Networks in Computational Biology
Professor Jeffrey Varner, professor in the Chemical and Biomolecular Engineering Department here at Cornell, conducts his research in computational systems biology. The objective of his research lab is defined as developing physiochemical modeling tools that can be used to reprogram signal flow in various pathways within the body. For example, one of the topics the Varner lab has researched is coagulation, or the process of blood clot formation. Physiologically, this process involves a cascade of different species and signaling molecules that together result in a successful clot, a natural protection mechanism used when one’s blood system is exposed to the outside environment.
In order to make such complex and cross linking biological systems and pathways manageable for alteration in a computer program or solver, networks are created. These networks relate different proteins or protein complexes. The nodes then, relate to the different species involved in a defined network, and the connections would represent interactions between the proteins. For the coagulation model example, the Varner lab defined 193 proteins and 301 interactions between these proteins. To assess the effect of varying conditions on the physiology of this cascade, ordinary differential equations are formulated and mass action kinetics were used to estimate the rates of the chemical interactions. With a network in place, the extent of a certain conditional change can be tracked and assessed to determine how sensitive the network is to such changes quickly and without expensive lab work. The Varner Lab group has its own website at www.varnerlab.org, and the publications are listed at www.varnerlab.org/papers/ if you would like more information on the coagulation project or others.