Fabrice Legeai
- Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)
Présentation
Research Engineer and Project Manager in bioinformatics Research interests :
❖ Genomics of insect crop pests and their interactions with plants
❖ Integration of omics data with Semantic Web technologies Tools:
❖ Askomics: Integration and data extraction with Semantic Web tools
❖ AskoR: R library for RNA-Seq data analysis
❖ MTG-Link: Gap-filling with linked-reads data
❖ LRez: library for manipulation of linked-reads data
❖ Leviathan: Identification of structural variants with linked-reads data
❖ MinYS: reconstruction of symbiont genomes
❖ FEELnc: Prediction of long non-coding RNAs
Domaines de recherche
Compétences
Publications
Publications
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Modular composition of SPARQL queries for focusing on what to look for rather than how to get itSWAT4HCLS 2026 - Semantic Web Applications and Tools for Healthcare and Life Sciences, Mar 2026, Amsteram, Netherlands |
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Enhanced Genome Assemblies of French-Bred Dactylis glomerata and Medicago sativa: Achieving High-Quality Tetraploid GenomesFCAG 2025 - 36th Meeting of the EUCARPIA Fodder Crops and Amenity Grasses Section, Aberystwyth University, Sep 2025, Aberystwyth, United Kingdom. pp.1-2 |
Search for key regulators of endogenous viruses replication in ichneumonid wasps through differential gene expression analysis8. International Entomophagous Insects Conference (IEIC), Jul 2025, Tours, France |
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SVJedi-Tag : a novel method for genotyping large inversions with linked-read dataJOBIM 2025 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.1-9 |
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Understanding the limits of pangenome graphs for the analysis of large inversions in a complex of butterfly species2024 - International Environmental and Agronomical Genomics symposium, Feb 2024, Toulouse, France. pp.1-1 |
Multiple expansion and contraction events in two major chemosensory gene families in aphidsCongrès de la Société Européenne de Biologie Evolutive, Aug 2022, Prague, Czech Republic |
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Intégration de données de phénotypiques, environnementales et de biodiversité à l'aide des technologies du Web SémantiqueSYSINFO-INRAe 2022 - Journées INRAE systèmes d'information pour les données agro-environnementales, Nov 2022, Clermont-Ferrand, France |
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MTG-Link: filling gaps in draft genome assemblies with linked read dataJOBIM 2021 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. pp.1-8 |
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AskoR, A R Package for Easy RNASeq Data AnalysisIECE 2021 - 1st International Electronic Conference on Entomology, Jul 2021, Virtual, France. pp.1-8, ⟨10.3390/IECE-10646⟩ |
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LEVIATHAN: efficient discovery of large structural variants by leveraging long-range information from Linked-Reads dataJOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. pp.1-8 |
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Reference-guided genome assembly in metagenomic samplesJOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1-8 |
Co-evolution of chloroplast and nuclear genomes in flowering plants and impact of allopolyploidy on fine tune cytonuclear interactions.International Conference on Polyploidy, Jun 2019, Ghent, Belgium |
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The virus particles of Bathyplectes spp., parasitoids of the alfalfa weevil, are related to ichnoviruses6. International Entomophagous Insects Conference, Sep 2019, Perugia, Italy |
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Cytonuclear interactions remain stable during allopolyploid evolution despite repeated wholegenome duplications21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint Malo, France |
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AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resourcesJOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1 |
Structural and functional evolutionary dynamics of duplicated genes and genomes in nascent and natural B. napus21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2019, Saint-Malo, France |
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Plant resistance and architecture for protection of pulses against pathogensTransversal Symposium GIS BV, Investment for the future, Projects in plant Biology, Oct 2019, Paris, France |
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Key Note speaker Plant resistance and architecture for protection of pulses against biotic stresses9. International Conference on Legume Genetics and Genomics (ICLGG 2019), Let's harness the potential of legumes, May 2019, Dijon, France |
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Identification of differentially expressed long non-coding RNAs (lncRNAs) in response to viral infection in S. frugiperda hemocytes10. International Workshop on Molecular Biology and Genetics of the Lepidoptera, Aug 2018, Kolympari, Greece |
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Influence of nitrogen constraint on quantitative resistance to clubroot in Brassica napus21st Crucifer Genetics Conference - Brassica - Wokshop Clubroot, 2018, Saint-Malo, France |
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How a polyploid becomes a new species: example from the Brassica model.International Conference on Environmental and Agronomical Genomics, 2018, Paris, France |
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From diploids to a huge diversity ready-to-use for oilseed rape breeding.21st Crucifer Genetics Conference on Brassica - Brassica 2018, Jul 2018, Saint-Malo, France |
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Quantitative resistance to clubroot and interactions with abiotic stressesIOBC-WPRS WG 'Pesticides and Beneficial Organisms', 2018, Zagreb, Croatia. pp.25-26 |
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Influence of nitrogen constraint on quantitative resistance to clubroot in Brassica napusInternational Clubroot Workshop, 2018, Edmonton, Canada |
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Cytonuclear interactions overcome inter-genomic conflict resulting from interspecific hybridization and genome doublingSecond Joint Congress on Evolutionary Biology, Aug 2018, Montpellier, France |
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Integrative genomics and gene networks for studying phenotypic plasticity in the pea aphid10th Arthropod Genomics Symposium, Jun 2017, Notre Dame, United States |
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AskOmics, a web tool to integrate and query biological data using semantic web technologiesJOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1 |
Integration of Linked Data into Galaxy using AskomicsGalaxy Community Conference, Jun 2017, Montpellier, France |
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Spodoptera genomes in the BIPAA information systemInternational Conference on Management of Destructive Agricultural Pests Spodoptera (Noctuidae), Nov 2017, Chongqing, China |
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Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approachesInternational Conference on Holobionts, Apr 2017, Paris, France |
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Recurrent domestication of viral genomes leads to different virulence strategies in ichneumonid waspsRéunion du réseau ADALEP, 2016, Paris, France |
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BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interactionXXVth International Congress of Entomology 2016, Sep 2016, Orlando, Florida, United States |
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Mechanisms of transfer of virulence molecules in ichneumonid wasps25th International Congress of Entomology (ICE 2016), Sep 2016, Orlando, United States |
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Genome scans on experimentaly evolved globodera pallida populations to identify molceular basis of adaptation to GPAV(VRN) potato resistanceJoint Meeting of the Society of Nematologists and the Organization of Nematologists of Tropical America (ONTA), 2016, Jul 2016, Montreal, Canada. 387 p |
Using genomic tools to unravel parasitic wasp genome evolution via acquisition of viral genomesArthropod Genomics Symposium, 2015, Manhattan, Kansas, United States |
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The chemosensory transcriptome of the cotton leafworm Spodoptera littoralis24. Annual Meeting of the European-Chemoreception-Research-Organization (ECRO), 2015, NA, France |
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AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomiqueIN OVIVE (INtégration de sources/masses de données hétérogènes et Ontologies, dans le domaine des sciences du VIVant et de l’Environnement), Institut National de Recherche en Informatique et en Automatique (INRIA). Rennes, FRA., Jun 2015, Rennes, France. pp.7 |
The grape phylloxera genome sequencing project6. International Phylloxera Symposium, Aug 2013, Bordeaux, France |
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Long non-‐coding RNA in the pea aphid; identification and comparative expression in sexual and asexual embryosArthropod Genomics Symposium, Jun 2014, Urbana, United States |
Integration of miRNAs data into a gene network of the pea aphid.7th International Symposium on Molecular Insect Science., 2014, Amsterdam, Netherlands |
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AphidAtlas : avancées récentesBAPOA 2013 MOP, Oct 2013, Montpellier, France |
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A study of phylloxera transcriptomes, comparing root and leaf feeding morphs6. International Phylloxera Symposium, Institut National de Recherche Agronomique (INRA). UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne (1287)., Aug 2013, Bordeaux, France. 59 p |
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Whole genome re-sequencing : lessons from unmapped readsJournées Ouvertes Biologie Informatique Mathématiques, Jul 2013, Toulouse, France |
The antennal transcriptome of a mothThe 20th Congress of the European Chemoreception Research Organisation (ECRO), Sep 2010, Avignon, France. pp.E29 |
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Physical mapping and re-sequencing of a set of resistance related genes in grapevine17. Conference Plant and Animal Genomes, Labo/service de l'auteur, Ville service, Pays service., Jan 2009, San Diego, United States. 1 p |
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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 |
The antennal transcriptome of a moth20. Congress of European Chemoreception Research Organization (ECRO-2010), Sep 2010, Avignon, France. pp.E29-E30 |
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Prediction and analyzes of non coding RNA sequences in the pea aphid genomeArthropods Genomics, Jun 2010, Kansas City, United States |
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GnpAnnot community annotation system: features, qualifiers, values3. International Biocuration Conference, Apr 2009, Berlin, Germany |
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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 |
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From AphidBase and Lepido-DB to an Information System for Insect Plant pest genomics studies.1st Workshop on Information System for Insect Pest, Nov 2009, Rennes, France |
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Apollo: a tool for the manual annotation of the pea aphid genomePea Aphid Genome Annotation Workshop, Jul 2008, Princeton, United States |
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BReIF: une e-infrastructure pour accélérer l'utilisation de ressources biologiques diversifiéesTrans Numériques 2026, Feb 2026, Rennes, France. |
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Holograph: a generic RDF schema to handle data from agroecological holobiontsSWAT4HCLS, Mar 2026, Amsterdam, France. 2026 |
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A Strategy for Balanced Haplotype-Resolved De Novo Assembly of the Autotetraploid Genome of Medicago sativaJOBIM 2025 (Journées ouvertes de Bio-Informatique 2025), Jul 2025, Bordeaux, France |
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GWASpipe: a Nexflow pipeline for GWAS analyses incorporating quality controlJOBIM, événement annuel de la bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France. ⟨10.15454/1.5572369328961167E12⟩ |
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Data modeling in agroecology: a schema to characterize plant holobiont and environmental dataJOBIM, Jul 2025, Bordeaux, France |
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GrAuFlow: A snakemake workflow for pangenome graph augmentation using short read dataJournées Ouvertes Biologie, Informatique, Mathématiques (JOBIM2025), Jul 2025, Bordeaux, France |
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Discovering domestication mutations in cauliflowerJournées scientifiques 2025 Agroécologie et Numérique, Jan 2025, Dijon, France. |
A characterization of piRNAs, their biogenesis and their targets in Spodoptera frugiperda (Lepidoptera, Noctuidae)The 12th International workshop on Molecular Biology and Genetics of the Lepidoptera, Jul 2025, Kolympari, Greece |
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Identification of viral gene involved in genome replication of domesticated endogenous virus in parasitoid waspJacques Monod Conference on “Virus evolution: the mutualism-antagonism continuum of virus- virus interactions”, Oct 2024, Roscoff, France |
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Establishment of pangenome graphs for the analysis and monitoring of fungal plant pathogen populationsISCLB 2024 International Symposium on Cereal Leaf Blights, Jun 2024, Zürich, Switzerland. ⟨10.15454/1.5572369328961167E12⟩ |
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BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané (Brest Métropole), France. pp.1-1, 2023 |
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AskoR, an R package for easy RNA-Seq data analysis.Journées Ouvertes en Biologie, Informatique et Mathématiques (Jobim), Jun 2023, Tours, France. pp.263, 2018, JOBIM2023. ⟨10.1080/02664763.2018.1454894⟩ |
BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.The 11th international workshop on Molecular Biology and Genetics of the Lepidoptera, Aug 2022, Kolympari, Greece |
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AskoR, an R package for easy RNA-Seq data analysis illustrated by the analysis of plant/pathogen/microbiote interactions.Journées Ouvertes en Biologie, Informatique et Mathématiques (Jobim), Jul 2022, Rennes, France |
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LRez: C++ API and toolkit for analyzing and managing Linked-Reads dataJOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. pp.1 |
MTG-Link: filling gaps in draft genome assemblies with linked read dataJOBIM 2020 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier, France. |
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MTG-Link: filling gaps in draft genome assemblies with linked read dataBiodiversity Genomics 2020, Oct 2020, Online, France. |
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Functional consequences of transposable elements on duplicated gene transcription and retention in polyploid Brassica speciesInternational Conference on Polyploidy, Jun 2019, Ghent, Belgium |
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Identification and functional characterization of ovarian and maternally-inherited miRNAs in medaka7. International Workshop on the Biology of Fish Gametes, Sep 2019, Rennes, France. , pp.153-153, 2019 |
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Reference guided genome assembly in metagenomic samplesRECOMB 2018 - 22nd International Conference on Research in Computational Molecular Biology, Apr 2018, Paris, France. pp.1 |
BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2018, Marseille (FR), France |
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Une nouvelle facette du génome de poule : les genes “longs non-codants12. Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, Apr 2017, Tours, France. ITAVI - Institut Technique de l'Aviculture, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras, 2017, Journées de la Recherche Avicole et des Palmipèdes à Foie Gras |
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Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approachesJOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France |
Integration and query of biological datasets with Semantic Web technologies: AskOmicsJournées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Jun 2016, Lyon, France |
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Comparative genomic analysis of Clubroot resistance in the Brassicaceae familyBrassica2016, Oct 2016, Melbourne, Australia. |
Long-non coding RNAs repertoire in liver and adipose tissue in chickenXXIV International Plant & Animal Genome (Pag), Jan 2016, San Diego, United States. 2016 |
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Improvement of the assembly of heterozygous genomes of non-model organismsGenome Informatics, Oct 2015, Cold Spring Harbor Laboratory, United States. 2015 |
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Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strainsArthropod Genomics 2015, Jun 2015, Manhattan (Kansas), United States. 2015 |
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How to Design a good RNA-Seq experiment in an interdisciplinary context?European conference on Computational Biology, Sep 2014, Strasbourg, France. , 2014 |
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Identification and correction of genome mis-assemblies due to heterozygosityEuropean Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , ECCB 2014, 2014 |
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A tale of genome, annotations, metabolism and phylogenomics: the pea aphid genome resources10. Cold Spring Harbor Laboratory / Wellcome Trust conference on Genome Informatics, Sep 2010, Hinxton, United Kingdom. 1 p., 2010 |
Analyse des données RNA-seq (RNA-sequencing)Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3 |
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Assemblage de génomesPrincipes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3 |
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La programmationPrincipes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3 |
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Genomics of Phenotypic plastity in AphidsHenryk Czosnek; Murad Ghanim. Management of Insect Pests to Agriculture, Springer International Publishing, pp.65-96, 2016, 978-3-319-24049-7. ⟨10.1007/978-3-319-24049-7_3⟩ |
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Whole genome sequencing projects of the plant pathogenic fungi Botrytis Cinerea and Sclerotinia SclerotiorumMacromolecules and secondary metabolites of grapevine and wine : fruit development, biotic and abiotic stresses, mechanisms of plant defense responses, proteins, glycoproteins, polysaccharides, polyphenolics, aroma compounds and secondar, EDITIONS TEC ET DOC, 2007, 978-2-7430-0965-9 |
SfruDB: Spodoptera frugiperda genome assembly, version 62019 |
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LepidoDB Information system2017 |
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Rapport d'étape chantier entrepôt et annuaire institutionnels pour les données de la recherche[0] 2014, 18 p |
bioperl : Bibliothèque perl pour la modélisation et le traitement de données issues de la biologie[Technical Report] 2008 |
Pan1c (Pangenome at chromosome level)Logiciel hal-05034842v1 |
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MTG-LinkLogiciel hal-04823104v1 |
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LEVIATHANLogiciel hal-04823122v1 |
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LRezLogiciel hal-04823115v1 |