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During the course of the project, several external partners will be able to assist us on various aspects. We briefly describe here the partnerships with people with which we already have contacts relative to the current project.

Active collaborators

K. Gorbunov and V. Lyubetsky, Institute for Information Transmission Problem RAS & Russian Academy of Sciences, Moscow, Russia.
Since 10 years, the team of Prof. Lyubetsky, including K. Gorbunov, is studying duplication and transfer events, in particular proposing reconciliation methods between gene and species trees. His algorithms are based on numerical analysis principles teamed with combinatorial descriptions of evolutionary scenarios. He visited Partner 1 in June 2009 together with Leonid Rusin and Kostantine Gorbunov. We currently work on extending the reconciliation method produced in Moscow and apply it experimentally on Hogenom to detect hot spots of evolution in Bacteria

Le Sy Vinh, Hanoi University.
Le is studying genomic distances on the basis of macro-evolutionary events (translocations, reversals, etc) and is working on reconstruction methods for large phylogenies, such as those to be proposed in this project. We currently work on building phylogenies while directly taking into account macro-events. A visit is planned in 2010.

Philippe Normand, University of Lyon, and Alison Berry, University of California, Davies.
They are currently collaborating with partner 3 on the evolution of Actinobacteria, and more particularly on the reconstruction of the genome evolution of this ancient and diverse group of bacteria. The sequence of several genomes from Actinobacteria have been acquired and analyzed through this collaboration. This group will be a good model to test our species supertree and our transfer detection approach, as several other methods have failed to identify a consensus phylogeny for this group (personal results not shown). In addition, this close collaboration with specialists of the ecology of Actinobacteria will be a very good basis for understanding the functional role of transfers in this group.

Mountaz Hascoët, LIRMM, Montpellier.
She is working on various apsects of visualization techniques: clustering methods based on the structure of objects for multi-scale visualization of graphs, automatic building of graphical representations for collections of documents, "focus+context" visualization. She will provide expertise in the design of our graphical representation of gene histories, and in the representation of multi-scale data.

Daniel Huson, University of Tübingen

Pr. C. Semple, Departement of Mathematics and Statistics, University of Canterbury, New Zealand.
Located at the Allan Wilson Centre for Molecular Ecology and Evolution, he performs research in combinatorics, algorithmics and mathematical biology, particularly phylogenetics and matroid theory.

Other visitors

Jens Lagergren, Feb 2009 (LBBE)

Tony Gabaldon, Nov 2009 (LIRMM)

François-Joseph Lapointe, Dec 2009 (LIRMM)

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