Claudine MEDIGUE

Identifiants chercheurs

IdHAL :

claudine-medigue

ORCID :

0000-0002-3905-1054

IdRef :

08942719X

VIAF :

197918831

ISNI :

0000000139824099

Publications

Article dans une revue (137)

Establishing the ELIXIR Microbiome Community Robert D Finn,Bachir Balech,Josephine Burgin,Physilia Chua,Erwan Correet al. F1000Research, 2025, 13, pp.50. ⟨10.12688/f1000research.144515.2⟩ Article dans une revue (article de synthèse) hal-04796156v1
A model industrial workhorse: $Bacillus\ subtilis$ strain 168 and its genome after a quarter of a century Erhard Bremer,Alexandra Calteau,Antoine Danchin,Colin Harwood,John D Helmannet al. Microbial Biotechnology, 2023, 16 (6), pp.1203-1231. ⟨10.1111/1751-7915.14257⟩ Article dans une revue cea-04284953v1
ProMetIS, deep phenotyping of mouse models by combined proteomics and metabolomics analysis Alyssa Imbert,Magali Rompais,Mohammed Selloum,Florence Castelli,Emmanuelle Mouton-Barbosaet al. Scientific Data , 2021, 8 (1), pp.311. ⟨10.1038/s41597-021-01095-3⟩ Article dans une revue pasteur-03453736v1
panRGP: a pangenome-based method to predict genomic islands and explore their diversity Adelme Bazin,Guillaume Gautreau,Claudine Médigue,David Vallenet,Alexandra Calteau Bioinformatics, 2020, 36 (Supplément 2), pp.i651 - i658. ⟨10.1093/bioinformatics/btaa792⟩ Article dans une revue hal-03322363v1
TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages Daria Bottai,Wafa Frigui,Fadel Sayes,Mariagrazia Di Luca,Dalila Spadoniet al. Nature Communications, 2020, 11 (1), pp.684. ⟨10.1038/s41467-020-14508-5⟩ Article dans une revue pasteur-02473990v1
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph Guillaume Gautreau,Adelme Bazin,Mathieu Gachet,Rémi Planel,Laura Burlotet al. PLoS Computational Biology, 2020, ⟨10.1371/journal.pcbi.1007732⟩ Article dans une revue hal-03089210v1
Ancestral state reconstruction of metabolic pathways across pangenome ensembles Fotis Psomopoulos,Jacques van Helden,Claudine Médigue,Anastasia Chasapi,Christos Ouzounis Microbial Genomics, 2020, 6 (11), ⟨10.1099/mgen.0.000429⟩ Article dans une revue hal-03089213v1
The arginine deiminase operon is responsible for a fitness trade-off in extended-spectrum-beta-lactamase-producing strains of Escherichia coli Typhaine Billard-Pomares,Olivier Clermont,Miguel Castellanos,Fatma Magdoud,Guilhem Royeret al. Antimicrobial Agents and Chemotherapy, 2019, 63 (8), pp.e00635-19. ⟨10.1128/AAC.e00635-19⟩ Article dans une revue cea-04307623v1
The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-␤-Lactamase-Producing Strains of Escherichia coli Typhaine Billard-Pomares,Olivier P Clermont,Miguel Castellanos,Fatma Magdoud,Guilhem Royeret al. Antimicrobial Agents and Chemotherapy, 2019, ⟨10.1128/AAC⟩ Article dans une revue hal-02413136v1
The Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli Typhaine Billard-Pomares,Olivier Clermont,Miguel Castellanos,Fatma Magdoud,Guilhem Royeret al. Antimicrobial Agents and Chemotherapy, 2019, 63 (8), pp.1521-1530. ⟨10.1128/AAC.00635-19⟩ Article dans une revue hal-04283183v1
Specialization of small non-conjugative plasmids in Escherichia coli according to their family types Catherine Branger,Alice Ledda,Typhaine Billard-Pomares,Benoît Doublet,Valérie Barbeet al. Microbial Genomics, 2019, 5 (9), 13p. ⟨10.1099/mgen.0.000281⟩ Article dans une revue hal-02403160v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis David Vallenet,Alexandra Calteau,Mathieu Dubois,Paul Amours,Adelme Bazinet al. Nucleic Acids Research, 2019, 48 (D1), pp.D579-D589. ⟨10.1093/nar/gkz926⟩ Article dans une revue hal-02403170v1
MicroScope—an integrated resource for community expertise of gene functions and comparative analysis of microbial genomic and metabolic data Claudine Médigue,Alexandra Calteau,Stéphane Cruveiller,Mathieu Gachet,Guillaume Gautreauet al. Briefings in Bioinformatics, 2019, 20 (4), pp.1071-1084. ⟨10.1093/bib/bbx113⟩ Article dans une revue hal-02626039v1
GROOLS: reactive graph reasoning for genome annotation through biological processes Jonathan Mercier,Adrien Josso,Claudine Medigue,David Vallenet BMC Bioinformatics, 2018, 19, pp.132. ⟨10.1186/s12859-018-2126-1⟩ Article dans une revue cea-04313474v1
PlaScope: a targeted approach to assess the plasmidome from genome assemblies at the species level G. Royer,J. W. Decousser,C. Branger,M. Dubois,C. Medigueet al. Microbial Genomics, 2018, 4 (9), pp.000211. ⟨10.1099/mgen.0.000211⟩ Article dans une revue cea-02291353v1
The Odyssey of the Ancestral Escherich Strain through Culture Collections: an Example of Allopatric Diversification M. Desroches,G. Royer,D. Roche,M. Mercier-Darty,D. Vallenetet al. MSphere, 2018, 3 (1), ⟨10.1128/mSphere.00553-17⟩ Article dans une revue hal-04283164v1
Extended-spectrum b-lactamase-encoding genes are spreading on a wide range of Escherichia coli plasmids existing prior to the use of third-generation cephalosporins Catherine Branger,Alice Ledda,Typhaine Billard-Pomares,Benoît Doublet,Stéphanie Fouteauet al. Microbial Genomics, 2018, 4 (9), 16 p. ⟨10.1099/mgen.0.000203⟩ Article dans une revue hal-02403119v1
Vibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs Graciela M. Dias,Adeline Bidault,Patrick Le Chevalier,Gwenaëlle Choquet,Clio Der Sarkissianet al. Frontiers in Microbiology, 2018, 9, pp.227. ⟨10.3389/fmicb.2018.00227⟩ Article dans une revue hal-02177600v1
Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation Evelyne Krin,Sebastian Aguilar Pierlé,Odile Sismeiro,Bernd Jagla,Marie-Agnès Dillieset al. BMC Genomics, 2018, 19 (1), pp.373. ⟨10.1186/s12864-018-4716-8⟩ Article dans une revue pasteur-02562431v1
Bacillus subtilis, the model Gram-positive bacterium: 20years of annotation refinement Rainer Borriss,Antoine Danchin,Colin R. Harwood,Claudine Médigue,Eduardo P. C. Rochaet al. Microbial Biotechnology, 2018, 11 (1), pp.3-17. ⟨10.1111/1751-7915.13043⟩ Article dans une revue cea-02291345v1
MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes David Vallenet,Alexandra Calteau,Stéphane Cruveiller,Mathieu Gachet,Aurélie Lajuset al. Nucleic Acids Research, 2017, 45 (D1), pp.D517-D528. ⟨10.1093/nar/gkw1101⟩ Article dans une revue cea-04320303v1
Parallel evolution of non-homologous isofunctional enzymes in methionine biosynthesis Karine Bastard,Alain Perret,Aline Mariage,Thomas Bessonnet,Agnès Pinet-Turpaultet al. Nature Chemical Biology, 2017, 13, pp.858-866. ⟨10.1038/nchembio.2397⟩ Article dans une revue cea-02132779v1
Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21 Françoise Bringel,Christiaan Postema,Sophie Mangenot,Sabrina Bibi-Triki,Pauline Chaignaudet al. Genome Announcements, 2017, 5 (30), ⟨10.1128/genomeA.00622-17⟩ Article dans une revue hal-02328278v1
Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria Elizabeth Ficko-Blean,Aurelie Prechoux,François Thomas,Tatiana Rochat,Robert Larocqueet al. Nature Communications, 2017, 8, pp.1685. ⟨10.1038/s41467-017-01832-6⟩ Article dans une revue hal-01899178v1
Comparative genomics between two Xenorhabdus bovienii strains highlights differential evolutionary scenarios within an entomopathogenic bacterial species Gaelle Bisch,Jean-Claude Ogier,Claudine Médigue,Zoé Rouy,Stéphanie Vincentet al. Genome Biology and Evolution, 2016, 8 (1), pp.148-160. ⟨10.1093/gbe/evv248⟩ Article dans une revue hal-01837293v1
The chimeric nature of the genomes of marine magnetotactic coccoid-ovoid bacteria defines a novel group of Proteobacteria. Boyang Ji,Sheng-Da Zhang,Wei-Jia Zhang,Zoe Rouy,François Albertoet al. Environmental Microbiology, 2016, pp.doi: 10.1111/1462-2920.13637. ⟨10.1111/1462-2920.13637⟩ Article dans une revue hal-01410134v1
Complete Genome Sequence of Bacillus methylotrophicus Strain B25, a Potential Plant Growth-Promoting Rhizobacterium Jonathan Gerbore,Aline Brutel,Arnaud Lemainque,Barbara Mairey,Claudine Medigueet al. Genome Announcements, 2016, 4 (2), ⟨10.1128/genomeA.00058-16⟩ Article dans une revue cea-04541792v1
RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori Yulia Redko,Eloïse Galtier,Hélène Arnion,Fabien Darfeuille,Odile Sismeiroet al. RNA Biology, 2016, 13 (2), pp.243-253. ⟨10.1080/15476286.2015.1132141⟩ Article dans une revue cea-04541794v1
Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria Jessica Plucain,Antonia Suau,Stéphane Cruveiller,Claudine Médigue,Dominique Schneideret al. BMC Evolutionary Biology, 2016, 16 (1), ⟨10.1186/s12862-016-0662-8⟩ Article dans une revue hal-01653387v1
The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis Eugeni Belda,Ruben G. A. Van Heck,Maria José Lopez-Sanchez,Stéphane Cruveiller,Valérie Barbeet al. Environmental Microbiology, 2016, 18 (10), pp.3403-3424. ⟨10.1111/1462-2920.13230⟩ Article dans une revue cea-04541789v1
Tempo and mode of genome evolution in a 50,000-generation experiment Olivier Tenaillon,Jeffrey E. Barrick,Noah Ribeck,Daniel E. Deatherage,Jeffrey L. Blanchardet al. Nature, 2016, 536 (7615), pp.165 - 170. ⟨10.1038/nature18959⟩ Article dans une revue hal-01653393v1
Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain Benoit Remenant,Frederic Borges,Catherine Cailliez-Grimal,Anne-Marie Revol-Junelles,Laurent Marchéet al. Genome Announcements, 2016, 4 (5), pp.e01109-16. ⟨10.1128/genomeA.01109-16⟩ Article dans une revue hal-02498294v1
Genomic and physiological analysis reveals versatile metabolic capacity of deep-sea Photobacterium phosphoreum ANT-2200. Sheng-Da Zhang,Claire-Lise Santini,Wei-Jia Zhang,Valérie Barbe,Sophie Mangenotet al. Extremophiles life under extreme conditions, 2016, 20 (3), pp.301-10. ⟨10.1007/s00792-016-0822-1⟩ Article dans une revue hal-01410136v1
16S rRNA and As-Related Functional Diversity: Contrasting Fingerprints in Arsenic-Rich Sediments from an Acid Mine Drainage Anne Fahy,L. Giloteaux,Philippe N. Bertin,D. Le Paslier,C. Médigueet al. Microbial ecology, 2015, 70 (1), pp.154-167. ⟨10.1007/s00248-014-0558-3⟩ Article dans une revue hal-01631845v1
Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment Rohan Maddamsetti,Philip J. Hatcher,Stéphane Cruveiller,Claudine Medigue,Jeffrey E. Barricket al. Molecular Biology and Evolution, 2015, 32 (11), pp.2897-2904. ⟨10.1093/molbev/msv161⟩ Article dans une revue cea-04573295v1
Candidatus Frankia Datiscae Dg1, the Actinobacterial Microsymbiont of Datisca glomerata, Expresses the Canonical nod Genes nodABC in Symbiosis with Its Host Plant T. Persson,K. Battenberg,I. V. Demina,T. Vigil-Stenman,B. Vanden Heuvelet al. PLoS ONE, 2015, 10 (5), pp.e0127630. ⟨10.1371/journal.pone.0127630⟩ Article dans une revue hal-02487299v1
A new network representation of the metabolism to detect chemical transformation modules Maria Sorokina,Claudine Medigue,David Vallenet BMC Bioinformatics, 2015, 16, pp.385. ⟨10.1186/s12859-015-0809-4⟩ Article dans une revue cea-04573300v1
Revealing the hidden functional diversity of an enzyme family Karine Bastard,Adam Alexander Thil Smith,Carine Vergne-Vaxelaire,Alain Perret,Anne Zaparuchaet al. Nature Chemical Biology, 2014, 10 (1), pp.42-49. ⟨10.1038/nchembio.1387⟩ Article dans une revue hal-02504067v1
Comparative genomic analysis provides insights into the evolution and niche adaptation of marine Magnetospira sp. QH-2 strain Boyang Ji,Sheng-Da Zhang,Pascal Arnoux,Zoe Rouy,François Albertoet al. Environmental Microbiology, 2014, 16 (2), pp.525-544. ⟨10.1111/1462-2920.12180⟩ Article dans une revue istex hal-02463127v1
Genome Features of the Endophytic Actinobacterium Micromonospora lupini Strain Lupac 08: On the Process of Adaptation to an Endophytic Life Style? Martha E Trujillo,Rodrigo Bacigalupe,Petar Pujic,Yasuhiro Igarashi,Patricia Benitoet al. PLoS ONE, 2014, 9 (9), pp.e108522. ⟨10.1371/journal.pone.0108522⟩ Article dans une revue hal-04576462v1
Comparative analyses of Legionella species identifies genetic features of strains causing Legionnaires' disease Laura Gomez-Valero,Christophe Rusniok,Monica Rolando,Mario Neou,Delphine Dervins-Ravaultet al. Genome Biology, 2014, 15 (11), pp.505. ⟨10.1186/s13059-014-0505-0⟩ Article dans une revue hal-01329875v1
Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii Jean-Claude Ogier,Sylvie Pages,Gaelle Bisch,Helene Chiapello,Claudine Médigueet al. Genome Biology and Evolution, 2014, 6, pp.1495-1513. ⟨10.1093/gbe/evu119⟩ Article dans une revue hal-01837258v1
Characterization of a P1-Like Bacteriophage Carrying an SHV-2 Extended-Spectrum β-Lactamase from an Escherichia coli Strain Typhaine Billard-Pomares,Stéphanie Fouteau,Marie Elise Jacquet,David Roche,Valérie Barbeet al. Antimicrobial Agents and Chemotherapy, 2014, 58 (11), pp.6550-6557. ⟨10.1128/aac.03183-14⟩ Article dans une revue hal-04575101v1
Profiling the orphan enzymes Maria Sorokina,Mark Stam,Claudine Médigue,Olivier Lespinet,David Vallenet Biology Direct, 2014, 9 (1), pp.10. ⟨10.1186/1745-6150-9-10⟩ Article dans une revue (article de synthèse) hal-04011158v1
Characterization of a P1-like bacteriophage encoding an SHV-2 extended-spectrum β-lactamase from an Escherichia coli strain. T. Billard-Pomares,,S. Fouteau,M.E. Jacquet,D. Roche,,V. Barbe,et al. Antimicrobial Agents and Chemotherapy, 2014, 58 (11), pp.6550-7 Article dans une revue hal-01117145v1
Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli C. Raeside,J. Gaffé,D. Deatherage,O. Tenaillon,A. Briskaet al. mBio, 2014, 5 (5), ⟨10.1128/mbio.01377-14⟩ Article dans une revue hal-01980589v1
Comparative analysis of the complete genome of KPC-2-producing Klebsiella pneumoniae Kp13 reveals remarkable genome plasticity and a wide repertoire of virulence and resistance mechanisms Pablo Ivan Pereira Ramos,Renata Christina Picão,Luiz Gonzaga Paula de Almeida,Nicholas Costa B Lima,Raquel Girardelloet al. BMC Genomics, 2014, 15 (1), pp.54. ⟨10.1186/1471-2164-15-54⟩ Article dans une revue cea-04646589v1
Epistasis and Allele Specificity in the Emergence of a Stable Polymorphism in Escherichia coli. Jessica Plucain,Thomas Hindré,Mickaël Le Gac,Olivier Tenaillon,Stéphane Cruveilleret al. Science, 2014, epub ahead of print. ⟨10.1126/science.1248688⟩ Article dans une revue hal-00961496v1
Sinorhizobium strains comprising five genospecies Masayuki Sugawara,Brendan Epstein,Brian Badgley,Tatsuya Unno,Lei Xuet al. Genome Biology, 2013, 14 (2), pp.R17. ⟨10.1186/gb-2013-14-2-r17⟩ Article dans une revue cea-04669820v1
Evolutionary history and genetic parallelism affect correlated responses to evolution. Mickael Le Gac,Tim F Cooper,Stéphane Cruveiller,Claudine Médigue,Dominique Schneider Molecular Ecology, 2013, 22 (12), pp.3292-3303. ⟨10.1111/mec.12312⟩ Article dans une revue hal-00961479v1
A Tribute to Disorder in the Genome of the Bloom- Forming Freshwater Cyanobacterium Microcystis aeruginosa Jean-François Humbert,Valérie Barbe,Amel Latifi,Muriel Gugger,Alexandra Calteauet al. PLoS ONE, 2013, 8 (8), pp.e70747. ⟨10.1371/journal.pone.0070747⟩ Article dans une revue bioemco-00851371v1
Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T). Oulfat Amin,Marie-Laure Fardeau,Odile Valette,Agnès Hirschler-Réa,Valérie Barbeet al. Genome Announcements, 2013, 1 (1), epub ahead of print. ⟨10.1128/genomeA.00114-12⟩ Article dans une revue hal-00807485v1
Genome sequence of the obligate gammaproteobacterial methanotroph Methylomicrobium album strain BG8. K Dimitri Kits,Marina G Kalyuzhnaya,Martin G Klotz,Mike S M Jetten,Huub J M Op den Campet al. Genome Announcements, 2013, 1 (2), pp.e0017013. ⟨10.1128/genomeA.00170-13⟩ Article dans une revue hal-00880898v1
Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26. Jérémy Andres,Florence Arsène-Ploetze,Valérie Barbe,Céline Brochier-Armanet,Jessica Cleiss-Arnoldet al. Genome Biology and Evolution, 2013, 5 (5), pp.934-53. ⟨10.1093/gbe/evt061⟩ Article dans une revue hal-00972245v1
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Sébastien Wielgoss,Jeffrey E Barrick,Olivier Tenaillon,Michael J Wiser,W James Dittmaret al. Proceedings of the National Academy of Sciences of the United States of America, 2013, 110 (1), pp.222-7. ⟨10.1073/pnas.1219574110⟩ Article dans une revue hal-00800700v1
An updated metabolic view of the Bacillus subtilis 168 genome Eugeni Belda,Agnieszka Sekowska,François Le Fèvre,Anne Morgat,Damien Mornicoet al. Microbiology, 2013, 159 (Pt_4), pp.757-770. ⟨10.1099/mic.0.064691-0⟩ Article dans une revue hal-04578023v1
Comparative genomics of pathogenic lineages of Vibrio nigripulchritudo identifies virulence-associated traits David Goudenège,Yannick Labreuche,Evelyne Krin,Dominique Ansquer,Sophie Mangenotet al. The International Society of Microbiologial Ecology Journal, 2013, Integrated genomics and post-genomics approaches in microbial ecology, 7 (10), pp.1985-1996. ⟨10.1038/ismej.2013.90⟩ Article dans une revue pasteur-01699814v1
Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis Philip Supply,Michael Marceau,Sophie Mangenot,David Roche,Carine Rouanetet al. Nature Genetics, 2013, 45 (2), pp.172-179. ⟨10.1038/ng.2517⟩ Article dans une revue pasteur-02615220v1
Experimental evolution of nodule intracellular infection in legume symbionts Suhua Guan,Carine Gris,Stéphane Cruveiller,Cecile Pouzet,Lena Tasseet al. The International Society of Microbiologial Ecology Journal, 2013, 7 (7), pp.1367 - 1377. ⟨10.1038/ismej.2013.24⟩ Article dans une revue hal-02646600v1
Genome Sequence of Blastococcus saxobsidens DD2, a Stone-Inhabiting Bacterium B. Chouaia,E. Crotti,L. Brusetti,D. Daffonchio,I. Essoussiet al. Journal of Bacteriology, 2012, 194 (10), pp.2752-2753. ⟨10.1128/JB.00320-12⟩ Article dans une revue hal-02532799v1
Complete genome sequences of six strains of the genus Methylobacterium. Christopher J Marx,Françoise Bringel,Ludmila Chistoserdova,Lionel Moulin,Muhammad Farhan Ul Haqueet al. Journal of Bacteriology, 2012, 194 (17), pp.4746-8. ⟨10.1128/JB.01009-12⟩ Article dans une revue hal-00749347v1
Genome Sequence of Radiation-Resistant Modestobacter marinus Strain BC501, a Representative Actinobacterium That Thrives on Calcareous Stone Surfaces Philippe Normand,Jérome Gury,Petar Pujic,B. Chouaia,E. Crottiet al. Journal of Bacteriology, 2012, 194 (17), pp.4773-4774. ⟨10.1128/JB.01029-12⟩ Article dans une revue hal-02531835v1
Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC Stefan Engelen,David Vallenet,Claudine Médigue,Antoine Danchin BMC Genomics, 2012, 13 (1), pp.69. ⟨10.1186/1471-2164-13-69⟩ Article dans une revue hal-04579011v1
The CanOE strategy: integrating genomic and metabolic contexts across multiple prokaryote genomes to find candidate genes for orphan enzymes. Adam Alexander Thil Smith,Eugeni Belda,Alain Viari,Claudine Médigue,David Vallenet PLoS Computational Biology, 2012, 8 (5), ⟨10.1371/journal.pcbi.1002540⟩ Article dans une revue hal-00763496v1
MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data David Vallenet,Eugeni Belda,Alexandra Calteau,Stéphane Cruveiller,Stefan Engelenet al. Nucleic Acids Research, 2012, 41 (D1), pp.D636 - D647. ⟨10.1093/nar/gks1194⟩ Article dans une revue hal-04578153v1
Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z. Stéphane Vuilleumier,Valentina N Khmelenina,Françoise Bringel,Alexandr S Reshetnikov,Aurélie Lajuset al. Journal of Bacteriology, 2012, 194 (2), pp.551-2. ⟨10.1128/JB.06392-11⟩ Article dans une revue hal-00749350v1
Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum Benoit Remenant,Lavanya Babujee,Aurélie Lajus,Claudine Medigue,Philippe Prioret al. Journal of Bacteriology, 2012, 194 (10), pp.2742-2743. ⟨10.1128/JB.00249-12⟩ Article dans une revue hal-02645685v1
Comparative Genomics of Aeschynomene Symbionts: Insights into the Ecological Lifestyle of Nod-Independent Photosynthetic Bradyrhizobia Damien Mornico,Lucie Miche,Gilles Bena,Nico Nouwen,Andre Vermeglioet al. Genes, 2012, 3 (1), pp.35-61. ⟨10.3390/genes3010035⟩ Article dans une revue hal-01791870v1
Draft Genome Sequence of the Volcano-Inhabiting Thermoacidophilic Methanotroph Methylacidiphilum fumariolicum Strain SolV Ahmad F Khadem,Adam S Wieczorek,Arjan Pol,Stéphane Vuilleumier,Harry R Harhangiet al. Journal of Bacteriology, 2012, 194 (14), pp.3729 - 3730. ⟨10.1128/jb.00501-12⟩ Article dans une revue hal-04578787v1
The entomopathogenic bacterial endosymbionts xenorhabdus and photorhabdus: convergent lifestyles from divergent genomes John M. Chaston,Garret Suen,Sarah L. Tucker,Aaron W. Andersen,Archna Bhasinet al. PLoS ONE, 2011, 6 (11), ⟨10.1371/journal.pone.0027909⟩ Article dans une revue hal-02647677v1
Mutation Rate Inferred From Synonymous Substitutions in a Long-Term Evolution Experiment With Escherichia coli. Sébastien Wielgoss,Jeffrey E Barrick,Olivier Tenaillon,Stéphane Cruveiller,Béatrice Chane-Woon-Minget al. G3, 2011, 1 (3), pp.183-186. ⟨10.1534/g3.111.000406⟩ Article dans une revue hal-00800695v1
Genome sequence of the arctic methanotroph Methylobacter tundripaludum SV96. Mette M Svenning,Anne Grethe Hestnes,Ingvild Wartiainen,Lisa y Stein,Martin G Klotzet al. Journal of Bacteriology, 2011, 193 (22), pp.6418-9. ⟨10.1128/JB.05380-11⟩ Article dans une revue hal-00644077v1
Genome sequence of Methyloversatilis universalis FAM5T, a methylotrophic representative of the order Rhodocyclales. Weerayuth Kittichotirat,Nathan M Good,Rob Hall,Françoise Bringel,Aurélie Lajuset al. Journal of Bacteriology, 2011, 193 (17), pp.4541-2. ⟨10.1128/JB.05331-11⟩ Article dans une revue hal-00644081v1
Complete genome sequence of the chloromethane-degrading Hyphomicrobium sp. strain MC1. Stéphane Vuilleumier,Thierry Nadalig,Muhammad Farhan Ul Haque,Ghislaine Magdelenat,Aurélie Lajuset al. Journal of Bacteriology, 2011, 193 (18), pp.5035-6. ⟨10.1128/JB.05627-11⟩ Article dans une revue hal-00644071v1
Genome sequence of the methanotrophic alphaproteobacterium Methylocystis sp. strain Rockwell (ATCC 49242). Lisa y Stein,Françoise Bringel,Alan A Dispirito,Sukkyun Han,Mike S M Jettenet al. Journal of Bacteriology, 2011, 193 (10), pp.2668-9. ⟨10.1128/JB.00278-11⟩ Article dans une revue hal-00644085v1
Metabolic diversity among main microorganisms inside an arsenic-rich ecosystem revealed by meta-and proteo-genomics P.N. Bertin,A. Heinrich-Salmeron,E. Pelletier,F. Goulhen-Chollet,F. Arsène-Ploetzeet al. The International Society of Microbiologial Ecology Journal, 2011, 5 (11), pp.1735-1747. ⟨10.1038/ismej.2011.51⟩ Article dans une revue hal-01631857v1
Reannotation of the genome sequence of Clostridium difficile strain 630. Marc Monot,Caroline Boursaux-Eude,Marie Thibonnier,David Vallenet,Ivan Moszeret al. Journal of Medical Microbiology, 2011, 60 (8), pp.1193-9. ⟨10.1099/jmm.0.030452-0⟩ Article dans une revue pasteur-01370838v1
Ralstonia syzygii, the Blood Disease Bacterium and Some Asian R. solanacearum Strains Form a Single Genomic Species Despite Divergent Lifestyles Benoît Remenant,Jean-Charles de Cambiaire,Gilles Cellier,Jonathan M Jacobs,Sophie Mangenotet al. PLoS ONE, 2011, 6 (9), pp.e24356. ⟨10.1371/journal.pone.0024356⟩ Article dans une revue hal-04579060v1
Extensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes Laura Gomez-Valero,Christophe Rusniok,Sophie Jarraud,Benoit Vacherie,Zoé Rouyet al. BMC Genomics, 2011, 12 (1), pp.536. ⟨10.1186/1471-2164-12-536⟩ Article dans une revue pasteur-00642457v1
Core and Panmetabolism in Escherichia coli Gilles Vieira,Victor Sabarly,Pierre-Yves Bourguignon,Maxime Durot,Francois Le Fevreet al. Journal of Bacteriology, 2011, 193 (6), pp.1461 - 1472. ⟨10.1128/JB.01192-10⟩ Article dans une revue hal-02646830v1
Parallel Evolution of a Type IV Secretion System in Radiating Lineages of the Host-Restricted Bacterial Pathogen Bartonella Philipp Engel,Walter Salzburger,Marius Liesch,Chao-Chin Chang,Soichi Maruyamaet al. PLoS Genetics, 2011, 7 (2), pp.e1001296. ⟨10.1371/journal.pgen.1001296⟩ Article dans une revue hal-04580576v1
Complete Nucleotide Sequence of Plasmid pTN48, Encoding the CTX-M-14 Extended-Spectrum β-Lactamase from an &lt;i&gt;Escherichia coli&lt;/i&gt; O102-ST405 Strain Typhaine Billard-Pomares,Olivier Tenaillon,Hervé Le Nagard,Zoé Rouy,Stéphane Cruveilleret al. Antimicrobial Agents and Chemotherapy, 2011, 55 (3), pp.1270 - 1273. ⟨10.1128/aac.01108-10⟩ Article dans une revue hal-04579228v1
Complete genome sequence of Crohn's disease-associated adherent-invasive E. coli strain LF82. Sylvie Miquel,Eric Peyretaillade,Laurent Claret,Amélie de Vallée,Carole Dossatet al. PLoS ONE, 2010, 5 (9), epub ahead of print. ⟨10.1371/journal.pone.0012714⟩ Article dans une revue hal-00529639v1
Experimental Evolution of a Plant Pathogen into a Legume Symbiont Marta Marchetti,Delphine Capela,Michelle Glew,Stéphane Cruveiller,Béatrice Chane-Woon-Minget al. PLoS Biology, 2010, 8 (1), pp.e1000280. ⟨10.1371/journal.pbio.1000280⟩ Article dans une revue hal-02665813v1
The Complete Genome Sequence of Cupriavidus metallidurans Strain CH34, a Master Survivalist in Harsh and Anthropogenic Environments Paul J Janssen,Rob van Houdt,Hugo Moors,Pieter Monsieurs,Nicolas Morinet al. PLoS ONE, 2010, 5 (5), pp.e10433. ⟨10.1371/journal.pone.0010433⟩ Article dans une revue hal-04580603v1
Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, &lt;em&gt;Photorhabdus&lt;/em&gt; and &lt;em&gt;Xenorhabdus&lt;/em&gt; Jean-Claude Ogier,Alexandra Calteau,Steve Forst,Heidi Goodrich-Blair,David Rocheet al. BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-568⟩ Article dans une revue hal-02660280v1
Structure, function, and evolution of the Thiomonas spp. genome. Florence Arsène-Ploetze,Sandrine Koechler,Marie Marchal,Jean-Yves Coppée,Michael Chandleret al. PLoS Genetics, 2010, 6 (2), pp.e1000859. ⟨10.1371/journal.pgen.1000859⟩ Article dans une revue hal-00463879v1
Genomes of three tomato pathogens within the Ralstonia solanacearum species complex reveal significant evolutionary divergence Benoît Remenant,Bénédicte Coupat-Goutaland,Alice Guidot,Gilles Cellier,Emmanuel Wickeret al. BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-379⟩ Article dans une revue hal-02936853v1
Delineation and Analysis of Chromosomal Regions Specifying Yersinia pestis Anne Derbise,Viviane Chenal-Francisque,Christèle Huon,Corinne Fayolle,Christian Demeureet al. Infection and Immunity, 2010, 78 (9), pp.3930-3941. ⟨10.1128/IAI.00281-10⟩ Article dans une revue pasteur-03260318v1
The Frankia alni Symbiotic Transcriptome Nicole Alloisio,Clothilde Queiroux,Pascale Fournier,Petar Pujic,Philippe Normandet al. Molecular Plant-Microbe Interactions, 2010, 23 (5), pp.593-607. ⟨10.1094/MPMI⟩ Article dans une revue hal-00599356v1
Genomic, proteomic, and transcriptomic analysis of virulent and avirulent&lt;i&gt;Rickettsia prowazekii&lt;/i&gt;reveals its adaptive mutation capabilities Yassina Bechah,Khalid El Karkouri,Oleg Mediannikov,Quentin Leroy,Nicolas Pelletieret al. Genome Research, 2010, 20 (5), pp.655 - 663. ⟨10.1101/gr.103564.109⟩ Article dans une revue hal-04580605v1
Genome Sequence of the Obligate Methanotroph Methylosinus trichosporium Strain OB3b. Lisa y Stein,Sukhwan Yoon,Jeremy D Semrau,Alan A Dispirito,Andrew Crombieet al. Journal of Bacteriology, 2010, 192 (24), pp.6497-8. ⟨10.1128/JB.01144-10⟩ Article dans une revue hal-00542790v1
Small variable segments constitute a major type of diversity of bacterial genomes at the species level. Fabrice Touzain,Erick Denamur,Claudine Médigue,Valérie Barbe,Meriem El Karouiet al. Genome Biology, 2010, 11 (4), pp.R45. ⟨10.1186/gb-2010-11-4-r45⟩ Article dans une revue inserm-00622573v1
From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma. Jean-Michel Thiberge,Caroline Boursaux-Eude,Philippe Lehours,Marie-Agnès Dillies,Sophie Crenoet al. BMC Genomics, 2010, 11 (1), pp.368. ⟨10.1186/1471-2164-11-368⟩ Article dans une revue pasteur-00668206v1
The Genome Sequence of the Cyanobacterium Oscillatoria sp. PCC 6506 Reveals Several Gene Clusters Responsible for the Biosynthesis of Toxins and Secondary Metabolites Annick Méjean,Rabia Mazmouz,Stéphane Mann,Alexandra Calteau,Claudine Médigueet al. Journal of Bacteriology, 2010, 192 (19), pp.5264-5265. ⟨10.1128/jb.00704-10⟩ Article dans une revue hal-04580588v1
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later Valérie Barbe,Stéphane Cruveiller,Frank Kunst,Patricia Lenoble,Guillaume Meuriceet al. Microbiology, 2009, 155 (6), pp.1758-1775. ⟨10.1099/mic.0.027839-0⟩ Article dans une revue hal-04581597v1
Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths. Marie Touchon,Claire Hoede,Olivier Tenaillon,Valérie Barbe,Simon Baeriswylet al. PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩ Article dans une revue hal-00390293v1
Genome sequence of Vibrio splendidus : an abundant planctonic marine species with a large genotypic diversity Frédérique Le Roux,Mohamed Zouine,Nesrine Chakroun,Johan Binesse,Denis Saulnieret al. Environmental Microbiology, 2009, 11 (8), pp.1959-1970. ⟨10.1111/j.1462-2920.2009.01918.x⟩ Article dans une revue hal-04581544v1
MicroScope: a platform for microbial genome annotation and comparative genomics David Vallenet,S. Engelen,D. Mornico,S. Cruveiller,L. Fleuryet al. Database - The journal of Biological Databases and Curation, 2009, 2009, bap021. ⟨10.1093/database/bap021⟩ Article dans une revue hal-04581832v1
NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis Christophe Rusniok,D. Vallenet,S. Floquet,H. Ewles,C. Mouzé-Soulamaet al. Genome Biology, 2009, 10 (10), pp.R110. ⟨10.1186/gb-2009-10-10-r110⟩ Article dans une revue pasteur-00663857v1
A Module Located at a Chromosomal Integration Hot Spot Is Responsible for the Multidrug Resistance of a Reference Strain from Escherichia coli Clonal Group A Mathilde Lescat,Alexandra Calteau,Claire Hoede,Valérie Barbe,Marie Touchonet al. Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩ Article dans une revue hal-03612468v1
Complete genome of the cellulolytic thermophile Acidothermus cellulolyticus 11B provides insights into its ecophysiological and evolutionary adaptations Ravi D. Barabote,Gary Xie,David H. Leu,Philippe Normand,Anamaria Necsuleaet al. Genome Research, 2009, 19, pp.1033-1043. ⟨10.1101/gr.084848.108⟩ Article dans une revue halsde-00526039v1
Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data. Stéphanie Weiss,Christine Carapito,Jessica Cleiss,Sandrine Koechler,Evelyne Turlinet al. Biochimie, 2009, 91 (2), pp.192-203. ⟨10.1016/j.biochi.2008.07.013⟩ Article dans une revue istex hal-00370778v1
Methylobacterium Genome Sequences: A Reference Blueprint to Investigate Microbial Metabolism of C1 Compounds from Natural and Industrial Sources Stéphane Vuilleumier,Ludmila Chistoserdova,Ming-Chun Lee,Françoise Bringel,Aurélie Lajuset al. PLoS ONE, 2009, 4 (5), pp.e5584. ⟨10.1371/journal.pone.0005584⟩ Article dans une revue hal-00390607v1
The Plasmid of &lt;i&gt;Escherichia coli&lt;/i&gt; Strain S88 (O45:K1:H7) That Causes Neonatal Meningitis Is Closely Related to Avian Pathogenic &lt;i&gt;E. coli&lt;/i&gt; Plasmids and Is Associated with High-Level Bacteremia in a Neonatal Rat Meningitis Model Chantal Peigne,Philippe Bidet,Farah Mahjoub-Messai,Céline Plainvert,Valérie Barbeet al. Infection and Immunity, 2009, 77 (6), pp.2272 - 2284. ⟨10.1128/iai.01333-08⟩ Article dans une revue hal-04581643v1
Advances in environmental genomics: towards an integrated view of micro-organisms and ecosystems Philippe Bertin,Claudine Médigue,Philippe Normand Microbiology, 2008, 154, pp.347-359. ⟨10.1099/mic.0.2007/011791-0⟩ Article dans une revue (article de synthèse) halsde-00254466v1
Effect of heavy exercise on spectral baroreflex sensitivity, heart rate, and blood pressure variability in well-trained humans F. Cottin,C. Médigue,Y. Papelier AJP - Heart and Circulatory Physiology, 2008, 295 (3), pp.H1150-H1155. ⟨10.1152/ajpheart.00003.2008⟩ Article dans une revue hal-02489960v1
Genome Sequence of the Saprophyte Leptospira biflexa Provides Insights into the Evolution of Leptospira and the Pathogenesis of Leptospirosis Mathieu Picardeau,Dieter M. Bulach,Christiane Bouchier,Richard L. Zuerner,Nora Zidaneet al. PLoS ONE, 2008, 3 (2), pp.e1607. ⟨10.1371/journal.pone.0001607⟩ Article dans une revue hal-03020737v1
Breathing cardiovascular variability and baroreflex in mechanically ventilated patients A. van de Louw,C. Médigue,Y. Papelier,F. Cottin American Journal of Physiology - Regulatory, Integrative and Comparative Physiology, 2008, 295 (6), pp.R1934-R1940. ⟨10.1152/ajpregu.90475.2008⟩ Article dans une revue hal-02489936v1
“ Candidatus Cloacamonas Acidaminovorans”: Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division Eric Pelletier,Annett Kreimeyer,Stéphanie Bocs,Zoé Rouy,Gábor Gyapayet al. Journal of Bacteriology, 2008, 190 (7), pp.2572-2579. ⟨10.1128/jb.01248-07⟩ Article dans une revue hal-04582001v1
A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1 Véronique de Berardinis,David Vallenet,Vanina Castelli,Marielle Besnard,Agnès Pinetet al. Molecular Systems Biology, 2008, 4 (1), pp.174. ⟨10.1038/msb.2008.10⟩ Article dans une revue hal-02503013v1
Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression Marie-Laure Rosso,Sylvie Chauvaux,Rodrigue Dessein,Caroline Laurans,Lionel Frangeulet al. BMC Microbiology, 2008, 8, pp.211. ⟨10.1186/1471-2180-8-211⟩ Article dans une revue inserm-02064904v1
Genome sequence of the -rhizobium Cupriavidus taiwanensis and comparative genomics of rhizobia Claire Amadou,Géraldine Pascal,Sophie Mangenot,Michelle Glew,Cyril Bontempset al. Genome Research, 2008, 18 (9), pp.1472 - 1483. ⟨10.1101/gr.076448.108⟩ Article dans une revue hal-01655676v1
Comparative analysis of acinetobacters: three genomes for three lifestyles David Vallenet,Patrice Nordmann,Valérie Barbe,Laurent Poirel,Sophie Mangenotet al. PLoS ONE, 2008, 3 (3), pp.e1805. ⟨10.1371/journal.pone.0001805⟩ Article dans une revue cea-04585511v1
Legumes Symbioses: Absence of Nod Genes in Photosynthetic Bradyrhizobia Eric Giraud,Lionel Moulin,David Vallenet,Valérie Barbe,Eddie Cytrynet al. Science, 2007, 316, pp.1307 - 1312. ⟨10.1126/science.1139548⟩ Article dans une revue halsde-00151340v1
A Genomic Island of the Pathogen Leptospira interrogans Serovar Lai Can Excise from Its Chromosome Pascale Bourhy,Laurence Salaün,Aurélie Lajus,Claudine Médigue,Caroline Boursaux-Eudeet al. Infection and Immunity, 2007, 75 (2), pp.677-683. ⟨10.1128/iai.01067-06⟩ Article dans une revue cea-04586169v1
Annotation, comparison and databases for hundreds of bacterial genomes Claudine Médigue,Ivan Moszer Research in Microbiology, 2007, 158 (10), pp.724-736. ⟨10.1016/j.resmic.2007.09.009⟩ Article dans une revue istex cea-04585543v1
Ventilatory thresholds assessment from heart rate variability during an incremental exhaustive running test. F. Cottin,Claudine Médigue,P. Lopes,Pierre-Marie Leprêtre,R. Heubertet al. International Journal of Sports Medicine, 2007, 28 (4), pp.287-94. ⟨10.1055/s-2006-924355⟩ Article dans une revue hal-00306354v1
A tale of two oxidation states: bacterial colonization of arsenic-rich environments. Daniel Muller,Claudine Médigue,Sandrine Koechler,Valérie Barbe,​mohamed Barakatet al. PLoS Genetics, 2007, 3 (4), pp.e53. ⟨10.1371/journal.pgen.0030053⟩ Article dans une revue hal-00340034v1
Genome characteristics of facultatively symbiotic Frankia sp. strains reflect host range and host plant biogeography Philippe Normand,Pascal Lapierre,Louis S. Tisa,Johann Peter Gogarten,Nicole Alloisioet al. Genome Research, 2007, 17, pp.7-15. ⟨10.1101/gr.5798407⟩ Article dans une revue halsde-00140365v1
A New O-Antigen Gene Cluster Has a Key Role in the Virulence of the Escherichia coli Meningitis Clone O45:K1:H7 Céline Plainvert,Philippe Bidet,Chantal Peigne,Valérie Barbe,Claudine Médigueet al. Journal of Bacteriology, 2007, 189 (23), pp.8528-8536. ⟨10.1128/jb.01013-07⟩ Article dans une revue cea-04585566v1
Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague Sylvie Chauvaux,Marie-Laure Rosso,L. Frangeul,Céline Lacroix,Laurent Labarreet al. Microbiology, 2007, 153 (9), pp.3112-3124. ⟨10.1099/mic.0.2007/006213-0⟩ Article dans une revue pasteur-03252353v1
Identification of the Last Unknown Genes in the Fermentation Pathway of Lysine Annett Kreimeyer,Alain Perret,Christophe Lechaplais,David Vallenet,Claudine Médigueet al. Journal of Biological Chemistry, 2007, 282 (10), pp.7191-7197. ⟨10.1074/jbc.M609829200⟩ Article dans une revue hal-02502995v1
Frankia alni proteome under nitrogen-fixing and nitrogen-replete conditions Nicole Alloisio,Servane Felix,Joelle Marechal,Pierre Pujic,Zoé Rouyet al. Physiologia Plantarum, 2007, 130 (3), pp.440-453. ⟨10.1111/j.1399-3054.2007.00859.x⟩ Article dans une revue istex halsde-00156090v1
Exploring the genomes of Frankia Philippe Normand,Clothilde Queiroux,Louis S. Tisa,David R. Benson,Zoé Rouyet al. Physiologia Plantarum, 2007, 130 (3), pp.331-343. ⟨10.1111/j.1399-3054.2007.00918.x⟩ Article dans une revue istex halsde-00156095v1
Assessment of ventilatory thresholds from heart rate variability in well-trained subjects during cycling. F. Cottin,Pierre-Marie Leprêtre,P. Lopes,Y. Papelier,C. Médigueet al. International Journal of Sports Medicine, 2006, 27 (12), pp.959-67 Article dans une revue hal-00306418v1
Comparative and Functional Genomic Analyses of Iron Transport and Regulation in Leptospira spp H. Louvel,S. Bommezzadri,Nora Zidane,Caroline Boursaux-Eude,S. Crenoet al. Journal of Bacteriology, 2006, 188 (22), pp.7893-7904. ⟨10.1128/jb.00711-06⟩ Article dans une revue cea-04586222v1
Complete genome sequence of the entomopathogenic and metabolically versatile soil bacterium Pseudomonas entomophila. Nicolas Vodovar,David Vallenet,Stéphane Cruveiller,Zoé Rouy,Valérie Barbeet al. Nat Biotechnol, 2006, 24 (6), pp.673-9. ⟨10.1038/nbt1212⟩ Article dans une revue hal-00133119v1
Persistent biases in the amino acid composition of prokaryotic proteins Géraldine Pascal,Claudine Médigue,Antoine Danchin BioEssays, 2006, 28 (7), pp.726-738. ⟨10.1002/BIES.20431⟩ Article dans une revue istex hal-02985564v1
Universal biases in protein composition of model prokaryotes Géraldine Pascal,Claudine Médigue,Antoine Danchin Proteins - Structure, Function and Bioinformatics, 2005, 60 (1), pp.27-35. ⟨10.1002/PROT.20475⟩ Article dans une revue istex hal-02985536v1
Insights into the evolution of Yersinia pestis through whole-genome comparison with Yersinia pseudotuberculosis P. Chain,E. Carniel,F. Larimer,J. Lamerdin,P. Stoutlandet al. Proceedings of the National Academy of Sciences of the United States of America, 2004, 101 (38), pp.13826-13831. ⟨10.1073/pnas.0404012101⟩ Article dans une revue hal-04463119v1
Integration of data and methods for genome analysis. Patrick Durand,Claudine Médigue,Anne Morgat,Yves Vandenbrouck,Alain Viariet al. Current Opinion in Drug Discovery and Development, 2003, 6 (3), pp.346-52 Article dans une revue hal-02072584v1
AMIGene: Annotation of Microbial Genes Gregory Nuel,S. Bocs,S. Cruveiller,D. Vellenet,C. Medigue Progress in Nucleic Acid Research and Molecular Biology, 2003, 13 (31), pp.3723-3726 Article dans une revue hal-00271511v1
The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens Éric Duchaud,Christophe Rusniok,Lionel Frangeul,Carmen Buchrieser,Alain Givaudanet al. Nature Biotechnology, 2003, 21 (11), pp.1307-1313. ⟨10.1038/nbt886⟩ Article dans une revue hal-02681540v1
Exploring the Penicillium marneffei genome Kwok-Yung Yuen,Géraldine Pascal,Samson Wong,Philippe Glaser,Patrick Wooet al. Archives of Microbiology, 2003, 179 (5), pp.339-353. ⟨10.1007/S00203-003-0533-8⟩ Article dans une revue istex hal-02985518v1
The complete genome sequence of the gram-positive bacterium Bacillus subtilis Frank Kunst,N. Ogasawara,Ivan Moszer,A.M. Albertini,G. Alloniet al. Nature, 1997, 390 (6657), pp.249-256. ⟨10.1038/36786⟩ Article dans une revue hal-02694553v1
Building large knowledge bases in molecular biology O. Schmeltzer,C. Medigue,P. Uvietta,F. Rechenmann,F. Dorkeldet al. In Proceedings of the First International Conference on Intelligent Systems for Molecular Biology, 1993, 1, pp.345-353 Article dans une revue hal-00698218v1

Communication dans un congrès (25)

A multi-modal and temporal antibiotic resistance knowledge graph Brieuc Quemeneur,Audrey Bihouée,Samuel Chaffron,Claudine Médigue,Hervé Ménageret al. SWAT4HCLS 2025 - 16th International SWAT4HCLS conference : Semantic Web Applications and Tools for Health Care and Life Sciences, Scientifika, Feb 2025, Barcelone, Spain Communication dans un congrès hal-04976716v1
ABRomics : Une plateforme basée sur Galaxy pour la recherche sur la résistance aux antibiotiques et la santé publique Cléa Siguret,Bérénice Batut,Raphaël Tackx,Julie Lao,Amanda Dieuaideet al. Journée d’animation annuelle de la plateforme AuBi 2024, Plateforme Auvergne Bioinformatique (AuBi), Dec 2024, Aubière / Clermont-Ferrand, France Communication dans un congrès hal-05084079v1
ABRomics : une plateforme intégrée multiomique pour la recherche sur la résistance aux antibiotiques et la santé publique Claudine Médigue 43ème Réunion Interdisciplinaire de Chimiothérapie anti-infectieuse (RICAI 2023), Centres Hospitaliers nationaux, Dec 2023, Palais des Congrès, Paris, France Communication dans un congrès hal-04369206v1
Current challenges in the analysis of microbiome data – roles of national bioinformatics infrastructures Claudine Médigue MICROBIOTA IN HEALTH AND DISEASE - The meeting of microbiota experts, CNRS orléans, Nov 2023, Orléans, France Communication dans un congrès hal-04369022v1
The MicroScope platform: 20 years of expertise in microbial genomics Claudine Médigue,Alexandra Calteau,David Vallenet The 20th MicroScope anniversary, Alexandra Calteau; David Vallenet, Sep 2023, Evry-Courcouronnes, France Communication dans un congrès hal-04370626v1
ABRomics: An integrated multi-omics platform for antibiotic resistance research and public health Julie Lao,Pierre Marin,Romain Dallet,Fabien Mareuil,Alix De Toisyet al. 18ème congrès national de la SFM: MICROBES 2023, Société Français de Microbiologie, Oct 2023, Le couvant des Jacobins, Rennes, France Communication dans un congrès hal-04369101v1
EMERGEN-BioInfo The digital platform for the French SARS-CoV-2 genomic surveillance and research program Thomas Denecker,Imane Messak,Anliat Mohamed,Chiara Antoinat,Arthur Le Barset al. JOBIM 2022 - Les Journées Ouvertes en Biologie, Informatique et Mathématiques, Jul 2022, Rennes, France. ⟨10.5281/ZENODO.6778707⟩ Communication dans un congrès hal-04495542v1
ABRomics: a numerical platform to store, integrate, analyse and share multiomics data about antimicrobial resistance Claudine Médigue Scientific Symposium “RESEARCH AND INNOVATION TO REDUCE THE BURDEN OF ANTIBIOTIC RESISTANCE: STRENGHTEN THE EUROPEAN ACTION”, Inserm, Jun 2022, PariSanté Campus, Paris 75015, France Communication dans un congrès hal-04369018v1
ABRomics-PF: a numerical platform on antimicrobial resistance to store, integrate, analyse and share multi-omics data. Claudine Médigue Colloque scientifique Antibiorésistance Recherche et Innovation, Inserm, Nov 2021, Espace Condorcet, Aubervilliers, France Communication dans un congrès hal-04369011v1
panRGP: a pangenome-based method to predict genomic islands and explore their diversity Adelme Bazin,Guillaume Gautreau,Claudine Médigue,David Vallenet,Alexandra Calteau JOBIM 2021 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris (virtual), France Communication dans un congrès hal-04360257v1
ABRomics: une plate-forme antibiorésistance multiomique pour la recherche et la surveillance Claudine Médigue,Philippe Glaser Antibiorésistance : mécanismes et innovation thérapeutique, Aviesan, alliance nationale pour les sciences de la vie et de la santé, Jul 2021, Webconférence, France Communication dans un congrès hal-04368999v1
ABRomics, une plate-forme numérique multi-omique pour la recherche et la surveillance en antibiorésistance Claudine Médigue Webinar microbiotes et antibiorésistance, Pôle de compétitivité Atlanpole Biothérapies & Inserm, Oct 2021, Webinar, France Communication dans un congrès hal-04369004v1
panRGP: a pangenome-based method to predict genomic islands and explore their diversity Adelme Bazin,Guillaume Gautreau,Claudine Médigue,David Vallenet,Alexandra Calteau the 19th European Conference on Computational Biology, ECCB 2020, Aug 2020, Barcelona (Virtual), Spain Communication dans un congrès hal-04360043v1
Cartographie des infrastructures en bioinformatique au niveau national et international Claudine Médigue L’ÉCOSYSTÈME FRANÇAIS DES PLATEFORMES DE BIOINFORMATIQUE FACE AUX DÉFIS DE L’ANALYSE DES DONNÉES DE BIOLOGIE ET DE SANTÉ, Inserm & IFB, Jan 2019, Paris Aviesan & 12 villes (visioconférence), France Communication dans un congrès hal-04367648v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis David Vallenet,Alexandra Calteau,Mathieu Dubois,Mylène Beuvin,Laura Burlotet al. The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom Communication dans un congrès hal-04358401v1
Comparative microbial pangenomics to explore mobilome dynamics Adelme Bazin,Guillaume Gautreau,Claudine Médigue,Alexandra Calteau,David Vallenet The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom Communication dans un congrès hal-04359455v1
PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph Guillaume Gautreau,Christophe Ambroise,Catherine Matias,Amandine Perrin,Rémi Planelet al. JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France Communication dans un congrès hal-04355945v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions using genomic and metabolic comparative analysis Claudine Médigue Conference "Marine Flavobacteria ", INRAE (E. Duchaud) au Centre CNRS de Cargèse, Jun 2018, Cargèse (Corse), France Communication dans un congrès hal-04367514v1
Action Thématique Incitative Genopole : Annotation in silico de génome de Micro-organismes Claudine Médigue Conférence DYNAMISER LA RECHERCHE Les dispositifs d’aide à la recherche : de l’Europe à Genopole, Genopole d'Evry, May 2018, Paris Hémicycle Simone Veil, France Communication dans un congrès hal-04367453v1
PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph Guillaume Gautreau,Christophe Ambroise,Catherine Matias,Amandine Perrin,Rémi Planelet al. Genome Informatics 2018, Sep 2018, Hinxton, Cambridge, United Kingdom Communication dans un congrès hal-04356757v1
Genomic comparison within Xenorhabdus genus: X. poinarii species characterized by a small genome and attenuated virulence toward insects Jean-Claude Ogier,Sylvie Pages,Gaelle Bisch,Sebastien Carrere,Helene Chiapelloet al. 5. Congress of European Microbiologists (FEMS 2013), Jul 2013, Leipzig, Allemagne Communication dans un congrès hal-01837266v1
Genomic comparison within Xenorhabdus bovienii species: the avirulent strain X. bovienii CS03 is characterized by its pseudogene content Gaelle Bisch,Jean-Claude Ogier,Sylvie Pages,Roba El Hajj,Claudine Médigueet al. 5. Congress of European Microbiologists (FEMS 2013), Jul 2013, Leipzig, Germany Communication dans un congrès hal-01837265v1
Prediction of superovulatory responses in the cow: effects of the estrous cycle and breeding conditions on anti-Müllerian hormone endocrine concentrations Charlène Rico,Claudine Medigue,F. Clement,Eric Briant,Mickaël Dupontet al. 8. International Symposium on Reproduction in Domestic Ruminants, Sep 2010, Anchorage, United States Communication dans un congrès hal-02754626v1
L'hormone anti-Müllérienne, un prédicteur endocrinien de la réponse à une stimulation ovarienne chez les bovins Danielle Monniaux,Charlène Rico,Helene H. Larroque,Rozenn Dalbies-Tran,Claudine Medigueet al. 41. Journée Thématique de la Société Française pour l'Etude de la Fertilité (SFEF) "Des follicules dans tous leurs états..", Mar 2010, Paris, France Communication dans un congrès hal-02756860v1
Unités de plasticité dans le génome de Photorhabdus : des réarrangements chromosomiques à l’échelle du temps du laboratoire à l’évolution des espèces. Jean-Claude Ogier,Alexandra Calteau,Anne Lanois,Sylvie Pages,David Rocheet al. 8. Congrès National de la Société Française de Microbiologie (SFM), Jun 2010, Palais des Congrès, Parc Chanot, Marseille, France Communication dans un congrès hal-02823581v1

Poster de conférence (22)

PanGBank: a database of pangenome graphs for comparative microbial genomics Jean Mainguy,Téo Lemane,Claudine Médigue,Alexandra Calteau,David Vallenet EAGS 2026 - International Environmental and Agronomical Genomics symposium, Feb 2026, Paris, France. Poster de conférence hal-05523557v1
A multi-modal and temporal antibiotic resistance knowledge graph Brieuc Quemeneur,Audrey Bihouée,Samuel Chaffron,Claudine Médigue,Hervé Ménageret al. JOBIM 2025, Jul 2025, Bordeaux, France. , 2025 Poster de conférence hal-05126299v2
ABRomics-analysis : developing Metagenomic Workflows for National Antibiotic Resistance Surveillance Platform Hugo Lefeuvre,Audrey Bihouée,Bérénice Batut,Samuel Chaffron,Claudine Médigueet al. JOBIM, Jul 2025, Bordeaux, France Poster de conférence hal-05127516v2
ProMetIS 2.0: proteomics and metabolomics data analysis and integration, applied to the characterization of the Lat and Mx2 knock-out phenotypes Oneeb Nasir,Alyssa Imbert,Sylvain Dechaumet,Pierrick Roger,Thomas Burgeret al. Journées Ouvertes en Biologie, Informatique, et Mathématiques (JOBIM 2024), Jun 2024, Toulouse, France. 2007 Poster de conférence hal-05035118v1
The ABRomics platform — a One Health Antimicrobial resistance analysis service Julie Lao,Raphael Tackx,Pierre Marin,Amanda Dieuaide,Thomas Mignonet al. Journées Ouvertes en Biologie, Informatique, et Mathématiques - 2024, Jun 2024, Toulouse, France Poster de conférence hal-04618645v1
ABRomics: A Galaxy-based one health antimicrobial resistance platform Pierre Marin,Bérénice Batut,Kenzo-Hugo Hillion,Clea Siguret,Raphael Tackxet al. GCC 2024 - Galaxy Community Conference 2024, Jun 2024, Brno, Czech Republic. , ⟨10.7490/f1000research.1119762.1⟩ Poster de conférence hal-04619528v1
ABRomics: An integrated multi-omics platform for antibiotic resistance research and public health Julie Lao,Pierre Marin,Romain Dallet,Fabien Mareuil,Alix De Toisyet al. 9ème symposium sur la résistance aux antimicrobiens chez les animaux et dans l'environnement (ARAE 2023), Jul 2023, Vinci International Convention Centre, Tours, France Poster de conférence hal-04369175v1
ABRomics: An integrated multi-omics platform for antibiotic resistance research and public health Julie Lao,Pierre Marin,Romain Dallet,Fabien Mareuil,Alix De Thoisyet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM ) 2023, Jun 2023, Plouzané, France Poster de conférence hal-04369161v1
ABRomics - an open access online platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data Julie Lao,Pierre Marin,Romain Dallet,Fabien Mareuil,Alix De Toisyet al. FEMS 2023 European Congress of Microbiology, Jul 2023, Congress Center Hamburg Hamburg, Germany, Germany Poster de conférence hal-04369134v1
ABRomics - a digital platform on antimicrobial resistance to store, integrate, analyze and share multi-omics data Pierre Marin,Julie Lao,Kenzo-Hugo Hillion,Aurélien Birer,Nadia Gouéet al. JOURNÉES OUVERTES EN BIOLOGIE, INFORMATIQUE ET MATHÉMATIQUES ( JOBIM ) 2022, Jul 2022, Rennes, France. Actes JOBIM 2022 Poster de conférence hal-04369049v1
MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis Alexandra Calteau,Mathieu Dubois,Jérôme Arnoux,Adelme Bazin,Mylène Beuvinet al. The 2nd FEMS Conference on Microbiology, Jun 2022, Belgrade, Serbia Poster de conférence hal-04371191v1
MicroScope: a web platform for microbial genome annotation through pangenomic and metabolic analysis Alexandra Calteau,Mathieu Dubois,Jérôme Arnoux,Lucie Coffion,Stéphanie Fouteauet al. Journées Ouvertes en Biologie, Informatique et Mathématiques (JOBIM) 2022, Jul 2022, Rennes, France Poster de conférence hal-04360324v1
MicroScope: an integrated platform for the annotation and axploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis Alexandra Calteau,Mathieu Dubois,Jérôme Arnoux,Adelme Bazin,Mylène Beuvinet al. JOBIM 2021 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2021, Paris (virtual), France Poster de conférence hal-04360241v1
MicroScope: an Integrated Platform for the Annotation and Exploration of Microbial Gene Functions through Genomic, Pangenomic and Metabolic Comparative Analysis Alexandra Calteau,Mathieu Dubois,Adelme Bazin,Mylène Beuvin,Stéphanie Fouteauet al. World Microbe Forum 2021, Jun 2021, Virtual, United States Poster de conférence hal-04360076v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis David Vallenet,Alexandra Calteau,Paul Amours,Jérôme Arnoux,Adelme Bazinet al. JOBIM 2020 Journées Ouvertes Biologie, Informatique et Mathématiques, Jun 2020, Montpellier (virtual), France Poster de conférence hal-04359963v1
PanGBank: depicting microbial species diversity via PPanGGOLiN Guillaume Gautreau,Adelme Bazin,Rémi Planel,Mathieu Gachet,Mathieu Duboiset al. JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France Poster de conférence hal-04358380v1
Comparative microbial pangenomics to explore mobilome dynamics Adelme Bazin,Guillaume Gautreau,Claudine Médigue,Alexandra Calteau,David Vallenet JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France Poster de conférence hal-04358338v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis David Vallenet,Alexandra Calteau,Mathieu Dubois,Mylène Beuvin,Laura Burlotet al. JOBIM 2019 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2019, Nantes, France Poster de conférence hal-04358357v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis David Vallenet,Alexandra Calteau,Mathieu Dubois,Aurélie Lajus,David Rocheet al. International symposium on environmental and agronomical genomics, Nov 2018, Paris, France Poster de conférence hal-04357657v1
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic and metabolic comparative analysis Claudine Médigue,Alexandra Calteau,Stéphane Cruveiller,Mathieu Gachet,Guillaume Gautreauet al. JOBIM 2018 Journées Ouvertes Biologie, Informatique et Mathématiques, Jul 2018, Marseille, France Poster de conférence hal-04356218v1
Génomique comparative dans le genre Xenorhabdus : l'espèce X. Poinarii caractérisée par un pouvoir pathogène atténué et un génome de petite taille Jean-Claude Ogier,Sylvie Pages,Patrick Tailliez,Gaëlle Bisch,Corinne Teyssieret al. Journées des Microbiologistes de l’INRA 2012, Nov 2012, L'Isle-sur-la-Sorgue, France. , 2012 Poster de conférence hal-02810864v1
Units of plasticity in bacterial genomes: new insight from the comparative genomics of two bacteria interacting with invertebrates, Photorhabdus and Xenorhabdus Jean-Claude Ogier,Alexandra Calteau,Steve Forst,Heidi Goodrich-Blair,David Rocheet al. 4. Congress of the FEMS, Jun 2011, Geneva, Suisse. , 2011 Poster de conférence hal-02808493v1

Autre publication scientifique (1)

Livre Blanc sur les Données au CNRS État des Lieux et Pratiques Mission Calcul et données (MiCaDo) Denis Veynante,Michel Bidoit,Michel Daydé,Pierre-Etienne Macchi,Denis Girouet al. 2018 Autre publication scientifique hal-02044528v1

Pré-publication, Document de travail (2)

NetSyn: genomic context exploration of protein families Mark Stam,Jordan Langlois,Céline Chevalier,Guillaume Reboul,Karine Bastardet al. 2023 Pré-publication, Document de travail (preprint/prepublication) hal-04301713v1
panModule: detecting conserved modules in the variable regions of a pangenome graph Adelme Bazin,Claudine Medigue,David Vallenet,Alexandra Calteau 2021 Pré-publication, Document de travail hal-04371147v1

Rapport (1)

French Institute of Bioinformatics - 2017-2018 Activity Report Claudine Médigue,Jacques van Helden [Technical Report] Zenodo. 2019 Rapport (rapport technique) hal-05130628v1