I study the evolution and functioning of (gene) regulatory networks in eukaryotes using computer simulations, mathematics, and bioinformatic data analysis. I like to pursue both theoretical questions and experimentally driven ones. In the latter case, I team up with experimental biologists.
Development, health and disease
Developmental processes, such as cell type specification and spatial patterning, are known for their intricate regulatory circuits. During development, cells need to respond to external signals, tune cell division, and become capable of performing specialized functions. Especially animals have evolved an elaborate repertoire of specialized cells organized in a variety of tissues. And when tissues experience uncontrolled growth, cancer may result. In summary, development and later organismal life are excellent areas for studying the evolution and (mal)functioning of regulatory networks. Plus, they provide ample room for working with experimentalists.
The game that organisms play, is one of survival and reproduction. To this end, the cell regulates the expression of its genes such that the right proteins (and non-coding RNAs etc.) are produced in a timely fashion and in the correct amount. One important process is that of genes activating and inhibiting each other’s expression: the gene regulatory network. This network is, of course, evolving. Understanding network evolution is a core theme of my research.
Gene and genome structure
Eukaryotes have a richly structured genome. It folds in a hierarchical fashion to fit in the nucleus, is full of the leftovers of transposable elements and viruses, dedicates only a small part of its DNA sequence to protein-coding genes, and encodes its genes in pieces. “How do genomes evolve?”, is a question I asked in my first publication and that keeps on intriguing me.