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Olivier Collin

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The bio.tools registry of software tools and data resources for the life sciences

Jon Ison , Hans Ienasescu , Piotr Chmura , Emil Rydza , Hervé Ménager
Genome Biology, 2019, 20 (164), pp.1-4. ⟨10.1186/s13059-019-1772-6⟩
Journal articles hal-02408472v1
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The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

Thomas Darde , Estelle Lecluze , Aurélie Lardenois , Isabelle Stévant , Nathan Alary
Bioinformatics, 2019, 35 (17), pp.3133-3139. ⟨10.1093/bioinformatics/btz047⟩
Journal articles hal-02015545v1
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TOXsIgN: a cross-species repository for toxicogenomic signatures

Thomas A. Darde , Pierre Gaudriault , Rémi Béranger , Clement Lancien , Annaelle Caillarec-Joly
Bioinformatics, 2018, 34 (12), pp.2116-2122. ⟨10.1093/bioinformatics/bty040⟩
Journal articles hal-01863047v1
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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
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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
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Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities

Sarah Cohen-Boulakia , Khalid Belhajjame , Olivier Collin , Jérôme Chopard , Christine Froidevaux
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Journal articles hal-01516082v1
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Colib’read on galaxy: a tools suite dedicated to biological information extraction from raw NGS reads

Yvan Le Bras , Olivier Collin , Cyril Monjeaud , Vincent Lacroix , Eric Rivals
GigaScience, 2016, 5 (1), ⟨10.1186/s13742-015-0105-2⟩
Journal articles hal-01280238v1

PepPSy: a web server to prioritize gene products in experimental and biocuration workflows

Olivier Sallou , Paula D. Duek , Thomas A. Darde , Olivier Collin , Lydie Lane
Database - The journal of Biological Databases and Curation, 2016, 2016, pp.baw070. ⟨10.1093/database/baw070⟩
Journal articles hal-01342472v1
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BioShaDock: a community driven bioinformatics shared Docker-based tools registry

François Moreews , Olivier Sallou , Hervé Ménager , Yvan Le Bras , Cyril Monjeaud
Journal articles hal-01243520v1
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The ReproGenomics Viewer: an integrative cross-species toolbox for the reproductive science community.

Thomas A Darde , Olivier Sallou , Emmanuelle Becker , Bertrand Evrard , Cyril Monjoeaud
Nucleic Acids Research, 2015, 43 (W1), pp.8. ⟨10.1093/nar/gkv345⟩
Journal articles hal-01146120v1
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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
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The BioMart community portal: an innovative alternative to large, centralized data repositories

Damian Smedley , Syed Haider , Steffen Durinck , Luca Pandini , Paolo Provero
Nucleic Acids Research, 2015, 43 (W1), pp.W589-W598. ⟨10.1093/nar/gkv350⟩
Journal articles hal-01146849v1

LIMLE, a New Molecule Over-Expressed following Activation, Is Involved in the Stimulatory Properties of Dendritic Cells

Laëtitia Le Texier , Justine Durand , Amélie Lavault , Philippe Hulin , Olivier Collin
PLoS ONE, 2014, pp.10. ⟨10.1371/journal.pone.0093894⟩
Journal articles hal-01093223v1

LIME, a new molecule associated with cytoskeleton is involved in stimulatory properties of DC

Laëtitia Le Texier , Justine Durand , Amélie Lavault , Philippe Hulin , Olivier Collin
PLoS ONE, 2014, pp.10. ⟨10.1371/journal.pone.0093894⟩
Journal articles hal-01183591v1

High-resolution profiling of novel transcribed regions during rat spermatogenesis

Frédéric Chalmel , Aurélie Lardenois , Bertrand Evrard , Antoine D. Rolland , Olivier Sallou
Biology of Reproduction, 2014, 91 (1), pp.5. ⟨10.1095/biolreprod.114.118166⟩
Journal articles hal-01063924v1

Fitness of macrolide resistant Campylobacter coli and Campylobacter jejuni.

Salman Zeitouni , Olivier Collin , Mathieu Andraud , Gwennola Ermel , Isabelle Kempf
Microbial Drug Resistance, 2012, 18 (2), pp.101-108. ⟨10.1089/mdr.2011.0188⟩
Journal articles hal-00796472v1
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GPSy: a cross-species gene prioritization system for conserved biological processes--application in male gamete development.

Ramona Britto , Olivier Sallou , Olivier Collin , Grégoire Michaux , Michael Primig
Nucleic Acids Research, 2012, 40 (W1), pp.W458-W465. ⟨10.1093/nar/gks380⟩
Journal articles inserm-00696905v1
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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

Un déluge de données

Christophe Blanchet , Olivier Collin
Biofutur, 2011
Journal articles hal-00639962v1

GermOnline 4.0 is a genomics gateway for germline development, meiosis and the mitotic cell cycle

Aurélie Lardenois , Alexandre Gattiker , Olivier Collin , Frédéric Chalmel , Michael Primig
Database -Weston-, 2010, pp.baq030. ⟨10.1093/database/baq030⟩
Journal articles hal-00639961v1
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MIMAS 3.0 is a Multiomics Information Management and Annotation System.

Alexandre Gattiker , Leandro Hermida , Robin Liechti , Ioannis Xenarios , Olivier Collin
BMC Bioinformatics, 2009, 10, pp.151. ⟨10.1186/1471-2105-10-151⟩
Journal articles inserm-00516451v1
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BioMAJ: a flexible framework for databanks synchronization and processing

Olivier Filangi , Yoann Beausse , Anthony Assi , Ludovic Legrand , Jean-Marc Larré
Bioinformatics, 2008, 24 (16), pp.1823-1825. ⟨10.1093/bioinformatics/btn325⟩
Journal articles inria-00327502v1

An expressed sequence tag analysis of thallus and regenerating protoplasts of Chondrus crispus (Gigartinales, Rhodophyceae)

Jonas Collén , Vincent Roeder , Sylvie Rousvoal , Olivier Collin , Bernard Kloareg
Journal of Phycology, 2006
Journal articles inria-00327543v1

An application suite based on the IFB Container as a Service platform

François Moreews , Olivier Sallou , Olivier Collin
ECCB 2016 (Elixir Talks) , ISCB, Sep 2016, Den Haag, Netherlands
Conference papers hal-01394295v1
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A curated Domain centric shared Docker registry linked to the Galaxy toolshed

François Moreews , Olivier Sallou , Yvan Le Bras , Grosjean Marie , Cyril Monjeaud
Galaxy Community Conference 2015, Jul 2015, Norwich, United Kingdom
Conference papers hal-01160514v1

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

Integrating GALAXY workflows in a metadata management environment

François Moreews , Yvan Le Bras , Olivier Dameron , Cyril Monjeaud , Olivier Collin
Galaxy Community Conference, Jul 2014, Baltimore, United States
Conference papers hal-01093058v1

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
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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
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SLICEE: A Service oriented middleware for intensive scientific computation

Jonathan Piat , François Moreews , Olivier Collin , Dominique Lavenier , Alexandre Cornu
SERVICES 2011, Jul 2011, WASHINGTON DC, United States
Conference papers inria-00638694v1

RENABI GRISBI Infrastructure Distribuée pour la Bioinformatique

Christophe Blanchet , Clément Gauthey , Christophe C. Caron , Olivier Collin , Stephane Delmotte
JOBIM 2011 - Journées Ouvertes Biologie Informatique Mathématique, Jun 2011, Paris, France
Conference papers hal-00640007v1

Présentation des Centres Bioinformatiques Régionaux : RENABI-GO

Tiphaine Martin , Christophe C. Caron , Olivier Collin
Journées GRISBI 2011 : scientifiques et technologique, Christophe Blanchet and Christophe Caron and Olivier Collin and Stéphane Delmotte and Clément Gauthey and Tiphaine Martin and Franck Samson and Bruno Spataro, May 2011, Lyon, France
Conference papers inria-00614475v1

ReNaBi-GRISBI: grande infrastructure pour la bioinformatique

Christophe Blanchet , Clément Gauthey , Olivier Collin , Tiphaine Martin , Nouredine Melab
JOBIM 2010 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Sep 2010, Montpellier, France
Conference papers inria-00540940v1

BioDesc : gestion d'un entrepôt multiformat de descriptions de ressources bioinformatiques

Philippe Picouet , Z. Doughi , Loraine Brillet , Erwan Corre , Christophe Caron
JOBIM, Sep 2010, Montpellier, France
Conference papers inria-00540815v1

From AphidBase and Lepido-DB to an Information System for Insect Plant pest genomics studies.

Fabrice Legeai , Jean-Pierre Gauthier , François Cousserans , Emmanuelle d'Alençon , Olivier Collin
1st Workshop on Information System for Insect Pest, Nov 2009, Rennes, France
Conference papers inria-00435823v1

BioWorkFlow: Web Services toolkit and workflow applications evaluation to deploy a confidence network

Marc Wessner , Martin Senger , Franck Samson , Philippe Picouet , François Moreews
Jobim (Journées Ouvertes Biologie Informatique Mathématiques), Jun 2008, Lille, France
Conference papers inria-00327528v1

The ReproGenomics Viewer: a multi-omics and cross-species resource compatible with single-cell studies for the reproductive science community

Thomas Alain Darde , Estelle Lecluze , Nathan Alary , Lardenois Aurélie , Olivier Collin
European Congress of Andrology, Oct 2018, Budapest, Hungary
Conference poster hal-02445089v1

ChemPSy : Identification, classification et priorisation de nouveaux perturbateurs endocriniens par intégration massive de données de toxicogénomiques

Thomas Alain Darde , Estelle Lecluze , Becker Emmanuelle , Victoria Potdevin , Olivier Collin
10 ans PNREST, ANSES, Nov 2016, Paris, France.
Conference poster hal-02445078v1

TOXsIgN – un espace de dépôt publique dédié aux signatures toxicologiques

Thomas Alain Darde , Pierre Gaudriault , Rémi Béranger , Lancien Clément , Annaelle Caillarec-Joly
10 ans PNREST, ANSES, Nov 2016, Paris, France
Conference poster hal-02445079v1

The ReproGenomics Viewer: An integrative cross-species toolbox for the reproductive science community

Thomas Alain Darde , Olivier Sallou , Becker Emmanuelle , Bertrand Evrard , Cyril Monjeaud
ReproScience, Apr 2015, Rennes, France
Conference poster hal-02445070v1

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