This is a short and self-contained introduction to the field of mathematical modeling of
gene-networks in bacteria. As an entry point to the field we focus on the analysis of simple
gene-network dynamics. The notes commence with an introduction to the deterministic modeling of
gene-networks with extensive reference to applicable results coming from dynamical systems
theory. The second part of the notes treats extensively several approaches to the study of
gene-network dynamics in the presence of noise-either arising from low numbers of molecules
involved or due to noise external to the regulatory process. The third and final part of the
notes gives a detailed treatment of three well studied and concrete examples of gene-network
dynamics by considering the lactose operon the tryptophan operon and the lysis-lysogeny
switch. The notes contain an index for easy location of particular topics as well as an
extensive bibliography of the current literature. The target audience of these notes are mainly
graduates students and young researchers with a solid mathematical background (calculus
ordinary differential equations and probability theory at a minimum) as well as with basic
notions of biochemistry cell biology and molecular biology. They are meant to serve as a
readable and brief entry point into a field that is currently highly active and will allow the
reader to grasp the current state of research and so prepare them for defining and tackling new
research problems.
