Bioinformatician

The interdisciplinary Clinical Genomics Lab ( http://www.cgl.insel.ch ) combines the genomic and cytogenetic laboratory diagnostics of human genetics, haematology and clinical chemistry of the Inselspital as well as the Institute of Tissue Medicine and Pathology of the University of Bern. Using state-of-the-art technologies, we investigate, among other things, hereditary diseases, genetic changes in cancer cells and the effects of drugs. To strengthen our team, we are looking for a motivated and eager-to-learn bioinformatician. In close collaboration with various specialist disciplines, you will be involved in the clinical routine diagnostics of high-throughput sequencing (NGS) as well as in the development and implementation of new analytics. You will gradually take on responsibility for the development, validation, maintenance and continuous improvement of clinical NGS workflows.

What to expect

• Development, validation, maintenance and troubleshooting of clinical NGS workflows for panels, WES and WGS - from variant calling and annotation to quality control and data transfer
• Automation and optimisation of reproducible bioinformatics workflows using scripts, workflow management systems and containerised environments
• Development and maintenance of databases, quality metrics and monitoring tools for sequencing performance, workflows and metadata
• Further development of applications and user interfaces for easy access to sequencing data, quality metrics and variant annotations
• Integration and optimisation of laboratory workflows in sLIMS as well as ensuring data exchange between laboratory systems, devices and bioinformatics pipelines in close interdisciplinary collaboration

Your profile

• Master’s degree in bioinformatics, computational biology, computer science or a related field, or equivalent practical experience
• Good practical knowledge of Python, Linux and shell scripting as well as a basic understanding of high-throughput sequencing and associated analysis workflows
• Enjoyment of complex technical challenges as well as a structured, reliable and independent working style
• Willingness to learn and motivation to gradually develop professionally in clinical bioinformatics and NGS workflow engineering
• Good communication and teamwork skills as well as good German and English language skills
• Advantageous: experience with SQL, Nextflow, Snakemake, HPC environments, NGS analysis tools, Java or Groovy, clinical diagnostic processes as well as Docker or Singularity

Our offer

• Meaningful work with a direct contribution to patient care in the growing field of precision medicine
• Work with state-of-the-art technologies in a professional clinical environment with high quality standards
• Interdisciplinary, dynamic team with open and cooperative collaboration
• Structured induction, professional support and room for new ideas as well as personal development

Questions about the position?

For further information, please contact Ursula Amstutz, CGL Head

+41 31 63 2 74 70