Searching journal content for articles similar to Weising et al. 4 (5): 249.

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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
    ..., compression, classification, and simulation of genomic data with several worldwide whole data sets from both humans and canids, and evaluate the performance of the proposed applications with and without ancestry conditioning. The unsupervised setting of autoencoders allows for the detection and learning...
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  2. 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
    ...prediction; however, it often struggles with interpretability because of its black-box nature. Here, we evaluate 12 ML models alongside GBLUP and BayesR to identify key factors influencing genomic prediction performance across traits with different genetic architectures in multiple agricultural species...
  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. April 2026 36: 754-768; Published in Advance February 3, 2026, doi:10.1101/gr.281001.125
    ...), and PCR comparison score. All of the metrics are in (0,1) and higher values mean better model performance. Details of our evaluation framework are summarized in the Methods section.To measure the effectiveness of imputation, we considered some existing imputation methods, including VISTA (Liu et al. 2026...
    OPEN ACCESS ARTICLE
  4. Method: Enabling efficient and robust analysis of tandem repeats in genomic data using wavefront-based string decomposer
    • Junhai Qi,
    • Zhidong Yang,
    • Ting Yu,
    • and Guojun Li
    Genome Res. April 8, 2026 gr.281346.125; Published in Advance April 8, 2026, doi:10.1101/gr.281346.125
    ...16 TRs are genomic sequences composed of tandemly arranged DNA repeat units. TRs are broadly categorized into short17 tandem repeats (STRs) and long tandem repeats (LTRs) based on repeat unit length. STRs typically consist of 1–6 base18 pair (bp) repeat units, whereas LTRs can span hundreds of base...
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  5. 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
    ...-time qPCR primers were designed using the PrimerQuest tool of the Syntezza-Israel IDT portal and UCSC Genome Bioinformatics (Supplemental Table S1). All samples were amplified in triplicate in a 384-well plate using the following cycling conditions: 10 min at 95°C, 45 cycles of 10 sec at 95°C, 30 sec...
  6. Method: Evaluation of N6-methyldeoxyadenosine antibody-based genomic profiling in eukaryotes
    • Brian M. Debo,
    • Benjamin J. Mallory,
    • and Andrew B. Stergachis
    Genome Res. March 2023 33: 427-434; Published in Advance February 14, 2023, doi:10.1101/gr.276696.122
    ...), duplicate end prep and adaptor ligation reactions were prepared and combined into single immunoprecipitations (including IgG controls). The samples were end-repaired by combining 1 μg of DNA in 50 μL of 10 mM Tris (pH 8.0) with 7 μL of end prep reaction buffer and 3 μL of end prep enzyme mix in PCR strip...
  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...
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  8. 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 eigenvectors corresponding to the smallest eigenvalues of this matrix comprise the set of SPCs.Evaluating performance to detect fine-scale population structure on a simulated data setTo evaluate the performance of SPCs for capturing fine-scale population structure in genomic data sets, we first simulated...
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  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
    .... briggsae strains and nine C. nigoni strains, including both reference strains. Through comparative pan-genomic analyses of both nematode species, we aim to identify the critical structural and genetic variations that drive intra- and interspecific evolution, ultimately leading to speciation...
  10. 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
    ...for Chinese Spring wheat and both short-arm (S) and long-arm (L) telosomes of ditelosomic lines. The bottom track presents annotated gene distributions. Triangles in the CS tracks denote primer positions used for PCR validation of genomic regions near breakpoints. (D) Agarose gel electrophoresis results...
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