Table of Contents

May 2024; 34 (5)

Mini-Review

  • Toward telomere-to-telomere cat genomes for precision medicine and conservation biology

    • William J. Murphy and
    • Andrew J. Harris
    Genome Res. May 2024 34: 655-664; Published in Advance June 7, 2024, doi:10.1101/gr.278546.123

Research

  • Single-cell spatial transcriptomics reveals a dystrophic trajectory following a developmental bifurcation of myoblast cell fates in facioscapulohumeral muscular dystrophy

    • Lujia Chen,
    • Xiangduo Kong,
    • Kevin G. Johnston,
    • Ali Mortazavi,
    • Todd C. Holmes,
    • Zhiqun Tan,
    • Kyoko Yokomori,
    • and Xiangmin Xu
    Genome Res. May 2024 34: 665-679; Published in Advance May 22, 2024, doi:10.1101/gr.278717.123
    OPEN ACCESS ARTICLE

  • Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer

    • Milad Razavi-Mohseni,
    • Weitai Huang,
    • Yu A. Guo,
    • Dustin Shigaki,
    • Shamaine Wei Ting Ho,
    • Patrick Tan,
    • Anders J. Skanderup,
    • and Michael A. Beer
    Genome Res. May 2024 34: 680-695; Published in Advance May 22, 2024, doi:10.1101/gr.278565.123

  • Neuron-specific chromatin disruption at CpG islands and aging-related regions in Kabuki syndrome mice

    • Leandros Boukas,
    • Teresa Romeo Luperchio,
    • Afrooz Razi,
    • Kasper D. Hansen,
    • and Hans T. Bjornsson
    Genome Res. May 2024 34: 696-710; Published in Advance May 3, 2024, doi:10.1101/gr.278416.123

  • Rapid evolution of piRNA clusters in the Drosophila melanogaster ovary

    • Satyam P. Srivastav,
    • Cédric Feschotte,
    • and Andrew G. Clark
    Genome Res. May 2024 34: 711-724; Published in Advance May 15, 2024, doi:10.1101/gr.278062.123

  • Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)

    • Pengfei Lv,
    • Xingzhuo Yang,
    • Xianguo Zhao,
    • Zhangwu Zhao,
    • and Juan Du
    Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123

  • Semiconservative transmission of DNA N6-adenine methylation in a unicellular eukaryote

    • Yalan Sheng,
    • Yuanyuan Wang,
    • Wentao Yang,
    • Xue Qing Wang,
    • Jiuwei Lu,
    • Bo Pan,
    • Bei Nan,
    • Yongqiang Liu,
    • Fei Ye,
    • Chun Li,
    • Jikui Song,
    • Yali Dou,
    • Shan Gao,
    • and Yifan Liu
    Genome Res. May 2024 34: 740-756; Published in Advance May 14, 2024, doi:10.1101/gr.277843.123

Methods

  • GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes

    • Tomáš Brůna,
    • Alexandre Lomsadze,
    • and Mark Borodovsky
    Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
    OPEN ACCESS ARTICLE

  • BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA

    • Lars Gabriel,
    • Tomáš Brůna,
    • Katharina J. Hoff,
    • Matthis Ebel,
    • Alexandre Lomsadze,
    • Mark Borodovsky,
    • and Mario Stanke
    Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
    OPEN ACCESS ARTICLE

  • Simulation of nanopore sequencing signal data with tunable parameters

    • Hasindu Gamaarachchi,
    • James M. Ferguson,
    • Hiruna Samarakoon,
    • Kisaru Liyanage,
    • and Ira W. Deveson
    Genome Res. May 2024 34: 778-783; Published in Advance May 1, 2024, doi:10.1101/gr.278730.123
    OPEN ACCESS ARTICLE

  • Identifying genes within pathways in unannotated genomes with PaGeSearch

    • Sohyoung Won,
    • Jaewoong Yu,
    • and Heebal Kim
    Genome Res. May 2024 34: 784-795; Published in Advance June 10, 2024, doi:10.1101/gr.278566.123
    OPEN ACCESS ARTICLE

Resource

  • A harmonized public resource of deeply sequenced diverse human genomes

    • Zan Koenig,
    • Mary T. Yohannes,
    • Lethukuthula L. Nkambule,
    • Xuefang Zhao,
    • Julia K. Goodrich,
    • Heesu Ally Kim,
    • Michael W. Wilson,
    • Grace Tiao,
    • Stephanie P. Hao,
    • Nareh Sahakian,
    • Katherine R. Chao,
    • Mark A. Walker,
    • Yunfei Lyu,
    • gnomAD Project Consortium,
    • Heidi L. Rehm,
    • Benjamin M. Neale,
    • Michael E. Talkowski,
    • Mark J. Daly,
    • Harrison Brand,
    • Konrad J. Karczewski,
    • Elizabeth G. Atkinson,
    • and Alicia R. Martin
    Genome Res. May 2024 34: 796-809; Published in Advance May 15, 2024, doi:10.1101/gr.278378.123

Erratum

  • Erratum: Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic

    • Jim Shaw and
    • Yun William Yu
    Genome Res. May 2024 34: 810; doi:10.1101/gr.279618.124
    OPEN ACCESS ARTICLE
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This Issue

May 2024; 34 (5)
Cover
  1. Mini-Review
  2. Research
  3. Methods
  4. Resource
  5. Erratum

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