GenOuest

Adress
263 avenue du Général Leclerc
Campus de Beaulieu 35000 Rennes
Structure(s)
INRIA
Unit:
INRIA Rennes Bretagne Atlantique IRISA UMR6074
Regional Center
IFB West
Website
GENOUEST
Scientific leader(s)
Technical leader(s)
Certificat(s)
  • CNOC (INRA)
  • ISO 9001
  • Label IBiSA
Infrastructure
Propriétaire
Effective storage
1 200.00 To
Cluster: cores number
800 cores
Data collections number
8
CPU/hours a year
4 000 000 H / an
Bioinformatic tools number
350
Users number (last year)
480
Servers description

Compute cluster

The computing resources can be accessed anonymously for certain tools or after authentication (command line or Galaxy portal).

The cluster is based on a forty servers using the SGE task scheduler. 

This computing ensemble is associated with two storage areas: a high performance space of 110 To and a NFS conventional space of 120 terabytes.

 

Cloud

The Genocloud infrastructure consists of 8 servers with 224 cores to 650 GB of memory. This set is associated with 8 TB of stockage.Several preconfigured images are made ​​available to users.


Access conditions

Access to the resources is free. The account application is available on https://my.genouest.org

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
19
Latest update:
Not documented

Crispi

Description

Base de données de séquences CRISPR. (mise en production en 2009).

Access conditions

Accès libre.

No website documented
Annual visits:
2 588 an
Unique visits:
1 930 an
Quotes:
5
Latest update:
Not documented

AnnotQTL

Description

Outil d’annotation fonctionnelle (mise en production en 2011).

Access conditions

Accès libre.

No website documented
Annual visits:
4 672 an
Unique visits:
3 484 an
Quotes:
2
Latest update:
Not documented

Cyanolyase

Description

Base de séquences et de motifs des phycobiline lyases (mise en production en 2012-13).

Access conditions

Accès libre.

No website documented
Annual visits:
1 an
Unique visits:
141 an
Quotes:
Not documented
Latest update:
Not documented

GAG

Description

Genomic Annotation Gathering : base de données de références croisées. (mise en production en 2013).

Access conditions

Accès libre.

Annual visits:
6 943 an
Unique visits:
4 336 an
Quotes:
45
Latest update:
Not documented

Aphidbase

Description

Banque de données génomique de référence pour plusieurs espèces de pucerons (Acyrthosiphon pisum, Myzus persicae)

Access conditions
No website documented
Annual visits:
1 590 an
Unique visits:
829 an
Quotes:
Not documented
Latest update:
Not documented

LepidoDB

Description

Banque de données génomique de référence pour des lépidoptères ravageurs de cultures (Spodoptera frugiperda notamment).

Access conditions
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
35
Latest update:
Not documented

Germonline

Description

The GermOnline 4.0 gateway is a cross-species microarray expression database focusing on germline development, meiosis and gametogenesis as well as the mitotic cell cycle. (created in 2009).

Access conditions

Free access

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
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Latest update:
Not documented

Staphylococcal regulatory RNAs

Description

The ‘Staphylococcal Regulatory RNA Database’ compiled all published data in a single interface including genetic locations, sequences and other features. SRD proposes a simplified and unified identifier for Staphylococcal regulatory RNAs (srn) based on the sRNA’s genetic location in S. aureus strain N315 which served as a reference.

 

Launched in 2015.

 

Access conditions

Free access

Available at http://srd.genouest.org/

 

No website documented
Annual visits:
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Unique visits:
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Quotes:
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Latest update:
21-01-2016

eDystrophin

Description

eDystrophin is a locus specific database for in-frame mutations and SNPs found in the DMD gene and the associated dystrophin variants

Access conditions

Accès libre

http://edystrophin.genouest.org/

Annual visits:
Not documented
Unique visits:
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Quotes:
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Latest update:
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Dog CNV database

Description

DoG_CNV is the Database of Genomic Copy Number Variants in the canine genome.

Access conditions

Free access

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
4
Downloads:
Not documented

ReproGenomics Viewer

Description

The ReproGenomics Viewer (RGV) is a cross-species genomic toolbox for the reproductive community. The system is based on the implementation of a JBrowse genome browser and a Galaxy bioinformatics workflow environment.

Mis en place en 2015

Access conditions

Accès libre

http://rgv.genouest.org/

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
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Logol

Description

Langage pour la recherche de motifs complexes. Interface web évoluée et téléchargement possible. La ressource a été mise en ligne en 2013 pour une première phase d’utilisation interne pour finaliser les développements et aboutir à un système stable.

Access conditions

Utilisation interne.

Accès libre.

Annual visits:
Not documented
Unique visits:
2 833 an
Quotes:
Not documented
Downloads:
Not documented

e-BGO

Description

Portail de collaboration scientifique (mise en production en 2013).

Access conditions

Accès public.

No website documented
Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
11
Downloads:
Not documented

BioQuali

Description

Plugin de visualisation et d’analyse de réseaux pour Cytoscape (mis en production en 2009).

Access conditions

Accès libre.

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
11
Downloads:
Not documented

BioMAJ

Description
BioMAJ (BIOlogie Mise A Jour) is a workflow engine dedicated to data synchronization and processing.

The software automates the update cycle and the supervision of the locally mirrored databank repository.

The software is free and released under AGPL v3 based licence.

Access conditions

Téléchargement libre : https://github.com/genouest/biomaj

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

BioMAJ2Galaxy

Description

BioMAJ2Galaxy makes it possible to configure BioMAJ to automatically download some reference data, to then convert them and/or index it in various formats, and then make this data available in a Galaxy server using data libraries or data managers.

Access conditions

Téléchargement libre : https://github.com/genouest/biomaj2galaxy

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

GO-Docker

Description

It is a cluster management tool using Docker as execution/isolation system. The software does not manage however itself the dispatch of the commands on the remote nodes. For this, it integrates with container management tools (Docker Swarm, Apache Mesos, ...)

Access conditions

Téléchargement libre : http://www.genouest.org/godocker/index.html

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

BioShaDock

Description

BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists.

Access conditions

Accès libre sur docker-ui.france-bioinformatique.fr/

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

PepPSY

Description

PepPSy has been developed as a user-friendly gene expression-based prioritization system, to help investigators to determine in which human tissues they should look for an unseen protein and curators to quickly look at available transcriptomics/proteomics data for a list of proteins.

Access conditions

Accès libre

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
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GO2Pub

Description

GO2PUB to automatically enrich PubMed queries with gene names, symbols and synonyms annotated by a GO term of interest or one of its descendants

Access conditions

Accès libre

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

Autograph

Description

AutoGRAPH is an integrated web server for multi-species comparative genomic analysis. It is designed for constructing and visualizing synteny maps between two or three species, determination and display of macrosynteny and microsynteny relationships among species, and for highlighting evolutionary breakpoints.
 

Access conditions

Free access.

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

Askomics

Description

AskOmics is a visual SPARQL query builder for RDF database.

Access conditions

Free

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

Caspo

Description

The caspo pipeline is dedicated to automated reasoning on logical signaling networks

Access conditions

Free

Annual visits:
Not documented
Unique visits:
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Quotes:
Not documented
Downloads:
Not documented

Cadbiom

Description

CADBIOM is an open source modelling software. Based on Guarded transition semantic, it gives a formal framework to help the modelling of biological systems such as cell signaling network.

Access conditions

Free

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

Protomata

Description

Given a sample of (unaligned) sequences belonging to a structural or functional family of proteins, Protomata-Learner infers automata characterizing the family. Automata are graphical models representing a (potentially infinite) set of sequences.

Access conditions

Free

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
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CesGO

Description

CeSGO offers a complete Virtual Research Environment (VRE) for Life Sciences. This VRE is based on a collaborative environment built on Wordpress and BuddyPress. It associated to the data sharing services of Owncloud and the SEEK platform.

Main site : https://www.cesgo.org/en/

Collaborative platform : https://www.cesgo.org/collaboration

Data management platform : https://data-access.cesgo.org

Scientific data platform : https://seek.cesgo.org/

 

 

Access conditions
Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
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Aureme

Description

The toolbox AuReMe allows for the Automatic Reconstruction of Metabolic networks based on the combination
of multiple heteregeneous data and knowledge sources. Since 2016, the workflow has been made available
as a Docker image to facilitate its distribution among the scientific community

Access conditions

Free

Annual visits:
Not documented
Unique visits:
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Quotes:
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Downloads:
Not documented

Minia

Description

Minia is a short-read assembler based on a de Bruijn graph, capable of assembling a human genome on a desktop computer in a day. The output of Minia is a set of contigs. Minia produces results of similar contiguity and accuracy to other de Bruijn assemblers (e.g. Velvet).

Access conditions

Free

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Downloads:
Not documented

GATB

Description

The Genome Analysis Toolbox with de-Bruijn graph (GATB) provides a set of highly efficient algorithms to analyse NGS datasets. These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes).

 

 

Access conditions

Freely available.

Domains of activity
  • Biomedical
  • Agri-food
  • Environment
  • Biotechnology
  • Biology
Description of expertise domains

GenOuest offers many services: 1) a bioinformatics infrastructure: a complete environment for users with or without the support of the core facility members. 2) bioinformatics application development : for the projects requiring software development the coders of the facility bring their expertise to build specific environments or interface of databases. 3) expertise and consulting : GenOuest members can provide help for scientific projects (data analysis, data management plans, etc.)   4) Technological transfer: since the GenOuest core facility is hosted by a computer science institute many tools originating from computer science research can be transferred.  5) Training: many training sessions on tools, environments or methodologies are provided by GenOuest engineers.  6) Scientific hosting : in partnership with GenOuest, users can install or setup new resources to disseminate their research activities.

 

Besides, GenOuest carries out research and developments in several fields :

 Developments focusing on sequence analysis (Logol, DrMotifs), biological data integration (BioMAJ, SeqCrawler, Danaïdes), and also metadata in Biology (EMME).

Technological developments of tools and environments to ease the administration and usage of bioinformatics applications (BioMAJ, MobyleNet, Galaxy) or technological developments on new computation paradigms for bioinformatics (cloud computing : genocloud, grod computing : Grisbi).

These two main fields are federated in a E-science project centered on Virtual Research Environments.

 

The platform is in close interaction with two local bioinformatics teams, Dyliss and GenScale. The Dyliss team specializes on sequence analysis and systems biology using formal systems to characterize the genetic factors controlling phenotypic responses depending on the environment. The GenScale team focuses on analysis of genomic data on a large scale in developing optimized algorithms (CPU and memory), and which can also be run in parallel environments.  The areas of expertise of these two teams contribute to reinforce the expertise of the GenOuest platform and offer innovative tools.

The GenOuest platform is also associated very closely with INRA Bipaa platform which offers resources bioinformatics for Genomics and post-Genomics of insects.

 

From a thematic point of view, the tools and methodologies developed within this group of fifty people are used in the traditional scientific domains of Biogenouest: sea, agriculture, health and environment.

 

Keywords:
  • NGS data analysis
  • Sequence analysis
  • Sequence algorithmics
  • Sequence motif discovery
  • Machine learning
  • Integration of heterogeneous data
  • Knowledge representation
  • Ontologies
  • Semantic Web
  • System biology
  • Metabolic network modelling
  • Regulatory network modelling
  • System modelling
  • Information and communication technology developments
  • Tools
  • Tool integration
  • Interoperability
  • Interfaces, web portals
  • Workflows developments
  • Data
  • Data integration
  • Data management and transfer
  • Databases and information systems
  • Computing environments
  • Cluster
  • Cloud

Formation professionnelle

No website documented
Trainees:
45 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Initiation à la plateforme web GALAXY : L’analyse de données biologiques pour tous !

Description

Présentation

L’analyse des données biologiques nécessite de plus en plus l’utilisation de ressources et d’environnements informatiques difficiles à maîtriser pour le biologiste.
Cette formation présente et décompose l’utilisation de l’environnement Galaxy.
En se basant sur une plateforme web, comme c’est la cas avec Mobyle, cet environnement propose une nouvelle approche pour rendre l’analyse biologique plus aisée pour les non- informaticiens.

Objectifs 

Prise en main de l’environnement Galaxy et des différentes fonctionnalités proposées.

Organisation pédagogique 

La formation comprendra un exposé théorique avec démonstrations pratiques complété par une rapide application sur la manipulation de données de régions génomiques.

Public visé

Chercheurs et ingénieurs, biologistes et bio-informaticiens possédant des compétences en développement bio-informatique souhaitant intégrer des outils dans le portail web Galaxy.

Pré-requis

Aucun.

Access conditions

Pas de pré-requis.

No website documented
Trainees:
13 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Analyse de données RNAseq sous Galaxy

Description

L’analyse des données biologiques nécessite de plus en plus l’utilisation de ressources et d’environnements informatiques difficiles à maîtriser pour le biologiste.
Cette formation présente et décompose l’utilisation de l’environnement Galaxy.
En se basant sur une plateforme web, comme c’est la cas avec Mobyle, cet environnement propose une nouvelle approche pour rendre l’analyse biologique plus aisée pour les non- informaticiens.

Objectifs 

Prise en main de l’environnement Galaxy et des différentes fonctionnalités proposées.

Organisation pédagogique 

La formation est exclusivement orientée pratique! Il s’agir d’utiliser des données de RNAseq fournies par l’UMR 0598 Agrocampus-Ouest / INRA pour utiliser les outils classiques d’analyse de données RNAseq (Tophat, flagstat, Cufflinks, Cuffcompare, Cuffdiff, ou htseq-count, Deseq…)

Public visé

Chercheurs et ingénieurs, biologistes souhaitant s’initier à l’analyse de données RNAseq.

Access conditions

Pas de pré-requis.

No website documented
Trainees:
20 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Initiation à l’analyse de données de type RAD par le pipeline Stacks sous la plateforme web d’analyse de données Galaxy

Description

Cette formation initie l’utilisation de Stacks dans l’environnement Galaxy.
En se basant sur une plateforme web, comme c’est la cas avec Mobyle, nous proposons une nouvelle utilisation de Stacks pour rendre l’analyse biologique plus aisée pour les non- informaticiens.

Objectifs 

Principe de l’analyse de données RAD-seq via Stacks.

Organisation pédagogique 

La formation comprendra un exposé théorique avec démonstrations pratiques.

Le programme :
1/ Présentation théorique du fonctionnement global de Stacks. Compter 1h
2/ Analyse de données RAD avec Stacks sous Galaxy. 3h
a) cartographie génétique
b) génomique des populations
c) assemblage de données pairées

Public visé

Chercheurs et ingénieurs, biologistes et bio-informaticiens souhaitant analyser des données de type RAD-seq dans le portail web Galaxy.

Access conditions

 

No website documented
Trainees:
6 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

HUBzero : Plateforme web open-source de collaboration scientifique

Description

Les projets de recherche sont de plus en plus multi-disciplinaires et multi-site. Afin de faciliter la gestion de groupe, la gestion de projet et le partage de ressources, de nombreux outils généraux ou dédiés entreprise existent. HUBzero représente la meilleure solution open-source et dédiée science. Nous proposons de vous présenter son fonctionnement global à travers une démonstration interactive.
Objectifs 

Prise en main de l’environnement HUBzero et des différentes fonctionnalités proposées.

Organisation pédagogique 

La formation est exclusivement orientée démonstration!

Public visé

Chercheurs et ingénieurs, biologistes souhaitant s’initier à l’utilisation d’HUBzero pour la gestion de groupes et de projets et le partage de ressources.

Access conditions
Not documented
No website documented
Trainees:
10 trainees / year
Training time:
1 day(s) / year
No upcoming session scheduled

Intégration d’outils dans la plateforme web GALAXY

Description
Not documented
Access conditions
Not documented
Users distribution
International
2 %
National
15 %
Regional
61 %
Local
22%
Explanation about this distribution:

Les chiffres donnés ci-dessus correspondent aux personnes accédant de manière authentifiée à l’environnement offert par la plate-forme. La partie locale correspond, outre les besoins propres des développements de la plate-forme, à deux équipes de recherche en bioinformatique de l’Irisa/Inria qui apportent des contributions régulières d’outils originaux à la plate-forme.

Platform's own projects

- DrMotifs : mise en place d’un portail de recherche et découverte de motifs (financement IBISA 2010)

- EMME : environnement de gestion des métadonnées expérimentales (financement IBISA 2012)

- e-Biogenouest : mise en place d’un environnement virtuel de recherche (financement Région Bretagne et Région Pays de la Loire 2011-2014)

- Genocloud : mise en place d’un environnement cloud expérimental pour la bioinformatique (auto-financement et financement Région Bretagne 2014)

- Hadoopizer : développement d’un framework pour l’utilisation du map-reduce en bioinformatique (financement Région Bretagne 2013)

- BioMAJ : outil de gestion des banques de données biologiques (financement INRIA 2009)

- CPER CeSGO : développement d'une plate-forme e-Science centrée sur les Sciences de la Vie (2015-2018)

- GO-Docker : gestionnaire de tâches sous Docker (auto-financement 2015)

 

Collaborations
National projets

- PELICAN : ANR 2012

- ECS : ANR 2012

- Rapsodyn : PIA : Optimisation de la teneur et du rendement en huile chez le colza cultivé sous contrainte azotée.

- France Génomique : PIA :

- BioDataCloud : PIA : Developpement de l'Economie Numerique «Cloud computing» Call, n.3 - Big data

- Projet INCa : «Structuration du séquençage de nouvelle génération à visée diagnostique en cancérologie»

 

A ces projets viennent s’ajouter les projets dans lesquels est impliquée Bipaa : -LepidOLF (ANR) - mirnADAPT (ANR) - Spéciaphid (ANR) - ADA-Spodo (ANR)

International and European projects

- Projet Excelerate

Projects with industry
Not documented
Collaboration projects not founded through an external organism
Not documented
Provision of services not founded through an external organism
Not documented
Animations (Workshops, Work-groups, seminars, conferences ... )

Groupe de travail Galaxy Grand Ouest : la plate-forme GenOuest est à l’origine des activités de ce groupe de travail qui va tout naturellement interagir avec le groupe de travail Galaxy de l’IFB.

Journée d’animation de l’axe bioinformatique de Biogenouest : Depuis 10 ans la plate-forme organise annuellement, en octobre-novembre, des rencontres à Rennes. Ces rencontres, ciblées sur un thème d’actualité, rassemblent de 80 à 100 personnes en moyenne.

Journée d’animation du projet fédérateur e-Biogenouest : Dans le cadre du projet E-science, une journée d’animation a été proposée en juin 2013. Cette journée a rassemblé plus de 80 personnes.

Participation au groupe de travail GRISBI : Depuis le projet GRISBI , la plate-forme GenOuest participe aux diverses réunions du groupe de travail.

La plate-forme GenOuest participe régulièrement au congrès Gen2Bio que ce soit pour des ateliers ou des conférences .
 

Internal publications
Seqcrawler: biological data indexing and browsing platform. Olivier Sallou, Anthony Bretaudeau, Aurelien Roult - BMC Bioinformatics (2012) vol. 13 (1) pp. 175-175

Obadia, T., Sallou, O., Ouedraogo, M., Guernec, G. & Lecerf, F. The GAG database: A new resource to gather genomic annotation cross-references. Gene, (2013).

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. A Bretaudeau, F Coste, F Humily, L Garczarek, G Le Corguille, C Six, M Ratin, O Collin, W. M Schluchter, F Partensky. Nucleic Acids Research (2013) vol. 41 (D1) pp. D396-D401

Bretaudeau, A., et al. (2015). "BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ." Gigascience 4: 22. 


Sallou, O., & Monjeaud, C. (2015, September). GO-Docker: Batch scheduling with containers. In IEEE Cluster 2015.

Moreews, F., Sallou, O., Ménager, H., Monjeaud, C., Blanchet, C., & Collin, O. (2015). BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Research, 4.
External publications

The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community. Darde T., Sallou, O., Becker, E., Evrard, B., Monjeaud, C., Le Bras, Y., Jegou, B., Collin, O., Rolland, A. D., Chalmel, F., Nucleic Acids Res.2015 Apr 16. pii: gkv345.


The BioMart community portal: an innovative alternative to large, centralized data repositories. Smedley, D., et al. (2015) - Nucleic Acids Res.


Boyer, F., Mercier, C., Bonin, A., Le Bras, Y., Taberlet, P., & Coissac, E. (2015). obitools: a unix‐inspired software package for DNA metabarcoding. Molecular ecology resources.

SRD: a Staphylococcus regulatory RNA database. Sassi M., Augagneur Y., Mauro T., Ivain L., Chabelskaya S., Hallier M., Sallou O., Felden B. RNA. 2015 Mar 24.

The first complete chloroplast genome of the Genistoid legume Lupinus luteus: evidence for a novel major lineage-specific rearrangement and new insights regarding plastome evolution in the legume family. G. E. Martin, M. Rousseau-Gueutin, S. Cordonnier, O. Lima, S. Michon-Coudouel, D. Naquin, J. Ferreira De Carvalho, M. L. Anouche, A. Salmon, A. Anouche. Ann Bot 113(7): 1197-1210.


High-Resolution Profiling of Novel Transcribed Regions During Rat Spermatogenesis. Chalmel F, Lardenois A, Evrard B, Rolland AD, Sallou O, Dumargne MC, Coiffec I, Collin O, Primig M, Jégou B. Biol. Reprod. biolreprod.114.118166– (2014).

Masculinization of the x chromosome in the pea aphid. J. Jaquiéry, C. Rispe, D. Roze, F. Legeai, G. Le Trionnaire, S. Stoeckel, L. Mieuzet, C. Da Silva, J. Poulain, N. Prunier-Leterme, B. Ségurens, D. Tagu, J.-C. Simon, PLoS Genet. 9, e1003690 (2013).

LIMLE, a New Molecule Over-Expressed following Activation, Is Involved in the Stimulatory Properties of Dendritic Cells. L. Le Texier, J. Durand, A. Lavault, P. Hulin, O. Collin, Y. Le Bras, M.-C. Cuturi, E. Chiffoleau, PLoS One 9, e93894 (2014).

Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. Marion Ouedraogo, Charles Bettembourg, Anthony Bretaudeau, Olivier Sallou, Christian Diot, Olivier Demeure, Frédéric Lecerf - PLoS One (2012) vol. 7 (11) pp. e50653

GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development. Ramona Britto, Olivier Sallou, Olivier Collin, Grégoire Michaux, Michael Primig, Frédéric Chalmel - Nucleic Acids Research (2012) vol. 40 (Web Server issue) pp. W458-65

PHYMYCO-DB: a curated database for analyses of fungal diversity and evolution. Stéphane Mahé, Marie Duhamel, Thomas Le Calvez, Laetitia Guillot, Ludmila Sarbu, Anthony Bretaudeau, Olivier Collin, Alexis Dufresne, E Toby Kiers, Philippe Vandenkoornhuyse - PLoS ONE (2012) vol. 7 (9) pp. e43117

Fitness of Macrolide Resistant Campylobacter coli and Campylobacter jejuni. Salman Zeitouni, Olivier Collin, Mathieu Andraud, Gwennola Ermel, Isabelle Kempf.- Microbial drug resistance (Larchmont, NY) (2012) pp.

Transcriptome de novo assembly from next-generation sequencing and comparative analyses in the hexaploid salt marsh species Spartina maritima and Spartina alterniflora (Poaceae). Ferreira de Carvalho J, Poulain J, Da Silva C, Wincker P, Michon-Coudouel S, Dheilly A, Naquin D, Boutte J, Salmon A, Ainouche M Heredity (Edinb). 110, 181–93 (2013).

Rousseau-Gueutin, M., Bellot, S., Martin, G. E., Boutte, J., Chelaifa, H., Lima, O., ... & Ainouche, M. (2015). The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating. Molecular phylogenetics and evolution, 93, 5-16.
Publications with the hosting laboratory
Abdou-Arbi, O., Lemosquet, S., Van Milgen, J., Siegel, A. & Bourdon, J. Exploring metabolism flexibility in complex organisms through quantitative study of precursor sets for system outputs. BMC Syst. Biol. 8, 8 (2014).

Blavy, P., Gondret, F., Lagarrigue, S., van Milgen, J. & Siegel, A. Using a large-scale knowledge database on reactions and regulations to propose key upstream regulators of various sets of molecules participating in cell metabolism. BMC Syst. Biol. 8, 32 (2014).

Andrieux, G., Le Borgne, M. & Théret, N. An integrative modeling framework reveals plasticity of TGF-beta signaling. BMC Syst. Biol. 8, 30 (2014).

Chikhi, R. & Rizk, G. Space-efficient and exact de Bruijn graph representation based on a Bloom filter. Algorithms Mol. Biol. 8, 22 (2013).

Guziolowski, C. et al. Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming. Bioinformatics 29, 2320–2326 (2013).

Transcriptomic profiling of the reproductive mode switch in the pea aphid in response to natural autumnal photoperiod Le Trionnaire G, Jaubert-Possamai S, Bonhomme J, Gauthier JP, Guernec G, Le Cam A, Legeai F, Monfort J, Tagu D.. J Insect Physiol. 2012 Dec;58(12):1517-24.

Candidate chemosensory genes in female antennae of the noctuid moth Spodoptera littoralis Jacquin-Joly E, Legeai F, Montagné N, Monsempes C, François MC, Poulain J,Gavory F, Walker WB 3rd, Hansson BS, Larsson MC.. Int J Biol Sci.2012;8(7):1036-50.

Comparison of gene repertoires and patterns of evolutionary rates in eight aphid species that differ by reproductive mode. Ollivier M, Gabaldón T, Poulain J, Gavory F, Leterme N, Gauthier JP, Legeai F, Tagu D, Simon JC, Rispe C. Genome Biol Evol. 2012;4(2):155-67.

Accelerated evolution of sex chromosomes in aphids, an x0 system. Jaquiéry J, Stoeckel S, Rispe C, Mieuzet L, Legeai F, Simon JC. Mol Biol Evol. 2012 Feb;29(2):837-47.

Candidate Chemosensory Genes In The Stemborer Sesamia nonagrioides, Glaser N, Gallot A, Legeai F, Montagné N, Poivet E, Harry M, Calatayud P-A, Jacquin-Joly E. Int J Biol Sci 2013; 9(5):481-495

A Comparison of the Olfactory Gene Repertoires of Adults and Larvae in the Noctuid Moth Spodoptera littoralis. Poivet E, Gallot A, Montagné N, Glaser N, Legeai F, Jacquin-Joly E. PLoS One. 2013;8(4):e60263

GOUIN, Anaïs, BRETAUDEAU, Anthony, LABADIE, K., et al. Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains. In : Arthropod Genomics 2015. 2015.

Dumas, P., Legeai, F., Lemaitre, C., Scaon, E., Orsucci, M., Labadie, K., ... & Aury, J. M. (2015). Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?. Genetica, 143(3), 305-316.
Acknowledgement
  • Noiret et al. (2016) Robust identification of Ptbp1-dependent splicing events by a junction-centric approach in Xenopus laevis. Dev Biol. 2016 Aug 19. pii: S0012-1606(16)30197-X
  • Le Tonquèze et al. (2016) Identification of CELF1 RNA targets by CLIP-seq in human HeLa cells. Genom Data. 2016 Apr 19;8:97-103. doi: 10.1016/j.gdata.2016.04.009. eCollection 2016 Jun.
  • Boutet et al. (2016)  "SNP discovery and genetic mapping using genotyping by sequencing of whole genome genomic DNA from a pea RIL population. " BMC Genomics (2016) 17:121
  • Loux, V., et al. (2015). "Mutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii." BMC Genomics 16(1): 296.
  • Chevignon, G., Cambier, S., Da Silva, C., Poulain, J., Drezen, J. M., Huguet, E., & Moreau, S. (2015). Transcriptomic response of Manduca sexta immune tissues to parasitization by the bracovirus associated wasp Cotesia congregata. Insect biochemistry and molecular biology.
  • Becker, E., Liu, Y., Lardenois, A., Walther, T., Horecka, J., Stuparevic, I., ... & Primig, M. (2015). Integrated RNA-and protein profiling of fermentation and respiration in diploid budding yeast provides insight into nutrient control of cell growth and development. Journal of proteomics, 119, 30-44.
  • Liu, Y., Stuparevic, I., Xie, B., Becker, E., Law, M. J., & Primig, M. (2015). The conserved histone deacetylase Rpd3 and the DNA binding regulator Ume6 repress BOI1's meiotic transcript isoform during vegetative growth in Saccharomyces cerevisiae. Molecular microbiology.
  • Silva, L. G., Genteluci, G. L., de Mattos, M. C., Glatthardt, T., Figueiredo, A. M. S., & Ferreira-Carvalho, B. T. (2015). Group C Streptococcus dysgalactiae subsp. equisimilis in south-east Brazil: Genetic diversity, resistance profile, and the first report of human and equine isolates belonging to the same MLST lineage. Journal of medical microbiology,
  • Lardenois, A., Stuparevic, I., Liu, Y., Law, M. J., Becker, E., Smagulova, F., ... & Primig, M. (2015). The conserved histone deacetylase Rpd3 and its DNA binding subunit Ume6 control dynamic transcript architecture during mitotic growth and meiotic development. Nucleic acids research, 43(1), 115-128.
  • Gaboyer, F., Burgaud, G., & Alain, K. (2015). Physiological and evolutionary potential of microorganisms from the Canterbury 1 Basin subseafloor, a metagenomic approach 2. FEMS Microbiology Ecology, fiv029.
  • Stuparevic, I., Becker, E., Law, M. J., & Primig, M. (2015). The histone deacetylase Rpd3/Sin3/Ume6 complex represses an acetate-inducible isoform of VTH2 in fermenting budding yeast cells. FEBS letters, 589(8), 924-932.
  • Emily, M., Talvas, A. & Delamarche, C. MetAmyl: a METa-predictor for AMYLoid proteins. PLoS One 8, e79722 (2013).
  • Mathieu et al. Expression screening of cancer/testis genes in prostate cancer identifies nr6a1 as a novel marker of disease progression and aggressiveness. Prostate. 2013 Jul;73(10):1103-14
  • Chalmel et al. Genome-wide identification of Sox8-, and Sox9-dependent genes during early post-natal testis development in the mouse. Andrology. 2013 Mar;1(2):281-92.
  • Genomic analysis of the biocontrol strain Pseudomonas fluorescens Pf29Arp with evidence of T3SS and T6SS gene expression on plant roots
  • Genome scans reveal candidate regions involved in the adaptation to host plant in the pea aphid complex. J Jaquiéry, S Stoeckel, P Nouhaud, L Mieuzet, F Mahéo, F Legeai, N Bernard, A Bonvoisin, R Vitalis, J-C Simon - Mol Ecol (2012) vol. 21 (21) pp. 5251-64
  • Nicolas et al. Assessment of the structural and functional impact of in-frame mutations of the DMD gene, using the tools included in the eDystrophin online database. Orphanet J Rare Dis (2012) vol. 7 pp. 45
  • Bettembourg et al. GO2PUB: Querying PubMed with semantic expansion of gene ontology terms. J Biomed Semantics (2012) vol. 3 (1) pp. 7
  • Chalmel et al. Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility. Hum Reprod (2012) vol. 27 (11) pp. 3233-48
  • Salmon et al. Targeted capture of homoeologous coding and noncoding sequence in polyploid cotton. G3 (Bethesda) (2012) vol. 2 (8) pp. 921-30
  • A new twist to coiled coil. Le Rumeur et al. FEBS Lett (2012) vol. 586 (17) pp. 2717-22
  • The bioinformatics tool box for reproductive biology. Primig M. Biochimica et biophysica acta (2012) pp. Global human tissue profiling and protein network analysis reveals distinct levels of transcriptional germline-specificity and identifies target genes for male infertility. Chalmel et al. Hum Reprod (2012) vol. 27 (11) pp. 3233-48
Development
GenOuest porte divers développements centrés sur la gestion des ressources (BioMAJ, BioMAJ2Galaxy, SeqCrawler, etc.), sur le calcul (GO-Docker, BioShaDock) et sur la collaborarion (utilisation de HubZero, ISAtools, Galaxy).
 
La plupart des logiciels développés au sein de la plate-forme et du laboratoire d’accueil font l’objet de dépôts APP.
- GenOuest : 4 (BioMAJ, ManBand, SeqCrawler, Cassiopee)
- Dyliss/GenOuest : 1 (Logol)
- GenScale : 9 (PLAST, MapSembler, GASSST, Minia, DSK, GATB CORE, Minia-GATB, TakeABreak, Bloocoo)
 
D’autre part, l’outil BioMAJ a été packagé pour des distributions Debian et est disponible au sein des distributions Debian-med et Ubuntu.
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