Camille Meslin, Pauline Mainet, Nicolas Montagné, Stéphanie Robin, Fabrice Legeai, et al.. Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae. G3, Genetics Society of America, 2022, 12 p. ⟨10.1093/g3journal/jkac131⟩. ⟨hal-03713321⟩

Jérémy Gauthier, Hélène Boulain, Joke J F A van Vugt, Lyam Baudry, Emma Persyn, et al.. Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization. Communications Biology, Nature Publishing Group, 2021, 4 (1), pp.1-15. ⟨10.1038/s42003-020-01623-8⟩. ⟨hal-03127732⟩

Rosanna Giordano, Ravi Kiran Donthu, Aleksey Zimin, Irene Consuelo Julca Chavez, Toni Gabaldon, et al.. Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest. Insect Biochemistry and Molecular Biology, Elsevier, 2020, 120, pp.1-24. ⟨10.1016/j.ibmb.2020.103334⟩. ⟨hal-03065382⟩

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⟩

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 (Art. 376), pp.1-27. ⟨10.1186/s12864-020-6764-0⟩. ⟨hal-02649295⟩

Ki Woong Nam, Sandra Nhim, Stéphanie Robin, Anthony Bretaudeau, Nicolas Nègre, et al.. Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm. BMC Evolutionary Biology, BioMed Central, 2020, 20 (1), ⟨10.1186/s12862-020-01715-3⟩. ⟨hal-03099735⟩

Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife, eLife Sciences Publication, 2020, 9, ⟨10.7554/eLife.61968⟩. ⟨hal-02395024v2⟩

Fabrice F. Legeai, Bernardo F Santos, Stéphanie Robin, Anthony Bretaudeau, Rebecca B 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⟩

Sylvie Gimenez, Heba Abdelgaffar, Gaelle Le Goff, Frédérique Hilliou, Carlos Blanco, et al.. Adaptation by copy number variation increases insecticide resistance in the fall armyworm. Communications Biology, Nature Publishing Group, 2020, 3 (1), pp.1-10. ⟨10.1038/s42003-020-01382-6⟩. ⟨hal-03065279⟩

Shawna Spoor, Chun-Huai Cheng, Lacey-Anne Sanderson, Bradford Condon, Abdullah Almsaeed, et al.. Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.. Database - The journal of Biological Databases and Curation, Oxford University Press, 2019, 2019, pp.baz077. ⟨10.1093/database/baz077⟩. ⟨hal-02318314⟩

Bernhard Gschloessl, Franck Dorkeld, Philippe Audiot, Anthony Bretaudeau, Carole Kerdelhue, et al.. De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae). Data in Brief, Elsevier, 2018, 17, pp.781-787. ⟨10.1016/j.dib.2018.01.073⟩. ⟨hal-02627842⟩

Bernhard Gschloessl, Franck Dorkeld, Helene Berges, Genséric Beydon, Olivier Bouchez, et al.. Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae). Molecular Ecology Resources, Wiley/Blackwell, 2018, 18 (3), pp.602-619. ⟨10.1111/1755-0998.12756⟩. ⟨hal-02627784⟩

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.. 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⟩

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⟩

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⟩

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⟩

Claude Rispe, Fabrice Legeai, Daciana Papura, Anthony Bretaudeau, Sylvie Hudaverdian, et al.. De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms. BMC Genomics, BioMed Central, 2016, 17 (1), pp.219. ⟨10.1186/s12864-016-2530-8⟩. ⟨hal-01286528⟩

Jon Ison, Kristoffer Rapacki, Hervé Ménager, Matúš Kalaš, Emil Rydza, et al.. Tools and data services registry: a community effort to document bioinformatics resources.. Nucleic Acids Research, Oxford University Press, 2016, 44 (D1), pp.D38-47. ⟨10.1093/nar/gkv1116⟩. ⟨hal-01594840⟩

Anthony Bretaudeau, Cyril Monjeaud, yvan Le Bras, Fabrice Legeai, Olivier Collin. BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience, Oxford Univ Press, 2015, 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⟩

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⟩

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⟩

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⟩

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⟩

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⟩

Clémence Frioux, Arnaud Belcour, Meziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metabolic complementarity applied to the screening of microbiota and the identification of key species. JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France. ⟨hal-03440232⟩

Clémence Frioux, Arnaud Belcour, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metabolic complementarity applied to the screening of microbiota and the identification of key species. MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27. ⟨hal-03440221⟩

Susete Alves Carvalho, Kévin Gazengel, Anthony Bretaudeau, Stéphanie Robin, Stéphanie Daval, et al.. AskoR, A R Package for Easy RNASeq Data Analysis. IECE 2021 - 1st International Electronic Conference on Entomology, Jul 2021, Virtual, France. pp.1-8, ⟨10.3390/IECE-10646⟩. ⟨hal-03347665⟩

Clémence Frioux, Arnaud Belcour, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metabolic complementarity applied to the screening of microbiota and the identification of key species. CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27. ⟨hal-03440212⟩

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, 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⟩

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⟩

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⟩

Delphine Eoche-Bosy, Magali Esquibet, Sylvain Fournet, Mathieu Gautier, Fabrice Legeai, et al.. Genome scans on experimentaly evolved globodera pallida populations to identify molceular basis of adaptation to GPAV(VRN) potato resistance. Joint Meeting of the Society of Nematologists and the Organization of Nematologists of Tropical America (ONTA), 2016, Jul 2016, Montreal, Canada. 387 p. ⟨hal-01602955⟩

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⟩

Claude Rispe, Daciana Papura, Fabrice Legeai, Julie Jaquiéry, Anthony Bretaudeau, et al.. A study of phylloxera transcriptomes, comparing root and leaf feeding morphs. 6. International Phylloxera Symposium, Institut National de Recherche Agronomique (INRA). UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne (1287)., Aug 2013, Bordeaux, France. 59 p. ⟨hal-01208647⟩

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⟩

Clémence Frioux, Arnaud Belcour, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species. IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1. ⟨hal-03438983⟩

Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species. JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩. ⟨hal-03151934⟩

Bernhard Gschloessl, Franck Dorkeld, Philippe Audiot, Anthony Bretaudeau, Christian Burban, et al.. Genomic and transcriptomic resources of two Lepidoptera: the Notodontidae Thaumetopoea pityocampa and the Crambidae Ostrinia scapulalis. 10. International Workshop on the Molecular Biology and Genetics of the Lepidoptera, Aug 2019, Crête, Greece. 2018. ⟨hal-02786428⟩

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⟩

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⟩

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⟩

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⟩

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⟩

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⟩

Anthony Bretaudeau. Annotation de génomes. Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3. ⟨hal-03319007⟩

Anthony Bretaudeau. Galaxy. Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3. ⟨hal-03319006⟩

Anthony Bretaudeau, Fabrice Legeai. Assemblage de génomes. Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3. ⟨hal-03319003⟩

Ki Woong Nam, Anthony Bretaudeau, Stéphanie Robin. SfruDB database :Spodoptera frugiperda genome assembly, Version 5. 2018. ⟨hal-02154692⟩

Emmanuelle d'Alençon, Fabrice Legeai, Anthony Bretaudeau, Stéphanie Robin, Nicolas Negre, et al.. LepidoDB Information system. 2017. ⟨hal-02154691⟩

Jérémy Gauthier, Hélène Boulain, Joke J.F.A. van Vugt, Lyam Baudry, Emma Persyn, et al.. Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes. 2020. ⟨hal-03090838⟩

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⟩

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

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

Alice B. Dennis, Gabriel I. 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. 2019. ⟨hal-02788571⟩

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⟩

Ki Woong Nam, Sandra Nhim, Stéphanie Robin, Anthony Bretaudeau, Nicolas Nègre, et al.. Genomic differentiation is initiated without physical linkage among targets of divergent selection in Fall armyworms. 2018. ⟨hal-02788771⟩