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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?

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up vote 3 down vote accepted

The following papers are a good starting point:

  1. René Thomas, Boolean formalization of genetic control circuits, Journal of Theoretical Biology, Volume 42, Issue 3, December 1973, Pages 563-585 <= A classic paper in the field.

  2. Thieffry D. Dynamical roles of biological regulatory circuits. Brief Bioinform. 2007 Jul;8(4):220-5.

  3. Remy E, Ruet P. From minimal signed circuits to the dynamics of Boolean regulatory networks. Bioinformatics. 2008 Aug 15;24(16):i220-6

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,

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Thank you for the comprehensive list of starting references. – user560 Oct 22 '12 at 23:10

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

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Thank you for the recommendation of Tyson's papers. I find his writing style to be quite clear and descriptive. – user560 Oct 27 '12 at 1:43

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