Current approaches to gene regulatory network modelling

Many different approaches have been developed to model and simulate gene regulatory networks.
We proposed the following categories for gene regulatory network models: network parts lists,
network topology models, network control logic models, and dynamic models. Here we will
describe some examples for each of these categories. We will study the topology of gene
regulatory networks in yeast in more detail, comparing a direct network derived from transcription
factor binding data and an indirect network derived from genome-wide expression data in mutants.
Regarding the network dynamics we briefly describe discrete and continuous approaches to
network modelling, then describe a hybrid model called Finite State Linear Model and demonstrate
that some simple network dynamics can be simulated in this model.


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