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Reference : UMR8199-HELDEG0-016
Workplace : LILLE,LILLE
Date of publication : Thursday, October 08, 2020
Type of Contract : FTC Scientist
Contract Period : 36 months
Expected date of employment : 1 January 2021
Proportion of work : Full time
Remuneration : Between 2675 et 3805 euros brut per month
Desired level of education : PhD
Experience required : 1 to 4 years
A post-doctoral position is available at the European Genomic Institute for Diabetes (UMR 8199 CNRS, INSERM, Institut Pasteur de Lille, CHU Lille, Université Lille) in the “Microbiome and Metabolome in Cardiometabolism” group supervised by Prof. Marc-Emmanuel Dumas, in Lille, France.
The successful candidate will develop Bioinformatic workflows “from sequencer to paper” for analysis of shotgun metagenomic sequences of the human microbiome.
He/She will contribute to the identification of microbial taxa, species, genes and pathways involved in cardiometabolism, including characterization of their metabolic output and delineation of their genomic and environmental determinants.
The objective is to develop a comprehensive metagenomic sequence analysis workflow for human microbiome and characterize its role in cardiometabolism and associated fields
The successful candidate will overview the processing of shotgun sequencing data related to the microbiome generated by the LIGAN-PM platform (“equipment of excellence” label), within the Unit and development of bioinformatic workflows for handling shotgun sequence data:
• Management of project data
• Development of a full metagenome workflow for de novo assembly, taxonomical analysis, generation of gene clusters, mapping on integrated gene catalogs as well as functional analysis
• Identification of metagenomic species (MGS) or metagenomically-assembled genomes (MAGs)
• Functional annotation using various databases such as integrated gene catalog, KEGG, etc…
He/She will be responsible for data processing and scientific dissemination of results (drafting of scientific articles in English and participation in conferences). The successful candidate will play a role in influencing the project: design of workflow, optimisation and benchmarking, prioritisation of projects, interpretation of results.
The candidate will:
• hold a PhD in computer science, bioinformatics, computational, human or microbial genomics
• have experience in genomic sequence pre-processing and development in Unix environments
• have experience in pre-processing shotgun metagenomics data and/or biochemical network data
• have knowledge of current shotgun metagenomics sequence analysis workflows such as MOCAT, HUMAnN 2.0
• have knowledge of metagenome mining and identification of biosynthetic gene clusters
• have knowledge of microbial taxonomy and metabolism
• master the English language (written and spoken)
• have an interest in multidisciplinary work
• demonstrate autonomy, rigor, critical thinking, problem solving and ability to work within an international team
The researcher will join the “Microbial Metabolome in Cardiometabolic diseases” team at EGID (recognised by a 'Laboratory of Excellence' award), whose research objectives are to study the microbiome and its metabolic output to identify microbial metabolites and lipids associated with cardiometabolism and study the bioactivities of the microbial metabolome in cardiometabolic processes. The Institute provides an excellent intellectual environment and most of the infrastructure required to carry out the project, with direct access to state-of-the-art platforms including high-throughput sequencing (LIGAN-PM, 'Equipment of Excellence' platform award), animal facilities with a small imaging platform and a core facility for metabolic studies (metabolic cages, treadmill, CTscan, PET scan, MRI), cell imaging facility (confocal microscopy, electron microscopy), flow (INFLUX BD) and mass (CyTOF) cytometry. More specifically, the candidate will be part of the 'Accueil Talent International' project awarded to Prof. Dumas and funded by ISite, Région Hauts-de-France and Métropole Européenne de Lille. The project integrates expertise in analytical chemistry, chemometrics, metagenomics and validations in cellular and animal models to identify metabolic pathways disrupted in cardiometabolism. The researcher will strongly interact with colleagues within the group, the Institute and international collaborators.
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