Searching journal content for articles similar to Perszyk et al. 31 (8): 1447.

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  1. Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
    • Shuai Wang,
    • Merritt Khaipho-Burch,
    • Lynn C. Johnson,
    • Zachary R. Miller,
    • Peter J. Bradbury,
    • Doug Speed,
    • William J. Allen,
    • M. Cinta Romay,
    • Jiquan Xue,
    • Edward S. Buckler,
    • Guillaume P. Ramstein,
    • and Baoxing Song
    Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
    ...functional molecules. The biological function of a given protein is dictated by the arrangement of the atoms and functional groups in its three-dimensional (3D) structure. Therefore, variation in protein 3D structure is an essential source of information to explain how coding sequence variants impact gene...
  2. 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
    ...-RVIS (Gussow et al. 2016) for when there is limited resolution in the sequence region of interest. This approach uses the observed to expected missense ratio in a domain (OE-ratio), which is equivalent to a domain-based missense tolerance ratio (MTR) (Traynelis et al. 2017). In short, the expected rate...
  3. Perspective: Genomic approaches for understanding the genetics of complex disease
    • William L. Lowe, Jr. and
    • Timothy E. Reddy
    Genome Res. October 2015 25: 1432-1441; doi:10.1101/gr.190603.115
    ...with specific histone modifications, may be more likely to alter regulatory element activity. Another possibility is that the three-dimensional structure of the will help tomodel genetic effects on target gene expression. Early indications suggest that prioritization based on such models will be helpful...
    OPEN ACCESS ARTICLE
  4. Resource: ProPhylER: A curated online resource for protein function and structure based on evolutionary constraint analyses
    • Jonathan Binkley,
    • Kalpana Karra,
    • Andrew Kirby,
    • Midori Hosobuchi,
    • Eric A. Stone,
    • and Arend Sidow
    Genome Res. January 2010 20: 142-154; Published in Advance October 21, 2009, doi:10.1101/gr.097121.109
    ...protein, the TP53 (also known as p53) tumor suppressor, has many thousands of documented cancerassociated somatic missense mutations (Hollstein et al. 1994; Olivier et al. 2002). The phenotype information associated with the five data sets allowed us to generate numerical scores reflecting the tolerance...
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