Theoretical Biology & Bioinformatics

tree of life


Biological systems are complex systems composed of many interacting building blocks, like molecules, cells, and organisms. These large networks of interactions have been shaped by trial and error during evolution, and nowadays account for the functional behavior of living systems. Understanding the behavior of such complex systems on a mechanistic level, and revealing the routes by which they have evolved, cannot be achieved by experimental biology only, and requires theoretical approaches like mathematical modeling, computer simulation and bioinformatics. In our group we use a computational biology approach to study biological processes.

The Theoretical Biology & Bioinformatics group is home to several research groups, all using computational approaches to address biological questions within their own biological focus area. Together we cover a range of biological areas, including immunology (De Boer, Bontrop & Kesmir), evolutionary (meta-)genomics (Snel & Dutilh), evolutionary development (Ten Tusscher), bacterial evolution (Hermsen), and multi-level evolution (Hogeweg). Some groups use bioinformatics, others use modeling and quantitative biology, or evolutionary agent based modeling. In order to address our research questions, we team up with various experimental partners to model and analyze biological data, and design novel experiments.

The group is part of the Institute for Biodynamics and Biocomplexity (IBB) which aims to decipher fundamental principles regulating dynamic biological processes, and we play leading roles in the University's focus areas Complex systems, the Utrecht Center for Quantitaive Immunology, and the Utrecht Bioinformatics Center.


The group has a long history in studying complex systems and bioinformatics. The group was founded in the seventies, and at that time Paulien Hogeweg and Ben Hesper coined the term bioinformatics for the study of informatic processes in biotic systems. According to the Oxford English Dictionary this was the first use of the term bioinformatics.