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Damien M. de Vienne

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Publications

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Response to “On the impact of incomplete taxon sampling on the relative timing of gene transfer events”

Théo Tricou , Eric Tannier , Damien de Vienne
PLoS Biology, 2024, 22 (3), pp.e3002557. ⟨10.1371/journal.pbio.3002557⟩
Journal articles hal-04515190v1
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PhylteR: Efficient Identification of Outlier Sequences in Phylogenomic Datasets

Aurore Comte , Théo Tricou , Eric Tannier , Julien Joseph , Aurélie Siberchicot
Molecular Biology and Evolution, 2023, 40 (11), pp.msad234. ⟨10.1093/molbev/msad234⟩
Journal articles hal-03995366v3
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Endoparasitoid lifestyle promotes endogenization and domestication of dsDNA viruses

Benjamin Guinet , D. Lepetit , S. Charlat , Peter N Buhl , David G Notton
eLife, 2023, 12, pp.e85993. ⟨10.7554/eLife.85993⟩
Journal articles hal-03861307v2
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Ghost lineages highly influence the interpretation of introgression tests

Théo Tricou , Eric Tannier , Damien M. de Vienne
Systematic Biology, 2022, 71 (5), pp.1147-1158. ⟨10.1093/sysbio/syac011⟩
Journal articles hal-03455377v2
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Ghost lineages can invalidate or even reverse findings regarding gene flow

Théo Tricou , Eric Tannier , Damien M. de Vienne
PLoS Biology, 2022, 20 (9), pp.e3001776. ⟨10.1371/journal.pbio.3001776⟩
Journal articles hal-03781025v2
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tidy tree : A New Layout for Phylogenetic Trees

Simon Penel , Damien de Vienne
Molecular Biology and Evolution, 2022, 39 (10), pp.msac204. ⟨10.1093/molbev/msac204⟩
Journal articles hal-03844239v1
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Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages

Adrian A Davin , Theo Tricou , Eric Tannier , Damien M. de Vienne , Gergely J Szöllosi
Journal articles hal-02302010v1
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Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot

Daphné Reiss , Gladys Mialdea , Vincent Miele , Damien M. de Vienne , Jean Peccoud
PLoS Genetics, 2019, 15 (2), pp.e1007965. ⟨10.1371/journal.pgen.1007965⟩
Journal articles hal-02140494v1

Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence

Damien M. de Vienne
Molecular Biology and Evolution, 2019, 36 (1), pp.174-176. ⟨10.1093/molbev/msy196⟩
Journal articles hal-02301092v1
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Co-occurrence among three divergent plant-castrating fungi in the same Silene host species

Jessica Lee Abbate , Pierre Gladieux , Michael E Hood , Damien de Vienne , Janis Antonovics
Molecular Ecology, 2018, 27 (16), pp.3357 - 3370. ⟨10.1111/mec.14805⟩
Journal articles hal-01921830v1

Coexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie

Ondine Filippi-Codaccioni , Marie-Pauline Beugin , Damien M. de Vienne , Elodie Portanier , David Fouchet
Plume de Naturalistes, 2018, 2, pp.169-190
Journal articles hal-02326861v1
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Multiple convergent supergene evolution events in mating-type chromosomes

Sara E Branco , Fantin E Carpentier , Ricardo Rodriguez de La Vega , Hélène Badouin , Alodie Snirc
Nature Communications, 2018, 9 (1), pp.2000. ⟨10.1038/s41467-018-04380-9⟩
Journal articles hal-01796609v1
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Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data

Ondine Filippi-Codaccioni , Marie-Pauline Beugin , Damien de Vienne , Elodie Portanier , David Fouchet
BMC Evolutionary Biology, 2018, 18 (1), ⟨10.1186/s12862-018-1289-8⟩
Journal articles hal-01936895v1
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Pitfalls in supermatrix phylogenomics

Herve Philippe , Damien M. de Vienne , Vincent Ranwez , Béatrice Roure , Denis Baurain
European Journal of Taxonomy, 2017, 283, pp.1-25. ⟨10.5852/ejt.2017.283⟩
Journal articles hal-01606389v1

RiboDB database: a comprehensive resource for prokaryotic systematics

Frédéric Jauffrit , Simon Penel , Stéphane Delmotte , Carine Rey , Damien M de Vienne
Molecular Biology and Evolution, 2016, 33 (8), pp.2170--2172. ⟨10.1093/molbev/msw088⟩
Journal articles hal-01800061v1
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Lifemap: Exploring the Entire Tree of Life

Damien M. de Vienne
PLoS Biology, 2016, 14 (12), ⟨10.1371/journal.pbio.2001624⟩
Journal articles hal-01799964v1
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Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi

Eric Fontanillas , Michael E Hood , Hélène Badouin , Elsa Petit , Valérie Barbe
Molecular Biology and Evolution, 2015, 32 (4), pp.928-943. ⟨10.1093/molbev/msu396⟩
Journal articles hal-01302682v1
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Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes

Pierre P. Gladieux , Jeanne Ropars , Helene Badouin , Antoine Branca , Gabriela G. Aguileta
Molecular Ecology, 2014, 23 (4), pp.753-773. ⟨10.1111/mec.12631⟩
Journal articles hal-01302695v1
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Massive gene swamping among cheese-making Penicillium fungi

Jeanne Ropars , Gabriela Aguileta , Damien M. de Vienne , Tatiana Giraud
Microbial Cell , 2014, ⟨10.15698/mic2014.01.135⟩
Journal articles hal-01302705v1
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High Variability of Mitochondrial Gene Order among Fungi

Gabriela Aguileta , Damien M. de Vienne , Oliver N. Ross , Michael E Hood , Tatiana Giraud
Genome Biology and Evolution, 2014, 6 (2), pp.451-465. ⟨10.1093/gbe/evu028⟩
Journal articles hal-01302669v1

Lineage selection and the maintenance of sex

Damien M. de Vienne , Tatiana Giraud , Pierre-Henri Gouyon
PLoS ONE, 2013, 8 (6), pp.e66906. ⟨10.1371/journal.pone.0066906⟩
Journal articles hal-01800063v1

Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis

Damien M. de Vienne , Sébastien Ollier , Gabriela Aguileta
Molecular Biology and Evolution, 2012, 29 (6), pp.1587--1598. ⟨10.1093/molbev/msr317⟩
Journal articles hal-01800064v1
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Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes

Elsa Petit , Tatiana Giraud , Damien M. de Vienne , Marco A Coelho , Gabriela Aguileta
Evolution - International Journal of Organic Evolution, 2012, 66 (11), pp.3519-3533. ⟨10.1111/j.1558-5646.2012.01703.x⟩
Journal articles hal-01190628v1

Efficient Prediction of Co-Complexed Proteins Based on Coevolution

Damien M. de Vienne , Jérôme Azé
PLoS ONE, 2012, 7 (11), pp.1-13. ⟨10.1371/journal.pone.0048728⟩
Journal articles hal-00756120v1

Euclidean nature of phylogenetic distance matrices

Damien M. de Vienne , Gabriela Aguileta , Sébastien Ollier
Systematic Biology, 2011, 60 (6), pp.826--832. ⟨10.1093/sysbio/syr066⟩
Journal articles hal-01800065v1

Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum

Damien de Vienne , G Refrégier , Me Hood , A Guigue , B Devier
Journal of Evolutionary Biology, 2009, 22 (4), pp.683--698
Journal articles hal-01800066v1

Phylogenetic determinants of potential host shifts in fungal pathogens

Damien de Vienne , Me Hood , T Giraud
Journal of Evolutionary Biology, 2009, 22 (12), pp.2532--2541
Journal articles hal-01800067v1

In response to comment on ‘A congruence index for testing topological similarity between trees’

Damien de Vienne , Tatiana Giraud , Olivier C Martin
Bioinformatics, 2008, 25 (1), pp.150--151. ⟨10.1093/bioinformatics/btn535⟩
Journal articles hal-01800068v1

Speciation in fungi

Tatiana Giraud , Guislaine Refrégier , Mickaël Le Gac , Damien M. de Vienne , Michael E Hood
Fungal Genetics and Biology, 2008, 45 (6), pp.791--802. ⟨10.1016/j.fgb.2008.02.001⟩
Journal articles hal-01800069v1

A congruence index for testing topological similarity between trees

Damien M de Vienne , Tatiana Giraud , Olivier C Martin
Bioinformatics, 2007, 23 (23), pp.3119--3124. ⟨10.1093/bioinformatics/btm500⟩
Journal articles hal-01800070v1

When can host shifts produce congruent host and parasite phylogenies? A simulation approach

Damien M de Vienne , Tatiana Giraud , J A Shykoff
Journal of Evolutionary Biology, 2007, 20 (4), pp.1428--1438
Journal articles hal-01800071v1

Vers une représentation sonore des arbres phylogénétiques

Arthur Paté , Henri Boutin , Damien de Vienne
16ème Congrès Français d'Acoustique, CFA2022, Société Française d'Acoustique; Laboratoire de Mécanique et d'Acoustique, Apr 2022, Marseille, France
Conference papers hal-03848536v1
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SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION

Henri Boutin , Damien de Vienne
Journées d'Informatique Musicale (JIM) 2017, May 2017, Paris, France
Conference papers hal-01893569v1

Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli

Thomas Bourquard , Damien Mathieu de Vienne , Jérôme Azé
EGC 2013 - 13eme conférence Francophone sur l'Extraction et la Gestion des Connaissances, Florence Sèdes (IRIT Toulouse - Université Paul Sabatier) et André Péninou (IRIT Toulouse - Université Toulouse 2), Jan 2013, Toulouse, France. pp.419-430
Conference papers hal-00785473v1
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L'arbre du vivant

Damien de Vienne
Denis Faure, Dominique Joly, Sylvie Salamitou. 101 secrets de l'adn, CNRS Éditions, pp.358, 2019, SOCIETE, 978-2-271-12323-7
Book sections hal-02323928v1

Sex and evolution

Pierre-Henri Gouyon , Damien De Vienne , Tatiana Giraud
Th. Heams; P. Huneman; G. Lecointre; M. Silberstein. Handbook of Evolutionary Thinking in the Sciences, Springer Netherlands, pp.499--507, 2015, 978-94-017-9013-0
Book sections hal-01800062v1
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Theory and examples of reciprocal influence between hosts and pathogens, from short-term to long term interactions: coevolution, cospeciation and pathogen speciation following host shifts

Aurélien Tellier , Damien M. de Vienne , Tatiana Giraud , Michael Hood , Guislaine Refrégier
Annette W. Barton. Host-Pathogen Interactions: Genetics, Immunology, and Physiology, Nova Science Publishers, Inc.; 1 edition (September 1, 2010), 2010, Immunology and Immune System Disorders, 978-1608762866
Book sections hal-02326400v1