Searching journal content for articles similar to Wang et al. 35 (11): 2389.

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  1. 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
    ...of HCC. Long-read RNA sequencing reveals that some HBV-induced SVs impact cancer-associated genes, with TRAs being capable of inducing the formation of fusion genes. These findings enhance our understanding of somatic SVs in HCC and their role in early tumorigenesis.As the most prevalent form of primary...
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  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
    ...our understanding of inherited variations in cancer. Kramer et al. (2024) performed long-read whole- sequencing with ONT PromethION on three families with early onset cancer probands, including two colorectal cancer trios and a quad with two siblings affected by testicular cancer, all with unaffected...
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  3. 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
    ...variants in the transcriptome (Glinos et al. 2022). Furthermore, long-read sequencing enables comprehensive analysis of splicing (Tilgner et al. 2015, 2018; Joglekar et al. 2021) which has fundamental importance for determining mRNA modifications due to their dependence on splicing patterns and transcript...
  4. 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...
  5. 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
    ...methods.Two leading long-read sequencing technologies currently dominate the market and have significantly impacted the genomics field (Fig. 1A): Pacific Biosciences (PacBio) HiFi and Oxford Nanopore Technologies (ONT) sequencing. While both technologies produce continuous long reads, they present...
  6. 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
    ...55421, USA Corresponding author: jshaw@ds.dfci.harvard.eduAbstractReconstructing exact haplotypes is important when sequencing a mixture of similar sequences. Long-read sequencing can connect distant alleles to disentangle similar haplotypes, but handling sequencing errors requires specialized...
  7. Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
    • Carolina Monzó,
    • Adam Frankish,
    • and Ana Conesa
    Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
    ...annotation of transcriptome diversity. (A) Benefits and challenges of annotating the transcriptome diversity revealed by long-read sequencing methods. Challenges include storage, interpretation, and visualization of vast amounts of transcripts and are outweighed by the benefits of using a comprehensive...
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  8. 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
    ...to genetic variants (Cheung et al. 2023). DNA methylation patterns captured by long-read sequencing can help reveal the parent of origin of genetic variation extending to chromosome-length haplotypes, as well as detect parent-specific methylation patterns to help resolve genomic imprinting and disease...
  9. Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
    • Alicja Pacholewska,
    • Matthias Lienhard,
    • Mirko Brüggemann,
    • Heike Hänel,
    • Lorina Bilalli,
    • Anja Königs,
    • Felix Heß,
    • Kerstin Becker,
    • Karl Köhrer,
    • Jesko Kaiser,
    • Holger Gohlke,
    • Norbert Gattermann,
    • Michael Hallek,
    • Carmen D. Herling,
    • Julian König,
    • Christina Grimm,
    • Ralf Herwig,
    • Kathi Zarnack,
    • and Michal R. Schweiger
    Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
    ...mediated by mutated SF3B1 in CLL (bulk or single cell) (Tang et al. 2020; Peng et al. 2024) and MDS (single-cell) (Cortés-López et al. 2023).Here, we used long-read Iso-Seq (Pacific Biosciences [PacBio]) sequencing of 44 patients to investigate the impact of SF3B1 mutations on alternative splicing. Our...
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  10. 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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