Searching journal content for articles similar to Guo et al. 13 (8): 1810.

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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
    ...et al. (2021) has attempted to use VAEs for genotype simulation.To summarize the contributions: In this work, we demonstrate how a single model can address several critical tasks in genomics research. By leveraging the nonlinearities and the modular architecture of our VAE, we implicitly model...
    OPEN ACCESS ARTICLE
  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
    ..., highlighting the practical value of dimensionality reduction in large-scale genomic analyses. Design of integrated artificial intelligence software for GP We integrated a user-friendly toolkit named artificial intelligence GP (AIGP) (Fig. 6). Specifically, AIGP begins with raw feature data that undergo...
  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
    ...using Telofinder, a script designed to specifically detect the degenerated yeast telomere motif TG1–3/C1–3A (O'Donnell et al. 2023). Finally, after filtering steps ensuring that the telomere sequences are not truncated or internal (Supplemental Fig. S1A), the lengths of all validated telomere sequences...
  4. 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
    ...Encoder, which generates spot embeddings and data set–specific gene embeddings simultaneously. It then imputes and denoises the given data by multiplying the learned embeddings to output a new matrix with improved expression levels. Results Overview of spRefine We design spRefine with a decomposed auto...
    OPEN ACCESS ARTICLE
  5. 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
    ...the polygenic phenotype with a heritability of 0.3 and the environmental smooth phenotype (reweighted to comprise 0.7 of the variance of the phenotype). The hybrid sharp phenotype is generated similarly using the environmental sharp with the same weighting scheme. The environmental category was designed...
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  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
    ...and the Natural Science Foundation of Hubei Province of China (2024AFB116).Author contributions: H.D.S. designed the research; J.W.Z., Y.H.H., H.M., Y.Q.C., and C.Y.C. performed the research; J.W.Z., Y.H.H., F.P.H., and H.D.S. analyzed the data; H.D.S. wrote the article.Footnotes [Supplemental material...
  7. 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
  8. 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
    ...(Coster et al. 2021). The choice of either analysis approach often impacts the experimental design itself (Harvey et al. 2023). Other factors influencing this decision include computational resources, DNA quality and quantity, sequencing depth, and the ability of assembly-based approaches to improve...
  9. 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
    ...families, we employed CAFE5 (Mendes et al. 2020), a computational tool designed to evaluate the evolution of gene families using phylogenetic data. Using C. nigoni and C. briggsae reference strains (JU1421 and AF16), along with three outgroup nematodes (C. elegans, C. remanei, and C. brenneri), we...
  10. Resource: Full-length RNA transcript sequencing traces brain isoform diversity in house mouse natural populations
    • Wenyu Zhang,
    • Anja Guenther,
    • Yuanxiao Gao,
    • Kristian Ullrich,
    • Bruno Huettel,
    • Aftab Ahmad,
    • Lei Duan,
    • Kaizong Wei,
    • and Diethard Tautz
    Genome Res. November 2024 34: 2118-2132; Published in Advance September 17, 2024, doi:10.1101/gr.279166.124
    ...–E) are based on the 1.5 IQR values for both sides; black dots in G and H represent outliers.In total, we found only 51% of the 117,728 distinct isoforms matching perfectly to a whole (FSM, 34.9%) or subsection (ISM, 16.1%) of a reference annotated isoform, designated as known isoforms following the convention...
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