Ludovic Cottret

93
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Publications

Publications

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Insights into the metabolic specificities of pathogenic strains from the Ralstonia solanacearum species complex

Caroline Baroukh , Ludovic Cottret , Emma Pires , Rémi Peyraud , Alice Guidot et al.

mSystems, 2023, 18 p. ⟨10.1128/msystems.00083-23⟩

Article dans une revue hal-04172034v1
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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 Gaston et al.

Protein Science, 2022, 31 (6), 17 p. ⟨10.1002/pro.4327⟩

Article dans une revue hal-03684572v1
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MtEFD and MtEFD2: Two transcription factors with distinct neofunctionalization in symbiotic nodule development

Marie-Françoise Jardinaud , Justine Fromentin , Marie-Christine Auriac , Sandra Moreau , Yann Pecrix et al.

Plant Physiology, 2022, 189 (3), pp.1587 - 1607. ⟨10.1093/plphys/kiac177⟩

Article dans une revue hal-03728310v1
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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
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Rhizobium leguminosarum symbiovar viciae strains are natural wheat endophytes that can stimulate root development

Claudia Bartoli , Stéphane Boivin , Marta Marchetti , Carine Gris , Virginie Gasciolli et al.

Environmental Microbiology, 2022, 24 (11), pp.5509-5523. ⟨10.1111/1462-2920.16148⟩

Article dans une revue hal-04204399v2
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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-Erckelboudt et al.

Microorganisms, 2022, 10 (9), pp.1859. ⟨10.3390/microorganisms10091859⟩

Article dans une revue hal-04204410v2
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MERRIN: MEtabolic Regulation Rule INference from time series data

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et al.

Bioinformatics, 2022, 38 (Supplement_2), pp.ii127-ii133. ⟨10.1093/bioinformatics/btac479⟩

Article dans une revue hal-03701755v2
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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 Cazalé et al.

Molecular Plant Pathology, 2020, 21 (10), pp.1257-1270. ⟨10.1111/mpp.12965⟩

Article dans une revue hal-03052440v1
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An ancestral signalling pathway is conserved in intracellular symbioses-forming plant lineages

Guru Radhakrishnan , Jean Keller , Mélanie K Rich , Tatiana Vernié , Duchesse Lacour Mbadinga Mbadinga et al.

Nature Plants, 2020, 6 (3), pp.280-289. ⟨10.1038/s41477-020-0613-7⟩

Article dans une revue hal-02550894v1
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Genome-Scale Investigation of the Metabolic Determinants Generating Bacterial Fastidious Growth

Léo Gerlin , Ludovic Cottret , Sophie Cesbron , Geraldine G. Taghouti , Marie-Agnès Jacques et al.

mSystems, 2020, 5 (2), 15 p. ⟨10.1128/mSystems.00698-19⟩

Article dans une revue hal-02901652v1
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Computational analysis of the Plasmodiophora brassicae genome: mitochondrial sequence description and metabolic pathway database design

Stéphanie Daval , Arnaud Belcour , Kévin Gazengel , Ludovic Legrand , Jerome Gouzy et al.

Genomics, 2019, 111 (6), pp.1629-1640. ⟨10.1016/j.ygeno.2018.11.013⟩

Article dans une revue hal-01943250v1
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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 Legrand et al.

The Plant Journal, 2019, 97 (4), ⟨10.1111/tpj.14157⟩

Article dans une revue hal-01990159v1
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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
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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
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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
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MetExplore: collaborative edition and exploration of metabolic networks

Ludovic Cottret , Clément Frainay , Maxime Chazalviel , Floréal Cabanettes , Yoann Gloaguen et al.

Nucleic Acids Research, 2018, 46 (W1), 8 p. ⟨10.1093/nar/gky301⟩

Article dans une revue hal-01886470v1
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MetExploreViz: web component for interactive metabolic network visualization

Maxime Chazalviel , Clément Frainay , Nathalie Poupin , Florence Vinson , Benjamin Merlet et al.

Bioinformatics, 2018, 34 (2), pp.312-313. ⟨10.1093/bioinformatics/btx588⟩

Article dans une revue hal-02621786v1
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The Rosa genome provides new insights into the domestication of modern roses

Olivier Raymond , Jerome Gouzy , Jérémy Just , Hélène Badouin , Marion Verdenaud et al.

Nature Genetics, 2018, 50 (6), pp.772-777. ⟨10.1038/s41588-018-0110-3⟩

Article dans une revue hal-01798003v1
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The sunflower genome provides insights into oil metabolism, flowering and Asterid evolution

Hélène Badouin , Jerome Gouzy , Christopher Grassa , Florent Murat , S Evan Staton et 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-Mestries et al.

Frontiers in Plant Science, 2017, 8, ⟨10.3389/fpls.2017.01633⟩

Article dans une revue hal-04779355v1
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Genomic Prediction of Sunflower Hybrids Oil Content

Brigitte Mangin , Fanny Bonnafous , Nicolas Blanchet , Marie-Claude Boniface , Emmanuelle Bret-Mestries et al.

Frontiers in Plant Science, 2017, 8, pp.1-12. ⟨10.3389/fpls.2017.01633⟩

Article dans une revue hal-02624895v1

Reprogramming of DNA methylation is critical for nodule development in Medicago truncatula.

Carine Satge , Sandra Moreau , Erika Sallet , Gaëlle Lefort , Marie-Christine Auriac et al.

Nature Plants, 2016, 2, pp.16166. ⟨10.1038/nplants.2016.166⟩

Article dans une revue hal-02636585v1

A laser dissection-RNAseq analysis highlights the activation of cytokinin pathways by nod factors in the <em>Medicago truncatula</em> root epidermis

Marie-Françoise Jardinaud , Stephane Boivin , Nathalie N. Rodde , Olivier Catrice , Anna Kisiala et al.

Plant Physiology, 2016, 171 (3), pp.2256-2276. ⟨10.1104/pp.16.00711⟩

Article dans une revue hal-02639350v1
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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
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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
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TrypanoCyc: a community-led biochemical pathways database for <em>Trypanosoma brucei</em>

Sanu Shameer , Flora J. Logan-Klumpler , Florence Vinson , Ludovic Cottret , Benjamin Merlet et al.

Nucleic Acids Research, 2015, 43 (D1), pp.D637 - D644. ⟨10.1093/nar/gku944⟩

Article dans une revue hal-02631222v1
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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 Sauviac et al.

The Plant Journal, 2014, 77 (6), pp.817-837. ⟨10.1111/tpj.12442⟩

Article dans une revue hal-03082945v1
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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. Birmelé et al.

Bioinformatics, 2014, 30 (1), pp.61-70. ⟨10.1093/bioinformatics/btt597⟩

Article dans une revue hal-00922567v1
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Exploration of the core metabolism of symbiotic bacteria

Cecilia Coimbra Klein , Ludovic Cottret , Janice Kielbassa , Hubert Charles , Christian Gautier et al.

BMC Genomics, 2012, 13 (1), pp.438. ⟨10.1186/1471-2164-13-438⟩

Article dans une revue hal-00784396v1
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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 et al.

Theoretical Computer Science, 2012, 457, pp.1--9. ⟨10.1016/j.tcs.2012.07.023⟩

Article dans une revue istex hal-00764025v1
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Transcriptome database resource and gene expression atlas for the rose

André Dubois , S. Carrere , O. Raymond , B. Pouvreau , L. Cottret et 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 Stougie et al.

Bioinformatics, 2012, 28 (19), pp.2474-2483. ⟨10.1093/bioinformatics/bts423⟩

Article dans une revue hal-00751715v1
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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-Brocal et al.

PLoS ONE, 2011, 6 (12), pp.e29096. ⟨10.1371/journal.pone.0029096⟩

Article dans une revue hal-00659506v1
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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 et al.

Database - The journal of Biological Databases and Curation, 2011, 2011, pp.bar008. ⟨10.1093/database/bar008⟩

Article dans une revue hal-00632965v1
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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 et al.

PLoS Computational Biology, 2010, 6 (9), epub ahead of print. ⟨10.1371/journal.pcbi.1000904⟩

Article dans une revue hal-00690650v1

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

Ludovic Cottret , David Wildridge , Florence Vinson , Michael P Barrett , Hubert Charles et al.

Nucleic Acids Research, 2010, 38 (Web Server issue), pp.W132-7. ⟨10.1093/nar/gkq312⟩

Article dans une revue hal-00690651v1
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Use of reconstituted metabolic networks to assist in metabolomic data visualization and mining

Fabien Jourdan , Ludovic Cottret , Laurence Huc , David Wildridge , Richard Scheltema et al.

Metabolomics, 2010, 6 (2), pp.312-321. ⟨10.1007/s11306-009-0196-9⟩

Article dans une revue hal-02662801v1
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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

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

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 Rahbé et 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
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Metabolic network visualization eliminating node redundance and preserving metabolic pathways

Romain Bourqui , L. Cottret , Vincent Lacroix , D. Auber , P. Mary et al.

BMC Biology, 2007, 1 - n°29, pp.1-19. ⟨10.1186/1752-0509-1-29⟩

Article dans une revue hal-00434765v1

Microbiota-Host interactions during juvenile growth: exploration of interconnected metabolic networks

Edern Cahoreau , Pavel Melentev , Hanna Kulyk , Lindsay Peyriga , Justine Bertrand-Michel et al.

NMR metabolomics symposium, Jun 2025, Nantes (France), France

Communication dans un congrès hal-05460083v1
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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

Investigation of the metabolic network of Xylella fastidiosa responsible of its fastidious growth

Leo Gerlin , Ludovic Cottret , Sophie Cesbron , Geraldine G. Taghouti , Marie-Agnès Jacques et 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
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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
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Learning Boolean controls in regulated metabolic networks: a case-study

Kerian Thuillier , Caroline Baroukh , Alexander Bockmayr , Ludovic Cottret , Loïc Paulevé et 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
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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
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Genome-scale investigation of the metabolic determinants generating bacterial fastidious growth

Leo Gerlin , Ludovic Cottret , Sophie Cesbron , Géraldine Taghouti , Marie-Agnès Jacques et 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 Girou et 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
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Visualization of time-series data in the context of metabolic networks with Systrip Software

Jonathan Dubois , Ludovic Cottret , Amine Ghozlane , David Auber , Frédéric Bringaud et al.

Journées Ouvertes Biologie Informatique Mathématiques (JOBIM 2013), Jul 2013, France

Communication dans un congrès hal-00838725v1
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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 et 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-Brocal et 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

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 Gales et al.

X-meeting, 2011, Florianópolis, Brazil

Communication dans un congrès hal-00748781v1
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Absence of a core metabolic network common to symbiotic bacteria

Cecilia Coimbra Klein , Ludovic Cottret , Hubert Charles , Christian Gautier , Ana Tereza Ribeiro de Vasconcelos et al.

6. Meeting GDRE-RA Comparative genomics, Nov 2011, Lyon, France. 33 diapositives

Communication dans un congrès hal-02806316v1

Telling Stories

Vicente Acuña , Etienne Birmele , Ludovic Cottret , Pierluigi Crescenzi , Fabien Jourdan et al.

ICALP 2011 satellite workshop: Graph Algorithms and Applications (GA), 2011, Zurich, Switzerland. ⟨10.1016/j.tcs.2012.07.023⟩

Communication dans un congrès istex hal-00748788v1

Metabolic network comparison of bacteria in the context of symbiosis

Cecilia C. Klein , Ludovic Cottret , Hubert Charles , Christian Gautier , Ana T Vasconcelos et al.

Otto Warburg International Summer School and Research Symposium on Evolutionary Genomics, 2011, Berlin, Germany

Communication dans un congrès hal-00748784v1

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 Calevro et 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) and CycADS (Cyc Annotation Database System): moving from genome sequence annotation to metabolic network analyses

Stefano Colella , A. Vellozo , L. Cottret , G. Febvay , Federica Calevro et al.

8th International Symposium on Aphids (8 ISA 2009), 2009, Catania (Italie), juin 2009, France. pp.1-1

Communication dans un congrès hal-00391280v1

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 Calevro et al.

6. International Symbiosis Society (ISS) Congress, 2009, Madison, août 2009, United States

Communication dans un congrès hal-02814342v1

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 Cottret et al.

1st International Workshop on Information Systems for Insect Pests, Rennes, FRANCE, 2009, France

Communication dans un congrès hal-00496032v1

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 Calevro et al.

Réseau Français de Biologie Adaptative des Pucerons, 2009, Paris, juin 2009, France

Communication dans un congrès hal-02815123v1

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 Calevro et al.

8. International Symposium on Aphids (8 ISA 2009), 2009, Catania, juin 2009, Italy

Communication dans un congrès hal-02814863v1

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 Calevro et 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 Calevro et al.

Integrative Post-Genomics - IPG'08, 2008, Lyon (France), novembre 2008, France. pp.1-1

Communication dans un congrès hal-00391519v1

Development of the Acyrthosiphon pisum Cyc database (ApsCyc) : from genome sequence to metabolic network analyses

Augusto Vellozo , Stefano Colella , Ludovic Cottret , Gérard Febvay , Federica Calevro et 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 Febvay et al.

Séminaire INRA AgroBI, 2008, Bordeaux, décembre 2008, France

Communication dans un congrès hal-02824972v1

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

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. Febvay et al.

Séminaire INRA AgroBI, 2008, Bordeaux (France), décembre 2008, France. pp.1-1

Communication dans un congrès hal-00391273v1

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 Rahbé et al.

Réseau Français de Biologie Adaptative des Pucerons, 2008, Paris (France), janvier 2008, France. pp.1-1

Communication dans un congrès hal-00391259v1

Enumerating precursor sets of target metabolites in a metabolic network

L. Cottret , P.V. Milreu , Vicente Acuna , A. Marchetti-Spaccamela , F. Viduani Martinez et 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, "Is there any life left?

Yvan Rahbé , H. Charles , J. Vinuelas , N. Reymond , Federica Calevro et 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 Martinez et 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 Calevro et 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
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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
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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 Peyriga et 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 Dufour et al.

15th European Nitrogen Fixation Conference, Aug 2023, Naples, Italy

Poster de conférence hal-04909369v1
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MetExplore: Omics data analysis in the context of metabolic networks

Maxime Chazalviel , Adrien Rohan , Nathalie Poupin , Florence Vinson , Clément Frainay et al.

European RFMF Metabomeeting 2020, Jan 2020, Toulouse, France.

Poster de conférence hal-02948391v1
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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 Zalko et 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 Sagot et 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 Calevro et 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