Section: Other Grants and Activities
HUPO Proteomics Standards Initiative
Participants : David James Sherman [ correspondant ] , Julie Bourbeillon.
We participate actively in the Proteomics Standards Initiative (PSI) of the Human Proteome Organization (HUPO), and international structure for the development and the advancement of technologies for proteomics. The HUPO PSI develops quality and representation standards for proteomic and interactomic data. The principal standards and PSI-MI, for molecular interactions, and PSI-MS, for mass spectometric data. These standards were presented in reference  in the journal Nature Biotechnology . Our project ProteomeBinders (see below) has been accepted as a HUPO PSI working group.
Participants : David James Sherman, Pascal Durrens [ correspondant ] , Macha Nikolski, Tiphaine Martin.
Since 2000 our team is a member of the Génolevures Consortium (GDR CNRS), a large-scale comparative genomics project that aims to address fundamental questions of molecular evolution through the sequencing and the comparison of 14 species of hemiascomycetous yeasts. The Consortium is comprised of 16 partners, in France, Belgium, and England (see http://cbi.labri.fr/Genolevures/ ). Within the Consortium our team is responsible for bioinformatics, both for the development of resources for exploiting comparative genomic data and for research in new methods of analysis.
In 2004 this collaboration with the 60+ biologists of the Consortium realized the complete genomic annotation and global analysis of four eukaryotic genomes sequenced for us by the National Center for Sequencing (Génoscope, Évry). This annotation consisted in: the ab initio identification of candidate genes and gene models though analysis of genomic DNA, the determination of genes coding for proteins and pseudo-genes, the association of information about the supposed function of the protein and its relations phylogenetics. For this global analysis in particular we developed a novel method for constructing multi-species protein families and detailled analyses of the gain and loss of genes and functions throughout evolution.
This perennial collaboration continues in two ways. First, a number of new projects are underway, concerning several new genomes currently being sequenced, and new questions about the mechanisms of gene formation. Second, through the development and improvement of the Génolevures On Line database, in whose maintenance our team has a longstanding committment.
Systems Biology Markup Language
Participant : Macha Nikolski [ correspondant ] .
Macha Nikolski has recently been implicated in the standards process for version 3 of the SMBL standard, in particular in defining a rigorous mathematical semantics for timed events and hierarchical compositions.