Master 2011 2012
proposition de these (amsterdam)

At the Department of Computer Science at the VU University Amsterdam, a PhD position for four years is available on a research project devoted to

Engineering Executable Models of Biological Networks

The project

The goal of the project is to describe gene regulatory networks by formal interaction patterns/models. Using these formal models, we aim to derive new insights in the behaviour of gene networks. These models, ultimately, describe cells’ behaviour, and cell components, as independent, communicating entities. Simulating cell behaviour this way at the same time promises new insights and poses new challenges on the execution and verification environment due to the complexity, heterogeneity and variability of the modeled entities.

The work will start with the application of our formal framework using Petri nets to model gene network behaviour. Additionally, extensions of the framework and new methods and tools for analysis of the behaviour patterns will be developed.

For more detailed information on the project, see feenstra/proj...

Research groups

This project is a collaboration between two research groups at the VU : Bioinformatics (Anton Feenstra and Jaap Heringa) and Theoretical Computer Science (Wan Fokkink). For experimental validation of predictions, we collaborate with two experimental groups ; the group Receptor Systems Biology at the VU (Martine Smit), and Bertie Göttgens at the Cambridge Institute for Medical Research.

For more information on the involved research groups, see tcs


Candidates should have completed their studies in computer science, bioinformatics or a closely related area. Experience with biological systems, a good theoretical background, and an open attitude to applications are considered advantages. You should enjoy working in an internationally oriented and interdisciplinary research environment. Communicative skills and the ability to work in a team are important.

Information and application

For further information about these positions please contact either :

Dr. Anton Feenstra tel. +31 (0)20 5987783 Prof.dr. Wan Fokkink tel. +31 (0)20 5987735 Prof.dr. Jaap Heringa tel. +31 (0)20 5987649

You are invited to send an application by email to the above email addresses no later than September 1, 2012. Your application should consist of a cover letter, a curriculum vitae (including detailed information regarding your academic degree), and the names and addresses of two references.