Searching journal content for Jared T. Simpson in author.

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  1. Resource: Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly
    • Valerie A. Schneider,
    • Tina Graves-Lindsay,
    • Kerstin Howe,
    • Nathan Bouk,
    • Hsiu-Chuan Chen,
    • Paul A. Kitts,
    • Terence D. Murphy,
    • Kim D. Pruitt,
    • Françoise Thibaud-Nissen,
    • Derek Albracht,
    • Robert S. Fulton,
    • Milinn Kremitzki,
    • Vincent Magrini,
    • Chris Markovic,
    • Sean McGrath,
    • Karyn Meltz Steinberg,
    • Kate Auger,
    • William Chow,
    • Joanna Collins,
    • Glenn Harden,
    • Timothy Hubbard,
    • Sarah Pelan,
    • Jared T. Simpson,
    • Glen Threadgold,
    • James Torrance,
    • Jonathan M. Wood,
    • Laura Clarke,
    • Sergey Koren,
    • Matthew Boitano,
    • Paul Peluso,
    • Heng Li,
    • Chen-Shan Chin,
    • Adam M. Phillippy,
    • Richard Durbin,
    • Richard K. Wilson,
    • Paul Flicek,
    • Evan E. Eichler,
    • and Deanna M. Church
    Genome Res. May 2017 27: 849-864; Published in Advance April 10, 2017, doi:10.1101/gr.213611.116
    OPEN ACCESS ARTICLE
  2. Method: Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes
    • Dirk D. Dolle,
    • Zhicheng Liu,
    • Matthew Cotten,
    • Jared T. Simpson,
    • Zamin Iqbal,
    • Richard Durbin,
    • Shane A. McCarthy,
    • and Thomas M. Keane
    Genome Res. February 2017 27: 300-309; Published in Advance December 16, 2016, doi:10.1101/gr.211748.116
  3. Resource: Efficient de novo assembly of large genomes using compressed data structures
    • Jared T. Simpson and
    • Richard Durbin
    Genome Res. March 2012 22: 549-556; Published in Advance December 7, 2011, doi:10.1101/gr.126953.111
    OPEN ACCESS ARTICLE
  4. 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
  5. Method: Revealing the genetic structure of a trait by sequencing a population under selection
    • Leopold Parts,
    • Francisco A. Cubillos,
    • Jonas Warringer,
    • Kanika Jain,
    • Francisco Salinas,
    • Suzannah J. Bumpstead,
    • Mikael Molin,
    • Amin Zia,
    • Jared T. Simpson,
    • Michael A. Quail,
    • Alan Moses,
    • Edward J. Louis,
    • Richard Durbin,
    • and Gianni Liti
    Genome Res. July 2011 21: 1131-1138; Published in Advance March 21, 2011, doi:10.1101/gr.116731.110
    OPEN ACCESS ARTICLE
  6. Resource: ABySS: A parallel assembler for short read sequence data
    • Jared T. Simpson,
    • Kim Wong,
    • Shaun D. Jackman,
    • Jacqueline E. Schein,
    • Steven J.M. Jones,
    • and İnanç Birol
    Genome Res. June 2009 19: 1117-1123; Published in Advance February 27, 2009, doi:10.1101/gr.089532.108
    OPEN ACCESS ARTICLE
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