• 2024
  Bryan Brancotte, Elodie Chapeaublanc, Shiny-K8s, a toolkit to easily and reproducibly deploy your (R)Shiny app thanks to docker and Kubernetes (without mastering them!), JOBIM 2024, Jun 2024, Toulouse (FRANCE), France. .
• 2024
  Juliette Bonche, Bryan Brancotte, Elodie Chapeaublanc, Amanda Dieuaide, Simon Malesys, Fabien Mareuil, Rémi Planel, Marie Schmit, Raphael Tackx, Rachel Torchet, Web development, expertise of the Web INTEgRation group in the Bioinformatic and Biostatistics Hub, Journée Départementale du Département de Biologie Computationnelle de l'Institut Pasteur, Mar 2024, Annecy (France), France.
• 2023
  Groeneveld CS, Sanchez-Quiles V, Dufour F, Shi M, Dingli F, Nicolle R, Chapeaublanc E, Poullet P, Jeffery D, Krucker C, Maillé P, Vacherot F, Vordos D, Benhamou S, Lebret T, Micheau O, Zinovyev A, Loew D, Allory Y, de Reyniès A, Bernard-Pierrot I, Radvanyi F, Proteogenomic Characterization of Bladder Cancer Reveals Sensitivity to Apoptosis Induced by Tumor Necrosis Factor-related Apoptosis-inducing Ligand in FGFR3-mutated Tumors., Eur Urol 2024 May; 85(5): 483-494.
• 2023
  Neyret-Kahn H, Fontugne J, Meng XY, Groeneveld CS, Cabel L, Ye T, Guyon E, Krucker C, Dufour F, Chapeaublanc E, Rapinat A, Jeffery D, Tanguy L, Dixon V, Neuzillet Y, Lebret T, Gentien D, Davidson I, Allory Y, Bernard-Pierrot I, Radvanyi F, , Epigenomic mapping identifies an enhancer repertoire that regulates cell identity in bladder cancer through distinct transcription factor networks., Oncogene 2023 Mar; (): .
• 2022
  Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Bogdan Gavrilović, Carole Goble, The Cwl Community, Methods Included, Communications of the ACM, 2022.
• 2021
  Marvin Martens, Rob Stierum, Emma L. Schymanski, Chris T. Evelo, Reza Aalizadeh, Hristo Aladjov, Kasia Arturi, Karine Audouze, Pavel Babica, Karel Berka, Jos Bessems, Ludek Blaha, Evan E. Bolton, Montserrat Cases, Dimitrios Ε. Damalas, Kirtan Dave, Marco Dilger, Thomas Exner, Daan P. Geerke, Roland Grafström, Alasdair Gray, John M. Hancock, Henner Hollert, Nina Jeliazkova, Danyel Jennen, Fabien Jourdan, Pascal Kahlem, Jana Klanova, Jos Kleinjans, Todor Kondic, Boï Kone, Iseult Lynch, Uko Maran, Sergio Martinez Cuesta, Hervé Ménager, Steffen Neumann, Penny Nymark, Herbert Oberacher, Noelia Ramirez, Sylvie Remy, Philippe Rocca-Serra, Reza M. Salek, Brett Sallach, Susanna-Assunta Sansone, Ferran Sanz, Haralambos Sarimveis, Sirarat Sarntivijai, Tobias Schulze, Jaroslav Slobodnik, Ola Spjuth, Jonathan Tedds, Nikolaos Thomaidis, Ralf J.M. Weber, Gerard J.P. van Westen, Craig E. Wheelock, Antony J. Williams, Hilda Witters, Barbara Zdrazil, Anže Županič, Egon L. Willighagen, ELIXIR and Toxicology: a community in development, F1000Research 2021, 10(ELIXIR):1129.
• 2021
  Julienne H, Laville V, McCaw ZR, He Z, Guillemot V, Lasry C, Ziyatdinov A, Nerin C, Vaysse A, Lechat P, Ménager H, Le Goff W, Dube MP, Kraft P, Ionita-Laza I, Vilhjálmsson BJ, Aschard H, Multitrait GWAS to connect disease variants and biological mechanisms., PLoS Genet 2021 Aug; 17(8): e1009713.
• 2021
  Tatfi M, Perthame E, Hillion KH, Dillies MA, Menager H, Hermine O, Suarez F, , Gene expression analysis in EBV-infected ataxia-telangiectasia cell lines by RNA-sequencing reveals protein synthesis defect and immune abnormalities., Orphanet J Rare Dis 2021 06; 16(1): 288.
• 2021
  Lamy-Besnier Q, Brancotte B, Ménager H, Debarbieux L, , Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions., Bioinformatics 2021 Feb; (): .
• 2021
  Ison J, Ienasescu H, Rydza E, Chmura P, Rapacki K, Gaignard A, Schwämmle V, van Helden J, Kalaš M, Ménager H, , biotoolsSchema: a formalized schema for bioinformatics software description., Gigascience 2021 Jan; 10(1): .
• 2021
  Torchet R, Druart K, Ruano LC, Moine-Franel A, Borges H, Doppelt-Azeroual O, Brancotte B, Mareuil F, Nilges M, Ménager H, Sperandio O, The iPPI-DB initiative: a community-centered database of protein-protein interaction modulators., Bioinformatics 2021 Apr; 37(1): 89-96.
• 2021
  Lamprecht AL, Palmblad M, Ison J, Schwämmle V, Al Manir MS, Altintas I, Baker CJO, Ben Hadj Amor A, Capella-Gutierrez S, Charonyktakis P, Crusoe MR, Gil Y, Goble C, Griffin TJ, Groth P, Ienasescu H, Jagtap P, Kalaš M, Kasalica V, Khanteymoori A, Kuhn T, Mei H, Ménager H, Möller S, Richardson RA, Robert V, Soiland-Reyes S, Stevens R, Szaniszlo S, Verberne S, Verhoeven A, Wolstencroft K, , Perspectives on automated composition of workflows in the life sciences., F1000Res 2021 ; 10(): 897.
• 2021
  Paul-Gilloteaux P, Tosi S, Hériché JK, Gaignard A, Ménager H, Marée R, Baecker V, Klemm A, Kalaš M, Zhang C, Miura K, Colombelli J, , Bioimage analysis workflows: community resources to navigate through a complex ecosystem., F1000Res 2021 ; 10(): 320.
• 2020
  Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lièvremont D, Coppée JY, Barbe V, Arsène-Ploetze F, , Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2., Microb Genom 2020 Oct; (): .
• 2020
  Allain F, Mareuil F, Ménager H, Nilges M, Bardiaux B, , ARIAweb: a server for automated NMR structure calculation., Nucleic Acids Res. 2020 May; (): .
• 2020
  Cyril Addi, Adrien Presle, Stéphane Frémont, Frédérique Cuvelier, Murielle Rocancourt, Florine Milin, Sandrine Schmutz, Julia Chamot-Rooke, Thibaut Douche, Magalie Duchateau, Quentin Giai Gianetto, Audrey Salles, Hervé Ménager, Mariette Matondo, Pascale Zimmermann, Neetu Gupta-Rossi, Arnaud Echard, The Flemmingsome reveals an ESCRT-to-membrane coupling via ALIX/syntenin/syndecan-4 required for completion of cytokinesis, Nature Communications, 2020, 11 (1), pp.1941. ⟨10.1038/s41467-020-15205-z⟩.
• 2020
  Julienne H, Lechat P, Guillemot V, Lasry C, Yao C, Araud R, Laville V, Vilhjalmsson B, Ménager H, Aschard H, JASS: command line and web interface for the joint analysis of GWAS results., NAR Genom Bioinform 2020 Mar; 2(1): lqaa003.
• 2019
  Ison J, Ménager H, Brancotte B, Jaaniso E, Salumets A, Raček T, Lamprecht AL, Palmblad M, Kalaš M, Chmura P, Hancock JM, Schwämmle V, Ienasescu HI, Community curation of bioinformatics software and data resources, Brief. Bioinformatics 2019 Oct;.
• 2019
  Ison J, Ienasescu H, Chmura P, Rydza E, Ménager H, Kalaš M, Schwämmle V, Grüning B, Beard N, Lopez R, Duvaud S, Stockinger H, Persson B, Vařeková RS, Raček T, Vondrášek J, Peterson H, Salumets A, Jonassen I, Hooft R, Nyrönen T, Valencia A, Capella S, Gelpí J, Zambelli F, Savakis B, Leskošek B, Rapacki K, Blanchet C, Jimenez R, Oliveira A, Vriend G, Collin O, van Helden J, Løngreen P, Brunak S, The bio.tools registry of software tools and data resources for the life sciences, Genome Biol. 2019 08;20(1):164.
• 2019
  Buchrieser J, Degrelle SA, Couderc T, Nevers Q, Disson O, Manet C, Donahue DA, Porrot F, Hillion KH, Perthame E, Arroyo MV, Souquere S, Ruigrok K, Dupressoir A, Heidmann T, Montagutelli X, Fournier T, Lecuit M, Schwartz O, , IFITM proteins inhibit placental syncytiotrophoblast formation and promote fetal demise., Science 2019 Jul; 365(6449): 176-180.
• 2019
  Lemoine F, Correia D, Lefort V, Doppelt-Azeroual O, Mareuil F, Cohen-Boulakia S, Gascuel O, NGPhylogeny.fr: new generation phylogenetic services for non-specialists, Nucleic Acids Res. 2019 Jul;47(W1):W260-W265.
• 2018
  Bryan Brancotte, Christophe Blanchet, Hervé Ménager, A reusable tree-based web-visualization to browse EDAM ontology, and contribute to it., JOSS 2018.
• 2018
  Batut B, Hiltemann S, Bagnacani A, Baker D, Bhardwaj V, Blank C, Bretaudeau A, Brillet-Guéguen L, Čech M, Chilton J, Clements D, Doppelt-Azeroual O, Erxleben A, Freeberg MA, Gladman S, Hoogstrate Y, Hotz HR, Houwaart T, Jagtap P, Larivière D, Le Corguillé G, Manke T, Mareuil F, Ramírez F, Ryan D, Sigloch FC, Soranzo N, Wolff J, Videm P, Wolfien M, Wubuli A, Yusuf D, , Taylor J, Backofen R, Nekrutenko A, Grüning B, Community-Driven Data Analysis Training for Biology, Cell Syst 2018 Jun;6(6):752-758.e1.
• 2018
  Bjorn Gruening , Olivier Sallou , Pablo Moreno , Felipe da Veiga Leprevost , Hervé Ménager , Dan Søndergaard , Hannes Röst , Timo Sachsenberg , Brian O'Connor , Fábio Madeira , Victoria Dominguez Del Angel , Michael R. Crusoe , Susheel Varma , Daniel Blankenberg , Rafael C. Jimenez , BioContainers Community , Yasset Perez-Riverol, Recommendations for the packaging and containerizing of bioinformatics software, F1000Research 2018, 7(ELIXIR):742 .
• 2017
  Kenzo-Hugo Hillion, Ivan Kuzmin, Anton Khodak, Eric Rasche, Michael Crusoe, Hedi Peterson, Jon Ison, Hervé Ménager, Using bio.tools to generate and annotate workbench tool descriptions, F1000Research 2017, 6(ELIXIR):2074.
• 2017
  Friedman RC, Kalkhof S, Doppelt-Azeroual O, Mueller SA, Chovancová M, von Bergen M, Schwikowski B, Common and phylogenetically widespread coding for peptides by bacterial small RNAs, BMC Genomics 2017 07;18(1):553.
• 2017
  Fabien Mareuil, Olivia-Doppelt Azeroual, Hervé Ménager, Galaxy@pasteur, Mareuil F, Doppelt-Azeroual O and Ménager H. A public Galaxy platform at Pasteur used as an execution engine for web services [version 1; not peer reviewed]. F1000Research 2017, 6:1030 (poster) (doi: 10.7490/f1000research.1114334.1) .
• 2017
  Doppelt-Azeroual O, Mareuil F, Deveaud E, Kalaš M, Soranzo N, van den Beek M, Grüning B, Ison J, Ménager H, ReGaTE: Registration of Galaxy Tools in Elixir, Gigascience 2017 Jun;6(6):1-4.
• 2017
  Sarah Cohen-Boulakia, Khalid Belhajjame, Olivier Collin, Jérôme Chopard, Christine Froidevaux, Alban Gaignard, Konrad Hinsen, Pierre Larmande, Yvan Le Bras, Frédéric Lemoine, Fabien Mareuil, Hervé Ménager, Christophe Pradal, Christophe Blanchet, Scientific workflows for computational reproducibility in the life sciences: Status, challenges and opportunities, Future Generation Computer Systems.
• 2016
  Damien Correia , Olivia Doppelt-Azeroual , Jean-Baptiste Denis , Mathias Vandenbogaert , Valérie Caro, MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data, Correia D, Doppelt-Azeroual O, Denis JB et al. MetaGenSense: A web-application for analysis and exploration of high throughput sequencing metagenomic data. F1000Research 2016, 4:86 (doi: 10.12688/f1000research.6139.3) .
• 2016
  Tammimies K, Bieder A, Lauter G, Sugiaman-Trapman D, Torchet R, Hokkanen ME, Burghoorn J, Castrén E, Kere J, Tapia-Páez I, Swoboda P, , Ciliary dyslexia candidate genes DYX1C1 and DCDC2 are regulated by Regulatory Factor X (RFX) transcription factors through X-box promoter motifs., FASEB J 2016 10; 30(10): 3578-3587.
• 2015
  Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S, Tools and data services registry: a community effort to document bioinformatics resources, Nucleic Acids Res. 2015 Nov;.