Researcher in Bioinformatics (Karolinska Institute)

Reference Number: STÖD 2-3670/2025 Location: Biomedicum, Solna, Stockholm County, Sweden Type of Employment: Special fixed-term employment, Full-time (100%) First Day of Employment: Upon agreement Salary: Monthly salary Number of Positions: 1 About the Position 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 nation-wide infrastructure and research community combining advanced life science technologies with data and AI expertise, the Chemical Proteomics unit at the Department of Medical Biochemistry and Biophysics is seeking a Research Engineer in Bioinformatics with a focus on MS-based proteomics. Your Mission We are seeking a bioinformatician to analyze complex proteomics datasets and develop innovative tools for data processing, visualization, and generation of databases and prediction models. Responsibilities include: Building and maintaining reproducible pipelines for analysis of high-throughput chemical proteomics experiments. Applying statistical and pathway analysis methods. Ensuring all datasets follow FAIR principles. Supporting users of the Chemical Proteomics unit in all data-related aspects. Contributing to multi-modal data integration through AI/ML approaches. Specific Tasks: Analyze, visualize, and interpret complex chemical proteomics datasets, including PISA, RedOX proteomics, PTMs, HDX-MS, and quantitative mass spectrometry data. Develop novel analysis tools, pipelines, and visualization methods tailored to chemical proteomics workflows. Apply robust statistical approaches for hit calling, differential protein quantification, and enrichment analysis. Ensure datasets are well-managed and compliant with FAIR principles. Contribute to multi-modal (multi-omics) data integration using AI/ML approaches. Your Profile Eligibility Requirements: MSc or PhD in Bioinformatics, Computational Biology, Systems Biology, Computer Science, Biochemistry (related to proteomics and mass spectrometry), or a related field. Strong Python and R skills for omics data processing, QC, statistical testing, and visualization. Solid foundation in statistical and quantitative methods. Strong communication skills and a collaborative, service-minded approach. Fluency in English, spoken and written. Other Assessment Criteria (Merits): Experience with specialized tools for MS-based proteomics data analysis, statistical testing, and visualization. Knowledge of website building (Django, RShiny, etc.). Specialized knowledge in MS-based proteomics: peptide-spectrum matching, FDR estimation, etc. Proficiency in protein and peptide level analysis, including normalization, missing-value handling, differential quantification, clustering, and correlations. Experience with database search engines (MaxQuant, Proteome Discoverer, Peaks Studio, DIA-NN, HDX-Examiner) and MS RAW data analysis software (Xcalibur, Freestyle). Protein-centric pathway analysis, enrichment, and network analysis using ReactomePA, clusterProfiler, Cytoscape, and databases such as Reactome, KEGG, and GO. Multi-modal data integration: combining proteomics with transcriptomics, imaging, or other complementary data types. Knowledge of AlphaFold for structural protein analysis/proteomics. AI/ML applications for predicting gene function or discovering functional relationships. Familiarity with proteomics-specific public repositories (e.g., PRIDE) and metadata standards, ensuring FAIR data management. What We Offer Karolinska Institutet is one of the world's leading medical universities. Employees enjoy benefits such as extended holidays, a generous occupational pension, free access to a modern gym, and reimbursement for medical care. The workplace at Biomedicum, Solna, hosts top-ranked research groups and infrastructure facilities. The work environment is creative, international, and inspiring. The Chemical Proteomics unit encourages personal and professional growth through access to courses, workshops, conferences, and specialized training. The position is initially limited to one year, with potential renewal and permanent appointment contingent on performance. Application Applications must be submitted through the Varbi recruitment system. Preferred language: English (Swedish also acceptable). Must include a cover letter detailing why you are a strong match for the position (personal, not AI-generated). Deadline for Application: 31 October 2025 Contact: Massimiliano Gaetani – Massimiliano.gaetani@ki.se Union Representatives: Anurupa Nagchowdhury, OFR – anurupa.nagchowdhury@ki.se Daisy Hjelmqvist, SACO – daisy.hjelmqvist@ki.se If you apply for this position please say you saw it on Engineeroxy

Reference Number: STÖD 2-3670/2025

Location: Biomedicum, Solna, Stockholm County, Sweden
Type of Employment: Special fixed-term employment, Full-time (100%)
First Day of Employment: Upon agreement
Salary: Monthly salary
Number of Positions: 1

About the Position

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 nation-wide infrastructure and research community combining advanced life science technologies with data and AI expertise, the Chemical Proteomics unit at the Department of Medical Biochemistry and Biophysics is seeking a Research Engineer in Bioinformatics with a focus on MS-based proteomics.

Your Mission

We are seeking a bioinformatician to analyze complex proteomics datasets and develop innovative tools for data processing, visualization, and generation of databases and prediction models. Responsibilities include:

Building and maintaining reproducible pipelines for analysis of high-throughput chemical proteomics experiments.
Applying statistical and pathway analysis methods.
Ensuring all datasets follow FAIR principles.
Supporting users of the Chemical Proteomics unit in all data-related aspects.
Contributing to multi-modal data integration through AI/ML approaches.

Specific Tasks:

Analyze, visualize, and interpret complex chemical proteomics datasets, including PISA, RedOX proteomics, PTMs, HDX-MS, and quantitative mass spectrometry data.
Develop novel analysis tools, pipelines, and visualization methods tailored to chemical proteomics workflows.
Apply robust statistical approaches for hit calling, differential protein quantification, and enrichment analysis.
Ensure datasets are well-managed and compliant with FAIR principles.
Contribute to multi-modal (multi-omics) data integration using AI/ML approaches.

Your Profile

Eligibility Requirements:

MSc or PhD in Bioinformatics, Computational Biology, Systems Biology, Computer Science, Biochemistry (related to proteomics and mass spectrometry), or a related field.
Strong Python and R skills for omics data processing, QC, statistical testing, and visualization.
Solid foundation in statistical and quantitative methods.
Strong communication skills and a collaborative, service-minded approach.
Fluency in English, spoken and written.

Other Assessment Criteria (Merits):

Experience with specialized tools for MS-based proteomics data analysis, statistical testing, and visualization.
Knowledge of website building (Django, RShiny, etc.).
Specialized knowledge in MS-based proteomics: peptide-spectrum matching, FDR estimation, etc.
Proficiency in protein and peptide level analysis, including normalization, missing-value handling, differential quantification, clustering, and correlations.
Experience with database search engines (MaxQuant, Proteome Discoverer, Peaks Studio, DIA-NN, HDX-Examiner) and MS RAW data analysis software (Xcalibur, Freestyle).
Protein-centric pathway analysis, enrichment, and network analysis using ReactomePA, clusterProfiler, Cytoscape, and databases such as Reactome, KEGG, and GO.
Multi-modal data integration: combining proteomics with transcriptomics, imaging, or other complementary data types.
Knowledge of AlphaFold for structural protein analysis/proteomics.
AI/ML applications for predicting gene function or discovering functional relationships.
Familiarity with proteomics-specific public repositories (e.g., PRIDE) and metadata standards, ensuring FAIR data management.

What We Offer

Karolinska Institutet is one of the world's leading medical universities. Employees enjoy benefits such as extended holidays, a generous occupational pension, free access to a modern gym, and reimbursement for medical care.

The workplace at Biomedicum, Solna, hosts top-ranked research groups and infrastructure facilities. The work environment is creative, international, and inspiring.

The Chemical Proteomics unit encourages personal and professional growth through access to courses, workshops, conferences, and specialized training. The position is initially limited to one year, with potential renewal and permanent appointment contingent on performance.

Application

Applications must be submitted through the Varbi recruitment system.

Preferred language: English (Swedish also acceptable).
Must include a cover letter detailing why you are a strong match for the position (personal, not AI-generated).

Deadline for Application: 31 October 2025

Contact:
Massimiliano Gaetani – Massimiliano.gaetani@ki.se

Union Representatives: