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  1. 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
    ...an overly large window size, which might lose fine-grained structure) and encoding efficiency (not using an excessively small window size, which would require a large bottleneck to capture all local information). In our analysis, w = 2500 results in a good compromise between capturing local genomic...
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  2. Method: Automated interpretable artificial intelligence genomic prediction with AlGP
    • Lei Wei,
    • Ziqin Jiang,
    • Baoliang Fan,
    • Yidan Yan,
    • Zhenqiang Xu,
    • Xiaoxiang Hu,
    • and Yuzhe Wang
    Genome Res. March 5, 2026 ; Published in Advance March 5, 2026, doi:10.1101/gr.281006.125
    ...approaches, integration of prior information, and parameter optimization. The AIGP toolkit enables automated model optimization and interpretability, making ML-driven genomic selection more accessible and providing new tools to support genomic research. [Supplemental material is available for this article...
  3. 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. February 3, 2026 ; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...performed worse than spRefine, suggesting that spRefine can better capture information than the pretrained models or generated niches based on spatial location. Moreover, Liu et al. 2 Genome Research www..org there was better cell type separation after imputation for the xenium_breast sample, supported...
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  4. 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
    ...Ruhollah Shemirani1, Gillian M. Belbin1,9, Sinead Cullina1,2, Christa Caggiano1, Christopher R. Gignoux3,4, Noah Zaitlen5,6,7 and Eimear E. Kenny1,2,8 1Institute for Genomic Health, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA; 2Department of Genetics and Genomic Sciences...
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  5. Research: Pangenome analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility
    • Dongying Xie,
    • Pohao Ye,
    • Yiming Ma,
    • and Zhongying Zhao
    Genome Res. March 2026 36: 506-521; Published in Advance February 17, 2026, doi:10.1101/gr.280885.125
    ...Pan analysis reveals families of ubiquitin-ligase adaptors as key genomic divergence drivers that lead to hybrid incompatibility Dongying Xie1,2,3, Pohao Ye1,3, Yiming Ma1 and Zhongying Zhao1 1Department of Biology, Hong Kong Baptist University, Hong Kong SAR, China; 2Institute for Research...
  6. 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
    ...Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; 3State Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy...
  7. Mini-Review: A Hitchhiker's Guide to long-read genomic analysis
    • Medhat Mahmoud,
    • Daniel P. Agustinho,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 545-558; doi:10.1101/gr.279975.124
    ...Medhat Mahmoud1,4, Daniel P. Agustinho1,4 and Fritz J. Sedlazeck1,2,3 1Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas 77030, USA; 2Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA; 3Department of Computer Science, Rice...
  8. Research: The genomic consequences and persistence of sociality in spiders
    • Jilong Ma,
    • Jesper Bechsgaard,
    • Anne Aagaard,
    • Palle Villesen,
    • Trine Bilde,
    • and Mikkel Heide Schierup
    Genome Res. March 2025 35: 499-511; Published in Advance February 20, 2025, doi:10.1101/gr.279503.124
    ...determined the divergence time of lineages and the age of individual transitions to sociality to assess whether speciation coincides with the evolution of sociality. This information further serves to investigate the progression of genomic consequences caused by the transition to sociality via comparisons...
  9. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...). Although informative, they are not quantitative, incapable of determining direct enhancer activity, and cannot uncouple epigenomic from genomic mechanisms. On the other hand, reporter assays overcome some of these limitations by measuring enhancer activity on nonchromatinized DNA templates, isolating...
  10. 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
    ...Genome Res GENOME Genome Research Genome Res. Genome Res 1088-9051 1549-5469 Cold Spring Harbor Laboratory Press 9509184 10.1101/gr.280534.125 ;gr.280534.125v1 ;gr.280534.125 gr.280534.125 gr.280534.125 Research Abaev-Schneiderman et al. ACTB methylation regulates transcription 1 The Shraga Segal...
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