Searching journal content for articles similar to Daubin and Ochman 14 (6): 1036.

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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
    ...of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial s. Genome Biol 10: R65. doi:10.1186/gb-2009-10-6-r65 ↵Daubin V, Ochman H. 2004a. Bacterial s as new gene homes: the genealogy of ORFans in E. coli. Genome Res 14: 1036–1042. doi:10.1101/gr.2231904...
  2. 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
    ...of the entire Streptococcus genus.Soon after the first bacterial was sequenced (Fleischmann et al. 1995), it became clear that the genomic contents varied between individual strains within a prokaryotic species. Variable genomic content is caused by the gain or loss of singleton ORFan genes (Daubin and Ochman...
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  3. LETTER: Operon formation is driven by co-regulation and not by horizontal gene transfer
    • Morgan N. Price,
    • Katherine H. Huang,
    • Adam P. Arkin,
    • and Eric J. Alm
    Genome Res. June 2005 15: 809-819; doi:10.1101/gr.3368805
    ...than individually transcribed genes. We will present evidence from comparative genomics that this is indeed the case. View larger version: In this window In a new window Figure 1. The evolutionary history of genes and operons. For each gene in E. coli K12, we determined which groups of s contained...
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  4. 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
    ...origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external...
  5. Research: Young proteins experience more variable selection pressures than old proteins
    • Anchal Vishnoi,
    • Sergey Kryazhimskiy,
    • Georgii A. Bazykin,
    • Sridhar Hannenhalli,
    • and Joshua B. Plotkin
    Genome Res. November 2010 20: 1574-1581; Published in Advance October 4, 2010, doi:10.1101/gr.109595.110
    ...recognition. Cell 65: 175–187. Cai J, Zhao R, Jiang H, Wang W. 2008. De novo origination of a new protein-coding gene in Saccharomyces cerevisiae. Genetics 179: 487– 496. Daubin V, Ochman H. 2004. Bacterial s as new genes homes: The genealogy of ORFans in E. coli. Genome Res 14: 1036–1042. Domazet-Loso T...
  6. LETTER: Unique genes in giant viruses: Regular substitution pattern and anomalously short size
    • Hiroyuki Ogata and
    • Jean-Michel Claverie
    Genome Res. September 2007 17: 1353-1361; Published in Advance July 25, 2007, doi:10.1101/gr.6358607
    .... Virus Res. 117 : 133 – 144 . ↵ Daubin, V. , Ochman, H. ( 2004 ) Bacterial s as new gene homes: The genealogy of ORFans in E. coli . Genome Res. 14 : 1036 – 1042 . ↵ Daubin, V. , Lerat, E. , Perriere, G. ( 2003 ) The source of laterally transferred genes in bacterial s . Genome Biol. 4 : R57 , doi: 10...
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  7. LETTER: The fate of laterally transferred genes: Life in the fast lane to adaptation or death
    • Weilong Hao and
    • G. Brian Golding
    Genome Res. May 2006 16: 636-643; doi:10.1101/gr.4746406
    ...transfer and parallel evolution in the history of glutathione biosynthesis genes. Genome Biol. 3 : 0025.1 – 0025.16 . ↵ Daubin V. , Ochman H. ( 2004 ) Bacterial s as new gene homes: The genealogy of ORFans in E. coli. Genome Res. 14 : 1036 – 1042 . ↵ Daubin V. , Lerat E. , Perriere G. ( 2003a ) The source...
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