Methods to Identify Cellular Architecture and Dynamics from Experimental Data
Rudiyanto Gunawan, Kapil G. Gadkar, Francis J. Doyle · The MIT Press eBooks · 2006
This chapter highlights the methodologies and challenges in the reverse engineering of cellular networks, in particular the identification of network dynamics using engineering approaches. The chapter is organized as follows. Section 11.2 gives a motivating example, which highlights some of the difficulties in a cellular network inference problem. Section 11.3 discusses the different issues and methodologies in reverse engineering with respect to both topology and dynamics. Tutorials are presented in the form of case studies involving a metabolic network in E. coli and a signal transduction pathway in a caspase-activated apoptosis. Finally, open research problems in this area are identified based on the analysis of the case studies.