• 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 2022 Nov; (): 103997.
• 2022
  Vabret N, Najburg V, Solovyov A, Gopal R, McClain C, Šulc P, Balan S, Rahou Y, Beauclair G, Chazal M, Varet H, Legendre R, Sismeiro O, Sanchez David RY, Chauveau L, Jouvenet N, Markowitz M, van der Werf S, Schwartz O, Tangy F, Bhardwaj N, Greenbaum BD, Komarova AV, , Y RNAs are conserved endogenous RIG-I ligands across RNA virus infection and are targeted by HIV-1., iScience 2022 Jul; 25(7): 104599.
• 2022
  Daunesse Maëlle, Legendre Rachel, Varet Hugo, Pain Adrien, Chica Claudia , ePeak: from replicated chromatin profiling data to epigenomic dynamics., NAR Genom Bioinform 2022 Jun; 4(2): lqac041.
• 2022
  Jacob JM, Di Carlo SE, Stzepourginski I, Lepelletier A, Ndiaye PD, Varet H, Legendre R, Kornobis E, Benabid A, Nigro G, Peduto L, , PDGFRα-induced stromal maturation is required to restrain postnatal intestinal epithelial stemness and promote defense mechanisms., Cell Stem Cell 2022 May; 29(5): 856-868.e5.
• 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
  Piel L, Rajan KS, Bussotti G, Varet H, Legendre R, Proux C, Douché T, Giai-Gianetto Q, Chaze T, Cokelaer T, Vojtkova B, Gordon-Bar N, Doniger T, Cohen-Chalamish S, Rengaraj P, Besse C, Boland A, Sadlova J, Deleuze JF, Matondo M, Unger R, Volf P, Michaeli S, Pescher P, Späth GF, , Experimental evolution links post-transcriptional regulation to Leishmania fitness gain., PLoS Pathog 2022 Mar; 18(3): e1010375.
• 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.
• 2021
  Giraud É, Varet H, Legendre R, Sismeiro O, Aubry F, Dabo S, Dickson LB, Valiente Moro C, Lambrechts L, , Mosquito-bacteria interactions during larval development trigger metabolic changes with carry-over effects on adult fitness., Mol Ecol 2021 Dec; (): .
• 2021
  Kim S, Larrous F, Varet H, Legendre R, Feige L, Dumas G, Matsas R, Kouroupi G, Grailhe R, Bourhy H, , Early Transcriptional Changes in Rabies Virus-Infected Neurons and Their Impact on Neuronal Functions., Front Microbiol 2021 ; 12(): 730892.
• 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
  Mazzuoli MV, Daunesse M, Varet H, Rosinski-Chupin I, Legendre R, Sismeiro O, Gominet M, Kaminski PA, Glaser P, Chica C, Trieu-Cuot P, Firon A, , The CovR regulatory network drives the evolution of Group B Streptococcus virulence., PLoS Genet 2021 Sep; 17(9): e1009761.
• 2021
  Rachez C, Legendre R, Costallat M, Varet H, Yi J, Kornobis E, Muchardt C, , HP1γ binding pre-mRNA intronic repeats modulates RNA splicing decisions., EMBO Rep 2021 Jul; (): e52320.
• 2021
  Robbe-Saule M, Foulon M, Poncin I, Esnault L, Varet H, Legendre R, Besnard A, Grzegorzewicz AE, Jackson M, Canaan S, Marsollier L, Marion E, Transcriptional adaptation of Mycobacterium ulcerans in an original mouse model: New insights into the regulation of mycolacton, Virulence . 2021 Dec;12(1):1438-1451.
• 2021
  Liu Z, Raj S, van Rhijn N, Fraczek M, Michel JP, Sismeiro O, Legendre R, Varet H, Fontaine T, Bromley M, Latgé JP, , Functional Genomic and Biochemical Analysis Reveals Pleiotropic Effect of Congo Red on Aspergillus fumigatus., mBio 2021 May; 12(3): .
• 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): .
• 2021
  Huot N, Rascle P, Petitdemange C, Contreras V, Stürzel CM, Baquero E, Harper JL, Passaes C, Legendre R, Varet H, Madec Y, Sauermann U, Stahl-Hennig C, Nattermann J, Saez-Cirion A, Le Grand R, Keith Reeves R, Paiardini M, Kirchhoff F, Jacquelin B, Müller-Trutwin M, , SIV-induced terminally differentiated adaptive NK cells in lymph nodes associated with enhanced MHC-E restricted activity., Nat Commun 2021 02; 12(1): 1282.
• 2021
  Machado L, Geara P, Camps J, Dos Santos M, Teixeira-Clerc F, Van Herck J, Varet H, Legendre R, Pawlotsky JM, Sampaolesi M, Voet T, Maire P, Relaix F, Mourikis P, , Tissue damage induces a conserved stress response that initiates quiescent muscle stem cell activation., Cell Stem Cell 2021 Feb; (): .
• 2021
  Danion F, van Rhijn NV, Dufour AC, Legendre R, Sismeiro O, Varet H, Olivo-Marin JC, Mouyna I, Chamilos G, Bromley M, Beauvais A, Latgé JP, Aspergillus fumigatus, One Uninucleate Species with Disparate Offspring., J Fungi (Basel) 2021 Jan; 7(1): .
• 2021
  Proutière A, du Merle L, Périchon B, Varet H, Gominet M, Trieu-Cuot P, Dramsi S, , Characterization of a Four-Component Regulatory System Controlling Bacteriocin Production in Streptococcus gallolyticus., mBio 2021 01; 12(1): .
• 2021
  Huot N, Rascle P, Planchais C, Contreras V, Passaes C, Le Grand R, Beignon AS, Kornobis E, Legendre R, Varet H, Saez-Cirion A, Mouquet H, Jacquelin B, Müller-Trutwin M, , CD32+CD4+ T Cells Sharing B Cell Properties Increase With Simian Immunodeficiency Virus Replication in Lymphoid Tissues., Front Immunol 2021 ; 12(): 695148.
• 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
  Lacerda Mariano L, Rousseau M, Varet H, Legendre R, Gentek R, Saenz Coronilla J, Bajenoff M, Gomez Perdiguero E, Ingersoll MA, , Functionally distinct resident macrophage subsets differentially shape responses to infection in the bladder., Sci Adv 2020 Nov; 6(48): .
• 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
  Latis E, Michonneau D, Leloup C, Varet H, Peffault de Latour R, , Bianchi E, Socié G, Rogge L, , Cellular and molecular profiling of T-cell subsets at the onset of human acute GVHD., Blood Adv 2020 Aug; 4(16): 3927-3942.
• 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
  Soler-Bistué A, Aguilar-Pierlé S, Garcia-Garcerá M, Val ME, Sismeiro O, Varet H, Sieira R, Krin E, Skovgaard O, Comerci DJ, Rocha EPC, Mazel D, , Macromolecular crowding links ribosomal protein gene dosage to growth rate in Vibrio cholerae., BMC Biol 2020 04; 18(1): 43.
• 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
  Derbise A, Echenique-Rivera H, Garcia-Lopez M, Beau R, Mattei M, Varet H, Dersch P, Pizarro-Cerdá J, , Bread Feeding Is a Robust and More Physiological Enteropathogen Administration Method Compared to Oral Gavage., Infect Immun 2020 03; 88(4): .
• 2020
  Lecoeur H, Prina E, Rosazza T, Kokou K, N'Diaye P, Aulner N, Varet H, Bussotti G, Xing Y, Milon G, Weil R, Meng G, Späth GF, , Targeting Macrophage Histone H3 Modification as a Leishmania Strategy to Dampen the NF-κB/NLRP3-Mediated Inflammatory Response., Cell Rep 2020 02; 30(6): 1870-1882.e4.
• 2020
  Merkling SH, Raquin V, Dabo S, Henrion-Lacritick A, Blanc H, Moltini-Conclois I, Frangeul L, Varet H, Saleh MC, Lambrechts L, , Tudor-SN Promotes Early Replication of Dengue Virus in the Aedes aegypti Midgut., iScience 2020 Feb; 23(2): 100870.
• 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
  Hommel B, Sturny-Leclère A, Volant S, Veluppillai N, Duchateau M, Yu CH, Hourdel V, Varet H, Matondo M, Perfect JR, Casadevall A, Dromer F, Alanio A, , Cryptococcus neoformans resists to drastic conditions by switching to viable but non-culturable cell phenotype., PLoS Pathog 2019 07; 15(7): e1007945.
• 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.
• 2019
  Reynard S, Journeaux A, Gloaguen E, Schaeffer J, Varet H, Pietrosemoli N, Mateo M, Baillet N, Laouenan C, Raoul H, Mullaert J, Baize S, Immune parameters and outcomes during Ebola virus disease, JCI Insight 2019 Jan;4(1).
• 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.
• 2018
  Cui L, Vigouroux A, Rousset F, Varet H, Khanna V, Bikard D, A CRISPRi screen in E. coli reveals sequence-specific toxicity of dCas9, Nat Commun. 2018 May 15;9(1):1912. doi: 10.1038/s41467-018-04209-5.
• 2017
  Léo Machado, Joana Esteves de Lima, Odile Fabre, Caroline Proux, Rachel Legendre, Anikó Szegedi, Hugo Varet, Lars Roed Ingerslev, Romain Barrès, Frédéric Relaix, Philippos Mourikis, In Situ Fixation Redefines Quiescence and Early Activation of Skeletal Muscle Stem Cells, Cell Reports , Volume 21 , Issue 7 , 1982 - 1993.
• 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
  Ribet D, Lallemand-Breitenbach V, Ferhi O, Nahori M-A, Varet H, de Thé H, Cossart P., Promyelocytic Leukemia Protein (PML) Controls Listeria monocytogenes Infection, mBio 8:e02179-16..
• 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
  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
  Dogan C, De Antonio M, Hamroun D, Varet H, Fabbro M, Rougier F, Amarof K, Arne Bes MC, Bedat-Millet AL, Behin A, Bellance R, Bouhour F, Boutte C, Boyer F, Campana-Salort E, Chapon F, Cintas P, Desnuelle C, Deschamps R, Drouin-Garraud V, Ferrer X, Gervais-Bernard H, Ghorab K, Laforet P, Magot A, Magy L, Menard D, Minot MC, Nadaj-Pakleza A, Pellieux S, Pereon Y, Preudhomme M, Pouget J, Sacconi S, Sole G, Stojkovich T, Tiffreau V, Urtizberea A, Vial C, Zagnoli F, Caranhac G, Bourlier C, Riviere G, Geille A, Gherardi RK, Eymard B, Puymirat J, Katsahian S, Bassez G., Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study, PLoS One. 2016 Feb 5;11(2):e0148264.
• 2015
  Tebbi A, Levillayer F, Jouvion G, Fiette L, Soubigou G, Varet H, Boudjadja N, Cairo S, Hashimoto K, Suzuki AM, Carninci P, Carissimo A, di Bernardo D, Wei Y, Deficiency of multidrug resistance 2 contributes to cell transformation through oxidative stress, Carcinogenesis 2016 Jan;37(1):39-48.
• 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.
• 2014
  Mekontso Dessap A, Katsahian S, Roche-Campo F, Varet H, Kouatchet A, Tomicic V, Beduneau G, Sonneville R, Jaber S, Darmon M, Castanares-Zapatero D, Brochard L, Brun-Buisson C, Ventilator-associated pneumonia during weaning from mechanical ventilation: role of fluid management, Chest 2014 Jul;146(1):58-65.
• 2012
  Mahr A, Katsahian S, Varet H, Guillevin L, Hagen EC, Höglund P, Merkel PA, Pagnoux C, Rasmussen N, Westman K, Jayne DR, , Revisiting the classification of clinical phenotypes of anti-neutrophil cytoplasmic antibody-associated vasculitis: a cluster analysis, Ann. Rheum. Dis. 2013 Jun;72(6):1003-10.