Searching journal content for James K.M. Brown in author.

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  1. Research: Extensive cross-regulation of post-transcriptional regulatory networks in Drosophila
    • Marcus H. Stoiber,
    • Sara Olson,
    • Gemma E. May,
    • Michael O. Duff,
    • Jan Manent,
    • Robert Obar,
    • K.G. Guruharsha,
    • Peter J. Bickel,
    • Spyros Artavanis-Tsakonas,
    • James B. Brown,
    • Brenton R. Graveley,
    • and Susan E. Celniker
    Genome Res. November 2015 25: 1692-1702; Published in Advance August 20, 2015, doi:10.1101/gr.182675.114
    OPEN ACCESS ARTICLE
  2. Resource: Comparative validation of the D. melanogaster modENCODE transcriptome annotation
    • Zhen-Xia Chen,
    • David Sturgill,
    • Jiaxin Qu,
    • Huaiyang Jiang,
    • Soo Park,
    • Nathan Boley,
    • Ana Maria Suzuki,
    • Anthony R. Fletcher,
    • David C. Plachetzki,
    • Peter C. FitzGerald,
    • Carlo G. Artieri,
    • Joel Atallah,
    • Olga Barmina,
    • James B. Brown,
    • Kerstin P. Blankenburg,
    • Emily Clough,
    • Abhijit Dasgupta,
    • Sai Gubbala,
    • Yi Han,
    • Joy C. Jayaseelan,
    • Divya Kalra,
    • Yoo-Ah Kim,
    • Christie L. Kovar,
    • Sandra L. Lee,
    • Mingmei Li,
    • James D. Malley,
    • John H. Malone,
    • Tittu Mathew,
    • Nicolas R. Mattiuzzo,
    • Mala Munidasa,
    • Donna M. Muzny,
    • Fiona Ongeri,
    • Lora Perales,
    • Teresa M. Przytycka,
    • Ling-Ling Pu,
    • Garrett Robinson,
    • Rebecca L. Thornton,
    • Nehad Saada,
    • Steven E. Scherer,
    • Harold E. Smith,
    • Charles Vinson,
    • Crystal B. Warner,
    • Kim C. Worley,
    • Yuan-Qing Wu,
    • Xiaoyan Zou,
    • Peter Cherbas,
    • Manolis Kellis,
    • Michael B. Eisen,
    • Fabio Piano,
    • Karin Kionte,
    • David H. Fitch,
    • Paul W. Sternberg,
    • Asher D. Cutter,
    • Michael O. Duff,
    • Roger A. Hoskins,
    • Brenton R. Graveley,
    • Richard A. Gibbs,
    • Peter J. Bickel,
    • Artyom Kopp,
    • Piero Carninci,
    • Susan E. Celniker,
    • Brian Oliver,
    • and Stephen Richards
    Genome Res. July 2014 24: 1209-1223; Published in Advance July 1, 2014, doi:10.1101/gr.159384.113
    OPEN ACCESS ARTICLE
  3. Research: Long noncoding RNAs are rarely translated in two human cell lines
    • Balázs Bánfai,
    • Hui Jia,
    • Jainab Khatun,
    • Emily Wood,
    • Brian Risk,
    • William E. Gundling, Jr.,
    • Anshul Kundaje,
    • Harsha P. Gunawardena,
    • Yanbao Yu,
    • Ling Xie,
    • Krzysztof Krajewski,
    • Brian D. Strahl,
    • Xian Chen,
    • Peter Bickel,
    • Morgan C. Giddings,
    • James B. Brown,
    • and Leonard Lipovich
    Genome Res. September 2012 22: 1646-1657; doi:10.1101/gr.134767.111
    OPEN ACCESS ARTICLE
  4. Resource: The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
    • Thomas Derrien,
    • Rory Johnson,
    • Giovanni Bussotti,
    • Andrea Tanzer,
    • Sarah Djebali,
    • Hagen Tilgner,
    • Gregory Guernec,
    • David Martin,
    • Angelika Merkel,
    • David G. Knowles,
    • Julien Lagarde,
    • Lavanya Veeravalli,
    • Xiaoan Ruan,
    • Yijun Ruan,
    • Timo Lassmann,
    • Piero Carninci,
    • James B. Brown,
    • Leonard Lipovich,
    • Jose M. Gonzalez,
    • Mark Thomas,
    • Carrie A. Davis,
    • Ramin Shiekhattar,
    • Thomas R. Gingeras,
    • Tim J. Hubbard,
    • Cedric Notredame,
    • Jennifer Harrow,
    • and Roderic Guigó
    Genome Res. September 2012 22: 1775-1789; doi:10.1101/gr.132159.111
    OPEN ACCESS ARTICLE
  5. Resource: ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia
    • Stephen G. Landt,
    • Georgi K. Marinov,
    • Anshul Kundaje,
    • Pouya Kheradpour,
    • Florencia Pauli,
    • Serafim Batzoglou,
    • Bradley E. Bernstein,
    • Peter Bickel,
    • James B. Brown,
    • Philip Cayting,
    • Yiwen Chen,
    • Gilberto DeSalvo,
    • Charles Epstein,
    • Katherine I. Fisher-Aylor,
    • Ghia Euskirchen,
    • Mark Gerstein,
    • Jason Gertz,
    • Alexander J. Hartemink,
    • Michael M. Hoffman,
    • Vishwanath R. Iyer,
    • Youngsook L. Jung,
    • Subhradip Karmakar,
    • Manolis Kellis,
    • Peter V. Kharchenko,
    • Qunhua Li,
    • Tao Liu,
    • X. Shirley Liu,
    • Lijia Ma,
    • Aleksandar Milosavljevic,
    • Richard M. Myers,
    • Peter J. Park,
    • Michael J. Pazin,
    • Marc D. Perry,
    • Debasish Raha,
    • Timothy E. Reddy,
    • Joel Rozowsky,
    • Noam Shoresh,
    • Arend Sidow,
    • Matthew Slattery,
    • John A. Stamatoyannopoulos,
    • Michael Y. Tolstorukov,
    • Kevin P. White,
    • Simon Xi,
    • Peggy J. Farnham,
    • Jason D. Lieb,
    • Barbara J. Wold,
    • and Michael Snyder
    Genome Res. September 2012 22: 1813-1831; doi:10.1101/gr.136184.111
    OPEN ACCESS ARTICLE
  6. Research: Genomic analysis of circulating cell-free DNA infers breast cancer dormancy
    • Jacqueline A. Shaw,
    • Karen Page,
    • Kevin Blighe,
    • Natasha Hava,
    • David Guttery,
    • Becky Ward,
    • James Brown,
    • Chetana Ruangpratheep,
    • Justin Stebbing,
    • Rachel Payne,
    • Carlo Palmieri,
    • Suzy Cleator,
    • Rosemary A. Walker,
    • and R. Charles Coombes
    Genome Res. February 2012 22: 220-231; Published in Advance October 11, 2011, doi:10.1101/gr.123497.111
    OPEN ACCESS ARTICLE
  7. Research: Genome-wide analysis of promoter architecture in Drosophila melanogaster
    • Roger A. Hoskins,
    • Jane M. Landolin,
    • James B. Brown,
    • Jeremy E. Sandler,
    • Hazuki Takahashi,
    • Timo Lassmann,
    • Charles Yu,
    • Benjamin W. Booth,
    • Dayu Zhang,
    • Kenneth H. Wan,
    • Li Yang,
    • Nathan Boley,
    • Justen Andrews,
    • Thomas C. Kaufman,
    • Brenton R. Graveley,
    • Peter J. Bickel,
    • Piero Carninci,
    • Joseph W. Carlson,
    • and Susan E. Celniker
    Genome Res. February 2011 21: 182-192; Published in Advance December 22, 2010, doi:10.1101/gr.112466.110
    OPEN ACCESS ARTICLE
  8. ARTICLE: Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome
    • Elliott H. Margulies,
    • Gregory M. Cooper,
    • George Asimenos,
    • Daryl J. Thomas,
    • Colin N. Dewey,
    • Adam Siepel,
    • Ewan Birney,
    • Damian Keefe,
    • Ariel S. Schwartz,
    • Minmei Hou,
    • James Taylor,
    • Sergey Nikolaev,
    • Juan I. Montoya-Burgos,
    • Ari Löytynoja,
    • Simon Whelan,
    • Fabio Pardi,
    • Tim Massingham,
    • James B. Brown,
    • Peter Bickel,
    • Ian Holmes,
    • James C. Mullikin,
    • Abel Ureta-Vidal,
    • Benedict Paten,
    • Eric A. Stone,
    • Kate R. Rosenbloom,
    • W. James Kent,
    • Gerard G. Bouffard,
    • Xiaobin Guan,
    • Nancy F. Hansen,
    • Jacquelyn R. Idol,
    • Valerie V.B. 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 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,
    • Angie Hinrichs,
    • Heather Trumbower,
    • Hiram Clawson,
    • Ann Zweig,
    • Robert M. Kuhn,
    • Galt Barber,
    • Rachel Harte,
    • Donna Karolchik,
    • Matthew A. Field,
    • Richard A. Moore,
    • Carrie A. Matthewson,
    • Jacqueline E. Schein,
    • Marco A. Marra,
    • Stylianos E. Antonarakis,
    • Serafim Batzoglou,
    • Nick Goldman,
    • Ross Hardison,
    • David Haussler,
    • Webb Miller,
    • Lior Pachter,
    • Eric D. Green,
    • and Arend Sidow
    Genome Res. June 2007 17: 760-774; doi:10.1101/gr.6034307
    OPEN ACCESS ARTICLE
  9. LETTER: Genome Size Reduction through Illegitimate Recombination Counteracts Genome Expansion in Arabidopsis
    • Katrien M. Devos,
    • James K.M. Brown,
    • and Jeffrey L. Bennetzen
    Genome Res. July 1, 2002 12: 1075-1079; doi:10.1101/gr.132102
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