Searching journal content for articles similar to Lomsadze et al. 28 (7): 1079.

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  1. Review: De novo gene birth and the conundrum of ORFan genes in bacteria
    • Md. Hassan uz-Zaman and
    • Howard Ochman
    Genome Res. August 2025 35: 1679-1688; Published in Advance July 10, 2025, doi:10.1101/gr.280157.124
    ...; Stern and Han 2022). Remote homology has been detected by searching hidden Markov model profiles derived from gene alignments against outgroup sequence or profile databases (Remmert et al. 2011; Lobb et al. 2015). The recent advent of protein structure prediction tools, such as ESMFold (Lin et al. 2023...
  2. Method: Accurate and fast graph-based pangenome annotation and clustering with ggCaller
    • Samuel T. Horsfield,
    • Gerry Tonkin-Hill,
    • Nicholas J. Croucher,
    • and John A. Lees
    Genome Res. September 2023 33: 1622-1637; Published in Advance August 24, 2023, doi:10.1101/gr.277733.123
    ...the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We...
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  3. Research: Parallel evolution of transcriptome architecture during genome reorganization
    • Sung Ho Yoon,
    • David J. Reiss,
    • J. Christopher Bare,
    • Dan Tenenbaum,
    • Min Pan,
    • Joseph Slagel,
    • Robert L. Moritz,
    • Sujung Lim,
    • Murray Hackett,
    • Angeli Lal Menon,
    • Michael W.W. Adams,
    • Adam Barnebey,
    • Steven M. Yannone,
    • John A. Leigh,
    • and Nitin S. Baliga
    Genome Res. November 2011 21: 1892-1904; Published in Advance July 12, 2011, doi:10.1101/gr.122218.111
    ...architectures Wehave previously demonstrated through TA analysis of Hsa that even the of a simple prokaryote is fraught with a higher than anticipated prevalence of transcriptional promoters inside genes and operons (Koide et al. 2009). Further, we demonstrated that conditional activation of such promoters...
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