Searching journal content for articles similar to Kumar et al. 19 (9): 1562.

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  1. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...processes of selection on somatic mutations, driving tumor growth through aberrant regulation of the cell cycle. Somatic mutations caused by multiple endogenous and exogenous factors are mostly neutral passengers, with only a few drivers of clonal expansion under strong positive selection. Cancer genomic...
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  2. 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
    ...with small gradients strongly favor substitutions to large polar or charged amino acids (Fig. 1C). These trends are specific to every amino acid pair: Alanine to valine substitution odds form a bell-shaped distribution as the evolutionary gradient at the mutated position varies from minimum to maximum; those...
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  3. Research: Loss of exon identity is a common mechanism of human inherited disease
    • Timothy Sterne-Weiler,
    • Jonathan Howard,
    • Matthew Mort,
    • David N. Cooper,
    • and Jeremy R. Sanford
    Genome Res. October 2011 21: 1563-1571; Published in Advance July 12, 2011, doi:10.1101/gr.118638.110
    ...by disease-causing mutations share hallmarks of functional splicing enhancers Since evolutionary conservationusually implies functionality (Boffelli et al. 2003; Margulies et al. 2003; Siepel et al. 2005), we opted to determine whether there was a difference in average evolutionary conservation between those...
  4. Perspective: Human genomic disease variants: A neutral evolutionary explanation
    • Joel T. Dudley,
    • Yuseob Kim,
    • Li Liu,
    • Glenn J. Markov,
    • Kristyn Gerold,
    • Rong Chen,
    • Atul J. Butte,
    • and Sudhir Kumar
    Genome Res. August 2012 22: 1383-1394; Published in Advance June 4, 2012, doi:10.1101/gr.133702.111
    ...). These footprints of neutral evolutionary processes in personal exomes ultimately shape the allele frequencies of nSNVs in populations (Fig. 3). Furthermore, it is expected that the balance between mutations and purifying selection across the human will result in rare minor alleles at the majority of polymorphic...
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