At Utrecht University, we have built a specialized team focusing on the discovery of previously unidentified antigens for immunotherapies through mass spectrometry (MS)-based proteomics and immunopeptidomics. We now seek a highly motivated and experienced Postdoctoral Researcher to join our multidisciplinary research team.
As a Postdoctoral Researcher in the group of dr Marino, 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
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Develop and maintain scalable pipelines for mass spectrometry (MS)-based proteomics and immunopeptidomics data analysis.
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Design integrative frameworks combining genomics, transcriptomics, ribosomal profiling and proteomics datasets.
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Develop and maintain high-quality pipelines for processing and visualizing large-scale proteogenomics, MS-based immunopeptidomics/proteomics data.
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Ensure reproducibility and scalability of workflows using modern workflow tools (es. Nextflow, Snakemake, CWL etc.).
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Contribute to scientific publications, grant writing, and presentations.
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Collaborate with internal/external groups to develop new analysis pipelines tailored to immunopeptidomics experiments.
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Stay at the forefront of scientific advances in mass spectrometry-based immunopeptidomics/proteomics including software and new methodologies.
Required qualifications and experience
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PhD in bioinformatics, computational biology, or a related field.
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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.
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Solid background in state-of-the-art packages and analysis pipelines in mass spectrometry-based immunopeptidomics.
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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).
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Experience in multi-modal data integration for prioritizing disease-specific targets: combining quantitative multi-omics approaches (es. RNA-seq, Ribo-seq, proteomics, immunopeptidomics).
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Strong programming skills in Python, R, or similar languages.
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Self-starting and collaborative attitude.
Preferred qualifications and experience
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AI/ML applications: applying machine learning or AI to integrate, discover and prioritize disease-specific targets across omics.
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access to the newest and most advanced mass spectrometry instruments and computing infrastructures;
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a multidisciplinary environment within the group, with exposure to and collaborations with external partners beyond the lab;
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a social and diverse environment across the entire BioMS group with a strong sense of community, in including shared lunches and coffee breaks, a joint running group, Friday drinks and other social activities that extend beyond the laboratory;
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a position for initially 1 year;
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a gross monthly salary, depending on qualifications and experience, between € 3.706 and €5.760 in the case of full-time employment (salary scale 10 under the Collective Labour Agreement for Dutch Universities (CAO NU));
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8% holiday pay and 8.3% year-end bonus;
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a pension scheme, partially paid parental leave and flexible terms of employment based on the CAO NU.
In addition to the terms of employment laid down in the CAO NU, Utrecht University also offers a range of its own schemes for employees. This includes arrangements for professional development, various types of leave, and options for sports and cultural activities. You can also tailor your employment conditions through our Terms of Employment Options Model. In this way, we encourage you to keep investing in your personal and professional development. For more information, please visit Working at Utrecht University.
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The Utrecht Institute for Pharmaceutical Sciences (UIPS) is the research institute of the department of Pharmaceutical Sciences of Utrecht University. UIPS focuses on processes around discovery, development, and use of drugs and medical nutrition using molecular and technological principles from the Natural and Life Sciences.
You will be embedded in the division of Biomolecular Mass Spectrometry and Proteomics. The group consist of more than 60 researchers and supportive staff, with 18 different nationalities and many different expertise, including chemists, biologists, bioinformaticians and technical staff. The research in this division focuses on the use of mass spectrometry based enabling technologies to deeply understand the inner workings of cells at the molecular level. The group houses an excellent infrastructure that includes more than a dozen state-of-the-art mass spectrometers, combined with cell culture facilities and access to microscopes etc. The BioMS group is world-renown for mass spectrometry-based proteomics and structural biology, and applies these technologies to study amongst others cancer, auto-immune disorders, immunology, infections, and infectious diseases.
Within the BioMS group you will work in the team and under the guidance of dr. Fabio Marino. Dr. Marino received his PhD in the BioMS group, after which he moved to the biotech industry. With several years of industry experience, he came back to the BioMS group as an assistant professor, leading his own immunopeptidomics group. His group focuses on enhancing our knowledge of the Human Leukocyte Antigen (HLA) class I/II processes of antigen processing/presentation by mass spectrometry-based proteomics and immuopeptidomics from the perspectives of the immune system and diseased cells. Those learnings will make it possible to improve clinical products, provide new strategies for finding targetable HLA-bound antigens and to decipher what/how T cell Antigen discovery recognize. Currently, the group consists of 1 phd student, 1 technician and 5 post docs. The group has many close collaborations with industry, and academic partners, including Princes Maxima Centre, and is part of the NGF project Oncode Accelerator.
For more information, please contact Celine Miedema at [email protected].
Do you have a question about the application procedure? Please send an email to [email protected].
As Utrecht University, we want to be a home for everyone. We value staff with diverse backgrounds, perspectives and identities, including cultural, religious or ethnic background, gender, sexual orientation, disability or age. We strive to create a safe and inclusive environment in which everyone can flourish and contribute.
Knowledge security screening can be part of the selection procedures of academic staff. We do this, among other things, to prevent the unwanted transfer of sensitive knowledge and technology.
If you are enthusiastic about this position, just apply via the "Apply now" button! Please enclose:
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your letter of motivation;
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your Curriculum vitae;
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the names, telephone numbers, and email addresses of at least two references.
If this specific opportunity isn’t for you, but you know someone else who may be interested, please forward this vacancy to them.
Applications will be reviewed on a rolling basis until the position is filled. The vacancy may close earlier if a suitable candidate is identified.
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