Searching journal content for articles similar to Parts et al. 24 (8): 1363.

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  1. 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
    .... 2023).The phylogenetic trees also provide a rich genomic landscape to explore possible regions of cryptic genetic variation among strains; namely, variation that may have little effect on phenotypic variation within populations but may contribute to trait heritability across populations (Paaby...
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  2. Research: Variation in histone configurations correlates with gene expression across nine inbred strains of mice
    • Anna L Tyler,
    • Catrina Spruce,
    • Romy Kursawe,
    • Annat Haber,
    • Robyn L Ball,
    • Wendy A Pitman,
    • Alexander D Fine,
    • Narayanan Raghupathy,
    • Michael Walker,
    • Vivek M Philip,
    • Christopher L Baker,
    • J. Matthew Mahoney,
    • Gary A. Churchill,
    • Jennifer J Trowbridge,
    • Michael L Stitzel,
    • Kenneth Paigen,
    • Petko M Petkov,
    • and Gregory W Carter
    Genome Res. May 22, 2023 gr.277467.122; Published in Advance May 22, 2023, doi:10.1101/gr.277467.122
    ...and was associated with variation in gene expression across strains. We found that epigenetic24 state imputed into a population of DO mice recapitulated the association with gene expression25 seen in the founders suggesting that both histone modifications and DNA methylation are highly26 heritable mechanisms of gene...
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  3. Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
    • Wen Huang,
    • Andreas Massouras,
    • Yutaka Inoue,
    • Jason Peiffer,
    • Miquel Ràmia,
    • Aaron M. Tarone,
    • Lavanya Turlapati,
    • Thomas Zichner,
    • Dianhui Zhu,
    • Richard F. Lyman,
    • Michael M. Magwire,
    • Kerstin Blankenburg,
    • Mary Anna Carbone,
    • Kyle Chang,
    • Lisa L. Ellis,
    • Sonia Fernandez,
    • Yi Han,
    • Gareth Highnam,
    • Carl E. Hjelmen,
    • John R. Jack,
    • Mehwish Javaid,
    • Joy Jayaseelan,
    • Divya Kalra,
    • Sandy Lee,
    • Lora Lewis,
    • Mala Munidasa,
    • Fiona Ongeri,
    • Shohba Patel,
    • Lora Perales,
    • Agapito Perez,
    • LingLing Pu,
    • Stephanie M. Rollmann,
    • Robert Ruth,
    • Nehad Saada,
    • Crystal Warner,
    • Aneisa Williams,
    • Yuan-Qing Wu,
    • Akihiko Yamamoto,
    • Yiqing Zhang,
    • Yiming Zhu,
    • Robert R.H. Anholt,
    • Jan O. Korbel,
    • David Mittelman,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Antonio Barbadilla,
    • J. Spencer Johnston,
    • Eric A. Stone,
    • Stephen Richards,
    • Bart Deplancke,
    • and Trudy F.C. Mackay
    Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
    ...to improve our understanding of the effects of naturally occurring genetic variation on molecular and organismal phenotypes. We used an integrated genotyping strategy to identify 4,853,802 single nucleotide polymorphisms (SNPs) and 1,296,080 non-SNP variants. Our molecular population genomic analyses show...
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  4. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...exon, altering only the 3′ UTR sequence while leaving the protein-coding sequence unchanged. Because the 3′ UTR contains many essential regulatory elements—such as microRNA and RNA-binding protein (RBP) binding sites—variation in 3′ UTR length can modulate target mRNA function, stability...
  5. Mini-Review: Large-scale genomic analysis of the domestic dog informs biological discovery
    • Reuben M. Buckley and
    • Elaine A. Ostrander
    Genome Res. June 2024 34: 811-821; Published in Advance July 2, 2024, doi:10.1101/gr.278569.123
    ...coefficients, calculated as the fraction of the within runs of homozygosity, can also indicate the diversity of the population from which a dog was sampled. For inbred populations, the landscape of common variation can be captured with fewer samples than in outbred populations. Importantly, dogs in groups 2, 3...
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  6. Research: Genetic analysis in the Collaborative Cross breeding population
    • Vivek M. Philip,
    • Greta Sokoloff,
    • Cheryl L. Ackert-Bicknell,
    • Martin Striz,
    • Lisa Branstetter,
    • Melissa A. Beckmann,
    • Jason S. Spence,
    • Barbara L. Jackson,
    • Leslie D. Galloway,
    • Paul Barker,
    • Ann M. Wymore,
    • Patricia R. Hunsicker,
    • David C. Durtschi,
    • Ginger S. Shaw,
    • Sarah Shinpock,
    • Kenneth F. Manly,
    • Darla R. Miller,
    • Kevin D. Donohue,
    • Cymbeline T. Culiat,
    • Gary A. Churchill,
    • William R. Lariviere,
    • Abraham A. Palmer,
    • Bruce F. O'Hara,
    • Brynn H. Voy,
    • and Elissa J. Chesler
    Genome Res. August 2011 21: 1223-1238; Published in Advance July 6, 2011, doi:10.1101/gr.113886.110
    ...effects underlying QTLs. Our analyses address phenotypic diversity, heritability, and genetic mapping and reveal the impact of novel allelic combinations in this population. Results Variation in breeding productivity and fecundity in the Collaborative Cross A total of 650 CC lines were initiated at ORNL...
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  7. Resource: Genetic dissection of a model complex trait using the Drosophila Synthetic Population Resource
    • Elizabeth G. King,
    • Chris M. Merkes,
    • Casey L. McNeil,
    • Steven R. Hoofer,
    • Saunak Sen,
    • Karl W. Broman,
    • Anthony D. Long,
    • and Stuart J. Macdonald
    Genome Res. August 2012 22: 1558-1566; Published in Advance April 10, 2012, doi:10.1101/gr.134031.111
    ...genetic variation in genome-wide association studies (GWAS). Thus, much of the heritability remains unexplained for most complex traits. Here we describe a novel, freely available resource for the Drosophila community consisting of two sets of recombinant inbred lines (RILs), each derived from...
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  8. Method: Revealing the genetic structure of a trait by sequencing a population under selection
    • Leopold Parts,
    • Francisco A. Cubillos,
    • Jonas Warringer,
    • Kanika Jain,
    • Francisco Salinas,
    • Suzannah J. Bumpstead,
    • Mikael Molin,
    • Amin Zia,
    • Jared T. Simpson,
    • Michael A. Quail,
    • Alan Moses,
    • Edward J. Louis,
    • Richard Durbin,
    • and Gianni Liti
    Genome Res. July 2011 21: 1131-1138; Published in Advance March 21, 2011, doi:10.1101/gr.116731.110
    ...of standing variation segregating in the pool. Therefore, we have the potential to establish an artificial outbred yeast population that can be used as a model for natural diploid wide association studies as carried out in humans. Methods Intercross Parental strains YPS128 (MATa, hoTHphMX4, ura3TKanMX4...
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  9. REVIEW: The influence of genetic variation on gene expression
    • Rohan B.H. Williams,
    • Eva K.F. Chan,
    • Mark J. Cowley,
    • and Peter F.R. Little
    Genome Res. December 2007 17: 1707-1716; doi:10.1101/gr.6981507
    ...The influence of genetic variation on gene expression Rohan B.H. Williams 1 , 2 , 3 , 4 , Eva K.F. Chan 1 , 3 , 5 , Mark J. Cowley 1 , 4 , and Peter F.R. Little 1 , 6 1 School of Biotechnology and Biomolecular Sciences...
  10. LETTER: Genetic Variation in Coding Regions Between and Within Commonly Used Inbred Rat Strains
    • Bart M.G. Smits,
    • Bert F.M. van Zutphen,
    • Ronald H.A. Plasterk,
    • and Edwin Cuppen
    Genome Res. July 2004 14: 1285-1290; doi:10.1101/gr.2155004
    ...populations. Their significance is illustrated by their potential contribution to common disease but also by their potential for use in genetic association and mapping experiments. We have examined the genetic variation between commonly used inbred rat strains by using an efficient SNP discovery and typing...
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