Amamam

Daphné Reiss, Gladys Mialdea, Vincent Miele, Damien M. de Vienne, Jean Peccoud, et al.. Global survey of mobile DNA horizontal transfer in arthropods reveals Lepidoptera as a prime hotspot. PLoS Genetics, Public Library of Science, 2019, 15 (2), pp.e1007965. ⟨10.1371/journal.pgen.1007965⟩. ⟨hal-02140494⟩

Adrian Davin, Theo Tricou, Eric Tannier, Damien M. de Vienne, Gergely J Szöllosi. Zombi: A phylogenetic simulator of trees, genomes and sequences that accounts for dead lineages. Bioinformatics, Oxford University Press (OUP), 2019, ⟨10.1093/bioinformatics/btz710⟩. ⟨hal-02302010⟩

Damien M. de Vienne. Tanglegrams Are Misleading for Visual Evaluation of Tree Congruence. Molecular Biology and Evolution, Oxford University Press (OUP), 2019, 36 (1), pp.174-176. ⟨10.1093/molbev/msy196⟩. ⟨hal-02301092⟩

Sara Branco, Fantin Carpentier, Ricardo Rodriguez de la Vega, Hélène Badouin, Alodie Snirc, et al.. Multiple convergent supergene evolution events in mating-type chromosomes. Nature Communications, Nature Publishing Group, 2018, 9 (1), pp.2000. ⟨10.1038/s41467-018-04380-9⟩. ⟨hal-01796609⟩

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien M. de Vienne, Elodie Portanier, David Fouchet, et al.. Coexistence de deux espèces cryptiques de chauves-souris en Guyane française : apprentissages à partir de la génétique de l’acoustique et de l’écologie. Plume de Naturalistes, Maxime LEUCHTMANN, 2018, 2, pp.169-190. ⟨hal-02326861⟩

Ondine Filippi-Codaccioni, Marie-Pauline Beugin, Damien de Vienne, Elodie Portanier, David Fouchet, et al.. Coexistence of two sympatric cryptic bat species in French Guiana: insights from genetic, acoustic and ecological data. BMC Evolutionary Biology, BioMed Central, 2018, 18 (1), ⟨10.1186/s12862-018-1289-8⟩. ⟨hal-01936895⟩

Jessica Lee Abbate, Pierre Gladieux, Michael Hood, Damien de Vienne, Janis Antonovics, et al.. Co-occurrence among three divergent plant-castrating fungi in the same Silene host species. Molecular Ecology, Wiley, 2018, 27 (16), pp.3357 - 3370. ⟨10.1111/mec.14805⟩. ⟨hal-01921830⟩

Hervé Philippe, Damien M. de Vienne, Vincent Ranwez, B. Roure, Denis Baurain, et al.. Pitfalls in supermatrix phylogenomics. European Journal of Taxonomy, Consortium of European Natural History Museums, 2017, 283, pp.1-25. ⟨10.5852/ejt.2017.283⟩. ⟨hal-01606389⟩

Damien M. de Vienne. Lifemap: Exploring the Entire Tree of Life. PLoS Biology, Public Library of Science, 2016, 14 (12), ⟨10.1371/journal.pbio.2001624⟩. ⟨hal-01799964⟩

Frédéric Jauffrit, Simon Penel, Stéphane Delmotte, Carine Rey, Damien de Vienne, et al.. RiboDB database: a comprehensive resource for prokaryotic systematics. Molecular Biology and Evolution, Oxford University Press (OUP), 2016, 33 (8), pp.2170--2172. ⟨10.1093/molbev/msw088⟩. ⟨hal-01800061⟩

Eric Fontanillas, Michael E Hood, Hélène Badouin, Elsa Petit, Valérie Barbe, et al.. Degeneration of the Nonrecombining Regions in the Mating-Type Chromosomes of the Anther-Smut Fungi. Molecular Biology and Evolution, Oxford University Press (OUP), 2015, 32 (4), pp.928-943. ⟨10.1093/molbev/msu396⟩. ⟨hal-01302682⟩

Gabriela Aguileta, Damien de Vienne, Oliver N. Ross, Michael E Hood, Tatiana Giraud, et al.. High Variability of Mitochondrial Gene Order among Fungi. Genome Biology and Evolution, Society for Molecular Biology and Evolution, 2014, 6 (2), pp.451-465. ⟨10.1093/gbe/evu028⟩. ⟨hal-01302669⟩

Jeanne Ropars, Gabriela Aguileta, Damien de Vienne, Tatiana Giraud. Massive gene swamping among cheese-making Penicillium fungi. Microbial Cell , Shared Science Publishers OG, 2014, ⟨10.15698/mic2014.01.135⟩. ⟨hal-01302705⟩

Pierre Gladieux, Jeanne Ropars, Helene Badouin, Antoine Branca, Gabriela Aguileta, et al.. Fungal evolutionary genomics provides insight into the mechanisms of adaptive divergence in eukaryotes. Molecular Ecology, Wiley, 2014, 23 (4), pp.753-773. ⟨10.1111/mec.12631⟩. ⟨hal-01302695⟩

Damien M. de Vienne, Tatiana Giraud, Pierre-Henri Gouyon. Lineage selection and the maintenance of sex. PLoS ONE, Public Library of Science, 2013, 8 (6), pp.e66906. ⟨hal-01800063⟩

Elsa Petit, Tatiana Giraud, Damien M. de Vienne, Marco A Coelho, Gabriela Aguileta, et al.. Linkage to the mating-type locus across the genus microbotryum: insights into nonrecombining chromosomes. Evolution - International Journal of Organic Evolution, Wiley, 2012, 66 (11), pp.3519-3533. ⟨10.1111/j.1558-5646.2012.01703.x⟩. ⟨hal-01190628⟩

Damien M. de Vienne, Sébastien Ollier, Gabriela Aguileta. Phylo-MCOA: a fast and efficient method to detect outlier genes and species in phylogenomics using multiple co-inertia analysis. Molecular Biology and Evolution, Oxford University Press (OUP), 2012, 29 (6), pp.1587--1598. ⟨10.1093/molbev/msr317⟩. ⟨hal-01800064⟩

Damien de Vienne, Jérôme Azé. Efficient Prediction of Co-Complexed Proteins Based on Coevolution. PLoS ONE, Public Library of Science, 2012, 7 (11), pp.1-13. ⟨10.1371/journal.pone.0048728⟩. ⟨hal-00756120⟩

Elsa Petit, Tatiana Giraud, Damien de Vienne, Marco Coelho, Gabriela Aguileta, et al.. LINKAGE TO THE MATING-TYPE LOCUS ACROSS THE GENUS MICROBOTRYUM : INSIGHTS INTO NONRECOMBINING CHROMOSOMES. Evolution - International Journal of Organic Evolution, Wiley, 2012, 66 (11), pp.3519-3533. ⟨10.1111/j.1558-5646.2012.01703.x⟩. ⟨hal-02328980⟩

Damien M. de Vienne, Gabriela Aguileta, Sébastien Ollier. Euclidean nature of phylogenetic distance matrices. Systematic Biology, Oxford University Press (OUP), 2011, 60 (6), pp.826--832. ⟨10.1093/sysbio/syr066⟩. ⟨hal-01800065⟩

Damien de Vienne, G Refrégier, Me Hood, A Guigue, B Devier, et al.. Hybrid sterility and inviability in the parasitic fungal species complex Microbotryum. Journal of Evolutionary Biology, Wiley, 2009, 22 (4), pp.683--698. ⟨hal-01800066⟩

Damien de Vienne, Me Hood, T Giraud. Phylogenetic determinants of potential host shifts in fungal pathogens. Journal of Evolutionary Biology, Wiley, 2009, 22 (12), pp.2532--2541. ⟨hal-01800067⟩

Damien de Vienne, Tatiana Giraud, Olivier C Martin. In response to comment on ‘A congruence index for testing topological similarity between trees’. Bioinformatics, Oxford University Press (OUP), 2008, 25 (1), pp.150--151. ⟨10.1093/bioinformatics/btn535⟩. ⟨hal-01800068⟩

Tatiana Giraud, Guislaine Refrégier, Mickaël Le Gac, Damien de Vienne, Michael E Hood. Speciation in fungi. Fungal Genetics and Biology, Elsevier, 2008, 45 (6), pp.791--802. ⟨hal-01800069⟩

Tatiana Giraud, Guislaine Refrégier, Mickael Le Gac, Damien de Vienne, Michael Hood. Speciation in fungi. Fungal Genetics and Biology, Elsevier, 2008, 45 (6), pp.791-802. ⟨10.1016/j.fgb.2008.02.001⟩. ⟨hal-02333172⟩

Damien de Vienne, Tatiana Giraud, Olivier C Martin. A congruence index for testing topological similarity between trees. Bioinformatics, Oxford University Press (OUP), 2007, 23 (23), pp.3119--3124. ⟨hal-01800070⟩

Damien de Vienne, Tatiana Giraud, J Shykoff. When can host shifts produce congruent host and parasite phylogenies? A simulation approach. Journal of Evolutionary Biology, Wiley, 2007, 20 (4), pp.1428--1438. ⟨hal-01800071⟩

Henri Boutin, Damien de Vienne. SONIFICATION OF PHYLOGENETIC TREES: LISTENING TO EVOLUTION. Journées d'Informatique Musicale (JIM) 2017, May 2017, Paris, France. ⟨hal-01893569⟩

Thomas Bourquard, Damien de Vienne, Jérôme Azé. Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia coli. 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. ⟨hal-00785473⟩

Damien de Vienne. L'arbre du vivant : Etat des lieux et visualisation. Denis Faure, Dominique Joly, Sylvie Salamitou. 101 secrets de l'adn, CNRS Éditions, pp.358, 2019, SOCIETE, 978-2-271-12323-7. ⟨hal-02323928⟩

Pierre-Henri Gouyon, Damien Vienne, Tatiana Giraud. Sex and evolution. 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. ⟨hal-01800062⟩

Aurélien Tellier, Damien M. de Vienne, Tatiana Giraud, Michael Hood, Guislaine Refrégier. 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. 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. ⟨hal-02326400⟩

Damien M. de Vienne. Tanglegrams are misleading for visual evaluation of tree congruence. 2018. ⟨hal-01807411⟩

Damien M. de Vienne, Fran Supek, Toni Gabaldon. Overtraining often results in topologically incorrect species trees with maximum likelihood methods. 2018. ⟨hal-01800059⟩