URGI

Adress
INRA Versailles
RD10 Route de Saint-Cyr 78000 Versailles
Structure(s)
INRA
Unit:
URGI - UR1164
Regional Center
ApliBio, Ile-de-France
Technical leader
Amselem Joelle
Certificat(s)
  • CNOC (INRA)
  • ISO 9001
  • Label IBiSA
Infrastructure
Propriétaire
Effective storage
207.00 To
Cluster: cores number
904 cores
CPU/hours a year
1 334 776 H / an
Bioinformatic tools number
163
Users number (last year)
942
Servers description

• 1 High-performance cluster
• 1 NFS server for storage management
• 1 server dedicated to the website
• 1 server for backup management
• 3 servers for virtual machines (Databases, Information sytem, web applications)


Access conditions

Web portal: acces to data and tool resources is public or restricted to collaborters in the frame of running project
Cluster: authentified access

Annual visits:
65 634 an
Unique visits:
16 721 an
Quotes:
11
Latest update:
05-01-2017

GnplS

Description

GnpIS is a multi-species integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data including genome-wide association studies, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, markers, single nucleotide polymorphisms, germplasms and genotypes) and genomic data (e.g. genomic sequences, physical maps, genome annotation and expression data) for species of agronomical interest.

Steinbach D, M Alaux, Amselem J, Choisne N, S Durand, Flores R, AO Keliet, Kimmel E, N Lapalu, I Luyten et al: GnpIS: an information system to integrate genetic and genomic data from plants and fungi. Database: the journal of biological databases and curation 2013, DOI: 10.1093 / database / bat058

Access conditions

GnpIS is accessible through a public  web portal allowing to browse each data modules or by searching through all the data simultaneously using a quick search ('google like search') or advanced search (Biomart, Galaxy, Intermine) tools

Some data are  under restricted access in the frame of collaborating project before publication.

Annual visits:
203 200 an
Unique visits:
27 900 an
Quotes:
Not documented
Latest update:
11-01-2017

Wheat@URGI

Description

Portal dedicated to wheat resources data including sequences from the IWGSC (International Wheat Genome Sequencing Consortium) and tools to analyse them.

Access conditions

https://wheat-urgi.versailles.inra.fr/

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
Not documented
Latest update:
11-01-2017

Plant data discovery portal

Description
The Plant Data Discovery Portal allows data discovery in information systems maintained by an international network managing plant data.
Access conditions

Access to the data through the portal : https://urgi.versailles.inra.fr/ifb/

The portal gives access to public data using an indexation tool easy to implement (https://wheat-urgi.versailles.inra.fr/Projects/Wheat-Information-System/SolR-tool-package ). Any plateforme willing to give access to its data through the Plant Data Discovery Portal is welcome to contact us.

Annual visits:
1 390 an
Unique visits:
646 an
Quotes:
189
Downloads:
476

REPET

Description
Analysis of sequences

 

The REPET package integrates bioinformatics programs in order to tackle biological issues at the genomic scale. Its two main pipelines are dedicated to de novo detect [1], classify [2], annotate and analyze repeats [3] in genomic sequences, specifically designed for transposable elements (TEs).

 

1. Flutre T, Duprat E, Feuillet C, Quesneville H: Considering transposable element diversification in de novo annotation approaches. PloS one 2011, 6(1):e16526.
2. Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H: PASTEC: An Automatic Transposable Element Classification Tool. PloS one 2014, 9(5):e91929.
3. Quesneville H, Bergman CM, Andrieu O, Autard D, Nouaud D, Ashburner M, Anxolabehere D: Combined evidence annotation of transposable elements in genome sequences. PLoS computational biology 2005, 1(2):166-175.

Access conditions

Download : https://urgi.versailles.inra.fr/Tools/REPET

Annual visits:
316 an
Unique visits:
208 an
Quotes:
17
Downloads:
81

S-MART

Description
Analysis of the data NGS - Analysis of transcripts (RNA-seq)

S-MART is a toolbox which handles mapped RNA-Seq and ChIP-Seq data. it is is an intuitive and lightweight tool, performing several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization.

It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis (between two conditions, for instance). S-MART also provides many ways to visualize your data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots).

 

Zytnicki M, Quesneville H (2011) S-MART, A Software Toolbox to Aid RNA-seq Data Analysis. PLoS ONE 6(10): e25988. doi:10.1371/journal.pone.0025988

Access conditions

Dowload at: https://urgi.versailles.inra.fr/Tools/S-Mart

Annual visits:
Not documented
Unique visits:
Not documented
Quotes:
6
Downloads:
Not documented

Tedna

Description

Tedna is a lightweight de novo transposable element assembler. It assembles the transposable elements directly from the raw reads.

 Zytnicki M, Akhunov E, Quesneville H: Tedna: a transposable element de novo assemblerBioinformatics 0, 30:2656–8.

Access conditions

Download

 

Annual visits:
133 an
Unique visits:
67 an
Quotes:
Not documented
Downloads:
Not documented

Galaxy server@URGI

Description
Analysis of sequences

 

Web-based access to tools including those developed at URGI

- S-MART tool box

- workflows for Differential Expression Analysis (RNA-Seq) and polymorphism (SNP, structural variations)

Access conditions

https://urgi.versailles.inra.fr/galaxy

Restricted access in the frame of collaborative project or URGI Service offering

Domains of activity
  • Environment
  • Biology
  • Agri-food
  • Computer Science
Description of expertise domains

URGI research activity (data integration, repeat annotation, genome structure and dynamics) is closely related the platform activity (Information System and genome analyses). On the one hand, the platform benefits from the research expertise (analysis and tools development) on the other hand it offers a strong support to our research activity with the resources and expertise of its staff (mainly engineers).

The areas of competence and expertise of the platform members are mainly focused on:

  • Interface development (Java J2EE)
  • Development of analysis pipelines (Python)
  • Databases (PostgreSQL, MySQL)
  • NoSQL technologies (ElasticSearch, Solr)
  • Data integration (ETL Talend) of genomics and genetic data (genome annotation, RNA-Seq, polymorphism, Genome wide association studies, phenotype, genetic resources)
  • Genome analysis (structure and dynamics)
    • Polymorphism analysis (SNP, structural variants)
    • RNA-Seq
    • Gene Annotation (structural and functional)
    • Repeat annotation (specifically transposable elements)
Keywords:
  • NGS data analysis
  • Sequence analysis
  • Cartography
  • Evolution and phylogeny
  • Comparative genomics

Formation professionnelle

Trainees:
10 trainees / year
Training time:
3 day(s) / year
Upcoming session :
21-11-2016

Formation "Détection et Annotation des éléments transposables dans les génomes eucaryotes"

Description

Objectifs

1. Acquérir des connaissances sur les éléments transposables
2. Réaliser l’annotation des éléments transposables dans un génome en utilisant le pipeline REPET
3. Pouvoir être autonome sur ces propres données.

Cette formation est composée de 2 modules 

21-22/11/2016 : module 1

23/11/2016 : module 2 (optionnel)

24/11/2016 : nous proposons aux participants qui le souhaitent d’analyser leurs propres données. Nous les accueillerons à l'URGI où ils pourront travailler de façon autonome sur leur machine, avec un support en cas de problème.

Module 1 : "REPET-lite"

- Introduction générale aux éléments transposables
- Présentation du pipeline REPET et des différentes stratégies d’annotation
- Présentation et utilisation de l’environnement Galaxy
- TP: lancement de REPET-lite sous Galaxy : paramètrage, analyse des résultats, masquage des répétitions dans un génome, ...

Module 2 "curation manuelle des éléments transposables"

- Présentation des différentes démarches possibles pour la curation
- Présentation des outils de visualisation et d'analyse des données
- TP "curation manuelle" : lancement des outils, analyse et traitement d’exemples, "parsing" de fichiers

 

Cette formation est ouverte à la fois aux biologistes et aux bioinformaticiens. Le module 1 ne nécessite pas de pré-requis et est destiné aux personnes dont l’objectif est d’obtenir un génome masqué. Le module 2 vise un public intéressé par l’analyse des éléments transposables dans le génome annoté et nécessite d’avoir des notions de ligne de commande.

 

Access conditions

La formation est gratuite, mais le nombre de place est limité (10 max)

Les inscriptions se font directement par mail auprès de :
nathalie.choisne@versailles.inra.fr "ET" olivier.inizan@versailles.inra.fr

Lors de votre inscription, veuillez préciser si vous êtes intéressés par la journée du 24 novembre. Dans ce cas, vous recevrez un questionnaire qui nous permettra d’évaluer la faisabilité de vos analyses.

No website documented
Trainees:
10 trainees / year
Training time:
Not documented
No upcoming session scheduled

Training to the GnpIS information system

Description

Detailed presentation of GnpIS:
- How to request through various forms (quick-search or module specific)
- How to browse the system: use cases to highlight inter-operability between data in the different modules.

Access conditions

Information and registering at: urgi-contact@versailles.inra.fr

Trainees:
6 trainees / year
Training time:
2 day(s) / year
Upcoming session :
11-04-2016

Galaxy for NGS data analysis

Description

The training combines presentations and use cases-based practices
General presentation of Galaxy
• Data management and history
• Workflows designing
• Visualization tools
Use of 2 workflows
• Polymorphism analysis: Mapping, SNP calling
• RNA-Seq: Differential Expression Analysis (DEA)

Access conditions

Information and registering at: urgi-contact@versailles.inra.fr

No website documented
Trainees:
6 trainees / year
Training time:
Not documented
No upcoming session scheduled

Cluster job submission training

Description

How to launch and manage jobs on URGI cluster

Access conditions

Information and registering at: urgi­-contact@versailles.inra.fr

Users distribution
International
85 %
National
15 %
Regional
0 %
Local
0%
Explanation about this distribution:

The percentages provided are related to the french and international visitors accessing the public data (GnpIS) and tools (e.g. REPET, S-MART).

Platform's own projects

Projets contributing to the development of an Information System for plans and fungi
GnpIS ”Development of the URGI genetic and genomic information system. It includes all Gnp* components, datamarts, Gbrowse, and GRS “; URGI project manager: D. Steinbach
GnpSNP “Development of a sequence variations information system managing SNP, Indel, PAV, CNV, transposable element insertions. “; URGI project manager: N. Mohellibi
Ephesis “Development of a phenotypic information system managing GxE experiments “; URGI project manager: C. Pommier
Siregal “Development of a genetic resources information system managing stocks, passport data, orders, primary phenotypic descriptions. “; URGI project manager: S. Durand
 
Projets contributing to the development of tools and pipeline for structure and dynamics analysis
Pipeline-common “Development of a toolbox for developing pipelines “; URGI project manager: O. Inizan
REPET “Development of a toolbox for detection, annotation and analysis of repeats in a genome. “; URGI project manager: V. Jamilloux
RNAseq “RNAseq tools developments “: URGI project manager: J. Amselem

Collaborations
National projets
  • France Genomique “French Bioinformatics infrastructure for NGS” 2012-2021; Funding: Investissement d'avenir; URGI coord.: J. Amselem; Project coord.: J. Weissenbach, CEA, Evry
  • AKER “French Research Initiative for a Sustainable Beet Improvement: Innovative breeding strategies based on allelic variation mining and novel -omic tools” 2012-2020; Funding: Investissement d'avenir; URGI coord.: D. Steinbach; Project coord.: C. Huyghe, INRA, DG, Lusignan; CDD: 12 months
  • BFF “Biomass For the Future". Development of local miscanthus and sorghum biomass production and valorization chains focused on heat-generation, anaerobic digestion and bio-based construction materials and plastics.” 2012- 2020; Funding: Investissement d'avenir; URGI coord.: H. Quesneville; Project coord.: H. Hofte, INRA, IJPB, Versailles
  • PEAMUST “Pea MUlti-STress adaptation and biological regulations for yield improvement and stability” 2012-2020; Funding: Investissement d'avenir; URGI coord.: D. Steinbach; Project coord.: J. Burstin, INRA, Agroécologie, Dijon
  • Phenome “French Plant Phenomic Centre; 2012-2020; Funding: Investissement d'avenir” URGI coord.: C. Pommier; Project coord.: F. Tardieu, INRA-LEPSE, Montpellier
  • Rapsodyn “Optimisation of the RAPeSeed Oil content and Yield under low Nitrogen input: improving breedin” 2012- 2020; Funding: Investissement d'avenir; URGI coord.: D. Steinbach; Project coord.: N. Nési, INRA-EGPP, Rennes
  •  
  • Gandalf “Genomic AND Adaptation for fungal LiFe history traits involved in host plant interactions” 2012-2015; Funding: ANR Bioadapt; URGI coord.: J. Amselem; Project coord.: F. Delmotte, INRA, SAV, Bordeaux
  • Breedwheat “Breeding for economically and environmentally sustainable wheat varieties: an integrated approach from genomics to selection” 2011-2020; Funding: Investissement d'avenir; URGI coord.: M. Alaux / H. Quesneville; Project coord.: J. Le Gouis, INRA, GDEC, Clermont-Ferrand
  • Amaizing “ Improving the efficiency of maize breeding programs in France, and to further characterize the varieties by implementing biotechnology advances and developing tools, biological knowledge, reference data and strategic know-how” 2011-2019; Funding: Investissement d'avenir; URGI coord.: D. Steinbach; Project coord.: A. Charcosset, Génétique Végétale, Gif-sur-Yvette
  • IFBPlant "The IFB plant node" 2014-2017; Funding IFB Tech; URGI coord.: H. Quesneville; Project coord.: H. Quesneville
  • PAGE “The PAGE program will develop resources and approaches in comparative genomics and deliver publicly applicable tools for the scientific community” 2011-2015; Funding: ANR Blanc; URGI coord.: H. Quesneville; Project coord.: J. Salse, INRA, GDEC, Clermont-Ferrand
  • Renabi-IFB “French Bioinformatics infrastructure” 2011-2015; Funding: Investissement d'avenir; URGI coord.: H. Quesneville; Project coord.: J-F. Gibrat, INRA, UR MIG, Jouy-En-Josas
  • GenOak “Sequencing of the oak genome and identification of genes that matter for forest tree adaptation” 2011- 2015; Funding: ANR Blanc; URGI coord.: H. Quesneville; Project coord.: C. Plomion, INRA, BIOGECO, Bordeaux
  • GnpAsso “Developing new bioinformatics resources to deal with large scale genome-wide association studies data” 2011-2015; Funding: ANR Génomique; URGI coord.: D. Steinbach; Project coord.: D. Steinbach, INRA, URGI, Versailles
  • ADA-SPODO “Molecular determinism of ecological adaptation and speciation in two strains of the Lepidoptera Spodoptera frugiperda” 2011-2015; Funding: ANR Blanc; URGI coord.: H. Quesneville; Project coord.: E. D'Alençon, INRA, UMR DGIMI, Montpellier
  • IBISA-Aplibio “The RENABI Ile de France platform“ 2010-2014; Funding: IBISA; URGI coord.: D. Steinbach; Project coord.: Y. Moszer, Institut Pasteur, Paris
  • 3Bseq “Sequencing, annotation and characterization of the bread wheat chromosome 3B” 2010-2013; Funding: ANR; URGI coord.: M. Alaux / H. Quesneville; Project coord.: C. Feuillet, INRA, GDEC, Clermont-Ferrand
  • FungIsochores “Isochores and effectors: genome reshaping and the birth of highly pathogenic species in fungal phytopathogens” 2010-2013; Funding: ANR; URGI coord.: J. Amselem; Project coord.: T. Rouxel, INRA, BIOGER, Thiverval-Grignon
  • Triannot-lifegrid “Annotation structurale et fonctionnelle automatique des génomes de plantes couplé à un Système d'Information” 2013-2014; Funding: Lifegrid; URGI coord.: M. Alaux; Project coord.: P. Leroy, INRA, GDEC, Clermont-Ferrand
International and European projects
  • Excelerate “ELIXIR-EXCELERATE: fast-track ELIXIR implementation and drive early user exploitation across the life sciences » 2015-2018; Funding EU-H2020 ; A-F Adam-Blondon; Project coord.: N. Blomberg
  • Whealbi “Wheat and barley Legacy for Breeding Improvement” 2013-2017; Funding: EU-FP7; URGI coord.: M. Alaux; Project coord.: G. Charmet, INRA, GDEC, Clermont-Ferrand
  • Whealbi “Wheat and barley Legacy for Breeding Improvement” 2013-2017; Funding: EU-FP7; URGI coord.: M. Alaux; Project coord.: G. Charmet, INRA, GDEC, Clermont-Ferrand
  • InnoVine “Combining innovation in vineyard management and genetic diversity for a sustainable European viticulture” 2013-2016; Funding: FP7; URGI coord.: A-F Adam-Blondon; Project coord.: A-F Adam-Blondon, INRA, Versailles.
  • TransPLANT “Trans-national Infrastructure for Plant Genomic Science” 2011-2015; Funding: EU-FP7; URGI coord.: H. Quesneville; Project coord.: P. Kersey, EBI, Cambridge, UK
Projects with industry

National projects: AKER, Amaizing, BFF, Breadwheat
International projects: TransPLANT, Whealbi

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 ... )

The plateform is member or coordinator of various working groups and networks
 
International networks
- Wheat Initiative (Coord. H. Quesneville)

National networks
- Joint coordination with SouthGreen  platform (Montpellier, France) of IFB-Plants
- Member of the working group  IFB-Galaxy

INRA network and working groups
Co-animation (member of the steering comitee) of the INRA PEPI networks (Partage d'Expérience et de Pratique en Informatique)
- PEPI GD : gestion de données
- PEPI IDL : développement logiciel
- PEPI GPI : gestion de projets en informatique
Member of the  OpenData network

Working groups of  INRA-BAP (Biologie et Amélioration des Plantes)
- Bioinformatics .
- Phénotyping (Information System).

Internal publications
Hoede C, Arnoux S, Moisset M, Chaumier T, Inizan O, Jamilloux V, Quesneville H: PASTEC: An Automatic Transposable Element Classification Tool. PloS one 2014, 9(5):e91929.

Steinbach D, Alaux M, Amselem J, Choisne N, Durand S, Flores R, Keliet AO, Kimmel E, Lapalu N, Luyten I, Michotey C, Mohellibi N, Pommier C, Reboux S, Valdenaire D, Verdelet D and Quesneville H: GnpIS: an information system to integrate genetic and genomic data from plants and fungi. Database : the journal of biological databases and curation 2013, 2013:bat058.
External publications
Cvikova K, Cattonaro F, Alaux M, Stein N, Mayer KF, Dolezel J, Bartos J: High-throughput physical map anchoring via BAC-pool sequencing. BMC plant biology 2015, 15:99.

El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC, Jackson SA: A new approach for annotation of transposable elements using small RNA mapping. Nucleic acids research 2015.

Krajewski P, Chen D, Cwiek H, van Dijk AD, Fiorani F, Kersey P, Klukas C, Lange M, Markiewicz A, Nap JP, van Oeveren J, Pommier C, Scholz U, van Schriek M, Usadel B, Weise S.: Towards recommendations for metadata and data handling in plant phenotyping. Journal of experimental botany 2015.

Lesur I, Le Provost G, Bento P, Da Silva C, Leple JC, Murat F, Ueno S, Bartholome J, Lalanne C, Ehrenmann F et al: The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC genomics 2015, 16(1):112.

Morel G, Sterck L, Swennen D, Marcet-Houben M, Onesime D, Levasseur A, Jacques N, Mallet S, Couloux A, Labadie K et al: Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Scientific reports 2015, 5:11571.

Murat F, Zhang R, Guizard S, Gavranovic H, Flores R, Steinbach D, Quesneville H, Tannier E, Salse J: Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome biology and evolution 2015, 7(3):735-749.

Perlin MH, Amselem J, Fontanillas E, Toh SS, Chen Z, Goldberg J, Duplessis S, Henrissat B, Young S, Zeng Q et al: Sex and parasites: genomic and transcriptomic analysis of Microbotryum lychnidis-dioicae, the biotrophic and plant-castrating anther smut fungus. BMC genomics 2015, 16:461.

Plomion C, Aury JM, Amselem J, Alaeitabar T, Barbe V, Belser C, Berges H, Bodenes C, Boudet N, Boury C et al: Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Molecular ecology resources 2015.

Smedley D, Haider S, Durinck S, Pandini L, Provero P, Allen J, Arnaiz O, Awedh MH, Baldock R, Barbiera G et al: The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic acids research 2015, 43(W1):W589-598.

Willing E-M, Rawat V, Mandáková T, Maumus F, James GV, Nordström KJV, Becker C, Warthmann N, Chica C, Szarzynska B et al: Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants 2015, 1:14023.

Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sorensen I, Lichtenstein G et al: The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature genetics 2014, 46(9):1034-1038.

Daron J, Glover N, Pingault L, Theil S, Jamilloux V, Paux E, Barbe V, Mangenot S, Alberti A, Wincker P et al: Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome biology 2014, 15(12).

Foulongne-Oriol M, Lapalu N, Ferandon C, Spataro C, Ferrer N, Amselem J, Savoie JM: The first set of expressed sequence tags (EST) from the medicinal mushroom Agaricus subrufescens delivers resource for gene discovery and marker development. Applied microbiology and biotechnology 2014, 98(18):7879-7892.

Geering ADW, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA et al: Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature communications 2014, 5.

Grandaubert J, Lowe RGT, Soyer JL, Schoch CL, Van de Wouw AP, Fudal I, Robbertse B, Lapalu N, Links MG, Ollivier B et al: Transposable element-assisted evolution and adaptation to host plant within the Leptosphaeria maculans-Leptosphaeria biglobosa species complex of fungal pathogens. BMC genomics 2014, 15:891.

Grimplet J, Adam-Blondon AF, Bert PF, Bitz O, Cantu D, Davies C, Delrot S, Pezzotti M, Rombauts S, Cramer GR: The grapevine gene nomenclature system. BMC genomics 2014, 15:1077.

Maumus F, Epert A, Nogue F, Blanc G: Plant genomes enclose footprints of past infections by giant virus relatives. Nature communications 2014, 5:4268.

Mayer KFX, Rogers J, Dolezel J, Pozniak C, Eversole K, Feuillet C, Gill B, Friebe B, Lukaszewski AJ, Sourdille P et al: A chromosome-based draft sequence of the hexaploid bread wheat (Triticum aestivum) genome. Science 2014, 345(6194).

Murat F, Zhang R, Guizard S, Flores R, Armero A, Pont C, Steinbach D, Quesneville H, Cooke R, Salse J: Shared subgenome dominance following polyploidization explains grass genome evolutionary plasticity from a seven protochromosome ancestor with 16K protogenes. Genome biology and evolution 2014, 6(1):12-33.

Pauchet Y, Saski CA, Feltus FA, Luyten I, Quesneville H, Heckel DG: Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome. Insect Mol Biol 2014, 23(3):286-300.

Zytnicki M, Akhunov E, Quesneville H: Tedna: a transposable element de novo assembler. Bioinformatics 2014, 30(18):2656-2658.

Campo S, Peris-Peris C, Sire C, Moreno AB, Donaire L, Zytnicki M, Notredame C, Llave C, San Segundo B: Identification of a novel microRNA (miRNA) from rice that targets an alternatively spliced transcript of the Nramp6 (Natural resistance-associated macrophage protein 6) gene involved in pathogen resistance. The New phytologist 2013, 199(1):212-227.

Pont C, Murat F, Guizard S, Flores R, Foucrier S, Bidet Y, Quraishi UM, Alaux M, Dolezel J, Fahima T et al: Wheat syntenome unveils new evidences of contrasted evolutionary plasticity between paleo- and neoduplicated subgenomes. The Plant journal : for cell and molecular biology 2013, 76(6):1030-1044.

Read BA, Kegel J, Klute MJ, Kuo A, Lefebvre SC, Maumus F, Mayer C, Miller J, Monier A, Salamov A et al: Pan genome of the phytoplankton Emiliania underpins its global distribution. Nature 2013, 499(7457):209-213.

Slotte T, Hazzouri KM, Agren JA, Koenig D, Maumus F, Guo Y-L, Steige K, Platts AE, Escobar JS, Newman LK et al: The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nature genetics 2013, 45(7):831-835.

Toffano-Nioche C, Luo Y, Kuchly C, Wallon C, Steinbach D, Zytnicki M, Jacq A, Gautheret D: Detection of non-coding RNA in bacteria and archaea using the DETR'PROK Galaxy pipeline. Methods (San Diego, Calif ) 2013, 63(1):60-65.

Toffano-Nioche C, Ott A, Crozat E, Nguyen AN, Zytnicki M, Leclerc F, Forterre P, Bouloc P, Gautheret D: RNA at 92 °C: the non-coding transcriptome of the hyperthermophilic archaeon Pyrococcus abyssi. RNA biology 2013, 10(7):1211-1220.

Veluchamy A, Lin X, Maumus F, Rivarola M, Bhavsar J, Creasy T, O'Brien K, Sengamalay NA, Tallon LJ, Smith AD et al: Insights into the role of DNA methylation in diatoms by genome-wide profiling in Phaeodactylum tricornutum. Nature communications 2013, 4:2091

Wicker T, Oberhaensli S, Parlange F, Buchmann JP, Shatalina M, Roffler S, Ben-David R, Dolezel J, Simkova H, Schulze-Lefert P et al: The wheat powdery mildew genome shows the unique evolution of an obligate biotroph. Nature genetics 2013, 45(9):1092-1096.

Zanni V, Eymery A, Coiffet M, Zytnicki M, Luyten I, Quesneville H, Vaury C, Jensen S: Distribution, evolution, and diversity of retrotransposons at the flamenco locus reflect the regulatory properties of piRNA clusters. Proceedings of the National Academy of Sciences of the United States of America 2013, 110(49):19842-19847.

Bourras S, Meyer M, Grandaubert J, Lapalu N, Fudal I, Linglin J, Ollivier B, Blaise F, Balesdent M-H, Rouxel T: Incidence of genome structure, DNA asymmetry, and cell physiology on T-DNA integration in chromosomes of the phytopathogenic fungus Leptosphaeria maculans. G3 (Bethesda, Md ) 2012, 2(8):891-904.

Guignon V, Droc G, Alaux M, Baurens FC, Garsmeur O, Poiron C, Carver T, Rouard M, Bocs S: Chado controller: advanced annotation management with a community annotation system. Bioinformatics 2012, 28(7):1054-1056.

Leroy P, Guilhot N, Sakai H, Bernard A, Choulet F, Theil S, Reboux S, Amano N, Flutre T, Pelegrin C et al: TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes. Frontiers in plant science 2012, 3:5.

Petit E, Giraud T, de Vienne DM, Coelho MA, Aguileta G, Amselem J, Kreplak J, Poulain J, Gavory F, Wincker P et al: Linkage to the mating-type locus accross the genus Microbotryum: insights into non recombining chromosomes. Evolution 2012:no-no.

Schbath S, Martin V, Zytnicki M, Fayolle J, Loux V, Gibrat JF: Mapping reads on a genomic sequence: an algorithmic overview and a practical comparative analysis. Journal of computational biology : a journal of computational molecular cell biology 2012, 19(6):796-813.

Zambounis A, Elias M, Sterck L, Maumus F, Gachon CMM: Highly dynamic exon shuffling in candidate pathogen receptors ... what if brown algae were capable of adaptive immunity? Molecular biology and evolution 2012, 29(4):1263-1276.
Publications with the hosting laboratory
Amselem J, Lebrun MH, Quesneville H: Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC genomics 2015, 16(1):141.

Maumus F, Fiston-Lavier A, Quesneville H: Impact of transposable elements on insect genomes and biology. Current Opinion in Insect Science 2015, 7:30-36.

Maumus F, Quesneville H: Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nature communications 2014, 5:4104.

Maumus F, Quesneville H: Deep investigation of Arabidopsis thaliana junk DNA reveals a continuum between repetitive elements and genomic dark matter. PloS one 2014, 9(4):e94101.

Zytnicki M, Luo Y, Quesneville H: Efficient comparison of sets of intervals with NC-lists. Bioinformatics (Oxford, England) 2013, 29(7):933-939.

Permal E, Flutre T, Quesneville H: Roadmap for annotating transposable elements in eukaryote genomes. Methods Mol Biol 2012, 859:53-68
Development
Le SI GnpIS, ainsi que REPET et S-­Mart y ont été déposé à l'APP.
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