  Modelling gene regulatory networks not only requires a thorough understanding
of the biological system depicted but also the ability to accurately represent
this system from a mathematical perspective. Throughout this chapter, we aim to
familiarise the reader with the biological processes and molecular factors at
play in the process of gene expression regulation.We first describe the
different interactions controlling each step of the expression process, from
transcription to mRNA and protein decay. In the second section, we provide
statistical tools to accurately represent this biological complexity in the
form of mathematical models. Amongst other considerations, we discuss the
topological properties of biological networks, the application of deterministic
and stochastic frameworks and the quantitative modelling of regulation. We
particularly focus on the use of such models for the simulation of expression
data that can serve as a benchmark for the testing of network inference
algorithms.
