<p>Institut des Sciences de l’Evolution de Montpellier (ISEM, UMR-5556)</p>
A postdoctoral fellowship will be available at the Institut des Sciences de l’Evolution de Montpellier (ISEM, UMR-5556, http://www.isem.univ-montp2.fr) in the framework of the Ancestrome project, recently funded by the ANR agency on the Bioinformatics Investissement d’avenir call (http://lbbe-dmz.univ-lyon1.fr/ancestrome/spip_ancestrome/).
Ancestrome aims at studying genome organization and functioning of extant living organisms to build integrative models to reconstruct evolutionary intermediates together with the evolutionary processes that have generated them.
A critical step in the development of methods to reconstruct the evolution of genomes is the modeling of the processes that relate gene phylogenies to species phylogenies. We have developed methods for integrating events of gene duplication, gene loss and lateral gene transfer in the simultaneous reconstruction of species and gene histories. These methods yield much better estimates of the gene content of ancestral genome, and hence open the door to accurate reconstructions of ancestral species characteristics. This includes cellular and genome organizations, or metabolic capabilities as deduced from genome content, but also virtually any internal or external factors that have left a trace in the genomic record, such as the environment to which the species has adapted, its resources, parasites or demography.
The aim of this position is to define, implement and exploit measures of reconciliation similarities. Reconciliations are defined as mapping of gene tree nodes into the species tree nodes permitting to infer past events in the species’ history such as gene duplications, losses and transfers . Defining similarities between two such mappings will allow to study the diversity of equally parsimonious reconciliations on the same pair species tree-gene tree, to cluster them and to eventually summarize them through a consensus reconciliation. Measures to compare two reconciliations for the same species tree but for different gene trees on the same gene family and even on different gene families should also be proposed. This latter measure will be used to search for gene families, which have undergone concomitant gene losses, duplications and transfers, suggesting a physical or functional link between those genes.
Candidates should have a solid background in Combinatorics. A background in Probability and Statistics would be appreciated.
Applications including a detailed curriculum vitae, a cover letter, and contact information of at least three references should be sent electronically to Celine Scornavacca (email@example.com) and Vincent Ranwez (firstname.lastname@example.org) before October 1st 2012.
Starting date: November 1st 2012.
 J.P. Doyon, V. Ranwez, V. Daubin, and V. Berry. Models, algorithms and programs for phylogeny reconciliation. Brief. Bioinformatics, 12:392–400, 2011