Searching journal content for articles similar to Lefébure et al. 27 (6): 1016.

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  1. Method: Label-free selection of marker genes in single-cell and spatial transcriptomics with geneCover
    • An Wang,
    • Stephanie Hicks,
    • Donald Geman,
    • and Laurent Younes
    Genome Res. December 2025 35: 2744-2755; Published in Advance November 12, 2025, doi:10.1101/gr.280539.125
    ...aim to select gene panels that effectively recover the underlying structure of the entire transcriptome. For example, PERSIST (Covert et al. 2023) selects genes that are maximally predictive of the overall gene expression profile using a concrete autoencoder network. Similarly, SCMER (Liang et al...
  2. Method: Highly accurate reference and method selection for universal cross–data set cell type annotation with CAMUS
    • Qunlun Shen,
    • Shuqin Zhang,
    • and Shihua Zhang
    Genome Res. November 2025 35: 2527-2538; Published in Advance October 1, 2025, doi:10.1101/gr.280821.125
    ...–method pairs, which is positively correlated with the corresponding actual accuracy. The CAMUS score serves as a predictor to estimate annotation accuracy for users.CAMUS enables highly accurate reference selection for cross-species annotationTo demonstrate the effectiveness of CAMUS in prioritizing...
  3. Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
    • Xue Dong,
    • Mengzhu Hu,
    • Xiaonan Cui,
    • Wenjian Zhou,
    • Jingtao Cai,
    • Guangyao Mao,
    • and Weiyang Shi
    Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
    ...washes. Fluorescence microscopy confirmed that this approach effectively eliminated unwanted signal amplification (Supplemental Fig. 1D). To further validate the importance of stringent washing conditions, we cultured HEK293 (human) and NIH/3T3 (mouse) cells on adjacent regions of a slide and selectively...
  4. Method: EnDeep4mC predicts DNA N4-methylcytosine sites using a dual-adaptive feature encoding framework in deep ensembles
    • Shuyu Zhang,
    • Quan Zou,
    • Mengting Niu,
    • Zhibin Lv,
    • Antony Stalin,
    • and Ximei Luo
    Genome Res. March 2026 36: 589-599; Published in Advance February 17, 2026, doi:10.1101/gr.280977.125
    ...models (Dietterich 2000; Kuncheva and Whitaker 2003), we constructed three DL networks—CNN, Bi-LSTM, and Transformer—to collaboratively capture multiscale sequence features (for visual effect, Supplemental Fig. S2). This principled selection, validated by subsequent quantitative diversity analysis...
    OPEN ACCESS ARTICLE
  5. Method: Robust and efficient annotation of cell states through gene signature scoring
    • Laure Ciernik,
    • Agnieszka Kraft,
    • Florian Barkmann,
    • Josephine Yates,
    • and Valentina Boeva
    Genome Res. March 2026 36: 630-644; Published in Advance February 18, 2026, doi:10.1101/gr.280926.125
    ...of constructing a valid control gene set. Overall, ANS induced the smallest bias, confirming the proposed strategy for control gene selection as the optimal one.The influence of cell-type proportions, batch effects, signature length, and inclusion of irrelevant genes on gene signature scoringThe mean control...
    OPEN ACCESS ARTICLE
  6. 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
    ...heritable phenotype. Additionally, SPCs improve rare variant association analyses, reducing genomic inflation (e.g., from 7.6 to 1.2 in one analysis), and provide more accurate heritability estimates. Spatial autocorrelation analysis further confirms the ability of SPCs to account for environmental effects...
    OPEN ACCESS ARTICLE
  7. 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
    ...processes of selection on somatic mutations, driving tumor growth through aberrant regulation of the cell cycle. Somatic mutations caused by multiple endogenous and exogenous factors are mostly neutral passengers, with only a few drivers of clonal expansion under strong positive selection. Cancer genomic...
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  8. Research: Degrees of convergent evolution in rodent adaptations to arid environments
    • Domitille Chalopin,
    • Carine Rey,
    • Jeremy Ganofsky,
    • Juliana Blin,
    • Pascale Chevret,
    • Marion Mouginot,
    • Laurent Guéguen,
    • Bastien Boussau,
    • Sophie Pantalacci,
    • and Marie Sémon
    Genome Res. March 2026 36: 472-486; Published in Advance January 21, 2026, doi:10.1101/gr.280089.124
    ...of genomic and transcriptomic convergence.Here we studied the effects of timescale on repeated genomic and transcriptomic evolution associated with transition to arid environments (Fig. 1A). First, we quantified signals of repeated evolution at two timescales, corresponding to the order Rodentia...
    OPEN ACCESS ARTICLE
  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
    ...). Concurrently, comparative genomic analyses have become increasingly imperative for inferring HI mechanisms (Moran et al. 2021; Mohan et al. 2024). On one hand, HIs are predominantly polygenic (Nosil et al. 2021), requiring whole- approaches to unravel subtle, interconnected effects that traditional genetic...
  10. 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
    ...were, however, shorter than telomeres at other extremities, indicative of a negative cis effect.Overall, Y′ elements might provide a local genomic feature as a cause for interextremity TL differences, both through their trans and cis effects. Whether the Y′ element directly regulates TL through...
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