Research Infrastructure Specialist

Do you want to contribute to top quality medical research? Robust data infrastructure, reproducibility, and standardized computational pipelines are the backbone of modern biological research. As part of SciLifeLab, a unique nation-wide research infrastructure and research community, the CRISPR Functional Genomics unit at Karolinska Institutet is looking for a Research Infrastructure Specialist in Bioinformatics and Data Stewardship Your mission You will spend roughly half of your time on building and maintaining reproducible pipelines for the in-depth analysis of high-throughput CRISPR gene-perturbation data. The remaining half will be dedicated to routine data administration throughout the data lifecycle, including metadata annotation, FAIR compliance for data sharing, and long-term archiving. Within this allocation, you will also support CFG and its users with day-to-day data analysis, management, and project delivery. More specifically, you will engage in the following areas: - Pipeline Engineering & Quality Control: Implement, benchmark, and maintain containerized workflows (e.g., Nextflow/Snakemake) to automate standard QC of pooled CRISPR screens – standard readouts, single-cell based readouts, and soon optical pooled screening readouts. - Hit Calling & Statistical Frameworks: Apply statistical models and algorithms to prioritize candidate hits across pooled CRISPR screening datasets, including base-editing datasets. - Metadata Curation & Archival Infrastructure: Design and enforce structured metadata schemes, manage raw and processed data uploads to public/institutional repositories, and establish audit-ready archiving procedures to maintain long-term FAIR compliance. - User Consultation & Project Management: Conduct technical consultations with external and internal research groups to define analysis requirements, troubleshoot user data issues, and deliver clear summary reports and interactive visualizations. - Internal Computational Support: Maintain webpages and support the team in all computer- and virtual environment-related tasks. Eligibility requirements For employment as Research Infrastructure Specialist at Karolinska Institutet, the eligibility requirements stated in the Guidelines for non-teaching positions at Karolinska Institutet are applied in relation to the established profile of employment. To be eligible for an employment as Research Infrastructure Specialist the applicant must have demonstrated research expertise and been awarded a PhD or a qualification from a foreign higher education institution deemed equivalent to a Swedish PhD. The applicant must also have demonstrated technological and methodological expertise. In addition to these minimal requirements, eligible candidates need to meet the following requirements: - PhD in Bioinformatics or Molecular Biosciences with at least three years of full-time wet-lab experience, and at least three years of full-time computational work. - Proven track record in analyzing pooled CRISPR screening data, as well as single-cell data and spatial omics datasets with and without a perturbation context. Experience in image analysis and segmentation for OPS/spatial transcriptomics is viewed favourably. - Proficiency in Python, R, and Unix/Linux (Bash) for omics data processing, quality control, statistical modeling, and interactive data visualization (e.g., Shiny or HTML-based dashboards). - Experience with backend databases/UI, drive releases, CI/CD, deployment, and production readiness of scientific applications. - Practical skills in High-Performance Computing (HPC) such as NAISS, or cloud environments using version control, containerization, and automated workflow managers. - Experience with version control, Git/Github, structured code, and automated testing. - Strong commitment to routine data administration, metadata tracking, and enforcing strict institutional compliance for FAIR data sharing and long-term archival. - Fluency in English (written and spoken) with a client- and service-oriented approach to supporting researchers, managing user projects, and documenting computational pipelines. - Familiarity with applying off-the-shelf biological foundation models and integrating LLMs/agentic workflows to automate routine bioinformatics tasks and data curation is advantageous. Assessment criteria Experience or expertise in any of the following areas will be considered an advantage, with particular emphasis placed on candidates who demonstrate a strong commitment to service, infrastructure maintenance, and routine data stewardship: - Routine Data Stewardship & FAIR Compliance: Demonstrated experience in enforcing structured metadata schemas, handling routine bulk data submissions to public/institutional repositories, and maintaining strict, audit-ready data archives. - Pipeline Maintenance & Execution: Proficiency in maintaining, troubleshooting, and executing existing containerized workflows (Snakemake, Nextflow, Docker/Singularity) for standard quality control. - Standardized CRISPR & Omics Processing: Practical experience running established hit-calling frameworks (e.g., MAGeCK) and standard single-cell/spatial omics processing pipelines for external users. - Client-Oriented Technical Support: A proven track record of acting in a service or core-facility capacity, including troubleshooting user data issues, consulting on standard experimental designs, and generating visually appealing and functional summary reports (Shiny or HTML dashboards). - Cross-Functional Wet-Lab Knowledge: A strong background in the practical application of wet-lab methodologies that enables effective communication with experimental researchers and practical troubleshooting of user-generated data. - General IT & Administrative Support: Willingness and technical ability to manage day-to-day internal group support, including maintaining web pages, updating documentation, and assisting colleagues with basic computer-related tasks. - Applied AI Tooling for Automation: Practical experience integrating LLMs or agentic workflows specifically to automate routine bioinformatics tasks, pipeline documentation, or metadata curation. After an overall assessment of the expertise and merits of the applicants in relation to the subject area, Karolinska Institutet will determine which of them has the best potential to contribute to a positive development of the activities at KI. What do we offer? A creative, international and inspiring environment with wide-ranging expertise and interests. Karolinska Institutet is one of the world's leading medical universities. Here, we conduct successful medical research and hold the largest range of medical education in Sweden. At KI, you get to meet researchers working with a wide range of specialisms and methods, giving you ample opportunity to exchange knowledge and experience with the various scientific fields within medicine and health. It is the crossover collaborations, which have pushed KI to where it is today, at the forefront of global research. Several of the people you meet in healthcare are educated at KI. A close relationship with the health care providers is important for creating groundbreaking top quality education and research. Karolinska Institutet is also a state university, which entitles you to several good benefits through our collective agreement. 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 Karolinska Institutet Research Infrastructure SciLifeLab CRISPR Functional Genomics New Career Path for Research Infrastructure Specialists     Application We prefer that Your application is written in English, but You can also apply in Swedish.  An application must contain the following documents: PhD certificate, resumé, qualifications  presented in accordance with  Karolinska Institutet's qualifications portfolio for research infrastructure specialist/senior research infrastructure specialist. KI applies individual and differentiated salary setting in accordance with our collective agreements RALS and RALS-T. The application is to be submitted through the Varbi recruitment system. Welcome with your application latest 2026-11-30. Want to make a difference? Join us and contribute to better health for all!