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  1. Method: 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
    ...are used to investigate functional divergence following duplication. This analysis, the most comprehensive to date, reveals that, whereas the majority of paralogs display similar rates of sequence evolution, significant differences in branch lengths following gene duplication can be correlated...
  2. Method: scSHEFT enables multiomics label transfer from scRNA-seq to scATAC-seq through dual alignment
    • Zhitao Huang,
    • Ruiqing Zheng,
    • Pengzhen Jia,
    • Xuhua Yan,
    • Jinmiao Chen,
    • and Min Li
    Genome Res. February 2026 36: 387-396; Published in Advance January 20, 2026, doi:10.1101/gr.280410.125
    ...between scRNA-seq and scATAC-seq pose challenges for identifying different cell types, which hinders the discovery of novel types. In this study, we propose a new label transfer tool scSHEFT, which simultaneously considers gene expression count data, peak count data, and Gene Activity Scores as inputs...
  3. Research: Natural diversity of telomere length distributions across 100 Saccharomyces cerevisiae strains
    • Clotilde Garrido,
    • Cintia Gómez-Muñoz,
    • Etienne Kornobis,
    • Nicolas Agier,
    • Oana Ilioaia,
    • Gilles Fischer,
    • and Zhou Xu
    Genome Res. March 2026 36: 522-533; Published in Advance January 16, 2026, doi:10.1101/gr.281132.125
    ..., representing the genetic and ecological diversity of the species. Our analysis reveals a large diversity in TL distributions within the species, largely driven by interextremity differences, ploidy level, and subtelomere structure. Polyploid strains display significantly longer telomeres than diploid...
  4. Research: Modest increase in the de novo single-nucleotide mutation rate in house mice born by assisted reproduction
    • Laura Blanco-Berdugo,
    • Alexis Garretson,
    • and Beth L. Dumont
    Genome Res. January 2026 36: 50-60; Published in Advance November 13, 2025, doi:10.1101/gr.281180.125
    ...that the tested ART protocol adversely impacts stability in gametes, zygotes, or early-stage embryos. However, systematic differences in sequencing data quality could also lead to differences in the number of false-positive or false-negative dnSNV calls between cohorts. Importantly, the sequencing data quality...
  5. Research: Degrees of convergent evolution in rodent adaptations to arid environments
    • Domitille Chalopin,
    • Carine Rey,
    • Jeremy Ganofsky,
    • Juliana Blin,
    • Pascale Chevret,
    • Marion Mouginot,
    • Laurent Guéguen,
    • Bastien Boussau,
    • Sophie Pantalacci,
    • and Marie Sémon
    Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
    ...that there are many different, yet repeatedly selected, ways to adapt to aridity and that the degree of convergent evolution increases with both the age of the transitions and species relatedness.Repeated evolution, embracing parallel and convergent evolution, occurs when different lineages evolve similar traits...
    OPEN ACCESS ARTICLE
  6. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...probabilities of six different ML algorithms. Liu et al. (2022) addressed a sample imbalance of species via scale-aware learning, integrating class weights into cross-entropy loss to develop MSNet-4mC. Based on Hyb4mC (Liang et al. 2022), iDNA-MS (Lv et al. 2020), and DeepTorrent (Liu et al. 2021a), Li et al...
    OPEN ACCESS ARTICLE
  7. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...poly(A) tails to the 3′ end through the selection of different polyadenylation sites (PASs), generating diverse transcript isoforms with varying lengths of 3′ untranslated regions (3′ UTRs) (Reyes and Huber 2018). In general, the APA occurs in over 70% of protein-coding genes in mammals and manifests...
  8. Research: Developmental transcriptomics in Pristionchus reveals the environmental responsiveness of a plasticity gene-regulatory network
    • Shelley Reich,
    • Tobias Loschko,
    • Julie Jung,
    • Samantha Nestel,
    • Ralf J. Sommer,
    • and Michael S. Werner
    Genome Res. July 2025 35: 1560-1573; Published in Advance June 9, 2025, doi:10.1101/gr.279783.124
    ...Corresponding author: michael.werner@utah.eduAbstractDevelopmental plasticity enables the production of alternative phenotypes in response to different environmental conditions. Although significant advances in understanding the ecological and evolutionary implications of plasticity have been made...
    OPEN ACCESS ARTICLE
  9. Method: spRefine denoises and imputes spatial transcriptomics with a reference-free framework powered by genomic language model
    • Tianyu Liu,
    • Tinglin Huang,
    • Wengong Jin,
    • Tinyi Chu,
    • Rex Ying,
    • and Hongyu Zhao
    Genome Res. February 3, 2026 gr.281001.125; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...). Therefore, there is a need to develop computational tools50 to address the limitations of different platforms and improve the reliability of the51 interpretation of spatial transcriptomics.52 Efforts have been made to address the limitations of these two platforms. For53 imaging-based technologies...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  10. Method: Automated interpretable artificial intelligence genomic prediction with AIGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 gr.281006.125; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ..., it often 24 struggles with interpretability because of its black-box nature. We evaluate 12 ML models 25 alongside GBLUP and BayesR to identify key factors influencing genomic prediction 26 performance across traits with different genetic architectures in multiple agricultural species, 27 including pigs...
    ACCEPTED MANUSCRIPT
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