Supervisor: Roest Crollius, Hugues
E-mail: Cet e-mail est protégé contre les robots collecteurs de mails, votre navigateur doit accepter le Javascript pour le voir
Phone: 0144322370
Lab address:
Dyogen Group - CNRS UMR8541
Ecole Normale Supérieure
46 rue d'Ulm
75005 Paris

Unit Director: Marc Dreyfus
Key subjects: Bioinformatics, Genome Evolution
Keywords: Graph clustering, programming, sequence alignments, comparative genomics, phylogenetics

summary of lab's interests:

Our laboratory explores several avenues related to genome organisation and evolution in vertebrates. Three key projects concern 1) genome wide scans for Darwinian selection in genomes of individual primates 2) sequence dependent signals for nucleosome positionning in the human genome 3) the reconstruction of ancestral vertebrate genomes. We take advantage of the massive increase in vertebrate genome data available to the community in the last few years, together with state-of-the-art bioinformatic methods, to compare genomes in order to identify signatures of biological functions. Such signatures may lie in the statistical nature of particular nucleotide arrangements or frequencies, or in deviations from expected distributions for long range organisation of gene order across genomes. Most projects require solutions to computer science problems in order to answer a wider biological question.

Summary of project:

The subject is set within project (3) above: the reconstruction of ancestral vertebrate genomes. We have now reconstructed 12 ancestral vertebrate genomes: their chromosome content, gene content within chromosomes, and gene order. All the information is stored in a relational database equiped with powerful graphical navigation tools. This resources provides, for the first time, an opportunity to consider biological processes (evolutionary processes now, potentially physiological processes ultimately) in a new dimension: from ancestral states to modern states across 400 million years of evolution. The student will build on this new resource to integrate important new biological \"objects\" to this framework. In particular, we are interested in adding conserved non-coding DNA sequences interspersed between genes. In addition to their biological role in regulating gene expression, they are also known to constrain the evolution of gene organisation. The outcome of the project may shed new light on our understanding of the impact that such non-coding DNA may have had in genome evolution.