
Hadi Quesneville
Présentation
Thèse en génétique des populations et bioinformatique. Post-doc en génétique épidémiologique. Travail dans le domaine de la génomique depuis plus de 20 ans, développant des méthodes et des outils informatiques pour annoter et explorer les génomes à travers l’intégration et l’analyse des données “omics”.
Développe des e-infrastructures faisant évoluer leur organisation pour suivre les évolutions scientifiques et technologiques de la biologie. Initiateur et ancien pilote de la WheatIS, un système d’information pour la génétique et la génomique du blé, construit sous l’égide de la wheat initiative, une initiative internationale pour coodonner la recherche sur le blé, et ancien coordinateur d’un nœud plante de l’Institut Français de Bioinformatique, nœud français de l’infrastructure bioinformatique européenne Elixir.
Aujourd'hui, chargé de mission auprès de la Direction Générale Déléguée à la Science et l’Innovation d’INRAE pour la gouvernance des données, des algorithmes, des codes et de l'IA en tant qu’Administrateur des données scientifique d’INRAE (Chief Data Officer). Directeur adjoint en charge du numérique scientifique à la direction pour la science ouverte.
Compétences
Publications
Publications
The Brachypodium distachyon Pangenome Highlights Transposable Element Dynamics in the SpeciesInternational Plant & Animal Genome (PAG 32), Jan 2025, San Diego (California), United States
Communication dans un congrès
hal-04947937
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Evolutionary Dynamics of Transposable Elements in Brachypodium distachyon Based on a Pangenomic ApproachInternational Plant & Animal Genome (PAG 31), Jan 2024, San Diego, United States
Communication dans un congrès
hal-04419364
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The Brachypodium distachyon pangenome highlights Transposable Element dynamics in the speciesJournées "BioinfOmics" sur la pangénomique, BioinfOmics, Dec 2024, Toulouse, France
Communication dans un congrès
hal-04944985
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A Benchmark for Transposable Element annotation toolsTEhub Workshop / International Congress on Transposable Elements, Apr 2024, Saint-Malo, France
Communication dans un congrès
hal-04733449
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Characterization of Transposable Elements in PangenomesJournées du PEPI IBIS 2023, PEPI Ingénierie Bio Informatique et Statistique pour les données haut-débit (IBIS), Sep 2023, Paris, France
Communication dans un congrès
hal-04283863
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Characterization of Transposable Elements in Pangenomes24th National Congress on Transposable Elements 2023 (CNET 2023), French research community working on transposable elements (CNET), Jul 2023, Perpignan, France
Communication dans un congrès
hal-04158362
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How to use REPET for de novo TE annotation11th RepeatExplorer Workshop on the Application of Next Generation Sequencing to Repetitive DNA Analysis, Laboratory of Molecular Cytogenetics of the Biology Centre CAS, May 2023, České Budějovice, Czech Republic
Communication dans un congrès
hal-04117937
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REPET novelties : a versatile and modular packageCNET 2023 : 24th National Congress on Transposable Elements 2023, French research community working on transposable elements (CNET), Jul 2023, Perpignan, France
Communication dans un congrès
hal-04156193
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REPET evolutions: faster and easier23rd National Congress on Transposable Elements (CNET 2022), French research community working on transposable elements (CNET), Jul 2022, Gif-Sur-Yvette, France
Communication dans un congrès
hal-03815061
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Characterization of Transposable Elements in PangenomesGDR CNRS 3546 Mobil-ET Annual Meeting, Mobil-ET GDR CNRS 3546, Dec 2022, Paris, France
Communication dans un congrès
hal-03890780
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Characterization of Transposable Elements in Pangenomes23rd National Congress on Transposable Elements (CNET 2022), French research community working on transposable elements (CNET), Jul 2022, Gif-Sur-Yvette, France
Communication dans un congrès
hal-03819044
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Transposable elements, from their annotation to their integration into knowledge graphsJournée thématique - Annotation, Intelligence Artificielle et Text-mining, PEPI IBIS, Nov 2022, Jouy-en-Josas, France
Communication dans un congrès
hal-03876510
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Principles of data governance for research organizations -INRAE's approachData for policy 2020, Sep 2020, Virtuel, France. ⟨10.5281/zenodo.3964002⟩
Communication dans un congrès
hal-02955903
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Traces of past transposable element presence in <em>Brassicaceae</em> genome dark matterMobile DNA - FASEB Scientific Research Conference, Jun 2019, Palm Spring, United States
Communication dans un congrès
hal-02738388
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Traces of past transposable element presence in <em>Brassicaceae</em> genome dark matterCongrès National des Éléments Transposables (CNET 2019), Jul 2019, Lyon, France
Communication dans un congrès
hal-02734400
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Developing infrastructures for FAIR data in plant biologyGatersleben Research Conference - Applied Bioinformatics for crops (GRC2019), IPK, Mar 2019, Gatersleben, Germany
Communication dans un congrès
hal-03316569
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Traces of past transposable element presence in <em>Brassicaceae</em> genome dark matterALPHY 2019: Bioinformatics and Evolutionary Genomics, Feb 2019, Paris, France
Communication dans un congrès
hal-02734925
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URGI PlatformJournées PEPI IBIS, Jun 2019, Paris, France
Communication dans un congrès
hal-02734116
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The IWGSC Data repository and wheat data resources hosted at URGI: Overview and perspectivesPAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.32 slides
Communication dans un congrès
hal-02788401
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Gestion des données de séquençage (GnpIS)Colloque FRB: Séminaire de restitution de l’étude sur l’utilisation des données de séquençage de ressources génétiques pour l’agriculture et l’alimentation., Oct 2018, Paris, France
Communication dans un congrès
hal-02786496
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Apprendre à lire aux ordinateurs pour améliorer le bléJNSO - Journées Nationales de la Science Ouverte, Dec 2018, Paris, France
Communication dans un congrès
hal-02734405
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An integrated information system dedicated to oak genomics and geneticsPAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.27 slides
Communication dans un congrès
hal-01839185
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An E-infrastructure model for the plant research communitiesPAG XXVI Plant and Animal Genome Conference, Jan 2018, San Diego, United States
Communication dans un congrès
hal-02734402
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Developing grapevine FAIR DataPAG Conference 2018, Jan 2018, San Diego, United States
Communication dans un congrès
hal-02738117
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Improving the « FAIRness » of Inra’s data for plant biology and breedingPAG XXVI - Plant and Animal Genome Conference, Jan 2018, San Diego, United States. pp.14 slides
Communication dans un congrès
hal-02790227
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BreedWheat GWAS data in GnpIS information systemEucarpia Cereal Section - Breeding cereals for sustainable agriculture, Mar 2018, Clermont-Ferrand, France
Communication dans un congrès
hal-02340450
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De novo annotation of transposable elements: tackling the fat genome issuePAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Communication dans un congrès
hal-02734406
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De novo annotation of transposable elements: tackling the fat genome issuePAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Communication dans un congrès
hal-02785776
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WheatIS: a genetics and genomics nformation system for the wheat research communityRDA: Interest Group Agriculture Data, Apr 2017, Barcelone, Spain
Communication dans un congrès
hal-02734123
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Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRA4. International Symposium on Genomics of Plant Genetic Resources, Sep 2017, Giessen, Germany. pp.17 slides
Communication dans un congrès
hal-02791168
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« Big data » & pédictions dans les génomesTable ronde « Big data » IHEST, May 2017, Paris, France
Communication dans un congrès
hal-02786759
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Plant Cyber-infrastructures: wheatIS & French elixir nodeBIOTALENT, May 2017, Poznan, Poland
Communication dans un congrès
hal-02786556
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WheatIS: a genetics and genomics information system for the wheat research communityBioinformatics to advance wheat breeding, Nov 2017, Bologne, Italy
Communication dans un congrès
hal-02786318
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Transposable element annotation in complexe genomes.BiLille: Journée annotation des génomes, Mar 2017, Lille, France
Communication dans un congrès
hal-02785819
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WheatIS: a genetics and genomics information system for the wheat research communityPAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Communication dans un congrès
hal-02734407
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The IWGSC Reference genome browser, data mining and beyondPAG XXV - Plant and Animal Genome Conference, Jan 2017, San Diego, United States
Communication dans un congrès
hal-02788141
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IWGSC Sequence Repository: Moving towards tools to facilitate data integration for the reference sequence of wheatPAG XXIV - Plant and Animal Genome Conference, Jan 2016, San Diego, United States
Communication dans un congrès
hal-01266518
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Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomicsIUFRO Genomics and Forest Tree Genetics, May 2016, Arcachon, France
Communication dans un congrès
hal-02740283
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Contribution to a European roadmap for data standardisation in Plant Science at URGI-INRAPlant Biology Europe EPSO / FESBP 2016 Congress, Jun 2016, Prague, Czech Republic
Communication dans un congrès
hal-02794139
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Exposing French agronomic resources as Linked Open DataIN-OLIVE, Jun 2016, Montpellier, France
Communication dans un congrès
hal-01411759
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Oak genome sequencing and evolutionGenomics and Forest Tree Genetics Conference, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Communication dans un congrès
hal-02741698
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Sequencing and Analysis of Wheat Chromosome 1BPlant and Animal Genome XXIV Conference; IWGSC Standards and Protocoles Workshop, Jan 2016, San Diego, CA, United States
Communication dans un congrès
hal-02306172
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Annotation of the oak genome sequence and associated bioinformatic resourcesIUFRO Genomics and Forest Tree Genetics, Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., May 2016, Arcachon, France. 134 p
Communication dans un congrès
hal-02741128
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Developing methods and tools to annotate and explore genomes through "omics" data analysis and integrationVIB Meetings, Flanders Institute for Biotechnology (VIB). BEL., Jun 2015, Gand, Belgium
Communication dans un congrès
hal-02799228
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Towards efficient data integration and knowledge management in the Agronomic domainAPIA: Applications Pratiques de l'Intelligence Artificielle, Institut National de Recherche en Informatique et en Automatique (INRIA). FRA., Jul 2015, Rennes, France. pp.117-124
Communication dans un congrès
hal-01176903
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Exposing French agronomic resources as Linked Open DataSWAT4LS: Semantic Web Applications and Tools for Life Sciences, Dec 2015, Cambridge, United Kingdom
Communication dans un congrès
lirmm-01274884
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Evolution and impact of transposable elements in <em>Brassicaceae species</em>Plant Genome Evolution 2015, Elsevier. USA., Sep 2015, Amsterdam, Netherlands
Communication dans un congrès
hal-02739778
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De novo annotation with REPET and P-clouds : beyond default parametersAnalysis and Annotation of DNA Repeats and Dark Matter in Eukaryotic Genomes - Studium conferences, Université François Rabelais (Tours). FRA., Jul 2015, Tours, France
Communication dans un congrès
hal-02801139
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Phenotypic Data Exchange and Processing Using ISA-Tab Standard: transPLANT Project Use Case with GnpIS.Ephesis and Bii23. Plant and Animal Genome (PAG), Jan 2015, San Diego, United States
Communication dans un congrès
hal-02739236
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Grape@GnpIS: Overview of the GnpIS grape genomics and genetics integrative resource23. Plant and Animal Genome (PAG XXIII), Jan 2015, San Diego, Californie, United States. pp.24 slides
Communication dans un congrès
hal-02741780
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IWGSC sequence repository : how to facilitate pseudomolecule assembly?PAG XXIII - Plant and Animal Genome Conference, Jan 2015, San Diego, United States
Communication dans un congrès
hal-02741662
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Assembling a pseudomolecule for a wheat chromosome: the 3B experience22. Conference on Plant and Animal Genome, Jan 2014, San Diego, Californie, United States
Communication dans un congrès
hal-02743902
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URGI plant and fungi platform: distributed resources through GMOD toolsPlant and Animal Genome conference XXII, GMOD session, Jan 2014, San Diego (CA), United States
Communication dans un congrès
hal-02796293
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IWGSC Sequence repository at URGI: New features and blast toolPAG XXII - Plant and Animal Genome, Jan 2014, San Diego, United States
Communication dans un congrès
hal-02801480
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Plant biology open data interoperability in the big data eraPlant Biology Europe EPSO/FEPBS 2014, Jun 2014, Dublin, Germany
Communication dans un congrès
hal-02801067
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IWGSC Sequence repository : new data and browsers12. IWGS (International Wheat Genetics Symposium), Kyoto University [Kyoto] (KU). JPN., Sep 2013, Yokohama, Japan
Communication dans un congrès
hal-02806070
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Sequencing and Assembling a Reference Sequence of the 1 Gb Wheat Chromosome 3BIWGSC Wheat Genome Sequencing Strategy and Funding Workshop, International Wheat Genome Sequencing Consortium (IWGSC). USA., Apr 2013, Evry, France
Communication dans un congrès
hal-02747374
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IWGSC Sequence repository : Blast your favorite gene against the wheat survey sequencePAG XXI - Plant and Animal Genome, Jan 2013, San Diego, United States
Communication dans un congrès
hal-02804578
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A generic tool for managing and exploiting genetic association studies results using high throughput genotyping and phenotypingPlant Genomics Seminar 2012, Apr 2012, Pont-Royal en Provence, France
Communication dans un congrès
hal-01268379
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Analyse bioinformatique des données de métagénomique fongique9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.23-23
Communication dans un congrès
hal-00999906
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A strategy to assemble a reference sequence of the 1 Gb wheat chromosome 3BTGAC/ESF-LESC workshop, Strategies for de novo assemblies of complex crop genomes, Genome Analysis Centre (TGAC). Norwich, GBR., Oct 2012, Norwich, United Kingdom
Communication dans un congrès
hal-02809032
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Towards a reference sequence of the 1 Gb wheat chromosome 3B16. Annual Advances in Genome Biology and Technology (AGBT), Feb 2012, Marco Island, Floride, United States
Communication dans un congrès
hal-02807639
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Fungal species resources: an integrated system for structural and functional genome annotation9. Rencontres de Phytopathologie-Mycologie de la Société Française de Phytopathologie (SFP), Jan 2012, Aussois, France. pp.81-81
Communication dans un congrès
hal-00999954
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Development of genomic resources to study the structure, function and evolution of the oak genomeIUFRO working group "Genetics of Quercus and Nothofagus", Institut National de Recherche Agronomique (INRA). UMR Biodiversité, Gènes et Communautés (1202)., Oct 2012, Bordeaux, France. 1 p
Communication dans un congrès
hal-01019850
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Fungal genome analysis of transposable elements: genomes dynamics vs Repeat-Induced Point mutation (RIP)17. Congrès National sur les Eléments Transposables, Jul 2011, Lyon, France. pp.35
Communication dans un congrès
hal-01019794
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Fungal genome analysis of transposable elements: expansion vs RIP silencingPlant and Animal Genome: 19. Conference, Jan 2011, San Diego, United States. n.p
Communication dans un congrès
hal-00956370
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Botrytis/Sclerotinia resources: an integrated system for structural and functional genome annotationBSPGW 2011 : Botrytis/Sclerotinia Post-Genome Workshop, Sep 2011, Lyon, France. pp.71
Communication dans un congrès
hal-00999928
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URGI genome annotation system:an integrated system for structural and functional genome annotation12. Edition du colloque JOBIM : Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2 p
Communication dans un congrès
hal-01019754
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Report on sequencing the wheat chromosome 3B19. Plant and Animal Genome Conference, Jan 2011, San Diego, Californie, United States. 1 p
Communication dans un congrès
hal-02808854
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Sequencing and Analyses of the Hexaploid Wheat Chromosome 3B19. Conference on Plant and Animal Genome, Jan 2011, San Diego, CA, United States
Communication dans un congrès
hal-02747876
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Nature, nurture and the structure of macroalgal genomes5. European Phycological Congress, Sep 2011, Rhodes, Greece
Communication dans un congrès
hal-02749757
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Comparative genomics of Botrytis cinerea and related Ascomycota species8. Rencontres de Phytopathologie - Mycologie de la Société Française de Phytopathologie (SFP), Jan 2010, Aussois, France
Communication dans un congrès
hal-02751266
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Sequencing and analyses of the hexaploid wheat chromosome 3B10. conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom
Communication dans un congrès
hal-02753841
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Development of resources for comparative physical mapping between Muscadinia rotundifolia and Vitis vinifera6. International Workshop of Grapevine Downy and Powdery Mildew. GDPM 2010, Jul 2010, BORDEAUX, France
Communication dans un congrès
hal-02754937
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GnpAnnot community annotation system: features, qualifiers, values3. International Biocuration Conference, Apr 2009, Berlin, Germany
Communication dans un congrès
hal-02758372
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Lepido-DB, a new bioinformatic resource for the annotation and cross-comparisons of lepidopteran genomes.The Eighth International Workshop on MOLECULAR BIOLOGY AND GENETICS OF THE LEPIDOPTERA, Aug 2009, Kolimpari, Greece
Communication dans un congrès
inria-00435820
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RepetDB: A TE databaseInternational congress on transposable elements ICTE, Apr 2024, Saint Malo, France
Poster de conférence
hal-04570060
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panREPET: A Pipeline to characterize Transposable Elements in Pangenomes on de novo assembled genomesInternational Plant & Animal Genome (PAG 31), Jan 2024, San Diego (CA), United States
Poster de conférence
hal-04516410
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New REPET improvements: REPET V4.0, making life easierInternational Congress on Transposable Elements, Apr 2024, Saint-malo, France.
Poster de conférence
hal-05009167
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REPET evolutions: faster and easierAnnual Meeting of the Society for Molecular Biology and Evolution (SMBE), Jul 2023, Ferrara, Italy.
Poster de conférence
hal-04169996
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Characterization of Transposable Elements in PangenomesJOBIM 2023, Jun 2023, Tours, France
Poster de conférence
hal-04158902
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Characterization of Transposable Elements in PangenomesSMBE23, Jul 2023, Ferrara, Italy
Poster de conférence
hal-04516434
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REPET evolutions: faster and easier6th Uppsala Transposon Symposium, Oct 2022, Uppsala, Sweden.
Poster de conférence
hal-03838081
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REPET evolutions: faster and easierJobim 2022, Jul 2022, Rennes, France.
Poster de conférence
hal-03819511
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TE Hub: a community-oriented space for sharing and connecting tools, data, resources, and methods for transposable element annotationThe Mobile DNA Conference: Evolution, Diversity, and Impact, Jun 2021, Virtuel, France. 2021
Poster de conférence
hal-03357402
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Findable, Accessible, Interoperable and Reusable data linked to genetic resources for plant biology and breeding at INRACrop diversification in a changing world : Mobilizing the green gold of plant genetic resources, May 2017, Montpellier, France. , 2017, EUCARPIA Genetic Resources 2017
Poster de conférence
hal-01606277
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The complete apple genome : Evolutionary events revealed.XXV Plant and Animal Genome Conference., Jan 2017, San Diego, United States. 2017
Poster de conférence
hal-03106053
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The complete apple genomeJournées Ouvertes Biologie Informatique et Mathématiques (JOBIM’2016)., Jun 2016, Lyon, France. 2016
Poster de conférence
hal-03106007
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BreedWheat genotyping and phenotyping data in GnpIS information systemJOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. 2015
Poster de conférence
hal-02801654
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Forest tree GnpIS: an information system dedicated to forest tree genetics, genomics and phenomics35. New Phytologist Symposium, Jun 2015, Boston, United States. 2015
Poster de conférence
hal-02795537
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Data integration in the agronomic domain : national and international data discovery systemJOBIM: Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-Ferrand, France. , Post-105 (#59), 2015
Poster de conférence
lirmm-01274725
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A computational architecture designed for genome annotation: oak genome sequencing project as a use caseJOBIM 2015 - Journées Ouvertes Biologie Informatique Mathématiques, Jul 2015, Clermont-ferrand, France. 2015
Poster de conférence
hal-01246649
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Benchmarks for transcript assembly and differential gene expression (new isoforms) analysis in the context of transposable elementsAssemblée Générale France Génomique 2015, Nov 2015, Paris, France. 2015
Poster de conférence
hal-01243323
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Nucleotide variation at the Vitis chloroplast genome based on high-throughput sequencing and SNP genotyping11. International Conference on Grapevine Breeding and Genetics, Jul 2014, Beijing, China. 2014
Poster de conférence
hal-02796195
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Whole genome comparative analysis of transposable elements provide new insights on silencing mechanisms in fungal genomesMobile Genetic Elements & Genome Evolution symposium, Mar 2014, Santa Fe New mexico, United States. , 2014
Poster de conférence
hal-02797247
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The GrapeReSeq 18k Vitis genotyping chipIX International Symposium on Grapevine Physiology&Biotechnology, Apr 2013, La Serena, Chile. 2013
Poster de conférence
hal-02811055
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Wheat Crop Ontology: A Species Specific Trait Ontology. Use Case: The URGI Information SystemPlant and Animal Genome, Jan 2013, San Diego, United States. 2013
Poster de conférence
hal-02810186
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Analysis of fungal communities associated with grapevine wood diseases, based on fungal ITS pyrosequencing.27th Fungal Genetics Conference - Asilomar Conference Grounds,, Mar 2013, Asilomar, United States. 2013
Poster de conférence
hal-01190538
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GnpSeq NGS: a new tool to manage NGS data in URGI's information system (GnpIS)JOBIM 2012 : Journées Ouvertes en Biologie, Informatique et Mathématiques, 2012, 2012
Poster de conférence
hal-02807359
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Use cases and improvements of REPET package : pipeline and tools to identify and annotate TEs in genomic sequences17. Congrès National des Elements Transposables, Jul 2011, Lyon, France. 2011
Poster de conférence
hal-01190364
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Mining plant genomic and genetic data using the GnpIS information systemAalt D.J van Dijk. Plant Genomics Databases. Methods and Protocols, 1533, Springer, 2017, Methods in Molecular Biology, 978-1-4939-6658-5. ⟨10.1007/978-1-4939-6658-5_5⟩
Chapitre d'ouvrage
hal-03206731
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Roadmap for annotating transposable elements in eukaryote genomesMobile Genetic Elements, 859 (2 ed.), Springer Science + Business Media LLC, 308 p., 2012, Methods in molecular biology (Clifton, N.J.), 978-1-61779-602-9. ⟨10.1007/978-1-61779-603-6_3⟩
Chapitre d'ouvrage
hal-00956367
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Transposable element annotation in completely sequenced eukaryote genomesPlant Transposable Elements, 24, Springer-Verlag, 330 p., 2012, Topics in Current Genetics, 978-3-642-31841-2. ⟨10.1007/978-3-642-31842-9_2⟩
Chapitre d'ouvrage
hal-00956368
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Recommandations pour l'usage des IA génératives comme assistant personnel au sein d'INRAE2024, 7 p. ⟨10.17180/ztym-j930⟩
Autre publication scientifique
hal-04692524
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Recommandations sur les usages du webscraping au sein d'INRAE2024, 19 p. ⟨10.17180/vka1-ng75⟩
Autre publication scientifique
hal-04803028
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Toward a critical assessment of virus detection in plants2021, pp.100007. ⟨10.24072/pci.genomics.100007⟩
Autre publication scientifique
hal-03189070
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Traces of transposable elements in genome dark matter co-opted by flowering gene regulation networks2020
Pré-publication, Document de travail
hal-02956027
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Towards the construction of an integrated Wheat Information System[0] Wheat Initiative - International Research Initiative for Wheat Improvement. 2012, 12 p
Rapport
(rapport d’expertise collective)
hal-01601834
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Eléments transposables et génomes eucaryotesBio-Informatique, Biologie Systémique [q-bio.QM]. université Pierre et Marie Curie, 2004
HDR
tel-02962775
v1
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REPET v3.02019
Logiciel
hal-02790461
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REPET2010
Logiciel
hal-02820937
v1
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