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Theme : LBGI Bioinformatique et Génomique Intégratives lbgi.fr

LBGI Bioinformatics and Integrating Genomics, led by Olivier Poch and Julie Thompson, focuses on a thriving field of research in the field of health: translational bioinformatics. Our main objective is to develop a robust IT infrastructure capable of managing big data in order to extract relevant knowledge in a "bed-patient" approach. In this context, we are particularly interested in the study of rare genetic diseases and the understanding of the pathophysiological mechanisms involved in these diseases, which often have a potential interest in understanding altered biological processes in more common diseases, such as obesity, diabetes or cancer....

Research topics

The LBGI is devoted to the development of robust, automated and integrated in silico approaches (analytical approaches, statistics, data integration and mining, extraction and representation of knowledge...) in order to study the evolution and behavior of complex biological systems ("Hyperstructures", networks, etc.) in humans and various animal models. Taking advantage of our integrated IT approaches and long-standing collaborations at the international, national and local levels, the LBGI participates in the analysis of complex systems involved in various human diseases, including the study of functional deficiencies related to retinal diseases or the brain, the identification of genetic variations related to ciliopathies and the characterization of the genomic and transcriptomic context in various cancers.

Operations

The work of the LBGI is organized around two main complementary axes:

• "Translational IT" (Julie Thompson), to develop an IT infrastructure dedicated to the integrated analysis of the "big data" resulting from high-throughput studies of human genetic diseases. This includes the design and development of original data management systems (storage, quality control, heterogeneous data integration) and analysis tools dedicated to data mining and extraction of biomedical knowledge. An important aspect is the development of intuitive user interfaces to facilitate access by biologists and clinicians.
• "Systems bioinformatics" (Olivier Poch/Odile Lecompte), to develop research in the emerging field of the analysis of complex biological systems, in order to understand genotype-phenotype relationships and to anwser questions related to human diseases. This includes integrated studies of evolutive, "omics" and patient data, particularly those concerning ciliopathies, and the development of a systemic approach to the relationships between mutations and biological networks in diseases.

Keywords

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Theme : SONIC (Stochastic Optimisation and Nature Inspired Computing)

La thématique SONIC (Stochastic Optimisation and Nature Inspired Computing), led by Pierre Collet, studies and uses techniques to tackle complex problems that are insoluble by exact methods. Nature-inspired methods are privileged for their robustness and their very good exploration of the search space. The team uses mainly:

• evolutionary algorithms, including :
  • genetic algorithms (applied to discrete and combinatory problems),
  • evolutionary strategies (applied to continuous problems),
  • genetic programming (applied to learning and data mining problems),
  • multi-objective evolutionary optimisation (for all industrial problems that need to optimize several antagonistic criteria at the same time),
• optimisation by ant colonies,
• emerging approaches (BOIDS, optimisation by particle swarms).