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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⟩
Article dans une revue hal-01287963v1
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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
Poster de conférence hal-04122666v1
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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⟩
Article dans une revue hal-03834209v2
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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⟩
Article dans une revue pasteur-02769991v1
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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
Communication dans un congrès 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⟩
Article dans une revue pasteur-03680115v1
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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⟩
Article dans une revue pasteur-01080418v1
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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.
F1000Research, 2015, ⟨10.12688/f1000research.7536.1⟩
Article dans une revue hal-01243520v1
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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⟩
Article dans une revue pasteur-03680143v2
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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⟩
Article dans une revue 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⟩
Article dans une revue pasteur-02773823v1
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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⟩
Poster de conférence hal-03702557v1
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Representing bioinformatics Nextflow workflows in RO-Crate : challenges and opportunities

 George Marchment , Marie Schmit , Clémence Sebe , Frédéric Lemoine , Hervé Ménager , et al.
Semantic Web Applications and Tools for Health Care and Life Sciences, Feb 2024, Leiden, Netherlands. Zenodo, 2024, ⟨10.5281/zenodo.10822156⟩
Poster de conférence hal-04540040v1

Dayglow and auroral emissions of Uranus in H2 FUV bands

 M. Barthelemy , L. Lamy , H. Menager , M. Schulik , D. Bernard , et al.
Icarus, 2014, 239, pp.160-167. ⟨10.1016/j.icarus.2014.05.035⟩
Article dans une revue hal-02559141v1
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Tools and data services registry: a community effort to document bioinformatics resources.

 Jon Ison , Kristoffer Rapacki , Hervé Ménager , Matúš Kalaš , Emil Rydza , et al.
Nucleic Acids Research, 2016, 44 (D1), pp.D38-47. ⟨10.1093/nar/gkv1116⟩
Article dans une revue hal-01594840v1
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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⟩
Article dans une revue 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⟩
Article dans une revue 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⟩
Article dans une revue pasteur-02557366v1

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⟩
Chapitre d'ouvrage istex pasteur-03682347v1
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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⟩
Article dans une revue hal-03252561v1
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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 , et al.
Genome Biology, 2019, 20 (164), pp.1-4. ⟨10.1186/s13059-019-1772-6⟩
Article dans une revue hal-02408472v1
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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⟩
Article dans une revue pasteur-03526210v1
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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⟩
Article dans une revue pasteur-03680151v1
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Trait selection strategy in multi-trait GWAS: Boosting SNPs discoverability

 Yuka Suzuki , Hervé Ménager , Bryan Brancotte , Raphaël Vernet , Cyril Nerin , et al.
2023
Pré-publication, Document de travail hal-04368562v1
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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⟩
Article dans une revue 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⟩
Article dans une revue hal-01516082v1

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

 Hanna Julienne , Vincent Laville , Zachary Mccaw , Zihuai He , Vincent Guillemot , et al.
2021
Pré-publication, Document de travail pasteur-03279159v1
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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⟩
Article dans une revue hal-03208600v1
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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⟩
Article dans une revue 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⟩
Article dans une revue pasteur-02770716v1
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