Troy Ruths

Bioinformatics is a field awash in data -- sitting at the crossroads of biology, biochemistry, biophysics and computer science, this dynamic discipline is overwhelmed by voluminous, crucial data encoding genomic, cellular, and proteinic information. The open questions are so fundamental that each step made in this field is progress towards a broad range of immediate applications, including cancer, gene therapy, and stem cell research. At the same time, these questions are restricted by our ability to analyze and process the exponentially growing data repositories. Ultimately, bioinformatics is desperate for high-performance computational tools and methodologies to assuage its growing pains.

Interaction networks are a vital source of information for interpreting cell function. Consequently, advances made in understanding these networks expand our ability to modify, enhance, and repair cell behavior. One of the fundamental observations that has been guiding much of the computational research into comparative, or evolutionary, analysis of interaction networks is that components of interaction networks, such as paths and cycles, that are conserved across multiple species tend to reflect true functional modules; hence, their identification is of great significance. With that said, comparative analysis of these networks is still in its infancy.

Investigating the structure and formation of interaction networks from an evolutionary perspective will be a central theme of my work. My initial investigations will bring insight into two arenas: first, the role of evolution in constructing, preserving, and removing function in interaction networks, and secondly, the dynamics of evolution on a proteinic and genomic scale. These results will benefit not only practicing biology but will also extend our model of evolution.

Troy Ruths, Derek Ruths, and Luay Nakhleh. "GS2: An efficiently computable measure of GO-based similarity of gene sets". Bioinformatics, submitted.