Searching journal content for articles similar to Huang et al. 26 (12): 1687.

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  1. Method: Privacy-preserving biological age prediction over federated human methylation data using fully homomorphic encryption
    • Meir Goldenberg,
    • Loay Mualem,
    • Amit Shahar,
    • Sagi Snir,
    • and Adi Akavia
    Genome Res. September 2024 34: 1324-1333; Published in Advance September 5, 2024, doi:10.1101/gr.279071.124
    .... ↵Akavia A, Galili B, Shaul H, Weiss M, Yakhini Z. 2024. Privacy preserving feature selection for sparse linear regression. Proc Priv Enhancing Technol 2024: 300–313. doi:10.56553/popets-2024-0017 ↵Bajard JC, Eynard J, Hasan MA, Zucca V. 2016. A full RNS variant of FV like somewhat homomorphic encryption...
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  2. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...) to classify 16S rRNA reads and observed a substantial compression ratio (249×–275×) for all three index types using different digestion methods (Table 1). For the minimizer index, the average profile storage decreased from d = 9118 values to 5.137 pairs in the cliff-compressed profile, leading...
  3. 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
    ...models (HMMs) (Tang et al. 2006; Corbett-Detig and Nielsen 2017; Browning et al. 2018, 2023) become computationally expensive and slow when faced with biobank-sized data, neural networks can provide a powerful alternative.Genomic sequence compressionThe storage and transmission of high...
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  4. 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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  5. 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...
  6. 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 and emphasize the importance of explainable ML 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...
  7. 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
    ...). These findings suggest that C. nigoni populations may experience substantially higher selection pressure from pathogens in their native environments compared with C. briggsae populations.Genes encoding Cullin-E3 ubiquitin-ligase-adaptors are major contributors to both gene family and genomic sequence divergence...
  8. 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...
  9. 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. April 2026 36: 684-694; Published in Advance March 25, 2026, doi:10.1101/gr.280534.125
    ...to western blot assay using the indicated antibodies. (B) Same as A with HCT116 cells expressing Flag-ACTB wt (WT ACTB) or Flag-ACTB H73A (MUT ACTB H73A).ACTB H73 methylation regulates the selective genomic distribution of SMARCA4Given that SETD3-mediated methylation of ACTB influences its genomic...
  10. 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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