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.

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 such genomes have evolved?”, is a question I asked in my first publication and keeps on intriguing me.

The gene regulatory network

The game that cells 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 the core of my research.

Developmental gene networks

Developmental processes, such as cell specification and spatial patterning, are known for their intricate gene regulatory networks. During development, cells need to respond to external signals, regulate cell division, and become capable of performing specialized functions. Especially animals have evolved an elaborate repertoire of specialized cells. In summary, development is an excellent area for studying the evolution of gene networks. Moreover, it provides ample room for working with experimentalists.