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.

38 documents

Journal articles

  • 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, 2016, pp.baw070. <10.1093/database/baw070>. <hal-01342472>
  • 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>
  • 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>
  • 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 (OUP): Policy C - Option B, 2015, 43, pp.W589-W598. <10.1093/nar/gkv350>. <hal-01146849>
  • 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 (OUP): Policy C - Option B, 2015, 43, pp.8. <10.1093/nar/gkv345>. <hal-01146120>
  • 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>
  • François Moreews, Olivier Sallou, Hervé Ménager, 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>
  • 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, Wiley/Blackwell, 2015, pp.10.1111/1755-0998.12428. <10.1111/1755-0998.12428>. <hal-01183582>
  • 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>
  • 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, Society for the Study of Reproduction, 2014, 91 (1), pp.5. <10.1095/biolreprod.114.118166>. <hal-01063924>
  • 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 DC. PLoS ONE, Public Library of Science, 2014, pp.10. <10.1371/journal.pone.0093894>. <hal-01183591>
  • Laëtitia Le Texier, Justine Durand, Amélie 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>
  • Fabrice Legeai, Sylvie Gimenez, Bernard Duvic, Jean-Michel Escoubas, Anne-Sophie Gosselin Grenet, et al.. Establishment and analysis of a reference transcriptome for Spodoptera frugiperda. BMC Genomics, BioMed Central, 2014, 15 (1), pp.704. <10.1186/1471-2164-15-704>. <hal-01058982>
  • Anthony Bretaudeau, Cyril Monjeaud, Yvan Le Bras, Fabrice Legeai, Olivier Collin. BioMAJ2Galaxy: automatic update of reference data in Galaxy using BioMAJ. GigaScience, BioMed Central, 2014, 4, pp.22. <hal-01240449>
  • 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, 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, <10.1111/1755-0998.12179>. <hal-00880072>
  • Thomas Obadia, Olivier Sallou, Marion Ouedraogo, Grégory Guernec, Frederic 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 Corguillé, et al.. CyanoLyase: a database of phycobilin lyase sequences, motifs and functions. Nucleic Acids Research, Oxford University Press (OUP): Policy C - Option B, 2012, pp.6. <10.1093/nar/gks1091>. <hal-01094087>
  • 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, Oxford University Press (OUP): Policy C - Option B, 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>
  • 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>
  • 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, Springer Verlag, 2011, <10.1007/s10709-011-9623-8>. <hal-01183596>

Conference papers

  • Francois Moreews, Olivier Sallou, Olivier Collin. An application suite based on the IFB Container as a Service platform. ECCB 2016 (Elixir Talks) , Sep 2016, Den Haag, Netherlands. 2016, <>. <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. 2015, <>. <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), Jun 2015, Rennes, France. pp.7, <>. <hal-01184903>
  • Catherine Belleannée, Olivier Sallou, Jacques Nicolas. Logol: Expressive Pattern Matching in sequences. Application to Ribosomal Frameshift Modeling. Comin, Matteo; Kall, Lukas; Marchiori, Elena; Ngom, Alioune; Rajapakse, Jagath. PRIB2014 - Pattern Recognition in Bioinformatics, 9th IAPR International Conference, Aug 2014, Stockholm, Sweden. Springer International Publishing, 8626, pp.34-47, 2014, <10.1007/978-3-319-09192-1_4>. <hal-01059506>
  • Anthony Bretaudeau, Yvan Le Bras, Cyril Monjeaud, Olivier Collin. Automatic update of reference data in Galaxy using BioMAJ.. Galaxy Day 2014, Dec 2014, Paris, France. <hal-01102421>
  • Francois 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. 2014. <hal-01093058>
  • Yvan Le Bras, Aurélien Roult, Cyril Monjoeaud, Bahin Mathieu, Olivier Quenez, et al.. Towards a Life Sciences Virtual Research Environment. JOBIM 2013, May 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, 2012, <>. <hal-00726791>

Poster communications

  • Aurélie Evrard, Charles Bettembourg, Melanie 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>
  • 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>
  • Anaïs Gouin, Anthony Bretaudeau, K Labadie, Jean-Marc Aury, Emmanuelle D'Alençon, et al.. Improvement of the assembly of heterozygous genomes of non-model organisms, a case study of the genomes of two Spodoptera frugiperda host strains. Arthropod Genomics 2015, Jun 2015, Manhattan (Kansas), United States. 2015. <hal-01240443>
  • Anaïs Gouin, Anthony Bretaudeau, Emmanuelle D'Alençon, Claire Lemaitre, Fabrice Legeai. Improvement of the assembly of heterozygous genomes of non-model organisms. Genome Informatics, Oct 2015, Cold Spring Harbor Laboratory, United States. 2015. <hal-01231793>
  • Yvan Le Bras, Aurélien Roult, Cyril Monjoeaud, Bahin Mathieu, Olivier Quenez, et al.. e-Science in France, a Life science Western story. Galaxy Community Conference (GCC2014), Jun 2014, Baltimore, United States. <hal-01102432>
  • Anthony Bretaudeau, Olivier Collin. Dr Motifs: a web resource for pattern matching and discovery. JOBIM 2012, Jul 2012, Rennes, France. <hal-01102439>
  • Frédéric Lecerf, Anthony Bretaudeau, Olivier Sallou, Colette Désert, Yuna Blum, et al.. AnnotQTL: a new tool to gather functional and comparative information on a genomic region. 12è Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2011, Paris, France. 2011. <hal-01102407>