Searching journal content for articles similar to Bohaczuk et al. 34 (12): 2269.

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  1. 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
    ...years has revolutionized our ability to catalog cancer risk variants and understand the genomic landscape of cancer. Early studies relied on targeted sequencing and microarrays to detect genomic and transcriptomic variations enriched in cancer patients, revealing, for example, the prevalence...
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  2. 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
    ...out using tools like Modkit and Jasmine for PacBio or the basecaller Dorado for ONT (see Table 1). Fiber-seq (Stergachis et al. 2020), which requires prior handling of methyltransferases to alter the sample, allows the detection of open chromatin to provide additional insights. Long-read sequencing...
  3. Method: DNA-m6A calling and integrated long-read epigenetic and genetic analysis with fibertools
    • Anupama Jha,
    • Stephanie C. Bohaczuk,
    • Yizi Mao,
    • Jane Ranchalis,
    • Benjamin J. Mallory,
    • Alan T. Min,
    • Morgan O. Hamm,
    • Elliott Swanson,
    • Danilo Dubocanin,
    • Connor Finkbeiner,
    • Tony Li,
    • Dale Whittington,
    • William Stafford Noble,
    • Andrew B. Stergachis,
    • and Mitchell R. Vollger
    Genome Res. November 2024 34: 1976-1986; Published in Advance June 7, 2024, doi:10.1101/gr.279095.124
    ...applied Fiber-seq and fibertools center to resolve the role of CTCF co-occupancy in guiding higher-order chromatin architectures along the ∼175 kbp Epstein–Barr virus (EBV) . CTCF elements within the EBV OriP and LMP loci are known to form a cohesin-dependent loop important for maintaining viral latent...
  4. Mini-Review: Evolution of genome-wide methylation profiling technologies
    • Carolina Montano and
    • Winston Timp
    Genome Res. April 2025 35: 572-582; doi:10.1101/gr.278407.123
    ..., highlighting the ability to detect both structural variants and methylation changes in a single assay. Yamada et al. (2023) further explored the diagnostic potential of targeted LRS in Prader–Willi syndrome (PWS) and Angelman syndrome (AS), two disorders caused by aberrant imprinting in the 15q11.2–q13 region...
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