Claudine MEDIGUE

73 %

Libre accès

199

Documents

Affiliation actuelle

Analyse Bio-Informatique pour la Génomique et le Métabolisme (LABGeM)

Identifiants chercheurs

Contact

Compétences

Bio-informatique

Publications

PanGBank: a large-scale resource of precomputed microbial pangenomes built with PPanGGOLiN

Jean Mainguy , Téo Lemane , Adelme Bazin , Jérôme Arnoux , Guillaume Gautreau et al.

Nucleic Acids Research, 2026, ⟨10.1093/nar/gkag948⟩

Article dans une revue hal-05779522v1

NetSyn: prokaryotic genomic context exploration of protein families

Mark Stam , Jordan Langlois , Céline Chevalier , Jean Mainguy , Guillaume Reboul et al.

Peer Community Journal, 2026, 6, pp.e101. ⟨10.24072/pcjournal.805⟩

Article dans une revue hal-05777628v1

Establishing the ELIXIR Microbiome Community

Robert D Finn , Bachir Balech , Josephine Burgin , Physilia Chua , Erwan Corre et 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 Helmann et 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-Barbosa et al.

Scientific Data , 2021, 8, pp.311. ⟨10.1038/s41597-021-01095-3⟩

Article dans une revue (data paper) 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 Spadoni et 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 Burlot et 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 Royer et 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-β-Lactamase-Producing Strains of Escherichia coli

Typhaine Billard-Pomares , Olivier Clermont , Miguel Castellanos , Fatma Magdoud , Guilhem Royer et al.

Antimicrobial Agents and Chemotherapy, 2019, 63 (8), pp.1521-1530. ⟨10.1128/AAC.00635-19⟩

Article dans une revue hal-04283183v1

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 Royer et al.

Antimicrobial Agents and Chemotherapy, 2019, ⟨10.1128/AAC⟩

Article dans une revue hal-02413136v1

Specialization of small non-conjugative plasmids in Escherichia coli according to their family types

Catherine Branger , Alice Ledda , Typhaine Billard-Pomares , Benoît Doublet , Valérie Barbe et 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 Bazin et 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 Gautreau et 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. Medigue et 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. Vallenet et 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 Fouteau et 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 Sarkissian et 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 Dillies et 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. Rocha et 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 Lajus et 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-Turpault et al.

Nature Chemical Biology, 2017, 13, pp.858-866. ⟨10.1038/nchembio.2397⟩

Article dans une revue cea-02132779v1

Carrageenan catabolism is encoded by a complex regulon in marine heterotrophic bacteria

Elizabeth Ficko-Blean , Aurelie Prechoux , François Thomas , Tatiana Rochat , Robert Larocque et al.

Nature Communications, 2017, 8, pp.1685. ⟨10.1038/s41467-017-01832-6⟩

Article dans une revue hal-01899178v1

Genome Sequence of the Dichloromethane-Degrading Bacterium Hyphomicrobium sp. Strain GJ21

Françoise Bringel , Christiaan Postema , Sophie Mangenot , Sabrina Bibi-Triki , Pauline Chaignaud et al.

Genome Announcements, 2017, 5 (30), ⟨10.1128/genomeA.00622-17⟩

Article dans une revue hal-02328278v1

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 Vincent et 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 Alberto et 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 Medigue et 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 Sismeiro et al.

RNA Biology, 2016, 13 (2), pp.243-253. ⟨10.1080/15476286.2015.1132141⟩

Article dans une revue cea-04541794v1

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 Barbe et al.

Environmental Microbiology, 2016, 18 (10), pp.3403-3424. ⟨10.1111/1462-2920.13230⟩

Article dans une revue cea-04541789v1

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 Schneider et al.

BMC Evolutionary Biology, 2016, 16 (1), ⟨10.1186/s12862-016-0662-8⟩

Article dans une revue hal-01653387v1

Draft Genome Sequence of Carnobacterium divergens V41, a Bacteriocin-Producing Strain

Benoit Remenant , Frederic Borges , Catherine Cailliez-Grimal , Anne-Marie Revol-Junelles , Laurent Marché et al.

Genome Announcements, 2016, 4 (5), pp.e01109-16. ⟨10.1128/genomeA.01109-16⟩

Article dans une revue hal-02498294v1

Tempo and mode of genome evolution in a 50,000-generation experiment

Olivier Tenaillon , Jeffrey E. Barrick , Noah Ribeck , Daniel E. Deatherage , Jeffrey L. Blanchard et al.

Nature, 2016, 536 (7615), pp.165 - 170. ⟨10.1038/nature18959⟩

Article dans une revue hal-01653393v1

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 Mangenot et 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. Médigue et 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. Barrick et al.

Molecular Biology and Evolution, 2015, 32 (11), pp.2897-2904. ⟨10.1093/molbev/msv161⟩

Article dans une revue cea-04573295v1

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

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 Heuvel et al.

PLoS ONE, 2015, 10 (5), pp.e0127630. ⟨10.1371/journal.pone.0127630⟩

Article dans une revue hal-02487299v1

Revealing the hidden functional diversity of an enzyme family

Karine Bastard , Adam Alexander Thil Smith , Carine Vergne-Vaxelaire , Alain Perret , Anne Zaparucha et 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 Alberto et 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 Benito et 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-Ravault et al.

Genome Biology, 2014, 15 (11), pp.505. ⟨10.1186/s13059-014-0505-0⟩

Article dans une revue hal-01329875v1

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 Carrying an SHV-2 Extended-Spectrum β-Lactamase from an Escherichia coli Strain

Typhaine Billard-Pomares , Stéphanie Fouteau , Marie Elise Jacquet , David Roche , Valérie Barbe et al.

Antimicrobial Agents and Chemotherapy, 2014, 58 (11), pp.6550-6557. ⟨10.1128/aac.03183-14⟩

Article dans une revue hal-04575101v1

Attenuated virulence and genomic reductive evolution in the entomopathogenic bacterial symbiont species, Xenorhabdus poinarii

Jean-Claude Ogier , Sylvie Pages , Gaelle Bisch , Helene Chiapello , Claudine Médigue et al.

Genome Biology and Evolution, 2014, 6, pp.1495-1513. ⟨10.1093/gbe/evu119⟩

Article dans une revue hal-01837258v1

Large Chromosomal Rearrangements during a Long-Term Evolution Experiment with Escherichia coli

C. Raeside , J. Gaffé , D. Deatherage , O. Tenaillon , A. Briska et al.

mBio, 2014, 5 (5), ⟨10.1128/mbio.01377-14⟩

Article dans une revue hal-01980589v1

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

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 Girardello et 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 Cruveiller et al.

Science, 2014, epub ahead of print. ⟨10.1126/science.1248688⟩

Article dans une revue hal-00961496v1

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 Calteau et al.

PLoS ONE, 2013, 8 (8), pp.e70747. ⟨10.1371/journal.pone.0070747⟩

Article dans une revue bioemco-00851371v1

Sinorhizobium strains comprising five genospecies

Masayuki Sugawara , Brendan Epstein , Brian Badgley , Tatsuya Unno , Lei Xu et 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

Genome Sequence of the Sulfate-Reducing Bacterium Desulfotomaculum hydrothermale Lam5(T).

Oulfat Amin , Marie-Laure Fardeau , Odile Valette , Agnès Hirschler-Réa , Valérie Barbe et al.

Genome Announcements, 2013, 1 (1), epub ahead of print. ⟨10.1128/genomeA.00114-12⟩

Article dans une revue hal-00807485v1

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-Arnold et al.

Genome Biology and Evolution, 2013, 5 (5), pp.934-53. ⟨10.1093/gbe/evt061⟩

Article dans une revue hal-00972245v1

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 Camp et al.

Genome Announcements, 2013, 1 (2), pp.e0017013. ⟨10.1128/genomeA.00170-13⟩

Article dans une revue hal-00880898v1

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 Dittmar et 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 Mornico et 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 Mangenot et 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 Rouanet et 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 Tasse et 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. Essoussi et 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 Haque et 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. Crotti et 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

Genome sequence of the haloalkaliphilic methanotrophic bacterium Methylomicrobium alcaliphilum 20Z.

Stéphane Vuilleumier , Valentina N Khmelenina , Françoise Bringel , Alexandr S Reshetnikov , Aurélie Lajus et al.

Journal of Bacteriology, 2012, 194 (2), pp.551-2. ⟨10.1128/JB.06392-11⟩

Article dans une revue hal-00749350v1

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 Engelen et al.

Nucleic Acids Research, 2012, 41 (D1), pp.D636 - D647. ⟨10.1093/nar/gks1194⟩

Article dans une revue hal-04578153v1

Sequencing of K60, Type Strain of the Major Plant Pathogen Ralstonia solanacearum

Benoit Remenant , Lavanya Babujee , Aurélie Lajus , Claudine Medigue , Philippe Prior et 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 Vermeglio et 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 Harhangi et al.

Journal of Bacteriology, 2012, 194 (14), pp.3729 - 3730. ⟨10.1128/jb.00501-12⟩

Article dans une revue hal-04578787v1

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-Ming et al.

G3, 2011, 1 (3), pp.183-186. ⟨10.1534/g3.111.000406⟩

Article dans une revue hal-00800695v1

The entomopathogenic bacterial endosymbionts xenorhabdus and photorhabdus: convergent lifestyles from divergent genomes

John M. Chaston , Garret Suen , Sarah L. Tucker , Aaron W. Andersen , Archna Bhasin et al.

PLoS ONE, 2011, 6 (11), ⟨10.1371/journal.pone.0027909⟩

Article dans une revue hal-02647677v1

Genome sequence of the arctic methanotroph Methylobacter tundripaludum SV96.

Mette M Svenning , Anne Grethe Hestnes , Ingvild Wartiainen , Lisa y Stein , Martin G Klotz et 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 Lajus et al.

Journal of Bacteriology, 2011, 193 (17), pp.4541-2. ⟨10.1128/JB.05331-11⟩

Article dans une revue hal-00644081v1

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 Jetten et al.

Journal of Bacteriology, 2011, 193 (10), pp.2668-9. ⟨10.1128/JB.00278-11⟩

Article dans une revue hal-00644085v1

Complete genome sequence of the chloromethane-degrading Hyphomicrobium sp. strain MC1.

Stéphane Vuilleumier , Thierry Nadalig , Muhammad Farhan Ul Haque , Ghislaine Magdelenat , Aurélie Lajus et al.

Journal of Bacteriology, 2011, 193 (18), pp.5035-6. ⟨10.1128/JB.05627-11⟩

Article dans une revue hal-00644071v1

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-Ploetze et 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 Moszer et 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 Mangenot et 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 Rouy et al.

BMC Genomics, 2011, 12 (1), pp.536. ⟨10.1186/1471-2164-12-536⟩

Article dans une revue pasteur-00642457v1

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 Maruyama et al.

PLoS Genetics, 2011, 7 (2), pp.e1001296. ⟨10.1371/journal.pgen.1001296⟩

Article dans une revue hal-04580576v1

Core and Panmetabolism in Escherichia coli

Gilles Vieira , Victor Sabarly , Pierre-Yves Bourguignon , Maxime Durot , Francois Le Fevre et al.

Journal of Bacteriology, 2011, 193 (6), pp.1461 - 1472. ⟨10.1128/JB.01192-10⟩

Article dans une revue hal-02646830v1

Complete Nucleotide Sequence of Plasmid pTN48, Encoding the CTX-M-14 Extended-Spectrum β-Lactamase from an Escherichia coli O102-ST405 Strain

Typhaine Billard-Pomares , Olivier Tenaillon , Hervé Le Nagard , Zoé Rouy , Stéphane Cruveiller et 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 Dossat et 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-Ming et al.

PLoS Biology, 2010, 8 (1), pp.e1000280. ⟨10.1371/journal.pbio.1000280⟩

Article dans une revue hal-02665813v1

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 Roche et al.

BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-568⟩

Article dans une revue hal-02660280v1

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 Morin et al.

PLoS ONE, 2010, 5 (5), pp.e10433. ⟨10.1371/journal.pone.0010433⟩

Article dans une revue hal-04580603v1

Structure, function, and evolution of the Thiomonas spp. genome.

Florence Arsène-Ploetze , Sandrine Koechler , Marie Marchal , Jean-Yves Coppée , Michael Chandler et 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 Wicker et al.

BMC Genomics, 2010, 11, ⟨10.1186/1471-2164-11-379⟩

Article dans une revue hal-02936853v1

The Frankia alni Symbiotic Transcriptome

Nicole Alloisio , Clothilde Queiroux , Pascale Fournier , Petar Pujic , Philippe Normand et al.

Molecular Plant-Microbe Interactions, 2010, 23 (5), pp.593-607. ⟨10.1094/MPMI⟩

Article dans une revue hal-00599356v1

Delineation and Analysis of Chromosomal Regions Specifying Yersinia pestis

Anne Derbise , Viviane Chenal-Francisque , Christèle Huon , Corinne Fayolle , Christian Demeure et al.

Infection and Immunity, 2010, 78 (9), pp.3930-3941. ⟨10.1128/IAI.00281-10⟩

Article dans une revue pasteur-03260318v1

Genomic, proteomic, and transcriptomic analysis of virulent and avirulentRickettsia prowazekiireveals its adaptive mutation capabilities

Yassina Bechah , Khalid El Karkouri , Oleg Mediannikov , Quentin Leroy , Nicolas Pelletier et 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 Crombie et 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 Karoui et 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 Creno et 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 Médigue et al.

Journal of Bacteriology, 2010, 192 (19), pp.5264-5265. ⟨10.1128/jb.00704-10⟩

Article dans une revue hal-04580588v1

Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths.

Marie Touchon , Claire Hoede , Olivier Tenaillon , Valérie Barbe , Simon Baeriswyl et al.

PLoS Genetics, 2009, 5 (1), pp.e1000344. ⟨10.1371/journal.pgen.1000344⟩

Article dans une revue hal-00390293v1

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 Meurice et al.

Microbiology, 2009, 155 (6), pp.1758-1775. ⟨10.1099/mic.0.027839-0⟩

Article dans une revue hal-04581597v1

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 Saulnier et 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. Fleury et al.

Database - The journal of Biological Databases and Curation, 2009, 2009, bap021. ⟨10.1093/database/bap021⟩

Article dans une revue hal-04581832v1

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 Touchon et al.

Antimicrobial Agents and Chemotherapy, 2009, 53 (6), pp.2283-2288. ⟨10.1128/AAC.00123-09⟩

Article dans une revue hal-03612468v1

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-Soulama et al.

Genome Biology, 2009, 10 (10), pp.R110. ⟨10.1186/gb-2009-10-10-r110⟩

Article dans une revue pasteur-00663857v1

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 Necsulea et 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 Turlin et 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 Lajus et al.

PLoS ONE, 2009, 4 (5), pp.e5584. ⟨10.1371/journal.pone.0005584⟩

Article dans une revue hal-00390607v1

The Plasmid of Escherichia coli Strain S88 (O45:K1:H7) That Causes Neonatal Meningitis Is Closely Related to Avian Pathogenic E. coli Plasmids and Is Associated with High-Level Bacteremia in a Neonatal Rat Meningitis Model

Chantal Peigne , Philippe Bidet , Farah Mahjoub-Messai , Céline Plainvert , Valérie Barbe et 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 Zidane et al.

PLoS ONE, 2008, 3 (2), pp.e1607. ⟨10.1371/journal.pone.0001607⟩

Article dans une revue hal-03020737v1

“ Candidatus Cloacamonas Acidaminovorans”: Genome Sequence Reconstruction Provides a First Glimpse of a New Bacterial Division

Eric Pelletier , Annett Kreimeyer , Stéphanie Bocs , Zoé Rouy , Gábor Gyapay et al.

Journal of Bacteriology, 2008, 190 (7), pp.2572-2579. ⟨10.1128/jb.01248-07⟩

Article dans une revue hal-04582001v1

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

A complete collection of single‐gene deletion mutants of Acinetobacter baylyi ADP1

Véronique de Berardinis , David Vallenet , Vanina Castelli , Marielle Besnard , Agnès Pinet et 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 Frangeul et 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 Bontemps et 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 Mangenot et 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 Cytryn et 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-Eude et 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. Heubert et 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 Barakat et 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 Alloisio et al.

Genome Research, 2007, 17, pp.7-15. ⟨10.1101/gr.5798407⟩

Article dans une revue halsde-00140365v1

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 Labarre et al.

Microbiology, 2007, 153 (9), pp.3112-3124. ⟨10.1099/mic.0.2007/006213-0⟩

Article dans une revue pasteur-03252353v1

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 Médigue et al.

Journal of Bacteriology, 2007, 189 (23), pp.8528-8536. ⟨10.1128/jb.01013-07⟩

Article dans une revue cea-04585566v1

Identification of the Last Unknown Genes in the Fermentation Pathway of Lysine

Annett Kreimeyer , Alain Perret , Christophe Lechaplais , David Vallenet , Claudine Médigue et al.

Journal of Biological Chemistry, 2007, 282 (10), pp.7191-7197. ⟨10.1074/jbc.M609829200⟩

Article dans une revue hal-02502995v1

Exploring the genomes of Frankia

Philippe Normand , Clothilde Queiroux , Louis S. Tisa , David R. Benson , Zoé Rouy et al.

Physiologia Plantarum, 2007, 130 (3), pp.331-343. ⟨10.1111/j.1399-3054.2007.00918.x⟩

Article dans une revue istex halsde-00156095v1

Frankia alni proteome under nitrogen-fixing and nitrogen-replete conditions

Nicole Alloisio , Servane Felix , Joelle Marechal , Pierre Pujic , Zoé Rouy et al.

Physiologia Plantarum, 2007, 130 (3), pp.440-453. ⟨10.1111/j.1399-3054.2007.00859.x⟩

Article dans une revue istex halsde-00156090v1

Assessment of ventilatory thresholds from heart rate variability in well-trained subjects during cycling.

F. Cottin , Pierre-Marie Leprêtre , P. Lopes , Y. Papelier , C. Médigue et 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. Creno et 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 Barbe et 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. Stoutland et 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 Viari et 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 Givaudan et 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 Woo et 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. Alloni et 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. Dorkeld et 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

ABRomics: a platform for antibiotic resistance research and public health using an integrated "One Health" approach

Julie Lao , Raphaël Tackx , Amanda Dieuaide , Thomas Mignon , Cléa Siguret et al.

ECCB 2026 - 25th European Conference on Computational Biology, Aug 2026, Geneva, Switzerland

Communication dans un congrès hal-05725740v1

A multi-modal and temporal antibiotic resistance knowledge graph

Brieuc Quemeneur , Audrey Bihouée , Samuel Chaffron , Claudine Médigue , Hervé Ménager et 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 Dieuaide et 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 Toisy et 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 Bars et 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

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

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 Burlot et al.

The 8th Congress of European Microbiologists, FEMS 2019, Jul 2019, Glasgow, United Kingdom

Communication dans un congrès hal-04358401v1

PPanGGOLiN: Depicting microbial diversity via a Partitioned Pangenome Graph

Guillaume Gautreau , Christophe Ambroise , Catherine Matias , Amandine Perrin , Rémi Planel et 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 Planel et 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 Chiapello et 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 Médigue et 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 Dupont et 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 Medigue et 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 Roche et 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

PanGBank: a Database of Pangenome Graphs for Comparative Microbial Genomics

Jean Mainguy , Téo Lemane , Claudine Médigue , Alexandra Calteau , David Vallenet

JOBIM 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05693102v1

cgMLST typing in the ABRomics web platform

Julie Lao , Raphaël Tackx , Amanda Dieuaide , Thomas Mignon , Cléa Siguret et al.

JOBIM 2026 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2026, Strasboug, France.

Poster de conférence hal-05646295v1

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

ABRomics: a platform for antibiotic resistance research and public health using an integrated "One Health" approach

Julie Lao , Raphaël Tackx , Amanda Dieuaide , Thomas Mignon , Cléa Siguret et al.

ECCB 2026 - 25th European Conference on Computational Biology, Aug 2026, Geneva, Switzerland

Poster de conférence hal-05732017v1

Retrieval-Augmented Generation (RAG) over Genomic Reports in the ABRomics Platform: Towards AI-Assisted Antimicrobial Resistance Research

Thomas Mignon , Raphaël Tackx , Julie Lao , Amanda Dieuaide , Brieuc Quemeneur et al.

JOBIM 2026 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2026, Strasbourg, France

Poster de conférence hal-05649796v1

Balancing Open Science and Data Privacy: The Challenge of Human Microbiome Research

Guillaume Gautreau , Aicha El Jai , Nicolas Pons , Claudine Médigue , Hélène Chiapello et al.

Journées ouvertes en biologie, informatique et mathématiques 2026, Jul 2026, Strasbourg, France.

Poster de conférence hal-05673622v1

MetaPanG: a pangenome graph-based method for strain-level profiling of prokaryotic microbiomes

Téo Lemane , Jean Mainguy , Claudine Médigue , Alexandra Calteau , David Vallenet

JOBIM 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05736773v1

Cloud4SAMS: a trusted research environment to handle human gut microbiome data

Pauline Barbet , Eugeni Belda , Audrey Bihouee , Alexandrina Bodrug , Paul Breugnot et al.

JOBIM 2026, Jun 2026, Strasbourg, France

Poster de conférence hal-05673661v1

A multi-modal and temporal antibiotic resistance knowledge graph

Brieuc Quemeneur , Audrey Bihouée , Samuel Chaffron , Claudine Médigue , Hervé Ménager et 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 Médigue et 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 Burger et 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 Mignon et 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 Tackx et 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 Toisy et 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 Thoisy et 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 Toisy et 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 Goué et 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 Beuvin et 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 Fouteau et 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 Beuvin et 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 Fouteau et 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 Bazin et 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 Dubois et 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 Burlot et 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 Roche et 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 Gautreau et 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 Teyssier et 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 Roche et al.

4. Congress of the FEMS, Jun 2011, Geneva, Suisse. , 2011

Poster de conférence hal-02808493v1

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 Girou et al.

2018

Autre publication scientifique hal-02044528v1

Problématiques soulevées par l'analyse et la gestion des données du microbiome humain

Guillaume Gautreau , Eugeni Belda , Christophe Blanchet , Samuel Chaffron , Hélène Chiapello et al.

2026

Pré-publication, Document de travail (working paper) hal-05673743v1

NetSyn: genomic context exploration of protein families

Mark Stam , Jordan Langlois , Céline Chevalier , Guillaume Reboul , Karine Bastard et 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

French Institute of Bioinformatics - 2017-2018 Activity Report

Claudine Médigue , Jacques van Helden

[Technical Report] Zenodo. 2019

Rapport (rapport technique) hal-05130628v1

Chargement...