, Kevin

AU - Lamarre, Nathan Vincent

AU - Lindahl, Marianne Allen

AU - Miotto, Benoit

AU - Moqtaderi, Zarmik

AU - Fleming, Joseph D.

AU - Newburger, Peter

AU - Farnham, Peggy J.

AU - Frietze, Seth

AU - O'Geen, Henriette

AU - Xu, Xiaoqin

AU - Blahnik, Kim R.

AU - Cao, Alina R.

AU - Iyengar, Sushma

AU - Stamatoyannopoulos, John A.

AU - Kaul, Rajinder

AU - Thurman, Robert E.

AU - Wang, Hao

AU - Navas, Patrick A.

AU - Sandstrom, Richard

AU - Sabo, Peter J.

AU - Weaver, Molly

AU - Canfield, Theresa

AU - Lee, Kristen

AU - Neph, Shane

AU - Roach, Vaughan

AU - Reynolds, Alex

AU - Johnson, Audra

AU - Rynes, Eric

AU - Giste, Erika

AU - Vong, Shinny

AU - Neri, Jun

AU - Frum, Tristan

AU - Johnson, Ericka M.

AU - Nguyen, Eric D.

AU - Ebersol, Abigail K.

AU - Sanchez, Minerva E.

AU - Sheffer, Hadar H.

AU - Lotakis, Dimitra

AU - Haugen, Eric

AU - Humbert, Richard

AU - Kutyavin, Tanya

AU - Shafer, Tony

AU - Dekker, Job

AU - Lajoie, Bryan R.

AU - Sanyal, Amartya

AU - Kent, W. James

AU - Rosenbloom, Kate R.

AU - Dreszer, Timothy R.

AU - Raney, Brian J.

AU - Barber, Galt P.

AU - Meyer, Laurence R.

AU - Sloan, Cricket A.

AU - Malladi, Venkat S.

AU - Cline, Melissa S.

AU - Learned, Katrina

AU - Swing, Vanessa K.

AU - Zweig, Ann S.

AU - Rhead, Brooke

AU - Fujita, Pauline A.

AU - Roskin, Krishna

AU - Karolchik, Donna

AU - Kuhn, Robert M.

AU - Haussler, David

AU - Birney, Ewan

AU - Dunham, Ian

AU - Wilder, Steven P.

AU - Keefe, Damian

AU - Sobral, Daniel

AU - Herrero, Javier

AU - Beal, Kathryn

AU - Lukk, Margus

AU - Brazma, Alvis

AU - Vaquerizas, Juan M.

AU - Luscombe, Nicholas M.

AU - Bickel, Peter J.

AU - Boley, Nathan

AU - Brown, James B.

AU - Li, Qunhua

AU - Huang, Haiyan

AU - Gerstein, Mark

AU - Habegger, Lukas

AU - Sboner, Andrea

AU - Rozowsky, Joel

AU - Auerbach, Raymond K.

AU - Yip, Kevin Y.

AU - Cheng, Chao

AU - Yan, Koon Kiu

AU - Bhardwaj, Nitin

AU - Wang, Jing

AU - Lochovsky, Lucas

AU - Jee, Justin

AU - Gibson, Theodore

AU - Leng, Jing

AU - Du, Jiang

AU - Hardison, Ross C.

AU - Harris, Robert S.

AU - Song, Giltae

AU - Miller, Webb

AU - Haussler, David

AU - Roskin, Krishna

AU - Suh, Bernard

AU - Wang, Ting

AU - Paten, Benedict

AU - Noble, William S.

AU - Hoffman, Michael M.

AU - Buske, Orion J.

AU - Weng, Zhiping

AU - Dong, Xianjun

AU - Wang, Jie

AU - Xi, Hualin

AU - Tenenbaum, Scott A.

AU - Doyle, Frank

AU - Penalva, Luiz O.

AU - Chittur, Sridar

AU - Tullius, Thomas D.

AU - Parker, Stephen C J

AU - White, Kevin P.

AU - Karmakar, Subhradip

AU - Victorsen, Alec

AU - Jameel, Nader

AU - Bild, Nick

AU - Grossman, Robert L.

AU - Snyder, Michael

AU - Landt, Stephen G.

AU - Yang, Xinqiong

AU - Patacsil, Dorrelyn

AU - Slifer, Teri

AU - Dekker, Job

AU - Lajoie, Bryan R.

AU - Sanyal, Amartya

AU - Weng, Zhiping

AU - Whitfield, Troy W.

AU - Wang, Jie

AU - Collins, Patrick J.

AU - Trinklein, Nathan D.

AU - Partridge, E. Christopher

AU - Myers, Richard M.

AU - Giddings, Morgan C.

AU - Chen, Xian

AU - Khatun, Jainab

AU - Maier, Chris

AU - Yu, Yanbao

AU - Gunawardena, Harsha

AU - Risk, Brian

AU - Feingold, Elise A.

AU - Lowdon, Rebecca F.

AU - Dillon, Laura A L

AU - Good, Peter J.

PY - 2011/4

Y1 - 2011/4

N2 - The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

AB - The mission of the Encyclopedia of DNA Elements (ENCODE) Project is to enable the scientific and medical communities to interpret the human genome sequence and apply it to understand human biology and improve health. The ENCODE Consortium is integrating multiple technologies and approaches in a collective effort to discover and define the functional elements encoded in the human genome, including genes, transcripts, and transcriptional regulatory regions, together with their attendant chromatin states and DNA methylation patterns. In the process, standards to ensure high-quality data have been implemented, and novel algorithms have been developed to facilitate analysis. Data and derived results are made available through a freely accessible database. Here we provide an overview of the project and the resources it is generating and illustrate the application of ENCODE data to interpret the human genome.

UR - http://www.scopus.com/inward/record.url?scp=79955550445&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=79955550445&partnerID=8YFLogxK

U2 - 10.1371/journal.pbio.1001046

DO - 10.1371/journal.pbio.1001046

M3 - Article

AN - SCOPUS:79955550445

VL - 9

JO - PLoS Biology

JF - PLoS Biology

SN - 1544-9173

IS - 4

M1 - e1001046

ER -