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Yutao Fu
Researcher at Thermo Fisher Scientific
Publications - 31
Citations - 21099
Yutao Fu is an academic researcher from Thermo Fisher Scientific. The author has contributed to research in topics: Human genome & Genome. The author has an hindex of 25, co-authored 31 publications receiving 19511 citations. Previous affiliations of Yutao Fu include Boston University & Life Technologies.
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Journal ArticleDOI
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Ewan Birney,John A. Stamatoyannopoulos,Anindya Dutta,Roderic Guigó,Thomas R. Gingeras,Elliott H. Margulies,Zhiping Weng,Michael Snyder,Emmanouil T. Dermitzakis,Robert E. Thurman,Michael S. Kuehn,Christopher M. Taylor,Shane Neph,Christoph M. Koch,Saurabh Asthana,Ankit Malhotra,Ivan Adzhubei,Jason A. Greenbaum,Robert M. Andrews,Paul Flicek,Patrick J. Boyle,Hua Cao,Nigel P. Carter,Gayle K. Clelland,Sean Davis,Nathan Day,Pawandeep Dhami,Shane C. Dillon,Michael O. Dorschner,Heike Fiegler,Paul G. Giresi,Jeff Goldy,Michael Hawrylycz,Andrew Haydock,Richard Humbert,Keith D. James,Brett E. Johnson,Ericka M. Johnson,Tristan Frum,Elizabeth Rosenzweig,Neerja Karnani,Kirsten Lee,Gregory Lefebvre,Patrick A. Navas,Fidencio Neri,Stephen C. J. Parker,Peter J. Sabo,Richard Sandstrom,Anthony Shafer,David Vetrie,Molly Weaver,Sarah Wilcox,Man Yu,Francis S. Collins,Job Dekker,Jason D. Lieb,Thomas D. Tullius,Gregory E. Crawford,Shamil R. Sunyaev,William Stafford Noble,Ian Dunham,Alexandre Reymond,Alexandre Reymond,Philipp Kapranov,Joel Rozowsky,Deyou Zheng,Robert Castelo,Adam Frankish,Jennifer Harrow,Srinka Ghosh,Albin Sandelin,Ivo L. Hofacker,Robert Baertsch,Damian Keefe,Sujit Dike,Jill Cheng,Heather A. Hirsch,Edward A. Sekinger,Julien Lagarde,Josep F. Abril,Josep F. Abril,Atif Shahab,Christoph Flamm,Christoph Flamm,Claudia Fried,Jörg Hackermüller,Jana Hertel,Manja Lindemeyer,Kristin Missal,Andrea Tanzer,Andrea Tanzer,Stefan Washietl,Jan O. Korbel,Olof Emanuelsson,Jakob Skou Pedersen,Nancy Holroyd,Ruth Taylor,David Swarbreck,Nicholas Matthews,Mark Dickson,Daryl J. Thomas,Matthew T. Weirauch,James G. R. Gilbert,Jorg Drenkow,Ian Bell,Xiaodong Zhao,Kandhadayar G. Srinivasan,Wing-Kin Sung,Hong Sain Ooi,Kuo Ping Chiu,Sylvain Foissac,Tyler Alioto,Michael R. Brent,Lior Pachter,Michael L. Tress,Alfonso Valencia,Siew Woh Choo,Chiou Yu Choo,Catherine Ucla,Caroline Manzano,Carine Wyss,Evelyn Cheung,Taane G. Clark,James B. Brown,Madhavan Ganesh,Sandeep Patel,Hari Tammana,Jacqueline Chrast,Charlotte N. Henrichsen,Chikatoshi Kai,Jun Kawai,Ugrappa Nagalakshmi,Jia Qian Wu,Zheng Lian,Jin Lian,Peter E. Newburger,Xueqing Zhang,Peter J. Bickel,John S. Mattick,Piero Carninci,Yoshihide Hayashizaki,Sherman M. Weissman,Tim Hubbard,Richard M. Myers,Jane Rogers,Peter F. Stadler,Peter F. Stadler,Peter F. Stadler,Todd M. Lowe,Chia-Lin Wei,Yijun Ruan,Kevin Struhl,Mark Gerstein,Stylianos E. Antonarakis,Yutao Fu,Eric D. Green,Ulas Karaoz,Adam Siepel,Adam Siepel,James Taylor,Laura A. Liefer,Kris A. Wetterstrand,Peter J. Good,Elise A. Feingold,Mark S. Guyer,Gregory M. Cooper,Gregory M. Cooper,George Asimenos,Colin N. Dewey,Minmei Hou,Sergey Nikolaev,Juan I. Montoya-Burgos,Ari Löytynoja,Simon Whelan,Fabio Pardi,Tim Massingham,Haiyan Huang,Nan Zhang,Nan Zhang,Ian Holmes,James C. Mullikin,Abel Ureta-Vidal,Benedict Paten,Michael Seringhaus,Deanna M. Church,Kate R. Rosenbloom,W. James Kent,Eric A. Stone,Serafim Batzoglou,Nick Goldman,Ross C. Hardison,David Haussler,Webb Miller,Arend Sidow,Nathan D. Trinklein,Zhengdong D. Zhang,Leah O. Barrera,Rhona K. Stuart,David C. King,Adam Ameur,Stefan Enroth,Mark Bieda,Jonghwan Kim,Akshay Bhinge,Nan Jiang,Jun Liu,Fei Yao,Vinsensius B. Vega,Charlie W.H. Lee,Patrick Ng,Annie Yang,Zarmik Moqtaderi,Zhou Zhu,Xiaoqin Xu,Sharon L. Squazzo,Matthew J. Oberley,David R. Inman,Michael A. Singer,Todd Richmond,Kyle J. Munn,Kyle J. Munn,Alvaro Rada-Iglesias,Ola Wallerman,Jan Komorowski,Joanna C. Fowler,Phillippe Couttet,Alexander W. Bruce,Oliver M. Dovey,Peter D. Ellis,Cordelia Langford,David A. Nix,Ghia Euskirchen,Stephen Hartman,Alexander E. Urban,Peter Kraus,Sara Van Calcar,Nate Heintzman,Tae Hoon Kim,Kun Wang,Chunxu Qu,Gary C. Hon,Rosa Luna,Christopher K. Glass,M. Geoff Rosenfeld,Shelley Force Aldred,Sara J. Cooper,Anason S. Halees,Jane M. Lin,Hennady P. Shulha,Xiaoling Zhang,Mousheng Xu,Jaafar N. Haidar,Yong Yu,Vishwanath R. Iyer,Roland Green,Claes Wadelius,Peggy J. Farnham,Bing Ren,Rachel A. Harte,Angie S. Hinrichs,Heather Trumbower,Hiram Clawson,Jennifer Hillman-Jackson,Ann S. Zweig,Kayla E. Smith,Archana Thakkapallayil,Galt P. Barber,Robert M. Kuhn,Donna Karolchik,Lluís Armengol,Christine P. Bird,Paul I.W. de Bakker,Andrew D. Kern,Nuria Lopez-Bigas,Joel D. Martin,Barbara E. Stranger,Abigail Woodroffe,Eugene Davydov,Antigone S. Dimas,Eduardo Eyras,Ingileif B. Hallgrímsdóttir,Julian L. Huppert,Michael C. Zody,Gonçalo R. Abecasis,Xavier Estivill,Gerard G. Bouffard,Xiaobin Guan,Nancy F. Hansen,Jacquelyn R. Idol,Valerie Maduro,Baishali Maskeri,Jennifer C. McDowell,Morgan Park,Pamela J. Thomas,Alice C. Young,Robert W. Blakesley,Donna M. Muzny,Erica Sodergren,David A. Wheeler,Kim C. Worley,Huaiyang Jiang,George M. Weinstock,Richard A. Gibbs,Tina Graves,Robert S. Fulton,Elaine R. Mardis,Richard K. Wilson,Michele Clamp,James Cuff,Sante Gnerre,David B. Jaffe,Jean L. Chang,Kerstin Lindblad-Toh,Eric S. Lander,Eric S. Lander,Maxim Koriabine,Mikhail Nefedov,Kazutoyo Osoegawa,Yuko Yoshinaga,Baoli Zhu,Pieter J. de Jong +320 more
TL;DR: Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Journal ArticleDOI
Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome.
Nathaniel D. Heintzman,Rhona K. Stuart,Gary C. Hon,Yutao Fu,Christina W. Ching,R. David Hawkins,Leah O. Barrera,Sara Van Calcar,Chunxu Qu,Keith A. Ching,Wei Wang,Zhiping Weng,Roland Green,Gregory E. Crawford,Bing Ren +14 more
TL;DR: Insight is given into the connections between chromatin modifications and transcriptional regulatory activity and a novel functional enhancer for the carnitine transporter SLC22A5 (OCTN2) is uncovered, providing a new tool for the functional annotation of the human genome.
Journal ArticleDOI
The ENCODE (ENCyclopedia of DNA elements) Project
Elise A. Feingold,Peter J. Good,Mark S. Guyer,S. Kamholz,L. Liefer,Kris A. Wetterstrand,Francis S. Collins,Thomas R. Gingeras,Dione Kampa,E. A. Sekinger,Jill Cheng,H. Hirsch,Srinka Ghosh,Zhou Zhu,Sandeep Patel,Antonio Piccolboni,A. Yang,Hari Tammana,Stefan Bekiranov,Philipp Kapranov,Rhonda Harrison,George M. Church,Kevin Struhl,Bing Ren,Tae Hoon Kim,Leah O. Barrera,Chunxu Qu,S. van Calcar,R. Luna,C. K. Glass,M. G. Rosenfeld,Roderic Guigó,Stylianos E. Antonarakis,Ewan Birney,Michael R. Brent,Lior Pachter,Alexandre Reymond,Emmanouil T. Dermitzakis,Colin N. Dewey,Damian Keefe,F. Denoeud,Julien Lagarde,Jennifer L. Ashurst,Tim Hubbard,Jan-Jaap Wesselink,Robert Castelo,Eduardo Eyras,Richard M. Myers,Arend Sidow,Serafim Batzoglou,Nathan D. Trinklein,Sara J. Hartman,Shelley Force Aldred,Elizabeth Anton,Diane I. Schroeder,S. S. Marticke,Long H. Nguyen,Jeremy Schmutz,Jane Grimwood,Mark Dickson,Gregory M. Cooper,Eric A. Stone,George Asimenos,Michael Brudno,Anindya Dutta,Neerja Karnani,Christopher M. Taylor,H. K. Kim,Gabriel Robins,George Stamatoyannopoulos,John A. Stamatoyannopoulos,Michael O. Dorschner,Peter J. Sabo,Michael Hawrylycz,Richard Humbert,James C. Wallace,Min-Feng Yu,Patrick A. Navas,M. McArthur,William Stafford Noble,Ian Dunham,Christof Koch,Robert M. Andrews,Gayle K. Clelland,Sarah Wilcox,Joanna C. Fowler,Keith D. James,P. Groth,Oliver M. Dovey,Peter D. Ellis,Vicki L. Wraight,Andrew J. Mungall,Pawandeep Dhami,Heike Fiegler,Cordelia Langford,Nigel P. Carter,David Vetrie,Michael Snyder,Ghia Euskirchen,Alexander E. Urban,Ugrappa Nagalakshmi,John L. Rinn,George V. Popescu,Paul Bertone,Stephen Hartman,Joel Rozowsky,Olof Emanuelsson,Thomas Royce,Sambath Chung,Mark Gerstein,Zheng Lian,Jane B. Lian,Y. Nakayama,Sherman M. Weissman,Viktor Stolc,W. Tongprasit,H. Sethi,Steven J.M. Jones,Marco A. Marra,H. Shin,Jacquie Schein,Michele Clamp,Kerstin Lindblad-Toh,Jean L. Chang,David B. Jaffe,Michael Kamal,Eric S. Lander,Tarjei S. Mikkelsen,Jade P. Vinson,Michael C. Zody,P. J. De Jong,Kazutoyo Osoegawa,Mikhail Nefedov,Baoli Zhu,Andreas D. Baxevanis,Tyra G. Wolfsberg,Gregory E. Crawford,James R R Whittle,Ingeborg Holt,T. J. Vasicek,D. Zhou,Shu-Jin Luo,Eric D. Green,Gerry Bouffard,Elliott H. Margulies,Matthew E. Portnoy,Nancy F. Hansen,Pamela J. Thomas,Jenny McDowell,Baishali Maskeri,Alice C. Young,Jacquelyn R. Idol,Robert W. Blakesley,Greg Schuler,Webb Miller,Ross C. Hardison,Laura Elnitski,Prachi Shah,Steven L. Salzberg,Mihaela Pertea,William H. Majoros,David Haussler,Daryl J. Thomas,Kate R. Rosenbloom,Hiram Clawson,Adam Siepel,W. J. Kent,Zhiping Weng,S. Jin,Anason S. Halees,H. Burden,Ulas Karaoz,Yutao Fu,Yong Yu,C. Ding,Charles R. Cantor,Robert E. Kingston,Jonathan H. Dennis,Roland Green,Michael A. Singer,Todd Richmond,J. E. Norton,Peggy J. Farnham,Matthew J. Oberley,D. R. Inman,M. R. McCormick,H. Kim,C. L. Middle,Michael C. Pirrung,Xiang-Dong Fu,Y. S. Kwon,Z. Ye,Job Dekker,Tomoko M. Tabuchi,Nele Gheldof,Josée Dostie,S. C. Harvey +196 more
TL;DR: The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
Journal ArticleDOI
An integrated semiconductor device enabling non-optical genome sequencing
Jonathan M. Rothberg,Wolfgang Hinz,Todd Rearick,Jonathan Schultz,William J. Mileski,Melville Davey,John H. Leamon,Kim L. Johnson,Mark James Milgrew,Matthew D. Edwards,Jeremy Hoon,Jan Fredrik Simons,David Marran,Jason W. Myers,John F. Davidson,Annika Branting,John Nobile,Bernard P. Puc,David Light,Travis A. Clark,Martin Huber,Jeffrey T. Branciforte,Isaac B. Stoner,Simon Cawley,Michael R. Lyons,Yutao Fu,Nils Homer,Marina Sedova,Xin Miao,Brian Reed,Jeffrey Sabina,Erika Feierstein,Michelle Schorn,Mohammad Alanjary,Eileen T. Dimalanta,Devin Dressman,Rachel Kasinskas,Tanya Sokolsky,Jacqueline A. Fidanza,Eugeni Namsaraev,Kevin McKernan,Alan Williams,G. Thomas Roth,James Bustillo +43 more
TL;DR: A DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes, showing its robustness and scalability by producing ion chips with up to 10 times as many sensors and sequencing a human genome.
Journal ArticleDOI
Assessing computational tools for the discovery of transcription factor binding sites.
Martin Tompa,Nan Li,Timothy L. Bailey,George M. Church,Bart De Moor,Eleazar Eskin,Alexander V. Favorov,Martin C. Frith,Yutao Fu,W. James Kent,Vsevolod J. Makeev,Andrei A. Mironov,William Stafford Noble,Giulio Pavesi,Graziano Pesole,Mireille Régnier,Nicolas Simonis,Saurabh Sinha,Gert Thijs,Jacques van Helden,Mathias Vandenbogaert,Zhiping Weng,Christopher T. Workman,Chun Ye,Zhou Zhu +24 more
TL;DR: The purpose of the current assessment is to provide some guidance to users regarding the accuracy of currently available tools in various settings, and to provide a benchmark of data sets for assessing future tools.