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Current Issue of Genome Research

Table of Contents — October 2025, 35 (10)

Table of Contents

October 2025; 35 (10)

Research

  • Molecular and genetic landscapes of retina and brain microglia in neurodegenerative diseases

    • Khang Ma and
    • Rinki Ratnapriya
    Genome Res. October 2025 35: 2143-2157; Published in Advance August 26, 2025, doi:10.1101/gr.280554.125

  • APOBEC3A drives deaminase mutagenesis in human gastric epithelium

    • Yohan An,
    • Ji-Hyun Lee,
    • Joonoh Lim,
    • Jeonghwan Youk,
    • Seongyeol Park,
    • Ji-Hyung Park,
    • Kijong Yi,
    • Taewoo Kim,
    • Chang Hyun Nam,
    • Won Hee Lee,
    • Soo A Oh,
    • Yoo Jin Bae,
    • Thomas M. Klompstra,
    • Haeun Lee,
    • Jinju Han,
    • Junehwak Lee,
    • Jung Woo Park,
    • Jie-Hyun Kim,
    • Hyunki Kim,
    • Hugo Snippert,
    • Bon-Kyoung Koo,
    • and Young Seok Ju
    Genome Res. October 2025 35: 2158-2172; Published in Advance August 26, 2025, doi:10.1101/gr.280338.124
    OPEN ACCESS ARTICLE

  • Epigenetic drift score captures directional methylation variability and links aging to transcriptional, metabolic, and genetic alterations

    • Xiu Fan,
    • Qili Qian,
    • Wenran Li,
    • Tianzi Liu,
    • Changqing Zeng,
    • Peilin Jia,
    • Huandong Lin,
    • Xin Gao,
    • Li Jin,
    • Mingfeng Xia,
    • Sijia Wang,
    • and Fan Liu
    Genome Res. October 2025 35: 2173-2188; Published in Advance August 1, 2025, doi:10.1101/gr.280155.124
    OPEN ACCESS ARTICLE

  • Widespread specific intron retention events in nuclear RNA complexes identified by sedimentation analysis of pluripotent cellular extracts

    • Isabela T. Pereira,
    • Izabela Mamede,
    • Paulo P. Amaral,
    • Gloria R. Franco,
    • and John L. Rinn
    Genome Res. October 2025 35: 2189-2198; Published in Advance August 26, 2025, doi:10.1101/gr.280431.125

  • H3K27 and H3K9 methylation mask potential CTCF binding sites to maintain 3D genome integrity

    • Kei Fukuda,
    • Chikako Shimura,
    • and Yoichi Shinkai
    Genome Res. October 2025 35: 2199-2210; Published in Advance August 5, 2025, doi:10.1101/gr.280732.125

  • Mapping multitissue regulatory variants reveals a liver-centric coexpression network associated with duck egg-laying performance

    • Yang Xi,
    • Jingjing Qi,
    • Zhao Yang,
    • Yutian Zeng,
    • Huicong Zhang,
    • Qiuyu Tao,
    • Mengru Xu,
    • Anqi Huang,
    • Shenqiang Hu,
    • Chunchun Han,
    • Lili Bai,
    • Jiwei Hu,
    • Jiwen Wang,
    • Liang Li,
    • Lingzhao Fang,
    • and Hehe Liu
    Genome Res. October 2025 35: 2211-2225; Published in Advance September 10, 2025, doi:10.1101/gr.280345.124

  • Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence

    • Manuela Baquero Pérez,
    • Gertjan Laenen,
    • Isabelle Loïodice,
    • Mickaël Garnier,
    • Ugo Szachnowski,
    • Antonin Morillon,
    • Myriam Ruault,
    • and Angela Taddei
    Genome Res. October 2025 35: 2226-2239; Published in Advance August 12, 2025, doi:10.1101/gr.279874.124

Methods

  • Ultra-long sequencing for contiguous haplotype resolution of the human immunoglobulin heavy-chain locus

    • Mari B. Gornitzka,
    • Egil Røsjø,
    • Uddalok Jana,
    • Easton E. Ford,
    • Alan Tourancheau,
    • William D. Lees,
    • Zachary Vanwinkle,
    • Melissa L. Smith,
    • Corey T. Watson,
    • and Andreas Lossius
    Genome Res. October 2025 35: 2240-2251; Published in Advance August 21, 2025, doi:10.1101/gr.280400.125

  • FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data

    • Can Luo,
    • Zimeng Jamie Zhou,
    • Yichen Henry Liu,
    • and Xin Maizie Zhou
    Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
    OPEN ACCESS ARTICLE

  • Unveiling the functional fate of duplicated genes through expression profiling and structural analysis

    • Alex Warwick Vesztrocy,
    • Natasha Glover,
    • Paul D. Thomas,
    • Christophe Dessimoz,
    • and Irene Julca
    Genome Res. October 2025 35: 2273-2284; Published in Advance August 14, 2025, doi:10.1101/gr.280166.124

  • Efficient integration of spatial omics data for joint domain detection, matching, and alignment with stMSA

    • Han Shu,
    • Jing Chen,
    • Chang Xu,
    • Jialu Hu,
    • Yongtian Wang,
    • Jiajie Peng,
    • Qinghua Jiang,
    • Xuequn Shang,
    • and Tao Wang
    Genome Res. October 2025 35: 2285-2299; Published in Advance August 14, 2025, doi:10.1101/gr.280584.125

  • Deciphering context-specific gene programs from single-cell and spatial transcriptomics data with DeCEP

    • Lin Li,
    • Xianbin Su,
    • and Ze-Guang Han
    Genome Res. October 2025 35: 2300-2315; Published in Advance August 21, 2025, doi:10.1101/gr.279689.124

  • Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes

    • Philipp Rentzsch,
    • Aaron Kollotzek,
    • Kaushik Ram Ganapathy,
    • Pejman Mohammadi,
    • and Tuuli Lappalainen
    Genome Res. October 2025 35: 2316-2325; Published in Advance September 17, 2025, doi:10.1101/gr.280360.124
    OPEN ACCESS ARTICLE

  • Tree-based differential testing using inferential uncertainty for RNA-seq

    • Noor Pratap Singh,
    • Euphy Y. Wu,
    • Jason Fan,
    • Michael I. Love,
    • and Rob Patro
    Genome Res. October 2025 35: 2326-2338; Published in Advance August 21, 2025, doi:10.1101/gr.279981.124
    OPEN ACCESS ARTICLE

  • Multicondition and multimodal temporal profile inference during mouse embryonic development

    • Ran Zhang,
    • Chengxiang Qiu,
    • Galina N. Filippova,
    • Gang Li,
    • Jay Shendure,
    • Jean-Philippe Vert,
    • Xinxian Deng,
    • William Stafford Noble,
    • and Christine M. Disteche
    Genome Res. October 2025 35: 2339-2351; Published in Advance August 14, 2025, doi:10.1101/gr.279997.124
    OPEN ACCESS ARTICLE

Resources

  • Analyzing the large and complex SFARI autism cohort data using the Genotypes and Phenotypes in Families (GPF) platform

    • Liubomir Chorbadjiev,
    • Murat Cokol,
    • Zohar Weinstein,
    • Kevin Shi,
    • Christopher Fleisch,
    • Nikolay Dimitrov,
    • Svetlin Mladenov,
    • Ivo Todorov,
    • Iordan Ivanov,
    • Simon Xu,
    • Steven Ford,
    • Yoon-ha Lee,
    • Boris Yamrom,
    • Steven Marks,
    • Adriana Munoz,
    • Alex Lash,
    • Natalia Volfovsky,
    • and Ivan Iossifov
    Genome Res. October 2025 35: 2352-2362; Published in Advance September 16, 2025, doi:10.1101/gr.280356.124
    OPEN ACCESS ARTICLE

  • Interspecies systems biology links bacterial metabolic pathways to nematode gene expression, chemotaxis behavior, and survival

    • Marina Athanasouli,
    • Tobias Loschko,
    • and Christian Rödelsperger
    Genome Res. October 2025 35: 2363-2374; Published in Advance August 5, 2025, doi:10.1101/gr.280848.125

Corrigendum

  • Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes

    • Ran Li,
    • Mian Gong,
    • Xinmiao Zhang,
    • Fei Wang,
    • Zhenyu Liu,
    • Lei Zhang,
    • Qimeng Yang,
    • Yuan Xu,
    • Mengsi Xu,
    • Huanhuan Zhang,
    • Yunfeng Zhang,
    • Xuelei Dai,
    • Yuanpeng Gao,
    • Zhuangbiao Zhang,
    • Wenwen Fang,
    • Yuta Yang,
    • Weiwei Fu,
    • Chunna Cao,
    • Peng Yang,
    • Zeinab Amiri Ghanatsaman,
    • Niloufar Jafarpour Negari,
    • Hojjat Asadollahpour Nanaei,
    • Xiangpeng Yue,
    • Yuxuan Song,
    • Xianyong Lan,
    • Weidong Deng,
    • Xihong Wang,
    • Chuanying Pan,
    • Ruidong Xiang,
    • Eveline M. Ibeagha-Awemu,
    • Pat (J.S.) Heslop-Harrison,
    • Benjamin D. Rosen,
    • Johannes A. Lenstra,
    • Shangquan Gan,
    • and Yu Jiang
    Genome Res. October 2025 35: 2375; doi:10.1101/gr.281340.125
    OPEN ACCESS ARTICLE

This Issue

October 2025; 35 (10)
Cover
  1. Research
  2. Methods
  3. Resources
  4. Corrigendum

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