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Current Issue of Genome Research

Table of Contents — August 2025, 35 (8)

Table of Contents

August 2025; 35 (8)

Review

  • De novo gene birth and the conundrum of ORFan genes in bacteria

    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124

Research

  • Oxygen-induced stress reveals context-specific gene regulatory effects in human brain organoids

    • Benjamin D. Umans and
    • Yoav Gilad
    Genome Res. August 2025 35: 1689-1700; Published in Advance June 2, 2025, doi:10.1101/gr.280219.124
    OPEN ACCESS ARTICLE

  • Wnt signaling activation induces CTCF binding and loop formation at cis-regulatory elements of target genes

    • Anna Nordin,
    • Chaitali Chakraborty,
    • Mattias Jonasson,
    • Orgena Dano,
    • Gianluca Zambanini,
    • Pierfrancesco Pagella,
    • Silvia Remeseiro,
    • and Claudio Cantù
    Genome Res. August 2025 35: 1701-1716; Published in Advance June 23, 2025, doi:10.1101/gr.279684.124
    OPEN ACCESS ARTICLE

  • Androgen receptor–mediated assisted loading of the glucocorticoid receptor modulates transcriptional responses in prostate cancer cells

    • Johannes Hiltunen,
    • Laura Helminen,
    • Niina Aaltonen,
    • Kaisa-Mari Launonen,
    • Hanna Laakso,
    • Marjo Malinen,
    • Einari A. Niskanen,
    • Jorma J. Palvimo,
    • and Ville Paakinaho
    Genome Res. August 2025 35: 1717-1732; Published in Advance June 2, 2025, doi:10.1101/gr.280224.124
    OPEN ACCESS ARTICLE

  • Mitotic chromosomes harbor cell type– and species-specific structural features within a universal loop array conformation

    • Marlies E. Oomen,
    • A. Nicole Fox,
    • Inma Gonzalez,
    • Amandine Molliex,
    • Thaleia Papadopoulou,
    • Pablo Navarro,
    • and Job Dekker
    Genome Res. August 2025 35: 1733-1744; Published in Advance June 6, 2025, doi:10.1101/gr.280648.125
    OPEN ACCESS ARTICLE

  • Dynamic barriers modulate cohesin positioning and genome folding at fixed occupancy

    • Hadi Rahmaninejad,
    • Yao Xiao,
    • Maxime M.C. Tortora,
    • and Geoffrey Fudenberg
    Genome Res. August 2025 35: 1745-1757; Published in Advance July 8, 2025, doi:10.1101/gr.280108.124
    OPEN ACCESS ARTICLE

  • Accurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing

    • Nora Zidane,
    • Carla Rodrigues,
    • Valérie Bouchez,
    • Martin Rethoret-Pasty,
    • Virginie Passet,
    • Sylvain Brisse,
    • and Chiara Crestani
    Genome Res. August 2025 35: 1758-1766; Published in Advance June 2, 2025, doi:10.1101/gr.279829.124

  • Lambdoid phages with abundant Chi recombination hotspots reflect diverse viral strategies for recombination-dependent growth

    • Clarence Zheng,
    • Sherwood R. Casjens,
    • Alan R. Davidson,
    • Susan K. Amundsen,
    • and Gerald R. Smith
    Genome Res. August 2025 35: 1767-1780; Published in Advance July 10, 2025, doi:10.1101/gr.280248.124
    OPEN ACCESS ARTICLE

Methods

  • Uncovering methylation-dependent genetic effects on regulatory element function in diverse genomes

    • Rachel M. Petersen,
    • Christopher M. Vockley,
    • and Amanda J. Lea
    Genome Res. August 2025 35: 1781-1793; Published in Advance July 14, 2025, doi:10.1101/gr.279957.124
    OPEN ACCESS ARTICLE

  • A novel multislice framework for precision 3D spatial domain reconstruction and disease pathology analysis

    • Daijun Zhang,
    • Ren Qi,
    • Xun Lan,
    • and Bin Liu
    Genome Res. August 2025 35: 1794-1808; Published in Advance July 14, 2025, doi:10.1101/gr.280281.124

  • Integration of hyperspectral imaging and transcriptomics from individual cells with SpectralSeq

    • Yike Xie,
    • Abbas Habibalahi,
    • Ayad G. Anwer,
    • Kanu Wahi,
    • Jacqueline Bailey,
    • Francis Lin,
    • Catherine Gatt,
    • Emma M.V. Johansson,
    • Tatyana Chtanova,
    • Jeff Holst,
    • Ewa Goldys,
    • and Fabio Zanini
    Genome Res. August 2025 35: 1809-1820; Published in Advance July 8, 2025, doi:10.1101/gr.280014.124
    OPEN ACCESS ARTICLE

  • QuadST identifies cell–cell interaction–changed genes in spatially resolved transcriptomics data

    • Xiaoyu Song,
    • Yuqing Shang,
    • Michelle E. Ehrlich,
    • Panos Roussos,
    • Guo-Cheng Yuan,
    • and Pei Wang
    Genome Res. August 2025 35: 1821-1831; Published in Advance June 23, 2025, doi:10.1101/gr.279859.124
    OPEN ACCESS ARTICLE

  • Batch correction methods used in single-cell RNA sequencing analyses are often poorly calibrated

    • Sindri Emmanúel Antonsson and
    • Páll Melsted
    Genome Res. August 2025 35: 1832-1841; Published in Advance July 7, 2025, doi:10.1101/gr.279886.124
    OPEN ACCESS ARTICLE

  • Cancer driver topologically associated domains identify oncogenic and tumor-suppressive lncRNAs

    • Ziyan Rao,
    • Min Zhang,
    • Shaodong Huang,
    • Chenyang Wu,
    • Yuheng Zhou,
    • Weijie Zhang,
    • Xia Lin,
    • and Dongyu Zhao
    Genome Res. August 2025 35: 1842-1858; Published in Advance May 27, 2025, doi:10.1101/gr.280235.124

  • Overcoming limitations to customize DeepVariant for domesticated animals with TrioTrain

    • Jenna Kalleberg,
    • Jacob Rissman,
    • and Robert D. Schnabel
    Genome Res. August 2025 35: 1859-1874; Published in Advance June 2, 2025, doi:10.1101/gr.279542.124
    OPEN ACCESS ARTICLE

  • A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry

    • Meilin Zhang,
    • Heng Du,
    • Yu Zhang,
    • Yue Zhuo,
    • Zhen Liu,
    • Yahui Xue,
    • Lei Zhou,
    • Sixuan Zhou,
    • Wanying Li,
    • and Jian-Feng Liu
    Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
    OPEN ACCESS ARTICLE

Resources

  • A map of enhancer regions in primary human neural progenitor cells using capture STARR-seq

    • Sophia C. Gaynor-Gillett,
    • Lijun Cheng,
    • Manman Shi,
    • Jason Liu,
    • Gaoyuan Wang,
    • Megan Spector,
    • Qiuyu Guo,
    • Le Qi,
    • Mary Flaherty,
    • Martha Wall,
    • Ahyeon Hwang,
    • Mengting Gu,
    • Zhanlin Chen,
    • Yuhang Chen,
    • PsychENCODE Consortium,
    • Jennifer R. Moran,
    • Jing Zhang,
    • Donghoon Lee,
    • Mark Gerstein,
    • Daniel Geschwind,
    • and Kevin P. White
    Genome Res. August 2025 35: 1887-1901; Published in Advance July 11, 2025, doi:10.1101/gr.279584.124

  • CGC1, a new reference genome for Caenorhabditis elegans

    • Kazuki Ichikawa,
    • Massa J. Shoura,
    • Karen L. Artiles,
    • Dae-Eun Jeong,
    • Chie Owa,
    • Haruka Kobayashi,
    • Yoshihiko Suzuki,
    • Manami Kanamori,
    • Yu Toyoshima,
    • Yuichi Iino,
    • Ann E. Rougvie,
    • Lamia Wahba,
    • Andrew Z. Fire,
    • Erich M. Schwarz,
    • and Shinichi Morishita
    Genome Res. August 2025 35: 1902-1918; Published in Advance July 15, 2025, doi:10.1101/gr.280274.124
    OPEN ACCESS ARTICLE

This Issue

August 2025; 35 (8)
Cover
  1. Review
  2. Research
  3. Methods
  4. Resources

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