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Genomes and Genes | Vincent DaubinSummaryAffiliation: University of Arizona Country: USA Publications
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Publications
Comment on "The origins of genome complexity"Vincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona. Tuscon, AZ 85721, USA
Science 306:978; author reply 978. 2004- Bacterial genomes as new gene homes: the genealogy of ORFans in E. coliVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, Arizona 85721, USA
Genome Res 14:1036-42. 2004..Rather, ORFans in the genomes of free-living microorganisms apparently derive from bacteriophage and occasionally become established by assuming roles in key cellular functions... - Quartet mapping and the extent of lateral transfer in bacterial genomesVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, USA
Mol Biol Evol 21:86-9. 2004..Here, we focus on one of these methods, quartet mapping, and show that its application can lead to overestimation of the extent of inferred LGT in prokaryotes, particularly when applied to distantly related taxa... - The source of laterally transferred genes in bacterial genomesVincent Daubin
Laboratoire de Biometrie et Biologie Evolutive, UMR CNRS 5558, Universite Claude Bernard Lyon 1, Cedex, France
Genome Biol 4:R57. 2003.... - From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-ProteobacteriaEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, USA
PLoS Biol 1:E19. 2003.... - Evolutionary origins of genomic repertoires in bacteriaEmmanuelle Lerat
Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, Arizona, USA
PLoS Biol 3:e130. 2005..Although our analyses are limited to the gamma-Proteobacteria, these results resolve a long-standing paradox-i.e., the ability to make robust phylogenetic inferences in light of substantial LGT... - Phylogenetics and the cohesion of bacterial genomesVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ, 85721, USA
Science 301:829-32. 2003..Although comparisons of complete gene inventories indicate appreciable gain and loss of genes, orthologs available for phylogenetic reconstruction are consistent with a single tree... - Examining bacterial species under the specter of gene transfer and exchangeHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, 85721, USA
Proc Natl Acad Sci U S A 102:6595-9. 2005..Taken as a whole, the results derived from the analysis of complete gene inventories support several of the current means to recognize and define bacterial species... - Detecting lateral gene transfers by statistical reconciliation of phylogenetic forestsSophie S Abby
Université de Lyon Université Lyon 1 CNRS INRIA UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, 43 Boulevard du 11 Novembre 1918, F 69622 Villeurbanne, France
BMC Bioinformatics 11:324. 2010..In addition, the application of these methods to real data raises the problem of sorting out real and artifactual phylogenetic conflict... - Genomes as documents of evolutionary historyBastien Boussau
Universite de Lyon, UMR 5558, Laboratoire de Biometrie et Biologie Evolutive, 43 Boulevard du 11 Novembre 1918, F 69622 Villeurbanne, France
Trends Ecol Evol 25:224-32. 2010..In this article, we review the recent advances and discuss possible developments towards a comprehensive reconstruction of the history of life... - A bunch of fun-guys: the whole-genome view of yeast evolutionHoward Ochman
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 87521, USA
Trends Genet 21:1-3. 2005..The pattern of genome evolution in yeast differs from that in bacteria apparently as a result of stronger selective constraints on bacterial chromosomes... - Lateral gene transfer as a support for the tree of lifeSophie S Abby
Laboratoire de Biometrie et Biologie Evolutive, Centre National de la Recherche Scientifique, Unite Mixte de Recherche 5558, Universite Lyon 1, F 69622 Villeurbanne, France
Proc Natl Acad Sci U S A 109:4962-7. 2012.... - Databases of homologous gene families for comparative genomicsSimon Penel
Laboratoire de Biometrie et Biologie Evolutive, CNRS, Universite Claude Bernard Lyon 1, 43 bd, du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
BMC Bioinformatics 10:S3. 2009..and phylogenetics. In that context, databases providing users high quality homologous families and sequence alignments as well as phylogenetic trees based on state of the art algorithms are becoming indispensable... - Start-up entities in the origin of new genesVincent Daubin
Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721, USA
Curr Opin Genet Dev 14:616-9. 2004..This invention of such novel functions seems to be founded on a strategy that secures the short-term survival of parasitic elements and thereby contributes to the renovation of gene repertoires in their host... - Comparative genomics and the evolution of prokaryotesSophie Abby
Universite de Lyon, Universite Lyon 1, Centre National de la Recherche Scientifique, UMR5558, Laboratoire de Biometrie et Biologie Evolutive, Villeurbanne, F 69622 cedex, France
Trends Microbiol 15:135-41. 2007..In this review, we present some of the most important recent advances and promising leads in the field of microbial evolutionary genomics... - Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus SileneGabriel A B Marais
Laboratoire de Biometrie et Biologie Evolutive, UMR5558, Universite Lyon 1, Centre National de la Recherche Scientifique, Villeurbanne, France
PLoS ONE 6:e21915. 2011..latifolia and its closest relatives. We estimate that sex chromosomes emerged soon after the split with the ancestor of S. viscosa, the probable closest non-dioecious S. latifolia relative among the species included in our study... - Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraureliaJean-Marc Aury
Genoscope and CNRS UMR 8030, , 91057 Evry, France
Nature 444:171-8. 2006..The conclusion of this analysis is that many genes are maintained after whole-genome duplication not because of functional innovation but because of gene dosage constraints... - Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeographyPhilippe Normand
Universite de Lyon, UMR CNRS, 5557 Ecologie Microbienne, IFR41 Bio Environnement et Santé, Université Lyon I, Villeurbanne 69622 Cedex, France
Genome Res 17:7-15. 2007..The results support the idea that major genome expansions as well as reductions can occur in facultative symbiotic soil bacteria as they respond to new environments in the context of their symbioses... - G+C3 structuring along the genome: a common feature in prokaryotesVincent Daubin
, , Lyon 1, Villeurbanne, France
Mol Biol Evol 20:471-83. 2003.... - A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common historyVincent Daubin
, , , 69622 Villeurbanne Cedex, France
Genome Res 12:1080-90. 2002..We then used this core of genes to infer a tree. This phylogeny presents several differences with the rRNA phylogeny, notably for the position of hyperthermophilic bacteria... - Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD testMarina Zelwer
, , 43, Bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France
Mol Phylogenet Evol 33:687-93. 2004..We show that this new test, ILD-BIONJ, while being much faster, is often more accurate than the ILD test, especially when the alignments compared are simulated under different evolutionary models...