Searching journal content for David B. Jaffe in author.

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  1. Corrigendum: Corrigendum: Direct determination of diploid genome sequences
    • Neil I. Weisenfeld,
    • Vijay Kumar,
    • Preyas Shah,
    • Deanna M. Church,
    • and David B. Jaffe
    Genome Res. April 2018 28: 606.1; doi:10.1101/gr.235812.118
    OPEN ACCESS ARTICLE
  2. Method: Direct determination of diploid genome sequences
    • Neil I. Weisenfeld,
    • Vijay Kumar,
    • Preyas Shah,
    • Deanna M. Church,
    • and David B. Jaffe
    Genome Res. May 2017 27: 757-767; Published in Advance April 5, 2017, doi:10.1101/gr.214874.116
    OPEN ACCESS ARTICLE
  3. Method: Paired-end sequencing of Fosmid libraries by Illumina
    • Louise J.S. Williams,
    • Diana G. Tabbaa,
    • Na Li,
    • Aaron M. Berlin,
    • Terrance P. Shea,
    • Iain MacCallum,
    • Michael S. Lawrence,
    • Yotam Drier,
    • Gad Getz,
    • Sarah K. Young,
    • David B. Jaffe,
    • Chad Nusbaum,
    • and Andreas Gnirke
    Genome Res. November 2012 22: 2241-2249; Published in Advance July 16, 2012, doi:10.1101/gr.138925.112
  4. Method: Finished bacterial genomes from shotgun sequence data
    • Filipe J. Ribeiro,
    • Dariusz Przybylski,
    • Shuangye Yin,
    • Ted Sharpe,
    • Sante Gnerre,
    • Amr Abouelleil,
    • Aaron M. Berlin,
    • Anna Montmayeur,
    • Terrance P. Shea,
    • Bruce J. Walker,
    • Sarah K. Young,
    • Carsten Russ,
    • Chad Nusbaum,
    • Iain MacCallum,
    • and David B. Jaffe
    Genome Res. November 2012 22: 2270-2277; Published in Advance July 24, 2012, doi:10.1101/gr.141515.112
    OPEN ACCESS ARTICLE
  5. Resource: Assemblathon 1: A competitive assessment of de novo short read assembly methods
    • Dent Earl,
    • Keith Bradnam,
    • John St. John,
    • Aaron Darling,
    • Dawei Lin,
    • Joseph Fass,
    • Hung On Ken Yu,
    • Vince Buffalo,
    • Daniel R. Zerbino,
    • Mark Diekhans,
    • Ngan Nguyen,
    • Pramila Nuwantha Ariyaratne,
    • Wing-Kin Sung,
    • Zemin Ning,
    • Matthias Haimel,
    • Jared T. Simpson,
    • Nuno A. Fonseca,
    • İnanç Birol,
    • T. Roderick Docking,
    • Isaac Y. Ho,
    • Daniel S. Rokhsar,
    • Rayan Chikhi,
    • Dominique Lavenier,
    • Guillaume Chapuis,
    • Delphine Naquin,
    • Nicolas Maillet,
    • Michael C. Schatz,
    • David R. Kelley,
    • Adam M. Phillippy,
    • Sergey Koren,
    • Shiaw-Pyng Yang,
    • Wei Wu,
    • Wen-Chi Chou,
    • Anuj Srivastava,
    • Timothy I. Shaw,
    • J. Graham Ruby,
    • Peter Skewes-Cox,
    • Miguel Betegon,
    • Michelle T. Dimon,
    • Victor Solovyev,
    • Igor Seledtsov,
    • Petr Kosarev,
    • Denis Vorobyev,
    • Ricardo Ramirez-Gonzalez,
    • Richard Leggett,
    • Dan MacLean,
    • Fangfang Xia,
    • Ruibang Luo,
    • Zhenyu Li,
    • Yinlong Xie,
    • Binghang Liu,
    • Sante Gnerre,
    • Iain MacCallum,
    • Dariusz Przybylski,
    • Filipe J. Ribeiro,
    • Shuangye Yin,
    • Ted Sharpe,
    • Giles Hall,
    • Paul J. Kersey,
    • Richard Durbin,
    • Shaun D. Jackman,
    • Jarrod A. Chapman,
    • Xiaoqiu Huang,
    • Joseph L. DeRisi,
    • Mario Caccamo,
    • Yingrui Li,
    • David B. Jaffe,
    • Richard E. Green,
    • David Haussler,
    • Ian Korf,
    • and Benedict Paten
    Genome Res. December 2011 21: 2224-2241; Published in Advance September 16, 2011, doi:10.1101/gr.126599.111
    OPEN ACCESS ARTICLE
  6. Research: Integrative analysis of the melanoma transcriptome
    • Michael F. Berger,
    • Joshua Z. Levin,
    • Krishna Vijayendran,
    • Andrey Sivachenko,
    • Xian Adiconis,
    • Jared Maguire,
    • Laura A. Johnson,
    • James Robinson,
    • Roel G. Verhaak,
    • Carrie Sougnez,
    • Robert C. Onofrio,
    • Liuda Ziaugra,
    • Kristian Cibulskis,
    • Elisabeth Laine,
    • Jordi Barretina,
    • Wendy Winckler,
    • David E. Fisher,
    • Gad Getz,
    • Matthew Meyerson,
    • David B. Jaffe,
    • Stacey B. Gabriel,
    • Eric S. Lander,
    • Reinhard Dummer,
    • Andreas Gnirke,
    • Chad Nusbaum,
    • and Levi A. Garraway
    Genome Res. April 2010 20: 413-427; Published in Advance February 23, 2010, doi:10.1101/gr.103697.109
    OPEN ACCESS ARTICLE
  7. RESOURCE: ALLPATHS: De novo assembly of whole-genome shotgun microreads
    • Jonathan Butler,
    • Iain MacCallum,
    • Michael Kleber,
    • Ilya A. Shlyakhter,
    • Matthew K. Belmonte,
    • Eric S. Lander,
    • Chad Nusbaum,
    • and David B. Jaffe
    Genome Res. May 2008 18: 810-820; Published in Advance March 13, 2008, doi:10.1101/gr.7337908
  8. Methods: Quality scores and SNP detection in sequencing-by-synthesis systems
    • William Brockman,
    • Pablo Alvarez,
    • Sarah Young,
    • Manuel Garber,
    • Georgia Giannoukos,
    • William L. Lee,
    • Carsten Russ,
    • Eric S. Lander,
    • Chad Nusbaum,
    • and David B. Jaffe
    Genome Res. May 2008 18: 763-770; Published in Advance January 22, 2008, doi:10.1101/gr.070227.107
  9. 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
  10. Methods: Assembly of polymorphic genomes: Algorithms and application to Ciona savignyi
    • Jade P. Vinson,
    • David B. Jaffe,
    • Keith O'Neill,
    • Elinor K. Karlsson,
    • Nicole Stange-Thomann,
    • Scott Anderson,
    • Jill P. Mesirov,
    • Nori Satoh,
    • Yutaka Satou,
    • Chad Nusbaum,
    • Bruce Birren,
    • James E. Galagan,
    • and Eric S. Lander
    Genome Res. August 2005 15: 1127-1135; doi:10.1101/gr.3722605
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