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)

Enumerating Precursor Sets of Target Metabolites in a Metabolic Network. - Ludovic Cottret; Paulo Vieira Milreu; Vicente Acuña; Alberto Marchetti-Spaccamela; Fábio Viduani Martinez; Marie-France Sagot; Leen Stougie (WABI, 2008)

An Introduction to Metabolic Networks and Their Structural Analysis. - Vincent Lacroix; Ludovic Cottret; Patricia Thébault; Marie-France Sagot (IEEE ACM Trans. Comput. Biol. Bioinform., 2008)

Deciphering the connectivity structure of biological networks using MixNet. - Franck Picard; Vincent Miele; Jean-Jacques Daudin; Ludovic Cottret; Stéphane Robin (BMC Bioinform., 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)

Graph-Based Analysis of the Metabolic Exchanges between Two Co-Resident Intracellular Symbionts, Baumannia cicadellinicola and Sulcia muelleri, with Their Insect Host, Homalodisca coagulata. - Ludovic Cottret; Paulo Vieira Milreu; Vicente Acuña; Alberto Marchetti-Spaccamela; Leen Stougie; Hubert Charles; Marie-France Sagot (PLoS Comput. Biol., 2010)

CycADS: an annotation database system to ease the development and update of BioCyc databases. - Augusto F. Vellozo; Amélie S. Véron; Patrice Baa-Puyoulet; Jaime Huerta-Cepas; Ludovic Cottret; Gérard Febvay; Federica Calevro; Yvan Rahbé; Angela E. Douglas; Toni Gabaldón; Marie-France Sagot; Hubert Charles; et al. (Database J. Biol. Databases Curation, 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)

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. - Vicente Acuña; Paulo Vieira Milreu; Ludovic Cottret; Alberto Marchetti-Spaccamela; Leen Stougie; Marie-France Sagot (Bioinform., 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)

Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes. - Mehdi Khafif; Ludovic Cottret; Claudine Balagué; Sylvain Raffaele (BMC Bioinform., 2014)

FlexFlux: combining metabolic flux and regulatory network analyses. - Lucas Marmiesse; Rémi Peyraud; Ludovic Cottret (BMC Syst. Biol., 2015)

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)

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)

Learning Boolean Controls in Regulated Metabolic Networks: A Case-Study. - Kerian Thuillier; Caroline Baroukh; Alexander Bockmayr; Ludovic Cottret; Loïc Paulevé; Anne Siegel (CMSB, 2021)

MERRIN: MEtabolic regulation rule INference from time series data. - Kerian Thuillier; Caroline Baroukh; Alexander Bockmayr; Ludovic Cottret; Loïc Paulevé; Anne Siegel (Bioinform., 2022)