Searching journal content for articles similar to Gusev et al. 19 (2): 318.

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  1. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ..., or the genetic relatedness matrix (GRM), which stores pairwise genetic similarity based on variants. GLMMs complement this approach by simultaneously accounting for population structure and cryptic relatedness by modeling a random effect whose covariance structure is defined by the estimated GRM. Both PC...
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  2. Method: Leveraging family data to design Mendelian randomization that is provably robust to population stratification
    • Nathan LaPierre,
    • Boyang Fu,
    • Steven Turnbull,
    • Eleazar Eskin,
    • and Sriram Sankararaman
    Genome Res. July 2023 33: 1032-1041; Published in Advance May 17, 2023, doi:10.1101/gr.277664.123
    ...instruments on the exposure coupled with spurious correlation between genetic instruments and confounders (Burgess et al. 2011) can bias the results of MR analyses (“weak instrument bias”). The problem of population stratification has been extensively studied in the Genome-Wide Association Study (GWAS...
  3. Research: Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations
    • Mirte Bosse,
    • Hendrik-Jan Megens,
    • Ole Madsen,
    • Richard P.M.A. Crooijmans,
    • Oliver A. Ryder,
    • Frédéric Austerlitz,
    • Martien A.M. Groenen,
    • and M. Angeles R. de Cara
    Genome Res. July 2015 25: 970-981; Published in Advance June 10, 2015, doi:10.1101/gr.187039.114
    ...Using genome-wide measures of coancestry to maintain diversity and fitness in endangered and domestic pig populations Mirte Bosse 1 , Hendrik-Jan Megens 1 , Ole Madsen 1 , Richard P.M.A. Crooijmans 1 , Oliver A. Ryder 2 , Frédéric...
  4. Research: A genome-wide perspective on the evolutionary history of enigmatic wolf-like canids
    • Bridgett M. vonHoldt,
    • John P. Pollinger,
    • Dent A. Earl,
    • James C. Knowles,
    • Adam R. Boyko,
    • Heidi Parker,
    • Eli Geffen,
    • Malgorzata Pilot,
    • Wlodzimierz Jedrzejewski,
    • Bogumila Jedrzejewska,
    • Vadim Sidorovich,
    • Claudia Greco,
    • Ettore Randi,
    • Marco Musiani,
    • Roland Kays,
    • Carlos D. Bustamante,
    • Elaine A. Ostrander,
    • John Novembre,
    • and Robert K. Wayne
    Genome Res. August 2011 21: 1294-1305; Published in Advance May 12, 2011, doi:10.1101/gr.116301.110
    ...(Supplemental Table S1). Map depicts historic species distributions and admixture zone (data from Nowak 2009; Rutledge et al. 2010b). Genome Research 1295 www..org Genome-wide analysis of enigmatic wolf-like canids We found considerable -wide SNP variation at the population level in graywolves and coyotes...
  5. Research: Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance
    • Yang Xi,
    • Jingjing Qi,
    • Zhao Yang,
    • Yutian Zeng,
    • Huicong Zhang,
    • Qiuyu Tao,
    • Mengru Xu,
    • Anqi Huang,
    • Shenqiang Hu,
    • Chunchun Han,
    • Lili Bai,
    • Jiwei Hu,
    • Jiwen Wang,
    • Liang Li,
    • Lingzhao Fang,
    • and Hehe Liu
    Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124
    ...variance).Genome-wide association studyPopulation structure and cryptic relatedness were used to minimize false positives and to increase statistical power. The mixed linear model program, implemented in Emmax, was used for the association analysis (Kang et al. 2010). The first 10 genotypic PCs derived...
  6. Research: Dynamic evolution of satellite DNAs drastically differentiates the genomes of Tribolium sibling species
    • Damira Veseljak,
    • Evelin Despot-Slade,
    • Marin Volarić,
    • Lucija Horvat,
    • Tanja Vojvoda Zeljko,
    • Nevenka Meštrović,
    • and Brankica Mravinac
    Genome Res. November 2025 35: 2445-2460; Published in Advance September 16, 2025, doi:10.1101/gr.280516.125
    ...).The previously established relatedness between TfSat03 and yp-specific TfSat04 prompted us to investigate their relationship to Cast7 by analyzing randomly selected individual monomer/subunit sequences. The PCA showed that Cast7 monomers intermingle with the clusters of TfSat04 monomers and TfSat03_subunitA (Fig...
  7. Review: Population genetic inference from genomic sequence variation
    • John E. Pool,
    • Ines Hellmann,
    • Jeffrey D. Jensen,
    • and Rasmus Nielsen
    Genome Res. March 2010 20: 291-300; Published in Advance January 12, 2010, doi:10.1101/gr.079509.108
    ..., comparisons of markers with different modes of inheritance, and the distribution of shared haplotype lengths. While population genetic theory once far exceeded the data available to test it, today it is the models and methods that must catch up with the data. Conclusions Genome-wide data are becoming readily...
  8. LETTER: A bimodal pattern of relatedness between the Salmonella Paratyphi A and Typhi genomes: Convergence or divergence by homologous recombination?
    • Xavier Didelot,
    • Mark Achtman,
    • Julian Parkhill,
    • Nicholas R. Thomson,
    • and Daniel Falush
    Genome Res. January 2007 17: 61-68; Published in Advance November 7, 2006, doi:10.1101/gr.5512906
    ...housekeeping gene fragments sequenced from diverse S. enterica to investigate the evolution of these two virulent lineages. Results Genomic pattern of relatedness between Typhi and Paratyphi A Genome-wide recombination patterns were investigated using a novel statistical algorithm that infers genetic exchange...
  9. Resource: GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis
    • Robyn L. Ball,
    • Molly A. Bogue,
    • Hongping Liang,
    • Anuj Srivastava,
    • David G. Ashbrook,
    • Anna Lamoureux,
    • Matthew W. Gerring,
    • Alexander S. Hatoum,
    • Matthew J. Kim,
    • Hao He,
    • Jake Emerson,
    • Alexander K. Berger,
    • David O. Walton,
    • Keith Sheppard,
    • Baha El Kassaby,
    • Francisco Castellanos,
    • Govindarajan Kunde-Ramamoorthy,
    • Lu Lu,
    • John Bluis,
    • Sejal Desai,
    • Beth A. Sundberg,
    • Gary Peltz,
    • Zhuoqing Fang,
    • Gary A. Churchill,
    • Robert W. Williams,
    • Arpana Agrawal,
    • Carol J. Bult,
    • Vivek M. Philip,
    • and Elissa J. Chesler
    Genome Res. January 2024 34: 145-159; Published in Advance January 30, 2024, doi:10.1101/gr.278157.123
    ...of Psychiatry, Washington University School of Medicine, St. Louis, Missouri 63110, USA Corresponding author: Robyn.Ball@jax.orgAbstractHundreds of inbred mouse strains and intercross populations have been used to characterize the function of genetic variants that contribute to disease. Thousands of disease...
    OPEN ACCESS ARTICLE
  10. Research: Founder population-specific HapMap panel increases power in GWA studies through improved imputation accuracy and CNV tagging
    • Ida Surakka,
    • Kati Kristiansson,
    • Verneri Anttila,
    • Michael Inouye,
    • Chris Barnes,
    • Loukas Moutsianas,
    • Veikko Salomaa,
    • Mark Daly,
    • Aarno Palotie,
    • Leena Peltonen,
    • and Samuli Ripatti
    Genome Res. October 2010 20: 1344-1351; Published in Advance September 1, 2010, doi:10.1101/gr.106534.110
    ...Department of Medical Genetics, University of Helsinki, Helsinki University Hospital, FI-00014 Helsinki, Finland ↵ 10 These authors contributed equally to this work. Abstract The combining of genome-wide association (GWA) data across populations represents a major challenge...
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