Research Fellows Directory
Dr Tamas Nepusz
Royal Holloway, University of London
An important new field of research, coined as systems biology, has emerged recently with a view that cellular functions are carried out by many interacting molecules organised in complex networks, where nodes represent bio-molecules and the links the relations between them. For instance, protein-protein interaction networks encode whether two proteins can physically interact with each other in the cell or not. In this network, every node represents a protein, and two nodes are connected by an edge if the two proteins can interact. Similarly, gene co-expression networks are composed of genes which are connected if they show similar expression patterns (roughly speaking, similar behaviour) in some biological experiment.
A common feature of many biological networks is that they contain groups of nodes that are more connected to each other than to the rest of the network. These groups (also called clusters or communities) frequently co-incide with known functional modules of bio-molecules. Communities of a protein-protein interaction network show a high correspondence with multi-protein complexes (molecular machineries that perform specific biological functions). Communities in a gene co-expression network represent genes participating in the same biological process. The boundaries between modules are not clear; a protein may belong to more than one protein complex and a gene may participate in more than one biological pathway at the same time. My research is about developing computational methods that can discover such overlapping modules in biological networks with high confidence. Such methods will have an impact for the biological and biomedical research communities, enabling them to detect underlying cellular processes from experimental data more accurately than with current state-of-the-art methods that do not consider overlaps between modules, and also pinpointing key bio-molecules that participate in more than one essential biological process at the same time.