Searching journal content for Adam Frankish 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. Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    OPEN ACCESS ARTICLE
  3. 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
  4. Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
    • Jonathan M. Mudge,
    • Irwin Jungreis,
    • Toby Hunt,
    • Jose Manuel Gonzalez,
    • James C. Wright,
    • Mike Kay,
    • Claire Davidson,
    • Stephen Fitzgerald,
    • Ruth Seal,
    • Susan Tweedie,
    • Liang He,
    • Robert M. Waterhouse,
    • Yue Li,
    • Elspeth Bruford,
    • Jyoti S. Choudhary,
    • Adam Frankish,
    • and Manolis Kellis
    Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
    OPEN ACCESS ARTICLE
  5. Perspective: Functional transcriptomics in the post-ENCODE era
    • Jonathan M. Mudge,
    • Adam Frankish,
    • and Jennifer Harrow
    Genome Res. December 2013 23: 1961-1973; Published in Advance October 30, 2013, doi:10.1101/gr.161315.113
    OPEN ACCESS ARTICLE
  6. Method: Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome
    • Cédric Howald,
    • Andrea Tanzer,
    • Jacqueline Chrast,
    • Felix Kokocinski,
    • Thomas Derrien,
    • Nathalie Walters,
    • Jose M. Gonzalez,
    • Adam Frankish,
    • Bronwen L. Aken,
    • Thibaut Hourlier,
    • Jan-Hinnerk Vogel,
    • Simon White,
    • Stephen Searle,
    • Jennifer Harrow,
    • Tim J. Hubbard,
    • Roderic Guigó,
    • and Alexandre Reymond
    Genome Res. September 2012 22: 1698-1710; doi:10.1101/gr.134478.111
    OPEN ACCESS ARTICLE
  7. 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
  8. Method: Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and “resurrected” pseudogenes in the mouse genome
    • Markus Brosch,
    • Gary I. Saunders,
    • Adam Frankish,
    • Mark O. Collins,
    • Lu Yu,
    • James Wright,
    • Ruth Verstraten,
    • David J. Adams,
    • Jennifer Harrow,
    • Jyoti S. Choudhary,
    • and Tim Hubbard
    Genome Res. May 2011 21: 756-767; Published in Advance April 1, 2011, doi:10.1101/gr.114272.110
    OPEN ACCESS ARTICLE
  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. ARTICLE: Prominent use of distal 5′ transcription start sites and discovery of a large number of additional exons in ENCODE regions
    • France Denoeud,
    • Philipp Kapranov,
    • Catherine Ucla,
    • Adam Frankish,
    • Robert Castelo,
    • Jorg Drenkow,
    • Julien Lagarde,
    • Tyler Alioto,
    • Caroline Manzano,
    • Jacqueline Chrast,
    • Sujit Dike,
    • Carine Wyss,
    • Charlotte N. Henrichsen,
    • Nancy Holroyd,
    • Mark C. Dickson,
    • Ruth Taylor,
    • Zahra Hance,
    • Sylvain Foissac,
    • Richard M. Myers,
    • Jane Rogers,
    • Tim Hubbard,
    • Jennifer Harrow,
    • Roderic Guigó,
    • Thomas R. Gingeras,
    • Stylianos E. Antonarakis,
    • and Alexandre Reymond
    Genome Res. June 2007 17: 746-759; doi:10.1101/gr.5660607
    OPEN ACCESS ARTICLE
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