Modeling methods

• Introduction
  
• Cooperativity
• Deterministic modeling
• Stochastic modeling
• Quantitative model and stability analysis
• C#Sim - algorithmic modeling

Introduction

Cooperativity

Deterministic modeling

Stochastic modeling

Quantitative model and stability analysis

Based on experimental data, we constructed what we refer to as a quantitative model. Please see Quantitative and stability model for details.

C#Sim - algorithmic modeling

References

Andrecut M, Halley JD, Winkler DA, Huang S. (2011) A General Model for Binary Cell Fate Decision Gene Circuits with Degeneracy: Indeterminacy and Switch Behavior in the Absence of Cooperativity. PLoS ONE 6(5): e19358. doi:10.1371/journal.pone.0019358.

Kaern M, Blake WJ, Collins JJ. (2003) The engineering of gene regulatory networks. Annual Review of Biomedical Engineering. 5, 179-206.

Kaern M, Elston TC, Blake WJ, Collins JJ. (2005) Stochasticity in gene expression: from theories to phenotypes. Nature. 6, 451-464.

Ribeiro AS, Lloyd-Price J. (2007) SGN Sim, a Stochastic Genetic Networks Simulator. Bioinformatics. 23 (6): 777-779.

Sauro HM. (2012) Enzyme Kinetics for Systems Biology. Future Skill Software.

Siegal-Gaskins D, Mejia-Guerra MK, Smith GD, Grotewold E. (2011) Emergence of Switch-Like Behavior in a Large Family of Simple Biochemical Networks. PLoS Comput Biol 7(5): e1002039. doi:10.1371/journal.pcbi.1002039.

Widder S, Macía J, Solé R. (2009) Monomeric Bistability and the Role of Autoloops in Gene Regulation. PLoS ONE 4(4): e5399. doi:10.1371/journal.pone.0005399.