Research Engineer in Bioinformatics (CRISPR Functional Genomics)

Do you want to contribute to top quality medical research?

Computational methods and AI applied to large-scale molecular data are transforming biology - from molecular structures and cellular processes to human health and ecosystems. As part of SciLifeLab, a unique nation-wide infrastructure and research community that combines advanced life science technologies with data and AI expertise, the CRISPR Functional Genomics unit at Karolinska Institutet is looking for a Research Engineer in Bioinformatics.

Your mission

You will build and maintain reproducible pipelines for in-depth analysis of high-throughput CRISPR gene-perturbation data. You will support CFG and its users in data analysis, management, and delivery. You will have the opportunity to contribute to multi-modal data integration to shape how high-dimensional omics data are transformed into actionable biological insights. Together with CFG’s wet-lab scientists and our user community, you will help drive a new era of quantitative and predictive biology.

More specifically, you will engage in the following areas:

• Analysis, visualization, and interpretation of NGS-based perturbation datasets with existing and emerging methods
• Support of CFG users in all aspects of data analysis and data handling
• Application and development of robust statistical approaches for hit calling and data interpretation
• Management of datasets for FAIR compliance and AI/ML-based discovery
• Contribute to multi-modal data integration

Your profile

• MSc or PhD in Computational Biology, Bioinformatics, Systems Biology, or a related field
• Strong programming skills (Python, R, Bash or similar) for omics data processing, QC, statistical testing, and visualization to support biological discovery
• Familiarity with working with Unix/Linux environments
• An understanding of statistical and quantitative methods
• Strong communication skills and a collaborative, service-minded approach
• Fluency in English, spoken and written

Experience or expertise in any of the following areas will be considered meritable:

• NGS and Omics Data Analysis: Processing and visualization of large-scale sequencing data (FASTQ/BAM, alignment, QC, variant calling)
• CRISPR/Mutagenesis Screen Analysis: High-throughput screen analysis, including UMI handling and hit calling (e.g., MAGeCK, Bagel).
• Pathway and Gene Set Analysis: Gene set enrichment and pathway analysis using fgsea, clusterProfiler, Enrichr, ReactomePA, and databases such as KEGG, Reactome, and GO.
• Pipeline Development: Development and maintenance of reproducible pipelines (Snakemake, Nextflow) with version control and containerization (Docker/Singularity).
• FAIR & Metadata Management: Knowledge of public repositories, metadata standards, and ensuring datasets are FAIR and AI-ready.

What do we offer?

Karolinska Institutet is one of the world's leading medical universities. As part of the Department of Medical Biochemistry and Biophysics, CFG offers a collaborative, dynamic, and friendly work environment housed in one of Europe’s most modern research buildings. You will have the opportunity to work on diverse projects spanning molecular cell biology, from basic research to molecular medicine, supporting high-impact studies across cancer, neurodegenerative diseases, infectious disease, and model organisms.

CFG encourages personal and professional growth through access to courses, workshops, conferences, and specialized training in computational biology, functional genomics, and data science. We foster a flexible and supportive work culture, emphasizing collaboration, mentoring, and peer learning. While this position is initially limited to one year, it is anticipated to be advertised as a permanent position, and the current holder will be encouraged to apply, contingent on strong performance during the first year.

Location: Biomedicum, Solna

Application

Your application should preferably be in English, but you may also apply in Swedish. It must include a cover letter detailing why you are a strong match for the position. The cover letter should be written personally and not generated by AI tools.

The deadline for application is 2025-10-31. Applications must be submitted through the Varbi recruitment system.

Want to make a difference? Join us and contribute to better health for all

Type of employment: Special fixed-term employment

Contract type: Full time

First day of employment: Upon agreement

Salary: Monthly salary

Number of positions: 1

Full-time equivalent: 100%

City: Stockholm

County: Stockholms län

Country: Sweden

Reference number: STÖD 2-3645/2025

Contact: Bernhard Schmierer, +46852480000