A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

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.

Raymond K. Auerbach | William Stafford Noble | Stephen C. J. Parker | Nathan C. Sheffield | Shane J. Neph | Juan M. Vaquerizas | Orion J. Buske | Kevin Y. Yip | David G. Knowles | Hugo Y. K. Lam | Christopher W. Maier | Morgan C. Giddings | Michael F. Lin | Maxwell W. Libbrecht | Alex P. Reynolds | Timothy E. Reddy | Barbara N. Pusey | Bernard B. Suh | Timothy J. Durham | Robert S. Harris | Robert C. Altshuler | D. Haussler | P. Bickel | T. Mikkelsen | D. Absher | E. Birney | S. Batzoglou | M. Gerstein | Z. Weng | G. Sherlock | A. Sidow | Hagen U. Tilgner | Fabian Grubert | J. Harrow | A. Frankish | M. Diekhans | F. Kokocinski | S. Searle | A. Bignell | V. Boychenko | T. Hunt | M. Kay | Gaurab Mukherjee | Gloria Despacio-Reyes | R. Harte | C. Howald | Andrea Tanzer | T. Derrien | J. Chrast | S. Balasubramanian | M. Tress | M. Brent | Manolis Kellis | A. Valencia | A. Reymond | R. Guigó | T. Hubbard | R. Sandstrom | J. Stamatoyannopoulos | W. J. Kent | T. Furey | K. Roskin | B. Williams | A. Mortazavi | B. Wold | Brian D. Reed | E. H. Margulies | W. Miller | V. Iyer | A. Kundaje | R. Myers | Paolo Ribeca | K. White | R. Grossman | K. Struhl | Z. Lu | P. Good | A. Brazma | N. Luscombe | A. Abyzov | Philip Cayting | M. Snyder | R. Kaul | E. Haugen | M. Weaver | Ekta Khurana | Jing Leng | L. Elnitski | K. Rosenbloom | E. Green | S. Weissman | P. Collins | I. Dunham | M. Sammeth | D. Winter | T. Gingeras | R. Thurman | P. Giresi | R. Humbert | Tristan Frum | P. Navas | P. Sabo | J. Dekker | J. Lieb | T. Tullius | G. Crawford | P. Kapranov | J. Rozowsky | Damian Keefe | Julien Lagarde | Atif Shahab | J. Drenkow | I. Bell | T. Alioto | C. Ucla | Jin Lian | P. Newburger | Piero Carninci | Y. Hayashizaki | Chia-Lin Wei | Y. Ruan | S. Antonarakis | E. Feingold | Haiyan Huang | B. Paten | R. Hardison | N. Trinklein | A. Bhinge | Z. Moqtaderi | Xiaoqin Xu | G. Euskirchen | P. Farnham | A. Zweig | G. Barber | R. Kuhn | D. Karolchik | S. Pepke | B. Bernstein | Theodore Gibson | A. Boyle | M. Cline | Kenneth McCue | A. Sboner | Tianyuan Wang | J. Ernst | B. Raney | O. Buske | J. Vaquerizas | G. Hannon | S. Djebali | A. Merkel | Xiaoan Ruan | T. Lassmann | N. Bhardwaj | Qunhua Li | Frank Doyle | Randall H. Brown | M. Mariotti | A. Dobin | Wei Lin | F. Schlesinger | G. Marinov | Jainab Khatun | C. Zaleski | Rehab F. Abdelhamid | P. Batut | K. Bell | S. Chakrabortty | Xian Chen | E. Dumais | Jacqueline Dumais | Hui Gao | Assaf Gordon | H. Gunawardena | Sonali Jha | Brandon King | C. Kingswood | Jonathan Preall | Brian A. Risk | Hazuki Takahashi | Diane Trout | Huaien Wang | Yanbao Yu | D. London | D. Raha | L. D. Ward | P. Kheradpour | Eric Rynes | Hao Wang | Kristen Lee | T. Kutyavin | Audra K. Johnson | T. Canfield | Erika Giste | Preti Jain | Kathryn Beal | Javier Herrero | A. Bansal | M. M. Hoffman | Koon-Kiu Yan | S. Landt | N. Shoresh | M. Hariharan | Chao Cheng | Alexandra E. Charos | S. Frietze | Jason Gertz | Maya Kasowski | P. Lacroute | Hannah Monahan | E. Partridge | Dorrelyn Patacsil | F. Pauli | Minyi Shi | T. Slifer | Jing Wang | Linfeng Wu | Xinqiong Yang | B. Lajoie | C. Epstein | Xiaolan Zhang | R. Issner | Michael J. Coyne | Manching Ku | Gilberto Desalvo | S. Karmakar | J. Vielmetter | V. Sotirova | L. Habegger | H. O'Geen | S. Wilder | D. Sobral | Lingyun Song | Li Wang | Ryan McDaniell | Jie Wang | Abigail K. Ebersol | Bum-Kyu Lee | D. Lotakis | Eric D Nguyen | Minerva E. Sanchez | A. Sanyal | Shinny Vong | Zhancheng Zhang | C. Davis | Xianjun Dong | T. Whitfield | H. Xi | R. Lowdon | Laura A. L. Dillon | S. Tenenbaum | Thanh Truong | C. A. Sloan | K. Learned | V. Malladi | T. Dreszer | L. Meyer | L. Grasfeder | Anna M. Battenhouse | Kimberly A. Showers | Christopher Shestak | Seul K.C. Kim | Zheng Liu | K. Varley | Henry Amrhein | K. Bowling | M. Muratet | K. Newberry | Amy S. Nesmith | S. Parker | Gary Saunders | M. V. Baren | Alina R. Cao | J. D. Fleming | S. Iyengar | Nathan Lamarre-Vincent | Marianne Lindahl-Allen | B. Miotto | L. O. Penalva | Alec Victorsen | M. Lukk | Nathan Boley | L. Lochovsky | L. Waite | R. Robilotto | Jiang Du | B. Rhead | Yoichiro Shibata | C. Borel | Katalin Toth Fejes | E. Graison | W. Poh | T. Vales | Rebekka O. Sprouse | Jason A. Dilocker | Krista S. Thibeault | K. Roberts | Anthony Kirilusha | Katherine Fisher | Rami Rauch | B. Aken | Youhan Xu | Kimberly R. Blahnik | Vaughan Roach | Jun Neri | Hadar H. Sheffer | Tony Shafer | Vanessa Swing | P. Fujita | James B. Brown | J. Jee | Giltae Song | S. Chittur | Nader Jameel | N. Bild | Ting Wang | Jonathan B. Preall | Kimberly M. Newberry | Kimberly M Newberry | J. Dumais | L. Penalva | Florencia Pauli | Sushma Iyengar | Tian-yuan Wang | B. Risk | M. Baren | H. O’Geen | A. Shahab | K. Fejes | Kevin Roberts | E. Margulies | Kathryn M Beal | C. Sloan | K. McCue | Amartya Sanyal | Katalin Fejes | F. Doyle | W. Kent | Jacqueline Chrast | Colin Kingswood | A. Tanzer | Carrie A. Davis | B. Rhead | Veronika Boychenko | Emilie Aït Yahya Graison | Robbyn Issner | Kevin Y. Yip

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