Searching journal content for articles similar to Sharim et al. 29 (4): 646.

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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
    .... 2020) or Strainy for bacterial strain phasing (Table 1; Kazantseva et al. 2024). However, specialized methods for phasing multiple cancer clones are yet to be developed.De novo assembly, showcased by many recent germline long-read studies, could also reveal somatic variation in cryptic and difficult-to-map...
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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
    ..., Sundararajan K, Brown RR, Mishra R, Detweiler AM, Neff N, Miga KH, Straight AF, et al. 2022b. DiMeLo-seq: a long-read, single-molecule method for mapping protein–DNA interactions wide. Nat Methods 19: 711–723. doi:10.1038/s41592-022-01475-6 ↵Amarasinghe SL, Su S, Dong X, Zappia L, Ritchie ME, Gouil Q. 2020...
  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
    ...long-reads and surpassing the capabilities of antibody-based short-read approaches. This technological advance will further our understanding of the role of genetics in determining mRNA modifications.Allele-specific expression (ASE) refers to the differences in gene expression from two alleles...
  4. 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
    ...-throughput sequencing is challenging. Here, we applied long-read nanopore sequencing and multisite sampling in a cohort of 42 samples from five patients. We found that adjacent nontumor tissue is not entirely normal, as significant somatic SV alterations were detected in these nontumor s. The adjacent nontumor tissue...
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  5. 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
    ...-nucleotide resolution. Long-read epigenetic studies encompass both the direct identification of native cytosine methylation and the identification of exogenously placed DNA N6-methyladenine (DNA-m6A). However, detecting DNA-m6A modifications using single-molecule sequencing, as well as coprocessing single-molecule...
  6. Method: PoreMeth2 for decoding the evolution of methylome alterations with nanopore sequencing
    • Gianluca Mattei,
    • Marta Baragli,
    • Barbara Gega,
    • Alessandra Mingrino,
    • Martina Chieca,
    • Tommaso Ducci,
    • Gianmaria Frigè,
    • Luca Mazzarella,
    • Romina D'Aurizio,
    • Francesco De Logu,
    • Romina Nassini,
    • Pier Giuseppe Pelicci,
    • and Alberto Magi
    Genome Res. November 2025 35: 2501-2512; Published in Advance October 20, 2025, doi:10.1101/gr.280259.124
    ...to regions with high CpG density (more than two to three CpG per 100 bp) (Sun et al. 2015).However, the past decade has seen the emergence of long-read sequencing (LRS) technologies, based on nanopore sequencing (Clarke et al. 2009) and on single-molecule real-time (SMRT) sequencing (Rhoads and Au 2015...
  7. Method: Using long-read CAGE sequencing to profile cryptic-promoter-derived transcripts and their contribution to the immunopeptidome
    • Ju Heon Maeng,
    • H. Josh Jang,
    • Alan Y. Du,
    • Shin-Cheng Tzeng,
    • and Ting Wang
    Genome Res. December 2023 33: 2143-2155; Published in Advance December 8, 2023, doi:10.1101/gr.277061.122
    ...improve immunopeptidome detection by incorporating TE and other tumor transcripts into the proteome database. By applying our methods to human lung cancer cell line H1299 data, we show that long-read technology significantly improves mapping of promoters with low mappability scores and that LRCAGE...
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  8. Method: Nondestructive enzymatic deamination enables single-molecule long-read amplicon sequencing for the determination of 5-methylcytosine and 5-hydroxymethylcytosine at single-base resolution
    • Zhiyi Sun,
    • Romualdas Vaisvila,
    • Laura-Madison Hussong,
    • Bo Yan,
    • Chloé Baum,
    • Lana Saleh,
    • Mala Samaranayake,
    • Shengxi Guan,
    • Nan Dai,
    • Ivan R. Corrêa, Jr.,
    • Sriharsa Pradhan,
    • Theodore B. Davis,
    • Thomas C. Evans, Jr.,
    • and Laurence M. Ettwiller
    Genome Res. February 2021 31: 291-300; Published in Advance January 19, 2021, doi:10.1101/gr.265306.120
    ...sequencing platforms and produces accurate identification of both 5mC and 5hmC. Most significantly, at single-molecule resolution LR-EM-seq coupled with long-read sequencing technologies (PacBio and Nanopore) can provide complete 5mC and 5hmC information of entire molecules (Fig. 3C) and thus make...
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  9. Method: Simultaneous assessment of human genome and methylome data in a single experiment using limited deamination of methylated cytosine
    • Bo Yan,
    • Duan Wang,
    • and Laurence Ettwiller
    Genome Res. June 2024 34: 904-913; Published in Advance June 10, 2024, doi:10.1101/gr.278294.123
    ....Simultaneous germline variation and methylation identification are now routinely performed using long-read sequencing (Rand et al. 2017; Simpson et al. 2017) in the context of native DNA for which no prior amplification has been performed, limiting the range of applications to direct methylation sequencing. Comparison...
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  10. Method: Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing
    • Shijia Zhu,
    • John Beaulaurier,
    • Gintaras Deikus,
    • Tao P. Wu,
    • Maya Strahl,
    • Ziyang Hao,
    • Guanzheng Luo,
    • James A. Gregory,
    • Andrew Chess,
    • Chuan He,
    • Andrew Xiao,
    • Robert Sebra,
    • Eric E. Schadt,
    • and Gang Fang
    Genome Res. July 2018 28: 1067-1078; Published in Advance May 15, 2018, doi:10.1101/gr.231068.117
    ...(specific to the REs used) and therefore provide a largely incomplete view of m6dA methylome in any given organism.Single-molecule real-time (SMRT) sequencing (Eid et al. 2009) by Pacific Biosciences enabled the -wide mapping of m6dA in prokaryotes at single-nucleotide resolution (Fang et al. 2012...
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