Erik van Nimwegen is Professor for computational systems biology at the Biozentrum of the University of Basel. His main research interests concern the structure, function, and evolution of genome-wide gene regulatory networks. Much of the work in the group revolves around developing computational methods for reconstructing gene regulatory networks from high-throughput biological data. This includes methods for genome-wide prediction of regulatory sites, and methods that use these genome-wide regulatory site predictions in combination with transcriptomic and epigenomic data to model genome-wide gene expression and chromatin state dynamics with the aim of identifying the key regulatory interactions in different developmental and cellular differentiation processes. Relevant examples of such methods are our ISMARA (ismara.unibas.ch) and CRUNCH (crunch.unibas.ch) tools for the automated analysis of transcriptomic, epigenomic, and TF-binding data. His group routinely applies these methodologies in collaborations with experimental labs both in Basel and abroad on a wide-range of model systems from bacteria through flies, to mammals. Besides such collaborative work, the current interests of his group mainly concern fundamental theoretical questions regarding the functioning of gene regulatory networks such as how how cell `types’ can be rigorously defined, characteristics of stochastic gene regulation at the single cell level, how cell identity is stabilized in the face of the highly stochastic expression dynamics at the single-cell level, and understanding how regulatory interactions determine trajectories in differentiation and transdifferentiation dynamics.
For detail and recent publications: https://www.biozentrum.unibas.ch/nimwegen