|
|
|
| e-Pub |
Previous | 
Home
Section: Partnerships and Cooperations
National Initiatives
Long-term contracts
"Omics"-Line of the Chilean CIRIC-Inria Center
Participants : Anne Siegel, Jérémie Bourdon, François Coste, Damien Eveillard, Gaëlle Garet, Jacques Nicolas, Andres Aravena, Sven Thiele, 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. Co-funded by Inria and CORFO-chile from 2012 to 2022, the program includes a co-advised Ph-D student (A. Aravena) [13] and a post-doc (S. Thiele). 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 2013.
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, 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, Michel Le Borgne, Geoffroy Andrieux, Andres Aravena, Vincent Picard, Sylvain Prigent, 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 2014. Teams involved include LINA (Nantes), I3S (Nice), DIMPP (Montpellier), Contrainte 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, Olivier Quenez, 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 Lepidolf
Participants : François Coste, Jacques Nicolas.
The LEPIDOLF project aims at better understanding olfactory mechanisms in insects. The goal is to establish the antennal transcriptome of the cotton leafworm Spodoptera littoralis, a noctuid representative of crop pest insects. It is funded by ANR call Blanc and coordinated by E. Jacquin-Joly from UMR PISC (INRA Versailles) from 2009 to 2013. Our contribution is to use grammatical inference to build characteristic signatures of the Olfactory Receptor family, which will be used to scan directly 454-sequencing reads and available partial cDNAs of genes expressed in the antenna of Lepidoptera or deduced proteins.
ANR Mirnadapt
Participants : Jacques Nicolas, Catherine Belleannée, Anne Siegel, Valentin Wucher.
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 is strengthened by a co-tutored PhD thesis (V. Wucher). 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 Pelican
Participant : François Coste.
The PELICAN project addresses competition for light in the ocean. It proposes an integrative genomic approach of the ecology, diversity and evolution of cyanobacterial pigment types in the marine environment, which arises from differences in the composition of the light-harvesting complexes (PBS). Our work is to build characteristic signatures of targeted PBS enzymes. This ANR project (génomique et biotechnologies végétales) is coordinated by F. Partensky (CRNS Roscoff) from 2010 to 2013.
Programs funded by research institutions
Inria Bioscience Ressource
Participants : Claudia Hériveau, Jacques Nicolas.
This project started in november 2011 and aims at promoting bioinformatics software and resources developed by Inria teams and their partners. A web portal will be deployed to allow users to test the software online. A tool is also developed to enhance the search of a specific resource using different criteria. The project is funded by Inria ADT program from 2011 to 2013, involves 8 research teams and is coordinated by the GenOuest platform and the Dyliss team (J. Nicolas and O. Collin).
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.