Jean Yves Coppee

Summary

Affiliation: Institut Pasteur
Country: France

Publications

  1. doi request reprint The Listeria transcriptional landscape from saprophytism to virulence
    Alejandro Toledo-Arana
    Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
    Nature 459:950-6. 2009
  2. ncbi request reprint CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation
    Olga Soutourina
    Unité de Génétique des Génomes Bactériens, CNRS URA 2171, France
    Mol Microbiol 73:194-211. 2009
  3. pmc RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
    Sanjiveeni Dhamgaye
    Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
    BMC Genomics 13:396. 2012
  4. pmc Field-based evidence of fast and global increase of Plasmodium falciparum drug-resistance by DNA-microarrays and PCR/RFLP in Niger
    Maman Laminou Ibrahim
    Centre de Recherche Médicale et Sanitaire CERMES, BP 10887 Niamey, Niger
    Malar J 8:32. 2009
  5. pmc FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance
    Nicolas Steenkeste
    Laboratoire d Epidemiologie Moleculaire, Institut Pasteur du Cambodge, 5 Bd Monivong, BP 983, Phnom Penh, Cambodia
    Malar J 8:229. 2009
  6. pmc Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)
    Simon M Dittami
    UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
    BMC Mol Biol 12:2. 2011
  7. pmc Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
    Marie Laure Rosso
    Inserm U801, Lille, F 59019, université Lille II, faculté de médecine Henri Warembourg, Lille, France
    BMC Microbiol 8:211. 2008
  8. pmc Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans
    Sandrine Koechler
    UMR7156 Génétique Moléculaire, Génomique et Microbiologie, CNRS Universite de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France
    BMC Microbiol 10:53. 2010
  9. pmc Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia
    Claude Lamarre
    Unite des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
    BMC Genomics 9:417. 2008
  10. pmc Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate
    Onguma Natalang
    Institut Pasteur, Unité d Immunologie Moléculaire des Parasites, CNRS URA 2581, 28 rue du Docteur Roux, F 75724, Paris, Cedex 15, France
    BMC Genomics 9:388. 2008

Detail Information

Publications44

  1. doi request reprint The Listeria transcriptional landscape from saprophytism to virulence
    Alejandro Toledo-Arana
    Institut Pasteur, Unité des Interactions Bactéries Cellules, F 75015 Paris, France
    Nature 459:950-6. 2009
    ..Together, our data unravel successive and coordinated global transcriptional changes during infection and point to previously unknown regulatory mechanisms in bacteria...
  2. ncbi request reprint CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation
    Olga Soutourina
    Unité de Génétique des Génomes Bactériens, CNRS URA 2171, France
    Mol Microbiol 73:194-211. 2009
    ..aureus via an ica-independent mechanism. These data indicate that fine-tuning of sulphur metabolism plays an important part in the physiology of this major pathogen and its adaptation to environmental conditions and survival in the host...
  3. pmc RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans
    Sanjiveeni Dhamgaye
    Membrane Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi 110067, India
    BMC Genomics 13:396. 2012
    ..We used RNA sequencing (RNA-seq) to analyze the transcriptomes of a CDR (Candida Drug Resistance) strain and its isogenic drug sensitive counterpart...
  4. pmc Field-based evidence of fast and global increase of Plasmodium falciparum drug-resistance by DNA-microarrays and PCR/RFLP in Niger
    Maman Laminou Ibrahim
    Centre de Recherche Médicale et Sanitaire CERMES, BP 10887 Niamey, Niger
    Malar J 8:32. 2009
    ..Then, Niger adopted artemisinin-based combination therapy as first-line treatment...
  5. pmc FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance
    Nicolas Steenkeste
    Laboratoire d Epidemiologie Moleculaire, Institut Pasteur du Cambodge, 5 Bd Monivong, BP 983, Phnom Penh, Cambodia
    Malar J 8:229. 2009
    ..Here a new Zip-code array is described, called FlexiChip, linked to a dedicated software program, which largely overcomes this problem...
  6. pmc Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae)
    Simon M Dittami
    UPMC Univ Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique, 29680 Roscoff, France
    BMC Mol Biol 12:2. 2011
    ....
  7. pmc Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
    Marie Laure Rosso
    Inserm U801, Lille, F 59019, université Lille II, faculté de médecine Henri Warembourg, Lille, France
    BMC Microbiol 8:211. 2008
    ..However, in immunocompromised patients, the microorganism may disseminate from the digestive tract and thus cause a systemic infection with septicemia...
  8. pmc Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans
    Sandrine Koechler
    UMR7156 Génétique Moléculaire, Génomique et Microbiologie, CNRS Universite de Strasbourg, 28 rue Goethe, 67000 Strasbourg, France
    BMC Microbiol 10:53. 2010
    ..Herminiimonas arsenicoxydans has been isolated from an arsenic- contaminated environment and has developed various mechanisms for coping with arsenic, including the oxidation of As(III) to As(V) as a detoxification mechanism...
  9. pmc Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia
    Claude Lamarre
    Unite des Aspergillus, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris Cedex 15, France
    BMC Genomics 9:417. 2008
    ..fumigatus genome)...
  10. pmc Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate
    Onguma Natalang
    Institut Pasteur, Unité d Immunologie Moléculaire des Parasites, CNRS URA 2581, 28 rue du Docteur Roux, F 75724, Paris, Cedex 15, France
    BMC Genomics 9:388. 2008
    ..However, few studies to date have used this powerful approach to explore transcriptome alterations of P. falciparum parasites exposed to antimalarial drugs...
  11. pmc Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans
    Jessica Cleiss-Arnold
    Département Microorganismes, UMR7156 Université de Strasbourg CNRS, Genetique Moleculaire, Génomique et Microbiologie, 28 rue Goethe, 67083 Strasbourg Cedex, France
    BMC Genomics 11:709. 2010
    ..In particular our previous studies have suggested the existence of a temporal induction of arsenite oxidase, a key enzyme in arsenic metabolism, in the presence of As(III)...
  12. doi request reprint Do DNA microarrays have their future behind them?
    Jean Yves Coppee
    DNA microarray platform, Institut Pasteur, 75015 Paris, France
    Microbes Infect 10:1067-71. 2008
    ..This review will discuss on this paradoxical situation...
  13. ncbi request reprint Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA
    Eliane Milohanic
    Unité des Interactions Bactéries Cellules and Laboratoire de Génomique des Microorganismes Pathogènes, Institut Pasteur, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France
    Mol Microbiol 47:1613-25. 2003
    ..This study reveals that PrfA can act as an activator or a repressor and suggests that PrfA may directly or indirectly activate different sets of genes in association with different sigma factors...
  14. pmc Induction of the Cpx envelope stress pathway contributes to Escherichia coli tolerance to antimicrobial peptides
    Bianca Audrain
    Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
    Appl Environ Microbiol 79:7770-9. 2013
    ..While this study further extends the understanding of the array of peptide-induced stress signaling systems, it also provides insight into the contribution of Cpx envelope stress pathway to E. coli tolerance to antimicrobial peptides. ..
  15. pmc From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma
    Jean Michel Thiberge
    Institut Pasteur, Unité postulante de Pathogenèse de Helicobacter, Paris, France
    BMC Genomics 11:368. 2010
    ..To determine whether certain combinations of genetic markers can be used to predict the clinical source of the infection, we analyzed well documented and geographically homogenous clinical isolates using a comparative genomics approach...
  16. ncbi request reprint On the origin of leprosy
    Marc Monot
    Unite de Genetique Moleculaire Bacterienne, Institut Pasteur, Paris, France
    Science 308:1040-2. 2005
    ..The disease seems to have originated in Eastern Africa or the Near East and spread with successive human migrations. Europeans or North Africans introduced leprosy into West Africa and the Americas within the past 500 years...
  17. pmc Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide
    Julien Santi-Rocca
    Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France
    PLoS ONE 7:e31777. 2012
    ..Our data highlighted unique cellular responses of interest to understand the mechanisms of parasite death during amoebiasis...
  18. pmc A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans
    Azad Eshghi
    Institut Pasteur, Biology of Spirochetes Unit, Paris, France
    Infect Immun 82:2542-52. 2014
    ..We provide insight into a possible requirement for transcriptional regulation as it relates to leptospiral virulence and suggest various biological processes that are affected due to the loss of native expression of this genetic locus. ..
  19. pmc Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica
    Chung Chau Hon
    Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Département Biologie Cellulaire et Infection, F 75015 Paris, France, INSERM U786, F 75015 Paris, France
    Nucleic Acids Res 41:1936-52. 2013
    ..histolytica is limited. Lastly, we revised the gene models and annotated their 3'UTR in AmoebaDB, providing valuable resources to the community...
  20. pmc Expanding the RpoS/σS-Network by RNA Sequencing and Identification of σS-Controlled Small RNAs in Salmonella
    Corinne Lévi-Meyrueis
    Institut Pasteur, Unité de Génétique Moléculaire, Departement de Microbiologie, Paris, France CNRS, ERL3526, Paris, France Université Paris Sud XI, Orsay, France
    PLoS ONE 9:e96918. 2014
    ..These findings will inspire future studies to investigate molecular mechanisms and the physiological impact of post-transcriptional regulation by σS. ..
  21. doi request reprint Identification of RNA partners of viral proteins in infected cells
    Anastassia V Komarova
    Unité de Génomique Virale et Vaccination, Institut Pasteur, CNRS URA 3015, Paris, France
    RNA Biol 10:944-56. 2013
    ..Thus, this method provides a new platform to explore biologically active RNA-protein networks that viruses establish within infected cells. ..
  22. doi request reprint A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection
    Haig A Eskandarian
    Unité des Interactions Bactéries Cellules, Institut Pasteur, Paris, France
    Science 341:1238858. 2013
    ..Thus, SIRT2-mediated H3K18 deacetylation plays a critical role during infection, which reveals an epigenetic mechanism imposed by a pathogenic bacterium to reprogram its host. ..
  23. ncbi request reprint GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli
    Florence Hommais
    Unité de Génétique des Génomes Bactériens, URA CNRS 2185, Institut Pasteur, France
    Microbiology 150:61-72. 2004
    ..These results, along with the G+C signature of the chromosomal region, support the existence of a fitness island for acid adaptation on the E. coli chromosome...
  24. doi request reprint Extending KNIME for next-generation sequencing data analysis
    Bernd Jagla
    Département Génomes et Génétique, Institut Pasteur, Plate forme Transcriptome et Epigénome, 25 rue du Docteur Roux, F 75015 Paris, France
    Bioinformatics 27:2907-9. 2011
    ..We present here new functionality and workflows that open the door to performing next-generation sequencing analysis using the KNIME framework...
  25. ncbi request reprint AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests
    José Osorio y Fortéa
    Unité d Immunophysiologie et Parasitisme Intracellulaire, Département de Parasitologie et Mycologie, Institut Pasteur, 25 rue du Docteur Roux, 75724 Paris, France
    J Bioinform Comput Biol 6:317-34. 2008
    ..AffyGCQC has been designed as an easy-to-use Web-based interface (online supplementary information: http://www.transcriptome.ens.fr/AffyGCQC/; contact: affygcqc@biologie.ens.fr)...
  26. pmc Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes
    José Osorio y Fortéa
    Institut Pasteur, Unité d Immunophysiologie et Parasitisme Intracellulaire, Département de Parasitologie et Mycologie, Paris, France
    BMC Genomics 10:119. 2009
    ..Indeed, the intracellular development of L. amazonensis amastigote relies on the biogenesis and dynamic remodelling of a phagolysosome, termed the parasitophorous vacuole, primarily within dermal MPhi...
  27. pmc Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum
    T Nicolai Siegel
    Biology of Host Parasite Interactions Unit, Institut Pasteur, Paris, France
    BMC Genomics 15:150. 2014
    ....
  28. ncbi request reprint Adherence modifies the regulation of gene expression induced by interleukin-10
    Anne France Petit-Bertron
    UP Cytokines and Inflammation, Institut Pasteur, 28 rue Dr Roux, 75015 Paris, France
    Cytokine 29:1-12. 2005
    ..Furthermore, the inhibition of the expression of SOCS1 by IL-10 in the absence of adherence, may explain its priming effects on a subsequent LPS stimulation that we previously described...
  29. doi request reprint Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence
    Tobias Sahr
    Institut Pasteur, 28, rue du Dr Roux, Paris 75724, France
    RNA Biol 9:503-19. 2012
    ..pneumophila genome, identified many new ncRNAs and will provide a framework for the understanding of virulence and adaptation properties of L. pneumophila...
  30. pmc Identification of the Virulence Landscape Essential for Entamoeba histolytica Invasion of the Human Colon
    Roman Thibeaux
    Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, France INSERM U786, Paris, France Université de Versailles Saint Quentin en Yvelines, Versailles, France
    PLoS Pathog 9:e1003824. 2013
    ..In summary, our data suggest a potential role of carbohydrate metabolism in colon invasion by virulent E. histolytica. ..
  31. pmc Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin
    Steve P Bernier
    Institut Pasteur, Unité de Génétique des Biofilms, Paris, France
    PLoS Genet 9:e1003144. 2013
    ..Our results therefore show that the SOS stress response induced in heterogeneous and nutrient-deprived biofilm microenvironments is a molecular mechanism leading to biofilm-specific high tolerance to the fluoroquinolone ofloxacin...
  32. pmc Artesunate tolerance in transgenic Plasmodium falciparum parasites overexpressing a tryptophan-rich protein
    Guillaume Deplaine
    Institut Pasteur, Unité d Immunologie Moléculaire des Parasites, Departement de Parasitologie Mycologie, CNRS, URA2581, F 75015 Paris, France
    Antimicrob Agents Chemother 55:2576-84. 2011
    ..This is the first report of genetically manipulated parasites displaying a stable and reproducible decreased susceptibility to artesunate, providing new possibilities to investigate the parasite response to artemisinins...
  33. pmc Unusual composition of a yeast chromosome arm is associated with its delayed replication
    Celia Payen
    Institut Pasteur, CNRS, URA, Universite Pierre et Marie Curie, Paris, France
    Genome Res 19:1710-21. 2009
    ....
  34. pmc The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila
    Delphine Fagegaltier
    Centre National de la Recherche Scientifique, Unité de Recherche Associée 2578, Institut Pasteur, 25 rue du Dr Roux, F75015 Paris, France
    Proc Natl Acad Sci U S A 106:21258-63. 2009
    ..Similar effects were observed in dcr2, r2d2, and ago2 mutants. Our findings provide evidence that a nuclear pool of TE-derived endo-siRNAs is involved in heterochromatin formation in somatic tissues in Drosophila...
  35. pmc Distinct transcriptional signatures of bone marrow-derived C57BL/6 and DBA/2 dendritic leucocytes hosting live Leishmania amazonensis amastigotes
    Emilie Giraud
    Département de Parasitologie et Mycologie, Laboratoire Immunophysiologie et Parasitisme, Institut Pasteur, Paris, France
    PLoS Negl Trop Dis 6:e1980. 2012
    ....
  36. ncbi request reprint Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague
    Sylvie Chauvaux
    Yersinia Research Unit, Institut Pasteur, 28 rue du Dr Roux, F 75724 Paris Cedex 15, France
    Microbiology 153:3112-24. 2007
    ..Eleven of these genes were specifically transcribed at 37 degrees C and may thus represent new virulence factors that are important during the septicaemic phase of human plague...
  37. pmc The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence
    Willem van Schaik
    Unité Toxines et Pathogénie Bactérienne, Institut Pasteur, 28 rue du Dr Roux, 75724 Cedex 15, France
    Infect Immun 77:4437-45. 2009
    ..Overexpression of atxA restored toxin component synthesis in the codY mutant strain. These results suggest that CodY controls toxin gene expression by regulating AtxA accumulation posttranslationally...
  38. ncbi request reprint The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis
    Julien Santi-Rocca
    Institut Pasteur, Unité Biologie Cellulaire du Parasitisme, Paris, F 75015, France, and INSERM U786, Paris, F 75015, France
    Cell Microbiol 10:202-17. 2008
    ..Following its characterization as a marker for the progression of infection, KERP1 was also seen to be a virulence marker as trophozoites affected in kerp1 expression by an antisense strategy were unable to form liver abscesses...
  39. pmc Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism
    Aurélie Guyet
    Unité de Biologie des Bactéries Pathogènes à Gram Positif, Institut Pasteur, CNRS URA 2172, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France
    BMC Microbiol 14:81. 2014
    ..We recently discovered interplay between ClpP peptidases and AdpA in S. lividans. Here, we report the identification of genes directly regulated by AdpA in S. lividans...
  40. pmc Transcriptome analysis of antigenic variation in Plasmodium falciparum--var silencing is not dependent on antisense RNA
    Stuart A Ralph
    Institut Pasteur, Centre National de la Recherche Scientifique, Unité de Recherche Associée 2581, F 75724 Paris Cedex 15, France
    Genome Biol 6:R93. 2005
    ..To investigate transcriptional features of this mechanism, we conducted a microarray analysis of parasites that were selected to express different var genes by adhesion to chondroitin sulfate A (CSA) or CD36...
  41. pmc Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile
    Olga A Soutourina
    Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Paris, France
    PLoS Genet 9:e1003493. 2013
    ..difficile sRNAs provides a firm basis for future RNome characterization and identification of molecular mechanisms of sRNA-based regulation of gene expression in this emergent enteropathogen...
  42. ncbi request reprint Long oligonucleotide microarrays for African green monkey gene expression profile analysis
    Beatrice Jacquelin
    Unité de Régulations des Infections Rétrovirales, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris Cedex 15, France
    FASEB J 21:3262-71. 2007
    ..In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles...
  43. pmc Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica
    Christian Weber
    Unité Biologie Cellulaire du Parasitisme, INSERM 786, Institut Pasteur, 28 rue du Dr Roux, 75724 Paris Cedex 15, France
    Eukaryot Cell 5:871-5. 2006
    ....
  44. ncbi request reprint Chemotaxis of Entamoeba histolytica towards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the Galactose/N-acetylgalactosamine lectin activity
    Samantha Blazquez
    Institut Pasteur, Unité de Biologie Cellulaire du Parasitisme, Paris, F 75015, France
    Cell Microbiol 10:1676-86. 2008
    ..These results have given us an insight on how E. histolytica changes its cytoskeleton dynamics during chemotaxis and revealed the capital role of PI3K and Gal/GalNAc lectin signalling in chemotaxis...