Searching journal content for articles similar to Ahmed et al. 33 (7): 1069.

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  1. Method: Strain-level metagenomic profiling using pangenome graphs with PanTax
    • Wenhai Zhang,
    • Yuansheng Liu,
    • Guangyi Li,
    • Jialu Xu,
    • Enlian Chen,
    • Alexander Schönhuth,
    • and Xiao Luo
    Genome Res. February 2026 36: 405-420; Published in Advance January 14, 2026, doi:10.1101/gr.280858.125
    ...17.Performance evaluationTo evaluate taxonomic classifiers, we rely on metrics like precision, recall, and F1 score, which assess the performance in terms of the identification of taxa (i.e., strains in our case). It is important to realize that these metrics are dominated by performance rates...
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  2. Method: Robust 16S rRNA classification based on a compressed LCA index
    • Omar Ahmed,
    • Christina Boucher,
    • and Ben Langmead
    Genome Res. December 2025 35: 2650-2660; Published in Advance August 25, 2025, doi:10.1101/gr.279846.124
    ...for targeted nanopore sequencing. iScience 24: 102696. doi:10.1016/j.isci.2021.102696 ↵Ahmed O, Rossi M, Boucher C, Langmead B. 2023a. Efficient taxa identification using a pan index. Genome Res 33: 1069–1077. doi:10.1101/gr.277642.123 ↵Ahmed OY, Rossi M, Gagie T, Boucher C, Langmead B. 2023b. SPUMONI 2...
  3. Research: Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins
    • Nikolaos Vakirlis and
    • Anne Kupczok
    Genome Res. June 2024 34: 888-903; Published in Advance July 8, 2024, doi:10.1101/gr.278977.124
    ...: In this window In a new window Figure 2. Large scale-identification of species-specific orphan genes (SSOGs) in the human gut microbiome. (A) The main steps of the computational workflow of similarity searches. (B) Distribution of the SSOG proportion in a given species’ pan. The red dashed line denotes...
  4. Research: A butterfly pan-genome reveals that a large amount of structural variation underlies the evolution of chromatin accessibility
    • Angelo A. Ruggieri,
    • Luca Livraghi,
    • James J. Lewis,
    • Elizabeth Evans,
    • Francesco Cicconardi,
    • Laura Hebberecht,
    • Yadira Ortiz-Ruiz,
    • Stephen H. Montgomery,
    • Alfredo Ghezzi,
    • José Arcadio Rodriguez-Martinez,
    • Chris D. Jiggins,
    • W. Owen McMillan,
    • Brian A. Counterman,
    • Riccardo Papa,
    • and Steven M. Van Belleghem
    Genome Res. October 2022 32: 1862-1875; Published in Advance September 15, 2022, doi:10.1101/gr.276839.122
    ...efficiently (Hill and Robertson 1966). In contrast, if SVs have a similar maladaptive load as SNPs, we expect their abundance on chromosomes to be similar to SNPs, which have a higher abundance on smaller compared with larger chromosomes in Heliconius resulting from the higher recombination rate and thus...
  5. Method: Accurate reconstruction of bacterial pan- and core genomes with PEPPAN
    • Zhemin Zhou,
    • Jane Charlesworth,
    • and Mark Achtman
    Genome Res. November 2020 30: 1667-1679; Published in Advance October 14, 2020, doi:10.1101/gr.260828.120
    ...function (Goodhead and Darby 2015) and should therefore be included in pans. The identification of such gene fragments requires comparisons against intact analogs (Lerat and Ochman 2005), but automatic annotation pipelines instead annotate them as multiple intact genes, reducing the size of the estimated...
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  6. Method: Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome
    • Michael S. Fitzsimons,
    • Mark Novotny,
    • Chien-Chi Lo,
    • Armand E.K. Dichosa,
    • Joyclyn L. Yee-Greenbaum,
    • Jeremy P. Snook,
    • Wei Gu,
    • Olga Chertkov,
    • Karen W. Davenport,
    • Kim McMurry,
    • Krista G. Reitenga,
    • Ashlynn R. Daughton,
    • Jian He,
    • Shannon L. Johnson,
    • Cheryl D. Gleasner,
    • Patti L. Wills,
    • Beverly Parson-Quintana,
    • Patrick S. Chain,
    • John C. Detter,
    • Roger S. Lasken,
    • and Cliff S. Han
    Genome Res. May 2013 23: 878-888; Published in Advance March 14, 2013, doi:10.1101/gr.142208.112
    ..., including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations. Footnotes ↵ 4 Corresponding...
  7. Research: Plant genome evolution in the genus Eucalyptus is driven by structural rearrangements that promote sequence divergence
    • Scott Ferguson,
    • Ashley Jones,
    • Kevin Murray,
    • Rose Andrew,
    • Benjamin Schwessinger,
    • and Justin Borevitz
    Genome Res. April 2024 34: 606-619; Published in Advance April 8, 2024, doi:10.1101/gr.277999.123
    ...was evaluated with benchmarking universal single-copy orthologs (BUSCO) (Manni et al. 2021) and the long terminal repeat (LTR) assembly index (LAI) (Ou et al. 2018). A more complete will contain a high proportion of single-copy BUSCO genes, and all our s were found to be highly BUSCO complete (average: 97...
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