Integrative Biology of Emerging Infectious Diseases (IBEID) / Principal investigators
Genome Analysis Platform
Institut Pasteur 25-28 rue du docteur Roux, 75015 Paris
Website under construction
Research area of the Unit
The Platform “Bioanalyse Génomique” is dedicated to data integration and analysis of large-scale genomic information, by means of methodological developments and collaborative genome analysis studies. In particular, we are working on microbial population genomics projects for several bacterial species (e.g., methodological developments for filtering NGS reads, characterizing possible SNPs, etc.). We are also involved in research programs such as: identification of novel infectious agents in complex samples; exploration of host-viral interactions in the outcome of dengue infection. We have developed the GenoList environment, dedicated to comparative analysis of microbial genomes, whose latest release integrates data for 700 species and receives over 120,000 hits/month. Recent developments are related to a dynamic visualisation tool, SynTView, which enables interactive navigation through microbial genomic data (synteny organisation, polymorphism maps). Finally, we are developing an interactive system for analysis of high-throughput microbial genome data, which aims at integrating relevant bioinformatics tools in a workflow system.
Contribution to the programme
High-throughput technologies produce masses of information that require an extraordinary effort in bioinformatics. Adequate organisation, integration and data mining of heterogeneous information is a pivotal issue in tackling a systems-level understanding of infectious diseases. In the framework of the IBEID programme, we will provide our expertise to build novel bioinformatics environments, which are required to conceptually represent and functionally interpret information in area such as: multiple genome sequences of related organisms (population genomics); gene expression (e.g., mapping of promoters); host genetics (association studies); epidemiological and phenotypic data, etc. We also propose to collaborate with biologist partners to help them analyze their genomic data sets, through the implementation of relevant existing tools. Indeed, data integration and interpretation can be achieved through the construction of “information hubs” for managing and mining the data, where added value is generated by the synergy between individual components (data models, analysis tools, user interfaces) in an integrated software environment.
References over the past 5 years
1. Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, Vallenet D, Wang T, Moszer I, Médigue C, Danchin A (2009) From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758–1775.
2. Chauvaux S, Dillies MA, Marceau M, Rosso ML, Rousseau S, Moszer I, Simonet M, Carniel E (2011) In silico comparison of Yersinia pestis and Yersinia pseudotuberculosis transcriptomes reveals a higher expression level of crucial virulence determinants in the plague bacillus. Int. J. Med. Microbiol. 301:105–116.
3. Cheval J, Sauvage V, Frangeul L, Dacheux L, Guigon G, Dumey N, Pariente K, Rousseaux C, Dorange F, Berthet N, Brisse S, Moszer I, Bourhy H, Manuguerra JC, Lecuit M, Burguiere A, Caro V, Eloit M (2011) Evaluation of High Throughput Sequencing for identifying known and unknown viruses in biological samples. J. Clin. Microbiol. 49:3268–3275.
4. Clément-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S (2009) Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics 25:2617–2618.
5. Lechat P, Hummel L, Rousseau S, Moszer I (2008) GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res. 36:D469–474.
6. Médigue C, Moszer I (2007) Annotation, comparison and databases for hundreds of bacterial genomes. Res. Microbiol. 158:724–736.
7. Monot M, Boursaux-Eude C, Thibonnier M, Vallenet D, Moszer I, Médigue C, Martin-Verstraete I, Dupuy B (2011) Reannotation of the genome sequence of Clostridium difficile strain 630. J. Med. Microbiol. 60:1193–1199.