Daubin Vincent

Relative time constraints improve molecular dating

Gergely Szöllősi, Sebastian Höhna, Tom Williams, Dominik Schrempf, Vincent Daubin, Bastien Boussau

DOI: 10.1101/2020.10.17.343889

2021

Pré-publication

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

Gabriel A.B. Marais, Bérénice Batut, Vincent Daubin

Current Biology - CB . 30 ( 19 ) : R1083-R1085

DOI: 10.1016/j.cub.2020.07.093

2020

Article dans une revue

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Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Nicolas Comte, Benoît Morel, Damir Hasic, Laurent Guéguen, Bastien Boussau, Vincent Daubin...

Bioinformatics . 36 ( 18 ) : 4822-4824

DOI: 10.1093/bioinformatics/btaa615

2020

Article dans une revue

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Quand les branches de l’arbre du vivant s’entremêlent

Eric Tannier, Bastien Boussau, Vincent Daubin

Pour la science .

2019

Article dans une revue

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Tracing Human Ancestral Migrations Using Symbiotic Bacteria

Alexia Nguyen Trung, Bastien Boussau, Vincent Daubin

Groupe des Méthodes Pluridisciplinaires Contribuant à l'Archéologie (GMPCA) .

2019

Acte de congrès

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RecPhyloXML: a format for reconciled gene trees

Wandrille Duchemin, Guillaume Gence, Anne-Muriel Arigon Chifolleau, Lars Arvestad, Mukul Bansal, Vincent Berry...

Bioinformatics . 34 ( 21 ) : 3646-3652

DOI: 10.1093/bioinformatics/bty389

2018

Article dans une revue

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Gene transfers can date the tree of life

Adrián Davín, Eric Tannier, Tom Williams, Bastien Boussau, Vincent Daubin, Gergely Szöllősi

Nature Ecology & Evolution . 2 ( 5 ) : 904-909

DOI: 10.1038/s41559-018-0525-3

2018

Article dans une revue

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Gearing up to handle the mosaic nature of life in the quest for orthologs

Kristoffer Forslund, Cécile Pereira, Salvador Capella-Gutiérrez, Alan Sousa da Silva, Adrian Altenhoff, Jaime Huerta-Cepas...

Bioinformatics . 34 ( 2 ) : 323-329

DOI: 10.1093/bioinformatics/btx542

2018

Article dans une revue

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MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

Cédric Chauve, Akbar Rafiey, Adrian Davin, Celine Scornavacca, Philippe Veber, Bastien Boussau...

DOI: 10.1101/127548

2017

Autre publication

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DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

Wandrille Duchemin, Yoann Anselmetti, Murray Patterson, Yann Ponty, Sèverine Bérard, Cedric Chauve...

Genome Biology and Evolution . 9 ( 5 ) : 1312-1319

DOI: 10.1093/gbe/evx069

2017

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Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Florent Lassalle, Rémi Planel, Simon Penel, David Chapulliot, Valérie Barbe, Audrey Dubost...

Genome Biology and Evolution . 9 ( 12 ) : 3413 - 3431

DOI: 10.1093/gbe/evx255

2017

Article dans une revue

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Ecological networks to unravel the routes to horizontal transposon transfers

Samuel Venner, Vincent Miele, Christophe Terzian, Christian Biemont, Vincent Daubin, Cedric Feschotte...

PLoS Biology . 15 ( 2 ) : np

DOI: 10.1371/journal.pbio.2001536

2017

Article dans une revue

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Horizontal Gene Transfer and the History of Life

Vincent Daubin, Gergely Szöllősi

Cold Spring Harbor Perspectives in Biology . 8 ( 4 ) : 1312 - 1319

DOI: 10.1101/cshperspect.a018036

2016

Article dans une revue

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

Mathieu Groussin, Bastien Boussau, Gergely Szollosi, Laura Eme, Manolo Gouy, Céline Brochier-Armanet...

Molecular Biology and Evolution . 33 ( 2 ) : 305 - 310

DOI: 10.1093/molbev/msv249

2016

Article dans une revue

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Dating with transfers

Adrián Davín, Gergely J Szöllosi, Eric Tannier, Bastien Boussau, Vincent Daubin

Journées Ouvertes Biologie Informatique Mathématiques .

2016

Acte de congrès

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Nucleotide, gene and genome evolution : a score to bind them all

Wandrille Duchemin, Vincent Daubin, Eric Tannier

Journées Ouvertes Biologie Informatique Mathématiques .

2016

Acte de congrès

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Ancestral Reconstruction: Theory and Practice

Mathieu Groussin, Vincent Daubin, Eric Tannier, Manolo Gouy

Encyclopedia of Evolutionary Biology . : 70–77

DOI: 10.1016/B978-0-12-800049-6.00166-9

2016

Chapitre d'ouvrage

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

Wandrille Duchemin, Vincent Daubin, Eric Tannier

BMC Genomics . 16 ( Suppl 10 ) : S9

DOI: 10.1007/978-3-319-19048-8_16

2015

Article dans une revue

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

Florent Lassalle, Séverine Périan, Thomas Bataillon, Xavier Nesme, L. Duret, Vincent Daubin

PLoS Genetics . 11 ( 2 ) : 1-20

DOI: 10.1371/journal.pgen.1004941

2015

Article dans une revue

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Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

G.J. Szollosi, Adrián Davin, Eric Tannier, Vincent Daubin, Bastien Boussau

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences (1934–1990) . 370 : 20140335 (11 pages)

DOI: 10.1098/rstb.2014.0335

2015

Article dans une revue

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The inference of gene trees with species trees

Gergely Szöllősi, Eric Tannier, Vincent Daubin, Bastien Boussau

Systematic Biology . 64 ( 1 ) : e42-e62

DOI: 10.1093/sysbio/syu048

2015

Article dans une revue

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Reductive genome evolution at both ends of bacterial population size spectrum

Bérénice Batut, Carole Knibbe, Gabriel Marais, Vincent Daubin

Nature Reviews Microbiology . 12 ( 12 ) : 841-850

DOI: 10.1038/nrmicro3331

2014

Article dans une revue

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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. nov. an

A. Sen, Vincent Daubin, D. Abrouk, I. Gifford, A. M. Berry, P. Normand

International Journal of Systematic and Evolutionary Microbiology . 64 ( Pt 11 ) : 3821-32

DOI: 10.1099/ijs.0.063966-0

2014

Article dans une revue

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

Hemalatha Golaconda Ramulu, Mathieu Groussin, Emmanuel Talla, Rémi Planel, Vincent Daubin, Céline Brochier-Armanet

Molecular Phylogenetics and Evolution . 75 : 103 - 117

DOI: 10.1016/j.ympev.2014.02.013

2014

Article dans une revue

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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

Martha H. Ramírez-Bahena, Ludovic Vial, Florent Lassalle, Benjamin Diel, David Chapulliot, Vincent Daubin...

Molecular Phylogenetics and Evolution . 73 : 202-207

DOI: 10.1016/j.ympev.2014.01.005

2014

Article dans une revue

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A Bayesian Method for Analyzing Lateral Gene Transfer

Joel Sjöstrand, Ali Tofigh, Vincent Daubin, Lars Arvestad, Bengt Sennblad, Jens Lagergren

Systematic Biology . 63 ( 3 ) : 409 - 420

DOI: 10.1093/sysbio/syu007

2014

Article dans une revue

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L'ADN, mémoire numérique du vivant

Vincent Daubin, Simon Penel, Eric Tannier

Pour la science . : 102-108

2013

Article dans une revue

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

Thomas Bigot, Vincent Daubin, Florent Lassalle, Guy Perrière

BMC Bioinformatics . 14 : 109

DOI: 10.1186/1471-2105-14-109

2013

Article dans une revue

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

Subarna Thakur, Philippe Normand, Vincent Daubin, Louis Tisa, Arnab Sen

BMC Genomics . 14 ( 1 )

DOI: 10.1186/1471-2164-14-474

2013

Article dans une revue

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Lateral gene transfer, rearrangement, reconciliation

Murray Patterson, Gergely Szöllősi, Vincent Daubin, Eric Tannier

BMC Bioinformatics . 14 ( Suppl 15 ) : S4

2013

Article dans une revue

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Publications

Relative time constraints improve molecular dating

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

Treerecs: an integrated phylogenetic tool, from sequences to reconciliations.

Quand les branches de l’arbre du vivant s’entremêlent

Tracing Human Ancestral Migrations Using Symbiotic Bacteria

RecPhyloXML: a format for reconciled gene trees

Gene transfers can date the tree of life

Gearing up to handle the mosaic nature of life in the quest for orthologs

MaxTiC: Fast Ranking Of A Phylogenetic Tree By Maximum Time Consistency With Lateral Gene Transfers

DeCoSTAR: Reconstructing the ancestral organization of genes or genomes using reconciled phylogenies

Ancestral Genome Estimation Reveals the History of Ecological Diversification in Agrobacterium

Ecological networks to unravel the routes to horizontal transposon transfers

Horizontal Gene Transfer and the History of Life

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

Dating with transfers

Nucleotide, gene and genome evolution : a score to bind them all

Ancestral Reconstruction: Theory and Practice

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

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

Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

The inference of gene trees with species trees

Reductive genome evolution at both ends of bacterial population size spectrum

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. nov. an

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

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

A Bayesian Method for Analyzing Lateral Gene Transfer

L'ADN, mémoire numérique du vivant

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

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

Lateral gene transfer, rearrangement, reconciliation