Are you ready for a challenge? We are looking for a PhD candidate who will use recent developments in AI technology to gain understanding of complex proteomics data derived by mass-spectrometry.

Your job
In this PhD project, you will develop AI-driven methodologies for analysing a variety of mass spectrometry data, including metabolites, peptides, and intact proteins. This involves predicting different biochemical properties of molecules and interpreting the trained models. Additionally, you will apply protein structure prediction methods to assess how different post-translational modifications impact protein structure, and consequently, protein-protein interactions. Collaboration with the Biomolecular Mass Spectrometry and Proteomics groups at the Pharmaceutical Sciences department will be an integral part of your work, providing you with hands-on experience in planning, executing, and validating biological hypotheses.

Your daily supervisor will be Pavel Sinitcyn, Assistant Professor in the vibrant interdisciplinary research group AI Technology for Life. The PhD project is collaboration between the AI Technology for Life group (Sanne Abeln, Professor of AI Technology for Life), and the Biomolecular Mass Spectrometry and Proteomics group (Albert J.R. Heck, Professor of Biomolecular Mass Spectrometry and Proteomics) at Utrecht University.

We are looking for a PhD candidate with the following qualities:

• a (nearly) completed MSc degree in a relevant area such as Artificial Intelligence/Machine Learning, Computer Sciences or Bioinformatics with a strong AI component;
• demonstrable experience with development of machine learning methods;
• an interest in working with proteomics data;
• as you will have to collaborate with researchers in the life sciences, it is essential that you have strong oral and written communication skills in English.

• a position for 4 years (0.8 -1.0 FTE);
• a gross monthly salary between €2,770 and €3,539 in the case of full-time employment (salary scale P under the Collective Labour Agreement for Dutch Universities (CAO NU);
• 8% holiday pay and 8.3% year-end bonus;
• 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 has a number of schemes and facilities of its own for employees. This includes schemes facilitating professional development, leave schemes and schemes for sports and cultural activities, as well as discounts on software and other IT products. We also offer access to additional employee benefits through our Terms of Employment Options Model. In this way, we encourage our employees to continue to invest in their growth. For more information, please visit Working at Utrecht University.

Universiteit Utrecht

A better future for everyone. This ambition motivates our scientists in executing their leading research and inspiring teaching. At Utrecht University, the various disciplines collaborate intensively towards major strategic themes. Our focus is on Dynamics of Youth, Institutions for Open Societies, Life Sciences and Pathways to Sustainability. Shaping science, sharing tomorrow.

At the Faculty of Science there are 6 departments to make a fundamental connection with: Biology, Chemistry, Information and Computing Sciences, Mathematics, Pharmaceutical Sciences and Physics. Each of these is made up of distinct institutes that work together to focus on answering some of humanity’s most pressing challenges. More fundamental still are the individual research groups – the building blocks of our ambitious scientific projects.

You will be embedded in the interdepartmental research group AI Technology for Life, and the Biomolecular Mass Spectrometry and Proteomics group. As such you will be affiliated with both the Department of Pharmaceutical Sciences and the Department of Information and Computing Sciences.