Searching journal content for articles similar to Schutte et al. 10 (1): 81.

Displaying results 1-10 of 6321
For checked items
  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
    ....Regarding other nonlinear manifold learning techniques, such as t-SNE (Van der Maaten and Hinton 2008) and UMAP (McInnes et al. 2018), these are not directly comparable with our approach as they do not allow mapping new samples to the spanned space, which makes them not usable for the tasks of compression...
    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
    ...for predicting complex traits in animals and plants (Meuwissen et al. 2001, 2016; Alemu et al. 2024). With the continual decrease in genotyping costs, a variety of genomic best linear unbiased prediction methods—such as GBLUP (VanRaden 2008) and their improved algorithms (Yin et al. 2020; Moghaddar et al. 2019...
  3. Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
    • Sheila Lutz,
    • Megan Lawler,
    • Samuel Amidon,
    • and Frank W Albert
    Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
    ...-based mapping, we identified a 6.5-kb genomic region including 429 four genes, SNN1, MKT1, END3 and SAL1, that caused a growth difference in liquid YPD. 430 Mapping with distal isolates suggested SAL1 as the causal gene. Sequencing corroborated 431 these results and further increased mapping resolution. Genome...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  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
    ...exhibit 532 heterogeneous distribution patterns, with some, such as finTRIMs, in gene groups dispersed 533 across the while others, including MHC class I genes, form a few or a unique cluster 534 on a specific location (Van der Aa et al., 2009; Lukacs et al., 2010). These findings 535 underscore...
    OPEN ACCESS ARTICLEACCEPTED MANUSCRIPT
  5. Research: Analyzing super-enhancer temporal dynamics reveals potential critical enhancers and their gene regulatory networks underlying skeletal muscle development
    • Song Zhang,
    • Chao Wang,
    • Shenghua Qin,
    • Choulin Chen,
    • Yongzhou Bao,
    • Yuanyuan Zhang,
    • Lingna Xu,
    • Qingyou Liu,
    • Yunxiang Zhao,
    • Kui Li,
    • Zhonglin Tang,
    • and Yuwen Liu
    Genome Res. December 2024 34: 2190-2202; Published in Advance October 21, 2024, doi:10.1101/gr.278344.123
    ...) (Fig. 6C; Supplemental Fig. S6A), and sharing the same adjacent target genes (synteny conservation).View larger version: In this window In a new window Figure 6. Conservation analysis and functional assay of candidate critical enhancers within Con SEs. (A) Schematic diagram illustrating the mapping...
  6. 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
    ..., these methods are restricted to sequencing-based methods and cannot uncover the missing information from unmeasured genes, and they are not able to process large-scale SRT data sets. Therefore, it is critical to have a flexible and efficient method for processing data sets from different platforms as well...
    OPEN ACCESS ARTICLE
  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
    ...Caenorhabditis briggsae and its sister species Caenorhabditis nigoni provide an ideal model system to address this question, as they exhibit extensive genomic divergence with limited gene flow from C. briggsae to C. nigoni. Despite previous comparative genomic studies, a comprehensive analysis of both...
  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
    ...and Thompson 2025), which may capture additional fine-scale relatedness. Finally, SPCs could also be evaluated as covariates in IBD-based mapping of quantitative trait loci, as their ability to resolve fine-scale population structure differences suggests they may help improve mapping accuracy (Chen et al. 2023...
    OPEN ACCESS ARTICLE
  9. Method: Gene duplication is associated with gene diversification and potential neofunctionalization in lung cancer evolution
    • Paul Ashford,
    • Alexander M. Frankell,
    • Zofia Piszka,
    • Camilla S.M. Pang,
    • Mahnaz Abbasian,
    • Maise Al Bakir,
    • Mariam Jamal-Hanjani,
    • Nicholas McGranahan,
    • Charles Swanton,
    • and Christine A. Orengo
    Genome Res. March 2026 36: 561-577; Published in Advance February 19, 2026, doi:10.1101/gr.278663.123
    ...s (Van de Peer et al. 2009; Kondrashov 2012; Wang et al. 2012). Although increased ploidy following WGD incurs fitness costs to an organism, it can confer advantages during times of environmental change and stress, including increased adaptability and robustness of gene regulatory networks (Ebadi et...
    OPEN ACCESS ARTICLE
  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
    ...using long-read mapping-based methods.Finally, while variant calling can utilize existing reference annotations (e.g., from T2T-CHM13v2 or GRCh), direct functional annotation of a assembly can provide additional insights about genes or other functional elements. This is particularly valuable when...
For checked items

Search Results

Next 10 » New Search

Modify Results

Citation format:
Results / page:
Results order:

This search

  • Alert me when new articles matching this search are published
  • Download all citations on this page to my citation manager

Preprint Server



Current Issue

  1. March 2026, 36 (3)
  1. Current Issue
  1. Alert me to new issues of Genome Research