Postdoc Position in Computational Antigen Discovery

Postdoc Position in Computational Antigen Discovery

Utrecht University - Faculty of Science

Utrecht, Netherlands

€ 3.546 - € 5.538 per month gross

Your job

As a Postdoctoral Researcher in the group of dr Marino external link, you will play a central role in advancing the group's research through the development and application of state-of-the-art bioinformatics workflows for antigen identification, quantification, and validation.

You will support the whole team in data analysis and visualization for different proteogenomics projects. You will organize and merge multi-omics data (in collaboration with our partners at Princess Maxima Center) using AI/ML techniques, implement antigen data analysis and discovery processes, and contribute to the maintenance of data infrastructure in collaboration with internal team members and other multidisciplinary teams.

In this role, you will also take the lead in developing new ideas and initiatives that advance the group’s research. This position will significantly impact the team by developing innovative bioinformatics pipelines, and by pinpointing and measuring the most immunogenic antigens for integration into vaccine-based therapies aimed at improving outcomes for patients with cancer.

Finally, you will be involved in many different multicentered and multidisciplinary collaborations, with both industry as well as academia and medical institutes. This will increase your exposure and expand your own professional network, supporting your future scientific career.

Key Responsibilities

• Develop and maintain scalable pipelines for mass spectrometry (MS)-based proteomics and immunopeptidomics data analysis.
• Design integrative frameworks combining genomics, transcriptomics, ribosomal profiling and proteomics datasets.
• Develop and maintain high-quality pipelines for processing and visualizing large-scale proteogenomics, MS-based immunopeptidomics/proteomics data.
• Ensure reproducibility and scalability of workflows using modern workflow tools (es. Nextflow, Snakemake, CWL etc.).
• Contribute to scientific publications, grant writing, and presentations.
• Collaborate with internal/external groups to develop new analysis pipelines tailored to immunopeptidomics experiments.
• Stay at the forefront of scientific advances in mass spectrometry-based immunopeptidomics/proteomics including software and new methodologies.

Your qualities

Required qualifications and experience

• PhD in bioinformatics, computational biology, or a related field.
• Proven experience analysing different mass spectrometry-based immunopeptidomics/proteomics data (i.e. DDA, DIA, PRM) with platforms such as FragPipe, Peaks, Spectronaut, MaxQuant, Skyline or equivalent tools.
• Solid background in state-of-the-art packages and analysis pipelines in mass spectrometry-based immunopeptidomics.
• Experience with non-canonical HLA-bound peptide discovery pipelines, binding predictions and other in silico tools (es. Immunogenicity predictors and/or HLA-peptide-TCR binding etc.).
• Experience in multi-modal data integration for prioritizing disease-specific targets: combining quantitative multi-omics approaches (es. RNA-seq, Ribo-seq, proteomics, immunopeptidomics).
• Strong programming skills in Python, R, or similar languages.
• Self-starting and collaborative attitude.

Preferred qualifications and experience

• AI/ML applications: applying machine learning or AI to integrate, discover and prioritize disease-specific targets across omics.