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

Authors :
Zhi Lu
Giltae Song
Troy W. Whitfield
Vishwanath R. Iyer
Teresa Vales
Angelika Merkel
Max Libbrecht
David Haussler
Ting Wang
Kristen Lee
Lingyun Song
Richard M. Myers
Alfonso Valencia
Rachel A. Harte
Xiaoqin Xu
Lucas D. Ward
Hazuki Takahashi
Nathan C. Sheffield
Thomas Derrien
Georgi K. Marinov
Eric D. Nguyen
Bernard B. Suh
Brian J. Raney
Richard Sandstrom
Thomas D. Tullius
Benoit Miotto
Alexander Dobin
Youhan Xu
Lukas Habegger
Ian Dunham
Brian A. Risk
Paul G. Giresi
Morgan C. Giddings
Hualin Xi
Anshul Kundaje
Robert S. Harris
Devin Absher
Peter J. Bickel
Yanbao Yu
Browen Aken
Colin Kingswood
Bryan R. Lajoie
Peter J. Good
Katrina Learned
Laura Elnitski
Shirley Pepke
Brandon King
Piero Carninci
Xinqiong Yang
Ghia Euskirchen
Kathryn Beal
Christelle Borel
Michael Muratet
Robert L. Grossman
David G. Knowles
Zarmik Moqtaderi
Veronika Boychenko
Steven P. Wilder
Michael L. Tress
Florencia Pauli
Alan P. Boyle
Andrea Tanzer
Philipp Kapranov
Serafim Batzoglou
Audra K. Johnson
Jun Neri
Nitin Bhardwaj
Elise A. Feingold
Venkat S. Malladi
Michael M. Hoffman
William Stafford Noble
Andrea Sboner
Mark Gerstein
Stephanie L. Parker
Jacqueline Dumais
Felix Schlesinger
Deborah R. Winter
Randall H. Brown
Thanh Truong
Rebecca F. Lowdon
Paolo Ribeca
Brooke Rhead
Peggy J. Farnham
Krista Thibeault
Terrence S. Furey
Donna Karolchik
Alec Victorsen
Xiaoan Ruan
Rehab F. Abdelhamid
Amy S. Nesmith
Jing Wang
Nicholas M. Luscombe
Alina R. Cao
Diane Trout
Teri Slifer
Peter E. Newburger
Cricket A. Sloan
Dimitra Lotakis
Stephen M. J. Searle
Ali Mortazavi
Alexandra Bignell
Alex Reynolds
Orion J. Buske
Chris Zaleski
Theresa K. Canfield
Ian Bell
Jin Lian
Vanessa K. Swing
Katalin Toth Fejes
Catherine Ucla
Robert E. Thurman
Jacqueline Chrast
Wei Lin
Tim Hubbard
Gary Saunders
Minyi Shi
Vihra Sotirova
Sherman M. Weissman
Jason D. Lieb
Richard Humbert
Kevin M. Bowling
Assaf Gordon
Tarjei S. Mikkelsen
Jing Leng
Thomas R. Gingeras
Fabian Grubert
Nader Jameel
Jost Vielmetter
Hannah Monahan
Preti Jain
Lindsay L. Waite
Tony Shafer
Joel Rozowsky
Michael Coyne
Brian Reed
M. Kay
Harsha P. Gunawardena
Ross C. Hardison
Gavin Sherlock
Alexandra Charos
Joseph D. Fleming
Ann S. Zweig
Jason Gertz
Rajinder Kaul
Xianjun Dong
Alexandre Reymond
Carrie A. Davis
Haiyan Huang
Chao Cheng
Marco Mariotti
Phil Lacroute
Jason A. Dilocker
Kenneth McCue
R. Robilotto
Stylianos E. Antonarakis
Sridar V. Chittur
Justin Jee
Barbara J. Wold
Sudipto K. Chakrabortty
Erica Dumais
Amartya Sanyal
Nathan Boley
Tianyuan Wang
Julien Lagarde
Anthony Kirilusha
Jonathan B. Preall
Kevin Roberts
Erika Giste
Hugo Y. K. Lam
Alvis Brazma
Gregory J. Hannon
Eric Rynes
Philippe Batut
Kevin Struhl
Margus Lukk
Manching Ku
Suganthi Balasubramanian
Sonali Jha
Jorg Drenkow
W. James Kent
Michael Snyder
Jie Wang
Anna Battenhouse
Charles B. Epstein
Rami Rauch
Christopher Shestak
John A. Stamatoyannopoulos
Gaurab Mukherjee
Cédric Howald
Tanya Kutyavin
Huaien Wang
Scott A. Tenenbaum
Wan Ting Poh
Kate R. Rosenbloom
Manolis Kellis
Pauline A. Fujita
Linfeng Wu
Anita Bansal
Molly Weaver
Linda L. Grasfeder
Peter J. Sabo
Qiang Li
Melissa S. Cline
Robert M. Kuhn
Darin London
Seth Frietze
Atif Shahab
Shane Neph
Damian Keefe
James B. Brown
Mark Diekhans
Webb Miller
Katherine Aylor Fisher
Jiang Du
Hadar H. Sheffer
Sarah Djebali
Frank Doyle
Nathan Lamarre-Vincent
Chia-Lin Wei
Laura A.L. Dillon
Jennifer Harrow
Robert C. Altshuler
Tyler Alioto
Raymond K. Auerbach
Adam Frankish
Rebekka O. Sprouse
Patrick J. Collins
E. Christopher Partridge
Zheng Liu
Yoichiro Shibata
Elliott H. Margulies
Abigail K. Ebersol
Kimberly A. Showers
Eric D. Green
Krishna M. Roskin
Job Dekker
Barbara N. Pusey
Ekta Khurana
Gilberto DeSalvo
Yijun Ruan
Hao Wang
Jainab Khatun
Henriette O'Geen
Alexej Abyzov
Brian Williams
Ryan M. McDaniell
Maya Kasowski
Manoj Hariharan
Felix Kokocinski
Gloria Despacio-Reyes
Zhancheng Zhang
Subhradip Karmakar
Ewan Birney
Koon-Kiu Yan
Xian Chen
Shinny Vong
Daniel Sobral
Nick Bild
Seul K.C. Kim
Timo Lassmann
Li Wang
Minerva E. Sanchez
Vaughan Roach
Theodore Gibson
Stephen C. J. Parker
Michael F. Lin
Patrick A. Navas
Laurence R. Meyer
Luiz O. F. Penalva
Bradley E. Bernstein
Kevin P. White
Emilie Aït Yahya Graison
Juan M. Vaquerizas
Sushma Iyengar
Kimberly M. Newberry
Akshay Bhinge
Xiaolan Zhang
Kim Bell
Yoshihide Hayashizaki
Lucas Lochovsky
Noam Shoresh
Hagen Tilgner
Philip Cayting
Dorrelyn Patacsil
Timothy E. Reddy
Eric Haugen
Katherine E. Varley
M. van Baren
Nathan D. Trinklein
Bum Kyu Lee
Tristan Frum
Marianne Lindahl-Allen
Timothy Durham
Roderic Guigó
Christopher W. Maier
Micha Sammeth
Debasish Raha
Timothy R. Dreszer
Benedict Paten
Robbyn Issner
Michael R. Brent
Kevin Y. Yip
Kim Blahnik
Jason Ernst
Zhiping Weng
Henry Amrhein
Arend Sidow
Javier Herrero
Hui Gao
Stephen G. Landt
Pouya Kheradpour
Galt P. Barber
Gregory E. Crawford
Toby Hunt
HudsonAlpha Institute for Biotechnology [Huntsville, AL]
ENCODE Project Consortium : 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-Toth K, Preall J, Gordon A, Sotirova V, Reymond A, Howald C, Graison E, Chrast J, Ruan Y, Ruan X, Shahab A, Ting Poh W, 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 SK, 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-Aylor K, Amrhein H, Vielmetter J, Sherlock G, Sidow A, Batzoglou S, Rauch R, Kundaje A, Libbrecht M, Margulies EH, Parker SC, 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, Van Baren M, Brown RH, Khurana E, Balasubramanian S, Zhang Z, Lam H, Cayting P, Robilotto R, Lu Z, Guigo R, Derrien T, Tanzer A, Knowles DG, Mariotti M, James Kent W, Haussler D, Harte R, Diekhans M, Kellis M, Lin M, Kheradpour P, Ernst J, Reymond A, Howald C, Graison EA, Chrast J, 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-Vincent N, Lindahl-Allen M, 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, James Kent W, 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 SC, 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 LA, Good PJ, Harrow J, Searle S.
Becker, Peter B
Broad Institute of MIT and Harvard
Lincoln Laboratory
Massachusetts Institute of Technology. Computer Science and Artificial Intelligence Laboratory
Massachusetts Institute of Technology. Department of Electrical Engineering and Computer Science
Massachusetts Institute of Technology. Department of Physics
Kellis, Manolis
Epstein, Charles B.
Bernstein, Bradley E.
Shoresh, Noam
Ernst, Jason
Mikkelsen, Tarjei Sigurd
Kheradpour, Pouya
Zhang, Xiaolan
Wang, Li
Issner, Robbyn
Coyne, Michael J.
Durham, Timothy
Ku, Manching
Truong, Thanh
Ward, Lucas D.
Altshuler, Robert Charles
Lin, Michael F.
ENCODE Project Consortium
Antonarakis, Stylianos
Miotto, Benoit
Source :
PLoS Biology, PLoS Biology, Public Library of Science, 2011, 9 (4), pp.e1001046. ⟨10.1371/journal.pbio.1001046⟩, PLoS biology, vol 9, iss 4, Recercat. Dipósit de la Recerca de Catalunya, instname, PLoS Biology, Vol 9, Iss 4, p e1001046 (2011), PLoS biology, PLoS, PLOS Biology, Vol. 9, No 4 (2011) P. e1001046
Publication Year :
2011
Publisher :
Public Library of Science, 2011.

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.<br />National Human Genome Research Institute (U.S.)<br />National Institutes of Health (U.S.)

Details

Language :
English
ISSN :
15457885 and 15449173
Volume :
9
Issue :
4
Database :
OpenAIRE
Journal :
PLoS Biology
Accession number :
edsair.doi.dedup.....d94123649e2cabce4d97ed30da33b8a8
Full Text :
https://doi.org/10.1371/journal.pbio.1001046⟩