Genomic insights into the 2016-2017 cholera epidemic in Yemen
Cholera is thought by many to be a disease of the Victorian era. However, Yemen has recently experienced one of the largest ever cholera epidemics. The first cases were declared in September 2016, and […]
Historical antibiotic-resistant populations of S. enterica serotype Typhimurium
Little is known about the emergence and spread of the first antibiotic-resistant populations. It is believed, for example, that the very common penicillinase gene, blaTEM-1, discovered for the first time in E. coli in Greece […]
Oxford Nanopore sequencing for detection and surveillance of pathogens
This project intends to share expertise, developments, equipement and bioinformatics tools to apply Oxford Nanopore Technology sequencing to the detection, diagnostic and characterization of pathogens of public health importance. It corresponds to a collaboration […]
Phylogenomics of Shiga’s epidemic dysentery bacillus (Shigella dysenteriae type 1)
The agent of epidemic dysentery, the bacterium Shigella dysenteriae type 1, was isolated in Japan in 1897 by Dr Kyoshi Shiga during a massive epidemic of bloody diarrhea that caused 20,000 deaths over a […]
Genetic variability of non-segmented negative RNA virus populations and host adaptation (Viva&Host)
Non-segmented negative strand RNA viruses are characterized by an intrinsic genome instability, the result of an error-prone RNA dependant RNA polymerase. To date, most viral populations have been characterized by their consensus genome sequences. […]
Our main objective is to increase the knowledge regarding the human virome during homeostasis and diseases. We mainly focus on: immunocompromised patients, where new pathogens and new associations between known pathogens and diseases at found at higher frequency than […]
Sequana: a set of flexible NGS pipelines
Sequana is a Python framework designed to provide pipelines to analyse Next Generation Sequencing data sets. Sequana provides tools to access the sequence quality but also post-processing analysis such as depth of coverage or […]
2022Low CCR5 expression protects HIV-specific CD4+ T cells of elite controllers from viral entry., Nat Commun 2022 Jan; 13(1): 521.
2021Dynamics of extended-spectrum beta-lactamase-producing Enterobacterales colonization in long-term carriers following travel abroad., Microb Genom 2021 Jul; 7(7): .
2021Pathogenomic analyses of Mycobacterium microti, an ESX-1-deleted member of the Mycobacterium tuberculosis complex causing disease in various hosts., Microb Genom 2021 02; 7(2): .
2020TbD1 deletion as a driver of the evolutionary success of modern epidemic Mycobacterium tuberculosis lineages, Nat Commun 2020 Feb;11(1):684.
2019Genomic insights into the 2016-2017 cholera epidemic in Yemen., Nature 2019 01; 565(7738): 230-233.
2018Sequana Coverage: Detection and Characterization of Genomic Variations using Running Median and Mixture Models, GigaScience, giy110, https://doi.org/10.1093/gigascience/giy110.
2018Generating genomic platforms to study Candida albicans pathogenesis., Nucleic Acids Res 2018 08; 46(14): 6935-6949.
2018Unexpected genomic and phenotypic diversity of Mycobacterium africanum Lineage 5 affects drug resistance, protein secretion and immunogenicity, Genome Biol Evol 2018 Jul;.
2018Gene flow contributes to diversification of the major fungal pathogen Candida albicans, Nat Commun 2018 06;9(1):2253.
2018Sequanix: A Dynamic Graphical Interface for Snakemake Workflows, https://doi.org/10.1093/bioinformatics/bty034.
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