PRABI
Rhone-Alpes Bioinformatics Center


Research projects involving PRABI-AMSB

Mosqui-Target

Project funded by CNRS/INEE-APEGE 2013 (duration : 2013-2014)

Targeted analysis of SNP associated to dengue vectors insecticide metabolic resistance.

Coordinator : Jean-Philip David (LECA) Collaborators : Vincent Navratil(PRABI, UCBL)


Large-scale RNA-seq analysis of intracellularly grown Legionella pneumophila strains.

Project funded by FRM - Bioinformatic analysis for research in biology (duration : 2014-2017)

Coordinators : Sophie Jarraud (CIRI), Guy Perrière (LBBE) Collaborators : Amandine Fournier (PRABI/LBBE), Christine Oger (PRABI, UCBL) Vincent Navratil (PRABI, UCBL)

The objectives of this project are to (i) characterize the genetic differences among Lp1 strains with respect to the severity of the associated legionellosis and (ii) to achieve a large-scale study of differential gene expression (DGE) by RNA-Seq will allow us to identify the determinants of pathogenicity at a transcriptomic level.


Ancestrome

Project funded by grant ANR on the Bioinformatics Investissement d’avenir call (duration : 2012-2016)

Coordinator : Vincent Daubin (LBBE) WP7 coordinator : Guy Perriere (PRABI, LBBE), Laurent Duret (LBBE) External collaborators : Rémi Planel (PRABI, UCBL/LBBE), Dominique Guyot (PRABI, UCBL), Vincent Navratil (PRABI, UCBL)

Ancestrome is a research project that aims to study genome organization and functioning of extant living organisms to build integrative models to reconstruct evolutionary intermediates together with the evolutionary processes that have generated them.

The PRABI participate to the WP7 (Data management and valorization ).


LegCoxiNet

Project funded by the labex ECOFECT. (duration : 2013-2016)

Coordinators : Patricia Doublet (CIRI), Guy Perrière (LBBE), ecofect teams partners : Mathias Faure (CIRI), Elsa Jourdain (UR346), Lionel Zenner (LBBE) external teams partners : Elodie Rousset (CNRL), Sophie Jarraud (CNRL/CIRI), Vincent Navratil (PRABI, UCBL)

LegCoxiNet gathers complementary skills in infectiology, eco-immunology and bioinformatics to (1) gain further knowledge on the molecular mechanisms by which Legionella pneumophila and Coxiella burnetii manipulate host autophagy to successfully infect mammals, and to (2) lay foundations for understanding the evolutionary scenarii that could allow the emergence of common strategies to escape host defenses, in particular autophagy, for successful dissemination in environment and during infection.


Deciphering novel non-conventional functions of nucleolin in HSV-1 infected cells

Project funded by grant FINOVI-AO#08 (R12128CC) (duration : 2012-2015)

Coordinator : Anna Greco (CIRI) Collaborators : Philippe Bouvet (ENS, Lyon), Vincent Navratil (PRABI, UCBL)

The Goal of this projet is to decipher the non-conventional functions of the nucleolin in HSV-1 infected cells by using a systems biology approach based on the modelling of HSV-1/NUCL protein interaction network.

Nucleolin partners obtained by TAP/MS technology will be first mapped and visualized onto the Human protein-protein interaction network (i.e. the human interactome) but also onto the Virus-Human protein-protein interaction network based on a new release of VirHostNet knowledge base develop at PRABI. Systems biology modeling will help to propose best nucleolin partners candidates for further experimental validation.


Eumétasol

Project funded by grant ANR-09-GENM-033-001 (duration : 2009-2013)

Coordinator : Roland Marmeisse (UMR5557) Collaborators : François Bartolo, Christine Oger (PRABI, UCBL) Vincent Navratil (PRABI, UCBL), Christian Gautier (PRABI, UCBL), Guy Perrière (PRABI, CNRS)

Eumetasoil was a high-throughput sequencing metatranscriptomic project which aims were twofold : i) highlight the impact of plant soil cover and global changes on soil genetic diversity and ii) look for novel biocatalysts.

In this project, the PRABI was mainly involved in the tasks of taxonomic and functional identification. For that purpose we developed a pipeline integrating the following tools :

The analyses were performed on a set of 155 samples from three alpine soils (Breuil, Lautaret and Puéchabon). They contained a total of 3.94×109 reads of 100 bp Illumina HiSeq 2000 reads (paired-end).


Metasoil

Project funded by grant ANR-08-GENM-025 (duration : 2008-2012)

In this project, the PRABI had to perform the tasks of taxonomic identification as well as the development of the project database and Web service.