Genopole / Plates-formes / Publications

Publications

2010

[20951640] Chauvaux S, Dillies MA, Marceau M, Rosso ML, Rousseau S, Moszer I, Simonet M, Carniel E (2010). In silico comparison of Yersinia pestis and Yersinia pseudotuberculosis transcriptomes reveals a higher expression level of crucial virulence determinants in the plague bacillus. Int. J. Med. Microbiol.

[20174790] Chouari R, Le Paslier D, Daegelen P, Dauga C, Weissenbach J, Sghir A (2010). Molecular Analyses of the Microbial Community Composition of an Anoxic Basin of a Municipal Wastewater Treatment Plant Reveal a Novel Lineage of Proteobacteria. Microb. Ecol. 10.1007/s00248-009-9632-7.

[20092627] Despons L, Baret PV, Frangeul L, Leh Louis V, Durrens P, Souciet JL (2010). Genome-wide computational prediction of tandem gene arrays: application in yeasts. BMC Genomics 11:56.

[20093191] Michelet L, Carod JF, Rakontondrazaka M, Ma L, Gay F, Dauga C (2010). The pig tapeworm Taenia solium, the cause of cysticercosis: Biogeographic (temporal and spacial) origin in Madagascar. Mol. Phylogenet. Evol. 55:744-750.

[21078856] Muschiol S, Boncompain G, Vromman F, Dehoux P, Normark S, Henriques-Normark B, Subtil A (2010). Identification of a family of type III secreted effectors conserved in pathogenic Chlamydiae. Infect. Immun.

[20537153] Thiberge JM, Boursaux-Eude C, Lehours P, Dillies MA, Creno S, Coppée JY, Rouy Z, Lajus A, Ma L, Burucoa C, Ruskoné-Foumestraux A, Courillon-Mallet A, De Reuse H, Boneca IG, Lamarque D, Mégraud F, Delchier JC, Médigue C, Bouchier C, Labigne A, Raymond J (2010). From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma. BMC Genomics 11:368.

2009

[19383706] Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, Vallenet D, Wang T, Moszer I, Médigue C, Danchin A (2009). From a consortium sequence to a unified sequence: The Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758-1775.

[19379809] Chenal-Francisque V, Caro V, Boursaux-Eude C, Guiso N (2009). Genomic analysis of the adenylate cyclase-hemolysin C-terminal region of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Res. Microbiol. 160:330-336.

[19654116] Clément-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S (2009). Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks. Bioinformatics 25:2617-2618.

[19087965] Geffroy V, Macadré C, David P, Pedrosa-Harand A, Sévignac M, Dauga C, Langin T (2009). Molecular analysis of a large subtelomeric nucleotide-binding-site-leucine-rich-repeat family in two representative genotypes of the major gene pools of Phaseolus vulgaris. Genetics 181:450-419.

[19015150] Sherman DJ, Martin T, Nikolski M, Cayla C, Souciet JL, Durrens P; Génolevures Consortium (2009). Génolevures: protein families and synteny among complete hemiascomycetous yeast proteomes and genomes. Nucleic Acids Res. 37:D550-D554.

[19525356] Souciet JL, Dujon B, Gaillardin C, Johnston M, Baret PV, Cliften P, Sherman DJ, Weissenbach J, Westhof E, Wincker P, Jubin C, Poulain J, Barbe V, Segurence B, Artiguenave F, Anthouard V, Vacherie B, Val ME, Fulton RS, Minx P, Wilson R, Durrens P, Jean G, Marck C, Martin T, Nikolski M, Rolland T, Seret ML, Casaregola S, Despons L, Fairhead C, Fischer G, Lafontaine I, Leh V, Lemaire M, de Montigny J, Neuveglise C, Thierry A, Blanc-Lenfle I, Bleykasten C, Diffels J, Fritsch E, Frangeul L, Goeffon A, Jauniaux N, Kachouri-Lafond R, Payen C, Potier S, Pribylova L, Ozanne C, Richard GF, Sacerdot C, Straub ML, Talla E (2009). Comparative genomics of protoploid Saccharomycetaceae. Genome Res. 19:1696-1709.

2008

[] Dauga C, Breeuwer P (2008). Taxonomy and Physiology of Enterobacter sakazakii. In JM Farber & S. Forsythe (eds), Enterobacter sakazakii, chap. 1, pp. 1-26, American Society for Microbiology, Washington DC.

[18614525] Cadel-Six S, Dauga C, Castets AM, Rippka R, Bouchier C, Tandeau de Marsac N, Welker M (2008). Halogenase genes in nonribosomal peptide synthetase gene clusters of Microcystis (Cyanobacteria): sporadic distribution and evolution. Mol. Biol. Evol. 25:2031-2041.

[18369472] Delevoye C, Nilges M, Dehoux P, Paumet F, Perrinet S, Dautry-Varsat A, Subtil A (2008). SNARE protein mimicry by an intracellular bacterium. PLoS Pathog. 4:e1000022.

[18534010] Frangeul L, Quillardet P, Castets AM, Humbert JF, Matthijs HC, Cortez D, Tolonen A, Zhang CC, Gribaldo S, Kehr JC, Zilliges Y, Ziemert N, Becker S, Talla E, Latifi A, Billault A, Lepelletier A, Dittmann E, Bouchier C, Tandeau de Marsac N (2008). Highly plastic genome of Microcystis aeruginosa PCC7806, a ubiquitous toxic freshwater cyanobacterium. BMC Genomics 9:274.

[18768595] Ganesan A, Chaussonnerie S, Tarrade A, Dauga C, Bouchez T, Pelletier E, Le Paslier D, Sghir A (2008). Cloacibacillus evryensis gen. nov., sp. nov., a novel asaccharolytic, mesophilic, amino-acid-degrading bacterium within the phylum ’Synergistetes’, isolated from an anaerobic sludge digester. Int. J. Syst. Evol. Microbiol. 58:2003-2012.

[18459975] Guermazi S, Daegelen P, Dauga C, Rivière D, Bouchez T, Godon JJ, Gyapay G, Sghir A, Pelletier E, Weissenbach J, Le Paslier D (2008). Discovery and characterization of a new bacterial candidate division by an anaerobic sludge digester metagenomic approach. Environ. Microbiol. 10:2111-2123.

[18761981] Guigon G, Cheval J, Cahuzac R, Brisse S (2008). MLVA-NET – a standardised web database for bacterial genotyping and surveillance. Euro Surveill. 13:pii=18863.

[18032431] Lechat P, Hummel L, Rousseau S, Moszer I (2008). GenoList: an integrated environment for comparative analysis of microbial genomes. Nucleic Acids Res. 36:D469-D474.

[18682527] Manichanh C, Chapple CE, Frangeul L, Gloux K, Guigo R, Doré J (2008). A comparison of random sequence reads versus 16S rDNA sequences for estimating the biodiversity of a metagenomic library. Nucleic Acids Res. 36:5180-5188.

[18458128] Périchon B, Bogaerts P, Lambert T, Frangeul L, Courvalin P, Galimand M. (2008). Sequence of conjugative plasmid pIP1206 mediating resistance to aminoglycosides by 16S rRNA methylation and to hydrophilic fluoroquinolones by efflux. Antimicrob. Agents Chemother. 52:2581-2592.

[18270594] Picardeau M, Bulach DM, Bouchier C, Zuerner RL, Zidane N, Wilson PJ, Créno S, Kuczek ES, Bommezzadri S, Davis JC, McGrath A, Johnson MJ, Boursaux-Eude C, Seemann T, Rouy Z, Coppel RL, Rood JI, Lajus A, Davies JK, Médigue C, Adler B (2008). Genome sequence of the saprophyte Leptospira biflexa provides insights into the evolution of Leptospira and the pathogenesis of Leptospirosis. PLoS ONE 3:e1607.

[18493595] Raymond J, Thiberge JM, Kalach N, Bergeret M, Dupont C, Labigne A, Dauga C (2008). Using macro-arrays to study routes of infection of Helicobacter pylori in three families. PLoS ONE 3:e2259.

[18039716] Rossignol T, Lechat P, Cuomo C, Zeng Q, Moszer I, d’Enfert C (2008). CandidaDB: a multi-genome database for Candida species and related Saccharomycotina. Nucleic Acids Res. 36:D557-D561.

[19055764] Rosso ML, Chauvaux S, Dessein R, Laurans C, Frangeul L, Lacroix C, Schiavo A, Dillies MA, Foulon J, Coppée JY, Médigue C, Carniel E, Simonet M, Marceau M (2008). Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression. BMC Microbiol. 8:211.

2007

[17118975] Bourhy P, Salaun L, Lajus A, Médigue C, Boursaux-Eude C, Picardeau M (2007). A genomic island of the pathogen Leptospira interrogans serovar Lai can excise from its chromosome. Infect. Immun. 75:677-683.

[17768254] Chauvaux S, Rosso ML, Frangeul L, Lacroix C, Labarre L, Schiavo A, Marceau M, Dillies MA, Foulon J, Coppée JY, Médigue C, Simonet M, Carniel E (2007). Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague. Microbiology 153:3112-3124.

[17803924] Guljamow A, Jenke-Kodama H, Saumweber H, Quillardet P, Frangeul L, Castets AM, Bouchier C, Tandeau de Marsac N, Dittmann E (2007). Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium. Curr. Biol. 17:R757-R759.

[18031997] Médigue C, Moszer I (2007). Annotation, comparison and databases for hundreds of bacterial genomes. Res. Microbiol. 158:724-736.

[17210928] Stinear TP, Seemann T, Pidot S, Frigui W, Reysset G, Garnier T, Meurice G, Simon D, Bouchier C, Ma L, Tichit M, Porter JL, Ryan J, Johnson PD, Davies JK, Jenkin GA, Small PL, Jones LM, Tekaia F, Laval F, Daffe M, Parkhill J, Cole ST (2007). Reductive evolution and niche adaptation inferred from the genome of Mycobacterium ulcerans, the causative agent of Buruli ulcer. Genome Res. 17:192-200.

2006

[17021191] Krin E, Chakroun N, Turlin E, Givaudan A, Gaboriau F, Bonne I, Rousselle JC, Frangeul L, Lacroix C, Hullo MF, Marisa L, Danchin A, Derzelle S (2006). Pleiotropic role of quorum-sensing autoinducer 2 in Photorhabdus luminescens. Appl. Environ. Microbiol. 72:6439-6451.

[16980464] Louvel H, Bommezzadri S, Zidane N, Boursaux-Eude C, Creno S, Magnier A, Rouy Z, Médigue C, Saint Girons I, Bouchier C, Picardeau M (2006). Comparative and functional genomic analyses of iron transport and regulation in Leptospira spp. J. Bacteriol. 188:7893-7904.

[16188921] Manichanh C, Rigottier-Gois L, Bonnaud E, Gloux K, Pelletier E, Frangeul L, Nalin R, Jarrin C, Chardon P, Marteau P, Roca J, Doré J (2006). Reduced diversity of faecal microbiota in Crohn’s disease revealed by a metagenomic approach. Gut 55:205-211.

[16700631] Schuffenecker I, Iteman I, Michault A, Murri S, Frangeul L, Vaney MC, Lavenir R, Pardigon N, Reynes JM, Pettinelli F, Biscornet L, Diancourt L, Michel S, Duquerroy S, Guigon G, Frenkiel MP, Brehin AC, Cubito N, Despres P, Kunst F, Rey FA, Zeller H, Brisse S (2006). Genome microevolution of chikungunya viruses causing the Indian Ocean outbreak. PLoS Med. 3:e263.

[16682464] Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, Gouyette C, Mirelman D, Coppée JY, Guillen N (2006). Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica. Eukaryot. Cell 5:871-875.

2005

[15937155] Bourhy P, Frangeul L, Couvé E, Glaser P, Saint Girons I, Picardeau M (2005). Complete nucleotide sequence of the LE1 prophage from the spirochete Leptospira biflexa and characterization of its replication and partition functions. J. Bacteriol. 187:3931-3940.

[16103911] Braun BR, van Het Hoog M, d’Enfert C, Martchenko M, Dungan J, Kuo A, Inglis DO, Uhl MA, Hogues H, Berriman M, Lorenz M, Levitin A, Oberholzer U, Bachewich C, Harcus D, Marcil A, Dignard D, Iouk T, Zito R, Frangeul L, Tekaia F, Rutherford K, Wang E, Munro CA, Bates S, Gow NA, Hoyer LL, Kohler G, Morschhauser J, Newport G, Znaidi S, Raymond M, Turcotte B, Sherlock G, Costanzo M, Ihmels J, Berman J, Sanglard D, Agabian N, Mitchell AP, Johnson AD, Whiteway M, Nantel A (2005). A human-curated annotation of the Candida albicans genome. PLoS Genet. 1:36-57.

[15812049] Chouari R, Le Paslier D, Dauga C, Daegelen P, Weissenbach J, Sghir A (2005). Novel major bacterial candidate division within a municipal anaerobic sludge digester. Appl. Environ. Microbiol. 71:2145-2153.

[] Dauga C (2005). Genus II Balneatrix (section Oceanospirillum). Bergey’s manual of systematic bacteriology (2nd ed), Vol. 2 The Proteobacteria, Part B The Gamma Proteobacteria, pp. 282-284.

[15745704] Dauga C, Doré J, Sghir A (2005). Identification de bactéries non ou difficilement cultivables en clinique et dans l’environnement : une diversité insoupçonnée du monde microbien. Med. Sci. 21:290-296.

[15608215] d’Enfert C, Goyard S, Rodriguez-Arnaveilhe S, Frangeul L, Jones L, Tekaia F, Bader O, Albrecht A, Castillo L, Dominguez A, Ernst JF, Fradin C, Gaillardin C, Garcia-Sanchez S, de Groot P, Hube B, Klis FM, Krishnamurthy S, Kunze D, Lopez MC, Mavor A, Martin N, Moszer I, Onesime D, Perez Martin J, Sentandreu R, Valentin E, Brown AJ (2005). CandidaDB: a genome database for Candida albicans pathogenomics. Nucleic Acids Res. 33:D353-D357.

[15698474] Fang G, Ho C, Qiu Y, Cubas V, Yu Z, Cabau C, Cheung F, Moszer I, Danchin A (2005). Specialized microbial databases for inductive exploration of microbial genome sequences. BMC Genomics 6:14.

[15737580] Garrigues T, Dauga C, Ferquel E, Choumet V, Failloux AB (2005). Molecular phylogeny of Vipera Laurenti, 1768 and the related genus Macrovipera (Reuss, 1927) and Daboia (Gray, 1842) with comments about neurotoxic Vipera aspis aspis populations. Mol. Phylogenet. Evol. 35:35-47.

[15833126] Gomez SM, Eiglmeier K, Segurens B, Dehoux P, Couloux A, Scarpelli C, Wincker P, Weissenbach J, Brey PT, Roth CW (2005). Pilot Anopheles gambiae full-length cDNA study: sequencing and initial characterization of 35,575 clones. Genome Biol. 6:R39.

[15699189] Hejnova J, Dobrindt U, Nemcova R, Rusniok C, Bomba A, Frangeul L, Hacker J, Glaser P, Sebo P, Buchrieser C (2005). Characterization of the flexible genome complement of the commensal Escherichia coli strain A0 34/86 (O83 : K24 : H31). Microbiology 151:385-398.

[16181519] Mousson L, Dauga C, Garrigues T, Vazeille M, Schaffner F, Failloux AB (2005). Phylogeography of Aedes aegypti and Aedes albopictus based on mitochondrial DNA variations. Genet. Res. 86:1-11.

[15620687] Talla E, Anthouard V, Bouchier C, Frangeul L, Dujon B (2005). The complete mitochondrial genome of the yeast Kluyveromyces thermotolerans. FEBS Lett. 579:30-40.

2004

[14742555] Doumith M, Cazalet C, Simoes N, Frangeul L, Jacquet C, Kunst F, Martin P, Cossart P, Glaser P, Buchrieser C (2004). New aspects regarding evolution and virulence of Listeria monocytogenes revealed by comparative genomics and DNA arrays. Infect. Immun. 72:1072-1083.

[15229592] Dujon B, Sherman D, Fischer G, Durrens P, Casaregola S, Lafontaine I, de Montigny J, Marck C, Neuveglise C, Talla E, Goffard N, Frangeul L, Aigle M, Anthouard V, Babour A, Barbe V, Barnay S, Blanchin S, Beckerich JM, Beyne E, Bleykasten C, Boisrame A, Boyer J, Cattolico L, Confanioleri F, de Daruvar A, Despons L, Fabre E, Fairhead C, Ferry-Dumazet H, Groppi A, Hantraye F, Hennequin C, Jauniaux N, Joyet P, Kachouri R, Kerrest A, Koszul R, Lemaire M, Lesur I, Ma L, Muller H, Nicaud JM, Nikolski M, Oztas S, Ozier-Kalogeropoulos O, Pellenz S, Potier S, Richard GF, Straub ML, Suleau A, Swennen D, Tekaia F, Wesolowski-Louvel M, Westhof E, Wirth B, Zeniou-Meyer M, Zivanovic I, Bolotin-Fukuhara M, Thierry A, Bouchier C, Caudron B, Scarpelli C, Gaillardin C, Weissenbach J, Wincker P, Souciet JL (2004). Genome evolution in yeasts. Nature 430:35-44.

[15280269] Feurer C, Clermont D, Bimet F, Candréa A, Jackson M, Glaser P, Bizet C, Dauga C (2004). Taxonomic characterization of nine strains isolated from clinical and environmental specimens, and proposal of Corynebacterium tuberculostearicum sp. nov. Int. J. Syst. Evol. Microbiol. 54:1055-1061.

[14752000] Frangeul L, Glaser P, Rusniok C, Buchrieser C, Duchaud E, Dehoux P, Kunst F (2004). CAAT-Box, Contigs-Assembly and Annotation Tool-Box for genome sequencing projects. Bioinformatics 20:790-797.

[15504269] Raymond J, Thiberge JM, Chevalier C, Kalach N, Bergeret M, Labigne A, Dauga C (2004). Genetic and transmission analyses of Helicobacter pylori strains within a family. Emerg. Infect. Dis. 10:1816-1821.

[15131170] Trad S, Allignet J, Frangeul L, Davi M, Vergassola M, Couve E, Morvan A, Kechrid A, Buchrieser C, Glaser P, El-Solh N (2004). DNA macroarray for identification and typing of Staphylococcus aureus isolates. J. Clin. Microbiol. 42: 2054-2064.

2003

[12626712] Boneca IG, de Reuse H, Epinat JC, Pupin M, Labigne A, Moszer I (2003). A revised annotation and comparative analysis of Helicobacter pylori genomes. Nucleic Acids Res. 31:1704-1714.

[14500481] Bury-Moné S, Skouloubris S, Dauga C, Thiberge JM, Dailidiene D, Berg DE, Labigne A, de Reuse H (2003). Presence of active aliphatic amidases in Helicobacter species able to colonize the stomach. Infect. Immun. 71:5613-5622.

[14528314] Duchaud E, Rusniok C, Frangeul L, Buchrieser C, Givaudan A, Taourit S, Bocs S, Boursaux-Eude C, Chandler M, Charles JF, Dassa E, Derose R, Derzelle S, Freyssinet G, Gaudriault S, Médigue C, Lanois A, Powell K, Siguier P, Vincent R, Wingate V, Zouine M, Glaser P, Boemare N, Danchin A, Kunst F (2003). The genome sequence of the entomopathogenic bacterium Photorhabdus luminescens. Nat. Biotechnol. 21:1307-1313.

[12807202] Gardan L, Stead DE, Dauga C, Gillis M (2003). Acidovorax valerianellae sp. nov., a new pathogen for lamb’s lettuce [Valerianella locusta (L.) Laterr.]. Int. J. Syst. Evol. Microbiol. 53:795-800.

[12788972] Garnier T, Eiglmeier K, Camus JC, Medina N, Mansoor H, Pryor M, Duthoy S, Grondin S, Lacroix C, Monsempe C, Simon S, Harris B, Atkin R, Doggett J, Mayes R, Keating L, Wheeler PR, Parkhill J, Barrell BG, Cole ST, Gordon SV, Hewinson RG (2003). The complete genome sequence of Mycobacterium bovis. Proc. Natl. Acad. Sci. U.S.A. 100:7877-7882.

[12527359] Koszul R, Malpertuy A, Frangeul L, Bouchier C, Wincker P, Thierry A, Duthoy S, Ferris S, Hennequin C, Dujon B (2003). The complete mitochondrial genome sequence of the pathogenic yeast Candida (Torulopsis) glabrata. FEBS Lett. 534: 39-48.

[12622816] Milohanic E, Glaser P, Coppée JY, Frangeul L, Vega Y, Vazquez-Boland JA, Kunst F, Cossart P, Buchrieser C (2003). Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA. Mol. Microbiol. 47: 1613-1625.

[12803476] Roth CW, Holm I, Graille M, Dehoux P, Rzhetsky A, Wincker P, Weissenbach J, Brey PT (2003). Identification of the Anopheles gambiae ATP-binding cassette transporter superfamily genes. Mol. Cells 15: 150-158.

2002

[] Camus JC, Moszer I, Jones LM, Pryor MJ, Cole ST (2002). TubercuList: a regularly updated database dedicated to the Mycobacterium tuberculosis genome. In Genomics of GC-Rich Gram-Positive Bacteria, pp. 159-176, Caister Academic Press, Wymondham, UK.

[12368430] Camus JC, Pryor MJ, Médigue C, Cole ST (2002). Re-annotation of the genome sequence of Mycobacterium tuberculosis H37Rv. Microbiology 148:2967-2973.

[11931166] Dauga C (2002). Evolution of the gyrB gene and the molecular phylogeny of Enterobacteriaceae: a model molecule for molecular systematic studies. Int. J. Syst. Evol. Microbiol. 52:531-547.

[12354221] Glaser P, Rusniok C, Buchrieser C, Chevalier F, Frangeul L, Msadek T, Zouine M, Couve E, Lalioui L, Poyart C, Trieu-Cuot P, Kunst F (2002). Genome sequence of Streptococcus agalactiae, a pathogen causing invasive neonatal disease. Mol. Microbiol. 45:1499-1513.

[18628883] Harwood CR, Moszer I (2002). From gene regulation to gene function: regulatory networks in Bacillus subtilis. Comp. Func. Genom. 3:37-41.

[] Moszer I (2002). Bases de données génomiques microbiennes : principes, méthodes et applications. Annales de l’Institut Pasteur/actualités 11:85-103.

[11752255] Moszer I, Jones LM, Moreira S, Fabry C, Danchin A (2002). SubtiList: the reference database for the Bacillus subtilis genome. Nucleic Acids Res. 30:62-65.
Dernière mise à jour : 8 avril 2010
Commentaires : ivan.moszer@pasteur.fr