Searching journal content for articles similar to Majumder 11 (6): 931.

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  1. 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
    ...(predictive phenotype) because of their “black-box” nature (Novakovsky et al. 2023). For genomic researchers, interpretative information, which is often lacking, can bemore valuable than predictions themselves because it can provide new insights into genetic processes. Traditional linear models, such as -wide...
  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
    ...and regression are based on dimensionality reduction and clustering techniques (Tan and Atkinson 2023). Genomic sequences from known and unknown origins are jointly analyzed—unknown samples are assigned to the nearest labeled cluster of the feature space (e.g., PCA space). Yet there are some caveats (Baran et al...
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  3. 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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  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
    ...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 models to jointly denoise and impute spatial transcriptomic data. Our results demonstrate that sp...
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  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
    ...these approaches show promise, they currently have some limitations, such as implicating large genomic regions in variant association and requiring methodological improvements to LMM scalability. Future work could explore the use of PCs, ARGs, and SPCs in tandem as a powerful tool for addressing the challenges...
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  6. 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
    ..., sociality is accompanied by a transition from outcrossing to inbreeding. In concert, these traits reduce effective population size, potentially rendering transitions to sociality “evolutionarily dead-ends.” We addressed this hypothesis in a comparative genomic study in spiders, in which sociality has...
  7. 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
    ...coordinates are shown below. CENH3 relocation indicates centromere repositioning relative to CS. (C) Quantitative comparison of gene and transposable element (TE) density across three genomic regions: the original centromere (CEN), the neocentromere (NeoCEN), and the flanking pericentromeric regions (PERI...
  8. Resource: The ggRibo single-gene viewer reveals insights into translatome and other nucleotide-resolution omics data
    • Hsin-Yen Larry Wu,
    • Isaiah D. Kaufman,
    • and Polly Yingshan Hsu
    Genome Res. September 2025 35: 2130-2142; Published in Advance July 22, 2025, doi:10.1101/gr.280480.125
    ...(Weerasooriya et al. 2024). This example highlights ggRibo’s capacity to compare multiple data sets, enabling investigations into differential translation or isoform-specific translation across tissues/conditions and providing valuable insights for future functional characterization.Multiomic data comparisons...
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  9. 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
    ...to determine whether haplotype imputation by this PHG database (or future databases containing more assemblies) is accurate enough for effective incorporation of predicted protein structure information into genomic prediction models.MethodsProtein sequence diversity investigationTo investigate sequence...
  10. 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
    ...variants, and deeper insights into the interplay between epigenetics and genomic variation. This mini-review provides a comprehensive overview of the latest developments in long-read DNA sequencing analysis, encompassing reference-based and de novo assembly approaches. We explore the entire workflow, from...
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