Searching journal content for articles similar to Liu et al. 34 (11): 2025.

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  1. 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
    ...). In a bacterial , the forms of DNA methylation are relatively limited (m6dA, m5C, m4C) and highly motif driven, which fundamentally ease the detection and differentiation of m6dA events from other DNA modifications. In contrast, m6dA events in eukaryotic s are much less abundant, weakly motif driven, and possibly...
  2. Research: Arabidopsis retrotransposon virus-like particles and their regulation by epigenetically activated small RNA
    • Seung Cho Lee,
    • Evan Ernst,
    • Benjamin Berube,
    • Filipe Borges,
    • Jean-Sebastien Parent,
    • Paul Ledon,
    • Andrea Schorn,
    • and Robert A. Martienssen
    Genome Res. April 2020 30: 576-588; Published in Advance April 17, 2020, doi:10.1101/gr.259044.119
    ...with DNase I (Methods), and sequenced cDNA products from WT, ddm1, and ddm1rdr6 using both Illumina short-read and Oxford Nanopore Technologies (ONT) long-read sequencing platforms (Supplemental Fig. S2). The two most productive elements, EVADE and the ATCOPIA52 subfamily element AT3TE76225, constituted 1...
  3. Editorial: Revolutionizing genomics and medicine—one long molecule at a time
    • Ana Conesa,
    • Alexander Hoischen,
    • and Fritz J. Sedlazeck
    Genome Res. November 2024 34: ix-xi; doi:10.1101/gr.280179.124
    ....279292.124 ↵Liu X, Ni Y, Ye L, Guo Z, Tan L, Li J, Yang M, Chen S, Li R. 2024. Nanopore strand-specific mismatch enables de novo detection of bacterial DNA modifications. Genome Res (this issue) 34: 2025–2038. doi:10.1101/gr.279012.124 ↵Lohde M, Wagner GE, Dabernig-Heinz J, Viehweger A, Braun SD, Monecke...
  4. Review: Leveraging the power of long reads for targeted sequencing
    • Shruti V. Iyer,
    • Sara Goodwin,
    • and William Richard McCombie
    Genome Res. November 2024 34: 1701-1718; doi:10.1101/gr.279168.124
    ...binding, crRNAs designed in a strand-directed manner help define sequencing directionality. For detecting duplications, Watson et al. designed plus-strand and minus-strand crRNA guides positioned within the duplicated sequence. Dephosphorylated DNA was split into two separate strand-specific cleavage...
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