• 2024
  Hafner L, Gadin E, Huang L, Frouin A, Laporte F, Gaultier C, Vieira A, Maudet C, Varet H, Moura A, Bracq-Dieye H, Tessaud-Rita N, Maury M, Dazas M, Legendre R, Gastineau P, Tsai YH, Coppée JY, Charlier C, Patin E, Chikhi R, Rocha EPC, Leclercq A, Disson O, Aschard H, Lecuit M, Differential stress responsiveness determines intraspecies virulence heterogeneity and host adaptation in Listeria monocytogenes., Nat Microbiol 2024 Dec; 9(12): 3345-3361.
• 2024
  Dang TTV, Maufrais C, Colin J, Moyrand F, Mouyna I, Coppée JY, Onyishi CU, Lipecka J, Guerrera IC, May RC, Janbon G, Alternative TSS use is widespread in Cryptococcus fungi in response to environmental cues and regulated genome-wide by the transcription factor Tur1., PLoS Biol 2024 Jul; 22(7): e3002724.
• 2023
  Juliana Rizzo, Adèle Trottier, Frédérique Moyrand, Jean-Yves J.-Y. Coppée, Corinne Maufrais, Ana Claudia G. Zimbres, Thi Tuong Vi Dang, Alexandre Alanio, M. Desnos-Ollivier, Isabelle Mouyna, Gérard Péhau-Arnaude, Pierre-Henri Commere, Sophie Novault, Iuliana V. Ene, Leonardo Nimrichter, Marcio Rodrigues, Guilhem Janbon, Coregulation of extracellular vesicle production and fluconazole susceptibility in Cryptococcus neoformans, mBio, 2023, pp.e00870-23. ⟨10.1128/mbio.00870-23⟩.
• 2022
  Krin E, Baharoglu Z, Sismeiro O, Varet H, Coppée JY, Mazel D, , Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae., Res Microbiol 2023 ; 174(1-2): 103997.
• 2022
  Lourenço M, Chaffringeon L, Lamy-Besnier Q, Titécat M, Pédron T, Sismeiro O, Legendre R, Varet H, Coppée JY, Bérard M, De Sordi L, Debarbieux L, , The gut environment regulates bacterial gene expression which modulates susceptibility to bacteriophage infection., Cell Host Microbe 2022 04; 30(4): 556-569.e5.
• 2022
  Serafini N, Jarade A, Surace L, Goncalves P, Sismeiro O, Varet H, Legendre R, Coppee JY, Disson O, Durum SK, Frankel G, Di Santo JP, , Trained ILC3 responses promote intestinal defense., Science 2022 Feb; 375(6583): 859-863.
• 2022
  Damien Mornico, Chung-Chau Hon, Mikael Koutero, Christian Weber, Jean-Yves Coppée, C Graham Clark, Marie-Agnes Dillies and Nancy Guillén, RNA Sequencing Reveals Widespread Transcription of Natural Antisense RNAs in Entamoeba Species, Microorganisms.
• 2021
  Zavala-Alvarado C, G Huete S, Vincent AT, Sismeiro O, Legendre R, Varet H, Bussotti G, Lorioux C, Lechat P, Coppée JY, Veyrier FJ, Picardeau M, Benaroudj N, The oxidative stress response of pathogenic Leptospira is controlled by two peroxide stress regulators which putatively cooperate in controlling virulence., PLoS Pathog 2021 Dec; 17(12): e1009087.
• 2021
  Lang M, Krin E, Korlowski C, Sismeiro O, Varet H, Coppée JY, Mazel D, Baharoglu Z, , Sleeping ribosomes: Bacterial signaling triggers RaiA mediated persistence to aminoglycosides., iScience 2021 Oct; 24(10): 103128.
• 2021
  Fule L, Halifa R, Fontana C, Sismeiro O, Legendre R, Varet H, Coppée JY, Murray GL, Adler B, Hendrixson DR, Buschiazzo A, Guo S, Liu J, Picardeau M, , Role of the major determinant of polar flagellation FlhG in the endoflagella-containing spirochete Leptospira., Mol Microbiol 2021 Oct; (): .
• 2021
  Nagaraja S, Cai MW, Sun J, Varet H, Sarid L, Trebicz-Geffen M, Shaulov Y, Mazumdar M, Legendre R, Coppée JY, Begley TJ, Dedon PC, Gourinath S, Guillen N, Saito-Nakano Y, Shimokawa C, Hisaeda H, Ankri S, , Queuine Is a Nutritional Regulator of Entamoeba histolytica Response to Oxidative Stress and a Virulence Attenuator., mBio 2021 Mar; 12(2): .
• 2020
  Gaultney RA, Vincent AT, Lorioux C, Coppée JY, Sismeiro O, Varet H, Legendre R, Cockram CA, Veyrier FJ, Picardeau M, , 4-Methylcytosine DNA modification is critical for global epigenetic regulation and virulence in the human pathogen Leptospira interrogans., Nucleic Acids Res 2020 Dec; 48(21): 12102-12115.
• 2020
  Mornico D, Hon CC, Koutero M, Weber C, Coppee JY, Dillies MA, Guillen N, , Genomic determinants for initiation and length of natural antisense transcripts in Entamoeba histolytica., Sci Rep 2020 11; 10(1): 20190.
• 2020
  Freel KC, Fouteau S, Roche D, Farasin J, Huber A, Koechler S, Peres M, Chiboub O, Varet H, Proux C, Deschamps J, Briandet R, Torchet R, Cruveiller S, Lièvremont D, Coppée JY, Barbe V, Arsène-Ploetze F, , Effect of arsenite and growth in biofilm conditions on the evolution of Thiomonas sp. CB2., Microb Genom 2020 Oct; (): .
• 2020
  Zavala-Alvarado C, Sismeiro O, Legendre R, Varet H, Bussotti G, Bayram J, G Huete S, Rey G, Coppée JY, Picardeau M, Benaroudj N, The transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress., PLoS Pathog 2020 Oct; 16(10): e1008904.
• 2020
  Aguilar-Rojas A, Castellanos-Castro S, Matondo M, Gianetto QG, Varet H, Sismeiro O, Legendre R, Fernandes J, Hardy D, Coppée JY, Olivo-Marin JC, Guillen N, , Insights into amebiasis using a human 3D-intestinal model., Cell Microbiol 2020 Aug; 22(8): e13203.
• 2020
  Silvia Castellanos-Castro, Arturo Aguilar-Rojas, Mariette Matondo, Quentin Gian Gianetto, Hugo Varet, Odile Sismeiro, Rachel Legendre, Julien Fernandes, David Hardy, Jean Yves Coppée, Jean Christophe Olivo-Marin, Nancy Guillen, Human Immune Response Triggered by Entamoeba histolytica in a 3D-Intestinal Model, Eukaryome Impact on Human Intestine Homeostasis and Mucosal Immunology. Springer, Cham.
• 2020
  Pourpre R, Naudon L, Meziane H, Lakisic G, Jouneau L, Varet H, Legendre R, Wendling O, Selloum M, Proux C, Coppée JY, Herault Y, Bierne H, BAHD1 haploinsufficiency results in anxiety-like phenotypes in male mice, PLoS ONE 2020;15(5):e0232789.
• 2020
  Peyrusson F, Varet H, Nguyen TK, Legendre R, Sismeiro O, Coppée JY, Wolz C, Tenson T, Van Bambeke F, Intracellular Staphylococcus aureus persisters upon antibiotic exposure, Nat Commun 2020 May;11(1):2200.
• 2020
  Rey C, Chang YY, Latour-Lambert P, Varet H, Proux C, Legendre R, Coppée JY, Enninga J, Transcytosis subversion by M cell-to-enterocyte spread promotes Shigella flexneri and Listeria monocytogenes  intracellular bacterial dissemination, PLoS Pathog. 2020 Apr;16(4):e1008446.
• 2020
  Lecoeur H, Rosazza T, Kokou K, Varet H, Coppée JY, Lari A, Commère PH, Weil R, Meng G, Milon G, Späth GF, Prina E, , Leishmania amazonensis Subverts the Transcription Factor Landscape in Dendritic Cells to Avoid Inflammasome Activation and Stall Maturation., Front Immunol 2020 ; 11(): 1098.
• 2019
  Dubois V, Pawlik A, Bories A, Le Moigne V, Sismeiro O, Legendre R, Varet H, Rodríguez-Ordóñez MDP, Gaillard JL, Coppée JY, Brosch R, Herrmann JL, Girard-Misguich F, Mycobacterium abscessus virulence traits unraveled by transcriptomic profiling in amoeba and macrophages, PLoS Pathog. 2019 Nov;15(11):e1008069.
• 2019
  Carballido Lopez A, Cunrath O, Forster A, Pérard J, Graulier G, Legendre R, Varet H, Sismeiro O, Perraud Q, Pesset B, Saint Auguste P, Bumann D, Mislin GLA, Coppee JY, Michaud-Soret I, Fechter P, Schalk IJ, Non-specific interference of cobalt with siderophore-dependent iron uptake pathways, Metallomics 2019 Nov;11(11):1937-1951.
• 2019
  Van den Bossche A, Varet H, Sury A, Sismeiro O, Legendre R, Coppee JY, Mathys V, Ceyssens PJ, Transcriptional profiling of a laboratory and clinical Mycobacterium tuberculosis strain suggests respiratory poisoning upon exposure to delamanid, Tuberculosis (Edinb) 2019 Jul;117:18-23.
• 2018
  Hugo Varet, Jean-Yves Coppée, checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes, Bioinformatics, 2018.
• 2018
  Randrianjatovo-Gbalou I, Rosario S, Sismeiro O, Varet H, Legendre R, Coppée JY, Huteau V, Pochet S, Delarue M, Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries, Nucleic Acids Res. 2018 07;46(12):6271-6284.
• 2018
  Varet H, Shaulov Y, Sismeiro O, Trebicz-Geffen M, Legendre R, Coppée JY, Ankri S, Guillen N, Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica, Sci Rep 2018 Jun;8(1):9042.
• 2018
  Krin E, Pierlé SA, Sismeiro O, Jagla B, Dillies MA, Varet H, Irazoki O, Campoy S, Rouy Z, Cruveiller S, Médigue C, Coppée JY, Mazel D, Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation, BMC Genomics 2018 May;19(1):373.
• 2017
  Martins RM, Macpherson CR, Claes A, Scheidig-Benatar C, Sakamoto H, Yam XY, Preiser P, Goel S, Wahlgren M, Sismeiro O, Coppée JY, Scherf A, An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum, Sci Rep 2017 Oct;7(1):14042.
• 2017
  Leroy M, Piton J, Gilet L, Pellegrini O, Proux C, Coppée JY, Figaro S, Condon C, Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis, EMBO J. 2017 May;36(9):1167-1181.
• 2017
  Julien Farasin, Sandrine Koechler, Hugo Varet, Julien Deschamps, Marie-Agnès Dillies, Caroline Proux, Mathieu Erhardt, Aline Huber, Bernd Jagla, Romain Briandet, Jean-Yves Coppée, Florence Arsène-Ploetze, Comparison of biofilm formation and motility processes in arsenic-resistant Thiomonas spp. strains revealed divergent response to arsenite, Microb Biotechnol. 2017 Feb 7. doi: 10.1111/1751-7915.12556.
• 2017
  Sahr T, Rusniok C, Impens F, Oliva G, Sismeiro O, Coppée JY, Buchrieser C, , The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system., PLoS Genet 2017 02; 13(2): e1006629.
• 2016
  Christian Weber, Mikael Koutero, Marie-Agnes Dillies, Hugo Varet, Cesar Lopez-Camarillo, Jean Yves Coppée, Chung-Chau Hon, Nancy Guillén, Extensive transcriptome analysis correlates the plasticity of Entamoeba histolytica pathogenesis to rapid phenotype changes depending on the environment, Sci Rep. 2016 Oct 21;6:35852. doi: 10.1038/srep35852..
• 2016
  Mouyna I, Aimanianda V, Hartl L, Prevost MC, Sismeiro O, Dillies MA, Jagla B, Legendre R, Coppée JY, Latgé JP, GH16 and GH81 family β-(1,3)-glucanases in Aspergillus fumigatus are essential for conidial cell wall morphogenesis, Cell Microbiol. 2016 Jun 15. doi: 10.1111/cmi.12630.
• 2016
  Hugo Varet, Loraine Brillet-Guéguen, Jean-Yves Coppée, Marie-Agnès Dillies, SARTools: A DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data, PLoS One. 2016 Jun 9;11(6):e0157022. doi: 10.1371/journal.pone.0157022. eCollection 2016.
• 2016
  Redko Y, Galtier E, Arnion H, Darfeuille F, Sismeiro O, Coppée JY, Médigue C, Weiman M, Cruveiller S, De Reuse H., RNase J depletion leads to massive changes in mRNA abundance in Helicobacter pylori., RNA Biol. 2016;13(2):243-53. doi: 10.1080/15476286.2015.1132141..
• 2015
  Balloy V, Varet H, Dillies MA, Proux C, Jagla B, Coppée JY, Tabary O, Corvol H, Chignard M, Guillot L, Normal and Cystic Fibrosis Human Bronchial Epithelial Cells Infected with Pseudomonas aeruginosa Exhibit Distinct Gene Activation Patterns, PLoS ONE 2015;10(10):e0140979.
• 2015
  Vembar SS, Macpherson CR, Sismeiro O, Coppée JY, Scherf A, The PfAlba1 RNA-binding protein is an important regulator of translational timing in Plasmodium falciparum blood stages, Genome Biol. 2015;16:212.
• 2015
  Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Kolb A, Monot M, Dupuy B, Duarte SS, Jagla B, Coppée JY, Beraud M, Norel F, Repressor activity of the RpoS/σS-dependent RNA polymerase requires DNA binding, Nucleic Acids Res. 2015 Feb;43(3):1456-68.
• 2014
  Almelli T, Nuel G, Bischoff E, Aubouy A, Elati M, Wang CW, Dillies MA, Coppée JY, Ayissi GN, Basco LK, Rogier C, Ndam NT, Deloron P, Tahar R, Differences in gene transcriptomic pattern of Plasmodium falciparum in children with cerebral malaria and asymptomatic carriers, PLoS ONE 2014;9(12):e114401.
• 2014
  Jang SM, Azebi S, Soubigou G, Muchardt C, DYRK1A phoshorylates histone H3 to differentially regulate the binding of HP1 isoforms and antagonize HP1-mediated transcriptional repression, EMBO Rep. 2014 Jun;15(6):686-94.
• 2014
  Lévi-Meyrueis C, Monteil V, Sismeiro O, Dillies MA, Monot M, Jagla B, Coppée JY, Dupuy B, Norel F, Expanding the RpoS/σS-network by RNA sequencing and identification of σS-controlled small RNAs in Salmonella, PLoS ONE 2014;9(5):e96918.
• 2014
  Eshghi A, Becam J, Lambert A, Sismeiro O, Dillies MA, Jagla B, Wunder EA, Ko AI, Coppee JY, Goarant C, Picardeau M, A putative regulatory genetic locus modulates virulence in the pathogen Leptospira interrogans, Infect. Immun. 2014 Jun;82(6):2542-52.
• 2014
  Dubois-Colas N, Petit-Jentreau L, Barreiro LB, Durand S, Soubigou G, Lecointe C, Klibi J, Rezaï K, Lokiec F, Coppée JY, Gicquel B, Tailleux L, Extracellular adenosine triphosphate affects the response of human macrophages infected with Mycobacterium tuberculosis, J. Infect. Dis. 2014 Sep;210(5):824-33.
• 2014
  Siegel TN, Hon CC, Zhang Q, Lopez-Rubio JJ, Scheidig-Benatar C, Martins RM, Sismeiro O, Coppée JY, Scherf A, Strand-specific RNA-Seq reveals widespread and developmentally regulated transcription of natural antisense transcripts in Plasmodium falciparum, BMC Genomics 2014;15:150.
• 2014
  Guyet A, Benaroudj N, Proux C, Gominet M, Coppée JY, Mazodier P, Identified members of the Streptomyces lividans AdpA regulon involved in differentiation and secondary metabolism., BMC Microbiol 2014 Apr; 14(): 81.
• 2013
  Thibeaux R, Weber C, Hon CC, Dillies MA, Avé P, Coppée JY, Labruyère E, Guillén N, Identification of the virulence landscape essential for Entamoeba histolytica invasion of the human colon, PLoS Pathog. 2013;9(12):e1003824.
• 2013
  Audrain B, Ferrières L, Zairi A, Soubigou G, Dobson C, Coppée JY, Beloin C, Ghigo JM, Induction of the Cpx envelope stress pathway contributes to Escherichia coli tolerance to antimicrobial peptides, Appl. Environ. Microbiol. 2013 Dec;79(24):7770-9.
• 2013
  Pawlik A, Garnier G, Orgeur M, Tong P, Lohan A, Le Chevalier F, Sapriel G, Roux AL, Conlon K, Honoré N, Dillies MA, Ma L, Bouchier C, Coppée JY, Gaillard JL, Gordon SV, Loftus B, Brosch R, Herrmann JL, Identification and characterization of the genetic changes responsible for the characteristic smooth-to-rough morphotype alterations of clinically persistent Mycobacterium abscessus, Mol. Microbiol. 2013 Nov;90(3):612-29.
• 2013
  Eskandarian HA, Impens F, Nahori MA, Soubigou G, Coppée JY, Cossart P, Hamon MA, A role for SIRT2-dependent histone H3K18 deacetylation in bacterial infection, Science 2013 Aug;341(6145):1238858.
• 2013
  Quax TE, Voet M, Sismeiro O, Dillies MA, Jagla B, Coppée JY, Sezonov G, Forterre P, van der Oost J, Lavigne R, Prangishvili D, Massive activation of archaeal defense genes during viral infection, J. Virol. 2013 Aug;87(15):8419-28.
• 2013
  Soutourina OA, Monot M, Boudry P, Saujet L, Pichon C, Sismeiro O, Semenova E, Severinov K, Le Bouguenec C, Coppée JY, Dupuy B, Martin-Verstraete I, Genome-wide identification of regulatory RNAs in the human pathogen Clostridium difficile, PLoS Genet. 2013 May;9(5):e1003493.
• 2013
  Komarova AV, Combredet C, Sismeiro O, Dillies MA, Jagla B, Sanchez David RY, Vabret N, Coppée JY, Vidalain PO, Tangy F, Identification of RNA partners of viral proteins in infected cells., RNA Biol 2013 Jun; 10(6): 944-56.
• 2013
  Hon CC, Weber C, Sismeiro O, Proux C, Koutero M, Deloger M, Das S, Agrahari M, Dillies MA, Jagla B, Coppee JY, Bhattacharya A, Guillen N, Quantification of stochastic noise of splicing and polyadenylation in Entamoeba histolytica, Nucleic Acids Res. 2013 Feb;41(3):1936-52.
• 2013
  Bernier SP, Lebeaux D, DeFrancesco AS, Valomon A, Soubigou G, Coppée JY, Ghigo JM, Beloin C, Starvation, together with the SOS response, mediates high biofilm-specific tolerance to the fluoroquinolone ofloxacin, PLoS Genet. 2013;9(1):e1003144.
• 2013
  Andres J, Arsène-Ploetze F, Barbe V, Brochier-Armanet C, Cleiss-Arnold J, Coppée JY, Dillies MA, Geist L, Joublin A, Koechler S, Lassalle F, Marchal M, Médigue C, Muller D, Nesme X, Plewniak F, Proux C, Ramírez-Bahena MH, Schenowitz C, Sismeiro O, Vallenet D, Santini JM, Bertin PN, Life in an arsenic-containing gold mine: genome and physiology of the autotrophic arsenite-oxidizing bacterium rhizobium sp. NT-26, Genome Biol Evol 2013;5(5):934-53.
• 2012
  Giraud E, Lecoeur H, Soubigou G, Coppée JY, Milon G, Prina E, Lang T, Distinct transcriptional signatures of bone marrow-derived C57BL/6 and DBA/2 dendritic leucocytes hosting live Leishmania amazonensis amastigotes, PLoS Negl Trop Dis 2012;6(12):e1980.
• 2012
  Léger P, Lara E, Jagla B, Sismeiro O, Mansuroglu Z, Coppée JY, Bonnefoy E, Bouloy M, Dicer-2- and Piwi-mediated RNA interference in Rift Valley fever virus-infected mosquito cells, J. Virol. 2013 Feb;87(3):1631-48.
• 2012
  Dhamgaye S, Bernard M, Lelandais G, Sismeiro O, Lemoine S, Coppée JY, Le Crom S, Prasad R, Devaux F, RNA sequencing revealed novel actors of the acquisition of drug resistance in Candida albicans, BMC Genomics 2012;13:396.
• 2012
  Sahr T, Rusniok C, Dervins-Ravault D, Sismeiro O, Coppee JY, Buchrieser C, Deep sequencing defines the transcriptional map of L. pneumophila and identifies growth phase-dependent regulated ncRNAs implicated in virulence, RNA Biol 2012 Apr;9(4):503-19.
• 2012
  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, Human cryptochrome-1 confers light independent biological activity in transgenic Drosophila correlated with flavin radical stability, PLoS ONE 2012;7(3):e31867.
• 2012
  Santi-Rocca J, Smith S, Weber C, Pineda E, Hon CC, Saavedra E, Olivos-García A, Rousseau S, Dillies MA, Coppée JY, Guillén N, Endoplasmic reticulum stress-sensing mechanism is activated in Entamoeba histolytica upon treatment with nitric oxide, PLoS ONE 2012;7(2):e31777.
• 2012
  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, Myf5 haploinsufficiency reveals distinct cell fate potentials for adult skeletal muscle stem cells, J. Cell. Sci. 2012 Apr;125(Pt 7):1738-49.
• 2011
  Jouneau A, Ciaudo C, Sismeiro O, Brochard V, Jouneau L, Vandormael-Pournin S, Coppée JY, Zhou Q, Heard E, Antoniewski C, Cohen-Tannoudji M, Naive and primed murine pluripotent stem cells have distinct miRNA expression profiles, RNA 2012 Feb;18(2):253-64.
• 2011
  Martini E, Borde V, Legendre M, Audic S, Regnault B, Soubigou G, Dujon B, Llorente B, Genome-wide analysis of heteroduplex DNA in mismatch repair-deficient yeast cells reveals novel properties of meiotic recombination pathways, PLoS Genet. 2011 Sep;7(9):e1002305.
• 2011
  Jagla B, Wiswedel B, Coppée JY, Extending KNIME for next-generation sequencing data analysis, Bioinformatics 2011 Oct;27(20):2907-9.
• 2011
  Deplaine G, Lavazec C, Bischoff E, Natalang O, Perrot S, Guillotte-Blisnick M, Coppée JY, Pradines B, Mercereau-Puijalon O, David PH, Artesunate tolerance in transgenic Plasmodium falciparum parasites overexpressing a tryptophan-rich protein, Antimicrob. Agents Chemother. 2011 Jun;55(6):2576-84.
• 2011
  Dittami SM, Proux C, Rousvoal S, Peters AF, Cock JM, Coppée JY, Boyen C, Tonon T, Microarray estimation of genomic inter-strain variability in the genus Ectocarpus (Phaeophyceae), BMC Mol. Biol. 2011;12:2.
• 2011
  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, Overexpression of proinflammatory TLR-2-signalling lipoproteins in hypervirulent mycobacterial variants, Cell. Microbiol. 2011 May;13(5):692-704.
• 2010
  Cleiss-Arnold J, Koechler S, Proux C, Fardeau ML, Dillies MA, Coppee JY, Arsène-Ploetze F, Bertin PN, Temporal transcriptomic response during arsenic stress in Herminiimonas arsenicoxydans, BMC Genomics 2010;11:709.
• 2010
  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, From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma, BMC Genomics 2010;11:368.
• 2010
  Thiberge JM1, 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., From array-based hybridization of Helicobacter pylori isolates to the complete genome sequence of an isolate associated with MALT lymphoma., BMC Genomics. 2010 Jun 10;11:368. doi: 10.1186/1471-2164-11-368..
• 2010
  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, Decreased in vitro susceptibility of Plasmodium falciparum isolates to artesunate, mefloquine, chloroquine, and quinine in Cambodia from 2001 to 2007, Antimicrob. Agents Chemother. 2010 May;54(5):2135-42.
• 2010
  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, Structure, function, and evolution of the Thiomonas spp. genome, PLoS Genet. 2010 Feb;6(2):e1000859.
• 2010
  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, Multiple controls affect arsenite oxidase gene expression in Herminiimonas arsenicoxydans, BMC Microbiol. 2010;10:53.
• 2009
  Fagegaltier D, Bougé AL, Berry B, Poisot E, Sismeiro O, Coppée JY, Théodore L, Voinnet O, Antoniewski C, The endogenous siRNA pathway is involved in heterochromatin formation in Drosophila, Proc. Natl. Acad. Sci. U.S.A. 2009 Dec;106(50):21258-63.
• 2009
  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, FlexiChip package: an universal microarray with a dedicated analysis software for high-thoughput SNPs detection linked to anti-malarial drug resistance, Malar. J. 2009;8:229.
• 2009
  van Schaik W, Château A, Dillies MA, Coppée JY, Sonenshein AL, Fouet A, The global regulator CodY regulates toxin gene expression in Bacillus anthracis and is required for full virulence, Infect. Immun. 2009 Oct;77(10):4437-45.
• 2009
  Forquin MP, Duvergey H, Proux C, Loux V, Mounier J, Landaud S, Coppée JY, Gibrat JF, Bonnarme P, Martin-Verstraete I, Vallaeys T, Identification of brevibacteriaceae by multilocus sequence typing and comparative genomic hybridization analyses, Appl. Environ. Microbiol. 2009 Oct;75(19):6406-9.
• 2009
  Payen C, Fischer G, Marck C, Proux C, Sherman DJ, Coppée JY, Johnston M, Dujon B, Neuvéglise C, Unusual composition of a yeast chromosome arm is associated with its delayed replication, Genome Res. 2009 Oct;19(10):1710-21.
• 2009
  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, , The Listeria transcriptional landscape from saprophytism to virulence., Nature 2009 Jun; 459(7249): 950-6.
• 2009
  Soutourina O, Poupel O, Coppée JY, Danchin A, Msadek T, Martin-Verstraete I, CymR, the master regulator of cysteine metabolism in Staphylococcus aureus, controls host sulphur source utilization and plays a role in biofilm formation, Mol. Microbiol. 2009 Jul;73(2):194-211.
• 2009
  Osorio y Fortéa J, de La Llave E, Regnault B, Coppée JY, Milon G, Lang T, Prina E, Transcriptional signatures of BALB/c mouse macrophages housing multiplying Leishmania amazonensis amastigotes, BMC Genomics 2009;10:119.
• 2009
  Ibrahim ML, Steenkeste N, Khim N, Adam HH, Konaté L, Coppée JY, Ariey F, Duchemin JB, Field-based evidence of fast and global increase of Plasmodium falciparum drug-resistance by DNA-microarrays and PCR/RFLP in Niger, Malar. J. 2009;8:32.
• 2008
  Muller H, Thierry A, Coppée JY, Gouyette C, Hennequin C, Sismeiro O, Talla E, Dujon B, Fairhead C, Genomic polymorphism in the population of Candida glabrata: gene copy-number variation and chromosomal translocations, Fungal Genet. Biol. 2009 Mar;46(3):264-76.
• 2008
  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, Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data, Biochimie 2009 Feb;91(2):192-203.
• 2008
  Lamarre C, Sokol S, Debeaupuis JP, Henry C, Lacroix C, Glaser P, Coppée JY, François JM, Latgé JP, Transcriptomic analysis of the exit from dormancy of Aspergillus fumigatus conidia, BMC Genomics 2008;9:417.
• 2008
  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, Dynamic RNA profiling in Plasmodium falciparum synchronized blood stages exposed to lethal doses of artesunate, BMC Genomics 2008;9:388.
• 2008
  Coppée JY, Do DNA microarrays have their future behind them?, Microbes Infect. 2008 Jul;10(9):1067-71.
• 2008
  Blazquez S, Guigon G, Weber C, Syan S, Sismeiro O, Coppée JY, Labruyère E, Guillén N, Chemotaxis of Entamoeba histolytica towards the pro-inflammatory cytokine TNF is based on PI3K signalling, cytoskeleton reorganization and the Galactose/N-acetylgalactosamine lectin activity, Cell. Microbiol. 2008 Aug;10(8):1676-86.
• 2008
  Osorio Y Fortéa J, Prina E, Lang T, Milon G, Davory C, Coppée JY, Regnault B, AffyGCQC: a web-based interface to detect outlying genechips with extreme studentized deviate tests, J Bioinform Comput Biol 2008 Apr;6(2):317-34.
• 2008
  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, Plasmodium falciparum transcriptome analysis reveals pregnancy malaria associated gene expression, PLoS ONE 2008;3(3):e1855.
• 2007
  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, Whole-transcriptome analysis of Plasmodium falciparum field isolates: identification of new pathogenicity factors, J. Infect. Dis. 2007 Dec;196(11):1603-12.
• 2007
  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, , Long oligonucleotide microarrays for African green monkey gene expression profile analysis., FASEB J 2007 Oct; 21(12): 3262-71.
• 2007
  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, Rapid microarray-based method for monitoring of all currently known single-nucleotide polymorphisms associated with parasite resistance to antimalaria drugs, J. Clin. Microbiol. 2007 Nov;45(11):3685-91.
• 2007
  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, , Transcriptome analysis of Yersinia pestis in human plasma: an approach for discovering bacterial genes involved in septicaemic plague., Microbiology (Reading, Engl.) 2007 Sep; 153(Pt 9): 3112-3124.
• 2007
  Santi-Rocca J, Weber C, Guigon G, Sismeiro O, Coppée JY, Guillén N, The lysine- and glutamic acid-rich protein KERP1 plays a role in Entamoeba histolytica liver abscess pathogenesis, Cell. Microbiol. 2008 Jan;10(1):202-17.
• 2007
  Hamon MA, Batsché E, Régnault B, Tham TN, Seveau S, Muchardt C, Cossart P, Histone modifications induced by a family of bacterial toxins, Proc. Natl. Acad. Sci. U.S.A. 2007 Aug;104(33):13467-72.
• 2007
  Bruggemann H, Hagman, Sismeiro O, Dillies MA, Heuner K, Steinert M, Gouyette C, Coppee JY and Buchrieser C, Bringing the genome of Legionella pneumophila to life (book chapter), E d. N Cianciotto, ASM press Washington, D.C. .
• 2006
  Brüggemann H, Hagman A, Jules M, Sismeiro O, Dillies MA, Gouyette C, Kunst F, Steinert M, Heuner K, Coppée JY, Buchrieser C, Virulence strategies for infecting phagocytes deduced from the in vivo transcriptional program of Legionella pneumophila, Cell. Microbiol. 2006 Aug;8(8):1228-40.
• 2006
  Weber C, Guigon G, Bouchier C, Frangeul L, Moreira S, Sismeiro O, Gouyette C, Mirelman D, Coppee JY, Guillén N, Stress by heat shock induces massive down regulation of genes and allows differential allelic expression of the Gal/GalNAc lectin in Entamoeba histolytica, Eukaryotic Cell 2006 May;5(5):871-5.
• 2006
  Tien MT, Girardin SE, Regnault B, Le Bourhis L, Dillies MA, Coppée JY, Bourdet-Sicard R, Sansonetti PJ, Pédron T, Anti-inflammatory effect of Lactobacillus casei on Shigella-infected human intestinal epithelial cells, J. Immunol. 2006 Jan;176(2):1228-37.
• 2005
  Ralph SA, Bischoff E, Mattei D, Sismeiro O, Dillies MA, Guigon G, Coppee JY, David PH, Scherf A, Transcriptome analysis of antigenic variation in Plasmodium falciparum–var silencing is not dependent on antisense RNA, Genome Biol. 2005;6(11):R93.
• 2005
  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, On the origin of leprosy, Science 2005 May;308(5724):1040-2.
• 2005
  Petit-Bertron AF, Pedron T, Gross U, Coppée JY, Sansonetti PJ, Cavaillon JM, Adib-Conquy M, Adherence modifies the regulation of gene expression induced by interleukin-10, Cytokine 2005 Jan;29(1):1-12.
• 2004
  Hommais F, Krin E, Coppée JY, Lacroix C, Yeramian E, Danchin A, Bertin P, GadE (YhiE): a novel activator involved in the response to acid environment in Escherichia coli, Microbiology (Reading, Engl.) 2004 Jan;150(Pt 1):61-72.
• 2003
  Milohanic E, Glaser P, Coppée JY, Frangeul L, Vega Y, Vázquez-Boland JA, Kunst F, Cossart P, Buchrieser C, Transcriptome analysis of Listeria monocytogenes identifies three groups of genes differently regulated by PrfA, Mol. Microbiol. 2003 Mar;47(6):1613-25.