Searching journal content for David Haussler in author.

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  1. Method: Highly accurate assembly polishing with DeepPolisher
    • Mira Mastoras,
    • Mobin Asri,
    • Lucas Brambrink,
    • Prajna Hebbar,
    • Alexey Kolesnikov,
    • Daniel E. Cook,
    • Maria Nattestad,
    • Julian Lucas,
    • Taylor S. Won,
    • Pi-Chuan Chang,
    • Andrew Carroll,
    • Benedict Paten,
    • Kishwar Shafin,
    • and and the Human Pangenome Reference Consortium
    Genome Res. July 2025 35: 1595-1608; Published in Advance May 19, 2025, doi:10.1101/gr.280149.124
  2. Research: Gaps and complex structurally variant loci in phased genome assemblies
    • David Porubsky,
    • Mitchell R. Vollger,
    • William T. Harvey,
    • Allison N. Rozanski,
    • Peter Ebert,
    • Glenn Hickey,
    • Patrick Hasenfeld,
    • Ashley D. Sanders,
    • Catherine Stober,
    • Human Pangenome Reference Consortium,
    • Jan O. Korbel,
    • Benedict Paten,
    • Tobias Marschall,
    • and Evan E. Eichler
    Genome Res. April 2023 33: 496-510; Published in Advance May 10, 2023, doi:10.1101/gr.277334.122
    OPEN ACCESS ARTICLE
  3. Method: A complete pedigree-based graph workflow for rare candidate variant analysis
    • Charles Markello,
    • Charles Huang,
    • Alex Rodriguez,
    • Andrew Carroll,
    • Pi-Chuan Chang,
    • Jordan Eizenga,
    • Thomas Markello,
    • David Haussler,
    • and Benedict Paten
    Genome Res. May 2022 32: 893-903; Published in Advance April 28, 2022, doi:10.1101/gr.276387.121
  4. Research: A hidden layer of structural variation in transposable elements reveals potential genetic modifiers in human disease-risk loci
    • Elisabeth J. van Bree,
    • Rita L.F.P. Guimarães,
    • Mischa Lundberg,
    • Elena R. Blujdea,
    • Jimi L. Rosenkrantz,
    • Fred T.G. White,
    • Josse Poppinga,
    • Paula Ferrer-Raventós,
    • Anne-Fleur E. Schneider,
    • Isabella Clayton,
    • David Haussler,
    • Marcel J.T. Reinders,
    • Henne Holstege,
    • Adam D. Ewing,
    • Colette Moses,
    • and Frank M.J. Jacobs
    Genome Res. April 2022 32: 656-670; Published in Advance March 24, 2022, doi:10.1101/gr.275515.121
    OPEN ACCESS ARTICLE
  5. Research: Positive selection in noncoding genomic regions of vocal learning birds is associated with genes implicated in vocal learning and speech functions in humans
    • James A. Cahill,
    • Joel Armstrong,
    • Alden Deran,
    • Carolyn J. Khoury,
    • Benedict Paten,
    • David Haussler,
    • and Erich D. Jarvis
    Genome Res. November 2021 31: 2035-2049; Published in Advance October 19, 2021, doi:10.1101/gr.275989.121
    OPEN ACCESS ARTICLE
  6. Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
    • Ian T. Fiddes,
    • Joel Armstrong,
    • Mark Diekhans,
    • Stefanie Nachtweide,
    • Zev N. Kronenberg,
    • Jason G. Underwood,
    • David Gordon,
    • Dent Earl,
    • Thomas Keane,
    • Evan E. Eichler,
    • David Haussler,
    • Mario Stanke,
    • and Benedict Paten
    Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
  7. 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
  8. Resource: Alignathon: a competitive assessment of whole-genome alignment methods
    • Dent Earl,
    • Ngan Nguyen,
    • Glenn Hickey,
    • Robert S. Harris,
    • Stephen Fitzgerald,
    • Kathryn Beal,
    • Igor Seledtsov,
    • Vladimir Molodtsov,
    • Brian J. Raney,
    • Hiram Clawson,
    • Jaebum Kim,
    • Carsten Kemena,
    • Jia-Ming Chang,
    • Ionas Erb,
    • Alexander Poliakov,
    • Minmei Hou,
    • Javier Herrero,
    • William James Kent,
    • Victor Solovyev,
    • Aaron E. Darling,
    • Jian Ma,
    • Cedric Notredame,
    • Michael Brudno,
    • Inna Dubchak,
    • David Haussler,
    • and Benedict Paten
    Genome Res. December 2014 24: 2077-2089; Published in Advance October 1, 2014, doi:10.1101/gr.174920.114
    OPEN ACCESS ARTICLE
  9. Resource: GENCODE: The reference human genome annotation for The ENCODE Project
    • Jennifer Harrow,
    • Adam Frankish,
    • Jose M. Gonzalez,
    • Electra Tapanari,
    • Mark Diekhans,
    • Felix Kokocinski,
    • Bronwen L. Aken,
    • Daniel Barrell,
    • Amonida Zadissa,
    • Stephen Searle,
    • If Barnes,
    • Alexandra Bignell,
    • Veronika Boychenko,
    • Toby Hunt,
    • Mike Kay,
    • Gaurab Mukherjee,
    • Jeena Rajan,
    • Gloria Despacio-Reyes,
    • Gary Saunders,
    • Charles Steward,
    • Rachel Harte,
    • Michael Lin,
    • Cédric Howald,
    • Andrea Tanzer,
    • Thomas Derrien,
    • Jacqueline Chrast,
    • Nathalie Walters,
    • Suganthi Balasubramanian,
    • Baikang Pei,
    • Michael Tress,
    • Jose Manuel Rodriguez,
    • Iakes Ezkurdia,
    • Jeltje van Baren,
    • Michael Brent,
    • David Haussler,
    • Manolis Kellis,
    • Alfonso Valencia,
    • Alexandre Reymond,
    • Mark Gerstein,
    • Roderic Guigó,
    • and Tim J. Hubbard
    Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
    OPEN ACCESS ARTICLE
  10. 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
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