Searching journal content for articles similar to Thybert et al. 28 (4): 448.

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  1. Method: Chromosome assembly of large and complex genomes using multiple references
    • Mikhail Kolmogorov,
    • Joel Armstrong,
    • Brian J. Raney,
    • Ian Streeter,
    • Matthew Dunn,
    • Fengtang Yang,
    • Duncan Odom,
    • Paul Flicek,
    • Thomas M. Keane,
    • David Thybert,
    • Benedict Paten,
    • and Son Pham
    Genome Res. November 2018 28: 1720-1732; Published in Advance October 19, 2018, doi:10.1101/gr.236273.118
    ...for resolving complicated genomic structures, such as repeats or low-coverage regions. This technique was implemented in a number of assemblers/scaffolders (Zerbino and Birney 2008; Peng et al. 2010; Gnerre et al. 2011; Iqbal et al. 2012) and proved to be valuable when a close reference is available. Another...
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  2. Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
    • Ian T. Fiddes,
    • Joel Armstrong,
    • Mark Diekhans,
    • Stefanie Nachtweide,
    • Zev N. Kronenberg,
    • Jason G. Underwood,
    • David Gordon,
    • Dent Earl,
    • Thomas Keane,
    • Evan E. Eichler,
    • David Haussler,
    • Mario Stanke,
    • and Benedict Paten
    Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
    ...-project/). These projects will provide a new understanding of gene evolution.MethodsCAT produces as output a series of diagnostic plots, an annotation set for each target , and a UCSC comparative assembly hub (Nguyen et al. 2014). Both the pipeline and associated documentation can be found at https://github.com/ComparativeGenomics...
  3. Research: Diversity, duplication, and genomic organization of homeobox genes in Lepidoptera
    • Peter O. Mulhair,
    • Liam Crowley,
    • Douglas H. Boyes,
    • Amber Harper,
    • Owen T. Lewis,
    • Darwin Tree of Life Consortium,
    • and Peter W.H. Holland
    Genome Res. January 2023 33: 32-44; Published in Advance December 8, 2022, doi:10.1101/gr.277118.122
    ...homologous recombination, resulting in segmental duplications and gene cluster expansions (Startek et al. 2015; Janoušek et al. 2016; Thybert et al. 2018). Repeat content across the whole s of 66 representative species was estimated using a combination of RepeatModeler and RepeatMasker pipelines (see Methods...
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  4. 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
    ...to mammalian geneticists (Chang et al. 2017, Poltorak et al. 2018), represent different Mus species; namely, Mus pahari, Mus caroli, and Mus spretus. They are distinct from the most deeply characterized M. musculus domesticus strains, which include classical inbred strains, many of which have been sequenced...
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  5. Research: De novo transcriptome assembly of mouse male germ cells reveals novel genes, stage-specific bidirectional promoter activity, and noncoding RNA expression
    • Mark E. Gill,
    • Alexia Rohmer,
    • Serap Erkek-Ozhan,
    • Ching-Yeu Liang,
    • Sunwoo Chun,
    • Evgeniy A. Ozonov,
    • and Antoine H.F.M. Peters
    Genome Res. December 2023 33: 2060-2078; Published in Advance December 21, 2023, doi:10.1101/gr.278060.123
    ...findings suggest selection against a major role for repeat elements in testicular gene regulation and evolution. In contrast, monoexonic transcripts and multiexonic transcripts overlapping repeats in exons other than their first represent 8.4% and 39.0% of all identified genes, similar to what would...
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