Searching journal content for articles similar to Ng and Henikoff 11 (5): 863.

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  1. Method: Greater strength of selection and higher proportion of beneficial amino acid changing mutations in humans compared with mice and Drosophila melanogaster
    • Ying Zhen,
    • Christian D. Huber,
    • Robert W. Davies,
    • and Kirk E. Lohmueller
    Genome Res. January 2021 31: 110-120; Published in Advance November 18, 2020, doi:10.1101/gr.256636.119
    ...), despite the use of different analytical approaches. α is expected to be lower on the human lineage compared with the chimpanzee or macaque lineage owing to the higher proportion of weakly deleterious amino acid substitutions on the human lineage to their smaller population size (Ohta 1973, 1992). For D...
  2. Resource: The SynMall resource for characterizing the functional impact of synonymous variation
    • Chen Ye,
    • Xiaoyan Li,
    • Na Cheng,
    • Yansen Su,
    • and Junfeng Xia
    Genome Res. February 2026 36: 421-431; Published in Advance December 17, 2025, doi:10.1101/gr.281257.125
    ...with synVep (Zeng et al. 2021), in which mRNA stability features show limited predictive power. At the protein level, pseudo-K-tuple-reduced amino acid composition (PseKRAAC) and absolute solvent accessibility differ between pathogenic and benign variants (Fig. 2D), consistent with findings from reg...
  3. LETTER: Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome
    • Peter Andolfatto
    Genome Res. December 2007 17: 1755-1762; Published in Advance November 7, 2007, doi:10.1101/gr.6691007
    ...predict a similar correlation between levels of synonymous diversity and rates of amino acid evolution. Results Reduced synonymous site diversity at rapidly evolving proteins To detect predicted hitchhiking effects associated with recurrent fixation of beneficial amino acid substitutions, I surveyed...
  4. 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
    ...functional diversification during evolution. In this study, we seek to identify the diversification and potential gene neofunctionalization of lung tumors in the TRACERx cohort. We develop a novel computational protocol to identify preduplication and postduplication mutations predicted to affect protein...
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  5. 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
    ...line B73 and the 25 other NAM founder lines. Whether AlphaFold2 can predict the effects of single amino-acid polymorphisms (SAPs) is controversial (Stein and Mchaourab 2024), so we first compared the protein sequence from the same core pangene group to characterize the sequence diversity of orthologous...
  6. Research: Common cis-regulatory variation modifies the penetrance of pathogenic SHROOM3 variants in craniofacial microsomia
    • Hao Zhu,
    • Jiao Zhang,
    • Soumya Rao,
    • Matthew D. Durbin,
    • Ying Li,
    • Ruirui Lang,
    • Jiqiang Liu,
    • Baichuan Xiao,
    • Hailin Shan,
    • Ziqiu Meng,
    • Jinmo Wang,
    • Xiaokai Tang,
    • Zhenni Shi,
    • Liza L. Cox,
    • Shouqin Zhao,
    • Stephanie M. Ware,
    • Tiong Y. Tan,
    • Michelle de Silva,
    • Lyndon Gallacher,
    • Ting Liu,
    • Jie Mi,
    • Changqing Zeng,
    • Hou-Feng Zheng,
    • Qingguo Zhang,
    • Stylianos E. Antonarakis,
    • Timothy C. Cox,
    • and Yong-Biao Zhang
    Genome Res. May 2025 35: 1065-1079; Published in Advance April 15, 2025, doi:10.1101/gr.280047.124
    ..., 2625 healthy Chinese individuals from the SG10K data set (Wu et al. 2019). Previous association studies had identified several CFM-related risk genes (Zhang et al. 2016; Xu et al. 2021). Initially, we focused our efforts on interrogating the predicted deleterious variants within risk genes directly...
  7. Research: Predicting the virulence of MRSA from its genome sequence
    • Maisem Laabei,
    • Mario Recker,
    • Justine K. Rudkin,
    • Mona Aldeljawi,
    • Zeynep Gulay,
    • Tim J. Sloan,
    • Paul Williams,
    • Jennifer L. Endres,
    • Kenneth W. Bayles,
    • Paul D. Fey,
    • Vijaya Kumar Yajjala,
    • Todd Widhelm,
    • Erica Hawkins,
    • Katie Lewis,
    • Sara Parfett,
    • Lucy Scowen,
    • Sharon J. Peacock,
    • Matthew Holden,
    • Daniel Wilson,
    • Timothy D. Read,
    • Jean van den Elsen,
    • Nicholas K. Priest,
    • Edward J. Feil,
    • Laurence D. Hurst,
    • Elisabet Josefsson,
    • and Ruth C. Massey
    Genome Res. May 2014 24: 839-849; Published in Advance April 9, 2014, doi:10.1101/gr.165415.113
    ...Predicting the virulence of MRSA from its genome sequence Maisem Laabei 1 , 11 , Mario Recker 2 , 11 , Justine K. Rudkin 1 , Mona Aldeljawi 1 , Zeynep Gulay 3 , Tim J. Sloan 4 , Paul Williams 4 , Jennifer L...
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  8. 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...
  9. Research: Interlocus gene conversion events introduce deleterious mutations into at least 1% of human genes associated with inherited disease
    • Claudio Casola,
    • Ugne Zekonyte,
    • Andrew D. Phillips,
    • David N. Cooper,
    • and Matthew W. Hahn
    Genome Res. March 2012 22: 429-435; Published in Advance November 16, 2011, doi:10.1101/gr.127738.111
    ...-associatedmutations in;1% of analyzed human genes. In addition, we predict thousands of potential IGC-mediated amino acid replacements with deleterious effects in almost 900 different human genes, 158 of which have already been implicated in human disease. Results and Discussion Pathological mutations derived from...
  10. Research: Genome-wide patterns of selection–drift variation strongly associate with organismal traits across the green plant lineage
    • Kavitha Uthanumallian,
    • Andrea Del Cortona,
    • Susana M. Coelho,
    • Olivier De Clerck,
    • Sebastian Duchene,
    • and Heroen Verbruggen
    Genome Res. August 2024 34: 1130-1139; Published in Advance August 29, 2024, doi:10.1101/gr.279002.124
    ...).DiscussionBody architecture strongly correlates with molecular evolutionThe influence of effective population size on the efficacy of purifying selection, imposing constraints on amino acid-altering nonsynonymous substitutions, is supported by both theoretical and empirical work (Ohta 1992; Moran 1996...
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