Anthony Bretaudeau

Publications

Article dans une revue (41)

Ten common misconceptions about Galaxy (and why they are wrong!) Wendi Anne Bacon,Bérénice Batut,Sanjay Kumar Srikakulam,Paul Zierep,Anthony Bretaudeauet al. PLoS Computational Biology, 2026, 22 (2), pp.e1013869. ⟨10.1371/journal.pcbi.1013869⟩ Article dans une revue hal-05563178v1
Single-cell exploration of gonadal somatic cell lineage specification during human sex determination Aurélie Lardenois,Antonio Suglia,Chad Lewis Moore,Bertrand Evrard,Laurence Noëlet al. Developmental Cell, 2026, 61 (2), pp.400-415.e6. ⟨10.1016/j.devcel.2025.09.011⟩ Article dans une revue hal-05318023v1
Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis Ugo Szachnowski,Emmanuelle Becker,Igor Stuparevic,Maxime Wery,Olivier Sallouet al. RNA, 2025, 31 (4), pp.497-513. ⟨10.1261/rna.080290.124⟩ Article dans une revue hal-04935733v1
Genome sequences of four Ixodes species expands understanding of tick evolution Alexandra Cerqueira de Araujo,Benjamin Noël,Anthony Bretaudeau,Karine Labadie,Matéo Boudetet al. BMC Biology, 2025, 23, pp.17. ⟨10.1186/s12915-025-02121-1⟩ Article dans une revue hal-04707197v1
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 Wéryet al. Yeast, 2024, 41 (10), pp.629-640. ⟨10.1002/yea.3982⟩ Article dans une revue hal-04718291v1
The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update Linelle Ann L Abueg,Enis Afgan,Olivier Allart,Ahmed Awan,Wendi Baconet al. Nucleic Acids Research, 2024, 52 (W1), pp.W83-W94. ⟨10.1093/nar/gkae410⟩ Article dans une revue hal-04645009v1
Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps Ange Lorenzi,Fabrice Legeai,Véronique Jouan,Pierre-Alain Girard,Michael R Strandet al. PLoS Pathogens, 2024, 20 (4), pp.e1011980. ⟨10.1371/journal.ppat.1011980⟩ Article dans une revue hal-04572197v1
Training Infrastructure as a Service Helena Rasche,Cameron Hyde,John Davis,Simon Gladman,Nate Coraoret al. GigaScience, 2023, 12, pp.giad048. ⟨10.1093/gigascience/giad048⟩ Article dans une revue hal-04183845v1
Galaxy Training: A powerful framework for teaching! Saskia Hiltemann,Helena Rasche,Simon Gladman,Hans-Rudolf Hotz,Delphine Larivièreet al. PLoS Computational Biology, 2023, 19 (1), pp.e1010752. ⟨10.1371/journal.pcbi.1010752⟩ Article dans une revue hal-04069041v1
First chromosome scale genomes of ithomiine butterflies (Nymphalidae: Ithomiini): comparative models for mimicry genetic studies Jérémy Gauthier,Joana Meier,Fabrice Legeai,Melanie McClure,Annabel Whibleyet al. Molecular Ecology Resources, In press, 23 (4), pp.872-885. ⟨10.1111/1755-0998.13749⟩ Article dans une revue hal-03926527v2
The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update Enis Afgan,Anton Nekrutenko,Bjórn Grüning,Daniel Blankenberg,Jeremy Goeckset al. Nucleic Acids Research, 2022, 50 (W1), pp.W345-W351. ⟨10.1093/nar/gkac247⟩ Article dans une revue hal-04053853v1
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 Legeaiet al. G3, 2022, 12 (8), pp.jkac131. ⟨10.1093/g3journal/jkac131⟩ Article dans une revue hal-03713321v1
AskoR, A R Package for Easy RNASeq Data Analysis Susete Alves Carvalho,Kévin Gazengel,Anthony Bretaudeau,Stéphanie Robin,Stéphanie Davalet al. Proceedings of The 1st International Electronic Conference on Entomology, 2021, ⟨10.3390/iece-10646⟩ Article dans une revue hal-04717074v1
Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization Jérémy Gauthier,Hélène Boulain,Joke J F A van Vugt,Lyam Baudry,Emma Persynet al. Communications Biology, 2021, 4 (1), pp.1-15. ⟨10.1038/s42003-020-01623-8⟩ Article dans une revue hal-03127732v1
Author Correction: Chromosomal scale assembly of parasitic wasp genome reveals symbiotic virus colonization Jérémy Gauthier,Hélène Boulain,Joke J F A van Vugt,Lyam Baudry,Emma Persynet al. Communications Biology, 2021, 4, ⟨10.1038/s42003-021-02480-9⟩ Article dans une revue hal-04686846v1
Functional insights from the GC-poor genomes of two aphid parasitoids, &quot;Aphidius ervi&quot; and &quot;Lysiphlebus fabarum Alice Dennis,Gabriel Ballesteros,Stéphanie Robin,Lukas Schrader,Jens Bastet al. BMC Genomics, 2020, 21 (Art. 376), pp.1-27. ⟨10.1186/s12864-020-6764-0⟩ Article dans une revue hal-02649295v1
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 Nègreet al. BMC Evolutionary Biology, 2020, 20 (1), ⟨10.1186/s12862-020-01715-3⟩ Article dans une revue hal-03099735v1
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 Gabaldonet al. Insect Biochemistry and Molecular Biology, 2020, 120, pp.1-24. ⟨10.1016/j.ibmb.2020.103334⟩ Article dans une revue hal-03065382v1
Adaptation by copy number variation increases insecticide resistance in the fall armyworm Sylvie Gimenez,Heba Abdelgaffar,Gaëlle Le Goff,Frédérique Hilliou,Carlos Blancoet al. Communications Biology, 2020, 3 (1), pp.1-10. ⟨10.1038/s42003-020-01382-6⟩ Article dans une revue hal-03065279v1
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 Dikowet al. BMC Biology, 2020, 18 (1), pp.1-23. ⟨10.1186/s12915-020-00822-3⟩ Article dans une revue hal-02918230v1
Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species Arnaud Belcour,Clémence Frioux,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. eLife, 2020, 9, ⟨10.7554/eLife.61968⟩ Article dans une revue hal-02395024v2
Correction to: 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 Aroraet al. BMC Biology, 2020, 18 (1), pp.123. ⟨10.1186/s12915-020-00864-7⟩ Article dans une revue hal-05190973v1
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 Aroraet al. BMC Biology, 2020, 18 (1), pp.90. ⟨10.1186/s12915-020-00820-5⟩ Article dans une revue hal-02917617v1
Tripal v3: an ontology-based toolkit for construction of FAIR biological community databases. Shawna Spoor,Chun-Huai Cheng,Lacey-Anne Sanderson,Bradford Condon,Abdullah Almsaeedet al. Database - The journal of Biological Databases and Curation, 2019, 2019, pp.baz077. ⟨10.1093/database/baz077⟩ Article dans une revue hal-02318314v1
Community-Driven Data Analysis Training for Biology Bérénice Batut,Saskia Hiltemann,Andrea Bagnacani,Dannon Baker,Vivek Bhardwajet al. Cell Systems, 2018, 6 (6), pp.752-758.e1. ⟨10.1016/j.cels.2018.05.012⟩ Article dans une revue hal-04863943v1
Draft genome and reference transcriptomic resources for the urticating pine defoliator Thaumetopoea pityocampa (Lepidoptera: Notodontidae) Bernhard Gschloessl,Franck Dorkeld,Helene Berges,Genséric Beydon,Olivier Bouchezet al. Molecular Ecology Resources, 2018, 18 (3), pp.602-619. ⟨10.1111/1755-0998.12756⟩ Article dans une revue hal-02627784v1
&lt;em&gt;De novo&lt;/em&gt; genome and transcriptome resources of the Adzuki bean borer &lt;em&gt;Ostrinia scapulalis&lt;/em&gt; (Lepidoptera: Crambidae) Bernhard Gschloessl,Franck Dorkeld,Philippe Audiot,Anthony Bretaudeau,Carole Kerdelhueet al. Data in Brief, 2018, 17, pp.781-787. ⟨10.1016/j.dib.2018.01.073⟩ Article dans une revue (data paper) hal-02627842v1
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 Taguet al. Epigenetics & Chromatin, 2017, 10 (1), pp.1-17. ⟨10.1186/s13072-017-0137-1⟩ Article dans une revue hal-01555242v1
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. Mugfordet al. Genome Biology, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩ Article dans une revue 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,Mathieu Gautier,Magali Esquibet,Fabrice Legeai,Anthony Bretaudeauet al. Molecular Ecology, 2017, 26 (18), pp.4700-4711. ⟨10.1111/mec.14240⟩ Article dans une revue hal-01605681v2
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 Auryet al. Scientific Reports, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩ Article dans une revue hal-01633879v1
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. Mugfordet al. Genome Biology, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩ Article dans une revue hal-01588181v1
Tools and data services registry: a community effort to document bioinformatics resources. Jon Ison,Kristoffer Rapacki,Hervé Ménager,Matúš Kalaš,Emil Rydzaet al. Nucleic Acids Research, 2016, 44 (D1), pp.D38-47. ⟨10.1093/nar/gkv1116⟩ Article dans une revue 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 Hudaverdianet al. BMC Genomics, 2016, 17 (1), pp.219. ⟨10.1186/s12864-016-2530-8⟩ Article dans une revue 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⟩ Article dans une revue hal-01240449v1
Establishment and analysis of a reference transcriptome for Spodoptera frugiperda Fabrice Legeai,Sylvie Gimenez,Bernard Duvic,Jean-Michel Escoubas,Anne-Sophie Gosselin Grenetet al. BMC Genomics, 2014, 15 (1), pp.704. ⟨10.1186/1471-2164-15-704⟩ Article dans une revue hal-01058982v1
PHYMYCO-DB: A Curated Database for Analyses of Fungal Diversity and Evolution Stéphane Mahé,Marie Duhamel,Thomas Le Calvez,Laëtitia Guillot,Ludmila Sarbuet al. PLoS ONE, 2012, 7 (9), pp.e43117. ⟨10.1371/journal.pone.0043117⟩ Article dans une revue hal-00756250v1
The duplicated genes database: identification and functional annotation of co-localised duplicated genes across genomes Marion Ouedraogo,Charles Bettembourg,Anthony Bretaudeau,Olivier Sallou,Christian Diotet al. PLoS ONE, 2012, 7 (11), pp.e50653. ⟨10.1371/journal.pone.0050653⟩ Article dans une revue hal-00841104v1
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⟩ Article dans une revue hal-00728279v1
CyanoLyase: a database of phycobilin lyase sequences, motifs and functions Anthony Bretaudeau,François Coste,Florian Humily,Laurence Garczarek,Gildas Le Corguilléet al. Nucleic Acids Research, 2012, pp.6. ⟨10.1093/nar/gks1091⟩ Article dans une revue hal-01094087v1
AnnotQTL: a new tool to gather functional and comparative information on a genomic region Frédéric Lecerc,Anthony Bretaudeau,Olivier Sallou,Colette Désert,Yuna Blumet al. Nucleic Acids Research, 2011, 39 (Suppl 2), open access. ⟨10.1093/nar/gkr361⟩ Article dans une revue hal-00597398v1

Communication dans un congrès (22)

Misconceptions about Galaxy debunked by the (French) Galaxy Community Romane Libouban,Eva Mercier,Thomas Chaussepied,Bérénice Batut,Anthony Bretaudeauet al. JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024, TOULOUSE, France. pp.1-28 Communication dans un congrès hal-04694551v1
Galaxy France: an example of a national UseGalaxy server Clea Siguret,Thomas Chaussepied,Romane Libouban,Eva Mercier,Julien Seileret al. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. pp.1-15, ⟨10.7490/f1000research.1119767.1⟩ Communication dans un congrès hal-04644627v1
Plam weevil odorant receptors: Omics, functional characterization, and evolution Emmanuelle Jacquin-Joly,Stéphanie Robin,Fabrice Legeai,Anthony Bretaudeau,Rémi Capoduroet al. Entomology Society of America annual meeting, Entomology 2023, ESA, Nov 2023, National Harbor (Maryland), United States Communication dans un congrès hal-05567453v1
The red palm weevil chemical ecology in the OMICS and post-genomic eras Emmanuelle Jacquin-Joly,Stéphanie Robin,Fabrice Legeai,Anthony Bretaudeau,Rémi Capoduroet al. Annual meeting of the International Society of Chemical Ecology, International Society of Chemical Ecology, Jul 2023, Bangalore, India Communication dans un congrès hal-05567992v1
The red palm weevil Rhynchophorus ferrugineus in the OMICS and post-genomic eras Stéphanie Robin,Fabrice Legeai,Anthony Bretaudeau,Carole Vincent-Monégat,Nicolas Parisotet al. Seventh International Date Palm Conference, Khalifa, Mar 2022, Abu Dabi, United Arab Emirates Communication dans un congrès hal-05567958v1
Red palm weevil omics bring insights into its chemical ecology and the evolution of Coleoptera pheromone receptors Nicolas Montagné,Rémi Capoduro,Arthur Comte,Stéphanie Robin,Fabrice Legeaiet al. 17th European Symposium for insect taste and olfaction, May 2022, Kristianstadt, Sweden Communication dans un congrès hal-05567471v1
AskoR, A R Package for Easy RNASeq Data Analysis Susete Alves Carvalho,Kévin Gazengel,Anthony Bretaudeau,Stéphanie Robin,Stéphanie Davalet al. IECE 2021 - 1st International Electronic Conference on Entomology, Jul 2021, Virtual, France. pp.1-8, ⟨10.3390/IECE-10646⟩ Communication dans un congrès hal-03347665v1
Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux,Arnaud Belcour,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, Sep 2021, Bordeaux, France. pp.1-27 Communication dans un congrès hal-03440212v1
Metabolic complementarity applied to the screening of microbiota and the identification of key species Clémence Frioux,Arnaud Belcour,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. MPA 2021 - 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. pp.1-27 Communication dans un congrès 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 Hildebrandet al. JOBIM 2021 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2021, Paris, France Communication dans un congrès hal-03440232v1
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 Communication dans un congrès hal-02401750v1
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 Communication dans un congrès hal-01576870v1
AskOmics, a web tool to integrate and query biological data using semantic web technologies Xavier Garnier,Anthony Bretaudeau,Olivier Filangi,Fabrice Legeai,Anne Siegelet al. JOBIM 2017 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2017, Lille, France. pp.1 Communication dans un congrès hal-01577425v1
BIPAA/Askomics, a new and easy approach for querying genomics and epigenomics elements in interaction Fabrice Legeai,Charles Bettembourg,Anthony Bretaudeau,Yvanne Chaussin,Olivier Dameronet al. XXVth International Congress of Entomology 2016, Sep 2016, Orlando, Florida, United States Communication dans un congrès hal-01391080v1
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 Legeaiet al. Joint Meeting of the Society of Nematologists and the Organization of Nematologists of Tropical America (ONTA), 2016, Jul 2016, Montreal, Canada. 387 p Communication dans un congrès hal-01602955v1
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 Communication dans un congrès 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 Communication dans un congrès hal-01102421v1
A study of phylloxera transcriptomes, comparing root and leaf feeding morphs Claude Rispe,Daciana Papura,Fabrice Legeai,Julie Jaquiéry,Anthony Bretaudeauet al. 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 Communication dans un congrès hal-01208647v1
AphidAtlas : avancées récentes Anthony Bretaudeau,Olivier Dameron,Fabrice Legeai,Yvan Rahbé BAPOA 2013 MOP, Oct 2013, Montpellier, France Communication dans un congrès hal-00913155v1
Towards a Life Sciences Virtual Research Environment Yvan Le Bras,Aurélien Roult,Cyril Monjoeaud,Bahin Mathieu,Olivier Quenezet al. JOBIM 2013 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2013, Toulouse, France Communication dans un congrès hal-01102438v1
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 Communication dans un congrès 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 Blumet al. 15th QTLMAS, Institut National de Recherche Agronomique (INRA). UMR Génétique Animale (0598)., May 2011, Rennes, France Communication dans un congrès hal-02746678v1

Poster de conférence (26)

MLOps best practices for bioinformatics Pauline Le Corre,Anthony Bretaudeau,Yann Le Cunff JOBIM - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux (France), France. pp.1-1, 2025, ⟨10.1093/bioinformatics/btad6[2]⟩ Poster de conférence hal-05168225v1
BYTE-Sea: the digital infrastructure of ATLASea, the French marine genome sequencing programme Annie Lebreton,Loraine Brillet-Guéguen,Karine Massau,Alexandre Nicaise,Arthur Le Barset al. JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. 2025 Poster de conférence hal-05135947v1
The Environmental Cost of Bioinformatics at GenOuest Rémy Siminel,Stéphanie Robin,Erell Le Deun,Matéo Boudet,Anthony Bretaudeau JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.1-1, 2025 Poster de conférence hal-05174309v1
Exploring the Richness of the French Galaxy Ecosystem Bérénice Batut,Gildas Le Corguillé,Anthony Bretaudeau JOBIM 2025 - Journées Ouvertes en bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France. 2025 Poster de conférence hal-05132824v1
Genome Annotation tooling in Galaxy: contributions of the EuroScienceGateway project Romane Libouban,Anthony Bretaudeau JOBIM 2025 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2025, Bordeaux, France. pp.1-1, 2025 Poster de conférence hal-05144157v1
Breaking myths: The reality of Galaxy's capabilities and impact Gildas Le Corguillé,Anthony Bretaudeau,Björn Grüning,Wendi Bacon,Bérénice Batut JOBIM 2025 - Journées Ouvertes en bioinformatique et de la biostatistique francophone, Jul 2025, Bordeaux, France. 2025 Poster de conférence hal-05132787v1
Exploring the richness of the French Galaxy Ecosystem Bérénice Batut,Gildas Le Corguillé,Yvan Le Bras,Loraine Brillet-Guéguen,Fabien Mareuilet al. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. , pp.1-1, 2024, ⟨10.7490/f1000research.1119765.1⟩ Poster de conférence 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 Guévelet al. EUROTOX 2024 - 58th Congress of the European Societies of Toxicology, Sep 2024, Copenhagen, Denmark. pp.S159, 2024, ⟨10.1016/j.toxlet.2024.07.402⟩ Poster de conférence hal-04690377v1
Services deployed on the IFB National Network of Computing Resources (NNCR) David Benaben,Christophe Blanchet,Matéo Boudet,Guillaume Brysbaert,Anthony Bretaudeauet al. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques, Jun 2024, Toulouse, France. , 2024 Poster de conférence hal-04618059v1
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 Poster de conférence hal-04694519v1
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 Poster de conférence hal-04176786v1
AskoR, an R package for easy RNA-Seq data analysis. Susete Alves Carvalho,Kévin Gazengel,Anthony Bretaudeau,Stéphanie Robin,Stéphanie Davalet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (Jobim), Jun 2023, Tours, France. pp.263, 2018, JOBIM2023. ⟨10.1080/02664763.2018.1454894⟩ Poster de conférence hal-04720296v1
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 Robinet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (Jobim), Jul 2022, Rennes, France Poster de conférence hal-04720279v1
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 Poster de conférence hal-04176792v1
Assessment of metabolic complementarity in large-scale microbiotas for the identification of key species Clémence Frioux,Arnaud Belcour,Méziane Aite,Anthony Bretaudeau,Falk Hildebrandet al. IHMC 2021 - 8th International Human Microbiome Consortium Congress, Jun 2021, Barcelone, Spain. pp.1 Poster de conférence 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 Hildebrandet al. JOBIM 2020 - Journées Ouvertes de Biologie, Informatique et Mathématique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩ Poster de conférence 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 Burbanet al. 10. International Workshop on the Molecular Biology and Genetics of the Lepidoptera, Aug 2019, Crête, Greece. Poster de conférence 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 Poster de conférence hal-04176797v1
Integration and query of biological datasets with Semantic Web technologies: AskOmics Aurélie Evrard,Charles Bettembourg,Mélanie Jubault,Olivier Dameron,Olivier Filangiet al. Journées Ouvertes Biologie, Informatique et Mathématiques (JOBIM 2016), Jun 2016, Lyon, France Poster de conférence hal-01391087v1
Comparative genomic analysis of Clubroot resistance in the Brassicaceae family Aurélie Evrard,Charles Bettembourg,Olivier Dameron,Olivier Filangi,Anthony Bretaudeauet al. Brassica2016, Oct 2016, Melbourne, Australia. Poster de conférence hal-01391707v1
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 Poster de conférence 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'Alençonet al. Arthropod Genomics 2015, Jun 2015, Manhattan (Kansas), United States. 2015 Poster de conférence hal-01240443v1
e-Science in France, a Life science Western story Yvan Le Bras,Aurélien Roult,Cyril Monjoeaud,Bahin Mathieu,Olivier Quenezet al. Galaxy Community Conference (GCC2014), Jun 2014, Baltimore, United States Poster de conférence hal-01102432v1
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 Poster de conférence hal-01092959v1
Dr Motifs: a web resource for pattern matching and discovery Anthony Bretaudeau,Olivier Collin JOBIM 2012, Jul 2012, Rennes, France Poster de conférence 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 Blumet al. 12. Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011, JOBIM 2011 Poster de conférence hal-02746728v1

Chapitre d'ouvrage (3)

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 Chapitre d'ouvrage hal-03319003v1
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 Chapitre d'ouvrage hal-03319006v1
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 Chapitre d'ouvrage hal-03319007v1

Autre publication scientifique (2)

SfruDB database :Spodoptera frugiperda genome assembly, Version 5 Ki Woong Nam,Anthony Bretaudeau,Stéphanie Robin 2018 Autre publication scientifique hal-02154692v1
LepidoDB Information system Emmanuelle d'Alençon,Fabrice Legeai,Anthony Bretaudeau,Stéphanie Robin,Nicolas Negreet al. 2017 Autre publication scientifique hal-02154691v1

Pré-publication, Document de travail (11)

Ten Common Misconceptions About Galaxy (and Why They Are Wrong!) Wendi Anne Bacon,Sanjay Kumar Srikakulam,Bérénice Batut,Paul Zierep,Anthony Bretaudeauet al. 2025 Pré-publication, Document de travail hal-05249780v1
Identification of a viral gene essential for the genome replication of a domesticated endogenous virus in ichneumonid parasitoid wasps Ange Lorenzi,Fabrice Legeai,Véronique Jouan,Pierre-Alain Girard,Michael R Strandet al. 2024 Pré-publication, Document de travail hal-04558930v1
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 Legeaiet al. 2021 Pré-publication, Document de travail hal-04706490v1
Chromosomal resolution reveals symbiotic virus colonization of parasitic wasp genomes Jérémy Gauthier,Hélène Boulain,Joke J.F.A. van Vugt,Lyam Baudry,Emma Persynet al. 2020 Pré-publication, Document de travail hal-03090838v1
Functional insights from the GC-poor genomes of two aphid parasitoids, &lt;em&gt;Aphidius ervi&lt;/em&gt; and &lt;em&gt;Lysiphlebus fabarum&lt;/em&gt; Alice B. Dennis,Gabriel I. Ballesteros,Stéphanie Robin,Lukas Schrader,Jens Bastet al. 2019 Pré-publication, Document de travail (preprint/prepublication) hal-02788571v1
Adaptation by copy number variation increases insecticide resistance in fall armyworms Ki Woong Nam,Sylvie Gimenez,Frederique Hilliou,Carlos A Blanco,Sabine Hännigeret al. 2019 Pré-publication, Document de travail 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. Dikowet al. 2019 Pré-publication, Document de travail (preprint/prepublication) hal-02788577v1
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 Nègreet al. 2018 Pré-publication, Document de travail (preprint/prepublication) hal-02788771v1
Community-Driven Data Analysis Training for Biology Bérénice Batut,Saskia Hiltemann,Andrea Bagnacani,Dannon Baker,Vivek Bhardwajet al. 2018 Pré-publication, Document de travail pasteur-02613129v1
Bioconda: A sustainable and comprehensive software distribution for the life sciences Björn Grüning,Ryan Dale,Andreas Sjödin,Brad Chapman,Jillian Roweet al. 2017 Pré-publication, Document de travail hal-04863967v1
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 Mugfordet al. 2020 Pré-publication, Document de travail (preprint/prepublication) hal-02936181v1