Characterization of species-specific genes using a flexible, web-based querying systemRobert L Charlebois
NeuroGadgets Inc, www neurogadgets com, Ottawa, Ontario, Canada
FEMS Microbiol Lett 225:213-20. 2003
..Using a dual-threshold approach, we conclude that these are characteristics of true species-specific genes, rather than artifacts of mis-annotation...
- Inferring genome trees by using a filter to eliminate phylogenetically discordant sequences and a distance matrix based on mean normalized BLASTP scores
G D Paul Clarke
NeuroGadgets Inc, Ottawa, Ontario K1G 4B5, Canada
J Bacteriol 184:2072-80. 2002
..Many but not all features of the genome tree from which PDSs were excluded are consistent with the 16S rRNA tree...
- Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
Dave MacLeod
GenomeAtlantic, 1721 Lower Water Street, Suite 401, Halifax, NS, B3J 1S5, Canada
BMC Evol Biol 5:27. 2005
..Indeed, even when the true history is a mixture of vertical descent for some genes and lateral gene transfer (LGT) for others, such methods produce unique topologies...
- GANN: genetic algorithm neural networks for the detection of conserved combinations of features in DNA
Robert G Beiko
Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
BMC Bioinformatics 6:36. 2005
..The consideration of structural features requires the development of new detection tools that can deal with data types other than primary sequence...
- Microbial phylogenomics: Branching out
Robert L Charlebois
Department of Biology, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
Nature 421:217. 2003
- Distributional profiles of homologous open reading frames among bacterial phyla: implications for vertical and lateral transmission
Mark A Ragan
Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
Int J Syst Evol Microbiol 52:777-87. 2002
..ORFs that are neither distributed universally among the Bacteria, nor necessarily shared with topologically adjacent lineages, are preferentially enriched in large bacterial genomes...
- Phylogenetic analyses of cyanobacterial genomes: quantification of horizontal gene transfer events
Olga Zhaxybayeva
Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia B3H 1X5, Canada
Genome Res 16:1099-108. 2006
..However, in interphylum as compared to intraphylum transfers, the proportion of metabolic (operational) gene transfers increases, while the proportion of informational gene transfers decreases...
- Weighted genome trees: refinements and applications
Uri Gophna
Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia
J Bacteriol 187:1305-16. 2005
..Comparisons of results obtained with different methods can provide further clues to major events and processes in genome evolution...
- Have archaeal genes contributed to bacterial virulence?
Uri Gophna
Genome Atlantic and Department of Biochemistry and Molecular Biology, Dalhousie University, 5850 College Street, Halifax, Nova Scotia B3H 1X5, Canada
Trends Microbiol 12:213-9. 2004
- Ancient lateral gene transfer in the evolution of Bdellovibrio bacteriovorus
Uri Gophna
Department of Molecular Microbiology and Biotechnology, The George S Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel
Trends Microbiol 14:64-9. 2006
..Although there might be little evidence for the extensive recent transfer of genes, we demonstrate that ancient lateral gene acquisition has shaped the B. bacteriovorus genome to a great extent...
