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authIdHal_s : herve-menager
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Multitrait GWAS to connect disease variants and biological mechanisms

Hanna Julienne , Vincent Laville , Zachary Mccaw , Zihuai He , Vincent Guillemot , et al.
PLoS Genetics, 2021, 17 (8), pp.e1009713. ⟨10.1371/journal.pgen.1009713⟩
Journal articles pasteur-03526210v1
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Making Biomedical Research Software FAIR: Actionable Step-by-step Guidelines with a User-support Tool

Bhavesh Patel , Sanjay Soundarajan , Hervé Ménager , Zicheng Hu
Scientific Data , 2023, 10 (1), pp.557. ⟨10.1038/s41597-023-02463-x⟩
Journal articles hal-04206208v1
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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 , et al.
Future Generation Computer Systems, 2017, 75, pp.284-298. ⟨10.1016/j.future.2017.01.012⟩
Journal articles hal-01516082v1
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ELIXIR and Toxicology: a community in development

Marvin Martens , Rob Stierum , Emma Schymanski , Chris Evelo , Reza Aalizadeh , et al.
F1000Research, 2021, 10, pp.1129. ⟨10.12688/f1000research.74502.1⟩
Journal articles pasteur-03680151v1

Multitrait genetic-phenotype associations to connect disease variants and biological mechanisms

Hanna Julienne , Vincent Laville , Zachary Mccaw , Zihuai He , Vincent Guillemot , et al.
Preprints, Working Papers, ... pasteur-03279159v1

Nine Best Practices for Research Software Registries and Repositories: A Concise Guide

Task Force On Best Practices For Software Registries , Alain Monteil , Alejandra Gonzalez-Beltran , Alexandros Ioannidis , Alice Allen , et al.
Preprints, Working Papers, ... hal-03093837v1
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JASS: command line and web interface for the joint analysis of GWAS results

Hanna Julienne , Pierre Lechat , Vincent Guillemot , Carla Lasry , Chunzi Yao , et al.
NAR Genomics and Bioinformatics, 2020, 2 (1), pp.lqaa003. ⟨10.1093/nargab/lqaa003⟩
Journal articles pasteur-02635247v1
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ReGaTE: Registration of Galaxy Tools in Elixir

Olivia Doppelt-Azeroual , Fabien Mareuil , Eric Deveaud , Matúš Kalaš , Nicola Soranzo , et al.
GigaScience, 2017, 6 (6), pp.1-4. ⟨10.1093/gigascience/gix022⟩
Journal articles pasteur-02613125v1
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Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions

Quentin Lamy-Besnier , Bryan Brancotte , Hervé Ménager , Laurent Debarbieux
Bioinformatics, 2021, 60 (4), pp.921-925. ⟨10.1093/bioinformatics/btab070⟩
Journal articles pasteur-03166905v1
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Community curation of bioinformatics software and data resources

Jon Ison , Hervé Ménager , Bryan Brancotte , Erik Jaaniso , Ahto Salumets , et al.
Briefings in Bioinformatics, 2019, pp.bbz075. ⟨10.1093/bib/bbz075⟩
Journal articles pasteur-02770716v1

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

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

Bioinformatics applications discovery and composition with the Mobyle suite and MobyleNet

Hervé Ménager , Vivek Gopalan , Bertrand Néron , Sandrine Larroudé , Julien Maupetit , et al.
Resource Discovery, 6799, Springer Berlin Heidelberg, pp.11-22, 2012, Lecture Notes in Computer Science, ⟨10.1007/978-3-642-27392-6_2⟩
Book sections pasteur-03682347v1

Bioimage analysis workflows: community resources to navigate through a complex ecosystem

Perrine Paul-Gilloteaux , Sébastien Tosi , Jean-Karim Hériché , Alban Gaignard , Hervé Ménager , et al.
F1000Research, 2021, 10, pp.320. ⟨10.12688/f1000research.52569.1⟩
Journal articles hal-03208600v1
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The iPPI-DB initiative: a community-centered database of protein–protein interaction modulators

Rachel Torchet , Karen Druart , Luis Checa Ruano , Alexandra Moine-Franel , Hélène Borges , et al.
Bioinformatics, 2021, 37 (1), pp.89-96. ⟨10.1093/bioinformatics/btaa1091⟩
Journal articles hal-03252561v1
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The registry of software tools and data resources for the life sciences

Jon Ison , Hans Ienasescu , Piotr Chmura , Emil Rydza , Hervé Ménager , et al.
Genome Biology, 2019, 20 (164), pp.1-4. ⟨10.1186/s13059-019-1772-6⟩
Journal articles hal-02408472v1
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MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems.

Sophie S Abby , Bertrand Néron , Hervé Ménager , Marie Touchon , Eduardo P C Rocha
PLoS ONE, 2013, 9 (10), pp.e110726. ⟨10.1371/journal.pone.0110726⟩
Journal articles pasteur-01080418v1
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Redesign of iPPI-DB, a database for modulators of Protein-Protein Interactions

Rachel Torchet , Alexandra Moine-Franel , Hélène Borges , Bryan Brancotte , Olivia Doppelt-Azeroual , et al.
JOBIM (Journées Ouvertes Biologie, Informatique et Mathématiques), Société Française de BioInformatique; GdR Bioinformatique Moléculaire; Institut Francais de Bioinformatique, Jul 2019, Nantes, France
Conference papers pasteur-02867265v1
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Perspectives on automated composition of workflows in the life sciences

Anna-Lena Lamprecht , Magnus Palmblad , Jon Ison , Veit Schwämmle , Mohammad Sadnan Al Manir , et al.
F1000Research, 2021, 10, pp.897. ⟨10.12688/f1000research.54159.1⟩
Journal articles pasteur-03680115v1
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Recommendations for the packaging and containerizing of bioinformatics software

Bjorn Gruening , Olivier Sallou , Pablo Moreno , Felipe da Veiga Leprevost , Hervé Ménager , et al.
F1000Research, 2018, 7, pp.742. ⟨10.12688/f1000research.15140.2⟩
Journal articles pasteur-02769991v1
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Mobyle: a new full web bioinformatics framework

Bertrand Néron , Hervé Ménager , Corinne Maufrais , Nicolas Joly , Julien Maupetit , et al.
Bioinformatics, 2009, 25 (22), pp.3005-3011. ⟨10.1093/bioinformatics/btp493⟩
Journal articles hal-01287963v1
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HARIBOSS: a curated database of RNA-small molecules structures to aid rational drug design

F. P. Panei , R. Torchet , H. Menager , P. Gkeka , M. Bonomi
Bioinformatics, 2022, 38 (17), pp.4185-4193. ⟨10.1093/bioinformatics/btac483⟩
Journal articles hal-03834209v2
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EDAM Browser: visualization of EDAM and annotated bioinformatics resources

Hager Eldakroury , Sakshi Dhamija , Rashika Rathi , Drashti Patoliya , Guneet Singh , et al.
BOSC, Jul 2021, Online, France
Conference poster hal-04122666v1
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biotoolsSchema: a formalized schema for bioinformatics software description

Jon Ison , Hans Ienasescu , Emil Rydza , Piotr Chmura , Kristoffer Rapacki , et al.
GigaScience, 2021, 10 (1), pp.giaa157. ⟨10.1093/gigascience/giaa157⟩
Journal articles hal-03145289v1
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A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it.

Bryan Brancotte , Christophe Blanchet , Hervé Ménager
Journal of Open Source Software, 2018, 3 (27), pp.698. ⟨10.21105/joss.00698⟩
Journal articles pasteur-02770161v1
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The Flemmingsome reveals an ESCRT-to-membrane coupling via ALIX/syntenin/syndecan-4 required for completion of cytokinesis

Cyril Addi , Adrien Presle , Stéphane Frémont , Frédérique Cuvelier , Murielle Rocancourt , et al.
Nature Communications, 2020, 11 (1), pp.1941. ⟨10.1038/s41467-020-15205-z⟩
Journal articles pasteur-02557366v1
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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 , et al.
Journal articles hal-01243520v1
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ARIAweb: a server for automated NMR structure calculation

Fabrice Allain , Fabien Mareuil , Hervé Ménager , Michael Nilges , Benjamin Bardiaux
Nucleic Acids Research, 2020, ⟨10.1093/nar/gkaa362⟩
Journal articles pasteur-02569631v1
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On-target activity predictions enable improved CRISPR-dCas9 screens in bacteria

Alicia Calvo-Villamañán , Jérôme Wong Ng , Rémi Planel , Hervé Ménager , Arthur Chen , et al.
Nucleic Acids Research, 2020, gkaa294, ⟨10.1093/nar/gkaa294⟩
Journal articles pasteur-02773823v1
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Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language

Michael R. Crusoe , Sanne Abeln , Alexandru Iosup , Peter Amstutz , John Chilton , et al.
Communications of the ACM, 2021, 65 (6), pp.54-63. ⟨10.1145/3486897⟩
Journal articles pasteur-03680143v2
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EDAM, the life-science ontology for data analysis and management

Lucie Lamothe , Alban Gaignard , Mads Kierkegaard , Hager Eldakroury , Melissa Black , et al.
JOBIM, Jul 2022, Rennes, France. ⟨10.5281/zenodo.6769072⟩
Conference poster hal-03702557v1