Hypothesis Generation in Signaling Networks

Biological signaling networks comprise the chemical processes by which cells detect and respond to changes in their environment. Such networks have been implicated in the regulation of important cellular activities, including cellular reproduction, mobility, and death. Though technological and scientific advances have facilitated the rapid accumulation of information about signaling networks, utilizing these massive information resources has become infeasible except through computational methods and computer-based tools. To date, visualization and simulation tools have received significant emphasis. In this paper, we present a graph-theoretic formalization of biological signaling network models that are in wide but informal use, and formulate two problems on the graph: the Constrained Downstream and Minimum Knockout Problems. Solutions to these problems yield qualitative tools for generating hypotheses about the networks, which can then be experimentally tested in a laboratory setting...

• Type: Journal
• Year: 2006
• Where: JCB
• Authors: Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram
• Keywords: Biological Signaling Network, Constrained Downstream, JCB 2006, Minimum Knockout Problem