title: Network representations and methods for the analysis of chemical and biochemical pathways.
abstract: Systems biologists increasingly use network representations to investigate biochemical pathways and their dynamic behaviours. In this critical review, we discuss four commonly used network representations of chemical and biochemical pathways. We illustrate how some of these representations reduce network complexity but result in the ambiguous representation of biochemical pathways. We also examine the current theoretical approaches available to investigate the dynamic behaviour of chemical and biochemical networks. Finally, we describe how the critical chemical and biochemical pathways responsible for emergent dynamic behaviour can be identified using network mining and functional mapping approaches.
authors.affiliation: Cystic Fibrosis and Pulmonary Diseases Research and Treatment Center and Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.
authors.forename: Conner I
authors.initials: CI
authors.lastname: Sandefur
authors.forename: Maya
authors.initials: M
authors.lastname: Mincheva
authors.forename: Santiago
authors.initials: S
authors.lastname: Schnell
mesh_terms: D000818:Animals; D006801:Humans; D008954:Models, Biological; D049490:Systems Biology / Q000379:methods*