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Associated laboratories : Université Pierre-et-Marie-Curie (UPMC)

Integrative immunology & ImmunocomplexiT

Research : Global analysis of the immune system as a complex biological system. Objectives : produce, collect, integrate high amounts of experimental data corresponding to immune system-related biological networks ; Develop and implement computational approaches to propose operational & predictive models of the studied complex biological functions ; Apply these models to identify potential immunomodulatory intervention. Methodologies : mathematical, computational and statistical modelling, transcriptome analysis, multi-colour flow cytometry, repertoire diversity analysis.
Contacts : Véronique Thomas-Vaslin, Adrien Six

Institut de Biologie Paris Seine – IBPS

Computational and quantitative biology – LCQB

Gene network architecture

Thèmes de recherche : Analyse in vivo et in silico des réseaux génétiques contrôlant la réponse des levures aux stress chimiques. Étude des réseaux de régulation post-transcriptionnelle impliqués dans la biogenèse mitochondriale.
Méthodologies : analyses de transcriptome, imagerie de l’expression des gènes, analyse d’interactions protéines/acides nucléiques, modélisation informatique, phylogénie des réseaux de régulation.
Contact : Frédéric Devaux

Analytical Genomics
Thèmes de recherche : Analyses statistiques de génomes bactériens (prédictions de gènes essentiels et de réseaux métaboliques essentiels, organisation spatiale des gènes sur le chromosome, espace de génomes microbiales, biais des génomes des phages), prédiction ab initio de miRNA dans les génomes eucaryotes, prédiction de sites d’interactions protéine-protéine, détection de partenaires protéiques. Méthodologies : statistiques, combinatoire et algorithmique.
Contact : Alessandra Carbone

Genome biology

Our group is interested into the biology and the evolution of yeast genomes. We are combining an experimental approach based on molecular genetics and functional genomics and an analytical dimension requiring bio-informatic skills and the development of new tools.
We are studying the molecular mechanisms responsible for the formation of the chromosomal rearrangements and for the variations of the nucleotide composition in genomes. We are notably paying much attention to the relationships between replication/recombination processes and the evolution of the gene content and the genetic organization along chromosomes. We also study genome dynamics by characterizing the structural polymorphism of genomes at different scales, from cells to populations, strains and species.
Contact : Gilles Fischer


High throughput data analysis for genomic

Research topics : High throughput sequencing machines spread over the scientific community an exponentially increasing amount of data. At the same time, data analysis requires large computer infrastructures associated with expensive human and maintenance costs. This is the reason why outsourcing data analysis is economic and efficient. Our team try to answer this problem by focusing on 3 different objectives : ensuring high quality data from high throughput sequencer outputs, applying validated bioinformatics analyse workflows on the produced datasets, and facilitating technological transfers from bioinformatics teams towards the biology community. We worked on distributed calculation solutions and cloud computing infrastructures to help the scientific community working on functional genomic and evolution research themes.
Contact : Stéphane Le Crom


Neuronal Networks and Physiopathological Rhythms

As a gateway to the cortex and a hub for the intracortical connections, the thalamus plays a central role in information representation. Our group investigates the mechanisms underlying sensory information processing in thalamic networks, as well as the slow rhythmic activities occurring in the thalamocortical loop when the subjects are disconnected from the external world, as during sleep or absence epilepsy. The originality of our approach arises from multiple levels of investigation : biophysical and molecular studies at the subcellular and cellular level, and in vitro / in vivo analysis of network activities. We exploit a panel of experimental approaches : in vitro (slices) and in vivo electrophysiology, computational analysis, biphotonic calcium imaging, hybrid system (dynamic-clamp), etc.
Contacts : Régis Lambert, Nathalie Leresche

Development and Plasticity of Neural Networks
Research : Our group studies the local translation of mRNA and its role in the development and plasticity of neural networks. This work is performed on the adult mouse olfactory system, a model characterized by a continuous neurogenesis making it easy to manipulate. Our two main objectives are :

  1. To analyse the local translation of mRNAs in axons and its role in controlling the olfactory map formation ;
  2. To characterize the local translation of dendritic mRNAs and its role in dendritogenesis, spinogenesis and synaptogenesis.

Our project adresses fundamental issues and molecular mechanisms involved in neurodevelopmental pathologies like Fragile X mental retardation.
Approaches : Our studies are mainly performed in vivo and ex vivo, using genetically manipulated mice as well as viral vectors.
Techniques used : Biochemistry, molecular biology, molecular histology, fluorescence imaging, time lapse analysis, electron microscopy, olfactory behavior.
Contact : Alain Trembleau