Searching journal content for articles similar to Traynelis et al. 27 (10): 1715.

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  1. Method: Three-dimensional missense tolerance ratio analysis
    • Riley E. Perszyk,
    • Anders S. Kristensen,
    • Polina Lyuboslavsky,
    • and Stephen F. Traynelis
    Genome Res. August 2021 31: 1447-1461; Published in Advance July 22, 2021, doi:10.1101/gr.275528.121
    ...of the missense tolerance ratio (MTR). The MTR was defined as a running average over some number (typically 31) of adjacent residues in the polypeptide chain of the ratio of observed to expected variants (Traynelis et al. 2017). The intended function of the MTR is readily observed in the GRIN gene family, which...
  2. Method: Identification of pathogenic variant enriched regions across genes and gene families
    • Eduardo Pérez-Palma,
    • Patrick May,
    • Sumaiya Iqbal,
    • Lisa-Marie Niestroj,
    • Juanjiangmeng Du,
    • Henrike O. Heyne,
    • Jessica A. Castrillon,
    • Anne O'Donnell-Luria,
    • Peter Nürnberg,
    • Aarno Palotie,
    • Mark Daly,
    • and Dennis Lal
    Genome Res. January 2020 30: 62-71; Published in Advance December 23, 2019, doi:10.1101/gr.252601.119
    .... 2011). Still, variant interpretation remains challenging (Gilissen et al. 2012) particularly for missense variants—the most prevalent genomic alteration, with 10,000 to 12,000 events per individual (The 1000 Genomes Project Consortium 2015). Protein truncating variants (PTVs) and large deletions...
  3. Method: Genetic variant pathogenicity prediction trained using disease-specific clinical sequencing data sets
    • Perry Evans,
    • Chao Wu,
    • Amanda Lindy,
    • Dianalee A. McKnight,
    • Matthew Lebo,
    • Mahdi Sarmady,
    • and Ahmad N. Abou Tayoun
    Genome Res. July 2019 29: 1144-1151; Published in Advance June 24, 2019, doi:10.1101/gr.240994.118
    ..., Berkovic SF, Liu L, Ascher DB, Balding DJ, Petrovski S. 2017. Optimizing genomic medicine in epilepsy through a gene-customized approach to missense variant interpretation. Genome Res 27: 1715–1729. doi:10.1101/gr.226589.117 ↵The UniProt Consortium. 2017. UniProt: the universal protein knowledgebase...
  4. Method: A new approach for rare variation collapsing on functional protein domains implicates specific genic regions in ALS
    • Sahar Gelfman,
    • Sarah Dugger,
    • Cristiane de Araujo Martins Moreno,
    • Zhong Ren,
    • Charles J. Wolock,
    • Neil A. Shneider,
    • Hemali Phatnani,
    • Elizabeth T. Cirulli,
    • Brittany N. Lasseigne,
    • Tim Harris,
    • Tom Maniatis,
    • Guy A. Rouleau,
    • Robert H. Brown, Jr,
    • Aaron D. Gitler,
    • Richard M. Myers,
    • Slavé Petrovski,
    • Andrew Allen,
    • David B. Goldstein,
    • and Matthew B. Harms
    Genome Res. May 2019 29: 809-818; Published in Advance April 2, 2019, doi:10.1101/gr.243592.118
    ...in which the unit for collapsing is the entire gene, yet missense variants only qualify for the analysis if they reside in domains that are intolerant to variation (domain 1 and 3). Loss-of-function variants (big circles) continue to qualify regardless of whether they reside in a tolerant or intolerant...
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