Bibliography
Contents |
Generalities
- Hidde de Jong. Journal of Computational Biology. January 1, 2002, 9(1): 67-103. Modeling and Simulation of Genetic Regulatory Systems: A Literature Review
- Claudine Chaouiya et al. Lecture Notes in Computer Science 2004 3099:137-156 Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets
- Steggles et al. Bioinformatics 2007 23(3):336-343 Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach
Logical models
- Luis Mendoza, Ioannis Xenarios. Theoretical Biology and Medical Modelling 2006, 3:13 A method for the generation of standardized qualitative dynamical systems of regulatory networks
- Thieffry D, Thomas R. Pac Symp Biocomput. 1998;:77-88. Qualitative analysis of gene networks
Petri Nets
- Claudine Chaouiya. Bioinformatics 2007 8(4):210-219. Petri net modelling of biological networks
- Oliver Shaw et al. 2004 Applying Petri Nets to Systems Biology using XML Technologies
- Wolgang Reisig 1998. Lectures in Petri Net I: basic models
Pi-Calculus
- Claudio Eccher, Corrado Priami, Bioinformatics December 15 2006, Vol. 22, No. 24: 3075-3081. Design and implementation of a tool for translating SBML into the biochemical stochastic pi-calculus
- Andrew Philips, Concurrent Models in Molecular Biology 2004. A Correct Abstract Machine for the Stochastic Pi-calculus. Paper, Talk
- Mathias John. Electronic Notes in Theoretical Computer Science 2008, 194(3):133-148. A Spatial Extension to the pi-calculus