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ddevienne‘s blog

Comparative Genomics

2011-now Postdoc: Overtraining in phylogenetic trees reconstruction methods, Horizontal Gene Transfers.
Center for Genomic Regulation (CRG), Bioinformatics group, Barcelona, Spain.

2010 Postdoc: A Lineage selection model for the maintenance of sex in Eukaryotes.
National History Museum (MNHN), Paris, France & Center for applied Mathematics (CMAP), Ecole Polytechnique, Palaiseau, France.

2008-2009 Postdoc: Protein-protein interactions detection in Prokaryotes using coevolution and a new learning algorithm.
Laboratoire de Recherche en Informatique (LRI), Université Paris-Sud, Orsay, France.

2005-2008 PhD: Speciation in Parasites: reproductive isolation, cospeciation and host-switches.
Laboratoire Ecologie Systématique et Evolution (ESE), Université Paris-Sud, Orsay, France.

Publications:

  • de Vienne, DM., Giraud, T. and Gouyon, P.-H. 2013. Lineage selection and the maintenance of sex. PLoS ONE. In press. url: http://lineage-selection.cgenomics.org/
  • de Vienne, DM., Refrégier, G., López-Villavicencio, M., Tellier, A., Hood, ME. and Giraud, T. 2013. Cospeciation vs host-shift speciation: methods for testing, evidence from natural associations and relation to coevolution. New Phytologist. In press. [Tansley Review]
  • Bourquard T., de Vienne DM and Azé, J. 2013. Identification de complexes protéine-protéine par combinaison de classifieurs. Application à Escherichia Coli. Actes EGC'2013. In press.[First Price Best Application Paper]
  • de Vienne DM and Azé, J. 2012. Efficient Prediction of Co-Complexed Proteins Based on Coevolution. PLoS ONE. In press.
  • Petit E, Giraud T, de Vienne DM, Coelho M. et al. 2012. Linkage to the Mating-Type Locus across the Genus Microbotryum: Insights into Non-Recombining Chromosomes. Evolution. In press.
  • de Vienne DM, Ollier, S. and Aguileta, G. 2012. Phylo-MCOA: a Fast and Efficient Method to Detect Outlier Genes and Species in Phylogenomics using Multiple Co-Inertia Analysis. Molecular Biology and Evolution. doi:10.1093/molbev/msr317.
  • de Vienne DM, Aguileta, G. and Ollier, S. 2011. The Euclidean Nature of Phylogenetic Distance Matrices. Systematic Biology. 60(6):826-832.
  • López-Villavicencio M, Aguileta G, Giraud T, de Vienne DM, Lacoste S, Couloux A, Dupont J. 2010. Sex in Penicillium: combined phylogenetic and experimental approaches. Fungal Genetics and Biology. 47(8):693-706.
  • de Vienne, DM., Hood, ME., Giraud, T. (2009). Phylogenetic Determinants of Potential Host Shifts in Fungal Pathogens. Journal of Evolutionary Biology. 22(12):2532-41.
  • de Vienne, DM., Giraud, T., Martin, O. C. (2009). In response to comment on a congruence index for testing topological similarity between trees. Bioinformatics, 25(1), 150–151.
  • de Vienne, DM., Refrégier, G., Hood, M. E., Guigue, A., Devier, B., Vercken, E., et al. (2009). Hybrid sterility and inviability in the parasitic fungal species complex microbotryum. Journal of Evolutionary Biology, 22(4),683–698.
  • Tellier, A., de Vienne, DM., Giraud, T., Hood, ME., Refrégier, G. (2009). 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. In Host-Pathogen Interactions: Genetics, Immunology and Physiology. N.Y. Nova Science Publishers.
  • Giraud, T., Refrégier, G., Le Gac, M., de Vienne, DM., Hood, M. E. (2008). Speciation in fungi. Fung. Genet. Biol., 45, 791–802.
  • Giraud, T., Yockteng, R., Marthey, S., Chiapello, H., Jonot, O., Lopez-Villavicencio, M., de Vienne DM. et al. (2008). Isolation of 60 polymorphic microsatellite loci in est libraries of four sibling species of the phytopathogenic fungal complex microbotryum. Molecular Ecology Resources, 8, 387–392.
  • de Vienne, DM., Giraud, T., Martin, O. C. (2007). A congruence index for testing topological similarity between trees. Bioinformatics, 23(23), 3119–3124.
  • de Vienne, DM., Giraud, T., Shykoff, J. A. (2007). When can host shifts produce congruent host and parasite phylogenies? a simulation approach. Journal of Evolutionary Biology, 20(4), 1428–1438.

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