Theoretical Biology & Bioinformatics

tree of life

Master track

Computational Biology is defined as a track within the MCLS Master's programme to enable master students to explore this exciting new field, and develop a unique interdisciplinary expertise. This master track builds on 30 years of bioinformatics research and teaching at Utrecht University. Students will perform original research in Computational Systems Biology during two comprehensive research projects in modelling and/or bioinformatics. You will attend hands-on courses in modelling and bioinformatics provided by the Theoretical Biology and Bioinformatics groups and the Graduate School of Life Sciences (GS-LS), and you can add on optional computational courses (like computer programming). Since our research is addressing current questions in biology, a solid understanding of the relevant biology is required. Students from the natural sciences can attend appropriate biology courses to repair potential deficiencies. Students interested in combining Computational Biology with wet lab experiments can also perform part of the research in a relevant experimental laboratory.

Students in our master track will be trained in the conceptual and technical skills for doing research in Theoretical Biology and Bioinformatics. The conceptual training includes identifying and formulating theoretical research topics, that are interesting and relevant, and critical evaluation of published theoretical research. The technical training includes mathematics, biological sequence analysis, modeling and simulation. The students learn to go beyond using existing methods and develop improved methods and models that better address their own specific research questions. This master track will prepare the participants for a PhD thesis in theoretical biology and/or bioinformatics in the participating groups or in other laboratories (experimental and theoretical).

Excellent students in the track Computational Biology are advised to follow the QBio honours programme with a special focus on quantitative biology.

Possible Research projects

Our aim is to develop of computational models that enriches our mechanistic understanding of complex living systems at all scales, e.g., from molecules to cells, to organisms (or patients), and communities (or ecosystems). Research projects in the master program revolve around the main research lines of the group:

  • Developmental biology: Simulate multi-scale computational models to study complex developmental pattern formation processes and their evolution.
  • Quantitative Immunology : Analyse and model immunological data to improve our understanding of the functioning of the immune system in a quantitative manner.
  • Evolutionary Genomics: to compare genome sequences and integrate highthrougput data sets.
  • Multilevel evolution: To understand how different levels of selection, complex genotype phenotype mapping, and interactions over different timescales contribute to the evolution of complexity at the level of individuals and/or ecosystems.
  • Evolution in heterogeneous environments: How do environmental heterogeneities in biotic and abiotic factors affect evolutionary adaptation?
  • Bacterial physiology: Bacterial cells can change their composition dramatically upon a change of environment. What logic governs these adaptations?
  • Metagenomics: Metagenomics is the sequencing of genetic material directly from an environment. Countless new microbes and viruses are readily discovered, and we investigate their identity and role in the ecosystem. Our goal is a full understanding of metagenomic datasets based on bioinformatic data analysis and computational modelling.
  • Immunological Bioinformatics : The development of several data driven computational methods to predict which parts of pathogenic microorganisms but also tumors generate an immune response.

Study program

In this interdisciplinary field the basic knowledge will vary between students from different backgrounds (e.g., biosciences, computational sciences, mathematics or physics). Depending on that background the study program will be selected on a personal basis. Biology students should have a sufficient background in mathematics, modeling, or bioinformatics. The group gives two MSc courses, a modeling course called Computational Biology and a bioinformatics course called Bioinformatics and Evolutionary Genomics, that are mandatory for students attending this track. Students can add on general courses in biology, computational sciences, and/or select courses from our bachelor and advanced courses curriculum. An overview of the first year time planning is to be found here.

For bachelor students at Utrecht University the best preparation for the Computational Biology track in the MCLS master program is to attend a good selection of our bachelor courses, which we have organized in the "studiepad Theoretische Biologie & Bioinformatica".

Contact information

The master track Computation Biology is open to students from all over the world. For further information about the contents of courses and research projects please contact Dr. Can Kesmir. Information about the MCLS master program embedding this track can be obtained from the MCLS website, and from the program coordinator Dr. Bertrand Kleizen ( Please motivate your interest in Computation Biology.