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List of works by Vincent Daubin

A Bayesian method for analyzing lateral gene transfer.

scientific article

A bunch of fun-guys: the whole-genome view of yeast evolution.

scientific article published on January 2005

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history

scientific article

Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium.

scientific article

Bacterial genomes as new gene homes: the genealogy of ORFans in E. coli

scientific article

Bacterial molecular phylogeny using supertree approach.

scientific article published on January 2001

Comment on "The Origins of Genome Complexity"

scientific article published in Science

Comparative genomics and the evolution of prokaryotes.

scientific article published on 7 February 2007

Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations

scientific article (publication date: June 2009)

Contrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria

scientific article

Databases of homologous gene families for comparative genomics

scientific article

DeCoSTAR: Reconstructing the Ancestral Organization of Genes or Genomes Using Reconciled Phylogenies

scientific article published on 8 April 2017

Dealing with incongruence in phylogenomic analyses

scientific article published on December 2008

Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests

scientific article

Detecting phylogenetic incongruence using BIONJ: an improvement of the ILD test

scientific article published in December 2004

Divergence between Drosophila santomea and allopatric or sympatric populations of D. yakuba using paralogous amylase genes and migration scenarios along the Cameroon volcanic line.

scientific article

Ecological networks to unravel the routes to horizontal transposon transfers

scientific article published on 15 February 2017

Efficient exploration of the space of reconciled gene trees

scientific article

Evolution of gene neighborhoods within reconciled phylogenies

scientific article published on September 2012

Evolutionary origins of genomic repertoires in bacteria

scientific article

Examining bacterial species under the specter of gene transfer and exchange

scientific article

From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria

scientific article

G+C3 Structuring Along the Genome: A Common Feature in Prokaryotes

scientific article published on 05 March 2003

GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands

scientific article published on 6 February 2015

Gene Acquisitions from Bacteria at the Origins of Major Archaeal Clades Are Vastly Overestimated

scientific article published on 4 November 2015

Gene transfers can date the tree of life

article

Gene transfers, like fossils, can date the Tree of Life

article

Genome Evolution: Mutation Is the Main Driver of Genome Size in Prokaryotes

scientific article published on 01 October 2020

Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography

scientific article (publication date: 2007)

Genome-scale coestimation of species and gene trees.

scientific article published on 6 November 2012

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

scientific article

Genomes as documents of evolutionary history

scientific article published on 31 October 2009

Genomic species are ecological species as revealed by comparative genomics in Agrobacterium tumefaciens.

scientific article

Global trends of whole-genome duplications revealed by the ciliate Paramecium tetraurelia

scientific article

High-quality sequence clustering guided by network topology and multiple alignment likelihood

scientific article

Horizontal Gene Transfer and the History of Life

scientific article

Lateral gene transfer as a support for the tree of life

scientific article

Lateral gene transfer from the dead

scientific article (publication date: May 2013)

Lateral gene transfer, rearrangement, reconciliation

scientific article

Les transferts horizontaux de gènes et l’arbre de la vie ⬇️

scientific article published on August 22, 2012

Modeling gene family evolution and reconciling phylogenetic discord.

scientific article published on January 2012

Models, algorithms and programs for phylogeny reconciliation

scientific article published on September 2011

Multiple nuclear gene phylogenetic analysis of the evolution of dioecy and sex chromosomes in the genus Silene

scientific article

Origins of major archaeal clades do not correspond to gene acquisitions from bacteria

article

Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations

scientific article (publication date: 23 October 2012)

Phylogenetic reconciliation

scientific article published on 3 November 2022

Phylogenetics and the cohesion of bacterial genomes

scientific article

Phylogeny of the class Actinobacteria revisited in the light of complete genomes. The orders 'Frankiales' and Micrococcales should be split into coherent entities: proposal of Frankiales ord. nov., Geodermatophilales ord. nov., Acidothermales ord. n

scientific article

Quartet mapping and the extent of lateral transfer in bacterial genomes

scientific article

RecPhyloXML: a format for reconciled gene trees

article

Reconstruction of an ancestral Yersinia pestis genome and comparison with an ancient sequence

scientific article

Reductive genome evolution at both ends of the bacterial population size spectrum.

scientific article

Ribosomal proteins: toward a next generation standard for prokaryotic systematics?

scientific article published on 28 February 2014

Single acquisition of protelomerase gave rise to speciation of a large and diverse clade within the Agrobacterium/Rhizobium supercluster characterized by the presence of a linear chromid.

scientific article published on 17 January 2014

Start-up entities in the origin of new genes

scientific article

TPMS: a set of utilities for querying collections of gene trees

scientific article

The inference of gene trees with species trees

scientific article

The origin of eukaryotes and their relationship with the Archaea: are we at a phylogenomic impasse?

scientific article published on 01 October 2010

The source of laterally transferred genes in bacterial genomes

scientific article

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations

scientific article published on 16 July 2020

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