Searching journal content for Daniel S. Rokhsar in author.

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  1. Method: Chromosome-scale shotgun assembly using an in vitro method for long-range linkage
    • Nicholas H. Putnam,
    • Brendan L. O'Connell,
    • Jonathan C. Stites,
    • Brandon J. Rice,
    • Marco Blanchette,
    • Robert Calef,
    • Christopher J. Troll,
    • Andrew Fields,
    • Paul D. Hartley,
    • Charles W. Sugnet,
    • David Haussler,
    • Daniel S. Rokhsar,
    • and Richard E. Green
    Genome Res. March 2016 26: 342-350; Published in Advance February 4, 2016, doi:10.1101/gr.193474.115
    OPEN ACCESS ARTICLE
  2. 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
  3. Letter: Domain shuffling and the evolution of vertebrates
    • Takeshi Kawashima,
    • Shuichi Kawashima,
    • Chisaki Tanaka,
    • Miho Murai,
    • Masahiko Yoneda,
    • Nicholas H. Putnam,
    • Daniel S. Rokhsar,
    • Minoru Kanehisa,
    • Nori Satoh,
    • and Hiroshi Wada
    Genome Res. August 2009 19: 1393-1403; Published in Advance May 14, 2009, doi:10.1101/gr.087072.108
  4. Methods: Rapid whole-genome mutational profiling using next-generation sequencing technologies
    • Douglas R. Smith,
    • Aaron R. Quinlan,
    • Heather E. Peckham,
    • Kathryn Makowsky,
    • Wei Tao,
    • Betty Woolf,
    • Lei Shen,
    • William F. Donahue,
    • Nadeem Tusneem,
    • Michael P. Stromberg,
    • Donald A. Stewart,
    • Lu Zhang,
    • Swati S. Ranade,
    • Jason B. Warner,
    • Clarence C. Lee,
    • Brittney E. Coleman,
    • Zheng Zhang,
    • Stephen F. McLaughlin,
    • Joel A. Malek,
    • Jon M. Sorenson,
    • Alan P. Blanchard,
    • Jarrod Chapman,
    • David Hillman,
    • Feng Chen,
    • Daniel S. Rokhsar,
    • Kevin J. McKernan,
    • Thomas W. Jeffries,
    • Gabor T. Marth,
    • and Paul M. Richardson
    Genome Res. October 2008 18: 1638-1642; Published in Advance September 4, 2008, doi:10.1101/gr.077776.108
    OPEN ACCESS ARTICLE
  5. LETTER: The amphioxus genome illuminates vertebrate origins and cephalochordate biology
    • Linda Z. Holland,
    • Ricard Albalat,
    • Kaoru Azumi,
    • Èlia Benito-Gutiérrez,
    • Matthew J. Blow,
    • Marianne Bronner-Fraser,
    • Frederic Brunet,
    • Thomas Butts,
    • Simona Candiani,
    • Larry J. Dishaw,
    • David E.K. Ferrier,
    • Jordi Garcia-Fernàndez,
    • Jeremy J. Gibson-Brown,
    • Carmela Gissi,
    • Adam Godzik,
    • Finn Hallböök,
    • Dan Hirose,
    • Kazuyoshi Hosomichi,
    • Tetsuro Ikuta,
    • Hidetoshi Inoko,
    • Masanori Kasahara,
    • Jun Kasamatsu,
    • Takeshi Kawashima,
    • Ayuko Kimura,
    • Masaaki Kobayashi,
    • Zbynek Kozmik,
    • Kaoru Kubokawa,
    • Vincent Laudet,
    • Gary W. Litman,
    • Alice C. McHardy,
    • Daniel Meulemans,
    • Masaru Nonaka,
    • Robert P. Olinski,
    • Zeev Pancer,
    • Len A. Pennacchio,
    • Mario Pestarino,
    • Jonathan P. Rast,
    • Isidore Rigoutsos,
    • Marc Robinson-Rechavi,
    • Graeme Roch,
    • Hidetoshi Saiga,
    • Yasunori Sasakura,
    • Masanobu Satake,
    • Yutaka Satou,
    • Michael Schubert,
    • Nancy Sherwood,
    • Takashi Shiina,
    • Naohito Takatori,
    • Javier Tello,
    • Pavel Vopalensky,
    • Shuichi Wada,
    • Anlong Xu,
    • Yuzhen Ye,
    • Keita Yoshida,
    • Fumiko Yoshizaki,
    • Jr-Kai Yu,
    • Qing Zhang,
    • Christian M. Zmasek,
    • Pieter J. de Jong,
    • Kazutoyo Osoegawa,
    • Nicholas H. Putnam,
    • Daniel S. Rokhsar,
    • Noriyuki Satoh,
    • and Peter W.H. Holland
    Genome Res. July 2008 18: 1100-1111; Published in Advance June 18, 2008, doi:10.1101/gr.073676.107
  6. RESOURCE: Chromosomal mapping of 170 BAC clones in the ascidian Ciona intestinalis
    • Eiichi Shoguchi,
    • Takeshi Kawashima,
    • Yutaka Satou,
    • Makoto Hamaguchi,
    • Tadasu Sin-I,
    • Yuji Kohara,
    • Nik Putnam,
    • Daniel S. Rokhsar,
    • and Nori Satoh
    Genome Res. February 2006 16: 297-303; Published in Advance December 14, 2005, doi:10.1101/gr.4156606
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