COEVOL Multi-Scale Coevolution

The Cocoon Group

Daubin Vincent

Directeur de recherche

CNRS

Address: 43 bd du 11 novembre 1918
69622 VILLEURBANNE cedex

Tel: 33 04 26 23 44 74

Email

Publications

Display of 31 to 60 publications on 87 in total

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

Journal article

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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

Journal article

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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

Journal article

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Genome-scale phylogenetic analysis finds extensive gene transfer among fungi

G.J. Szollosi, Adrián Arellano 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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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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

Journal article

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Lateral Gene Transfer from the Dead.

Gergely J Szöllosi, Eric Tannier, Nicolas Lartillot, Vincent Daubin

Systematic Biology . 62 ( 3 ) : 386-397

DOI: 10.1093/sysbio/syt003

Journal article

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L'ADN, mémoire numérique du vivant

Vincent Daubin, Simon Penel, Eric Tannier

Pour la science . : 102-108

Journal article

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

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

BMC Genomics . 14 ( 1 )

DOI: 10.1186/1471-2164-14-474

Journal article

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Lateral gene transfer, rearrangement, reconciliation

Murray Patterson, Gergely Szöllősi, Vincent Daubin, Eric Tannier

BMC Bioinformatics . 14 ( Suppl 15 ) : S4

Journal article

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Efficient Exploration of the Space of Reconciled Gene Trees.

Gergely J Szöllosi, Wojciech Rosikiewicz, Bastien Boussau, Eric Tannier, Vincent Daubin

Systematic Biology . 62 ( 6 ) : 901-912

DOI: 10.1093/sysbio/syt054

Journal article

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Genome-scale coestimation of species and gene trees.

Bastien Boussau, Gergely J Szöllosi, L. Duret, Manolo Gouy, Eric Tannier, Vincent Daubin

Genome Research . 23 ( 2 ) : 323-330

DOI: 10.1101/gr.141978.112

Journal article

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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

Journal article

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

Gergely J Szöllosi, Bastien Boussau, Sophie S Abby, Eric Tannier, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 43 ) : 17513-17518

DOI: 10.1073/pnas.1202997109

Journal article

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Modeling Gene Family Evolution and Reconciling Phylogenetic Discord

G.J. Szollosi, Vincent Daubin

Methods in Molecular Biology . 856 : 29-51

Journal article

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Evolution of Prokaryotic Pangenomes

Florent Lassalle, Vincent Daubin

Horizontal Gene Transfer in Microorganisms . 978-1-908230-10-2 : 23-32

Book chapter

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Evolution of gene neighborhoods within reconciled phylogenies

Sèverine Bérard, Coralie Gallien, Bastien Boussau, Gergely J Szöllosi, Vincent Daubin, Eric Tannier

Bioinformatics . 28 ( 18 ) : i382-i388

DOI: 10.1093/bioinformatics/bts374

Journal article

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Lateral gene transfer as a support for the tree of life.

Sophie S Abby, Eric Tannier, Manolo Gouy, Vincent Daubin

Proceedings of the National Academy of Sciences of the United States of America . 109 ( 13 ) : 4962-4967

DOI: 10.1073/pnas.1116871109

Journal article

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

Vincent Miele, Simon Penel, Vincent Daubin, Franck Picard, Daniel Kahn, L. Duret

Bioinformatics . 28 ( 8 ) : 1078-85

DOI: 10.1093/bioinformatics/bts098

Journal article

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Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

Florent Lassalle, Tony Campillo, Ludovic Vial, Jessica Baude, Denis Costechareyre, David Chapulliot...

Genome Biology and Evolution . 3 ( 3 ) : 762-781

DOI: 10.1093/gbe/evr070

Journal article

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Multiple Nuclear Gene Phylogenetic Analysis of the Evolution of Dioecy and Sex Chromosomes in the Genus Silene

Gabriel Marais, A. Forrest, E. Kamau, Jos Käfer, Vincent Daubin, D. Charlesworth

PLoS ONE . 6 : e21915

DOI: 10.1371/journal.pone.0021915

Journal article

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Models, algorithms, and programs for phylogeny reconciliation

Jean-Philippe Doyon, Vincent Ranwez, Vincent Daubin, Vincent Berry

Briefings in Bioinformatics . 12 ( 5 ) : 392-400

DOI: 10.1093/bib/bbr045

Journal article

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Tpms: a Tree Pattern-matching Utility for Querying Gene Trees Collections

Thomas Bigot, Vincent Daubin, G. Perrière

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM) . : 111-112

Conference paper

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La notion d'espèce en écologie microbienne

T. Campillo, Malek Shams, Sally Burr, Martha Helena Ramírez-Bahena, Florent Lassalle, Franck Bertolla...

1er Colloque National d'Ecologie Scientifique .

Conference paper

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Toward an ecological concept for bacterial species in Agrobacterium

Tony Campillo, Florent Lassalle, M. Shams, Martha Helena Ramírez-Bahena, Jessica Baude, Celine Lavire...

12th International Conference on Plant Pathogenic Bacteria .

Conference paper

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Identification de fonctions « spécifiques d'espèce » impliquées dans l'individualisation en écovar de l’espèce G8 du complexe Agrobacterium tumefaciens

Florent Lassalle, Daniel Muller, Denis Costechareyre, David Chapulliot, Celine Lavire, Laurent Guéguen...

Journées des Microbiologistes de l'INRA .

Conference paper

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