Section: Partnerships and Cooperations
National Initiatives
Long-term contracts
"Omics"-Line of the Chilean CIRIC-Inria Center
Participants : Anne Siegel, Jérémie Bourdon, François Coste, Marie Chevallier, Damien Eveillard, Gaëlle Garet, Jacques Nicolas, Santiago Videla.
Cooperation with Univ. of Chile (MATHomics, A. Maass) on methods for the identification of biomarkers and software for biochip design. 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.
ANR Idealg
Participants : Anne Siegel, Catherine Belleannée, Jérémie Bourdon, Jeanne Cambefort, François Coste, Olivier Dameron, Damien Eveillard, Jacques Nicolas, Guillaume Collet, Clovis Galiez, Gaëlle Garet, Yann Guitton, Sylvain Prigent.
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 to workpackages 1 (establishment of a virtual platform for integrating omics studies on seaweed) and 4 (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) within workpackage 5 .[details]
Methodology: ANR Biotempo
Participants : Anne Siegel, Jérémie Bourdon, François Coste, Damien Eveillard, Jacques Nicolas, Olivier Dameron, Vincent Picard, Sylvain Prigent, Nathalie Théret, Santiago Videla.
The BioTempo projects aims at developing some original methods for studying biological systems. The goal is to introduce partial quantitative information either on time or on component observations to gain in the analysis and interpretation of biological data. Three biological applications are considered regulation systems used by biomining bacteria, TGF- signaling and initiation of sea-urchin translation. It is funded by ANR Blanc (SIMI2) and coordinated by A. Siegel from 2011 to Nov. 2014. Teams involved include LINA (Nantes), I3S (Nice), DIMPP (Montpellier), Contraintes/Lifeware project team (Inria), IRSET (Rennes) and Station biologique de Roscoff [details]
Proof-of-concept on dedicated applications
ANR Fatinteger
Participants : Aymeric Antoine-Lorquin, Catherine Belleannée, Jacques Nicolas, Anne Siegel.
This project (ANR Blanc SVE7 "biodiversité, évolution, écologie et agronomie" from 2012 to 2015) is leaded by INRA UMR1348 PEGASE (F. Gondret). Its goal is the identification of key regulators of fatty acid plasticity in two lines of pigs and chickens. To reach these objectives, this project has for ambition to test some combination of statistics, bioinformatics and phylogenetics approaches to better analyze transcriptional data of high dimension. Data and methods integration is a key issue in this context. We work on the recognition of specific common cis-regulatory elements in a set of differentially expressed genes and on the regulation network associated to fatty acid metabolism with the aim of extracting some key regulators.
ANR Mirnadapt
Participants : Jacques Nicolas, Catherine Belleannée, Anne Siegel, Olivier Dameron, Valentin Wucher, Charles Bettembourg.
This ANR project is coordinated by UMR IGEPP, INRA Le Rheu (D. Tagu) and funded by ANR SVSE 6 "Génomique, génétique, bioinformatique, biologie systémique" from 2012 to 2014. This cooperation was strengthened by a co-tutored PhD thesis (V. Wucher) defended in Nov. 2014 [13] . It proposes an integrative study between bioinformatics, genomics and mathematical modeling focused on the transcriptional basis of the plasticity of the aphid reproduction mode in response to the modification of environment. An important set of differentially expressed mRNAs and microRNAs are available for the two modes, asexual parthenogenesis and sexual reproduction. Our work is to combine prediction methods for the detection of putative microRNA/mRNA interactions as well as transcription factor binding sites from the knowledge of genomic sequences and annotations available on this and other insects. The results will be integrated within a coherent putative interaction network and serve as a filter for the design of new targeted experiments with the hope to improve functional annotations of implied genes.
ANR Samosa
Participants : Jacques Nicolas, Catherine Belleannée, Anne Siegel, Aymeric Antoine-Lorquin, Jérémie Bourdon, François Coste.
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.
Programs funded by research institutions
ADT Complex-biomarkers
Participants : Jeanne Cambefort, Guillaume Collet, Marie Chevallier, 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).
ANSES Mecagenotox
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.
PEPS VAG
Participants : François Coste, Jacques Nicolas, Clovis Galiez.
PEPS VAG started a collaboration between IMPMC UMR 7590, Institut de biologie de l'Ecole Normale Supérieure (IBENS) UMR8197, Atelier de Bioinformatique UPMC and Dyliss. It aims at defining the needs and means for a larger project about viruses in marine ecosystems. Indeed, we aim at developing new methods based on both sequential and structural information of proteins to improve the detection of viral sequences in marine metagenomes, to identify new viruses and to compare the viral populations specifically associated with different environment parameters (temperature, acidity, nutriments...) and ultimately to connect them with the potential hosts identified by population sequencing.