Multiscale Visualization of Small World Networks. - David Auber; Yves Chiricota; Fabien Jourdan; Guy Melançon (INFOVIS, 2003)

Software Components Capture Using Graph Clustering. - Yves Chiricota; Fabien Jourdan; Guy Melançon (IWPC, 2003)

Tool for metabolic and regulatory pathways visual analysis. - Fabien Jourdan; Guy Melançon (Visualization and Data Analysis, 2003)

Metric-Based Network Exploration and Multiscale Scatterplot. - Yves Chiricota; Fabien Jourdan; Guy Melançon (INFOVIS, 2004)

Multiscale hybrid MDS. - Fabien Jourdan; Guy Melançon (IV, 2004)

Une approche MDS hybride pour l'exploration visuelle interactive. - Fabien Jourdan; Guy Melançon; Christophe Douy; Alexandre Gasne (IHM, 2005)

Interactive Refinement of Multi-scale Network Clusterings. - David Auber; Fabien Jourdan (IV, 2005)

Metabolic network visualization using constraint planar graph drawing algorithm. - Romain Bourqui; David Auber; Vincent Lacroix; Fabien Jourdan (IV, 2006)

Multiscale Scatterplot Matrix for Visual and Interactive Exploration of Metabonomic Data. - Fabien Jourdan; Alain Paris; Pierre-Yves Koenig; Guy Melançon (VIEW, 2006)

Metabolic network visualization eliminating node redundance and preserving metabolic pathways. - Romain Bourqui; Ludovic Cottret; Vincent Lacroix; David Auber; Patrick Mary; Marie-France Sagot; Fabien Jourdan (BMC Syst. Biol., 2007)

Revealing Subnetwork Roles using Contextual Visualization: Comparison of Metabolic Networks. - Romain Bourqui; Fabien Jourdan (IV, 2008)

MetaNetter: inference and visualization of high-resolution metabolomic networks. - Fabien Jourdan; Rainer Breitling; Michael P. Barrett; David R. Gilbert (Bioinform., 2008)

Detecting Structural Changes and Command Hierarchies in Dynamic Social Networks. - Romain Bourqui; Frédéric Gilbert 001; Paolo Simonetto; Faraz Zaidi; Umang Sharan; Fabien Jourdan (ASONAM, 2009)

A Stable Decomposition Algorithm for Dynamic Social Network Analysis. - Romain Bourqui; Paolo Simonetto; Fabien Jourdan (EGC (best of volume), 2009)

Un algorithme stable de décomposition pour l'analyse des réseaux sociaux dynamiques. - Romain Bourqui; Paolo Simonetto; Fabien Jourdan (EGC, 2009)

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. - Ludovic Cottret; David Wildridge; Florence Vinson; Michael P. Barrett; Hubert Charles; Marie-France Sagot; Fabien Jourdan (Nucleic Acids Res., 2010)

Domain specific vs Generic Network Visualization: an Evaluation with Metabolic Networks. - Romain Bourqui; Helen C. Purchase; Fabien Jourdan (AUIC, 2011)

Communities and hierarchical structures in dynamic social networks: analysis and visualization. - Frédéric Gilbert 001; Paolo Simonetto; Faraz Zaidi; Fabien Jourdan; Romain Bourqui (Soc. Netw. Anal. Min., 2011)

Systrip: A Visual Environment for the Investigation of Time-series Data in the Context of Metabolic Networks. - Jonathan Dubois; Ludovic Cottret; Amine Ghozlane; David Auber; Frédéric Bringaud; Patricia Thébault; Fabien Jourdan; Romain Bourqui (IV, 2012)

Flux Analysis of the Trypanosoma brucei Glycolysis Based on a Multiobjective-Criteria Bioinformatic Approach. - Amine Ghozlane; Frédéric Bringaud; Hayssam Soueidan; Isabelle Dutour; Fabien Jourdan; Patricia Thébault (Adv. Bioinformatics, 2012)

Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets. - Vicente Acuña; Etienne Birmelé; Ludovic Cottret; Pierluigi Crescenzi; Fabien Jourdan; Vincent Lacroix; Alberto Marchetti-Spaccamela; Andrea Marino 001; Paulo Vieira Milreu; Marie-France Sagot; Leen Stougie (Theor. Comput. Sci., 2012)

Telling metabolic stories to explore metabolomics data: a case study on the yeast response to cadmium exposure. - Paulo Vieira Milreu; Cecilia Coimbra Klein; Ludovic Cottret; Vicente Acuña; Etienne Birmelé; Michele Borassi; Christophe Junot; Alberto Marchetti-Spaccamela; Andrea Marino 001; Leen Stougie; Fabien Jourdan; Pierluigi Crescenzi; et al. (Bioinform., 2014)

ProbMetab: an R package for Bayesian probabilistic annotation of LC-MS-based metabolomics. - Ricardo Roberto da Silva; Fabien Jourdan; Diego M. Salvanha; Fabien Létisse; Emilien L. Jamin; Simone Guidetti-Gonzalez; Carlos A. Labate; Ricardo Z. N. Vêncio (Bioinform., 2014)

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. - Sanu Shameer; Flora J. Logan-Klumpler; Florence Vinson; Ludovic Cottret; Benjamin Merlet; Fiona Achcar; Michael Boshart; Matthew Berriman; Rainer Breitling; Frédéric Bringaud; Peter Bütikofer; Amy M. Cattanach; et al. (Nucleic Acids Res., 2015)

Computational methods to identify metabolic sub-networks based on metabolomic profiles. - Clément Frainay; Fabien Jourdan (Briefings Bioinform., 2017)

The future of metabolomics in ELIXIR. - Merlijn N. van Rijswijk; Charlie Beirnaert; Christophe Caron; Marta Cascante; Victoria Dominguez Del Angel; Warwick B. Dunn; Timothy M. D. Ebbels; Franck Giacomoni; Alejandra N. González-Beltrán; Thomas Hankemeier; Kenneth Haug; Jose L. Izquierdo-García; et al. (F1000Research, 2017)

MetExploreViz: web component for interactive metabolic network visualization. - Maxime Chazalviel; Clément Frainay; Nathalie Poupin; Florence Vinson; Benjamin Merlet; Yoann Gloaguen; Ludovic Cottret; Fabien Jourdan (Bioinform., 2018)

MetExplore: collaborative edition and exploration of metabolic networks. - Ludovic Cottret; Clément Frainay; Maxime Chazalviel; Floréal Cabanettes; Yoann Gloaguen; Etienne Camenen; Benjamin Merlet; Stéphanie Heux; Jean-Charles Portais; Nathalie Poupin; Florence Vinson; Fabien Jourdan (Nucleic Acids Res., 2018)

MetaboRank: network-based recommendation system to interpret and enrich metabolomics results. - Clément Frainay; Sandrine Aros; Maxime Chazalviel; Thomas Garcia; Florence Vinson; Nicolas Weiss; Benoit Colsch; Frédéric Sedel; Dominique Thabut; Christophe Junot; Fabien Jourdan (Bioinform., 2019)

FORUM: building a Knowledge Graph from public databases and scientific literature to extract associations between chemicals and diseases. - Maxime Delmas; Olivier Filangi; Nils Paulhe; Florence Vinson; Christophe Duperier; William Garrier; Paul-Emeric Saunier; Yoann Pitarch; Fabien Jourdan; Franck Giacomoni; Clément Frainay (Bioinform., 2021)

DEXOM: Diversity-based enumeration of optimal context-specific metabolic networks. - Pablo Rodríguez-Mier; Nathalie Poupin; Carlo de Blasio; Laurent Le Cam; Fabien Jourdan (PLoS Comput. Biol., 2021)

Pathway analysis in metabolomics: Recommendations for the use of over-representation analysis. - Cecilia Wieder; Clément Frainay; Nathalie Poupin; Pablo Rodríguez-Mier; Florence Vinson; Juliette Cooke; Rachel P. J. Lai; Jacob G. Bundy; Fabien Jourdan; Timothy M. D. Ebbels (PLoS Comput. Biol., 2021)

A strategy to detect metabolic changes induced by exposure to chemicals from large sets of condition-specific metabolic models computed with enumeration techniques. - Louison Fresnais; Olivier Périn; Anne Riu; Romain Grall; Alban Ott; Bernard Fromenty; Jean-Clément Gallardo; Maximilian Stingl; Clément Frainay; Fabien Jourdan; Nathalie Poupin (BMC Bioinform., 2023)

PathIntegrate: Multivariate modelling approaches for pathway-based multi-omics data integration. - Cecilia Wieder; Juliette Cooke; Clément Frainay; Nathalie Poupin; Russell Bowler; Fabien Jourdan; Katerina J. Kechris; Rachel P. J. Lai; Timothy M. D. Ebbels (PLoS Comput. Biol., 2024)

Genome scale metabolic network modelling for metabolic profile predictions. - Juliette Cooke; Maxime Delmas; Cecilia Wieder; Pablo Rodríguez-Mier; Clément Frainay; Florence Vinson; Timothy M. D. Ebbels; Nathalie Poupin; Fabien Jourdan (PLoS Comput. Biol., 2024)