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  1. Research: Adaptation of centromeres to breakage through local genomic and epigenomic remodeling in wheat
    • Jingwei Zhou,
    • Yuhong Huang,
    • Huan Ma,
    • Yiqian Chen,
    • Chuanye Chen,
    • Fangpu Han,
    • and Handong Su
    Genome Res. November 2025 35: 2461-2471; Published in Advance September 30, 2025, doi:10.1101/gr.280913.125
    ...nucleosome remodeling and is accompanied by local transcription changes and chromatin reorganization, and subsequently may contribute to the stabilization of broken chromosomes. Our findings highlight the resilience and adaptability of plant chromosomes in response to centromere breakage and provide valuable...
  2. Method: Autoencoders for genomic variation analysis
    • Margarita Geleta,
    • Daniel Mas Montserrat,
    • Xavier Giro-i-Nieto,
    • and Alexander G. Ioannidis
    Genome Res. February 2026 36: 348-360; Published in Advance January 20, 2026, doi:10.1101/gr.280086.124
    ...of segments that could be classified as European and West African ancestry (Ali-Khan and Daar 2010). To characterize these different genomic segments, one can use local ancestry inference (LAI) methods like RFMix (Maples et al. 2013). These can rely on neural networks as well, for instance LAI-Net (Montserrat...
    OPEN ACCESS ARTICLE
  3. 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. April 2026 36: 814-826; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...models, outperforming both GBLUP and BayesR. These findings demonstrate a favorable trade-off between reduced accuracy (averaging <15%) and substantial computational savings, highlighting the practical value of dimensionality reduction in large-scale genomic analyses.View larger version: In this window...
  4. Research: ACTB methylation regulates SMARCA4 genomic occupancy to promote translation and reduce adhesion in colorectal cancer cells
    • Elina Abaev-Schneiderman,
    • Linh Nguyen,
    • Raz Shalev,
    • Tzofit Elbaz Biton,
    • Anand Chopra,
    • Giritharan Jagadeesan,
    • Daniel Sevilla-Sanchez,
    • Nili Tickotsky Moskovitz,
    • Liron Levin,
    • Michal Feldman,
    • Capucine Van Rechem,
    • and Dan Levy
    Genome Res. March 25, 2026 ; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
    ...localized ACTB-dependent mechanisms but also by broadly influencing SMARCA4 genomic occupancy. A question raised by our findings is how SETD3 expression itself is regulated in colorectal cancer cells. To gain preliminary insight into potential upstream regulatory mechanisms, we performed an in silico...
  5. Method: ML-MAGES enables multivariate genetic association analyses with genes and effect size shrinkage
    • Xiran Liu,
    • Lorin Crawford,
    • and Sohini Ramachandran
    Genome Res. December 2025 35: 2691-2700; Published in Advance November 19, 2025, doi:10.1101/gr.280440.125
    ..., or nonprioritized—among multiple traits based on their regularized effects. Clustering applied to our neural network shrinkage results also produces consistently higher precision and recall for distinguishing gene-level associations in simulations. We demonstrate the application of ML-MAGES on association analyses...
    OPEN ACCESS ARTICLE
  6. Method: spRefine denoises and imputes spatial transcriptomic data 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. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...transcriptomic data is hindered by high noise levels and missing gene measurements, challenges that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language...
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  7. Method: Predicted protein 3D structures provide essential insights into the genetic architecture underlying phenotypic diversity in maize
    • Shuai Wang,
    • Merritt Khaipho-Burch,
    • Lynn C. Johnson,
    • Zachary R. Miller,
    • Peter J. Bradbury,
    • Doug Speed,
    • William J. Allen,
    • M. Cinta Romay,
    • Jiquan Xue,
    • Edward S. Buckler,
    • Guillaume P. Ramstein,
    • and Baoxing Song
    Genome Res. January 2026 36: 214-225; Published in Advance October 31, 2025, doi:10.1101/gr.280514.125
    ...shaped protein 3D architecture is crucial for identifying functionally important regions that contribute to genetic adaptation to the environment.Genome-wide association studies (GWASs) have identified many candidate causal loci in protein-coding genes and regulatory regions. These genomic variations...
  8. Research: Genomic regulatory landscape underlying the antiviral response of Atlantic salmon
    • Shahmir Naseer,
    • Thomas C Clark,
    • Bertrand Collet,
    • Pooran Dewari,
    • Damir Baranasic,
    • Daniel J Macqueen,
    • Pierre Boudinot,
    • and Samuel A.M. Martin
    Genome Res. October 22, 2025 gr.280579.125; Published in Advance October 22, 2025, doi:10.1101/gr.280579.125
    ...provides novel insights into the genomic regulatory landscape underlying antiviral 33 immunity in a farmed fish with a complex . 34 Introduction 35 The innate immune response to viral infection, which is mainly based on the type I interferon 36 (type I IFN) pathway is crucial to both disease progression...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  9. Method: A spectral component approach leveraging identity-by-descent graphs to address recent population structure in genomic analysis
    • Ruhollah Shemirani,
    • Gillian M. Belbin,
    • Sinead Cullina,
    • Christa Caggiano,
    • Christopher R. Gignoux,
    • Noah Zaitlen,
    • and Eimear E. Kenny
    Genome Res. March 2026 36: 534-546; Published in Advance December 23, 2025, doi:10.1101/gr.280659.125
    ...heritable phenotype. Additionally, SPCs improve rare variant association analyses, reducing genomic inflation (e.g., from 7.6 to 1.2 in one analysis), and provide more accurate heritability estimates. Spatial autocorrelation analysis further confirms the ability of SPCs to account for environmental effects...
    OPEN ACCESS ARTICLE
  10. Research: Genomic insights into metabolic flux in hummingbirds
    • Ariel Gershman,
    • Quinn Hauck,
    • Morag Dick,
    • Jerrica M. Jamison,
    • Michael Tassia,
    • Xabier Agirrezabala,
    • Saad Muhammad,
    • Raafay Ali,
    • Rachael E. Workman,
    • Mikel Valle,
    • G. William Wong,
    • Kenneth C. Welch, Jr.,
    • and Winston Timp
    Genome Res. May 2023 33: 703-714; Published in Advance May 8, 2023, doi:10.1101/gr.276779.122
    ...University, Baltimore, Maryland 21205, USA Corresponding author: wtimp@jhu.eduAbstractHummingbirds are very well adapted to sustain efficient and rapid metabolic shifts. They oxidize ingested nectar to directly fuel flight when foraging but have to switch to oxidizing stored lipids derived from ingested...
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