Erik van Nimwegen’s main research topics concern genome evolution and the function and evolution of the regulatory networks by which cells control gene expression. He develops mathematical models for analyzing how regulatory networks evolve and function, and computational methods for the reconstruction of such networks from large biological data-sets. Van Nimwegen's work includes a general model for the evolution of robustness against mutations and the identification of a number of universal scaling laws of genome evolution. Further research topics are the development of general Bayesian methods for transcription factor and miRNA binding site prediction as well as models for inferring regulatory networks from genome-wide expression and chromatin state data.