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  1. Resource: Whole-genome sequencing of diverse 351 cultured prokaryotes including as-yet-unsequenced type strains
    • Shingo Kato,
    • Sachiko Masuda,
    • Arisa Shibata,
    • Takashi Itoh,
    • Mitsuo Sakamoto,
    • Ken Shirasu,
    • and Moriya Ohkuma
    Genome Res. April 2026 36: 875-884; Published in Advance April 7, 2026, doi:10.1101/gr.281026.125
    .... 2021). BGCs were detected using antiSMASH version 7.1.0 (Blin et al. 2023). Plasmids and viruses/phages were identified using geNomad version 1.8.1 (Camargo et al. 2024), mob-suite version 3.1.9 (Robertson and Nash 2018), and VirSorter version 2.2.4 (Guo et al. 2021).The quality of the determined s...
  2. Research: Single-cell sequencing provides clues about the host interactions of segmented filamentous bacteria (SFB)
    • Sünje J. Pamp,
    • Eoghan D. Harrington,
    • Stephen R. Quake,
    • David A. Relman,
    • and Paul C. Blainey
    Genome Res. June 2012 22: 1107-1119; Published in Advance March 20, 2012, doi:10.1101/gr.131482.111
    ...-mouse-NYU indicate the borders of contigs. Two similar flagellins (FliC3, and FliC4) in SFB-mouse-Japan are encoded at a position where only one copy is observed in the other s; sequence fragments from single cell SFB suggest the presence of two flagellins as well (this study). See Supplemental Figure S9...
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  3. Method: Discovery of recurrent structural variants in nasopharyngeal carcinoma
    • Anton Valouev,
    • Ziming Weng,
    • Robert T. Sweeney,
    • Sushama Varma,
    • Quynh-Thu Le,
    • Christina Kong,
    • Arend Sidow,
    • and Robert B. West
    Genome Res. February 2014 24: 300-309; Published in Advance November 8, 2013, doi:10.1101/gr.156224.113
    ...mapping split reads, which pinpoint breakpoint positions with nearly base-pair level accuracy. As a final filter, SMASH performs sequence homology Genome Research 301 www..org Structural variant discovery in NPC comparison of regions flanking the breakpoints using local alignment (Smith and Waterman 1981...
  4. Method: BiosyntheticSPAdes: reconstructing biosynthetic gene clusters from assembly graphs
    • Dmitry Meleshko,
    • Hosein Mohimani,
    • Vittorio Tracanna,
    • Iman Hajirasouliha,
    • Marnix H. Medema,
    • Anton Korobeynikov,
    • and Pavel A. Pevzner
    Genome Res. August 2019 29: 1352-1362; Published in Advance June 3, 2019, doi:10.1101/gr.243477.118
    ...in publicly available s, as found in the antiSMASH database (https://antismash-db.secondarymetabolites.org/#!/stats). Since NRPSs are very common (albeit elusive) in diverse bacterial data sets (Mukherjee et al. 2017) and since the downstream peptidogenomics analysis of NRPs is greatly impaired by fragmented...
  5. Review: A systematic guide for identifying transcription factors that directly regulate the expression of a gene of interest
    • Andrew D. Bates,
    • Dawid Grzela,
    • Maciej Studzian,
    • Louise Brennan,
    • Moli Williams,
    • Conor Fawcett,
    • Beth Hammond,
    • Manreen Grewal,
    • Marcin Ratajewski,
    • Lukasz Pulaski,
    • and Urszula L. McClurg
    Genome Res. March 2026 36: 433-459; Published in Advance February 17, 2026, doi:10.1101/gr.281154.125
    ...et al. 2018), or Halo- (Tovell et al. 2019) and SMASh-tags (Chung et al. 2015), allow acute and reversible depletion of TF proteins in response to a small molecule. These methods are particularly valuable because they bypass transcriptional adaptation and permit rapid TF loss, thereby minimizing...
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