Bioinformatician

The interdisciplinary Clinical Genomics Lab ( http://www.cgl.insel.ch ) brings together genomic and cytogenetic diagnostics in human genetics, haematology and clinical chemistry at Inselspital, Bern University Hospital, as well as at the Institute of Tissue Medicine and Pathology at the University of Bern. Using state-of-the-art technologies, we investigate hereditary diseases, genetic alterations in cancer cells and responses to medication.

To strengthen our team, we are looking for a motivated bioinformatician who is eager to learn. Working closely with specialists from various disciplines, you will contribute to routine next-generation sequencing (NGS) clinical diagnostics as well as the development and implementation of new analytical methods. You will progressively take responsibility for the development, validation, maintenance and continuous improvement of clinical NGS workflows.

What you can expect

• Development, validation, maintenance and troubleshooting of clinical NGS workflows for targeted 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 that facilitate access to sequencing data, quality metrics and variant annotations
• Integration and optimisation of laboratory workflows in sLIMS and ensuring data exchange between laboratory systems, instruments 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 the associated analysis workflows
• Enjoyment of complex technical challenges and a structured, reliable and independent way of working
• Eagerness to learn and motivation to further develop your expertise in clinical bioinformatics and NGS workflow engineering
• Good communication and teamwork skills as well as good command of German and English
• An advantage: experience with SQL, Nextflow, Snakemake, HPC environments, NGS analysis tools, Java or Groovy, clinical diagnostic workflows, Docker or Singularity

What we offer

• Meaningful work that directly contributes to patient care in the growing field of precision medicine
• The opportunity to work with state-of-the-art technologies in a professional clinical environment with high quality standards
• An interdisciplinary and dynamic team with an open and collaborative culture
• Structured onboarding, professional guidance and opportunities to contribute new ideas and develop personally and professionally

Questions about the job?

For further information, please contact Ursula Amstutz Head, Clinical Genomics Lab

+41 31 63 2 74 70