INRA Versailles
RD10 Route de Saint-Cyr 78000 Versailles
URGI - UR1164
Scientific leader(s)
Technical leader(s)
  • ISO 9001
  • Label IBiSA
Effective storage
358.00 To
Cluster: cores number
1 206 cores
CPU/hours a year
1 334 776 H / an
Bioinformatic tools number
Users number (last year)
Servers description

An infrastructure dedicated to bioinformatics: data storage, web site and high-throughput computing in a secure environment. They are hosted in the INRA DataCenter in Ile-de-France (Bruyère-Le-Chatel)

  • High Performance Computer (HPC)
  • High-performance NAS storage for unix , databases & cluster (200 To)
  • server dedicated to the web site
  • server dedicated to the back-ups management
  • 3 servers dedicated to virtualization (DBMS, Information System, Wevb applications)
  • 1 cloud

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:
138 180 an
Unique visits:
31 510 an
Latest update:



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:
20 498 an
Unique visits:
3 122 an
Not documented
Latest update:



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

Access conditions


Annual visits:
195 an
Unique visits:
157 an
Not documented
Latest update:

Plant data discovery portal

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:
1 491 an
Unique visits:
600 an


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:
474 an
Unique visits:
267 an


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:
1 872 an
Unique visits:
557 an



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



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)
  • NGS data analysis
  • Sequence analysis
  • Cartography
  • Evolution and phylogeny
  • Comparative genomics
Not documented
Training time:
Not documented
Upcoming session :

Manual curation of Transposable element annotation


URGI organizes a BYOD-­style (Bring Your Own Data) training course on manual curation of transposable elements reference sequences obtained with REPET pipelines.

Access conditions
Not documented

Formation professionnelle

10 trainees / year
Training time:
3 day(s) / year
Upcoming session :

Training on annotation of transposable elements


The objectives of this training are: 

  • To acquire knowledge on transposable elements
  • To achieve annotation of transposable elements in the genome using REPET pipelines
  • To be autonomous on your own data.


  • Opening presentations on transposable elements and their annotation
  • Strategies of repeat annotation
  • REPET pipelines overview and practices 
  • Post-analyze tools overview and practices


Access conditions

This training is dedicated to biologists and/or bioinformaticians (10 pers. max)

Cost : 150€

Registration and information by mail to: urgi-contact@inra.fr

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

Training to the GnpIS information system


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

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

Cluster job submission training


How to launch and manage jobs on URGI cluster

Access conditions

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

Users distribution
85 %
15 %
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

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

Adam Blondon, A.-F., Alaux, M., Durand, S., Letellier, T., Merceron, G., Mohellibi, N., Pommier, C., Steinbach, D., Alfama, F., Amselem, J., Charruaud, D., Choisne, N., Flores, R.-G., Guerche, C., Jamilloux, V., Kimmel, E., Lapalu, N., Loaec, M., Michotey, C., Quesneville, H. (2017). Mining plant genomic and genetic data using the GnpIS information system. In: Aalt D.J van Dijk, Plant genomics databases. Methods and protocols (p. 103-117). Methods in Molecular Biology, 1533. USA: Springer Science + Business Media B.V. 336 p., DOI: 10.1007/978-1-4939-6658-5_5

Dzale Yeumo, W. E., Alaux, M., Arnaud, E., Aubin, S., Baumann, U., Buche, P., Cooper, L., Ćwiek-Kupczyńska, H., Davey, R. P., Fulss, R. A., Jonquet, C., Laporte, Larmande, P., Pommier, C., Protonotarios, V., Reverte, C., Shrestha, Subirats, I., Venkatesan, A., Whan, A., Quesneville, H. (2017). Developing data interoperability using standards: a wheat community use case. F1000Research, 6, 1843. DOI: 10.12688/f1000research.12234.1

Hoede, C., Arnoux, S., Moissette, M., Chaumier, T., Inizan, O., Jamilloux, V., Quesneville, H. (2014). PASTEC: an automatic transposable element classification tool. Plos One, 9 (5), e91929. DOI: 10.1371/journal.pone.0091929

External publications

Darracq, A., Vitte, C., Nicolas, S., Duarte, J., Pichon, J.-P., Mary, T., Chevalier, C., Berard, A., Le Paslier, M.-C., Rogowsky, P., Charcosset, A., Joets, J. (2018). Sequence analysis of European maize inbred line F2 provides new insights into molecular and chromosomal characteristics of presence/absence variants. BMC Genomics, 19 (1), DOI: 10.1186/s12864-018-4490-7

Basu, S., Patil, S., Mapleson, D., Russo, MT., Vitale, L., Fevola, C., Maumus, F., Casotti, R., Mock, T., Caccamo, M., Montresor, M., Sanges, R., Ferrante, MI (2017). Finding a partner in the ocean: molecular and evolutionary bases of the response to sexual cues in a planktonic diatom. New Phytologist, 215 (1), 140-156. DOI: 10.1111/nph.14557

Mathers, T. C., Chen, Y., Kaithakottil, G., Legeai, F., Mugford, Baa-Puyoulet, P., Bretaudeau, A., Clavijo, B., Colella, S., Collin, O., Dalmay, T., Derrien, T., Feng, H., Gabaldón, T., Jordan, A., Julca, I., Kettles, G. J., Kowitwanich, K., Lavenier, Lenzi, P., Lopez-Gomollon, S., Loska, D., Mapleson, Maumus, F., Moxon, Price, D. R. G., Sugio, A., Van Munster, M., Uzest, M., Waite, Jander, G., Tagu, D., Wilson, van Oosterhout, C., Swarbreck, D., Hogenhout, S. A. (2017). Erratum to Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, 18 (63). DOI: 10.1186/s13059-017-1202-6

Schmidt, M. H.-W., Vogel, A., Denton, A. K., Istace, B., Wormit, van de Geest, H., Bolger, M. E., Alseekh, S., Maß, Pfaff, Schurr, Chetelat, R., Maumus, F., Aury, Koren, S., Fernie, A. R., Zamir, D., Bolger, A. M., Usadel, B. (2017). De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell, 29, 2336–2348. DOI: 10.1105/tpc.17.00521

Guizard, S., Piégu, B., Arensburger, P., Guillou, F., Bigot, Y. (2016). Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools. BMC Genomics, 17 (1), 1-23. DOI: 10.1186/s12864-016-3015-5

Mader, M., Le Paslier, M.-C., Bounon, R., Berard, A., Faivre-Rampant, P., Fladung, Leplé, J.-C., Kersten (2016). Whole-genome draft assembly of Populus tremula x P. alba clone INRA 717-1B4. Silvae Genetica, 65 (2), 74-79. DOI: 10.1515/sg-2016-0019

Maumus, F., Blanc, G. (2016). Study of gene trafficking between Acanthamoeba and giant viruses suggests an undiscovered family of Amoeba-infecting viruses. Genome Biology and Evolution, 8 (11), 3351-3363. DOI: 10.1093/gbe/evw260

Nicolas, S., Peros, J.-P., Lacombe, T., Launay, A., Le Paslier, M.-C., Berard, A., Mangin, B., Valiere, S., MARTINS, F., Le Cunff, L., Laucou, V., Bacilieri, R., Dereeper, A., Chatelet, P., This, D., Doligez, A. (2016). Genetic diversity, linkage disequilibrium and power of a large grapevine (Vitis vinifera L) diversity panel newly designed for association studies. BMC Plant Biology, 16 (1). DOI: 10.1186/s12870-016-0754-z

Olsen, J. L.Rouzé, P., Verhelst, B., Lin, Y.-C., Bayer, T., Collen, J., Dattolo, E., De Paoli, E., Dittami, S., Maumus, F., Michel, G., Kersting, A., Lauritano, C., Lohaus, R., Töpel, M., Tonon, T., Vanneste, K., Amirebrahimi, M., Brakel, J., Boström, C., Chovatia, M., Grimwood, J., Jenkins, J. W., Jueterbock, A., Mraz, A., Stam, W. T., Tice, H., Bornberg-Bauer, E., Green, P. J., Pearson, G. A., Procaccini, G., Duarte, C. M., Schmutz, J., Reusch, T. B. H., Van de Peer, Y. (2016). The genome of the seagrass Zostera marina reveals angiosperm adaptation to the sea. Nature, 331 (5), 1-17. DOI: 10.1038/nature16548

Tounsi, S., Ben Amar, S., Masmoudi, K., Sentenac, H., Brini, F., Véry, A.-A. (2016). Characterisation of two HKT1;4 Transporters from Triticum monococcum to elucidate the Determinants of the Wheat Salt Tolerance Nax1 QTL. Plant and Cell Physiology. DOI: 10.1093/pcp/pcw123

Blanc, G.Gallot-Lavallee, L., Maumus, F. (2015). Provirophages in the Bigelowiella genome bear testimony to past encounters with giant viruses. Proceedings of the National Academy of Sciences of the United States of America, 112 (38), E5318-E5326. DOI: 10.1073/pnas.1506469112

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).

Burstin, J., Salloignon, P., Chabert Martinello, M., Magnin Robert, J.-B., Siol, M., Jacquin, F., Chauveau, A., Pont, C., Aubert, G., Delaitre, C., Truntzer, C., Duc, G. (2015). Genetic diversity and trait genomic prediction in a pea diversity panel. BMC Genomics, 16. DOI: 10.1186/s12864-015-1266-1

El Baidouri, M., Kim, K. D., Abernathy, B., Arikit, S., Maumus, F., Panaud, O., Meyers, B. C., Jackson, S. A. (2015). A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acids Research, 43 (13). DOI: 10.1093/nar/gkv257

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.

Schumacher, J., Simon, A., Cohrs, K. C., Traeger, S., PORQUIER, A., Dalmais, B., Viaud, M., Tudzynski, B. (2015). The VELVET Complex in the Gray Mold Fungus Botrytis cinerea: Impact of BcLAE1 on Differentiation, Secondary Metabolism, and Virulence. Molecular Plant-Microbe Interactions, 28 (6), 659-674. DOI: 10.1094/mpmi-12-14-0411-r

Shamandi, N., Zytnicki, M., Charbonnel, C., Elvira-Matelot, E., Bochnakian, A., Comella, P., Mallory, A., Lepere, G., Saez-Vasquez, J., Vaucheret, H. (2015). Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses. Plos Biology, 13 (12), e1002326. DOI: 10.1371/journal.pbio.1002326

Willing, E.-M., Rawat, V., Mandáková, T., Maumus, F., James, G. V., Nordström, K. J., Becker, C., Warthmann, N., Chica, C., Szarzynska, B., Zytnicki, M., Albani, M. C., Kiefer, C., Bergonzi, S., Castaings, L., Mateos, J. L., Berns, M. C., Bujdoso, N., Piofczyk, T., de Lorenzo, L., Barrero-Sicilia, C., Mateos, I., Piednoël, M., Hagmann, J., Chen-Min-Tao, R., Iglesias-Fernández, R., Schuster, S. C., Alonso-Blanco, C., François, R., Carbonero, P., Paz-Ares, J., Davis, S. J., Pecinka, A., Quesneville, H., Colot, V., Lysak, M. A., Weigel, D., Coupland, G.Schneeberger, K. (2015). Genome expansion of Arabis alpina linked with retrotransposition and reduced symmetric DNA methylation. Nature Plants, 1 (2), 14023-14028. DOI: 10.1038/nplants.2014.23

Gastineau, R., Davidovich, N., Hansen, G., Rines, J., Wulff, A., Kaczmarska, I., Ehrman, J., Hermann, D., Maumus, F., Hardivillier, Y., Leignel, V., Jacquette, B., Meleder, V., Hallegraeff, G., Yallop, M., Perkins, R., Cadoret, J.-P., Saint-Jean, B., Carrier, G., Mouget, J.-L. (2014). Haslea ostrearia-like Diatoms: Biodiversity out of the Blue. In: Nathalie Bourgougnon, dir., Sea Plants (p. 441-465). Advances in Botanical Research, 71. GBR : Elsevier Ltd. 25DOI: 10.1016/B978-0-12-408062-1.00015-9

Geering, A. D. W., Maumus, F., Copetti, D., Choisne, N., Zwickl, D. J., Zytnicki, M., McTaggart, A. R., Scalabrin, S., Vezzulli, S., Wing, R. A., Quesneville, H., Teycheney, P.-Y. (2014). Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution. Nature Communications, 5. DOI: 10.1038/ncomms6269

Maumus, F., Epert, A., Nogué, F., Blanc, G. (2014). Plant genomes enclose footprints of past infections by giant virus relatives. Nature Communications, 5. DOI: 10.1038/ncomms5268

Lopez-Gomollon, S., Beckers, M., Rathjen, T., Moxon, S., Maumus, F., Mohorianu, I., Moulton, V., Dalmay, T., Mock, T. (2014). Global discovery and characterization of small non-coding RNAs in marine microalgae. BMC Genomics, 15. DOI: 10.1186/1471-2164-15-697

Ma, J., Stiller, J., Zhao, Q., Feng, Q., Cavanagh, C., Wang, P., Gardiner, D., Choulet, F., Feuillet, C., Zheng, Y.-L., Wei, Y., Yan, G., Han, B., Manners, J. M., Liu, C. (2014). Transcriptome and Allele Specificity Associated with a 3BL Locus for Fusarium Crown Rot Resistance in Bread Wheat. Plos One, 9 (11). DOI: 10.1371/journal.pone.0113309

Schumacher, J., Simon, A., Cohrs, K. C., Viaud, M., Tudzynski, P. (2014). The Transcription Factor BcLTF1 Regulates Virulence and Light Responses in the Necrotrophic Plant Pathogen Botrytis cinerea. Plos Genetics, 10 (1), e1004040. DOI: 10.1371/journal.pgen.1004040

Thomas, M., Pingault, L., Poulet, A., Duarte, J., Throude, M., Faure, S., Pichon, J.-P., Paux, E., Probst, A. V., Tatout, C. (2014). Evolutionary history of Methyltransferase 1 genes in hexaploid wheat. BMC Genomics, 15. DOI: 10.1186/1471-2164-15-922
Publications with the hosting laboratory

Dominguez Del Angel, V., Hjerde, E., Sterck, L., Capella-Gutierrez, S., Notredame, C., Vinnere Pettersson, O., Amselem, J., Bouri, L., Bocs, S., Klopp, C., Gibrat, J.-F., Vlasova, A., Leskosek, B. L., Soler, L., Binzer-Panchal, M., Lantz, H. (2018). Ten steps to get started in Genome Assembly and Annotation. F1000Research, 7, 19 p. DOI: 10.12688/f1000research.13598.1

Laucou V, Launay A,  Bacilieri R,  Lacombe T,  Adam-Blondon AF, Berard A,  Chauveau A, de Andres, MT,  Hausmann L, Ibanez J, Le Paslier MC,  Maghradze D, Martinez-Zapater JM, Maul E, Ponnaiah M ; Topfer R, Péros JP, Boursiquot JM (2018) Extended diversity analysis of cultivated grapevine Vitis vinifera with 10K genome-wide SNPs. PLOS ONE, 13, 2: e0192540 https://doi.org/10.1371/journal.pone.0192540

Castanera, R., Pérez, G., López-Varas, L., Amselem, J., LaButti, K., Singan, V., Lipzen, A., Haridas, S., Barry, K., Grigoriev, I. V., Pisabarro, A. G., Ramírez, L. (2017). Comparative genomics of Coniophora olivacea reveals different patterns of genome expansion in Boletales. BMC Genomics, 18 (1), 1-14. DOI: 10.1186/s12864-017-4243-z

Daccord, N., Celton, J.-M., Linsmith, G., Becker, C., Choisne, N., Schijlen, E., van de Geest, H., Bianco, L., Micheletti, D., Velasco, R., Di Pierro, E. A., Gouzy, J., Rees, D. J. G., Guérif, P., Muranty, H., Durel, C. E., Laurens, F., Lespinasse, Y., Gaillard, S., Aubourg, S., Quesneville, H., Weigel, D., van de Weg, E., Troggio, M., Bucher, E. (2017). High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, 49 (7), 1099-1108. DOI: 10.1038/ng.3886

Dallery, J.-F., Lapalu, N., Zampounis, A., Pigné, S., Luyten, I., Amselem, J., Wittenberg, A. H. J., Zhou, S., de Queiroz, M. V., Robin, G., Auger, A., Hainaut, M., Henrissat, B., Kim, K.-T., Lee, Y.-H., Lespinet, O., Schwartz, D. C., Thon, M. R., O'Connell, R. (2017). Gapless genome assembly of Colletotrichum higginsianum reveals chromosome structure and association of transposable elements with secondary metabolite gene clusters. BMC Genomics, 18. DOI: 10.1186/s12864-017-4083-x

El Baidouri, M., Murat, F., Veyssière, M., Molinier, M., Flores, R.-G., Burlot, L., Alaux, M., Quesneville, H., Pont, C., Salse, J. (2017). Reconciling the evolutionary origin of bread wheat (Triticum aestivum). New Phytologist, 213 (3), 1477-1486. DOI: 10.1111/nph.14113

Gouin, A., Bretaudeau, A. (Co-premier auteur), Nam, K. (Co-premier auteur), Gimenez, S., Aury, J.-M., Duvic, B., Hilliou, F., Durand, N., Montagné, N., Darboux, I., Kuwar, S., Chertemps, T., Siaussat, D., Bretschneider, A., Moné, Y., Ahn, S.-J., Hänniger, S., Grenet, A.-S. G., Neunemann, D., Maumus, F., Luyten, I., Labadie, K., Xu, W., Koutroumpa, F., Escoubas, J.-M., Llopis, A., Maïbèche-Coisne, M., Salasc, F., Tomar, A., Anderson, A. R., Khan, S. A., Dumas, P., Orsucci, M., Guy, J., Belser, C., Alberti, A., Noel, B., Couloux, A., Mercier, J., Nidelet, S., Dubois, E., Liu, N.-Y., Boulogne, I., Mirabeau, O., Le Goff, G., Gordon, K., Oakeshott, J., Consoli, F. L., Volkoff, A. N., Fescemyer, H. W., Marden, J. H., Luthe, D. S., Herrero, S., Heckel, D. G., Wincker, P., Kergoat, G. J., Amselem, J., Quesneville, H., Groot, A. T., Jacquin-Joly, E., Nègre, N.Lemaitre, C.Legeai, F., D'Alençon, E.Fournier, P. (2017). Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. Scientific Reports, 7, 1-12. DOI: 10.1038/s41598-017-10461-4

Jamilloux, V., Daron, J., Choulet, F., Quesneville, H. (2017). De novo annotation of transposable elements: tackling the fat genome issue. Proceedings of the IEEE, 105 (3), 474-481. DOI: 10.1109/JPROC.2016.2590833

Mock, T., Otillar, R. P., Strauss, J., McMullan, M., Paajanen, P., Schmutz, J., Salamov, A., Sanges, R., Toseland, A., Ward, B. J., Allen, A. E., Dupont, C. L., Frickenhaus, S., Maumus, F., Veluchamy, A., Wu, T., Barry, KW., Falciatore, A., Ferrante, M. I., Fortunato, A. E., Glöckner, G., Gruber, A., Hipkin, R., Janech, M. G., Kroth, P. G., Leese, F., Lindquist, E. A., Lyon, B. R., Martin, J., Mayer, C., Parker, M., Quesneville, H., Raymond, J. A., Uhlig, C., Valas, R. E., Valentin, K. U., Worden, A. Z., Armbrust, E. V., Clark, M. D., Bowler, C., Green, B. R., Moulton, V., van Oosterhout, C., Grigoriev, I. V. (2017). Evolutionary genomics of the cold-adapted diatom Fragilariopsis cylindrus. Nature, 541, 536-540. DOI: 10.1038/nature20803

Quraishi, U. M., Pont, C., Ain, Q.-u., Flores, R., Burlot, L., Alaux, M., Quesneville, H., Salse, J. (2017). Combined genomic and genetic data integration of major agronomical traits in bread wheat (Triticum aestivum L.). Frontiers in Plant Science, 8, 1-12. DOI: 10.3389/fpls.2017.01843

Zhong, Z., Marcel, T., Hartmann, F. E., Ma, X., Plissonneau, C., Zala, M., Ducasse, A., Confais, J., Compain, R., Lapalu, N., Amselem, J., McDonald, B. A., Croll, D., Palma-Guerrero, J. (2017). A small secreted protein in Zymoseptoria tritici is responsible for avirulence on wheat cultivars carrying the Stb6 resistance gene. New Phytologist, 214 (2), 619 - 631DOI: 10.1111/nph.14434

Adam-Blondon, A.-F., Alaux, M., Pommier, C., Cantu, D., Cheng, Z.-M., Cramer, G. R., Davies, C., Delrot, S., Deluc, L., di Gaspero, G., Grimplet, J., Fennell, A., Londo, J. P., Kersey, P., Mattivi, F., Naithani, S., Neveu, P., Nikolski, M., Pezzotti, M., Reisch, B. I., Topfer, R., Vivier, M., Ware, D., Quesneville, H. (2016). Towards an open grapevine information system. Horticulture Research, 3, 8 p. DOI: 10.1038/hortres.2016.56

Ćwiek-Kupczyńska, H., Altmann, T., Arend, D., Arnaud, E., Chen, D., Cornut, G., Fiorani, F., Frohmberg, W., Junker, A., Klukas, C., Lange, M., Mazurek, C., Nafissi, A., Neveu, P., van Oeveren, J., Pommier, C., Poorter, H., Rocca-Serra, P., Sansone, S.-A., Scholz, U., van Schriek, M., Seren, Ü., Usadel, B., Weise, S., Kersey, P., Krajewski, P. (2016). Measures for interoperability of phenotypic data: minimum information requirements and formatting. Plant Methods, 12, 1-18. DOI: 10.1186/s13007-016-0144-4

Elvirat-Matelot, E., Hachet, M., Shamandi, N., Comella, P., Saez-Vasquez, J., Zytnicki, M., Vaucheret, H. (2016). Arabidopsis rnase three like2 modulates the expression of protein-coding genes via 24-nucleotide small interfering rna-directed dna methylation. Plant Cell, 28 (2), 406-425. DOI: 10.1105/tpc.15.00540

Jouffroy, O., Saha, S., Mueller, L., Quesneville, H., Maumus, F. (2016). Comprehensive repeatome annotation reveals strong potential impact of repetitive elements on tomato ripening. BMC Genomics, 17 (1), 1-15. DOI: 10.1186/s12864-016-2980-z

Lesage, P., Betermier, M., Bridier-Nahmias, A., Chandler, M., Chambeyron, S., Cristofari, G., Gilbert, N., Quesneville, H., Vaury, C., Volff, J.-N. (2016). International Congress on Transposable elements (ICTE 2016) in Saint Malo: mobile elements under the sun of Brittany. Mobile DNA, 7, 1-8. DOI: 10.1186/s13100-016-0075-7

Maumus, F., Quesneville, H. (2016). Impact and insights from ancient repetitive elements in plant genomes. Current Opinion in Plant Biology, 30, 41-46. DOI: 10.1016/j.pbi.2016.01.003

Molitor, A. M., Latrasse, D., Zytnicki, M., Andrey, P., Houba Hérin, N., Hachet, M., Battail, C., Del Prete, S., Alberti, A., Quesneville, H., Gaudin, V. (2016). The Arabidopsis hnRNP-Q Protein LIF2 and the PRC1 subunit LHP1 function in concert to regulate the transcription of stress-responsive genes. Plant Cell, 28 (9). DOI: 10.1105/tpc.16.00244

Murat, F., Louis, A., Maumus, F., Armero, A., Cooke, R., Quesneville, H., Crollius, H. R., Salse, J. (2016). Understanding Brassicaceae evolution through ancestral genome reconstruction (vol 16, 262, 2015). Genome Biology, 17 (64). DOI: 10.1186/s13059-016-0887-2

Plomion, C1., Aury, J.-M1., Amselem, J. 1, Alaeitabar, T., Barbe, V., Belser, C., Berges, H., Bodenes-Brezard, C., Boudet, N., Boury, C., Canaguier, A., Couloux, A., Da Silva, C., Duplessis, S., Ehrenmann, F., Estrada-Mairey, B., Fouteau, S., Francillonne, N., Gaspin, C., Guichard, C., Klopp, C., Labadie, K., Lalanne, C., Le Clainche, I., Leplé, J.-C., Le Provost, G., Leroy, T., Lesur Kupin, I., Martin, F., Mercier, J., Michotey, C., Murat, F., Salin, F., Steinbach, D., Faivre-Rampant, P., Wincker, P., Salse, J., Quesneville, H., Kremer, A. (2016). Decoding the oak genome: public release of sequence data, assembly, annotation and publication strategies. Molecular Ecology Resources, 16 (1), 254-265. DOI: 10.1111/1755-0998.12425

Porquier, A., Morgant, G., Moraga, J., Dalmais, B., Luyten, I., Simon, A., Pradier, J.-M., Amselem, J., Gonzalez Collado, I., Viaud, M. (2016). The botrydial biosynthetic gene cluster of Botrytis cinerea displays a bipartite genomic structure and is positively regulated by the putative Zn(II)(2)Cys(6) transcription factor BcBot6. Fungal Genetics and Biology, 96 (Nov 2016), 33-46. DOI: 10.1016/j.fgb.2016.10.003

Spannagl, M. 1, Alaux, M. 1, Lange, M., Bolser, D. M., Bader, K. C., Letellier, T., Kimmel, E., Flores, R.-G., Pommier, C., Kerhornou, A., Walts, B., Nussbaumer, T., Grabmuller, C., Chen, J., Colmsee, C., Beier, S., Mascher, M., Schmutzer, T., Arend, D., Thanki, A., Ramirez-Gonzalez, R., Ayling, M., Ayling, S., Caccamo, M., Mayer, K. F. X., Scholz, U., Steinbach, D., Quesneville, H., Kersey, P. (2016). TransPLANT resources for triticeae genomic data. Plant Genome, 9 (1), 13 p. DOI: 10.3835/plantgenome2015.06.0038

Amselem, J., Lebrun, M.-H., Quesneville, H. (2015). Whole genome comparative analysis of transposable elements provides new insight into mechanisms of their inactivation in fungal genomes. BMC Genomics, 16 (1), 141. DOI: 10.1186/s12864-015-1347-1

Amselem, J., Vigouroux, M., Oberhaensli, S., Brown, J. K. M., Bindschedler, L. V., Skamnioti, P., Wicker, T., Spanu, P. D., Quesneville, H., Sacristán, S. (2015). Evolution of the EKA family of powdery mildew avirulence-effector genes from the ORF 1 of a LINE retrotransposon. BMC Genomics, 16 (1), 917. DOI: 10.1186/s12864-015-2185-x

Chiapello, H., Mallet, L., Guerin, C., Aguileta, G., Amselem, J., Kroj, T., Ortega-Abboud, E., Lebrun, M.-H., Henrissat, B., Gendrault, A., Rodolphe, F., Tharreau, D., Fournier, E. (2015). Deciphering Genome Content and Evolutionary Relationships of Isolates from the Fungus Magnaporthe oryzae Attacking Different Host Plants. Genome Biology and Evolution, 7 (10), 2896 - 2912. DOI: 10.1093/gbe/evv187

Cviková, K., Cattonaro, F., Alaux, M., Stein, N., Mayer, K. F. X., Doležel, J., Bartoš, J. (2015). High-throughput physical map anchoring via BAC-pool sequencing. BMC Plant Biology, 15. DOI: 10.1186/s12870-015-0429-1

Hoen, D. R., Hickey, G., Bourque, G., Casacuberta, J., Cordaux, R., Feschotte, C., Fiston-Lavier, A.-S., Hua-Van, A., Hubley, R., Kapusta, A., Lerat, E., Maumus, F., Pollock, D. D., Quesneville, H., Smit, A., Wheeler, T. J., Bureau, T. E., Blanchette, M. (2015). A call for benchmarking transposable element annotation methods. Mobile DNA, 6. DOI: 10.1186/s13100-015-0044-6

Krajewski, P., Chen, D., Ćwiek, H., van Dijk, A. D. J., Fiorani, F., Kersey, P., Klukas, C., Lange, M., Markiewicz, A., Nap, J. P., van Oeveren, J., Pommier, C., Scholz, U., van Schriek, M., Usadel, B., Weise, S. (2015). Towards recommendations for metadata and data handling in plant phenotyping. Journal of Experimental Botany, 66 (18), 5417-5427. DOI: 10.1093/jxb/erv271

Lesur, I., Le Provost, G., Bento, P., Da Silva, C., Leplé, J.-C., Murat, F., Saneyoshi, U., Bartholome, J., Lalanne, C., Ehrenmann, F., Noirot, C., Burban, C., Léger, V., Amselem, J., Belser, C., Quesneville, H., Stierschneider, M., Fluch, S., Feldhahn, L., Tarkka, M., Herrmann, S., Buscot, F., Klopp, C., Kremer, A., Salse, J., Aury, J.-M., Plomion, C. (2015). The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release. BMC Genomics, 16, 23 p. DOI: 10.1186/s12864-015-1331-9

Morel, G., Sterck, L., Swennen, D., Marcet-Houben, M., Onesime, D., Levasseur, A., Vignolles, N., Mallet, S., Couloux, A., Labadie, K., Amselem, J., Beckerich, J.-M., Henrissat, B., Van de Peer, Y., Wincker, P., Souciet, J.-L., Gabaldón, T., Tinsley, C., Casaregola, S. (2015). Differential gene retention as an evolutionary mechanism to generate biodiversity and adaptation in yeasts. Scientific Reports, 5. DOI: 10.1038/srep11571

Murat, F., Zhang, R., Guizard, S., Gavranovic, H., Flores, R.-G., Steinbach, D., Quesneville, H., Tannier, E., Salse, J. (2015). Karyotype and gene order evolution from reconstructed extinct ancestors highlight contrasts in genome plasticity of modern rosid crops. Genome Biology and Evolution, 7 (3), 735-749. DOI: 10.1093/gbe/evv014

Murat, F., Louis, A., Maumus, F., Armero, A., Cooke, R., Quesneville, H., Crollius, H. R., Salse, J. (2015). Understanding Brassicaceae evolution through ancestral genome reconstruction. Genome Biology, 16 (262). DOI: 10.1186/s13059-015-0814-y

Parent, J. S., Jauvion, V., Bouche, N., Beclin, C., Hachet, M., Zytnicki, M., Vaucheret, H. (2015). Post-transcriptional gene silencing triggered by sense transgenes involves uncapped antisense RNA and differs from silencing intentionally triggered by antisense transgenes. Nucleic Acids Research, 43 (17), 8464-8475. DOI: 10.1093/nar/gkv753

Smedley, D., Haider, S., Durinck, S., Pandini, L., Provero, P., Allen, J., Arnaiz, O., Awedh, M. H., Baldock, R., Barbiera, G., Bardou, P., Beck, T., Blake, A., Bonierbale, M., Brookes, A. J., Bucci, G., Buetti, I., Burge, S., Cabau, C., Carlson, J. W., Chelala, C., Chrysostomou, C., Cittaro, D., Collin, O., Cordova, R., Cutts, R. J., Dassi, E., Genova, A. D., Djari, A., Esposito, A., Estrella, H., Eyras, E., Fernandez-Banet, J., Forbes, S., Free, R. C., Fujisawa, T., Gadaleta, E., Garcia-Manteiga, J. M., Goodstein, D., Gray, K., Guerra-Assunção, J. A., Haggarty, B., Han, D.-J., Han, B. W., Harris, T., Harshbarger, J., Hastings, R. K., Hayes, R. D., Hoede, C., Hu, S., Hu, Z.-L., Hutchins, L., Kan, Z., Kawaji, H., Keliet, A., Kerhornou, A., Kim, S., Kinsella, R., Klopp, C., Kong, L., Lawson, D., Lazarevic, D., Lee, J.-H., Letellier, T., Li, C.-Y., Lio, P., Liu, C.-J., Luo, J., Maass, A., Mariette, J., Maurel, T., Merella, S., Mohamed, A. M., Moreews, F., Nabihoudine, I., Ndegwa, N., Noirot, C., Perez-Llamas, C., Primig, M., Quattrone, A., Quesneville, H., Rambaldi, D., Reecy, J., Riba, M., Rosanoff, S., Saddiq, A. A., Salas, E., Sallou, O., Shepherd, R., Simon, R., Sperling, L., Spooner, W., Staines, D. M., Steinbach, D., Stone, K., Stupka, E., Teague, J. W., Dayem Ullah, A. Z., Wang, J., Ware, D., Wong-Erasmus, M., Youens-Clark, K., Zadissa, A., Zhang, S.-J., Kasprzyk, A. (2015). The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research, 43 (W1), W589-W598. DOI: 10.1093/nar/gkv350

Bolger, A., Scossa, F., Bolger, M. E., Lanz, C., Maumus, F., Tohge, T., Quesneville, H., Alseekh, S., Sørensen, I., Lichtenstein, G., Fich, E. A., Conte, M., Keller, H., Schneeberger, K., Schwacke, R., Ofner, I., Vrebalov, J., Xu, Y., Osorio, S., Aflitos, S. A., Schijlen, E., Jimenez Gomez, J., Ryngajllo, M., Kimura, S., Kumar, R., Koenig, D., Headland, L. R., Maloof, J. N., Sinha, N., van Ham, R. C. H. J., Lankhorst, R. K., Mao, L., Vogel, A., Arsova, B., Panstruga, R., Fei, Z., Rose, J. K. C., Zamir, D., Carrari, F., Giovannoni, J. J., Weigel, D., Usadel, B., Fernie, A. R. (2014). The genome of the stress-tolerant wild tomato species Solanum pennellii. Nature Genetics, 46 (9), 1034-1038. DOI: 10.1038/ng.3046

Choulet, F., Alberti, A., Theil, S., Glover, N. M., Barbe, V., Daron, J., Pingault, L., Sourdille, P., Couloux, A., Paux, E., Leroy, P., Mangenot, S., Guilhot, N., Le Gouis, J., Balfourier, F., Alaux, M., Jamilloux, V., Julie, P., Durand, C., Bellec, A., Gaspin, C., Šafář, J., Doležel, J., Rogers, J., Vandepoele, K., Aury, J.-M., Mayer, K., Berges, H., Quesneville, H., Wincker, P., Feuillet, C. (2014). Structural and Functional Partitioning of Bread Wheat Chromosome 3B. Science, 345 (6194), online. DOI: 10.1126/science.1249721

Daron, J., Glover, N., Pingault, L., Theil, S., Jamilloux, V., Paux, E., Barbe, V., Mangenot, S., Alberti, A., Wincker, P., Quesneville, H., Feuillet, C., Choulet, F. (2014). Organization and evolution of transposable elements along the bread wheat chromosome 3B. Genome Biology, 15 (12), 1-15. DOI: 10.1186/s13059-014-0546-4

Denoeud, F., Carretero-Paulet, L., Dereeper, A., Droc, G., Guyot, R., Pietrella, M., Zheng, C., Alberti, A., Anthony, F., Aprea, G., Aury, J.-M., Bento, P., Bernard, M., Bocs, S., Campa, C., Cenci, A., Combes, M.-C., Crouzillat, D., Da Silva, C., Daddiego, L., De Bellis, F., Dussert, S., Garsmeur, O., Gayraud, T., Guignon, V., Jahn, K., Jamilloux, V., Joët, T., Labadie, K., Lan, T., Leclercq, J., Lepelley, M., Leroy, T., Li, L.-T., Librado, P., Lopez, L., Muñoz, A., Noel, B., Pallavicini, A., Perrotta, G., Poncet, V., Pot, D., Priyono, Rigoreau, M., Rouard, M., Rozas, J., Tranchant-Dubreuil, C., VanBuren, R., Zhang, Q., Andrade, A. C., Argout, X., Bertrand, B., de Kochko, A., Graziosi, G., Henry, R. J., Jayarama, Ming, R., Nagai, C., Rounsley, S., Sankoff, D., Giuliano, G., Albert, V. A., Wincker, P., Lashermes, P. (2014). The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science, 345 (6201), 1181-1184. DOI: 10.1126/science.1255274

Foulongne Oriol, M., Lapalu, N., Férandon, C., Spataro, C., Ferrer, N., Amselem, J., Savoie, J.-M. (2014). 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, 98 (18), 7879-92. DOI: 10.1007/s00253-014-5844-y

Grimplet, J., Adam-Blondon, A.-F., Bert, P.-F., Bitz, O., Cantu, D., Davies, C., Delrot, S., Pezzotti, M., Rombauts, S., Cramer, G. R. (2014). The grapevine gene nomenclature system. BMC Genomics, 15 (1077). DOI: 10.1186/1471-2164-15-1077

Hoede, C., Arnoux, S., Moissette, M., Chaumier, T., Inizan, O., Jamilloux, V., Quesneville, H. (2014). PASTEC: an automatic transposable element classification tool. Plos One, 9 (5), e91929. DOI: 10.1371/journal.pone.0091929

Maumus, F., Quesneville, H. (2014). Ancestral repeats have shaped epigenome and genome composition for millions of years in Arabidopsis thaliana. Nature Communications, 5, 9 p. DOI: 10.1038/ncomms5104

Maumus, F., Quesneville, H. (2014). Deep Investigation of Arabidopsis thaliana Junk DNA Reveals a Continuum between Repetitive Elements and Genomic Dark Matter. Plos One, 9 (4). DOI: 10.1371/journal.pone.0094101

Pauchet, Y., Saski, C. A., Feltus, F. A., Luyten, I., Quesneville, H., Heckel, D. G. (2014). Studying the organization of genes encoding plant cell wall degrading enzymes in Chrysomela tremula provides insights into a leaf beetle genome. Insect Molecular Biology, 23 (3), 286-300. DOI: 10.1111/imb.12081

Zytnicki, M., Akhunov, E., Quesneville, H. (2014). Tedna: a transposable element de novo assembler. Bioinformatics, (on-line), 1-3. DOI: 10.1093/bioinformatics/btu365

Le SI GnpIS, ainsi que REPET et S-­Mart y ont été déposé à l'APP.