Searching journal content for Jonathan Mudge 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: Ribosome decision graphs for the representation of eukaryotic RNA translation complexity
    • Jack A.S. Tierney,
    • Michał Świrski,
    • Håkon Tjeldnes,
    • Jonathan M. Mudge,
    • Joanna Kufel,
    • Nicola Whiffin,
    • Eivind Valen,
    • and Pavel V. Baranov
    Genome Res. April 2024 34: 530-538; Published in Advance May 7, 2024, doi:10.1101/gr.278810.123
    OPEN ACCESS ARTICLE
  3. 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
  4. 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
  5. 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
  6. LETTER: Neocentromeres in 15q24-26 Map to Duplicons Which Flanked an Ancestral Centromere in 15q25
    • Mario Ventura,
    • Jonathan M. Mudge,
    • Valeria Palumbo,
    • Sally Burn,
    • Elisabeth Blennow,
    • Mauro Pierluigi,
    • Roberto Giorda,
    • Orsetta Zuffardi,
    • Nicoletta Archidiacono,
    • Michael S. Jackson,
    • and Mariano Rocchi
    Genome Res. September 2003 13: 2059-2068; Published in Advance January 1, 2003, doi:10.1101/gr.1155103
  7. ARTICLE: Genomic Sequence and Transcriptional Profile of the Boundary Between Pericentromeric Satellites and Genes on Human Chromosome Arm 10p
    • Jane Guy,
    • Tom Hearn,
    • Moira Crosier,
    • Jonathan Mudge,
    • Luigi Viggiano,
    • Dirk Koczan,
    • Hans-Jurgen Thiesen,
    • Jeffrey A. Bailey,
    • Julie E. Horvath,
    • Evan E. Eichler,
    • Mark E. Earthrowl,
    • Panos Deloukas,
    • Lisa French,
    • Jane Rogers,
    • David Bentley,
    • and Michael S. Jackson
    Genome Res. February 1, 2003 13: 159-172; Published in Advance January 14, 2003, doi:10.1101/gr.644503
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