Ludovic Cottret

Publications

Article dans une revue (45)

Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex Caroline Baroukh,Ludovic Cottret,Emma Pires,Rémi Peyraud,Alice Guidotet al. mSystems, 2023, 18 p. ⟨10.1128/msystems.00083-23⟩ Article dans une revue hal-04172034v1
An integrated approach reveals how lipo‐chitooligosaccharides interact with the lysin motif receptor‐like kinase MtLYR3 Younes Bouchiba,Jérémy Esque,Ludovic Cottret,Maude Maréchaux,Mégane Gastonet al. Protein Science, 2022, 31 (6), 17 p. ⟨10.1002/pro.4327⟩ Article dans une revue hal-03684572v1
MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development Marie-Françoise Jardinaud,Justine Fromentin,Marie-Christine Auriac,Sandra Moreau,Yann Pecrixet al. Plant Physiology, 2022, 189 (3), pp.1587 - 1607. ⟨10.1093/plphys/kiac177⟩ Article dans une revue hal-03728310v1
A multi-organ metabolic model of tomato predicts plant responses to nutritional and genetic perturbations Léo Gerlin,Ludovic Cottret,Antoine Escourrou,Stéphane Genin,Caroline Baroukh Plant Physiology, 2022, 188 (3), pp.1709-1723. ⟨10.1093/plphys/kiab548⟩ Article dans une revue hal-03727243v1
Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development Claudia Bartoli,Stéphane Boivin,Marta Marchetti,Carine Gris,Virginie Gasciolliet al. Environmental Microbiology, 2022, 24 (11), pp.5509-5523. ⟨10.1111/1462-2920.16148⟩ Article dans une revue hal-04204399v2
Rhizocarpon geographicum Lichen Discloses a Highly Diversified Microbiota Carrying Antibiotic Resistance and Persistent Organic Pollutant Tolerance Alice Miral,Adam Kautsky,Susete Alves Carvalho,Ludovic Cottret,Anne-Yvonne Guillerm-Erckelboudtet al. Microorganisms, 2022, 10 (9), pp.1859. ⟨10.3390/microorganisms10091859⟩ Article dans une revue hal-04204410v2
MERRIN: MEtabolic Regulation Rule INference from time series data Kerian Thuillier,Caroline Baroukh,Alexander Bockmayr,Ludovic Cottret,Loïc Paulevéet al. Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩ Article dans une revue hal-03701755v2
EffectorK, a comprehensive resource to mine for Ralstonia, Xanthomonas, and other published effector interactors in the Arabidopsis proteome Manuel Gonzalez‐fuente,Sébastien Carrere,Dario Monachello,Benjamin G Marsella,Anne‐claire Cazaléet al. Molecular Plant Pathology, 2020, 21 (10), pp.1257-1270. ⟨10.1111/mpp.12965⟩ Article dans une revue hal-03052440v1
An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages Guru Radhakrishnan,Jean Keller,Mélanie K Rich,Tatiana Vernié,Duchesse Lacour Mbadinga Mbadingaet al. Nature Plants, 2020, 6 (3), pp.280-289. ⟨10.1038/s41477-020-0613-7⟩ Article dans une revue hal-02550894v1
Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth Léo Gerlin,Ludovic Cottret,Sophie Cesbron,Geraldine G. Taghouti,Marie-Agnès Jacqueset al. mSystems, 2020, 5 (2), 15 p. ⟨10.1128/mSystems.00698-19⟩ Article dans une revue hal-02901652v1
Sunflower resistance to multiple downy mildew pathotypes revealed by recognition of conserved effectors of the oomycete Plasmopara halstedii Yann Pecrix,Luis Fernando Buendia Martin,Charlotte Penouilh-Suzette,Maude Marechaux,Ludovic Legrandet al. The Plant Journal, 2019, 97 (4), ⟨10.1111/tpj.14157⟩ Article dans une revue hal-01990159v1
Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design Stéphanie Daval,Arnaud Belcour,Kévin Gazengel,Ludovic Legrand,Jerome Gouzyet al. Genomics, 2019, 111 (6), pp.1629-1640. ⟨10.1016/j.ygeno.2018.11.013⟩ Article dans une revue hal-01943250v1
Evolutionary History of Plant LysM Receptor Proteins Related to Root Endosymbiosis Clare Gough,Ludovic Cottret,Benoît Lefebvre,Jean-Jacques Bono Frontiers in Plant Science, 2018, 9, ⟨10.3389/fpls.2018.00923⟩ Article dans une revue hal-02366084v1
LysM Receptor-Like Kinase and LysM Receptor-Like Protein Families: An Update on Phylogeny and Functional Characterization Luis Fernando Buendia Martin,Ariane Girardin,Tongming Wang,Ludovic Cottret,Benoît Lefebvre Frontiers in Plant Science, 2018, 9, ⟨10.3389/fpls.2018.01531⟩ Article dans une revue hal-02621378v1
Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen Rémi Peyraud,Ludovic Cottret,Lucas Marmiesse,Stéphane Genin Nature Communications, 2018, 9, ⟨10.1038/s41467-017-02660-4⟩ Article dans une revue hal-02621546v1
MetExploreViz: web component for interactive metabolic network visualization Maxime Chazalviel,Clément Frainay,Nathalie Poupin,Florence Vinson,Benjamin Merletet al. Bioinformatics, 2018, 34 (2), pp.312-313. ⟨10.1093/bioinformatics/btx588⟩ Article dans une revue hal-02621786v1
MetExplore: collaborative edition and exploration of metabolic networks Ludovic Cottret,Clément Frainay,Maxime Chazalviel,Floréal Cabanettes,Yoann Gloaguenet al. Nucleic Acids Research, 2018, 46 (W1), 8 p. ⟨10.1093/nar/gky301⟩ Article dans une revue hal-01886470v1
The Rosa genome provides new insights into the domestication of modern roses Olivier Raymond,Jerome Gouzy,Jérémy Just,Hélène Badouin,Marion Verdenaudet al. Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩ Article dans une revue hal-01798003v1
The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution Hélène Badouin,Jerome Gouzy,Christopher Grassa,Florent Murat,S Evan Statonet al. Nature, 2017, 546 (7656), pp.148-152. ⟨10.1038/nature22380⟩ Article dans une revue hal-01603287v1
Genomic Prediction of Sunflower Hybrids Oil Content Brigitte Mangin,Fanny Bonnafous,Nicolas Blanchet,Marie-Claude Boniface,Emmanuelle Bret-Mestrieset al. Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01633⟩ Article dans une revue hal-02624895v1
A laser dissection-RNAseq analysis highlights the activation of cytokinin pathways by nod factors in the &lt;em&gt;Medicago truncatula&lt;/em&gt; root epidermis Marie-Françoise Jardinaud,Stephane Boivin,Nathalie N. Rodde,Olivier Catrice,Anna Kisialaet al. Plant Physiology, 2016, 171 (3), pp.2256-2276. ⟨10.1104/pp.16.00711⟩ Article dans une revue hal-02639350v1
Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula. Carine Satge,Sandra Moreau,Erika Sallet,Gaëlle Lefort,Marie-Christine Auriacet al. Nature Plants, 2016, 2, pp.16166. ⟨10.1038/nplants.2016.166⟩ Article dans une revue hal-02636585v1
A Resource Allocation Trade-Off between Virulence and Proliferation Drives Metabolic Versatility in the Plant Pathogen Ralstonia solanacearum Rémi Peyraud,Ludovic Cottret,Lucas Marmiesse,Jerome Gouzy,Stéphane Genin PLoS Pathogens, 2016, 12 (10), pp.e1005939. ⟨10.1371/journal.ppat.1005939⟩ Article dans une revue hal-01404552v1
FlexFlux: combining metabolic flux and regulatory network analyses Lucas Marmiesse,Rémi Peyraud,Ludovic Cottret BMC Systems Biology, 2015, 9, ⟨10.1186/s12918-015-0238-z⟩ Article dans une revue hal-02633823v1
TrypanoCyc: a community-led biochemical pathways database for &lt;em&gt;Trypanosoma brucei&lt;/em&gt; Sanu Shameer,Flora J. Logan-Klumpler,Florence Vinson,Ludovic Cottret,Benjamin Merletet al. Nucleic Acids Research, 2015, 43 (D1), pp.D637 - D644. ⟨10.1093/nar/gku944⟩ Article dans une revue hal-02631222v1
Identification and phylogenetic analyses of VASt, an uncharacterized protein domain associated with lipid-binding domains in Eukaryotes Mehdi Khafif,Ludovic Cottret,Claudine Balague,Sylvain Raffaele BMC Bioinformatics, 2014, 15, 12 p. ⟨10.1186/1471-2105-15-222⟩ Article dans une revue hal-02636200v1
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 Sauviacet al. The Plant Journal, 2014, 77 (6), pp.817-837. ⟨10.1111/tpj.12442⟩ Article dans une revue hal-03082945v1
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 E. Birmeléet al. Bioinformatics, 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩ Article dans une revue hal-00922567v1
Telling stories: Enumerating maximal directed acyclic graphs with a constrained set of sources and targets Vicente Acuña,Etienne Birmelé,Ludovic Cottret,Pierluigi Crescenzi,Fabien Jourdanet al. Theoretical Computer Science, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩ Article dans une revue hal-00764025v1
Exploration of the core metabolism of symbiotic bacteria Cecilia Coimbra Klein,Ludovic Cottret,Janice Kielbassa,Hubert Charles,Christian Gautieret al. BMC Genomics, 2012, 13 (1), pp.438. ⟨10.1186/1471-2164-13-438⟩ Article dans une revue hal-00784396v1
Transcriptome database resource and gene expression atlas for the rose André Dubois,S. Carrere,O. Raymond,B. Pouvreau,L. Cottretet al. BMC Genomics, 2012, 13, pp.638. ⟨10.1186/1471-2164-13-638⟩ Article dans une revue hal-00841830v1
Algorithms and complexity of enumerating minimal precursor sets in genome-wide metabolic networks. Vicente Acuña,Paulo Vieira Milreu,Ludovic Cottret,Alberto Marchetti-Spaccamela,Leen Stougieet al. Bioinformatics, 2012, 28 (19), pp.2474-2483. ⟨10.1093/bioinformatics/bts423⟩ Article dans une revue hal-00751715v1
A genomic reappraisal of symbiotic function in the aphid/buchnera symbiosis: reduced transporter sets and variable membrane organisations. Hubert Charles,Severine Balmand,Araceli Lamelas,Ludovic Cottret,Vicente Pérez-Brocalet al. PLoS ONE, 2011, 6 (12), pp.e29096. ⟨10.1371/journal.pone.0029096⟩ Article dans une revue hal-00659506v1
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 Cottretet al. Database - The journal of Biological Databases and Curation, 2011, 2011, pp.bar008. ⟨10.1093/database/bar008⟩ Article dans une revue hal-00632965v1
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 Stougieet al. PLoS Computational Biology, 2010, 6 (9), epub ahead of print. ⟨10.1371/journal.pcbi.1000904⟩ Article dans une revue hal-00690650v1
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks. Ludovic Cottret,David Wildridge,Florence Vinson,Michael P Barrett,Hubert Charleset al. Nucleic Acids Research, 2010, 38 (Web Server issue), pp.W132-7. ⟨10.1093/nar/gkq312⟩ Article dans une revue hal-00690651v1
Graph methods for the investigation of metabolic networks in parasitology Ludovic Cottret,Fabien Jourdan Parasitology, 2010, 137, pp.1393-1407. ⟨10.1017/S0031182010000363⟩ Article dans une revue istex hal-02661590v1
Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining Fabien Jourdan,Ludovic Cottret,Laurence Huc,David Wildridge,Richard Scheltemaet al. Metabolomics, 2010, 6 (2), pp.312-321. ⟨10.1007/s11306-009-0196-9⟩ Article dans une revue hal-02662801v1
Deciphering the connectivity structure of biological networks using MixNet Franck Picard,V. Miele,L. Cottret,J.J. Daudin,S. Robin BMC Bioinformatics, 2009, in press, pp.1-1 Article dans une revue hal-00391483v1
Deciphering the connectivity structure of biological networks using MixNet Franck Picard,Vincent Miele,Jean-Jacques J.-J. Daudin,Ludovic Cottret,Stephane S. Robin BMC Bioinformatics, 2009, 10, pp.1-11. ⟨10.1186/1471-2105-10-S6-S17⟩ Article dans une revue hal-02658961v1
Systemic analysis of the symbiotic function of Buchnera aphidicola, the primary endosymbiont of the pea aphid Acyrthosiphon pisum. Lilia Brinza,José Viñuelas,Ludovic Cottret,Federica Calevro,Yvan Rahbéet al. Comptes Rendus. Biologies, 2009, 332 (11), pp.1034-49. ⟨10.1016/j.crvi.2009.09.007⟩ Article dans une revue istex hal-00445861v1
Deciphering the connectivity structure of biological networks using MixNet Franck Picard,V. Miele,J.J. Daudin,L. Cottret,S. Robin BMC Bioinformatics, 2009, 10, pp.1-11 Article dans une revue hal-00428390v1
Analyse systémique de la symbiose intracellulaire : évolution et organisation du réseau métabolique des endocytobiotes L. Cottret incollection, 2009, pp.307-316 Article dans une revue hal-00539375v1
An introduction to metabolic networks and their structural analysis. Vincent Lacroix,Ludovic Cottret,Patricia Thebault,Marie-France Sagot IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2008, 5 (4), pp.594-617. ⟨10.1109/TCBB.2008.79⟩ Article dans une revue hal-00355497v1
Metabolic network visualization eliminating node redundance and preserving metabolic pathways Romain Bourqui,L. Cottret,Vincent Lacroix,D. Auber,P. Maryet al. BMC Biology, 2007, 1 - n°29, pp.1-19. ⟨10.1186/1752-0509-1-29⟩ Article dans une revue hal-00434765v1

Communication dans un congrès (33)

Microbiota-Host interactions during juvenile growth: exploration of interconnected metabolic networks Edern Cahoreau,Pavel Melentev,Hanna Kulyk,Lindsay Peyriga,Justine Bertrand-Michelet al. NMR metabolomics symposium, Jun 2025, Nantes (France), France Communication dans un congrès hal-05460083v1
MULTI-ORGAN GENOME-SCALE METABOLIC MODELING OF A TOMATO PLANT AT VEGETATIVE GROWTH STAGE Léo Gerlin,Antoine Escourrou,Ludovic Cottret,Stéphane Genin,Caroline Baroukh 13ème Congrès international de la SFBV, Société Française de la Biologie Végétale, Aug 2022, Montpellier, France Communication dans un congrès hal-04718279v1
Multi-organ genome-scale metabolic modeling of tomato plant Leo Gerlin,Antoine Escourrou,Ludovic Cottret,Stephane Genin,Caroline Baroukh 7th Conference on Constraint-Based Reconstruction and Analysis (COBRA 2021), Mar 2021, Virtual, France Communication dans un congrès hal-03350567v1
Investigation of the metabolic network of Xylella fastidiosa responsible of its fastidious growth Leo Gerlin,Ludovic Cottret,Sophie Cesbron,Geraldine G. Taghouti,Marie-Agnès Jacqueset al. 3rd European Conference on Xylella fastidiosa and the final meeting of the XF-ACTORS project, Apr 2021, Virtual, France Communication dans un congrès hal-03350588v1
Learning Boolean controls in regulated metabolic networks: a case-study Kerian Thuillier,Caroline Baroukh,Alexander Bockmayr,Ludovic Cottret,Loïc Paulevéet al. CMSB 2021 - 19th International Conference on Computational Methods in Systems Biology, 2021, Bordeaux, France. pp.159-180, ⟨10.1007/978-3-030-85633-5_10⟩ Communication dans un congrès hal-03207589v3
Exploration of the growth-virulence trade-off in the plant pathogen Ralstonia solanacearum species complex Caroline Baroukh,Emma Pires,Ludovic Cottret,Remi Peyraud,Stéphane Genin MicrobiOccitanie 2019 - Rencontre des Microbiologistes Région Occitanie, Feb 2019, Montpellier, France Communication dans un congrès hal-02786961v1
Genome-scale investigation of the metabolic determinants generating bacterial fastidious growth Leo Gerlin,Ludovic Cottret,Sophie Cesbron,Géraldine Taghouti,Marie-Agnès Jacqueset al. Symposium on Synthetic and Systemic Biology, Nov 2019, Bordeaux, France Communication dans un congrès hal-03350558v1
Phylogenetic and Phylogenomic Approaches to Decipher the Evolution of the Nitrogen Fixing Root Nodule Symbiosis Jean Keller,Tatiana Vernié,Hélène San Clemente,Ludovic Cottret,Camille Girouet al. 18th Congress of International-Society-for-Molecular-Plant-Microbe-Interactions (IS-MPMI), International Society for Molecular Plant-Microbe Interactions, Jul 2019, Glasgow, United Kingdom. pp.13-13 Communication dans un congrès hal-02961209v1
Visualization of time-series data in the context of metabolic networks with Systrip Software Jonathan Dubois,Ludovic Cottret,Amine Ghozlane,David Auber,Frédéric Bringaudet al. Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2013), Jul 2013, France Communication dans un congrès hal-00838725v1
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 Bringaudet al. 16th International Conference on Information Visualization (IV'12), Jul 2012, Montpellier, France. pp.4771a204 Communication dans un congrès hal-00742176v1
Réévaluation génomique de la fonction de transport chez Buchnera, endocytobiote des pucerons : une faible diversité de transporteurs et une organisation membranaire variable Hubert Charles,Severine Balmand,Araceli Lamelas,Ludovic Cottret,Vicente Pérez-Brocalet al. 4. Réunion Réseau Français de Biologie Adaptative des Pucerons et Organismes Associés, Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). FRA., Nov 2011, Paris, France Communication dans un congrès hal-02808863v1
Absence of a core metabolic network common to symbiotic bacteria Cecilia Coimbra Klein,Ludovic Cottret,Hubert Charles,Christian Gautier,Ana Tereza Ribeiro de Vasconceloset al. 6. Meeting GDRE-RA Comparative genomics, Nov 2011, Lyon, France. 33 diapositives Communication dans un congrès hal-02806316v1
Initial metabolic reconstruction of Klebsiella pneumoniae Kp13, a multidrug resistant pathogen involved in nosocomial outbreaks in Brazil P. Ivan,Cecilia C. Klein,Ludovic Cottret,Ana T Vasconcelos,Ac Galeset al. X-meeting, 2011, Florianópolis, Brazil Communication dans un congrès hal-00748781v1
Metabolic network comparison of bacteria in the context of symbiosis Cecilia C. Klein,Ludovic Cottret,Hubert Charles,Christian Gautier,Ana T Vasconceloset al. Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics, 2011, Berlin, Germany Communication dans un congrès hal-00748784v1
Telling Stories Vicente Acuña,Etienne Birmele,Ludovic Cottret,Pierluigi Crescenzi,Fabien Jourdanet al. ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩ Communication dans un congrès hal-00748788v1
AcypiCyc (Acyrthosiphon pisumCyc database) and CycADS (CycAnnotation Database System) : moving from genome sequence annotation to metabolic network analyses Stefano Colella,Augusto Vellozo,Ludovic Cottret,Gérard Febvay,Federica Calevroet al. Réseau Français de Biologie Adaptative des Pucerons, 2009, Paris, juin 2009, France Communication dans un congrès hal-02815123v1
The Acyrthosiphon pisum Cyc database (AcypiCyc) created using a novel BioCyc Annotation Database System (CycADS): a useful tool to explore and study the pea aphid metabolism Stefano Colella,A. Vellozo,Ludovic Cottret,Gérard Febvay,Federica Calevroet al. 5th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 2, Barcelona, Espagne, juin 2009, Jun 2009, France Communication dans un congrès hal-00498411v1
AcypiCyc (Acyrthosiphon pisum Cyc database) : a model database to visualize and study the metabolic network underlying the pea aphid-Buchnera symbiosis Stefano Colella,Augusto Vellozo,Ludovic Cottret,Gérard Febvay,Federica Calevroet al. 6. International Symbiosis Society (ISS) Congress, 2009, Madison, août 2009, United States Communication dans un congrès hal-02814342v1
AcypiCyc (Acyrthosiphon pisum Cyc database) and CycADS (Cyc Annotation Database System): moving from genome sequence annotation to metabolic network analyses Stefano Colella,A. Vellozo,L. Cottret,G. Febvay,Federica Calevroet al. 8th International Symposium on Aphids (8 ISA 2009), 2009, Catania (Italie), juin 2009, France. pp.1-1 Communication dans un congrès hal-00391280v1
CycADS: an annotation management system for the development and update of BioCyc metabolic network databases A. Vellozo,Patrice Baa-Puyoulet,A. Veron,Jaime Huerta-Cepas,Ludovic Cottretet al. 1st International Workshop on Information Systems for Insect Pests, Rennes, FRANCE, 2009, France Communication dans un congrès hal-00496032v1
Development of the Acyrthosiphon pisum Cyc database (ApsCyc) : from genome sequence to metabolic network analyses Augusto Vellozo,Stefano Colella,Ludovic Cottret,Gérard Febvay,Federica Calevroet al. Integrative Post-Genomics - IPG'08, 2008, Lyon, novembre 2008, France Communication dans un congrès hal-02821711v1
Caractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum Hubert Charles,Federica Calevro,Stefano Colella,Jean-Michel Fayard,Gérard Febvayet al. Séminaire INRA AgroBI, 2008, Bordeaux, décembre 2008, France Communication dans un congrès hal-02824972v1
Annotation of metabolism genes: towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses Stefano Colella,A. Vellozo,L. Cottret,G. Febvay,Federica Calevroet al. 4th Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1", 2008, Princetown (USA), juillet 2008, France. pp.1-1 Communication dans un congrès hal-00391279v1
Development of the Acyrthosiphon pisum Cyc database (ApsCyc): from genome sequence to metabolic network analyses A. Vellozo,Stefano Colella,L. Cottret,G. Febvay,Federica Calevroet al. Integrative Post-Genomics - IPG'08, 2008, Lyon (France), novembre 2008, France. pp.1-1 Communication dans un congrès hal-00391519v1
Metabolic network reconstruction from genomic annotations L. Cottret First Systryp meeting, 2008, Glasgow (UK), juin 2008, France. pp.1-1 Communication dans un congrès hal-00391287v1
Interactions trophiques dans la symbiose puceron - Buchnera : Régulations transcriptionnelles de la réponse à la carence en acides aminés essentiels Federica Calevro,H. Charles,J.M. Fayard,G. Febvay,Yvan Rahbéet al. Réseau Français de Biologie Adaptative des Pucerons, 2008, Paris (France), janvier 2008, France. pp.1-1 Communication dans un congrès hal-00391259v1
Caractérisation et modélisation de la « fonction symbiotique » de Buchnera aphidicola chez le puceron du pois Acyrthosiphon pisum H. Charles,Federica Calevro,Stefano Colella,J.M. Fayard,G. Febvayet al. Séminaire INRA AgroBI, 2008, Bordeaux (France), décembre 2008, France. pp.1-1 Communication dans un congrès hal-00391273v1
Enumerating precursor sets of target metabolites in a metabolic network L. Cottret,P.V. Milreu,Vicente Acuna,A. Marchetti-Spaccamela,F. Viduani Martinezet al. WABI 2008 - 8th International Workshop on Algorithms in Bioinformatics, Sep 2008, Karlsruhe, Germany. pp.233-244 Communication dans un congrès hal-00391292v1
SymBioCyc: Metabolic data on endosymbiotic, parasitic and free bacteria L. Cottret,H. Charles,M.F. Sagot Integrative Post-Genomics - IPG'07, 2007, Lyon (France), novembre 2007, France. pp.1-1 Communication dans un congrès hal-00391290v1
Regulation of expression following nutritional stresses in the reduced genome of Buchnera aphidicola, &quot;Is there any life left? Yvan Rahbé,H. Charles,J. Vinuelas,N. Reymond,Federica Calevroet al. Seminarios del Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE) - Univ. Valencia (ESP), 2007, Valencia (Espagne), juin 2007, France. pp.1-1 Communication dans un congrès hal-00391505v1
Enumerating precursor sets of target metabolites in a metabolic network L. Cottret,P.V. Milreu,Vicente Acuna,A. Marchetti-Spaccamela,F. Viduani Martinezet al. 8th Workshop on Algorithms in Bioinformatics (WABI), 2007, Karlsruhe (Allemagne), septembre 2008, France. pp.233-244 Communication dans un congrès hal-00391291v1
Recherche de précurseurs dans un réseau métabolique L. Cottret,Vicente Acuna,H. Charles,M.F. Sagot Réseaux d'interaction : analyse, modélisation et simulation (RIAMS), 2007, Villeurbanne (France), novembre 2007, France. pp.1-1 Communication dans un congrès hal-00391288v1
Régulation génétique et métabolique chez Buchnera aphidicola (AgroBi 2006) L. Cottret,L. Brinza,J. Vinuelas,G. Duport,Federica Calevroet al. Journée INRA-INRIA "Insertion des mathématiques dans les approches biologiques : du gène à l'organisme", 2006, Lyon (France), décembre 2006, France. pp.1-1 Communication dans un congrès hal-00391289v1

Poster de conférence (9)

MetExploreViz, online visualisation tool for metabolic networks Jean-clément Gallardo,Marion Liotier,Florence Vinson,Fabien Jourdan,Ludovic Cottret Metabolomics 2025, Jun 2025, Prague, Czech Republic. 12, 2016 Poster de conférence hal-05180188v1
Functional analysis of metabolic networks and host-microbiota interactions using multimodal Metabolomics. A Methodological Approach Using Mass Spectrometry, NMR, DESI Imaging, and Modeling. Hanna Kulyk,Pavel Melentev,Edern Cahoreau,Pauline Le Faouder,Lindsay Peyrigaet al. RFMF 2025, Jun 2025, Paris, France Poster de conférence hal-05479492v1
MtCel2, a new cellulase involved in the establishment of the Medicago truncatula-Sinorhizobium meliloti symbiosis María Isabel Rubia,Lisa Frances,Maria Fernanda Guerrero-Molina,Marilyne Renard,Anaïs Dufouret al. 15th European Nitrogen Fixation Conference, Aug 2023, Naples, Italy Poster de conférence hal-04909369v1
MetExplore: Omics data analysis in the context of metabolic networks Maxime Chazalviel,Adrien Rohan,Nathalie Poupin,Florence Vinson,Clément Frainayet al. European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France. Poster de conférence hal-02948391v1
Metabolic modelling of trophic interactions between a plant pathogen and its host plant Caroline Baroukh,Rémi Peyraud,Ludovic Cottret,Stéphane Genin International Plant Systems Biology, Sep 2018, Roscoff, France. , 2018 Poster de conférence hal-02786492v1
TrypanoCyc: a community effort towards the development of a metabolic pathway database for Trypanosoma brucei. Flora Logan-Klumpler,Ludovic Cottret,Florence Vinson,Fabien Jourdan,Michael Barrett Kinetoplastid Molecular Cell Biology Meeting (KMCB 2011), 2011, Inconnue, France. 2011 Poster de conférence hal-02803549v1
MetExplore, a framework for the analysis of metabolic networks: applications in the field of metabolomics data and the study of endocrine disruptors Ludovic Cottret,Florence Vinson,Nicolas J. Cabaton,Maria-Helena Meireles,Daniel Zalkoet al. 6th Copenhagen Workshop on Endocrine Disrupters, Apr 2011, Copenhague, Denmark. 2011 Poster de conférence hal-02802904v1
MetExplore: a web server to link metabolomic experiments and genome-scale metabolic networks Ludovic Cottret,David Wildridge,Florence Vinson,Michael P. Barrett,Marie-France Sagotet al. JOBIM 2010, Sep 2010, Montpellier, France. , 1 p., 2010, JOBIM 2010 Montpellier, Journée Ouvertes Biologie Informatique Mathématique, Montpellier, France, 7 - 9 septembre 2010 Poster de conférence hal-02821730v1
Annotation of metabolism genes : towads the implementation of an Acyrthosiphon pisum Cyc database (ApsCyc) to perform metabolic network analyses Stefano Colella,Augusto Vellozo,L. Cottret,Gérard Febvay,Federica Calevroet al. 4. Meeting of the International Aphid Genomics Consortium "Pea Aphid Genome Annotation Workshop 1", 2008, Princetown, juillet 2008, United States. 2008 Poster de conférence hal-02818508v1

Pré-publication, Document de travail (3)

Unlocking the Microbiome-Metabolome Nexus for Innovative One-Health Solution Nicolas Creusot,Floriant Bellvert,Samuel Bertrand,Cédric Bertrand,Simon Colaset al. 2026 Pré-publication, Document de travail hal-05228419v2
Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes and can stimulate root development and colonization by arbuscular mycorrhizal fungi Claudia Bartoli,Stéphane Boivin,Marta Marchetti,Carine Gris,Virginie Gasciolliet al. 2020 Pré-publication, Document de travail hal-02967159v1
Family-Companion: analyse, visualise, browse, query and share your homology clusters Ludovic Cottret,Corinne Rancurel,Martial Briand,Sébastien Carrere 2018 Pré-publication, Document de travail (preprint/prepublication) hal-02788818v1

Thèse (1)

Analyse systémique de la symbiose intracellulaire : évolution et organisation du réseau métabolique des endocytobiotes. Ludovic Cottret Sciences du Vivant [q-bio]. Université Claude Bernard - Lyon I, 2009. Français. ⟨NNT : ⟩ Thèse tel-00494581v1