Fabrice Legeai, Bernardo Santos, Stéphanie Robin, Anthony Bretaudeau, Rebecca Dikow, et al.. Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps. BMC Biology, BioMed Central, 2020, 18 (1), pp.1-23. ⟨10.1186/s12915-020-00822-3⟩. ⟨hal-02918230⟩

Alice Dennis, Gabriel Ballesteros, Stéphanie Robin, Lukas Schrader, Jens Bast, et al.. Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum. BMC Genomics, BioMed Central, 2020, 21 (1), pp.1-27. ⟨10.1186/s12864-020-6764-0⟩. ⟨hal-02649295⟩

Claude Rispe, Fabrice Legeai, Paul Nabity, Rosa Fernández, Arinder Arora, et al.. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest. BMC Biology, BioMed Central, 2020, 18 (1), pp.90. ⟨10.1186/s12915-020-00820-5⟩. ⟨hal-02917617⟩

Delphine Eoche-Bosy, Matthieu Gautier, Magali Esquibet, Fabrice Legeai, Anthony Bretaudeau, et al.. Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.. Molecular Ecology, Wiley, 2017, 26 (18), pp.4700-4711. ⟨10.1111/mec.14240⟩. ⟨hal-01605681v2⟩

Gautier Richard, Fabrice Legeai, Nathalie Prunier-Leterme, Anthony Bretaudeau, Denis Tagu, et al.. Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid.. Epigenetics & Chromatin, BioMed Central, 2017, 10 (1), pp.1-17. ⟨10.1186/s13072-017-0137-1⟩. ⟨hal-01555242⟩

Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, et al.. Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, BioMed Central, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩. ⟨hal-01500475⟩

Thomas C. Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam T. Mugford, et al.. Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species. Genome Biology, BioMed Central, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩. ⟨hal-01588181⟩

Anaïs Gouin, Anthony Bretaudeau, Kiwoong Nam, Sylvie Gimenez, Jean-Marc Aury, et al.. Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges. Scientific Reports, Nature Publishing Group, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩. ⟨hal-01633879⟩

Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin. BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience, BioMed Central, 2014, 4, pp.22. ⟨10.1186/s13742-015-0063-8⟩. ⟨hal-01240449⟩

Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin Grenet, et al.. Establishment and analysis of a reference transcriptome for Spodoptera frugiperda. BMC Genomics, BioMed Central, 2014, 15 (1), pp.704. ⟨10.1186/1471-2164-15-704⟩. ⟨hal-01058982⟩

Olivier Sallou, Anthony Bretaudeau, Aurelien Roult. Seqcrawler: biological data indexing and browsing platform.. BMC Bioinformatics, BioMed Central, 2012, 13 (1), pp.175. ⟨10.1186/1471-2105-13-175⟩. ⟨hal-00728279⟩

Anthony Bretaudeau, François Coste, Florian Humily, Laurence Garczarek, Gildas Le Corguillé, et al.. CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. Nucleic Acids Research, Oxford University Press, 2012, pp.6. ⟨10.1093/nar/gks1091⟩. ⟨hal-01094087⟩

Stéphane Mahé, Marie Duhamel, Thomas Le Calvez, Laëtitia Guillot, Ludmila Sarbu, et al.. PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution. PLoS ONE, Public Library of Science, 2012, 7 (9), pp.e43117. ⟨10.1371/journal.pone.0043117⟩. ⟨hal-00756250⟩

Marion Ouedraogo, Charles Bettembourg, Anthony Bretaudeau, Olivier Sallou, Christian Diot, et al.. The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes. PLoS ONE, Public Library of Science, 2012, 7 (11), pp.e50653. ⟨10.1371/journal.pone.0050653⟩. ⟨hal-00841104⟩

Frédéric Lecerc, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Yuna Blum, et al.. AnnotQTL: a new tool to gather functional and comparative information on a genomic region. Nucleic Acids Research, Oxford University Press, 2011, 39 (Suppl 2), open access. ⟨10.1093/nar/gkr361⟩. ⟨hal-00597398⟩

Xavier Garnier, Anthony Bretaudeau, Fabrice Legeai, Anne Siegel, Olivier Dameron. AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resources. JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1. ⟨hal-02401750⟩

Xavier Garnier, Olivier Dameron, Olivier Filangi, Fabrice Legeai, Anthony Bretaudeau. Integration of Linked Data into Galaxy using Askomics. Galaxy Community Conference, Jun 2017, Montpellier, France. ⟨hal-01576870⟩

Xavier Garnier, Anthony Bretaudeau, Olivier Filangi, Fabrice Legeai, Anne Siegel, et al.. AskOmics, a web tool to integrate and query biological data using semantic web technologies. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1. ⟨hal-01577425⟩

Fabrice Legeai, Charles Bettembourg, Anthony Bretaudeau, Yvanne Chaussin, Olivier Dameron, et al.. BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction. XXVth International Congress of Entomology 2016, Sep 2016, Orlando, Florida, United States. ⟨hal-01391080⟩

Charles Bettembourg, Olivier Dameron, Anthony Bretaudeau, Fabrice Legeai. AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomique. IN 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. ⟨hal-01184903⟩

Anthony Bretaudeau, Yvan Le Bras, Cyril Monjeaud, Olivier Collin. Automatic update of reference data in Galaxy using BioMAJ.. Galaxy Day 2014, Institut Français de Bioinformatique, Dec 2014, Paris, France. ⟨hal-01102421⟩

Anthony Bretaudeau, Olivier Dameron, Fabrice Legeai, Yvan Rahbé. AphidAtlas : avancées récentes. BAPOA 2013 MOP, Oct 2013, Montpellier, France. ⟨hal-00913155⟩

Yvan Le Bras, Aurélien Roult, Cyril Monjoeaud, Bahin Mathieu, Olivier Quenez, et al.. Towards a Life Sciences Virtual Research Environment. JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France. ⟨hal-01102438⟩

Anthony Bretaudeau, Olivier Sallou, Olivier Collin. Hadoopizer : a cloud environment for bio-informatics data analysis. journées scientifiques mésocentres et France Grilles 2012, Oct 2012, Paris, France. ⟨hal-00766066⟩

Frédéric Lecerf, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Anne Blum, et al.. AnnotQTL: a new tool to gather functional and comparative information on a genomic region. 15th QTLMAS, Institut National de Recherche Agronomique (INRA). UMR Génétique Animale (0598)., May 2011, Rennes, France. ⟨hal-02746678⟩

Aurélie Evrard, Charles Bettembourg, Mélanie Jubault, Olivier Dameron, Olivier Filangi, et al.. Integration and query of biological datasets with Semantic Web technologies: AskOmics. Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Jun 2016, Lyon, France. ⟨hal-01391087⟩

Aurélie Evrard, Charles Bettembourg, Olivier Dameron, Olivier Filangi, Anthony Bretaudeau, et al.. Comparative genomic analysis of Clubroot resistance in the Brassicaceae family. Brassica2016, Oct 2016, Melbourne, Australia. ⟨hal-01391707⟩

Anaïs Gouin, Anthony Bretaudeau, K Labadie, Jean-Marc Aury, Emmanuelle d'Alençon, et al.. Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains. Arthropod Genomics 2015, Jun 2015, Manhattan (Kansas), United States. 2015. ⟨hal-01240443⟩

Anaïs Gouin, Anthony Bretaudeau, Emmanuelle d'Alençon, Claire Lemaitre, Fabrice Legeai. Improvement of the assembly of heterozygous genomes of non-model organisms. Genome Informatics, Oct 2015, Cold Spring Harbor Laboratory, United States. 2015. ⟨hal-01231793⟩

Anaïs Gouin, Anthony Bretaudeau, Claire Lemaitre, Fabrice Legeai. Identification and correction of genome mis-assemblies due to heterozygosity. European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. ECCB 2014, 2014. ⟨hal-01092959⟩

Yvan Le Bras, Aurélien Roult, Cyril Monjoeaud, Bahin Mathieu, Olivier Quenez, et al.. e-Science in France, a Life science Western story. Galaxy Community Conference (GCC2014), Jun 2014, Baltimore, United States. ⟨hal-01102432⟩

Anthony Bretaudeau, Olivier Collin. Dr Motifs: a web resource for pattern matching and discovery. JOBIM 2012, Jul 2012, Rennes, France. ⟨hal-01102439⟩

Frédéric Lecerf, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Yuna Blum, et al.. AnnotQTL: a new tool to gather functional and comparative information on a genomic region. 12. Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011, JOBIM 2011. ⟨hal-02746728⟩

Frédéric Lecerf, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Yuna Blum, et al.. AnnotQTL: a new tool to gather functional and comparative information on a genomic region. 12è Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011. ⟨hal-01102407⟩

Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, et al.. Community-Driven Data Analysis Training for Biology. 2020. ⟨pasteur-02613129⟩

Thomas Mathers, Yazhou Chen, Gemy Kaithakottil, Fabrice Legeai, Sam Mugford, et al.. A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters. 2020. ⟨hal-02936181⟩

Kiwoong Nam, Sylvie Gimenez, Frederique Hilliou, Carlos Blanco, Sabine Hänniger, et al.. Adaptation by copy number variation increases insecticide resistance in fall armyworms. 2020. ⟨hal-02945633⟩

Fabrice Legeai, Bernardo F. Santos, Stéphanie Robin, Anthony Bretaudeau, Rebecca B. Dikow, et al.. Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps. 2019. ⟨hal-02788577⟩

Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Anne Siegel. Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species. 2019. ⟨hal-02395024⟩