Searching journal content for articles similar to Stone and Sidow 15 (7): 978.

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  1. Letter: Evolutionary constraint facilitates interpretation of genetic variation in resequenced human genomes
    • David L. Goode,
    • Gregory M. Cooper,
    • Jeremy Schmutz,
    • Mark Dickson,
    • Eidelyn Gonzales,
    • Ming Tsai,
    • Kalpana Karra,
    • Eugene Davydov,
    • Serafim Batzoglou,
    • Richard M. Myers,
    • and Arend Sidow
    Genome Res. March 2010 20: 301-310; Published in Advance January 12, 2010, doi:10.1101/gr.102210.109
    ...affecting mildly to strongly constrained positions (RS > 1), 78 are nonsynonymous substitutions and 840 are synonymous or noncoding (Fig. 4B; Supplemental Table S2). Noncoding variants are particularly prevalent among sites with weaker constraint, but even among the most constrained positions (RS > 3, N...
  2. 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
    ...from a common ancestor, substitutions compatible with that function are likely to be represented in extant sequences; conversely, conservation among extant homologs implies that evolutionary variation has been consistently rejected owing to functional or structural constraint (Kimura 1983). The logic...
  3. Methods: Identification of deleterious mutations within three human genomes
    • Sung Chun and
    • Justin C. Fay
    Genome Res. September 2009 19: 1553-1561; Published in Advance July 14, 2009, doi:10.1101/gr.092619.109
    ...for the association. A number of methods have been developed to identify deleterious and/or disease-causing mutations within protein-coding sequences. These methods predict whether an amino acid altering mutation is deleterious or disease causing based on physicochemical properties (Grantham1974), population...
  4. Method: A formal perturbation equation between genotype and phenotype determines the Evolutionary Action of protein-coding variations on fitness
    • Panagiotis Katsonis and
    • Olivier Lichtarge
    Genome Res. December 2014 24: 2050-2058; Published in Advance September 12, 2014, doi:10.1101/gr.176214.114
    ...and sporadic cancers. The GAA missense mutations and their Pompe’s disease severity classification were obtained from http://cluster15. erasmusmc.nl/klgn/pompe/mutations.html. The 278,179 human polymorphisms were obtained from the phase 1 analysis of the 1000 Genomes Project, at http://ftp.1000s.ebi.ac.uk/vol1...
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