Utrecht University >
Faculty of Science >
department of Biology >
Theoretical Biology & Bioinformatics >
The immune system is a fascinating complex system taking decisions on
how to respond to a wide variety of stimuli, varying from lethal
pathogens to harmless proteins in the food. Decisions are remembered
for life in the form of immunological memory. Most of the research in
immunology is of a qualitative nature, describing novel cell types,
molecules, and genes.
The proper understanding of such a complex systems also requires a
more quantitative approach describing the various population sizes,
the turnover rates of the cells within each population, their
migration rates, and the rates at which cells form contacts with other
cells. A major part of our work is to develop a more quantitative
immunology by describing the population dynamics of its major
populations using a variety of labeling techniques and mathematical
modeling to analyze the data.
Pathogens are also fascinating complex systems that by their faster
evolution manage to exploit properties of the immune system to elicit
inappropriate immune reactions. We study host-pathogen evolution by
bioinformatic methods predicting which parts of a pathogen trigger the
dominant immune responses in any particular host (using peptide MHC
One of our model pathogens is HIV-1, which is modifying the normal
population dynamics in the immune system in such a way that the system
slowly collapses, and for which an enormous amount of bioinformatic
data is available, that we use to study the evolution of this pathogen
in its new human host.
Teaching, honors, and other activities
I teach introductory courses in Theoretical Biology and Theoretical
Ecology for biology students on the bachelor level, which results Ebooks that are publicly available.
I am on the External Faculty of the Santa Fe Institute and am one of the
founding fathers of Institute Para
Limes, and listed in the Gallery of Honor of
We have developed public domain software
for simulating cellular automata, analyzing ordinary differential
equations, and making BibTex files from other citation formats,
and we maintain servers for estimating viral
fitness from competition experiments.
Open position: staff member
Please see the website for an open position
for a computation life scientist at the assistant/associate professor level.
My full address.
Theoretical Biology & Bioinformatics /
Last modified on 24 March 2013 /