Integrative methods for reconstructing ancestral genomes

Tuesday 20 November 2012
by  daubin
popularity : 0%

A 2 (+1) year post-doctoral position is available to work on integrative methods for reconstructing ancestral genomes in the Bioinformatics and Genome Evolution (BGE) group at the LBBE in Lyon, France.

The researcher will work in collaboration with Vincent Daubin, Bastien Boussau, Gergely Szollosi and Eric Tannier, in the context of the ANCESTROME project. ANCESTROME is a large collaborative project funded by the French National Research Agency .

The project aims at building integrative models and studying the genomes of extant living organisms 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. These include not only cellular and genome organisation, and metabolic capabilities, as deduced from genome content, but also virtually any internal or external factor that has left a trace in the genomic record, in particular details of the environment to which the species has adapted, its resources, parasites or demography.

In a series of recent papers, we have used probabilistic models and high performance computing methods on the HOGENOM database to start exploiting genomes as documents of evolutionary history (see references below).

Possible avenues of research include:

- Reconstructing ancestral genomes, phenotypes and environments

- Modelling coevolution of genes and genomes...

The successful candidate will have a strong background in computational biology or probabilistic models. Good programming skills are essential. A good understanding of the concepts of evolutionary biology is a plus.

The LBBE offers a highly stimulating scientific environment, and Lyon is a lively, beautiful, history rich city with great food. The researcher will also have the opportunity to visit collaborating labs in the no less interesting cities of Budapest and Berkeley.

Please send a CV and motivation letter including references to Vincent Daubin ( and Bastien Boussau (

Keywords: Probabilistic Models, Phylogenetics, Evolution of Life on Earth, Evolutionary Genomics, Coevolution, HPC

- Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V. Genome-scale coestimation of species and gene trees. Genome Res. 2012 Nov 6.
- Szöllosi GJ, Boussau B, Abby SS, Tannier E, Daubin V. Phylogenetic modeling of lateral gene transfer reconstructs the pattern and relative timing of speciations. Proc Natl Acad Sci U S A. 2012 Oct 23;109(43):17513-8.
- Bérard S, Gallien C, Boussau B, Szöllősi GJ, Daubin V, Tannier E. Evolution of gene neighborhoods within reconciled phylogenies. Bioinformatics. 2012 Sep 15;28(18):i382-i388.
- Abby SS, Tannier E, Gouy M, Daubin V. Lateral gene transfer as a support for the tree of life. Proc Natl Acad Sci U S A. 2012 Mar 27;109(13):4962-7.
- Szöllosi GJ, Daubin V. Modeling gene family evolution and reconciling phylogenetic discord. Methods Mol Biol. 2012;856:29-51.
- Abby SS, Tannier E, Gouy M, Daubin V. Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests. BMC Bioinformatics. 2010 Jun 15;11:324.
- Boussau B, Daubin V. Genomes as documents of evolutionary history. Trends Ecol Evol. 2010 Apr;25(4):224-32.
- Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G. Databases of homologous gene families for comparative genomics. BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S3.


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