Searching journal content for articles similar to Qin et al. 34 (1): 85.

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  1. Corrigendum: Corrigendum: A statistical learning method for simultaneous copy number estimation and subclone clustering with single-cell sequencing data
    • Fei Qin,
    • Guoshuai Cai,
    • Christopher I. Amos,
    • and Feifei Xiao
    Genome Res. March 2024 34: 514; doi:10.1101/gr.279293.124
    OPEN ACCESS ARTICLE
  2. 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
    ....beerenwinkel@bsse.ethz.chAbstractIn cancer, genetic and transcriptomic variations generate clonal heterogeneity, leading to treatment resistance. Long-read single-cell RNA sequencing (LR scRNA-seq) has the potential to detect genetic and transcriptomic variations simultaneously. Here, we present LongSom, a computational workflow leveraging...
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  3. Method: Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution
    • Qian Qin,
    • Victoria Popic,
    • Kirsty Wienand,
    • Houlin Yu,
    • Emily White,
    • Akanksha Khorgade,
    • Asa Shin,
    • Christophe Georgescu,
    • Catarina D. Campbell,
    • Arthur Dondi,
    • Niko Beerenwinkel,
    • Francisca Vazquez,
    • Aziz M. Al'Khafaji,
    • and Brian J. Haas
    Genome Res. April 2025 35: 967-986; Published in Advance March 14, 2025, doi:10.1101/gr.279200.124
    ...short-read sequences. Recent advances in long-read isoform sequencing enable the detection of fusion transcripts at unprecedented resolution in bulk and single-cell samples. Here, we developed a new computational tool, CTAT-LR-Fusion, to detect fusion transcripts from long-read RNA-seq with or without...
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  4. Perspective: Applications of single-cell genomics and computational strategies to study common disease and population-level variation
    • Benjamin J. Auerbach,
    • Jian Hu,
    • Muredach P. Reilly,
    • and Mingyao Li
    Genome Res. October 2021 31: 1728-1741; doi:10.1101/gr.275430.121
    ...haplotype-specific copy number changes seeding minor subclones throughout the course of cancer evolution. Furthermore, Alleloscope allows the detection of haplotype-differentiated subclones in single-cell ATAC-seq (scATAC-seq) data to examine the interplay of genetic and epigenetic evolution...
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  5. Method: SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data
    • Hamim Zafar,
    • Nicholas Navin,
    • Ken Chen,
    • and Luay Nakhleh
    Genome Res. November 2019 29: 1847-1859; Published in Advance October 18, 2019, doi:10.1101/gr.243121.118
    ...cannot be represented by a cell lineage tree model.Here, we propose SiCloneFit, a unified statistical framework and computational method that simultaneously addresses the problems of subclonal reconstruction and phylogeny inference from single-cell sequencing data. Our unified model simultaneously (1...
  6. Method: De novo antibody identification in human blood from full-length single B cell transcriptomics and matching haplotype-resolved germline assemblies
    • John Beaulaurier,
    • Lynn Ly,
    • J. Andrew Duty,
    • Carly Tyer,
    • Christian Stevens,
    • Chuan-Tien Hung,
    • Akash Sookdeo,
    • Alex W. Drong,
    • Shreyas Kowdle,
    • Axel Guzman-Solis,
    • Domenico Tortorella,
    • Daniel J. Turner,
    • Sissel Juul,
    • Scott Hickey,
    • and Benhur Lee
    Genome Res. April 2025 35: 929-941; Published in Advance March 21, 2025, doi:10.1101/gr.279392.124
    ...in the remaining clusters (Fig. 3C; Supplemental Table S3).View larger version: In this window In a new window Figure 3. Single-cell expression data from the MBC gate. (A) Uniform Manifold Approximation and Projection (UMAP) visualization of cells clustered by gene expression quantified by short-read sequencing...
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  7. Research: Telomerase-independent survival leads to a mosaic of complex subtelomere rearrangements in Chlamydomonas reinhardtii
    • Frédéric Chaux,
    • Nicolas Agier,
    • Clotilde Garrido,
    • Gilles Fischer,
    • Stephan Eberhard,
    • and Zhou Xu
    Genome Res. September 2023 33: 1582-1598; Published in Advance August 14, 2023, doi:10.1101/gr.278043.123
    ...of approximately 350 copies corresponding to ∼3 Mb. Two other repeated elements, called Suber and Subtile, were found next to Sultan elements at three subtelomeres, called class C. The Suber element, initially named pTANC (Hails et al. 1993), contains the most abundant interstitial telomere sequence (ITS...
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  8. Method: Analyzing rare mutations in metagenomes assembled using long and accurate reads
    • Marcus W. Fedarko,
    • Mikhail Kolmogorov,
    • and Pavel A. Pevzner
    Genome Res. November/December 2022 32: 2119-2133; Published in Advance November 23, 2022, doi:10.1101/gr.276917.122
    .... Additionally, machine-learning-based methods that have been trained on human sequencing data may not perform similarly well for metagenomic data (Sapoval et al. 2022).Simulation models of sequencing dataThe MetaSim simulation model of Illumina reads (Richter et al. 2008), which was used in benchmarking Lo...
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