Searching journal content for Benedict Paten 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: Assessing DNA methylation detection for primary human tissue using Nanopore sequencing
    • Rylee Genner,
    • Stuart Akeson,
    • Melissa Meredith,
    • Pilar Alvarez Jerez,
    • Laksh Malik,
    • Breeana Baker,
    • Abigail Miano-Burkhardt,
    • CARD-long-read Team,
    • Benedict Paten,
    • Kimberley J. Billingsley,
    • Cornelis Blauwendraat,
    • and Miten Jain
    Genome Res. April 2025 35: 632-643; Published in Advance March 7, 2025, doi:10.1101/gr.279159.124
    OPEN ACCESS ARTICLE
  3. Method: Phased nanopore assembly with Shasta and modular graph phasing with GFAse
    • Ryan Lorig-Roach,
    • Melissa Meredith,
    • Jean Monlong,
    • Miten Jain,
    • Hugh E. Olsen,
    • Brandy McNulty,
    • David Porubsky,
    • Tessa G. Montague,
    • Julian K. Lucas,
    • Chris Condon,
    • Jordan M. Eizenga,
    • Sissel Juul,
    • Sean K. McKenzie,
    • Sara E. Simmonds,
    • Jimin Park,
    • Mobin Asri,
    • Sergey Koren,
    • Evan E. Eichler,
    • Richard Axel,
    • Bruce Martin,
    • Paolo Carnevali,
    • Karen H. Miga,
    • and Benedict Paten
    Genome Res. March 2024 34: 454-468; Published in Advance April 16, 2024, doi:10.1101/gr.278268.123
  4. 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
  5. 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
  6. 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
  7. Method: Chromosome assembly of large and complex genomes using multiple references
    • Mikhail Kolmogorov,
    • Joel Armstrong,
    • Brian J. Raney,
    • Ian Streeter,
    • Matthew Dunn,
    • Fengtang Yang,
    • Duncan Odom,
    • Paul Flicek,
    • Thomas M. Keane,
    • David Thybert,
    • Benedict Paten,
    • and Son Pham
    Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
    OPEN ACCESS ARTICLE
  8. 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
  9. 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
  10. Research: Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes
    • David Thybert,
    • Maša Roller,
    • Fábio C.P. Navarro,
    • Ian Fiddes,
    • Ian Streeter,
    • Christine Feig,
    • David Martin-Galvez,
    • Mikhail Kolmogorov,
    • Václav Janoušek,
    • Wasiu Akanni,
    • Bronwen Aken,
    • Sarah Aldridge,
    • Varshith Chakrapani,
    • William Chow,
    • Laura Clarke,
    • Carla Cummins,
    • Anthony Doran,
    • Matthew Dunn,
    • Leo Goodstadt,
    • Kerstin Howe,
    • Matthew Howell,
    • Ambre-Aurore Josselin,
    • Robert C. Karn,
    • Christina M. Laukaitis,
    • Lilue Jingtao,
    • Fergal Martin,
    • Matthieu Muffato,
    • Stefanie Nachtweide,
    • Michael A. Quail,
    • Cristina Sisu,
    • Mario Stanke,
    • Klara Stefflova,
    • Cock Van Oosterhout,
    • Frederic Veyrunes,
    • Ben Ward,
    • Fengtang Yang,
    • Golbahar Yazdanifar,
    • Amonida Zadissa,
    • David J. Adams,
    • Alvis Brazma,
    • Mark Gerstein,
    • Benedict Paten,
    • Son Pham,
    • Thomas M. Keane,
    • Duncan T. Odom,
    • and Paul Flicek
    Genome Res. April 2018 28: 448-459; Published in Advance March 21, 2018, doi:10.1101/gr.234096.117
    OPEN ACCESS ARTICLE
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