Searching journal content for Mark Diekhans 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: 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
  4. Research: Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells
    • Tate Tunstall,
    • Richard Kock,
    • Jiri Vahala,
    • Mark Diekhans,
    • Ian Fiddes,
    • Joel Armstrong,
    • Benedict Paten,
    • Oliver A. Ryder,
    • and Cynthia C. Steiner
    Genome Res. June 2018 28: 780-788; Published in Advance May 24, 2018, doi:10.1101/gr.227603.117
    OPEN ACCESS ARTICLE
  5. 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
  6. 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
  7. Resource: Cactus: Algorithms for genome multiple sequence alignment
    • Benedict Paten,
    • Dent Earl,
    • Ngan Nguyen,
    • Mark Diekhans,
    • Daniel Zerbino,
    • and David Haussler
    Genome Res. September 2011 21: 1512-1528; Published in Advance June 10, 2011, doi:10.1101/gr.123356.111
    OPEN ACCESS ARTICLE
  8. Resource: The completion of the Mammalian Gene Collection (MGC)
    • The MGC Project Team,
    • Gary Temple,
    • Daniela S. Gerhard,
    • Rebekah Rasooly,
    • Elise A. Feingold,
    • Peter J. Good,
    • Cristen Robinson,
    • Allison Mandich,
    • Jeffrey G. Derge,
    • Jeanne Lewis,
    • Debonny Shoaf,
    • Francis S. Collins,
    • Wonhee Jang,
    • Lukas Wagner,
    • Carolyn M. Shenmen,
    • Leonie Misquitta,
    • Carl F. Schaefer,
    • Kenneth H. Buetow,
    • Tom I. Bonner,
    • Linda Yankie,
    • Ming Ward,
    • Lon Phan,
    • Alex Astashyn,
    • Garth Brown,
    • Catherine Farrell,
    • Jennifer Hart,
    • Melissa Landrum,
    • Bonnie L. Maidak,
    • Michael Murphy,
    • Terence Murphy,
    • Bhanu Rajput,
    • Lillian Riddick,
    • David Webb,
    • Janet Weber,
    • Wendy Wu,
    • Kim D. Pruitt,
    • Donna Maglott,
    • Adam Siepel,
    • Brona Brejova,
    • Mark Diekhans,
    • Rachel Harte,
    • Robert Baertsch,
    • Jim Kent,
    • David Haussler,
    • Michael Brent,
    • Laura Langton,
    • Charles L.G. Comstock,
    • Michael Stevens,
    • Chaochun Wei,
    • Marijke J. van Baren,
    • Kourosh Salehi-Ashtiani,
    • Ryan R. Murray,
    • Lila Ghamsari,
    • Elizabeth Mello,
    • Chenwei Lin,
    • Christa Pennacchio,
    • Kirsten Schreiber,
    • Nicole Shapiro,
    • Amber Marsh,
    • Elizabeth Pardes,
    • Troy Moore,
    • Anita Lebeau,
    • Mike Muratet,
    • Blake Simmons,
    • David Kloske,
    • Stephanie Sieja,
    • James Hudson,
    • Praveen Sethupathy,
    • Michael Brownstein,
    • Narayan Bhat,
    • Joseph Lazar,
    • Howard Jacob,
    • Chris E. Gruber,
    • Mark R. Smith,
    • John McPherson,
    • Angela M. Garcia,
    • Preethi H. Gunaratne,
    • Jiaqian Wu,
    • Donna Muzny,
    • Richard A. Gibbs,
    • Alice C. Young,
    • Gerard G. Bouffard,
    • Robert W. Blakesley,
    • Jim Mullikin,
    • Eric D. Green,
    • Mark C. Dickson,
    • Alex C. Rodriguez,
    • Jane Grimwood,
    • Jeremy Schmutz,
    • Richard M. Myers,
    • Martin Hirst,
    • Thomas Zeng,
    • Kane Tse,
    • Michelle Moksa,
    • Merinda Deng,
    • Kevin Ma,
    • Diana Mah,
    • Johnson Pang,
    • Greg Taylor,
    • Eric Chuah,
    • Athena Deng,
    • Keith Fichter,
    • Anne Go,
    • Stephanie Lee,
    • Jing Wang,
    • Malachi Griffith,
    • Ryan Morin,
    • Richard A. Moore,
    • Michael Mayo,
    • Sarah Munro,
    • Susan Wagner,
    • Steven J.M. Jones,
    • Robert A. Holt,
    • Marco A. Marra,
    • Sun Lu,
    • Shuwei Yang,
    • James Hartigan,
    • Marcus Graf,
    • Ralf Wagner,
    • Stanley Letovksy,
    • Jacqueline C. Pulido,
    • Keith Robison,
    • Dominic Esposito,
    • James Hartley,
    • Vanessa E. Wall,
    • Ralph F. Hopkins,
    • Osamu Ohara,
    • and Stefan Wiemann
    Genome Res. December 2009 19: 2324-2333; Published in Advance September 18, 2009, doi:10.1101/gr.095976.109
  9. Resource: The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes
    • Kim D. Pruitt,
    • Jennifer Harrow,
    • Rachel A. Harte,
    • Craig Wallin,
    • Mark Diekhans,
    • Donna R. Maglott,
    • Steve Searle,
    • Catherine M. Farrell,
    • Jane E. Loveland,
    • Barbara J. Ruef,
    • Elizabeth Hart,
    • Marie-Marthe Suner,
    • Melissa J. Landrum,
    • Bronwen Aken,
    • Sarah Ayling,
    • Robert Baertsch,
    • Julio Fernandez-Banet,
    • Joshua L. Cherry,
    • Val Curwen,
    • Michael DiCuccio,
    • Manolis Kellis,
    • Jennifer Lee,
    • Michael F. Lin,
    • Michael Schuster,
    • Andrew Shkeda,
    • Clara Amid,
    • Garth Brown,
    • Oksana Dukhanina,
    • Adam Frankish,
    • Jennifer Hart,
    • Bonnie L. Maidak,
    • Jonathan Mudge,
    • Michael R. Murphy,
    • Terence Murphy,
    • Jeena Rajan,
    • Bhanu Rajput,
    • Lillian D. Riddick,
    • Catherine Snow,
    • Charles Steward,
    • David Webb,
    • Janet A. Weber,
    • Laurens Wilming,
    • Wenyu Wu,
    • Ewan Birney,
    • David Haussler,
    • Tim Hubbard,
    • James Ostell,
    • Richard Durbin,
    • and David Lipman
    Genome Res. July 2009 19: 1316-1323; Published in Advance June 4, 2009, doi:10.1101/gr.080531.108
  10. RESOURCE: 28-Way vertebrate alignment and conservation track in the UCSC Genome Browser
    • Webb Miller,
    • Kate Rosenbloom,
    • Ross C. Hardison,
    • Minmei Hou,
    • James Taylor,
    • Brian Raney,
    • Richard Burhans,
    • David C. King,
    • Robert Baertsch,
    • Daniel Blankenberg,
    • Sergei L. Kosakovsky Pond,
    • Anton Nekrutenko,
    • Belinda Giardine,
    • Robert S. Harris,
    • Svitlana Tyekucheva,
    • Mark Diekhans,
    • Thomas H. Pringle,
    • William J. Murphy,
    • Arthur Lesk,
    • George M. Weinstock,
    • Kerstin Lindblad-Toh,
    • Richard A. Gibbs,
    • Eric S. Lander,
    • Adam Siepel,
    • David Haussler,
    • and W. James Kent
    Genome Res. December 2007 17: 1797-1808; Published in Advance November 5, 2007, doi:10.1101/gr.6761107
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