FlexFlux: combining metabolic flux and regulatory network analyses.

Lucas Marmiesse, Rémi Peyraud, Ludovic Cottret. BMC Systems Biology. 2015 

TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei
Sanu Shameer,...,Ludovic Cottret,...,Fabien Jourdan. Nucleic Acids Research2015

Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes

Mehdi Khafif, Ludovic Cottret, Claudine Balagué and Sylvain Raffaele. BMC Bioinformatics. 2014

An integrated analysis of plant and bacterial gene expression in symbiotic root nodules using laser-capture microdissection coupled to RNA sequencing
Brice Roux, Nathalie Rodde, Marie-Françoise Jardinaud, Ton Timmers, Laurent Sauviac, Ludovic Cottret, Sébastien Carrère, Erika Sallet, Emmanuel Courcelle, Sandra Moreau, Frédéric Debellé, Delphine Capela, Fernanda de Carvalho-Niebel, Jérôme Gouzy, Claude Bruand, Pascal Gamas.Plant Journal. 2014

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, Leen Stougie, Fabien Jourdan, Pierluigi Crescenzi, Vincent Lacroix, and Marie-France Sagot.Bioinformatics. 2013

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, Paulo Vieira Milreu, Marie-France Sagot, Leen Stougie.Theoretical Computer Science. 2012

Systrip: A Visual Environment for the Investigation of Time-series Data in the Context of Metabolic Networks
Dubois, J., Cottret, L., Ghozlane, A., Auber, D., Bringaud, F., Thebault, P., Jourdan, F., Bourqui, R. . Information Visualisation (IV), 2012 16th International Conference on. 2012

Transcriptome database resource and gene expression atlas for the rose.
Dubois A, Carrere S, Raymond O, Pouvreau B, Cottret L, Roccia A, Onesto J-P, Sakr S, Atanassova R, Baudino S, Foucher F, Le Bris M, Gouzy J and Bendahmane M. BMC Genomics. 2012

Exploration of the core metabolism of symbiotic bacteria.
Klein CC, Cottret L, Kielbassa J, Charles H, Gautier C, Vasconcelos AT, Lacroix V, Sagot MF. BMC Genomics. 2012

Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks.
Acuña V, Milreu PV, Cottret L, Marchetti-Spaccamela A, Stougie L, Sagot MF. Bioinformatics. 2012

A Genomic Reappraisal of Symbiotic Function in the Aphid/Buchnera Symbiosis: Reduced Transporter Sets and Variable Membrane Organisations.
Charles H, Balmand S, Lamelas A, Cottret L, Pérez-Brocal V, Burdin B, Latorre A, Febvay G, Colella S, Calevro F, Rahbé Y. Plos One. 2011

CycADS: an annotation database system to ease the development and update of BioCyc databases.
Vellozo A, Véron A, Baa-Puyoulet P, Huerta-Cepas J, Cottret L, Febvay G, Calevro F, Rahbé Y, Douglas AE, Gabaldon T, Sagot M-F, Charles H, Colella S. Accepted in DATABASE. 2O11

Genome sequence of the pea aphid Acyrthosiphon pisum.
International Aphid Genomics Consortium. Plos Biology. 2010 8(2)

Graph based analysis of the metabolic exchanges between two co-resident intracellular symbionts, Baumannia cicadellinicola and Sulcia muelleri, with their insect host, Homalodisca coagulata
Cottret L, Milreu P, Acuña V, Marchetti-Spaccamela A, Stougie L, Charles H, Sagot M-F. PLOS COMPUTATIONAL BIOLOGY. 2010 6(9)

MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks.

Cottret L
, Wildridge D, Vinson F, Barrett MP, Charles H, Sagot MF, Jourdan F. Nucleic Acids Res. 2010

Graph methods for the investigation of metabolic networks in parasitology

Cottret L and Jourdan F. Parasitology, 2010 6:1-15

Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining
Jourdan F, Cottret L, Huc L, Wildridge D, Scheltema R, Hillenweck A, Barrett M P, Zalko D, Watson D G and Debrauwer L, Metabolomics, 2010

Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum
Brinza L, Viñuelas J, Cottret L, Calevro F, Rahbé Y, Febvay G, Duport G, Colella S, Rabatel A, Gautier C, Fayard JM, Sagot MF, Charles H, C R Biol, 2009, 332, 1034-1049

Deciphering the connectivity structure of biological networks using MixNet.
Picard F, Miele V, Daudin JJ, Cottret L, Robin S., BMC Bioinformatics, 2009 Jun 16;10 Suppl 6:S17.

Enumerating Precursor Sets of Target Metabolites in a Metabolic Network.
Cottret L, Milreu P-V, Acuna V, Marchetti-Spaccamela A, Viduani-Martinez F, Sagot M-F, Stougie L. WABI 2008, Springer-Verlag, Lecture Notes in Bioinformatics, 2008 vol. LNBI 5251 pp.233-244.

An introduction to metabolic networks and their structural analysis.
Lacroix V, Cottret L, Thébault P, Sagot MF. IEEE/ACM Trans Comput Biol Bioinform. 2008 Oct-Dec;5(4):594-617. Review.

Metabolic network visualization eliminating node redundance and preserving metabolic pathways.
Bourqui R, Cottret L, Lacroix V, Auber D, Mary P, Sagot MF, Jourdan F. BMC Syst Biol. 2007 Jul 3;1:29.