Postdoc Position in Computational Antigen Discovery, Utrecht University, Netherlands

Summary

Utrecht University is seeking a highly motivated and experienced Postdoctoral Researcher to join the research group led by Dr. Fabio Marino within the Biomolecular Mass Spectrometry and Proteomics (BioMS) division. The position focuses on developing and deploying state-of-the-art bioinformatics workflows, AI/ML models, and multi-omics data integration pipelines to identify, quantify, and validate novel tumor antigens for cancer immunotherapies and vaccine-based treatments.

Key Position Details

Research Area

• Bioinformatics & Computational Biology
• Mass Spectrometry (MS)-based Proteomics & Immunopeptidomics
• Multi-Modal Data Integration (RNA-seq, Ribo-seq, Proteomics, Immunopeptidomics)
• Cancer Immunotherapy, Tumor Antigen Discovery & Vaccine Design
• Machine Learning / Artificial Intelligence in Multi-Omics Target Prioritization

Location

Utrecht University, Faculty of Science

Department of Pharmaceutical Sciences

Heidelberglaan 8, 3584 CS Utrecht, The Netherlands

Eligibility & Qualifications

Required Qualifications

• Education: A completed PhD in Bioinformatics, Computational Biology, Data Science, or a closely related field.
• Domain Experience: Proven hands-on experience analyzing mass spectrometry-based immunopeptidomics and proteomics data (DDA, DIA, PRM) using tools such as FragPipe, PEAKS, Spectronaut, MaxQuant, or Skyline.
• Computational Skills: Strong programming skills in Python, R, or similar data-science languages.
• Specialized Expertise: Experience with non-canonical HLA-bound peptide discovery pipelines, immunogenicity predictors, and in silico HLA–peptide–TCR binding prediction tools.
• Multi-Omics Integration: Familiarity with integrative frameworks linking quantitative genomics, transcriptomics, ribosomal profiling (Ribo-seq), and proteomics data.
• Mindset: Strong problem-solving, self-starting, and collaborative team-working abilities.

Preferred Qualifications

• Experience building and applying Machine Learning / AI models to discover and prioritize disease-specific targets across complex omics datasets.
• Experience using workflow management frameworks (e.g., Nextflow, Snakemake, CWL) for scalable, reproducible pipeline development.

Job Description & Responsibilities

• Pipeline Development: Design, build, and maintain scalable and reproducible data processing pipelines for large-scale MS-based proteomics and immunopeptidomics datasets.
• Multi-Omics Integration: Merge and analyze multi-omics data in close collaboration with partners such as the Princess Máxima Center and the Oncode Accelerator network.
• Antigen Prioritization: Implement AI/ML-driven analyses to pinpoint, quantify, and validate immunogenic antigens for translation into vaccine-based cancer therapies.
• Scientific Output: Author and contribute to high-impact scientific publications, research grant proposals, and conference presentations.
• Collaborative Research: Act as a bioinformatics anchor within the multidisciplinary BioMS group, working closely with molecular biologists, chemists, and medical oncologists across academia and industry.

How to Apply

Interested candidates should apply online via the official Utrecht University vacancy portal by clicking the “Apply now” button on the job page.

Required Application Documents:

1. Curriculum Vitae (CV)
2. Letter of Motivation
3. Contact details (names, email addresses, phone numbers) of at least two academic/professional references

Note: Applications are evaluated on a rolling basis, and the position may close earlier if a suitable candidate is selected.

• Inquiries regarding position content: Dr. Celine Miedema (t.c.miedema@uu.nl)
• Inquiries regarding application procedure: science.recruitment@uu.nl

Last Date for Apply

31 August 2026

Link