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Technical officer in Bioinformatics (m/f)

TYPE DE CONTRAT : CDD - temps plein

The Laboratoire national de santé (Luxembourg public institution) is recruiting a Technical officer in Bioinformatics (m/f) for the Department of Microbiology in a full time position (40h/week) with a fixed-term contract of 12 months (ending 30 september 2022).

About the Laboratoire national de santé

The “Laboratoire national de santé” (LNS) is a public institution under the supervision of the Ministry of Health in Luxembourg. LNS is organized as a multidisciplinary institute and supported by a professional services team, the LNS includes four scientific departments in the fields of medical biology, microbiology, forensic medicine, and health protection, in addition to hosting the National Center of Pathology and the National Center of Genetics. The LNS is based at Dudelange, with state of the art, modern infrastructure in line with recent developments in medical sciences.

 

The department of microbiology offers reference laboratory activities in partnership with various other public and private laboratories in the country. The department is nominated as National Reference Laboratory for Acute Respiratory Infections. At the same time, it works closely together with the Ministry of Health and the European Centre for Disease Prevention and Control (ECDC) ) on epidemiological matters, as well as the National Service for Infectious Diseases as far as diagnostics is concerned.

The Department of Microbiology has recently received a grant from the European Centre for Disease Prevention and Control (ECDC) for the strengthening of national whole genome sequencing (WGS) and/or reverse transcription polymerase chain reaction (RT-PCR) infrastructure and capacity to respond to the Covid-19 pandemic in the European Union and the European Economic Area.

The Grant will help to expand the computational power, storage and sharing capacity including automation of the bioinformatics pipeline, accompanied by frontend development improving user friendliness allowing an extended user group. This will lead to develop a data analytics framework that will include conceptual explanations of different analyses, as well as data assembly and analyses support. Ultimately, LNS strives to develop a team composed of data scientists and stewards, medical doctors and epidemiologists that together with partners will be able to deliver top-notch science and data analysis.

To complement our existing teams, the department of Microbiology is seeking to appoint a highly motivated, enthusiastic Bioinformatician. This post is available at full time basis on a determined contract.

The successful candidate will be competent to develop and collaborate on research projects and programmes in communicable diseases, but also IT infrastructure like laboratory information management systems. The position offers and requires a high range of creativity, motivation and room for professional development.

Job Description

The Technical officer in Bioinformatics will be responsible for :

  • COVID-19 data analysis including automation and phylogenetic anaylsis for automatic weekly reporting to ECDC and national authorities
  • Automation of Bioinformatics analysis with a user interface
  • Expansion of the local bioinformatics server capacity
  • Development of a data analytics framework with conceptual explanations of different analyses for various pathogens, compliant with ISO Technical Standards, currently in development
  • Development of regional data hub to facilitate the timely reporting of WGS and RT-PCR data to ECDC, and the sharing of data in the public domain (e.g. GISAID, ENA)
  • Building a universal database and catalogue with user interface
  • Development of nationally agreed standards for data collection, safe storage, data sharing, custodianship, analyses, reporting and privacy requirements, in collaboration with the ILNAS working group, currently working on a laboratory data management project.
  • Development of infrastructure to support secure storage of microbial genomic data
  • Development, implementation and optimization of bioinformatics workflows for analysing NGS data (mainly Illumina platform)
  • managing existing bioinformatic software packages and/or develop in-house pipelines enabling standardized, reproducible analyses
  • Integration of genomic characaterisation automatically into pathogen specific databases for further epidemiological analysis
  • Development of 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)
  • Liaision with IT department for managing appropriate computing, network and data storage infrastructure

Qualifications & Skills

To be successful in this role, you will need to demonstrate a high level of technical skill and intellectual rigor and be able to cope with multiple and changing demands in a fast paced and unpredictable environment.

Required Qualifications

  • The candidate will have Ph.D. degree in Bioinformatics or IT related field 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, polygenic risk score, eQTL analysis, correlation and association analyses)
  • Knowledge of open source and commercial microbial NGS analysis pipelines (Seqsphere, Bionumerics, Resfinder, Geneious)
  • Knowledge of programming tools (Python, bash and R programs, etc..)
  • Strong biological background, ideally with hands-on wetlab experience, in a microbial environment (DNA and RNA extraction, PCR, qPCR, NGS)
  • Visualisation / web development and experience in development of relational database systems is considered as strong advantage

Required Skills

  • Proven knowledge of the methods of statistical and scientific report writing including the ability to develop, prepare and use meaningful charts and diagrams
  • Effective interpersonal and influencing skills, be able to prioritise work, and work well against a background of change and uncertainty
  • Strong sense of data quality and consistency
  • Problem solver, communicator (including lay-audience) and team player
  • Open to move on grounds different form bioinformatics, like lab information management, web development and data curation/administration
  • Aptitude in adjusting to changing situations to meet emergency or changing program requirements, and follow-up to ensure that higher priority cases are followed up first and in greater detail than less urgent cases.
  • Skilled in eliciting sensitive and confidential information.
  • Able to work well independently.
  • Strong and proactive monitoring of the assigned tasks.
  • Excellent interpersonal skills.
  • Languages skills: excellent command of English and French, additional knowledge of German would be considered a strong asset.

The above list is not exhaustive and further tasks could be added according to the needs of the department.

If you meet the above profile requirements and wish to apply, please send your application (CV, letter of intent and copies of your degrees) by clicking on the application button below.

Applications will be processed in order of arrival. The utmost confidentiality will be granted to each application.

Prospective candidates are invited to contact Dr Tamir Abdelrahman, Head of Microbiology department +352 28 100 500 or via email tamir.abdelrahman@lns.etat.luYour application will be treated confidentiality.