Jean-Yves Coppee is managing the transcriptome and epigenome (PF2) platform. After a PhD in molecular biology (Universite de Louvain, Belgium), he spent 4 years at the “Centre de Génétique Moléculaire du CNRS” (head: Prof. P.P. Slonimski) working on the functional analysis of the yeast genome. He then joined the “Unité de Régulation de l’Expression Génétique” (headed by Antoine Danchin) at the Institut Pasteur where he used proteomics to study sulfur metabolism in Bacillus subtilis. Since 2000, he is responsible for the PF2 platform which is dedicated to the development and use of high throughput approaches (initially DNA arrays and since 2009 Next Generation Sequencing) for gene expression profiling.
Training: analysis of the transcriptome by RNAseq
The Transcriptome and Epigenome platform of the Biomics pole is organizing a one week (October 10, 2016 – October 14, 2016) training session dedicated to the analysis of the transcriptome by RNAseq. It is […]
Entamoeba histolytica – bacterium interaction and the role of this interaction in intestinal pathogenesis
Amoebiasis, a global medical problem, is a parasitic infection of the intestines caused by the protozoan Entamoeba histolytica. The consortium AMOEBAC, headed by Dr Serge Ankri (Technion Israel Institute of Technology, Israel) aims to […]
Deciphering dormancy in Cryptocococcus neoformans
Cryptococcus neoformans is a sugar-coated yeast that is able to interact closely with numerous organisms in the environment including amebae, paramecium of nematodes. The interaction with these organisms probably shaped its virulence. The ability […]
Deciphering the virulence factors of Mycobacterium abscessus activated in the presence of environmental amoebae
Mycobacterium abscessus (M. abs) is an emerging pathogen causing lung infections in cystic fibrosis patients. Although the environmental reservoir of M. abs is currently unknown, M. abs possesses a gene pool dedicated to a […]
Transcriptome of different quiescence sub-states of neural stem cells in adult zebrafish
Vertebrate adult neural stem cells (NSCs) are generally quiescent, and the frequency of their cell cycle re-entry (“activation”) conditions their lifespan. Little is known of the molecular pathways controlling the NSC quiescence/activation balance. We […]
The role of lncRNA H19 in Thymopoiesis
“The thymus is a specialized organ that provides a unique environment for T cell development and differentiation. The study the thymus-settling progenitors (TSPs) and how they differentiate is important for the characterization of the […]
Gene expression profiling in germinal center B cells
Germinal centers (GC) are essential for an effective humoral immune response. The GC provides an environment that stimulates B cells to proliferate in response to antigens and accumulate somatic mutations in immunoglobulin (Ig) genes, […]
Characterization of the SigmaS network by RNA sequencing and identification of SigmaS-controlled small regulatory RNAs in Salmonella
We have used directional RNA-sequencing and complementary assays to explore the SigmaS-dependent transcriptome of Salmonella enterica serovar Typhimurium. This study confirms the large regulatory scope of SigmaS and provides insights into its physiological functions […]
Escherichia coli transcriptomic analysis upon OmrA or OmrB overexpression
OmrA and OmrB are two small regulatory RNAs (sRNAs) conserved in enterobacteria. Their transcription is activated by the EnvZ-OmpR two-component system and their levels therefore increase in response to an increase in osmolarity. They […]
Intracellular membrane proliferation in E. coli
Overproduction of membrane proteins in the E. coli strains generally induce cell death. The multiple mutant C43 (DE3) derivative of BL21 (DE3) strain was selected to resist this overproduction. In this mutant, the membrane […]
S. cerevisiae gene regulation in quiescence
In wild life, yeast cells are able to survive in severe conditions, without nutriment for a long period of time because the cell is able to enter in stationary phase. During this phase, the […]
A personal database system for large scale quantitative results exploration (Cassandre, PTR 463)
Cassandre is a project of personal database system, integrating a “user-friendly” interface to manage and explore multiple sets of large-scale experimental results in biology. Large-scale experiments that generate quantitative data, such as changes in […]
HIV signature on RIG-I-like receptors
The pathogenesis of HIV infection, and in particular the development of immunodeficiency, remains incompletely understood. During HIV infection both innate and adaptive immune responses are raised, but they appear to be insufficient or too […]
Role of neuronal, microglial and glial cells during rabies virus infection in the modulation of innate immune response: MIME-RAB
Rabies is an untreatable disease of humans due to lyssaviruses and Rabies virus (RABV) in particular. RABV is a highly neurotropic virus which prevent inflammation during the early phase of infection. In the brain, […]
Dynamic regulation of chromatin and transcription by HP1 Heterochromatin Proteins in relationship with RNA.
The three HP1 (Heterochromatin Protein 1), HP1a, HP1b, and HP1g proteins are epigenetic markers of heterochromatin, the condensed, repressed form of chromatin. They are typically known to associate to the di-/tri-methylated lysine 9 of […]
Biostatistics for data analysis
The platform provides statistical analyses of RNA-seq count data. Before any project starts, we help the user to design his experiment in order to ensure that it really addresses the biological question he wishes […]
The platform also has important technological and bibliographical survey activities for the wet lab as well as for the dry lab. Over the last months, the platform has established methods for the transcriptome sequencing […]
Régulation transcriptionnelle par l’Enhancer de Trithorax et Polycomb Corto et la Protéine Ribosomique L12.
Il est aujourd’hui connu que les protéines ribosomiques ont des fonctions extra-ribosomiques, et qu’en particulier, certaines d’entre elles contrôlent la transcription. Nous avons montré que, chez la drosophile, RPL12 interagit avec le facteur épigénétique […]
2018checkMyIndex: a web-based R/Shiny interface for choosing compatible sequencing indexes, Bioinformatics, 2018.
2018Enteric bacteria boost defences against oxidative stress in Entamoeba histolytica, Sci Rep 2018 Jun;8(1):9042.
2018Expansion of the SOS regulon of Vibrio cholerae through extensive transcriptome analysis and experimental validation, BMC Genomics 2018 May;19(1):373.
2018Enzymatic synthesis of random sequences of RNA and RNA analogues by DNA polymerase theta mutants for the generation of aptamer libraries, Nucleic Acids Res. 2018 Jul;46(12):6271-6284.
2017An ApiAP2 member regulates expression of clonally variant genes of the human malaria parasite Plasmodium falciparum, Sci Rep 2017 Oct;7(1):14042.
2017Rae1/YacP, a new endoribonuclease involved in ribosome-dependent mRNA decay in Bacillus subtilis, EMBO J. 2017 May;36(9):1167-1181.
2017The Legionella pneumophila genome evolved to accommodate multiple regulatory mechanisms controlled by the CsrA-system, PLoS Genet. 2017 Feb;13(2):e1006629.
2017Comparison 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.
2016Extensive 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..
2016GH16 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.
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