Research Infrastructure Specialist in Bioinformatics systems

Do you want to contribute to improving human health?

Karolinska Institutet, Department of Oncology-Pathology

SciLifeLab

Computational methods and artificial intelligence on large-scale molecular data are transforming the study of biological systems at all levels, from molecular structures and cellular processes to human health and global ecosystems. Established in 2010, SciLifeLab (www.scilifelab.se) forms an internationally unique infrastructure and research community, bringing together groundbreaking life science technologies with data and AI expertise. We are currently launching a major recruitment call for outstanding staff scientists in areas such as bioinformatics, data management and IT to join our national research infrastructures. As a key infrastructure expert, you will have a central role in connecting our user communities and to develop new data services together with senior experts at the SciLifeLab Bioinformatics Platform and the SciLifeLab Data Centre, to catalyze groundbreaking research in a new era of quantitative and predictive biology. 

About the Global Proteomics and Proteogenomics unit at SciLifeLab

You will join SciLifeLab's Global Proteomics and Proteogenomics (GPPG) unit in Stockholm, a state-of-the-art facility equipped with the latest high-performance LC-MS instrumentation for comprehensive protein analysis. The unit specializes in cutting-edge proteogenomics research, combining proteomics data with sample-specific genomic and transcriptomic information to discover novel protein coding regions, detect variant proteins, and identify cancer neoantigens. Our facility offers a full spectrum of MS-based applications including quantitative proteomics, single-cell analysis, post-translational modification studies, and interaction analysis. The unit serves as a national resource supporting the Swedish life science community with expert knowledge in both discovery-scale and targeted proteomics approaches. You will work alongside a team of experienced scientists and have access to world-class infrastructure to advance proteogenomics research and applications.

Your mission

We are seeking a Bioinformatics Research Infrastructure Specialist to lead the development and management of SciLifeLab's global proteomics and proteogenomics (GPPG) units data infrastructure. This full-time position focuses on building robust data pipelines, optimizing analytical workflows, and integrating mass spectrometry proteomics data with multi-omics platforms. You will play a critical role in enabling seamless data management and cross-platform integration to advance systems biology and precision medicine research, while ensuring data assets align with FAIR (Findable, Accessible, Interoperable, Reusable) principles through robust metadata frameworks and standardization practices.

Key Responsibilities

• Design, build, and maintain scalable bioinformatics pipelines for MS proteomics data processing
• Optimize existing analytical workflows and integrate new tools into the data platform
• Manage omics data infrastructure, ensuring efficient data transfer and storage solutions
• Integrate proteomics data with genomic, transcriptomic, and clinical datasets
• Collaborate with internal teams and external partners to develop cross-platform solutions
• Provide technical support and training to users of the platform 

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.

Assessment criteria

It is particularly meritorious that the applicant has shown

•  Programming expertise: Proficiency in Python, R, and/or workflow management systems (Nextflow, Snakemake)
• Bioinformatics background: Degree in Bioinformatics, Computational Biology, Computer Science, or related field with demonstrated omics data experience
• Pipeline development: Proven experience building and maintaining omics data analysis workflows
• Communication: Excellent English communication skills and ability to work in collaborative research environments 

It is meritorious that the applicant has shown

•  Advanced degree: Ph.D. in relevant field, or Master's with 5+  years of specialized experience
• Technical tools: Experience with MaxQuant, OpenMS, DIA-NN, Spectronaut, or similar platforms
• Multi-omics integration: Experience combining proteomics with genomic/transcriptomic data
• Specialized knowledge: Understanding of peptide-spectrum matching, FDR estimation, protein inference
• AI/ML proficiency: Experience with machine learning frameworks and AI-assisted data analysis tools for omics applications

  Research applications: Background in translational research, biomarker discovery, or cancer proteogenomics

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.

Location: Science For Life Laboratory in Solna

Your career continues here

MS-based Protein Analysis - SciLifeLab

LehtiöLab

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.

Welcome to apply at the latest 9^th November.

The application is to be submitted through the Varbi recruitment system.

Permanent position is initiated by a six months trial period.

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