From genome to graph comparison

Comparative genomics consists in studying and understanding the structure and function of a genome by comparing different species (distance calculation, search for structural variants, etc.). This research axis benefits from the power of computer tools that make it possible to define models for the representation of different biological objects (DNA, RNA, protein), based on sequences or graphs, and to develop algorithmic and combinatorial analysis methods capable of managing the complexity and mass of data. The team is also developing methods adapted to new high-throughput sequencing data, for the comparison of unassembled genomes, the analysis of very high throughput transcription data (RNA-seq) or the analysis of single cell data (DGE-seq).

From biological process modeling to community modeling

The ComBi team also has an important activity in systems biology using the computer and mathematical expertise of its members. Mathematical and computer models are developed and analyzed by the team. These models make it possible to study the metabolism and its regulation from the cell to the interactions between the micro-organisms present in different microbiomes. The computer methods and models used here are based on graph theories, combinatorial optimization and probability.

Linking modeling scales to extract biomarkers

All the team's efforts, both in genomics and systems biology, are complemented by the development of decision support tools whose goal is to extract relevant biomarkers from the models of the different scales of living organisms we are considering.

Bioinformatics developments

The ComBi team develops a strong expertise in application development for biologist users. This expertise is concentrated around a bioinformatics platform, BiRD, shared with the Institut du Thorax.