Bioinformatician Wanted at Clinical Genomics Uppsala

The Department of Immunology, Genetics and Pathology at Uppsala University has a broad research profile with strong research groups focused on cancer, genetic, and autoimmune diseases. One of the core ideas at the department is to stimulate translational research and thus promote closer collaboration between medical research and healthcare. Research is conducted within six research programs: cancer precision medicine, cancer immunotherapy, genomics and neurobiology, molecular tools and functional genomics, neuro-oncology and neurodegeneration, as well as vascular biology. Parts of the operations are also integrated with the departments of oncology, clinical genetics, clinical immunology, clinical pathology, and hospital physics at Uppsala University Hospital. The department has teaching assignments in several program educations, independent courses, and international master's programs within the medical faculty. The department has a turnover of approximately 550 million SEK, of which about two-thirds are external research grants. The number of employees is about 400, of which about 100 are doctoral students, and there are over 850 active in the workforce. Read more about the department's activities here: http://www.uu.se/medarbetare/institution/immunologi-genetik-och-patologi (http://www.uu.se/medarbetare/institution/immunologi-genetik-och-patologi)

About Clinical Genomics Uppsala

Clinical Genomics Uppsala (CGU) is a collaboration between Uppsala University Hospital, Region Uppsala, and Uppsala University within the Clinical Genomics platform at SciLifeLab. CGU supports clinic-based research and development and provides clinical analyses based on large-scale DNA sequencing. The bioinformatics work is primarily conducted at Uppsala University, while laboratory work is performed at Uppsala University Hospital. In multidisciplinary teams with bioinformaticians, geneticists, and physicians, clinical assessments of genetic variants are made. The analyses focus on cancer, hereditary diseases, and microbiology, with over 10,000 samples analyzed annually. The demand for genetic diagnostics is increasing, and the operations are expected to grow further.

Job Responsibilities

CGU is seeking a full-time bioinformatician for the development of analyses aimed at cancer and hereditary diseases. The tasks will be tailored to skills and interests but will include the development and maintenance of diagnostic analyses based on whole genome, whole exome, and transcriptome sequencing, as well as broad gene panels. The analyses are used to identify genetic variants that affect diagnosis, prognosis, and treatment. Ongoing development projects include long-read technologies (PacBio, ONT), while current diagnostics primarily rely on short-read data.
The role involves continuous evaluation, improvement, and automation of robust bioinformatics pipelines for clinical use. The work also includes efficient data management, automation, and visualization to create smooth data flows and facilitate clinical interpretation and reporting. Collaboration occurs closely with clinically active staff and within Genomic Medicine Sweden (GMS). Experience or interest in database management and software development is advantageous, as the unit continuously develops its analyses, IT environments, and working methods. Pipeline development primarily occurs in Python and Snakemake, and the employee can contribute to the Hydra Genetics project.
A central part of the work is collaboration with healthcare personnel and the development of methods for clinically relevant questions. Since the operations handle sensitive data, data security is of great importance. Clinical genomics is a rapidly growing research area, and the employee will have the opportunity to contribute to publications and presentations of technical and medical results. The work takes place in teams with bioinformaticians, physicians, clinical geneticists, and molecular biologists, both locally and in national and international collaborations.

Qualifications

• Master's degree in bioinformatics, biotechnology, computer science, or a related field
• Documented experience with scripting languages (e.g., Python, Bash, Perl)
• Experience with NGS analysis in a Linux environment on computing clusters
• Experience with git, conda, and code review
• Experience with pipeline tools such as Snakemake or Nextflow
• Experience with automation solutions (e.g., Stackstorm)
• Experience with container software (Apptainer/Singularity, Docker, Podman)
• Experience with administration of Unix/Linux servers and virtual systems
• Basic knowledge of database management
• Good communication skills in Swedish and English
• The work requires precision, initiative, teamwork, and independence. Great emphasis is placed on personal suitability.

Desirable

A PhD in bioinformatics, genetics, or a similar field is desirable. Experience with sequencing technologies for cancer genetics, clinical bioinformatics, or clinical genomics is preferred. Experience from accredited operations and collaboration with clinical laboratories is also advantageous. Since documentation is conducted in Swedish, good proficiency in spoken and written Swedish is particularly valuable.

About the Employment

The employment is permanent, with a probationary period applicable. The extent is full-time. Start date according to agreement. Location: Uppsala

For inquiries about the position, please contact: Malin Melin, [email protected] (mailto:[email protected])

Welcome with your application by January 28, 2026, UFV-PA 2026/80

Uppsala University is a broad research university with a strong international position. The ultimate goal is to conduct education and research of the highest quality and relevance to make a difference in society. Our most important asset is all 7,600 employees and 53,000 students who, with curiosity and commitment, make Uppsala University one of the country's most exciting workplaces.

Read more about our benefits and what it is like to work at Uppsala University https://uu.se/om-uu/jobba-hos-oss/ (https://uu.se/om-uu/jobba-hos-oss/)

The employment may be subject to security clearance. A prerequisite for employment during security clearance is that the applicant is approved.

We kindly decline offers of recruitment and advertising assistance.

Applications are received in Uppsala University's recruitment system.

Union representatives: Saco-S - [email protected] (mailto:[email protected]), Seko - [email protected] (mailto:[email protected]), ST (OFR/S) - [email protected] (mailto:[email protected])