Bioinformatician

The interdisciplinary Clinical Genomics Lab (http://www.cgl.insel.ch (http://www.cgl.insel.ch/)) combines the genomic and cytogenetic laboratory diagnostics of human genetics, hematology and clinical chemistry of the Inselspital as well as the Institute for 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 effect of drugs.

To strengthen our team, we are looking for a motivated and eager-to-learn bioinformatician. In close cooperation with various specialist disciplines, you will participate in the clinical routine diagnostics of high-throughput sequencing (NGS) as well as in the development and introduction of new analytics. In doing so, you will gradually assume 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 optimization of reproducible bioinformatics workflows using scripts, workflow management systems and containerized 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 optimization of laboratory workflows in sLIMS as well as ensuring data exchange between laboratory systems, devices and bioinformatics pipelines in close interdisciplinary cooperation

What you bring with you

• Master's degree in bioinformatics, computational biology, computer science or a related field or equivalent practical experience
• Good practical knowledge in Python, Linux and shell scripting as well as a basic understanding of high-throughput sequencing and associated analysis workflows
• Enjoyment of complex technical issues as well as a structured, reliable and independent way of working
• Willingness to learn and motivation to professionally develop step by step in clinical bioinformatics and NGS workflow engineering
• Good communication and teamwork skills as well as good German and English 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 activity 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 guidance and space for new ideas as well as personal development

Questions about the position?

Further information will be gladly provided by

Ursula Amstutz
CGL Head

+41 31 63 2 74 70