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Ugrappa Nagalakshmi
Researcher at Yale University
Publications - 13
Citations - 10285
Ugrappa Nagalakshmi is an academic researcher from Yale University. The author has contributed to research in topics: Medicine & Biology. The author has an hindex of 8, co-authored 8 publications receiving 9659 citations.
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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
The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing
Ugrappa Nagalakshmi,Zhong Wang,Karl Waern,C. Shou,Debasish Raha,Mark Gerstein,Michael Snyder +6 more
TL;DR: A quantitative sequencing-based method is developed for mapping transcribed regions, in which complementary DNA fragments are subjected to high-throughput sequencing and mapped to the genome, and it is demonstrated that most (74.5%) of the nonrepetitive sequence of the yeast genome is transcribed.
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
RNA-Seq: A Method for Comprehensive Transcriptome Analysis
TL;DR: This unit describes protocols for performing RNA‐Seq using the Illumina sequencing platform, and has been used successfully to precisely quantify transcript levels, confirm or revise previously annotated 5′ and 3′ ends of genes, and map exon/intron boundaries.
Journal ArticleDOI
Assessing the performance of different high-density tiling microarray strategies for mapping transcribed regions of the human genome
Olof Emanuelsson,Ugrappa Nagalakshmi,Deyou Zheng,Joel Rozowsky,Alexander E. Urban,Jiang Du,Zheng Lian,Viktor Stolc,Sherman M. Weissman,Michael Snyder,Mark Gerstein +10 more
TL;DR: Overall, the performance improves with more data points per locus, coupled with statistical scoring approaches that properly take advantage of this, where this larger number of data points arises from higher genomic tiling density and the use of replicate arrays and mismatches.