Systems Biology Modeling of Epistasis

A recent paper by Nagasaki et al. (see below) highlights the use of Petri nets for modeling of biological systems. We have used Petri nets as a discrete dynamical systems modeling tool for carrying out thought experiments (see below) about the complexity of biochemical systems that are consistent with a statistical model that defines an epistatic relationship between two or more DNA sequence variations and disease susceptibility. Our review of this work was just published. See:

Moore JH, Boczko EM, Summar ML. Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human genetics. Mol Genet Metab. 2005 Feb;84(2):104-11. [PubMed]

Nagasaki M, Doi A, Matsuno H, Miyano S. A versatile Petri net based architecture for modelingand simulation of complex biological processes, Genome Inform. 2004;15(1):180-97. [PubMed] [JSBI]

Interested in thought experiments? Here is a great paper on the topic:

Di Paolo et al. Simulation models as opaque thought experiments. In: Bedau et al. Artificial Life VII, pp 497-506, 2000. [CiteSeer] [pdf]