Bioinformatician in In Situ Sequencing

The Department of Biochemistry and Biophysics. SciLifeLab (SciLifeLab) is a national center for molecular biosciences with focus on health and environmental research. The center combines frontline technical expertise with advanced knowledge of translational medicine and molecular bioscience. SciLifeLab is a national resource hosted by Karolinska Institutet, KTH Royal Institute of Technology, Stockholm University and Uppsala University. The center also collaborates with several other universities.
For more details about the facility, visit: www.scilifelab.se/facilities/in-situ-sequencing/.

The employment will be placed at the Department of Biochemistry and Biophysics, at Stockholm university. More information about us, please visit: www.dbb.su.se.

Main responsibilities

• Perform in-depth analysis of complex spatial transcriptomics / In situ sequencing datasets using established computational frameworks
• Ensure data management practices align with the FAIR (Findable, Accessible, Interoperable, Reusable) principles, including metadata annotation and long-term storage solutions
• Provide expert support to researchers on all data-related aspects, from experimental design to analysis and interpretation
• Contribute to the development of integrative, multi-modal analysis pipelines for spatial omics datasets
• Design and implement novel analytical approaches and interactive visualizations tailored to high-dimensional multi-modal spatial data.

Qualification requirements

Required Qualifications 

• A PhD (or MSc with significant experience) in Bioinformatics, Computational Biology, Systems Biology, or a related discipline
• Proficiency in Python and R, with experience in spatial transcriptomics data analysis and high-dimensional data visualization
• Demonstrated experience in building and maintaining reproducible and modular data analysis workflows
• Solid understanding of statistical methods and their application to transcriptomics and image-derived data
• Familiarity with public biological data repositories, metadata standards and best practices in open science
• A collaborative mindset, with the ability to work in interdisciplinary teams and communicate effectively with both computational and experimental scientists.

Desirable (but not required):

• Experience with imaging technologies (e.g., Xenium, MERFISH, seqFISH) and associated data formats
• Familiarity with cloud computing environments or high-performance computing clusters
• Knowledge of tissue segmentation, spatial registration, or histology-based data alignment.

Personal Skills
We believe success in this role requires curiosity for biological questions and enthusiasm for learning new bioinformatics tools and methods. You enjoy working as part of a team, with a structured and quality-focused mindset. Strong communication skills, both spoken and written, are essential. We place great emphasis on personal qualities.

About the employment

This is a full-time, indefinite-term employment with a six-month probationary period. Stockholm University applies individual salary setting. Start date is as soon as possible.

We offer

With us, you will experience the dynamic interaction between higher education and research that makes Stockholm University an exciting and creative environment. You will work in an international environment and get favourable conditions. 

Stockholm University strives to be a workplace free from discrimination and with equal opportunities for all.

Contact

Further information about the position can be obtained from Katarina Tiklova, katarina.tiklova@scilifelab.se, or Chika Yokota chika.yokota@scilifelab.se.

Application

Apply for the position at Stockholm University's recruitment system. It is the responsibility of the applicant to ensure that the application is complete and that it is submitted before the deadline.

The instructions for applicants are available at: How to apply for a position.