Publications – HAL

HAL is an open archive where authors can deposit scholarly documents from all academic fields. Here is a list of GenOuest references extracted from HAL.


97 documents

Journal articles47 document

  • Ugo Szachnowski, Emmanuelle Becker, Igor Stuparevic, Maxime Wery, Olivier Sallou, et al.. Pervasive formation of double-stranded RNAs by overlapping sense/antisense transcripts in budding yeast mitosis and meiosis. RNA, 2025, pp.rna.080290.124. ⟨10.1261/rna.080290.124⟩. ⟨hal-04935733⟩
  • Yael Tirlet, Matéo Boudet, Emmanuelle Becker, Fabrice Legeai, Olivier Dameron. Generic and queryable data integration schema for transcriptomics and epigenomics studies. Computational and Structural Biotechnology Journal, 2024, 23, pp.4232-4241. ⟨10.1016/j.csbj.2024.11.022⟩. ⟨hal-04818860⟩
  • Linelle Ann L Abueg, Enis Afgan, Olivier Allart, Ahmed Awan, Wendi Bacon, et al.. The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Research, 2024, 52 (W1), pp.W83-W94. ⟨10.1093/nar/gkae410⟩. ⟨hal-04645009⟩
  • Cyril Falentin, Houria Hadj-Arab, Fella Aissiou, Claudia Bartoli, Giuseppe Bazan, et al.. Combined cytogenetic and molecular methods for taxonomic verification and description of Brassica populations deriving from different origins. Genetic Resources, 2024, 5 (9), pp.61-71. ⟨10.46265/genresj.ryaj6068⟩. ⟨hal-04608007⟩
  • Ugo Szachnowski, Oliver Sallou, Matéo Boudet, Anthony Bretaudeau, Maxime Wéry, et al.. The 5-Fluorouracil RNA Expression Viewer (5-FUR) Facilitates Interpreting the Effects of Drug Treatment and RRP6 Deletion on the Transcriptional Landscape in Yeast. Yeast, 2024, 41 (10), pp.629-640. ⟨10.1002/yea.3982⟩. ⟨hal-04718291⟩
  • Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, et al.. Galaxy Training: A powerful framework for teaching!. PLoS Computational Biology, 2023, 19 (1), pp.e1010752. ⟨10.1371/journal.pcbi.1010752⟩. ⟨hal-04069041⟩
  • Sudeeptha Yainna, Wee Tek Tay, Karine Durand, Estelle Fiteni, Frédérique Hilliou, et al.. The evolutionary process of invasion in the fall armyworm (Spodoptera frugiperda). Scientific Reports, 2022, 12, pp.21063. ⟨10.1038/s41598-022-25529-z⟩. ⟨hal-03926301⟩
  • Estelle Fiteni, Karine Durand, Sylvie Gimenez, Robert L. Meagher Jr., Robert L Meagher Jr., et al.. Host-plant adaptation as a driver of incipient speciation in the fall armyworm ( Spodoptera frugiperda ). BMC Ecology and Evolution, 2022, 22, pp.133. ⟨10.1186/s12862-022-02090-x⟩. ⟨hal-03813221⟩
  • 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, 2022, 12 (8), pp.jkac131. ⟨10.1093/g3journal/jkac131⟩. ⟨hal-03713321⟩
  • Julie Jaquiéry, Jean-Christophe Simon, Stéphanie Robin, Gautier Richard, Jean Peccoud, et al.. Masculinization of the X-chromosome in aphid soma and gonads. Peer Community Journal, 2022, 2, pp.e53. ⟨10.24072/pcjournal.166⟩. ⟨hal-03999192⟩
  • Susete Alves Carvalho, Kévin Gazengel, Anthony Bretaudeau, Stéphanie Robin, Stéphanie Daval, et al.. AskoR, A R Package for Easy RNASeq Data Analysis. Proceedings of The 1st International Electronic Conference on Entomology, 2021, ⟨10.3390/iece-10646⟩. ⟨hal-04717074⟩
  • Arnaud Belcour, Clémence Frioux, Méziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife, 2020, 9, ⟨10.7554/eLife.61968⟩. ⟨hal-02395024v2⟩
  • Sylvie Gimenez, Heba Abdelgaffar, Gaëlle Le Goff, Frédérique Hilliou, Carlos Blanco, et al.. Adaptation by copy number variation increases insecticide resistance in the fall armyworm. Communications Biology, 2020, 3 (1), pp.1-10. ⟨10.1038/s42003-020-01382-6⟩. ⟨hal-03065279⟩
  • Rosa Fernández, Marina Marcet-Houben, Fabrice Legeai, Gautier Richard, Stéphanie Robin, et al.. Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. Molecular Biology and Evolution, 2020, 37 (9), pp.2601-2615. ⟨10.1093/molbev/msaa110⟩. ⟨hal-03065353⟩
  • Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, Hervé Ménager, et al.. The bio.tools registry of software tools and data resources for the life sciences. Genome Biology, 2019, 20 (164), pp.1-4. ⟨10.1186/s13059-019-1772-6⟩. ⟨hal-02408472⟩
  • Stéphanie Robin, Marc Ravallec, Marie Frayssinet, James Whitfield, Véronique Jouan, et al.. Evidence for an ichnovirus machinery in parasitoids of coleopteran larvae. Virus Research, 2019, 263, pp.189-206. ⟨10.1016/j.virusres.2019.02.001⟩. ⟨hal-02059774⟩
  • Thomas Darde, Estelle Lecluze, Aurélie Lardenois, Isabelle Stévant, Nathan Alary, et al.. The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community. Bioinformatics, 2019, 35 (17), pp.3133-3139. ⟨10.1093/bioinformatics/btz047⟩. ⟨hal-02015545⟩
  • Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, et al.. Community-Driven Data Analysis Training for Biology. Cell Systems, 2018, 6 (6), pp.752-758.e1. ⟨10.1016/j.cels.2018.05.012⟩. ⟨hal-04863943⟩
  • 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, 2018, 17, pp.781-787. ⟨10.1016/j.dib.2018.01.073⟩. ⟨hal-02627842⟩
  • Thomas A. Darde, Pierre Gaudriault, Rémi Béranger, Clement Lancien, Annaelle Caillarec-Joly, et al.. TOXsIgN: a cross-species repository for toxicogenomic signatures. Bioinformatics, 2018, 34 (12), pp.2116-2122. ⟨10.1093/bioinformatics/bty040⟩. ⟨hal-01863047⟩
  • 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, 2017, 18 (1), pp.27. ⟨10.1186/s13059-016-1145-3⟩. ⟨hal-01500475⟩
  • 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, 2017, 7 (1), pp.1-12. ⟨10.1038/s41598-017-10461-4⟩. ⟨hal-01633879⟩
  • 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, 2017, 18 (1), pp.63. ⟨10.1186/s13059-017-1202-6⟩. ⟨hal-01588181⟩
  • Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, et al.. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩. ⟨hal-01516082⟩
  • 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, 2017, 26 (18), pp.4700-4711. ⟨10.1111/mec.14240⟩. ⟨hal-01605681v2⟩
  • Yvan Le Bras, Olivier Collin, Cyril Monjeaud, Vincent Lacroix, Eric Rivals, et al.. Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads. GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩. ⟨hal-01280238⟩
  • Olivier Sallou, Paula D. Duek, Thomas A. Darde, Olivier Collin, Lydie Lane, et al.. PepPSy: a web server to prioritize gene products in experimental and biocuration workflows. Database - The journal of Biological Databases and Curation, 2016, 2016, pp.baw070. ⟨10.1093/database/baw070⟩. ⟨hal-01342472⟩
  • François Moreews, Olivier Sallou, Hervé Ménager, Yvan Le Bras, Cyril Monjeaud, et al.. BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Research, 2015, ⟨10.12688/f1000research.7536.1⟩. ⟨hal-01243520⟩
  • Mathieu Rousseau-Gueutin, Sidonie Bellot, Guillaume E. Martin, Julien Boutte, Houda Chelaifa, et al.. The chloroplast genome of the hexaploid Spartina maritima (Poaceae, Chloridoideae): Comparative analyses and molecular dating. Molecular Phylogenetics and Evolution, 2015, 93, pp.5-16. ⟨10.1016/j.ympev.2015.06.013⟩. ⟨hal-01187129⟩
  • Frédéric Boyer, Céline Mercier, Aurélie Bonin, Yvan Le Bras, Pierre Taberlet, et al.. OBITools: a Unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources, 2015, pp.10.1111/1755-0998.12428. ⟨10.1111/1755-0998.12428⟩. ⟨hal-01183582⟩
  • Thomas A Darde, Olivier Sallou, Emmanuelle Becker, Bertrand Evrard, Cyril Monjoeaud, et al.. The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.. Nucleic Acids Research, 2015, 43 (W1), pp.8. ⟨10.1093/nar/gkv345⟩. ⟨hal-01146120⟩
  • Mohamed Sassi, Yoann Augagneur, Tony Mauro, Lorraine Ivain, Svetlana Chabelskaya, et al.. SRD: a Staphylococcus regulatory RNA database.. RNA, 2015, RNA, 21 (5), pp.1005-1017. ⟨10.1261/rna.049346.114⟩. ⟨inserm-01136506⟩
  • Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin. BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience, 2015, 4, pp.22. ⟨10.1186/s13742-015-0063-8⟩. ⟨hal-01240449⟩
  • Damian Smedley, Syed Haider, Steffen Durinck, Luca Pandini, Paolo Provero, et al.. The BioMart community portal: an innovative alternative to large, centralized data repositories. Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩. ⟨hal-01146849⟩
  • Pascaline Dumas, Fabrice Legeai, Claire Lemaitre, Erwan Scaon, Marion Orsucci, et al.. Spodoptera frugiperda (Lepidoptera: Noctuidae) host-plant variants: two host strains or two distinct species?. Genetica, 2015, 143 (3), pp.305-316. ⟨10.1007/s10709-015-9829-2⟩. ⟨hal-01208780v2⟩
  • Laëtitia Le Texier, Justine Durand, Amélie Lavault, Philippe Hulin, Olivier Collin, et al.. LIME, a new molecule associated with cytoskeleton is involved in stimulatory properties of dendritic cells. PLoS ONE, 2014, 9 (4), pp.10. ⟨10.1371/journal.pone.0093894⟩. ⟨hal-01183591⟩
  • 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, 2014, 15 (1), pp.704. ⟨10.1186/1471-2164-15-704⟩. ⟨hal-01058982⟩
  • Frédéric Chalmel, Aurélie Lardenois, Bertrand Evrard, Antoine D. Rolland, Olivier Sallou, et al.. High-resolution profiling of novel transcribed regions during rat spermatogenesis. Biology of Reproduction, 2014, 91 (1), pp.5. ⟨10.1095/biolreprod.114.118166⟩. ⟨hal-01063924⟩
  • Denis Habauzit, Catherine Le Quément, Maxim Zhadobov, Catherine Martin, Marc Aubry, et al.. Transcriptome analysis reveals the contribution of thermal and the specific effects in cellular response to millimeter wave exposure.. PLoS ONE, 2013, 9 (10), pp.e109435. ⟨10.1371/journal.pone.0109435⟩. ⟨hal-01118066⟩
  • Elsa Quillery, Olivier Quenez, Pierre Peterlongo, Olivier Plantard. Development of genomic resources for the tick Ixodes ricinus: isolation and characterization of Single Nucleotide Polymorphisms. Molecular Ecology Resources, 2013, 14 (2), pp.393-400. ⟨10.1111/1755-0998.12179⟩. ⟨hal-00880072⟩
  • Thomas Obadia, Olivier Sallou, Marion Ouedraogo, Grégory Guernec, Frédéric Lecerf. The GAG database: A new resource to gather genomic annotation cross-references. Gene, 2013, 527 (2), pp.503-509. ⟨10.1016/j.gene.2013.06.063⟩. ⟨hal-01207750⟩
  • 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, 2012, pp.6. ⟨10.1093/nar/gks1091⟩. ⟨hal-01094087⟩
  • Olivier Sallou, Anthony Bretaudeau, Aurelien Roult. Seqcrawler: biological data indexing and browsing platform.. BMC Bioinformatics, 2012, 13 (1), pp.175. ⟨10.1186/1471-2105-13-175⟩. ⟨hal-00728279⟩
  • Ramona Britto, Olivier Sallou, Olivier Collin, Grégoire Michaux, Michael Primig, et al.. GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.. Nucleic Acids Research, 2012, 40 (W1), pp.W458-W465. ⟨10.1093/nar/gks380⟩. ⟨inserm-00696905⟩
  • 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, 2012, 7 (11), pp.e50653. ⟨10.1371/journal.pone.0050653⟩. ⟨hal-00841104⟩
  • Thomas Derrien, Rory Johnson, Giovanni Bussotti, Andrea Tanzer, Sarah Djebali, et al.. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research, 2012, 22, pp.1775-1789. ⟨10.1101/gr.132159.111⟩. ⟨hal-01205054⟩
  • Alain van Wormhoudt, Béatrice Gaume, Yvan Le Bras, Valérie Roussel, Sylvain Huchette. Two different and functional nuclear rDNA genes in the abalone Haliotis tuberculata : tissue differential expression. Genetica, 2011, http://link.springer.com/article/10.1007%2Fs10709-011-9623-8. ⟨10.1007/s10709-011-9623-8⟩. ⟨hal-01183596⟩

Conference papers19 document

  • Romane Libouban, Eva Mercier, Thomas Chaussepied, Bérénice Batut, Anthony Bretaudeau, et al.. Misconceptions about Galaxy debunked by the (French) Galaxy Community. JOBIM 2024 - Journées Ouvertes Biologie Informatique Mathématiques, Jun 2024, TOULOUSE, France. pp.1-28. ⟨hal-04694551⟩
  • Clea Siguret, Thomas Chaussepied, Romane Libouban, Eva Mercier, Julien Seiler, et al.. Galaxy France: an example of a national UseGalaxy server. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. pp.1-15, ⟨10.7490/f1000research.1119767.1⟩. ⟨hal-04644627⟩
  • Sylvain Grellet, Isabelle Braud, Fanny Arnaud, Kenneth Maussang, Anne Laurent, et al.. OneWater FAIR Data Platform : setting up a national FAIR water data platform and community. TERENO OZCAR 2023 - 2ème conférence internationale TERENO OZCAR, TERENO and OZCAR networks, Sep 2023, Bonn, Germany. pp.1-23. ⟨hal-04233630v3⟩
  • Olivier Dameron, Yael Tirlet, Matéo Boudet, Fabrice Legeai. Intégration de données de phénotypiques, environnementales et de biodiversité à l'aide des technologies du Web Sémantique. SYSINFO-INRAe 2022 - Journées INRAE systèmes d'information pour les données agro-environnementales, Nov 2022, Clermont-Ferrand, France. ⟨hal-03893738⟩
  • 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⟩
  • 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⟩
  • 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⟩
  • Stéphanie Robin, Fabrice Legeai. Spodoptera genomes in the BIPAA information system. International Conference on Management of Destructive Agricultural Pests Spodoptera (Noctuidae), Nov 2017, Chongqing, China. ⟨hal-04176810⟩
  • 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⟩
  • François Moreews, Olivier Sallou, Olivier Collin. An application suite based on the IFB Container as a Service platform. ECCB 2016 (Elixir Talks) , ISCB, Sep 2016, Den Haag, Netherlands. ⟨hal-01394295⟩
  • François Moreews, Olivier Sallou, Yvan Le Bras, Grosjean Marie, Cyril Monjeaud, et al.. A curated Domain centric shared Docker registry linked to the Galaxy toolshed. Galaxy Community Conference 2015, Jul 2015, Norwich, United Kingdom. ⟨hal-01160514⟩
  • 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⟩
  • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling. PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Lukas KALL, Aug 2014, Stockholm, Sweden. pp.34-47, ⟨10.1007/978-3-319-09192-1_4⟩. ⟨hal-01059506⟩
  • François Moreews, Yvan Le Bras, Olivier Dameron, Cyril Monjeaud, Olivier Collin. Integrating GALAXY workflows in a metadata management environment. Galaxy Community Conference, Jul 2014, Baltimore, United States. ⟨hal-01093058⟩
  • 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⟩
  • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Recherche d'instances de motifs expressifs avec Logol. Application à la modélisation d'événements de frameshift -1. JOBIM 2012- 13e Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2012, Rennes, France. pp.5-14. ⟨hal-00726791⟩
  • Benoît Calmes, Philippe Simoneau, Erwan Scaon, Nelly Bataille-Simoneau, Thomas Guillemette. Rôle des Glutathion-S-transférases fongiques dans la protection contre les métabolites de défenses des Brassicacées. 9èmes Rencontres de Phytopathologie - Mycologie, 2012, Aussois, France. ⟨hal-03281872⟩

Poster communications24 document

  • T. Darde, I. Kugathas, Matéo Boudet, Anthony Bretaudeau, R. Le Guével, et al.. P06-18 Enhancing prediction and priorisation of adverse effects: TOXsIgN as a comprehensive resource for toxicogenomics. EUROTOX 2024 - 58th Congress of the European Societies of Toxicology, Sep 2024, Copenhagen, Denmark. pp.S159, 2024, ⟨10.1016/j.toxlet.2024.07.402⟩. ⟨hal-04690377⟩
  • Konogan Bourhy, Laurent Bouri, Christophe Bruley, Olivier Collin, Frédéric De Lamotte, et al.. Orchestrating data flows throughout their whole life cycle. JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques, Jun 2024, Toulouse, France. , 2024. ⟨hal-04618277⟩
  • Guillaume Laisney, David Benaben, Christophe Duperier, Matéo Boudet, Franck Giacomoni, et al.. Metabolomic Semantic Datalake : A Scalable Approach to Managing Metabolomics Semantic Resources. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique, et Mathématiques, Jun 2024, Toulouse, France. pp.1-1, 2024. ⟨hal-04655538⟩
  • David Benaben, Christophe Blanchet, Matéo Boudet, Guillaume Brysbaert, Anthony Bretaudeau, et al.. Services deployed on the IFB National Network of Computing Resources (NNCR). JOBIM 2024 - Journées ouvertes en biologie, informatique, et mathématiques, Jun 2024, Toulouse, France. , 2024. ⟨hal-04618059⟩
  • Bérénice Batut, Gildas Le Corguillé, Yvan Le Bras, Loraine Brillet-Guéguen, Fabien Mareuil, et al.. Exploring the richness of the French Galaxy Ecosystem. GCC 2024 - Galaxy Community Conference, Jun 2024, Brno, Czech Republic. , pp.1-1, 2024, ⟨10.7490/f1000research.1119765.1⟩. ⟨hal-04644779⟩
  • Eva Mercier, Romane Libouban, Thomas Chaussepied, Anthony Bretaudeau. Building a Distributed Computing Network for Galaxy, Application to Genome Annotation. JOBIM 2024 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2024, Toulouse, France. 2024. ⟨hal-04694519⟩
  • Stéphanie Robin, Fabrice Legeai, Anthony Bretaudeau. 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. ⟨hal-04176786⟩
  • Susete Alves Carvalho, Kévin Gazengel, Anthony Bretaudeau, Stéphanie Robin, Stéphanie Daval, et al.. 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⟩. ⟨hal-04720296⟩
  • Stéphanie Robin, Anthony Bretaudeau, Fabrice Legeai. BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.. The 11th international workshop on Molecular Biology and Genetics of the Lepidoptera, Aug 2022, Kolympari, Greece. ⟨hal-04176792⟩
  • Susete Alves Carvalho, Kévin Gazengel, Masanelli Sylvin, Anthony Bretaudeau, Stéphanie Robin, et al.. 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. ⟨hal-04720279⟩
  • 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⟩
  • Thomas Alain Darde, Estelle Lecluze, Nathan Alary, Lardenois Aurélie, Olivier Collin, et al.. The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community. European Congress of Andrology, Oct 2018, Budapest, Hungary. ⟨hal-02445089⟩
  • Stéphanie Robin, Anthony Bretaudeau, Fabrice Legeai. BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM), Jul 2018, Marseille (FR), France. ⟨hal-04176797⟩
  • Thomas Alain Darde, Pierre Gaudriault, Rémi Béranger, Lancien Clément, Annaelle Caillarec-Joly, et al.. TOXsIgN – un espace de dépôt publique dédié aux signatures toxicologiques. 10 ans PNREST, ANSES, Nov 2016, Paris, France. ⟨hal-02445079⟩
  • Thomas Alain Darde, Estelle Lecluze, Becker Emmanuelle, Victoria Potdevin, Olivier Collin, et al.. ChemPSy : Identification, classification et priorisation de nouveaux perturbateurs endocriniens par intégration massive de données de toxicogénomiques. 10 ans PNREST, ANSES, Nov 2016, Paris, France. . ⟨hal-02445078⟩
  • 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, 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⟩
  • Olivier Sallou, Cyril Monjeaud. GO-Docker: Batch scheduling with containers. IEEE Cluster 2015, Sep 2015, CHICAGO, United States. , ⟨10.1109/CLUSTER.2015.89⟩. ⟨hal-01213323⟩
  • Thomas Alain Darde, François Moreews, Yvan Le Bras, Cyril Monjeaud, Frédéric Chalmel. Yet another Galaxy Genome viewer. GCC, Jul 2015, Norwich, United Kingdom. ⟨hal-02445072⟩
  • 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⟩
  • Thomas Alain Darde, Olivier Sallou, Becker Emmanuelle, Bertrand Evrard, Cyril Monjeaud, et al.. The ReproGenomics Viewer: An integrative cross-species toolbox for the reproductive science community. ReproScience, Apr 2015, Rennes, France. ⟨hal-02445070⟩
  • 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⟩

Books1 document


Preprints, Working Papers6 document

  • Bérénice Batut, Matthias Bernt, Mina Hojat Ansari, Matúš Kalaš, Paul Klemm, et al.. How to improve the annotation of Galaxy resources? Outcomes of an online hackathon for improving the annotation of Galaxy resources for microbial data resources. 2024. ⟨hal-04626280⟩
  • Cyril Falentin, Houria Hadj-Arab, Fella Aissiou, Claudia Bartoli, Giuseppe Bazan, et al.. Warnings/Cautions when collecting Brassica diversity along a large climatic gradient. 2024. ⟨hal-04701870⟩
  • Saskia Hiltemann, Helena Rasche, Simon Gladman, Hans-Rudolf Hotz, Delphine Larivière, et al.. Galaxy Training: A Powerful Framework for Teaching!. 2022. ⟨hal-04863959⟩
  • 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. 2021. ⟨hal-04706490⟩
  • Bérénice Batut, Saskia Hiltemann, Andrea Bagnacani, Dannon Baker, Vivek Bhardwaj, et al.. Community-Driven Data Analysis Training for Biology. 2018. ⟨pasteur-02613129⟩
  • Björn Grüning, Ryan Dale, Andreas Sjödin, Brad Chapman, Jillian Rowe, et al.. Bioconda: A sustainable and comprehensive software distribution for the life sciences. 2017. ⟨hal-04863967⟩

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