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.



64 documents

Journal articles

  • Arnaud Belcour, ClĂ©mence Frioux, MĂ©ziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metage2Metabo, microbiota-scale metabolic complementarity for the identification of key species. eLife, eLife Sciences Publication, 2020, 9, ⟨10.1101/803056⟩. ⟨hal-02395024v2⟩
  • Sylvie Gimenez, Heba Abdelgaffar, Gaelle Le Goff, FrĂ©dĂ©rique 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⟩
  • Rosa Fernández, Marina Marcet-Houben, Fabrice Legeai, Gautier Richard, StĂ©phanie Robin, et al.. Selection following Gene Duplication Shapes Recent Genome Evolution in the Pea Aphid Acyrthosiphon pisum. Molecular Biology and Evolution, Oxford University Press (OUP), 2020, 37 (9), pp.2601-2615. ⟨10.1093/molbev/msaa110⟩. ⟨hal-03065353⟩
  • Jon Ison, Hans Ienasescu, Piotr Chmura, Emil Rydza, HervĂ© MĂ©nager, et al.. The bio.tools registry of software tools and data resources for the life sciences. Genome Biology, BioMed Central, 2019, 20 (164), pp.1-4. ⟨10.1186/s13059-019-1772-6⟩. ⟨hal-02408472⟩
  • Thomas Darde, Estelle Lecluze, AurĂ©lie Lardenois, Isabelle StĂ©vant, 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, Oxford University Press (OUP), 2019, 35 (17), pp.3133-3139. ⟨10.1093/bioinformatics/btz047⟩. ⟨hal-02015545⟩
  • StĂ©phanie Robin, Marc Ravallec, Marie Frayssinet, James Whitfield, VĂ©ronique Jouan, et al.. Evidence for an ichnovirus machinery in parasitoids of coleopteran larvae. Virus Research, Elsevier, 2019, 263, pp.189-206. ⟨10.1016/j.virusres.2019.02.001⟩. ⟨hal-02059774⟩
  • Thomas A. Darde, Pierre Gaudriault, RĂ©mi BĂ©ranger, Clement Lancien, Annaelle Caillarec-Joly, et al.. TOXsIgN: a cross-species repository for toxicogenomic signatures. Bioinformatics, Oxford University Press (OUP), 2018, 34 (12), pp.2116-2122. ⟨10.1093/bioinformatics/bty040⟩. ⟨hal-01863047⟩
  • 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⟩
  • AnaĂŻs 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⟩
  • Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, JĂ©rĂ´me Chopard, Christine Froidevaux, et al.. Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities. Future Generation Computer Systems, Elsevier, 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, Wiley, 2017, 26 (18), pp.4700-4711. ⟨10.1111/mec.14240⟩. ⟨hal-01605681v2⟩
  • 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⟩
  • 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, BioMed Central, 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, Oxford University Press, 2016, 2016, pp.baw070. ⟨10.1093/database/baw070⟩. ⟨hal-01342472⟩
  • François Moreews, Olivier Sallou, HervĂ© MĂ©nager, Yvan Le Bras, Cyril Monjeaud, et al.. BioShaDock: a community driven bioinformatics shared Docker-based tools registry. F1000Research, Faculty of 1000, 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, Elsevier, 2015, 93, pp.5-16. ⟨10.1016/j.ympev.2015.06.013⟩. ⟨hal-01187129⟩
  • FrĂ©dĂ©ric Boyer, CĂ©line Mercier, AurĂ©lie Bonin, Yvan Le Bras, Pierre Taberlet, et al.. OBITools: a Unix-inspired software package for DNA metabarcoding. Molecular Ecology Resources, Wiley/Blackwell, 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, Oxford University Press, 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, Cold Spring Harbor Laboratory Press, 2015, RNA, 21 (5), pp.1005-1017. ⟨10.1261/rna.049346.114⟩. ⟨inserm-01136506⟩
  • 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, Oxford University Press, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩. ⟨hal-01146849⟩
  • Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin. BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience, BioMed Central, 2015, 4, pp.22. ⟨10.1186/s13742-015-0063-8⟩. ⟨hal-01240449⟩
  • 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, Springer Verlag, 2015, 143 (3), pp.305-316. ⟨10.1007/s10709-015-9829-2⟩. ⟨hal-01208780v2⟩
  • LaĂ«titia Le Texier, Justine Durand, AmĂ©lie Lavault, Philippe Hulin, Olivier Collin, et al.. LIMLE, a New Molecule Over-Expressed following Activation, Is Involved in the Stimulatory Properties of Dendritic Cells. PLoS ONE, Public Library of Science, 2014, pp.10. ⟨10.1371/journal.pone.0093894⟩. ⟨hal-01093223⟩
  • LaĂ«titia Le Texier, Justine Durand, AmĂ©lie Lavault, Philippe Hulin, Olivier Collin, et al.. LIME, a new molecule associated with cytoskeleton is involved in stimulatory properties of DC. PLoS ONE, Public Library of Science, 2014, pp.10. ⟨10.1371/journal.pone.0093894⟩. ⟨hal-01183591⟩
  • FrĂ©dĂ©ric Chalmel, AurĂ©lie Lardenois, Bertrand Evrard, Antoine D. Rolland, Olivier Sallou, et al.. High-resolution profiling of novel transcribed regions during rat spermatogenesis. Biology of Reproduction, Society for the Study of Reproduction, 2014, 91 (1), pp.5. ⟨10.1095/biolreprod.114.118166⟩. ⟨hal-01063924⟩
  • 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⟩
  • Denis Habauzit, Catherine Le QuĂ©ment, 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, Public Library of Science, 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, Wiley/Blackwell, 2013, 14 (2), pp.393-400. ⟨10.1111/1755-0998.12179⟩. ⟨hal-00880072⟩
  • Thomas Obadia, Olivier Sallou, Marion Ouedraogo, GrĂ©gory Guernec, FrĂ©dĂ©ric Lecerf. The GAG database: A new resource to gather genomic annotation cross-references. Gene, Elsevier, 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 CorguillĂ©, 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⟩
  • Ramona Britto, Olivier Sallou, Olivier Collin, GrĂ©goire Michaux, Michael Primig, et al.. GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.. Nucleic Acids Research, Oxford University Press, 2012, 40 (W1), pp.W458-W465. ⟨10.1093/nar/gks380⟩. ⟨inserm-00696905⟩
  • 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, Cold Spring Harbor Laboratory Press, 2012, 22, pp.1775-1789. ⟨10.1101/gr.132159.111⟩. ⟨hal-01205054⟩
  • 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⟩
  • Alain van Wormhoudt, BĂ©atrice Gaume, Yvan Le Bras, ValĂ©rie Roussel, Sylvain Huchette. Two different and functional nuclear rDNA genes in the abalone Haliotis tuberculata : tissue differential expression. Genetica, Springer Verlag, 2011, http://link.springer.com/article/10.1007%2Fs10709-011-9623-8. ⟨10.1007/s10709-011-9623-8⟩. ⟨hal-01183596⟩

Conference papers

  • ClĂ©mence Frioux, Arnaud Belcour, MĂ©ziane 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. ⟨hal-03440212⟩
  • ClĂ©mence Frioux, Arnaud Belcour, MĂ©ziane Aite, Anthony Bretaudeau, Falk Hildebrand, et al.. Metabolic complementarity applied to the screening of microbiota and the identification of key species. 8th Metabolic Pathway Analysis, Aug 2021, Knoxville, TN, United States. ⟨hal-03440221⟩
  • ClĂ©mence 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 - JournĂ©es Ouvertes en Biologie, Informatique et MathĂ©matiques, Jul 2021, Paris, France. ⟨hal-03440232⟩
  • 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 - JournĂ©es Ouvertes en Biologie, Informatique et MathĂ©matiques, 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 : IntĂ©gration et interrogation de rĂ©seaux de rĂ©gulation gĂ©nomique et post-gĂ©nomique. IN OVIVE (INtĂ©gration de sources/masses de donnĂ©es hĂ©tĂ©rogènes 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 BelleannĂ©e, 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, AurĂ©lien Roult, Cyril Monjoeaud, Bahin Mathieu, Olivier Quenez, et al.. Towards a Life Sciences Virtual Research Environment. JOBIM 2013 - JournĂ©es Ouvertes en Biologie, Informatique et MathĂ©matiques, Jul 2013, Toulouse, France. ⟨hal-01102438⟩
  • Catherine BelleannĂ©e, Olivier Sallou, Jacques Nicolas. Recherche d'instances de motifs expressifs avec Logol. Application Ă  la modĂ©lisation d'Ă©vĂ©nements de frameshift -1. JOBIM 2012- 13e JournĂ©es Ouvertes en Biologie, Informatique et MathĂ©matiques, Jul 2012, Rennes, France. pp.5-14. ⟨hal-00726791⟩
  • BenoĂ®t Calmes, Philippe Simoneau, Erwan Scaon, Nelly Bataille-Simoneau, Thomas Guillemette. RĂ´le des Glutathion-S-transfĂ©rases fongiques dans la protection contre les mĂ©tabolites de dĂ©fenses des BrassicacĂ©es. 9èmes Rencontres de Phytopathologie - Mycologie, 2012, Aussois, France. ⟨hal-03281872⟩

Poster communications

  • ClĂ©mence Frioux, Arnaud Belcour, MĂ©ziane 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 2021, Jun 2021, Barcelone, Spain. ⟨hal-03438983⟩
  • Arnaud Belcour, ClĂ©mence Frioux, MĂ©ziane 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 - JournĂ©es Ouvertes de Biologie, Informatique et MathĂ©matique, Jun 2020, Montpellier / Virtual, France. ⟨10.1101/803056⟩. ⟨hal-03151934⟩
  • Thomas Alain Darde, Estelle Lecluze, Nathan Alary, Lardenois AurĂ©lie, 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⟩
  • Thomas Alain Darde, Estelle Lecluze, Becker Emmanuelle, Victoria Potdevin, Olivier Collin, et al.. ChemPSy : Identification, classification et priorisation de nouveaux perturbateurs endocriniens par intĂ©gration massive de donnĂ©es de toxicogĂ©nomiques. 10 ans PNREST, ANSES, Nov 2016, Paris, France. ⟨hal-02445078⟩
  • Thomas Alain Darde, Pierre Gaudriault, RĂ©mi BĂ©ranger, Lancien ClĂ©ment, Annaelle Caillarec-Joly, et al.. TOXsIgN – un espace de dĂ©pĂ´t publique dĂ©diĂ© aux signatures toxicologiques. 10 ans PNREST, ANSES, Nov 2016, Paris, France. ⟨hal-02445079⟩
  • AurĂ©lie Evrard, Charles Bettembourg, MĂ©lanie Jubault, Olivier Dameron, Olivier Filangi, et al.. Integration and query of biological datasets with Semantic Web technologies: AskOmics. JournĂ©es Ouvertes Biologie, Informatique et MathĂ©matiques (JOBIM 2016), Jun 2016, Lyon, France. ⟨hal-01391087⟩
  • AnaĂŻs 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, FrĂ©dĂ©ric Chalmel. Yet another Galaxy Genome viewer. GCC, Jul 2015, Norwich, United Kingdom. ⟨hal-02445072⟩
  • AnaĂŻs 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, AurĂ©lien 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⟩

Preprints, Working Papers

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