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Publications de la plate-forme

2012

RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans.

Dhamgaye S, Bernard M, Lelandais G, Sismeiro O, Lemoine S, Coppée JY, Le Crom S, Prasad R, Devaux F.

BMC Genomics. 2012 Aug 16;13(1):396

Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence.

Sahr T, Rusniok C, Dervins-Ravault D, Sismeiro O, Coppee JY, Buchrieser C.

RNA Biol. 2012 Apr 1;9(4).

Human cryptochrome-1 confers light independent biological activity in transgenic Drosophila correlated with flavin radical stability.

Vieira J, Jones AR, Danon A, Sakuma M, Hoang N, Robles D, Tait S, Heyes DJ, Picot M, Yoshii T, Helfrich-Förster C, Soubigou G, Coppee JY, Klarsfeld A, Rouyer F, Scrutton NS, Ahmad M.

PLoS One. 2012;7(3):e31867. Epub 2012 Mar 12

Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide.

Santi-Rocca J, Smith S, Weber C, Pineda E, Hon CC, Saavedra E, Olivos-García A, Rousseau S, Dillies MA, Coppée JY, Guillén N.

PLoS One. 2012;7(2):e31777. Epub 2012 Feb 24

Myf5 haploinsufficiency reveals distinct cell fate potentials for adult skeletal muscle stem cells.

Gayraud-Morel B, Chrétien F, Jory A, Sambasivan R, Negroni E, Flamant P, Soubigou G, Coppée JY, Di Santo J, Cumano A, Mouly V, Tajbakhsh S.

J Cell Sci. 2012 Apr 1;125(Pt 7):1738-49. Epub 2012 Feb 24

Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles.

Jouneau A, Ciaudo C, Sismeiro O, Brochard V, Jouneau L, Vandormael-Pournin S, Coppée JY, Zhou Q, Heard E, Antoniewski C, Cohen-Tannoudji M.

RNA. 2012 Feb;18(2):253-64. Epub 2011 Dec 27

2011

Overexpression of proinflammatory TLR-2-signalling lipoproteins in hypervirulent mycobacterial variants.

Roux AL, Ray A, Pawlik A, Medjahed H, Etienne G, Rottman M, Catherinot E, Coppée JY, Chaoui K, Monsarrat B, Toubert A, Daffé M, Puzo G, Gaillard JL, Brosch R, Dulphy N, Nigou J, Herrmann JL.

Cell Microbiol. 2011 May;13(5):692-704. doi: 10.1111/j.1462-5822.2010.01565.x. Epub 2011 Jan 5

Extending KNIME for next-generation sequencing data analysis.

Jagla B, Wiswedel B, Coppée JY.

Bioinformatics. 2011 Oct 15;27(20):2907-9. Epub 2011 Aug 27

Artesunate tolerance in transgenic Plasmodium falciparum parasites overexpressing a tryptophan-rich protein.

Deplaine G, Lavazec C, Bischoff E, Natalang O, Perrot S, Guillotte-Blisnick M, Coppée JY, Pradines B, Mercereau-Puijalon O, David PH.

Antimicrob Agents Chemother. 2011 Jun;55(6):2576-84. Epub 2011 Apr 4

Global regulation of the response to sulfur availability in the cheese-related bacterium Brevibacterium aurantiacum.

Forquin MP, Hébert A, Roux A, Aubert J, Proux C, Heilier JF, Landaud S, Junot C, Bonnarme P, Martin-Verstraete I.

Appl Environ Microbiol. 2011 Feb;77(4):1449-59. Epub 2010 Dec 17

Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae).

Dittami SM, Proux C, Rousvoal S, Peters AF, Cock JM, Coppée JY, Boyen C, Tonon T.

BMC Mol Biol. 2011 Jan 13;12:2.

A bacterial protein targets the BAHD1 chromatin complex to stimulate type III interferon response.

Lebreton A, Lakisic G, Job V, Fritsch L, Tham TN, Camejo A, Matteï PJ, Regnault B, Nahori MA, Cabanes D, Gautreau A, Ait-Si-Ali S, Dessen A, Cossart P, Bierne H.

Science. 2011 Mar 11;331(6022):1319-21. Epub 2011 Jan 20.

2010

Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans.

Cleiss-Arnold J, Koechler S, Proux C, Fardeau ML, Dillies MA, Coppee JY, Arsène-Ploetze F, Bertin PN.

BMC Genomics. 2010 Dec 17;11:709.

Transcriptome analyses based on genetic screens for Pax3 myogenic targets in the mouse embryo.

Lagha M, Sato T, Regnault B, Cumano A, Zuniga A, Licht J, Relaix F, Buckingham M.

BMC Genomics. 2010 Dec 8;11:696.

From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma.

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.

BMC Genomics. 2010 Jun 10;11:368.

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

Arsène-Ploetze F, Koechler S, Marchal M, Coppée JY, Chandler M, Bonnefoy V, Brochier-Armanet C, Barakat M, Barbe V, Battaglia-Brunet F, Bruneel O, Bryan CG, Cleiss-Arnold J, Cruveiller S, Erhardt M, Heinrich-Salmeron A, Hommais F, Joulian C, Krin E, Lieutaud A, Lièvremont D, Michel C, Muller D, Ortet P, Proux C, Siguier P, Roche D, Rouy Z, Salvignol G, Slyemi D, Talla E, Weiss S, Weissenbach J, Médigue C, Bertin PN.

PLoS Genet. 2010 Feb 26;6(2):e1000859.

Decreased in vitro susceptibility of Plasmodium falciparum isolates to artesunate, mefloquine, chloroquine, and quinine in Cambodia from 2001 to 2007.

Lim P, Wongsrichanalai C, Chim P, Khim N, Kim S, Chy S, Sem R, Nhem S, Yi P, Duong S, Bouth DM, Genton B, Beck HP, Gobert JG, Rogers WO, Coppee JY, Fandeur T, Mercereau-Puijalon O, Ringwald P, Le Bras J, Ariey F.

Antimicrob Agents Chemother. 2010 May;54(5):2135-42. Epub 2010 Mar 1.

Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans.

Koechler S, Cleiss-Arnold J, Proux C, Sismeiro O, Dillies MA, Goulhen-Chollet F, Hommais F, Lièvremont D, Arsène-Ploetze F, Coppée JY, Bertin PN.

BMC Microbiol. 2010 Feb 18;10:53.

Control of flagellar gene regulation in Legionella pneumophila and its relation to growth phase.

Albert-Weissenberger C, Sahr T, Sismeiro O, Hacker J, Heuner K, Buchrieser C.

J Bacteriol. 2010 Jan;192(2):446-55. Epub 2009 Nov 13.

An adult tissue-specific stem cell in its niche: a gene profiling analysis of in vivo quiescent and activated muscle satellite cells.

Pallafacchina G, François S, Regnault B, Czarny B, Dive V, Cumano A, Montarras D, Buckingham M.

Stem Cell Res. 2010 Mar;4(2):77-91. Epub 2009 Oct 28.

2009

Nonpathogenic SIV infection of African green monkeys induces a strong but rapidly controlled type I IFN response.

Jacquelin B, Mayau V, Targat B, Liovat AS, Kunkel D, Petitjean G, Dillies MA, Roques P, Butor C, Silvestri G, Giavedoni LD, Lebon P, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC.

J Clin Invest. 2009 Dec;119(12):3544-55.

Human BAHD1 promotes heterochromatic gene silencing.

Bierne H, Tham TN, Batsche E, Dumay A, Leguillou M, Kernéis-Golsteyn S, Regnault B, Seeler JS, Muchardt C, Feunteun J, Cossart P.

Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13826-31. Epub 2009 Aug 3.

Basonuclin 2 has a function in the multiplication of embryonic craniofacial mesenchymal cells and is orthologous to disco proteins.

Vanhoutteghem A, Maciejewski-Duval A, Bouche C, Delhomme B, Hervé F, Daubigney F, Soubigou G, Araki M, Araki K, Yamamura K, Djian P.

Proc Natl Acad Sci U S A. 2009 Aug 25;106(34):14432-7. Epub 2009 Aug 12.

FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance.

Steenkeste N, Dillies MA, Khim N, Sismeiro O, Chy S, Lim P, Crameri A, Bouchier C, Mercereau-Puijalon O, Beck HP, Imwong M, Dondorp AM, Socheat D, Rogier C, Coppée JY, Ariey F.

Malar J. 2009 Oct 15;8:229.

The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence.

Van Schaik W, Château A, Dillies MA, Coppée JY, Sonenshein AL, Fouet A.

Infect Immun. 2009 Oct;77(10):4437-45. Epub 2009 Aug 3.

Unusual composition of a yeast chromosome arm is associated with its delayed replication.

Payen C, Fischer G, Marck C, Proux C, Sherman DJ, Coppée JY, Johnston M, Dujon B, Neuvéglise C.

Genome Res. 2009 Oct;19(10):1710-21. Epub 2009 Jul 10.

The Listeria transcriptional landscape from saprophytism to virulence.

Toledo-Arana A, Dussurget O, Nikitas G, Sesto N, Guet-Revillet H, Balestrino D, Loh E, Gripenland J, Tiensuu T, Vaitkevicius K, Barthelemy M, Vergassola M, Nahori MA, Soubigou G, Régnault B, Coppée JY, Lecuit M, Johansson J, Cossart P.

Nature. 2009 Jun 18;459(7249):950-6. Epub 2009 May 17.

Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses.

Forquin MP, Duvergey H, Proux C, Loux V, Mounier J, Landaud S, Coppée JY, Gibrat JF, Bonnarme P, Martin-Verstraete I, Vallaeys T.

Appl Environ Microbiol. 2009 Oct;75(19):6406-9. Epub 2009 Jul 31.

CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation.

Soutourina O, Poupel O, Coppée JY, Danchin A, Msadek T, Martin-Verstraete I.

Mol Microbiol. 2009 Jul;73(2):194-211. Epub 2009 Jun 8.

Field-based evidence of fast and global increase of Plasmodium falciparum drug-resistance by DNA-microarrays and PCR/RFLP in Niger.

Ibrahim ML, Steenkeste N, Khim N, Adam HH, Konaté L, Coppée JY, Ariey F, Duchemin JB.

Malar J. 2009 Feb 23;8:32.

Genomic polymorphism in the population of Candida glabrata: gene copy-number variation and chromosomal translocations.

Muller H, Thierry A, Coppée JY, Gouyette C, Hennequin C, Sismeiro O, Talla E, Dujon B, Fairhead C.

Fungal Genet Biol. 2009 Mar;46(3):264-76. Epub 2008 Dec 6.

Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes.

Osorio y Fortéa J, de La Llave E, Regnault B, Coppée JY, Milon G, Lang T, Prina E.

BMC Genomics. 2009 Mar 20;10:119.

2008

Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs.

Crameri A, Marfurt J, Mugittu K, Maire N, Regös A, Coppee JY, Sismeiro O, Burki R, Huber E, Laubscher D, Puijalon O, Genton B, Felger I, Beck HP.

J Clin Microbiol. 2007 Nov;45(11):3685-91. Epub 2007 Sep 5.

Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression.

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.

BMC Microbiol. 2008 Dec 3;8:211.

Temperature shift and host cell contact up-regulate sporozoite expression of Plasmodium falciparum genes involved in hepatocyte infection.

Siau A, Silvie O, Franetich JF, Yalaoui S, Marinach C, Hannoun L, van Gemert GJ, Luty AJ, Bischoff E, David PH, Snounou G, Vaquero C, Froissard P, Mazier D.

PLoS Pathog. 2008 Aug 8;4(8):e1000121.

The LIM-only protein FHL2 mediates ras-induced transformation through cyclin D1 and p53 pathways.

Labalette C, Nouët Y, Levillayer F, Armengol C, Renard CA, Soubigou G, Xia T, Buendia MA, Wei Y.

PLoS One. 2008;3(11):e3761. Epub 2008 Nov 19.

Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data.

Weiss S, Carapito C, Cleiss J, Koechler S, Turlin E, Coppee JY, Heymann M, Kugler V, Stauffert M, Cruveiller S, Médigue C, Van Dorsselaer A, Bertin PN, Arsène-Ploetze F.

Biochimie. 2009 Feb;91(2):192-203. Epub 2008 Sep 25.

Do DNA microarrays have their future behind them?

Coppée JY.

Microbes Infect. 2008 Jul;10(9):1067-71. Epub 2008 Jul 9. Review.

Interferon gamma-signature transcript profiling and IL-23 upregulation in response to Helicobacter pylori infection.

Vivas JR, Regnault B, Michel V, Bussière FI, Avé P, Huerre M, Labigne A, D' Elios MM, Touati E.

Int J Immunopathol Pharmacol. 2008 Jul-Sep;21(3):515-26.

Virulent Shigella flexneri subverts the host innate immune response through manipulation of antimicrobial peptide gene expression.

Sperandio B, Regnault B, Guo J, Zhang Z, Stanley SL Jr, Sansonetti PJ, Pédron T.

J Exp Med. 2008 May 12;205(5):1121-32. Epub 2008 Apr 21.

The LIM-only protein FHL2 regulates cyclin D1 expression and cell proliferation.

Labalette C, Nouët Y, Sobczak-Thepot J, Armengol C, Levillayer F, Gendron MC, Renard CA, Regnault B, Chen J, Buendia MA, Wei Y.

J Biol Chem. 2008 May 30;283(22):15201-8. Epub 2008 Mar 31.

Maturation of paneth cells induces the refractory state of newborn mice to Shigella infection.

Fernandez MI, Regnault B, Mulet C, Tanguy M, Jay P, Sansonetti PJ, Pédron T.

J Immunol. 2008 Apr 1;180(7):4924-30.

Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia.

Lamarre C, Sokol S, Debeaupuis JP, Henry C, Lacroix C, Glaser P, Coppée JY, François JM, Latgé JP.

BMC Genomics. 2008 Sep 16;9:417.

Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate.

Natalang O, Bischoff E, Deplaine G, Proux C, Dillies MA, Sismeiro O, Guigon G, Bonnefoy S, Patarapotikul J, Mercereau-Puijalon O, Coppée JY, David PH.

BMC Genomics. 2008 Aug 18;9:388.

AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests.

Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B.

J Bioinform Comput Biol. 2008 Apr;6(2):317-34.

Chemotaxis of Entamoeba histolytica towards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the Galactose/N-acetylgalactosamine lectin activity.

Blazquez S, Guigon G, Weber C, Syan S, Sismeiro O, Coppée JY, Labruyère E, Guillén N.

Cell Microbiol. 2008 Aug;10(8):1676-86. Epub 2008 Apr 16.

Plasmodium falciparum transcriptome analysis reveals pregnancy malaria associated gene expression.

Tuikue Ndam N, Bischoff E, Proux C, Lavstsen T, Salanti A, Guitard J, Nielsen MA, Coppée JY, Gaye A, Theander T, David PH, Deloron P.

PLoS One. 2008 Mar 26;3(3):e1855.

The Yak1 kinase is involved in the initiation and maintenance of hyphal growth in Candida albicans.

Goyard S, Knechtle P, Chauvel M, Mallet A, Prévost MC, Proux C, Coppée JY, Schwartz P, Dromer F, Park H, Filler SG, Janbon G, d'Enfert C.

Mol Biol Cell. 2008 May;19(5):2251-66. Epub 2008 Mar 5.

Whole-transcriptome analysis of Plasmodium falciparum field isolates: identification of new pathogenicity factors.

Siau A, Toure FS, Ouwe-Missi-Oukem-Boyer O, Ciceron L, Mahmoudi N, Vaquero C, Froissard P, Bisvigou U, Bisser S, Coppee JY, Bischoff E, David PH, Mazier D.

J Infect Dis. 2007 Dec 1;196(11):1603-12. Epub 2007 Oct 25.

The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis.

Santi-Rocca J, Weber C, Guigon G, Sismeiro O, Coppée JY, Guillén N.

Cell Microbiol. 2008 Jan;10(1):202-17. Epub 2007 Aug 17.

2007

Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague.

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.

Microbiology. 2007 Sep;153(Pt 9):3112-24.

An injected bacterial effector targets chromatin access for transcription factor NF-kappaB to alter transcription of host genes involved in immune responses.

Arbibe L, Kim DW, Batsche E, Pedron T, Mateescu B, Muchardt C, Parsot C, Sansonetti PJ.

Nat Immunol. 2007 Jan;8(1):47-56. Epub 2006 Dec 10.

Connexin30 deficiency causes instrastrial fluid-blood barrier disruption within the cochlear stria vascularis.

Cohen-Salmon M, Regnault B, Cayet N, Caille D, Demuth K, Hardelin JP, Janel N, Meda P, Petit C.

Proc Natl Acad Sci U S A. 2007 Apr 10;104(15):6229-34. Epub 2007 Mar 30.

Long oligonucleotide microarrays for African green monkey gene expression profile analysis.

Jacquelin B, Mayau V, Brysbaert G, Regnault B, Diop OM, Arenzana-Seisdedos F, Rogge L, Coppée JY, Barré-Sinoussi F, Benecke A, Müller-Trutwin MC.

FASEB J. 2007 Oct;21(12):3262-71. Epub 2007 May 16.

Histone modifications induced by a family of bacterial toxins.

Hamon MA, Batsché E, Régnault B, Tham TN, Seveau S, Muchardt C, Cossart P.

Proc Natl Acad Sci U S A. 2007 Aug 14;104(33):13467-72. Epub 2007 Aug 3. Erratum in: Proc Natl Acad Sci U S A. 2007 Oct 30;104(44):17555.

Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs.

Crameri A, Marfurt J, Mugittu K, Maire N, Regös A, Coppee JY, Sismeiro O, Burki R, Huber E, Laubscher D, Puijalon O, Genton B, Felger I, Beck HP.

J Clin Microbiol. 2007 Nov;45(11):3685-91. Epub 2007 Sep 5.

2006

Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica.

Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, Gouyette C, Mirelman D, Coppee JY, Guillén N.

Eukaryot Cell. 2006 May;5(5):871-5.

Anti-inflammatory effect of Lactobacillus casei on Shigella-infected human intestinal epithelial cells.

Tien MT, Girardin SE, Regnault B, Le Bourhis L, Dillies MA, Coppée JY, Bourdet-Sicard R, Sansonetti PJ, Pédron T.

J Immunol. 2006 Jan 15;176(2):1228-37. Erratum in: J Immunol. 2006 Mar 15;176(6):3841.

Anti-inflammatory effect of Lactobacillus casei on Shigella-infected human intestinal epithelial cells.

Tien MT, Girardin SE, Regnault B, Le Bourhis L, Dillies MA, Coppée JY, Bourdet-Sicard R, Sansonetti PJ, Pédron T.

J Immunol. 2006 Jan 15;176(2):1228-37. Erratum in: J Immunol. 2006 Mar 15;176(6):3841.

The protein kinase IKKepsilon can inhibit HCV expression independently of IFN and its own expression is downregulated in HCV-infected livers.

Vilasco M, Larrea E, Vitour D, Dabo S, Breiman A, Regnault B, Riezu JI, Eid P, Prieto J, Meurs EF.

Hepatology. 2006 Dec;44(6):1635-47.

2005

Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila.

Brüggemann H, Hagman A, Jules M, Sismeiro O, Dillies MA, Gouyette C, Kunst F, Steinert M, Heuner K, Coppée JY, Buchrieser C.

Cell Microbiol. 2006 Aug;8(8):1228-40.

Transcriptome analysis of antigenic variation in Plasmodium falciparum--var silencing is not dependent on antisense RNA.

Ralph SA, Bischoff E, Mattei D, Sismeiro O, Dillies MA, Guigon G, Coppee JY, David PH, Scherf A.

Genome Biol. 2005;6(11):R93. Epub 2005 Oct 31.

On the origin of leprosy.

Monot M, Honoré N, Garnier T, Araoz R, Coppée JY, Lacroix C, Sow S, Spencer JS, Truman RW, Williams DL, Gelber R, Virmond M, Flageul B, Cho SN, Ji B, Paniz-Mondolfi A, Convit J, Young S, Fine PE, Rasolofo V, Brennan PJ, Cole ST.

Science. 2005 May 13;308(5724):1040-2.

Cryptic pol II transcripts are degraded by a nuclear quality control pathway involving a new poly(A) polymerase.

Wyers F, Rougemaille M, Badis G, Rousselle JC, Dufour ME, Boulay J, Régnault B, Devaux F, Namane A, Séraphin B, Libri D, Jacquier A.

Cell. 2005 Jun 3;121(5):725-37.

Adherence modifies the regulation of gene expression induced by interleukin-10.

Petit-Bertron AF, Pedron T, Gross U, Coppée JY, Sansonetti PJ, Cavaillon JM, Adib-Conquy M.

Cytokine. 2005 Jan 7;29(1):1-12.