Anthony Bretaudeau

Documents

Publications

	The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update Linelle Ann L Abueg , Enis Afgan , Olivier Allart , Ahmed Awan , Wendi Bacon Nucleic Acids Research, 2024, 52 (W1), pp.W83-W94. ⟨10.1093/nar/gkae410⟩ Journal articles hal-04645009v1
	The 5-Fluorouracil RNA Expression Viewer (5-FUR) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast Ugo Szachnowski , Oliver Sallou , Matéo Boudet , Anthony Bretaudeau , Maxime Wéry Yeast, 2024, Online ahead of print. ⟨10.1002/yea.3982⟩ Journal articles hal-04718291v1
	First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies Jérémy Gauthier , Joana Meier , Fabrice Legeai , Melanie McClure , Annabel Whibley Molecular Ecology Resources, In press, 23 (4), pp.872-885. ⟨10.1111/1755-0998.13749⟩ Journal articles hal-03926527v2
	Galaxy Training: A powerful framework for teaching! Saskia Hiltemann , Helena Rasche , Simon Gladman , Hans-Rudolf Hotz , Delphine Larivière PLoS Computational Biology, 2022, 19 (1), pp.e1010752. ⟨10.1371/journal.pcbi.1010752⟩ Journal articles hal-04069041v1
	Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae Camille Meslin , Pauline Mainet , Nicolas Montagné , Stéphanie Robin , Fabrice Legeai G3, 2022, 12 (8), pp.jkac131. ⟨10.1093/g3journal/jkac131⟩ Journal articles hal-03713321v1
	Training Infrastructure as a Service Helena Rasche , Cameron Hyde , John Davis , Simon Gladman , Nate Coraor GigaScience, 2022, 12, pp.giad048. ⟨10.1093/gigascience/giad048⟩ Journal articles hal-04183845v1
	Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization Jérémy Gauthier , Hélène Boulain , Joke J F A van Vugt , Lyam Baudry , Emma Persyn Communications Biology, 2021, 4 (1), pp.1-15. ⟨10.1038/s42003-020-01623-8⟩ Journal articles hal-03127732v1
	AskoR, A R Package for Easy RNASeq Data Analysis Susete Alves Carvalho , Kévin Gazengel , Anthony Bretaudeau , Stéphanie Robin , Stéphanie Daval Proceedings of The 1st International Electronic Conference on Entomology, 2021, ⟨10.3390/iece-10646⟩ Journal articles hal-04717074v1
	Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand eLife, 2020, 9, ⟨10.7554/eLife.61968⟩ Journal articles hal-02395024v2
	Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps Fabrice F. Legeai , Bernardo F Santos , Stéphanie Robin , Anthony Bretaudeau , Rebecca B Dikow BMC Biology, 2020, 18 (1), pp.1-23. ⟨10.1186/s12915-020-00822-3⟩ Journal articles hal-02918230v1
	The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest Claude Rispe , Fabrice Legeai , Paul Nabity , Rosa Fernández , Arinder Arora BMC Biology, 2020, 18 (1), pp.90. ⟨10.1186/s12915-020-00820-5⟩ Journal articles hal-02917617v1
	Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest Rosanna Giordano , Ravi Kiran Donthu , Aleksey Zimin , Irene Consuelo Julca Chavez , Toni Gabaldon Insect Biochemistry and Molecular Biology, 2020, 120, pp.1-24. ⟨10.1016/j.ibmb.2020.103334⟩ Journal articles hal-03065382v1
	Adaptation by copy number variation increases insecticide resistance in the fall armyworm Sylvie Gimenez , Heba Abdelgaffar , Gaelle Le Goff , Frédérique Hilliou , Carlos Blanco Communications Biology, 2020, 3 (1), pp.1-10. ⟨10.1038/s42003-020-01382-6⟩ Journal articles hal-03065279v1
	Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm Ki Woong Nam , Sandra Nhim , Stéphanie Robin , Anthony Bretaudeau , Nicolas Nègre BMC Evolutionary Biology, 2020, 20 (1), ⟨10.1186/s12862-020-01715-3⟩ Journal articles hal-03099735v1
	Functional insights from the GC-poor genomes of two aphid parasitoids, "Aphidius ervi" and "Lysiphlebus fabarum" Alice Dennis , Gabriel Ballesteros , Stéphanie Robin , Lukas Schrader , Jens Bast BMC Genomics, 2020, 21 (Art. 376), pp.1-27. ⟨10.1186/s12864-020-6764-0⟩ Journal articles hal-02649295v1
	Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Shawna Spoor , Chun-Huai Cheng , Lacey-Anne Sanderson , Bradford Condon , Abdullah Almsaeed Database - The journal of Biological Databases and Curation, 2019, 2019, pp.baz077. ⟨10.1093/database/baz077⟩ Journal articles hal-02318314v1
	Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae) Bernhard Gschloessl , Franck Dorkeld , Helene Berges , Genséric Beydon , Olivier Bouchez Molecular Ecology Resources, 2018, 18 (3), pp.602-619. ⟨10.1111/1755-0998.12756⟩ Journal articles hal-02627784v1
	De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae) Bernhard Gschloessl , Franck Dorkeld , Philippe Audiot , Anthony Bretaudeau , Carole Kerdelhue Data in Brief, 2018, 17, pp.781-787. ⟨10.1016/j.dib.2018.01.073⟩ Journal articles hal-02627842v1
	Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩ Journal articles hal-01588181v1
	Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid. Gautier Richard , Fabrice Legeai , Nathalie Prunier-Leterme , Anthony Bretaudeau , Denis Tagu Epigenetics & Chromatin, 2017, 10 (1), pp.1-17. ⟨10.1186/s13072-017-0137-1⟩ Journal articles hal-01555242v1
	Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges Anaïs Gouin , Anthony Bretaudeau , Kiwoong Nam , Sylvie Gimenez , Jean-Marc Aury Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩ Journal articles hal-01633879v1
	Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species Thomas C. Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam T. Mugford Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩ Journal articles hal-01500475v1
	Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida. Delphine Eoche-Bosy , Matthieu Gautier , Magali Esquibet , Fabrice Legeai , Anthony Bretaudeau Molecular Ecology, 2017, 26 (18), pp.4700-4711. ⟨10.1111/mec.14240⟩ Journal articles hal-01605681v2
	Tools and data services registry: a community effort to document bioinformatics resources. Jon Ison , Kristoffer Rapacki , Hervé Ménager , Matúš Kalaš , Emil Rydza Nucleic Acids Research, 2016, 44 (D1), pp.D38-47. ⟨10.1093/nar/gkv1116⟩ Journal articles hal-01594840v1
	De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms Claude Rispe , Fabrice Legeai , Daciana Papura , Anthony Bretaudeau , Sylvie Hudaverdian BMC Genomics, 2016, 17 (1), pp.219. ⟨10.1186/s12864-016-2530-8⟩ Journal articles hal-01286528v1
	BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ Anthony Bretaudeau , Cyril Monjeaud , Yvan Le Bras , Fabrice Legeai , Olivier Collin GigaScience, 2015, 4, pp.22. ⟨10.1186/s13742-015-0063-8⟩ Journal articles hal-01240449v1
	Establishment and analysis of a reference transcriptome for Spodoptera frugiperda Fabrice Legeai , Sylvie Gimenez , Bernard Duvic , Jean-Michel Escoubas , Anne-Sophie Gosselin Grenet BMC Genomics, 2014, 15 (1), pp.704. ⟨10.1186/1471-2164-15-704⟩ Journal articles hal-01058982v1
	CyanoLyase: a database of phycobilin lyase sequences, motifs and functions Anthony Bretaudeau , François Coste , Florian Humily , Laurence Garczarek , Gildas Le Corguillé Nucleic Acids Research, 2012, pp.6. ⟨10.1093/nar/gks1091⟩ Journal articles hal-01094087v1
	Seqcrawler: biological data indexing and browsing platform. Olivier Sallou , Anthony Bretaudeau , Aurelien Roult BMC Bioinformatics, 2012, 13 (1), pp.175. ⟨10.1186/1471-2105-13-175⟩ Journal articles hal-00728279v1
	The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes Marion Ouedraogo , Charles Bettembourg , Anthony Bretaudeau , Olivier Sallou , Christian Diot PLoS ONE, 2012, 7 (11), pp.e50653. ⟨10.1371/journal.pone.0050653⟩ Journal articles hal-00841104v1
	PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution Stéphane Mahé , Marie Duhamel , Thomas Le Calvez , Laëtitia Guillot , Ludmila Sarbu PLoS ONE, 2012, 7 (9), pp.e43117. ⟨10.1371/journal.pone.0043117⟩ Journal articles hal-00756250v1
	AnnotQTL: a new tool to gather functional and comparative information on a genomic region Frédéric Lecerc , Anthony Bretaudeau , Olivier Sallou , Colette Désert , Yuna Blum Nucleic Acids Research, 2011, 39 (Suppl 2), open access. ⟨10.1093/nar/gkr361⟩ Journal articles hal-00597398v1

	Galaxy France: an example of a national UseGalaxy server Clea Siguret , Thomas Chaussepied , Romane Libouban , Eva Mercier , Julien Seiler GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. pp.1-15, ⟨10.7490/f1000research.1119767.1⟩ Conference papers hal-04644627v1
	Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27 Conference papers hal-03440221v1
	Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux , Arnaud Belcour , Meziane Aite , Anthony Bretaudeau , Falk Hildebrand JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Conference papers hal-03440232v1
	Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27 Conference papers hal-03440212v1
	AskoR, A R Package for Easy RNASeq Data Analysis Susete Alves Carvalho , Kévin Gazengel , Anthony Bretaudeau , Stéphanie Robin , Stéphanie Daval IECE 2021 - 1st International Electronic Conference on Entomology, Jul 2021, Virtual, France. pp.1-8, ⟨10.3390/IECE-10646⟩ Conference papers hal-03347665v1
	AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resources Xavier Garnier , Anthony Bretaudeau , Fabrice Legeai , Anne Siegel , Olivier Dameron JOBIM 2019 - Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France. pp.1 Conference papers hal-02401750v1
	AskOmics, a web tool to integrate and query biological data using semantic web technologies Xavier Garnier , Anthony Bretaudeau , Olivier Filangi , Fabrice Legeai , Anne Siegel JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1 Conference papers hal-01577425v1
	Integration of Linked Data into Galaxy using Askomics Xavier Garnier , Olivier Dameron , Olivier Filangi , Fabrice Legeai , Anthony Bretaudeau Galaxy Community Conference, Jun 2017, Montpellier, France Conference papers hal-01576870v1
	Genome scans on experimentaly evolved globodera pallida populations to identify molceular basis of adaptation to GPAV(VRN) potato resistance Delphine Eoche-Bosy , Magali Esquibet , Sylvain Fournet , Mathieu Gautier , Fabrice Legeai Joint Meeting of the Society of Nematologists and the Organization of Nematologists of Tropical America (ONTA), 2016, Jul 2016, Montreal, Canada. 387 p Conference papers hal-01602955v1
	BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction Fabrice Legeai , Charles Bettembourg , Anthony Bretaudeau , Yvanne Chaussin , Olivier Dameron XXVth International Congress of Entomology 2016, Sep 2016, Orlando, Florida, United States Conference papers hal-01391080v1
	AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomique Charles Bettembourg , Olivier Dameron , Anthony Bretaudeau , Fabrice Legeai 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 Conference papers hal-01184903v1
	Automatic update of reference data in Galaxy using BioMAJ. Anthony Bretaudeau , Yvan Le Bras , Cyril Monjeaud , Olivier Collin Galaxy Day 2014, Institut Français de Bioinformatique, Dec 2014, Paris, France Conference papers hal-01102421v1
	Towards a Life Sciences Virtual Research Environment Yvan Le Bras , Aurélien Roult , Cyril Monjoeaud , Bahin Mathieu , Olivier Quenez JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France Conference papers hal-01102438v1
	AphidAtlas : avancées récentes Anthony Bretaudeau , Olivier Dameron , Fabrice Legeai , Yvan Rahbé BAPOA 2013 MOP, Oct 2013, Montpellier, France Conference papers hal-00913155v1
	A study of phylloxera transcriptomes, comparing root and leaf feeding morphs Claude Rispe , Daciana Papura , Fabrice Legeai , Julie Jaquiéry , Anthony Bretaudeau 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 Conference papers hal-01208647v1
	Hadoopizer : a cloud environment for bio-informatics data analysis Anthony Bretaudeau , Olivier Sallou , Olivier Collin journées scientifiques mésocentres et France Grilles 2012, Oct 2012, Paris, France Conference papers hal-00766066v1
	AnnotQTL: a new tool to gather functional and comparative information on a genomic region Frédéric Lecerf , Anthony Bretaudeau , Olivier Sallou , Colette Désert , Anne Blum 15th QTLMAS, Institut National de Recherche Agronomique (INRA). UMR Génétique Animale (0598)., May 2011, Rennes, France Conference papers hal-02746678v1

	Building a Distributed Computing Network for Galaxy, Application to Genome Annotation Eva Mercier , Romane Libouban , Thomas Chaussepied , Anthony Bretaudeau JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. 2024 Conference poster hal-04694519v1
	Services deployed on the IFB National Network of Computing Resources (NNCR) David Benaben , Christophe Blanchet , Matéo Boudet , Guillaume Brysbaert , Anthony Bretaudeau JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques, Jun 2024, Toulouse, France. , 2024 Conference poster hal-04618059v1
	Exploring the richness of the French Galaxy Ecosystem Bérénice Batut , Gildas Le Corguillé , Yvan Le Bras , Loraine Brillet-Guéguen , Fabien Mareuil GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. , pp.1-1, 2024, ⟨10.7490/f1000research.1119765.1⟩ Conference poster hal-04644779v1
	P06-18 Enhancing prediction and priorisation of adverse effects: TOXsIgN as a comprehensive resource for toxicogenomics T. Darde , I. Kugathas , Matéo Boudet , Anthony Bretaudeau , R. Le Guével EUROTOX 2024 - 58th Congress of the European Societies of Toxicology, Sep 2024, Copenhagen, Denmark. pp.S159, 2024, ⟨10.1016/j.toxlet.2024.07.402⟩ Conference poster hal-04690377v1
	AskoR, an R package for easy RNA-Seq data analysis. Susete Alves Carvalho , Kévin Gazengel , Anthony Bretaudeau , Stéphanie Robin , Stéphanie Daval Journées Ouvertes en Biologie, Informatique et Mathématiques (Jobim), Jun 2023, Tours, France. pp.263, 2018, JOBIM2023. ⟨10.1080/02664763.2018.1454894⟩ Conference poster hal-04720296v1
	BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods. Stéphanie Robin , Fabrice Legeai , Anthony Bretaudeau JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané (Brest Métropole), France. pp.1-1, 2023 Conference poster hal-04176786v1
	BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods. Stéphanie Robin , Anthony Bretaudeau , Fabrice Legeai The 11th international workshop on Molecular Biology and Genetics of the Lepidoptera, Aug 2022, Kolympari, Greece Conference poster hal-04176792v1
	AskoR, an R package for easy RNA-Seq data analysis illustrated by the analysis of plant/pathogen/microbiote interactions. Susete Alves Carvalho , Kévin Gazengel , Masanelli Sylvin , Anthony Bretaudeau , Stéphanie Robin Journées Ouvertes en Biologie, Informatique et Mathématiques (Jobim), Jul 2022, Rennes, France Conference poster hal-04720279v1
	Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species Clémence Frioux , Arnaud Belcour , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1 Conference poster hal-03438983v1
	Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species Arnaud Belcour , Clémence Frioux , Méziane Aite , Anthony Bretaudeau , Falk Hildebrand JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩ Conference poster hal-03151934v1
	Genomic and transcriptomic resources of two Lepidoptera: the Notodontidae Thaumetopoea pityocampa and the Crambidae Ostrinia scapulalis Bernhard Gschloessl , Franck Dorkeld , Philippe Audiot , Anthony Bretaudeau , Christian Burban 10. International Workshop on the Molecular Biology and Genetics of the Lepidoptera, Aug 2019, Crête, Greece. Conference poster hal-02786428v1
	BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods. Stéphanie Robin , Anthony Bretaudeau , Fabrice Legeai Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2018, Marseille (FR), France Conference poster hal-04176797v1
	Comparative genomic analysis of Clubroot resistance in the Brassicaceae family Aurélie Evrard , Charles Bettembourg , Olivier Dameron , Olivier Filangi , Anthony Bretaudeau Brassica2016, Oct 2016, Melbourne, Australia. Conference poster hal-01391707v1
	Integration and query of biological datasets with Semantic Web technologies: AskOmics Aurélie Evrard , Charles Bettembourg , Mélanie Jubault , Olivier Dameron , Olivier Filangi Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Jun 2016, Lyon, France Conference poster hal-01391087v1
	Improvement of the assembly of heterozygous genomes of non-model organisms Anaïs Gouin , Anthony Bretaudeau , Emmanuelle d'Alençon , Claire Lemaitre , Fabrice Legeai Genome Informatics, Oct 2015, Cold Spring Harbor Laboratory, United States. 2015 Conference poster hal-01231793v1
	Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains Anaïs Gouin , Anthony Bretaudeau , K Labadie , Jean-Marc Aury , Emmanuelle d'Alençon Arthropod Genomics 2015, Jun 2015, Manhattan (Kansas), United States. 2015 Conference poster hal-01240443v1
	Identification and correction of genome mis-assemblies due to heterozygosity Anaïs Gouin , Anthony Bretaudeau , Claire Lemaitre , Fabrice Legeai European Conference on Computational Biology (ECCB), Sep 2014, Strasbourg, France. , ECCB 2014, 2014 Conference poster hal-01092959v1
	e-Science in France, a Life science Western story Yvan Le Bras , Aurélien Roult , Cyril Monjoeaud , Bahin Mathieu , Olivier Quenez Galaxy Community Conference (GCC2014), Jun 2014, Baltimore, United States Conference poster hal-01102432v1
	Dr Motifs: a web resource for pattern matching and discovery Anthony Bretaudeau , Olivier Collin JOBIM 2012, Jul 2012, Rennes, France Conference poster hal-01102439v1
	AnnotQTL: a new tool to gather functional and comparative information on a genomic region Frédéric Lecerf , Anthony Bretaudeau , Olivier Sallou , Colette Désert , Yuna Blum 12. Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011, JOBIM 2011 Conference poster hal-02746728v1

	Annotation de génomes Anthony Bretaudeau Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3 Book sections hal-03319007v1
	Galaxy Anthony Bretaudeau Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3 Book sections hal-03319006v1
	Assemblage de génomes Anthony Bretaudeau , Fabrice Legeai Principes des techniques de biologie moléculaire et génomique : 3e édition revue et augmentée, Quae, 2018, Savoir Faire, 978-2-7592-2389-3 Book sections hal-03319003v1

	SfruDB database :Spodoptera frugiperda genome assembly, Version 5 Ki Woong Nam , Anthony Bretaudeau , Stéphanie Robin 2018 Other publications hal-02154692v1
	LepidoDB Information system Emmanuelle d'Alençon , Fabrice Legeai , Anthony Bretaudeau , Stéphanie Robin , Nicolas Negre 2017 Other publications hal-02154691v1

	Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae Camille Meslin , Pauline Mainet , Nicolas Montagné , Stéphanie Robin , Fabrice Legeai 2021 Preprints, Working Papers, ... hal-04706490v1
	Community-Driven Data Analysis Training for Biology Bérénice Batut , Saskia Hiltemann , Andrea Bagnacani , Dannon Baker , Vivek Bhardwaj 2020 Preprints, Working Papers, ... pasteur-02613129v1
	A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters Thomas Mathers , Yazhou Chen , Gemy Kaithakottil , Fabrice Legeai , Sam Mugford 2020 Preprints, Working Papers, ... hal-02936181v1
	Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes Jérémy Gauthier , Hélène Boulain , Joke J.F.A. van Vugt , Lyam Baudry , Emma Persyn 2020 Preprints, Working Papers, ... hal-03090838v1
	Adaptation by copy number variation increases insecticide resistance in fall armyworms Ki Woong Nam , Sylvie Gimenez , Frederique Hilliou , Carlos A Blanco , Sabine Hänniger 2020 Preprints, Working Papers, ... hal-02945633v1
	Conserved and specific genomic features of endogenous polydnaviruses revealed by whole genome sequencing of two ichneumonid wasps Fabrice Legeai , Bernardo F. Santos , Stéphanie Robin , Anthony Bretaudeau , Rebecca B. Dikow 2019 Preprints, Working Papers, ... hal-02788577v1
	Functional insights from the GC-poor genomes of two aphid parasitoids, Aphidius ervi and Lysiphlebus fabarum Alice B. Dennis , Gabriel I. Ballesteros , Stéphanie Robin , Lukas Schrader , Jens Bast 2019 Preprints, Working Papers, ... hal-02788571v1
	Genomic differentiation is initiated without physical linkage among targets of divergent selection in Fall armyworms Ki Woong Nam , Sandra Nhim , Stéphanie Robin , Anthony Bretaudeau , Nicolas Nègre 2018 Preprints, Working Papers, ... hal-02788771v1

Anthony Bretaudeau

Publications

The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update

The 5-Fluorouracil RNA Expression Viewer (5-FUR) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast

First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies

Galaxy Training: A powerful framework for teaching!

Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Training Infrastructure as a Service

Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization

AskoR, A R Package for Easy RNASeq Data Analysis

Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species

Genomic architecture of endogenous ichnoviruses reveals distinct evolutionary pathways leading to virus domestication in parasitic wasps

The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Soybean aphid biotype 1 genome: Insights into the invasive biology and adaptive evolution of a major agricultural pest

Adaptation by copy number variation increases insecticide resistance in the fall armyworm

Positive selection alone is sufficient for whole genome differentiation at the early stage of speciation process in the fall armyworm

Functional insights from the GC-poor genomes of two aphid parasitoids, "Aphidius ervi" and "Lysiphlebus fabarum"

Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases.

Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae)

De novo genome and transcriptome resources of the Adzuki bean borer Ostrinia scapulalis (Lepidoptera: Crambidae)

Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Dosage compensation and sex-specific epigenetic landscape of the X chromosome in the pea aphid.

Two genomes of highly polyphagous lepidopteran pests (Spodoptera frugiperda, Noctuidae) with different host-plant ranges

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species

Genome scans on experimentally evolved populations reveal candidate regions for adaptation to plant resistance in the potato cyst nematode Globodera pallida.

Tools and data services registry: a community effort to document bioinformatics resources.

De novo transcriptome assembly of the grapevine phylloxera allows identification of genes differentially expressed between leaf- and root-feeding forms

BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ

Establishment and analysis of a reference transcriptome for Spodoptera frugiperda

CyanoLyase: a database of phycobilin lyase sequences, motifs and functions

Seqcrawler: biological data indexing and browsing platform.

The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes

PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution

AnnotQTL: a new tool to gather functional and comparative information on a genomic region

Galaxy France: an example of a national UseGalaxy server

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Metabolic complementarity applied to the screening of microbiota and the identification of key species

Metabolic complementarity applied to the screening of microbiota and the identification of key species

AskoR, A R Package for Easy RNASeq Data Analysis

AskOmics: a user-friendly interface to Semantic Web technologies for integrating local datasets with reference resources

AskOmics, a web tool to integrate and query biological data using semantic web technologies

Integration of Linked Data into Galaxy using Askomics

Genome scans on experimentaly evolved globodera pallida populations to identify molceular basis of adaptation to GPAV(VRN) potato resistance

BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction

AskOmics : Intégration et interrogation de réseaux de régulation génomique et post-génomique

Automatic update of reference data in Galaxy using BioMAJ.

Towards a Life Sciences Virtual Research Environment

AphidAtlas : avancées récentes

A study of phylloxera transcriptomes, comparing root and leaf feeding morphs

Hadoopizer : a cloud environment for bio-informatics data analysis

AnnotQTL: a new tool to gather functional and comparative information on a genomic region

Building a Distributed Computing Network for Galaxy, Application to Genome Annotation

Services deployed on the IFB National Network of Computing Resources (NNCR)

Exploring the richness of the French Galaxy Ecosystem

P06-18 Enhancing prediction and priorisation of adverse effects: TOXsIgN as a comprehensive resource for toxicogenomics

AskoR, an R package for easy RNA-Seq data analysis.

BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.

BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.

AskoR, an R package for easy RNA-Seq data analysis illustrated by the analysis of plant/pathogen/microbiote interactions.

Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species

Metage2Metabo: metabolic complementarity applied to genomes of large-scale microbiotas for the identification of keystone species

Genomic and transcriptomic resources of two Lepidoptera: the Notodontidae Thaumetopoea pityocampa and the Crambidae Ostrinia scapulalis

BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.

Comparative genomic analysis of Clubroot resistance in the Brassicaceae family

Integration and query of biological datasets with Semantic Web technologies: AskOmics

Improvement of the assembly of heterozygous genomes of non-model organisms

Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains

Identification and correction of genome mis-assemblies due to heterozygosity

e-Science in France, a Life science Western story

Dr Motifs: a web resource for pattern matching and discovery

AnnotQTL: a new tool to gather functional and comparative information on a genomic region

Annotation de génomes

Galaxy

Assemblage de génomes

SfruDB database :Spodoptera frugiperda genome assembly, Version 5

LepidoDB Information system

Spodoptera littoralis genome mining brings insights on the dynamic of expansion of gustatory receptors in polyphagous noctuidae

Community-Driven Data Analysis Training for Biology

A clonally reproducing generalist aphid pest colonises diverse host plants by rapid transcriptional plasticity of duplicated gene clusters

Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes