Searching journal content for articles similar to Zeng et al. 35 (4): 671.

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  1. Research: Long-read sequencing reveals HBV integration patterns and oncogenic impact on early-onset hepatocellular carcinoma
    • Yao Wang,
    • Dong Yu,
    • Yue Mei,
    • ZhiDa Fu,
    • Jian Lin,
    • Di Wu,
    • Yuan Yang,
    • and Hongli Yan
    Genome Res. November 2025 35: 2389-2405; Published in Advance September 16, 2025, doi:10.1101/gr.279889.124
    ...and transcriptomic levels, along with their regulatory effects on structural variations (SVs) and gene expression. Functional validation is performed using dual-luciferase assays and cell-based experiments. Our findings reveal that integrated HBV sequences form long concatemers, mediating inter- and intrachromosomal...
  2. Perspective: Unraveling the hidden complexity of cancer through long-read sequencing
    • Qiuhui Li,
    • Ayse G. Keskus,
    • Justin Wagner,
    • Michal B. Izydorczyk,
    • Winston Timp,
    • Fritz J. Sedlazeck,
    • Alison P. Klein,
    • Justin M. Zook,
    • Mikhail Kolmogorov,
    • and Michael C. Schatz
    Genome Res. April 2025 35: 599-620; Published in Advance March 20, 2025, doi:10.1101/gr.280041.124
    ...of the long-read sequencing workflow including downstream analysis options. (B) Somatic SNV and a structural variation in the COLO829 cell line resulting in haplotype-specific copy number change and loss of heterozygosity (data from Keskus et al. 2024). Reads are grouped and colored with the alleles using...
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  3. Research: Strong bias in long-read sequencing prevents assembly of Drosophila melanogaster Y-linked genes
    • A. Bernardo Carvalho,
    • Bernard Y. Kim,
    • and Fabiana Uno
    Genome Res. January 2026 36: 71-82; Published in Advance October 1, 2025, doi:10.1101/gr.280604.125
    ...fails at multiple levels: read initiation (very few reads start within satellite regions), read elongation (satellite-containing reads are shorter on average), and basecalling (quality scores drop as sequencing enters a satellite sequence). These findings challenge the assumption that long-read...
  4. Method: FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data
    • Can Luo,
    • Zimeng Jamie Zhou,
    • Yichen Henry Liu,
    • and Xin Maizie Zhou
    Genome Res. October 2025 35: 2252-2272; Published in Advance August 13, 2025, doi:10.1101/gr.280282.124
    ...FocalSV enables target region–based structural variant assembly and refinement using single-molecule long-read sequencing data Can Luo1,3, Zimeng Jamie Zhou2,3, Yichen Henry Liu2 and Xin Maizie Zhou1,2 1Department of Biomedical Engineering, Vanderbilt University, Nashville, Tennessee 37235, USA; 2...
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  5. Method: Long-read reconstruction of many diverse haplotypes with devider
    • Jim Shaw,
    • Christina Boucher,
    • Yun William Yu,
    • Noelle Noyes,
    • and Heng Li
    Genome Res. December 2025 35: 2637-2649; Published in Advance September 23, 2025, doi:10.1101/gr.280510.125
    ...deep, heterogeneous long-read amplicon sequences.DiscussionWe presented devider, a method for retrieving high-similarity haplotypes from long-read sequencing of heterogeneous sequences. devider leverages a PDBG assembly approach on a subset of informative alleles to disentangle variation...
  6. 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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  7. Method: Long-read RNA sequencing reveals allele-specific N6-methyladenosine modifications
    • Dayea Park and
    • Can Cenik
    Genome Res. April 2025 35: 999-1011; Published in Advance October 29, 2024, doi:10.1101/gr.279270.124
    ...). These assignments were based on 135,380 (replicate 1) and 134,585 (replicate 2) informative positions on the long-reads that overlapped known genetic variation between the strains (210,004 total SNPs).As an orthogonal approach to determine ASE, we used Illumina short-read sequencing. We found that RNA expression...
  8. 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
    ...University, Houston, Texas 77005, USA ↵4 These authors contributed equally to this work. Corresponding author: fritz.sedlazeck@bcm.eduAbstractOver the past decade, long-read sequencing has evolved into a pivotal technology for uncovering the hidden and complex regions of the . Significant cost efficiency...
  9. Perspective: The impact of long-read sequencing on human population-scale genomics
    • Tobias Rausch,
    • Tobias Marschall,
    • and Jan O. Korbel
    Genome Res. April 2025 35: 593-598; doi:10.1101/gr.280120.124
    ...of population-scale and disease studies. This capacity of long-read sequencing to detect genetic variants in regions inaccessible by short-read sequencing is positioning long-read technologies as a pivotal tool for human genetics, revealing connections between previously unexplored genetic variations and human...
  10. Mini-Review: The additional diagnostic yield of long-read sequencing in undiagnosed rare diseases
    • Giulia F. Del Gobbo and
    • Kym M. Boycott
    Genome Res. April 2025 35: 559-571; Published in Advance February 3, 2025, doi:10.1101/gr.279970.124
    ...the two technologies have been summarized elsewhere (Logsdon et al. 2020; Harvey et al. 2023; Mastrorosa et al. 2023; Oehler et al. 2023; van Dijk et al. 2023) and are beyond the scope of this mini-review.Additional diagnostic yield provided by long-read sequencingDetection and resolution of structural...
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