Searching journal content for Adam M. Phillippy 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. Method: Verkko2 integrates proximity-ligation data with long-read De Bruijn graphs for efficient telomere-to-telomere genome assembly, phasing, and scaffolding
    • Dmitry Antipov,
    • Mikko Rautiainen,
    • Sergey Nurk,
    • Brian P. Walenz,
    • Steven J. Solar,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. July 2025 35: 1583-1594; Published in Advance May 19, 2025, doi:10.1101/gr.280383.124
    OPEN ACCESS ARTICLE
  3. Method: Gapless assembly of complete human and plant chromosomes using only nanopore sequencing
    • Sergey Koren,
    • Zhigui Bao,
    • Andrea Guarracino,
    • Shujun Ou,
    • Sara Goodwin,
    • Katharine M. Jenike,
    • Julian Lucas,
    • Brandy McNulty,
    • Jimin Park,
    • Mikko Rautiainen,
    • Arang Rhie,
    • Dick Roelofs,
    • Harrie Schneiders,
    • Ilse Vrijenhoek,
    • Koen Nijbroek,
    • Olle Nordesjo,
    • Sergey Nurk,
    • Mike Vella,
    • Katherine R. Lawrence,
    • Doreen Ware,
    • Michael C. Schatz,
    • Erik Garrison,
    • Sanwen Huang,
    • William Richard McCombie,
    • Karen H. Miga,
    • Alexander H.J. Wittenberg,
    • and Adam M. Phillippy
    Genome Res. November 2024 34: 1919-1930; Published in Advance November 6, 2024, doi:10.1101/gr.279334.124
  4. Resource: The genome of the colonial hydroid Hydractinia reveals that their stem cells use a toolkit of evolutionarily shared genes with all animals
    • Christine E. Schnitzler,
    • E. Sally Chang,
    • Justin Waletich,
    • Gonzalo Quiroga-Artigas,
    • Wai Yee Wong,
    • Anh-Dao Nguyen,
    • Sofia N. Barreira,
    • Liam B. Doonan,
    • Paul Gonzalez,
    • Sergey Koren,
    • James M. Gahan,
    • Steven M. Sanders,
    • Brian Bradshaw,
    • Timothy Q. DuBuc,
    • Febrimarsa,
    • Danielle de Jong,
    • Eric P. Nawrocki,
    • Alexandra Larson,
    • Samantha Klasfeld,
    • Sebastian G. Gornik,
    • R. Travis Moreland,
    • Tyra G. Wolfsberg,
    • Adam M. Phillippy,
    • James C. Mullikin,
    • Oleg Simakov,
    • Paulyn Cartwright,
    • Matthew Nicotra,
    • Uri Frank,
    • and Andreas D. Baxevanis
    Genome Res. March 2024 34: 498-513; Published in Advance March 20, 2024, doi:10.1101/gr.278382.123
    OPEN ACCESS ARTICLE
  5. 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
  6. Method: HiCanu: accurate assembly of segmental duplications, satellites, and allelic variants from high-fidelity long reads
    • Sergey Nurk,
    • Brian P. Walenz,
    • Arang Rhie,
    • Mitchell R. Vollger,
    • Glennis A. Logsdon,
    • Robert Grothe,
    • Karen H. Miga,
    • Evan E. Eichler,
    • Adam M. Phillippy,
    • and Sergey Koren
    Genome Res. September 2020 30: 1291-1305; Published in Advance August 14, 2020, doi:10.1101/gr.263566.120
    OPEN ACCESS ARTICLE
  7. Method: Canu: scalable and accurate long-read assembly via adaptive k-mer weighting and repeat separation
    • Sergey Koren,
    • Brian P. Walenz,
    • Konstantin Berlin,
    • Jason R. Miller,
    • Nicholas H. Bergman,
    • and Adam M. Phillippy
    Genome Res. May 2017 27: 722-736; Published in Advance March 15, 2017, doi:10.1101/gr.215087.116
    OPEN ACCESS ARTICLE
  8. Editorial: New advances in sequence assembly
    • Adam M. Phillippy
    Genome Res. May 2017 27: xi-xiii; doi:10.1101/gr.223057.117
    OPEN ACCESS ARTICLE
  9. 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
  10. Resource: GAGE: A critical evaluation of genome assemblies and assembly algorithms
    • Steven L. Salzberg,
    • Adam M. Phillippy,
    • Aleksey Zimin,
    • Daniela Puiu,
    • Tanja Magoc,
    • Sergey Koren,
    • Todd J. Treangen,
    • Michael C. Schatz,
    • Arthur L. Delcher,
    • Michael Roberts,
    • Guillaume Marçais,
    • Mihai Pop,
    • and James A. Yorke
    Genome Res. March 2012 22: 557-567; Published in Advance December 6, 2011, doi:10.1101/gr.131383.111
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