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  • Bioinformatician (m/f) to support the Microbiology department

Bioinformatician (m/f) to support the Microbiology department

TYPE DE CONTRAT : CDI - temps plein

About the LNS and the department of Microbiology

The “Laboratoire national de santé” (LNS) is a public institution operating under the supervision of the Ministry of Health in Luxembourg. Organized as a multidisciplinary institute, its six departments include services and units related to pathology, clinical biochemistry, microbiology, genetics, legal medicine and health protection. www.lns.lu

The purpose of the LNS is to deliver clinical expertise and develop analytical and scientific activity related to the treatment, diagnosis, prevention and monitoring of human diseases. Furthermore, the LNS fulfils a role as national control and reference laboratory.

The department plays the role of national reference laboratory for a number of microbial pathogens (foodborne, vaccine-preventable and emerging viral diseases), as well as antibiotic resistance. Both human and non-human molecular surveillance data from the LNS is sent to international institutions ECDC, EFSA and WHO for international monitoring purposes.

The LNS is a key player in Luxembourg’s national strategy to combat antimicrobial resistance: “Plan National Antibiotiques 2018-2022” (http://www.sante.public.lu/fr/actualites/2017/06/plan-national-antibiotiques/index.html). We operate in a multidisciplinary and international scientific environment, mainly including the University of Luxembourg and its Luxembourg Centre for Systems Biomedicine (LCSB – http://wwwde.uni.lu/lcsb) as well as the Luxembourg Institute of Health (LIH – https://www.lih.lu), the Luxembourg Institute of Science and technology (LIST – www.list.lu).

Participation in research is actively encouraged and the candidate will be supported in developing as a leader in bioinformatics.

Microbiology at the LNS is subdivided into three services:

  • Bacteriology, Mycology, Antibiotic Resistance monitoring, and Infection Prevention and Control
  • Virology and Serology
  • Microbial Genomics and Epidemiology

Main activities

  • Implement microbial genomic analysis pipelines in  the following departmental priority areas:
    • antibiotic resistance (e.g. carbapenemase producing Enterobacteriaceae),
    • food and waterborne pathogens (Salmonella, Campylobacter, VTEC, Listeria, etc.)
    • vaccine-preventable infections (influenza, human papillomavirus)
    • bioterrorism-related and emerging viral pathogens
    • metagenomics
  • Develop, optimize bioinformatics workflows for analysing runs from Illumina sequencing platforms (e.g. MiniSeq) including for quality assurance purposes and accreditation
  • To maintain and manage existing bioinformatic software packages and/or develop homemade pipelines enabling standardized, replicable and accreditable analyses
  • Integrate genomic characaterisation automatically into pathogen specific databases for further epidemiological analysis
  • Develop appropriate tools for sharing and/or publishing next-generation sequencing data with external institutions (Ministry of Health, ECDC, EFSA, EURL) or data repositories (GISAID, Genbank, ENA, PubMLST)
  • Provide expertise with phylogenetic and genomic analysis
  • Liaise with IT department for managing appropriate computing, network and data storage infrastructure

Requirements

  • The candidate will have at least a Master degree in Bioinformatics and have significant experience with analysing microbial genomics data (e.g. de novo assembly, mapping, core genome MLST and phylogenetic analyses of both bacterial and viral pathogens)
  • Knowledge of open source and commercial microbial NGS analysis pipelines (Seqsphere, Bionumerics, Resfinder, Geneious)
  • Linux, Python and R programming skills
  • The ideal candidate will be fluent in English AND one of the following language French, German, or Luxembourgish

If you meet the above profile and wish to apply, please send your application (CV, letter of intent and copies of your degrees) to microbioinfo01@odoo.lns.etat.lu quoting the reference 2018-Microbio-Info. The applications will be treated in order of arrival and with the highest degree of confidentiality.