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  1. Method: Nanopore sequencing identifies high-frequency somatic structural variations in laryngeal squamous cell carcinoma genomes
    • Xuyan Liu,
    • Lin Xia,
    • Yixin Qiao,
    • Yang Li,
    • Yan Huang,
    • Bingyan Yue,
    • Xi Liang,
    • Xin Yang,
    • Honghui Zhang,
    • Jiaxun Zhang,
    • Xiao Chen,
    • Dan Xie,
    • and Jifeng Liu
    Genome Res. April 8, 2026 gr.281046.125; Published in Advance April 8, 2026, doi:10.1101/gr.281046.125
    ...(Beroukhim et al. 2016). Large-scale cancer cohort studies have shown that 63 somatic SVs are the most prevalent class of driver mutations in cancer, vastly outnumbering 64 single nucleotide variants (SNVs) and small insertions/deletions (indels)(Cosenza et al. 2022). 65 Given their abundance and diverse roles...
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  2. Research: Confounding factors in assessing the enriched expression of somatic mutant alleles in bulk tumor samples
    • Kohei Hagiwara,
    • Andrew Thrasher,
    • Nadezhda V. Terekhanova,
    • and Jinghui Zhang
    Genome Res. March 4, 2026 ; Published in Advance March 4, 2026, doi:10.1101/gr.281003.125
    ...(SNVs) can be constrained to certain genomic contexts (e.g., TCA>TGA and hotspots). Although the model parameters can confound the detection of true ASE, elevated AEV can be exploited for RNA-based somatic mutation detection to complement DNAbased approach. Using the TCGA RNA-seq data, we performed de...
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  3. Method: De novo detection of somatic variants in high-quality long-read single-cell RNA sequencing data
    • Arthur Dondi,
    • Nico Borgsmüller,
    • Pedro F. Ferreira,
    • Brian J. Haas,
    • Francis Jacob,
    • Viola Heinzelmann-Schwarz,
    • Tumor Profiler Consortium,
    • and Niko Beerenwinkel
    Genome Res. April 2025 35: 900-913; Published in Advance March 19, 2025, doi:10.1101/gr.279281.124
    ...using cell mutational profiles. LongSom distinguishes somatic SNVs from noise and germline polymorphisms by applying an extensive set of hard filters and statistical tests. Applying LongSom to human ovarian cancer samples, we detected clinically relevant somatic SNVs that were validated against matched...
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  4. Research: Closing the gaps, and improving somatic structural variant analysis and benchmarking using CHM13-T2T
    • Luis F. Paulin,
    • Jeremy Fan,
    • Kieran O'Neill,
    • Erin Pleasance,
    • Vanessa L. Porter,
    • Steven J.M. Jones,
    • and Fritz J. Sedlazeck
    Genome Res. April 2025 35: 621-631; Published in Advance March 17, 2025, doi:10.1101/gr.279352.124
    ...SV benchmark set for COLO829/COLO829BL across four replicates sequenced at different centers with different long-read technologies. We discovered instability of this cell line across these replicates; 346 SVs (1.13%) were only discoverable in a single replicate. We identify 54 somatic SVs, which...
  5. Method: Integrating SNVs and CNAs on a phylogenetic tree from single-cell DNA sequencing data
    • Liting Zhang,
    • Hank W. Bass,
    • Jerome Irianto,
    • and Xian Mallory
    Genome Res. November 2023 33: 2002-2017; Published in Advance November 22, 2023, doi:10.1101/gr.277249.122
    ...data sets shows highly consistent placement of SNV cells and SNVs with the original study while also supporting a refined placement of ATP7B, illustrating SCsnvcna's value in analyzing complex multitumor samples.Cancers result from a combination of abnormal cell growth along with metastasis...
  6. 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
    ...in the tens of thousands), the clustering results from well-profiled scRNA-seq data are relatively distinct, resulting in high accuracy of cell type annotation. Recently, as extensive scRNA-seq data sets are generated and annotated, reference-based annotation methods have gained prominence (Clarke et al. 2021...
  7. Research: Multisite long-read sequencing reveals the early contributions of somatic structural variations to HBV-related hepatocellular carcinoma tumorigenesis
    • Tianfu Zeng,
    • Haotian Liao,
    • Lin Xia,
    • Siyao You,
    • Yanqun Huang,
    • Jiaxun Zhang,
    • Yahui Liu,
    • Xuyan Liu,
    • and Dan Xie
    Genome Res. April 2025 35: 671-685; Published in Advance March 4, 2025, doi:10.1101/gr.279617.124
    ...based on somatic SVs, whereas no such pattern was evident in the case of somatic SNVs (Supplemental Fig. S7B). These results suggest that somatic SVs may represent the primary mutation type in the context of chronic liver disease during the early stages of HCC progression.HCC is characterized by somatic...
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  8. Resource: Multitissue single-nucleus RNA-seq reveals cell type–specific regulatory patterns of alternative polyadenylation in pigs
    • Qiuhan Wen,
    • Zhen Wang,
    • Qi Bao,
    • Tianli Ding,
    • Haihan Zhang,
    • Jianbo Li,
    • Zhuang Liu,
    • Jieping Huang,
    • and Guoqiang Yi
    Genome Res. September 2025 35: 2116-2129; Published in Advance June 16, 2025, doi:10.1101/gr.280095.124
    ...clustering analysis revealed that RBPs associated with 3′ UTR elongation are specifically upregulated in neuronal cells, distinctly segregating them from other somatic cell types (Fig. 6A). This specific expression pattern suggests that neurons may have longer 3′ UTRs. Consistent with this, enhanced PSI...
  9. Research: Mutational scanning of CRX classifies clinical variants and reveals biochemical properties of the transcriptional effector domain
    • James L. Shepherdson,
    • David M. Granas,
    • Jie Li,
    • Zara Shariff,
    • Stephen P. Plassmeyer,
    • Alex S. Holehouse,
    • Michael A. White,
    • and Barak A. Cohen
    Genome Res. October 2024 34: 1540-1552; Published in Advance September 25, 2024, doi:10.1101/gr.279415.124
    ..., with both increases and decreases in activity depending on substitution. While disordered regions lack a fixed 3D structure and are, therefore, often assumed to be relatively insensitive to mutations, our work clearly reveals chemically interpretable patterns in mutational sensitivity.As discussed...
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  10. Research: Global characterization of somatic mutations and DNA methylation changes during vegetative propagation in strawberries
    • Shaoqiang Hu,
    • Xiangguo Zeng,
    • Yuguo Liu,
    • Yongping Li,
    • Minghao Qu,
    • Wen-Biao Jiao,
    • Yongchao Han,
    • and Chunying Kang
    Genome Res. October 2024 34: 1582-1594; Published in Advance October 15, 2024, doi:10.1101/gr.279378.124
    .../deletions (indels) in each regenerated plantlet after transformation (Li et al. 2019). In contrast, much fewer SNVs (<200) and indels (<100) were found in rice transformants (Tang et al. 2018). When the size is taken into account, the mutation frequencies in cotton and rice are still quite different. Somatic...
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