Section: Partnerships and Cooperations
"Omics"-Line of the Chilean CIRIC-Inria Center
Participants : Meziane Aite, Jérémie Bourdon, François Coste, Marie Chevallier, Damien Eveillard, Clémence Frioux, Jacques Nicolas, Anne Siegel.
We have a cooperation with Univ. of Chile (MATHomics, A. Maass) on methods for the identification of biomarkers and software for biochip design, supported by a national Inria initiative. It aims at combining automatic reasoning on biological sequences and networks with probabilistic approaches to manage, explore and integrate large sets of heterogeneous omics data into networks of interactions allowing to produce biomarkers, with a main application to biomining bacteria. The program is co-funded by Inria and CORFO-chile from 2012 to 2022. In this context, IntegrativeBioChile is an Associate Team between Dyliss and the Laboratory of Bioinformatics and Mathematics of the Genome hosted at Univ. of Chile funded from 2011 to 2016.
Participants : Jérémie Bourdon, Marie Chevallier, François Coste, Damien Eveillard, Clémence Frioux, Jeanne Got, Jacques Nicolas, Anne Siegel.
IDEALG is one of the five laureates from the national call 2010 for Biotechnology and Bioresource and will run until 2020. It gathers 18 different partners from the academic field (CNRS, IFREMER, UEB, UBO, UBS, ENSCR, University of Nantes, INRA, AgroCampus), the industrial field (C-WEED, Bezhin Rosko, Aleor, France Haliotis, DuPont) as well as a technical center specialized in seaweeds (CEVA) in order to foster biotechnology applications within the seaweed field. It is organized in ten workpackages. We are participating in the tasks related to the establishment of a virtual platform for integrating omics studies on seaweed) and the integrative analysis of seaweed metabolism, in cooperation with SBR Roscoff. Major objectives are the building of brown algae metabolic maps, flux analysis and the selection extraction of important parameters for the production of targeted compounds. We will also contribute to the prediction of specific enzymes (sulfatases) [More details].
Programs funded by research institutions
PEPS PEPS: a platform for supporting studies in pharmaco-epidemiology using medico-administrative databases
Participants : Olivier Dameron, Yann Rivault.
As a partner of the PEPS platform, IRISA develops generic methods supporting efficient and semantically-rich queries for pharmaco-epidemiology studies on medico-administrative databases. The leader is Thomas Guyet (IRISA team Lacodam). We showed that Semantic Web technologies are technically suited for representing patients' data from medico-administrative databases as RDF and querying them using SPARQL. We also demonstrated that this approach is relevant as it supports the combination of patients' data with hierarchical knowledge in order to address the problem of reconciling precise patients data with more general query criteria , , . This work is mostly conducted by Yann Rivault, whose PhD thesis is supervized by Olivier Dameron and Nolwenn LeMeur (Ecole des Hautes Etudes en Santé Publique).
Cancer Plan: TGFSYSBIO
Participants : Nathalie Théret, Jacques Nicolas, Olivier Dameron, Anne Siegel, Jean Coquet.
The TGFSYSBIO project aims to develop the first model of extracellular and intracellular TGF-beta system that might permit to analyze the behaviors of TGF-beta activity during the course of liver tumor progression and to identify new biomarkers and potential therapeutic targets. Based on collaboration with Jerome Feret from ENS, Paris,we will combine a rule-based model (Kappa language) to describe extracellular TGF-beta activation and large-scale state-transition based (Cadbiom formalism) model for TGF-beta-dependent intracellular signaling pathways. The multi-scale integrated model will be enriched with a large-scale analysis of liver tissues using shotgun proteomics to characterize protein networks from tumor microenvironment whose remodeling is responsible for extracellular activation of TGF-beta. The trajectories and upstream regulators of the final model will be analyzed with symbolic model checking techniques and abstract interpretation combined with causality analysis. Candidates will be classified with semantic-based approaches and symbolic bi-clustering technics. The project is funded by the national program "Plan Cancer - Systems biology" from 2015 to 2018.
Participants : Damien Eveillard, Jeanne Got, Anne Siegel.
Oceans are particularly affected by global change, which can cause e.g. increases in average sea temperature and in UV radiation fluxes onto ocean surface or a shrinkage of nutrient-rich areas. This raises the question of the capacity of marine photosynthetic microorganisms to cope with these environmental changes both at short term (physiological plasticity) and long term (e.g. gene alterations or acquisitions causing changes in fitness in a specific niche). Synechococcus cyanobacteria are among the most pertinent biological models to tackle this question, because of their ubiquity and wide abundance in the field, which allows them to be studied at all levels of organization from genes to the global ocean.
The SAMOSA project is funded by ANR from 2014 to 2018, coordinated by F. Gaczarek at the Station Biologique de Roscoff/UPMC/CNRS. The goal of the project is to develop a systems biology approach to characterize and model the main acclimation (i.e., physiological) and adaptation (i.e. evolutionary) mechanisms involved in the differential responses of Synechococcus clades/ecotypes to environmental fluctuations, with the goal to better predict their respective adaptability, and hence dynamics and distribution, in the context of global change. For this purpose, following intensive omics experimental protocol driven by our colleagues from Station Biologique de Roscoff , we aim at constructing a gene network model sufficiently flexible to allow the integration of transcriptomic and physiological data.
ADT Complex-biomarkers and ADT Proof of concept
Participants : Jeanne Got, Marie Chevallier, Meziane Aite, Anne Siegel.
This project started in Oct. 2014 and aims at designing a working environment based on workflows to assist molecular biologists to integrate large-scale omics data on non-classical species. The main goal of the workflows will be to facilitate the identification of set of regulators involved in the response of a species when challenged by an environmental stress. Applications target extremophile biotechnologies (biomining) and marine biology (micro-algae).
Participants : Victorien Delannée, Anne Siegel, Nathalie Théret.
The objective of Mecagenotox project is to characterize and model the human liver ability to bioactivate environmental contaminants during liver chronic diseases in order to assess individual susceptibility. Indeed, liver pathologies which result in the development of fibrosis are associated with a severe dysfunction of liver functions that may lead to increased susceptibility against contaminants. In this project funded by ANSES and coordinated by S. Langouet at IRSET/inserm (Univ. Rennes 1), we will combine cell biology approaches, biochemistry, biophysics, analytical chemistry and bioinformatics to 1) understand how the tension forces induced by the development of liver fibrosis alter the susceptibility of hepatocytes to certain genotoxic chemicals (especially Heterocyclic Aromatic Amines) and 2) model the behavior of xenobiotic metabolism during the liver fibrosis. Our main goal is to identify "sensitive" biomolecules in the network and to understand more comprehensively bioactivation of environmental contaminants involved in the onset of hepatocellular carcinoma.
Participants : Olivier Dameron, Jean Coquet, Nathalie Théret, Jacques Nicolas, Anne Siegel, Pierre Vignet.
PEPS CONFOCAL aims at developing new bioinformatics methods for analyzing heterogeneous *omics data and for filtering them according to domain knowledge. The current approaches are facing four main limitations: (1) classic biclustering methods do not support partial overlap of clusters, which is too restrictive considering some genes' pleiotropic nature, (2) they assume that the items to analyze (the genes, the molecules, the signaling pathways...) are independent, (3) they tend to generate numerous clusters leaving to the experts the task of identifying the relevant ones, and (4) they are sensitive to noisy or incomplete data. We investigate the extension of Formal Concept Analysis (FCA) with symbolic knowledge from ontologies in order to process large and complex sets of associations between genes, signaling pathways and the molecules involved in these pathways. Future applications cover the discrete model analysis in molecular biology. CONFOCAL initiated a collaboration with Amedeo Napoli (LORIA Nancy) and Elisabeth Remy (Mathematics Institute Luminy, "Mathematical Methods for Genomics" team).