Searching journal content for articles similar to Burger et al. 34 (12): 2244.

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  1. Method: A high-throughput screening method for selecting feature SNPs to evaluate breed diversity and infer ancestry
    • Meilin Zhang,
    • Heng Du,
    • Yu Zhang,
    • Yue Zhuo,
    • Zhen Liu,
    • Yahui Xue,
    • Lei Zhou,
    • Sixuan Zhou,
    • Wanying Li,
    • and Jian-Feng Liu
    Genome Res. August 2025 35: 1875-1886; Published in Advance July 15, 2025, doi:10.1101/gr.280176.124
    ...for screening feature SNPs from high-coverage WGS is still imperative.Furthermore, the traditional ancestry inference methods are mainly based on clustering algorithms, such as STRUCTURE (Pritchard et al. 2000) and ADMIXTURE (Kosoy et al. 2009), and conduct ancestry inference through an unsupervised analysis...
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  2. Method: STCC enhances spatial domain detection through consensus clustering of spatial transcriptomics data
    • Congcong Hu,
    • Nana Wei,
    • Jiyuan Yang,
    • Hua-Jun Wu,
    • and Xiaoqi Zheng
    Genome Res. June 2025 35: 1415-1428; Published in Advance May 12, 2025, doi:10.1101/gr.280031.124
    ...the resilience of specific consensus strategies in maintaining clustering accuracy despite variations in the number of clusters, reinforcing their applicability in complex ST data sets.Finally, we visualized the clustering results and performed trajectory inference. By taking the BZ5 slice as an example, all...
  3. Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
    • Yanis Zekri,
    • Sebastian Gregoricchio,
    • Elif Yapıcı,
    • Chia-Chi Flora Huang,
    • Tunç Morova,
    • Umut Berkay Altıntaş,
    • Gozde Korkmaz,
    • Nathan A. Lack,
    • and Wilbert Zwart
    Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
    ...with distinct copy number variations (CNVs) (Kumaran et al. 2017; Wilcox et al. 2023). Using CopywriteR (Kuilman et al. 2015), which infers DNA copy from off-target sequencing reads, we reanalyzed ESR1 ChIP-seq data sets from normal breast tissue, primary tumors, liver metastases, and breast recurrences from...
  4. Method: Deep structural clustering reveals hidden systematic biases in RNA sequencing data
    • Qiang Su,
    • Yi Long,
    • Deming Gou,
    • Junmin Quan,
    • Xiaoming Zhou,
    • and Qizhou Lian
    Genome Res. November 2025 35: 2563-2577; Published in Advance September 19, 2025, doi:10.1101/gr.280713.125
    ...and robustness against conventional machine learning techniques, including Gaussian mixture models (GMM-only), principal component analysis-based GMMs, k-means clustering, and hierarchical clustering. These validations, using an extensive and diverse array of data sets, including synthetic RNA constructs...
  5. Research: Hierarchical architecture of neo-sex chromosomes and accelerated adaptive evolution in tortricid moths
    • Fangyuan Yang,
    • Li-Jun Cao,
    • Petr Nguyen,
    • Zhong-Zheng Ma,
    • Jin-Cui Chen,
    • Wei Song,
    • and Shu-Jun Wei
    Genome Res. January 2025 35: 66-77; Published in Advance January 6, 2025, doi:10.1101/gr.279569.124
    ...∼124 million years ago, accompanied by an SA fusion between the Merian elements M(20 + 17) and MZ. In contrast to partial autosomal fusions, the fused neo-Z Chromosome developed a hierarchical architecture, in which the three elements exhibit heterogeneous sequence features and evolutionary patterns...
  6. Method: Fast and space-efficient taxonomic classification of long reads with hierarchical interleaved XOR filters
    • Jens-Uwe Ulrich and
    • Bernhard Y. Renard
    Genome Res. June 2024 34: 914-924; Published in Advance June 17, 2024, doi:10.1101/gr.278623.123
    ...taxonomic classification methods have large computational requirements. This issue motivated us to develop a new data structure for fast and memory-efficient querying of long reads. Here, we present Taxor as a new tool for long-read metagenomic classification using a hierarchical interleaved XOR filter data...
  7. Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
    • Samuel T. Horsfield,
    • Gerry Tonkin-Hill,
    • Nicholas J. Croucher,
    • and John A. Lees
    Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
    ...homologous genes do not share enough sequence to be placed in the same cluster (Zhou et al. 2020; Tonkin-Hill et al. 2023). Orthologs may also be given inconsistent functional annotations (termed an “annotation error”), leading to ambiguity during functional inference of gene families (Tonkin-Hill et al...
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  8. Method: BINDER achieves accurate identification of hierarchical TADs by comprehensively characterizing consensus TAD boundaries
    • Yangyang Liu,
    • Bingqiang Liu,
    • and Juntao Liu
    Genome Res. May 2025 35: 1194-1208; Published in Advance March 17, 2025, doi:10.1101/gr.279647.124
    ...in mice housing the α-globin gene cluster, delineate the chromatin region where enhancers gain access and interact with responsive promoters, which underscored the association of hierarchical TADs with gene-specific regulation. Moreover, several studies have documented a category of partially overlapping...
  9. Method: Complex hierarchical structures in single-cell genomics data unveiled by deep hyperbolic manifold learning
    • Tian Tian,
    • Cheng Zhong,
    • Xiang Lin,
    • Zhi Wei,
    • and Hakon Hakonarson
    Genome Res. February 2023 33: 232-246; Published in Advance February 27, 2023, doi:10.1101/gr.277068.122
    ...; Amodio et al. 2019; Moon et al. 2019; Wolf et al. 2019), clustering (Levine et al. 2015; Wang et al. 2017; Tian et al. 2019), and pseudotime inference (Haghverdi et al. 2016; Qiu et al. 2017). Visualizing large-scale single-cell data in low dimensions will effectively reveal high-level structural...
  10. Method: Inferring disease progression stages in single-cell transcriptomics using a weakly supervised deep learning approach
    • Fabien Wehbe,
    • Levi Adams,
    • Jordan Babadoudou,
    • Samantha Yuen,
    • Yoon-Seong Kim,
    • and Yoshiaki Tanaka
    Genome Res. January 2025 35: 135-146; Published in Advance December 2, 2024, doi:10.1101/gr.278812.123
    ...between epileptogenic and nonepileptogenic cells in CL-MES and CL2 cluster. (CL) Classical, (MES) mesenchymal, and (PN) proneural.To validate the reliability of the inferred disease score, we identified 284 and 193 genes whose expression in oligodendrocytes were positively and negatively correlated...
    OPEN ACCESS ARTICLE
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