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Current Issue of Genome Research

Table of Contents — February 2025, 35 (2)

Table of Contents

February 2025; 35 (2)

Review

  • k-mer approaches for biodiversity genomics

    • Katharine M. Jenike,
    • Lucía Campos-Domínguez,
    • Marilou Boddé,
    • José Cerca,
    • Christina N. Hodson,
    • Michael C. Schatz,
    • and Kamil S. Jaron
    Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
    OPEN ACCESS ARTICLE

Research

  • Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations

    • Mikkel Dahl-Jessen,
    • Thorkild Terkelsen,
    • Rasmus O. Bak,
    • and Uffe Birk Jensen
    Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123

  • Aberrant homeodomain–DNA cooperative dimerization underlies distinct developmental defects in two dominant CRX retinopathy models

    • Yiqiao Zheng,
    • Gary D. Stormo,
    • and Shiming Chen
    Genome Res. February 2025 35: 242-256; Published in Advance December 23, 2024, doi:10.1101/gr.279340.124
    OPEN ACCESS ARTICLE

  • Ultraviolet damage and repair maps in Drosophila reveal the impact of domain-specific changes in nucleosome repeat length on repair efficiency

    • Benjamin Morledge-Hampton,
    • Kathiresan Selvam,
    • Manish Chauhan,
    • Alan G. Goodman,
    • and John J. Wyrick
    Genome Res. February 2025 35: 257-267; Published in Advance January 6, 2025, doi:10.1101/gr.279605.124

  • Timescale and genetic linkage explain the variable impact of defense systems on horizontal gene transfer

    • Yang Liu,
    • João Botelho,
    • and Jaime Iranzo
    Genome Res. February 2025 35: 268-278; Published in Advance January 10, 2025, doi:10.1101/gr.279300.124
    OPEN ACCESS ARTICLE

Methods

  • Identification of the shortest species-specific oligonucleotide sequences

    • Ioannis Mouratidis,
    • Maxwell A. Konnaris,
    • Nikol Chantzi,
    • Candace S.Y. Chan,
    • Michail Patsakis,
    • Kimonas Provatas,
    • Austin Montgomery,
    • Fotis A. Baltoumas,
    • Congzhou M. Sha,
    • Manvita Mareboina,
    • Georgios A. Pavlopoulos,
    • Dionysios V. Chartoumpekis,
    • and Ilias Georgakopoulos-Soares
    Genome Res. February 2025 35: 279-295; Published in Advance January 2, 2025, doi:10.1101/gr.280070.124
    OPEN ACCESS ARTICLE

  • Interactive visualization and interpretation of pangenome graphs by linear reference–based coordinate projection and annotation integration

    • Zepu Miao and
    • Jia-Xing Yue
    Genome Res. February 2025 35: 296-310; Published in Advance January 13, 2025, doi:10.1101/gr.279461.124
    OPEN ACCESS ARTICLE

  • Combining DNA and protein alignments to improve genome annotation with LiftOn

    • Kuan-Hao Chao,
    • Jakob M. Heinz,
    • Celine Hoh,
    • Alan Mao,
    • Alaina Shumate,
    • Mihaela Pertea,
    • and Steven L. Salzberg
    Genome Res. February 2025 35: 311-325; Published in Advance December 27, 2024, doi:10.1101/gr.279620.124

  • Proxy panels enable privacy-aware outsourcing of genotype imputation

    • Degui Zhi,
    • Xiaoqian Jiang,
    • and Arif Harmanci
    Genome Res. February 2025 35: 326-339; Published in Advance January 10, 2025, doi:10.1101/gr.278934.124
    OPEN ACCESS ARTICLE

  • Diffusion-based generation of gene regulatory networks from scRNA-seq data with DigNet

    • Chuanyuan Wang and
    • Zhi-Ping Liu
    Genome Res. February 2025 35: 340-354; Published in Advance December 18, 2024, doi:10.1101/gr.279551.124
    OPEN ACCESS ARTICLE

  • Kernel-bounded clustering for spatial transcriptomics enables scalable discovery of complex spatial domains

    • Hang Zhang,
    • Yi Zhang,
    • Kai Ming Ting,
    • Jie Zhang,
    • and Qiuran Zhao
    Genome Res. February 2025 35: 355-367; Published in Advance February 5, 2025, doi:10.1101/gr.278983.124
    OPEN ACCESS ARTICLE

  • Probing the eukaryotic microbes of ruminants with a deep-learning classifier and comprehensive protein databases

    • Ming Yan,
    • Thea O. Andersen,
    • Phillip B. Pope,
    • and Zhongtang Yu
    Genome Res. February 2025 35: 368-378; Published in Advance December 27, 2024, doi:10.1101/gr.279825.124

This Issue

February 2025; 35 (2)
Cover
  1. Review
  2. Research
  3. Methods

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