I've read a recent Nature Methods paper by Moon T.S. et al, in which a synthetic genetic circuit consisting of layered logic gates was created. For example, the paper, a circuit is modelled in Figure 4a. How is this circuit computationally modelled? Can you refer me to any graduate level texts on the subject?
The following papers are a good starting point:
You can also have a look at Computational Methods in Systems Biology, International Conference CMSB 2007, Edinburgh, Scotland, September 20-21, 2007. Proceedings, specifically the chapter "Decision diagrams for the representation and analysis of logical models of genetic networks" by A. Naldi, D. Thieffry and C. Chaouiya.
I would also suggest Uri Alon's An Introduction to Systems Biology.
Personally, I learned using JJ Tyson's body of work and I would particullary recommend Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell