Vacancies

PhD position, appointment for 4 years

Description of the position

Systems biology is rapidly developing as the scientific approach to understand complex biological systems consisting of a large number of components and their interactions. In this project, we will answer the question of how to encode the information present in a knowledge base in such a way that it can be used in explorative metabolomics data analysis to improve the interpretation of the results. However, detailed biological knowledge is often found scattered in literature, online databases and in the mind of the expert.

The underlying technology used in the BioExpert framework allows many knowledge-driven goals to be accomplished, such as the linking of knowledge to public databases, and the provision of high-level knowledge to non-experts in the domain of the knowledge base. The BioExpert framework provides a platform that supports the capture of knowledge from experts in a specific domain. This is achieved through providing experts with the tools to define their knowledge graphically as concept maps. Concept maps are a powerful tool as they allow the specification of complex knowledge in an intuitive way, much like the way in which diagrams are presented in journal articles. To explore this we will build a knowledge base of some of the key polyphenol degradation pathways. Polyphenols are plant secondary metabolites, ubiquitous in fruits, vegetables, tea or wine that have a role in the prevention of e.g. cardiovascular diseases, metabolic syndrome, etc. Their bioavailability however depends strongly on the variety of gut bacteria that break down the large aromatic molecules into smaller and simpler phenolics that are absorbed into the human body. Some of these phenolics are measured in blood and urine but it is not yet possible to deduct which degradation pathways were used. The knowledge base contains information on the phenolics, their connectivity, regulation, liver conjugation and kidney clearance effects. We will explore in what way the metabolic network information should be treated so that it can be used directly in the multivariate statistical analysis of metabolomics experiments.

In a joint effort with the project 'Grey systems biology models' the combined analysis should provide the mainly used degradation pathways for a specific individual after polyphenol intake, giving the possibility of phenotyping individuals.

The project is funded by the Netherlands Bioinformatics Centre (NBIC) and performed in collaboration with Unilever.

Requirements

  • MSc in bioinformatics or systems biology.
  • Strong affinity for knowledge base development and data analysis.
  • Ambition to perform pioneering research in a developing field of science.
  • Good communicative skills and a multidisciplinary mindset.

For more detailed information regarding these positions you are invited to contact: Dr. Johan Westerhuis, phone +31 20-5256546, e-mail