Chapter 7: Discrete dynamic models: Boolean networks #

Modelling and analysis of gene regulatory networks
Karlebach and Shamir (2008) Nature Reviews Molecular Cell Biology

An excellent review detailing multiple methods for modelling gene regulatory networks.

Boolean network simulations for life scientists
Albert et al. (2008) Source Code for Biology and Medicine

Describes the BooleanNet tool.

Boolean Modeling of Genetic Regulatory Networks
Albert et al. (2004) Lecture Notes in Physics

A classic paper on modelling genetic regulatory networks, with application to Drosophila melanogaster segment polarity genes.

Robustness and fragility of Boolean models for genetic regulatory networks
Chaves et al. (2005) Journal of Theoretical Biology

Integrates stochasticity nicely, into Boolean modelling.

Algebraic Models of Biochemical Networks
Laubenbacher and Jarrah (2009) Methods in Enzymology

Discusses generalisations of Boolean networks (algebraic models).

Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle
Faure et al. (2006) Bioinformatics

A lucid paper, explaining how the cell cycle can be well-modelled using Boolean networks.

BooleSim

BooleSim tool, which can be tinkered around with just a web browser.

BooleanNet

BooleanNet, a Python-based tool for Boolean Network analysis.

Predicting Essential Components of Signal Transduction Networks: A Dynamic Model of Guard Cell Abscisic Acid Signaling
Li et al. (2006) PLoS Biology

Another excellent illustration of using Boolean networks to model cellular signalling/regulation.