The goal of this course is to give an introduction to mathematical and algorithmic methods for the analysis of molecular networks in systems biology, which have numerous applications in biology, medicine and biotechnology. Molecular networks describe interactions between molecules in a cell and may contain several thousands of nodes and (hyper-)arcs.

We will focus on methods from discrete mathematics (polyhedra, matroids, Boolean functions, linear and integer optimization) for the analysis of metabolic and regulatory networks. We first study flux polyhedra of metabolic networks at steady state. Then we consider dynamic processes, cellular resource allocation and regulation/control of cellular processes. This leads to various static and dynamic optimization problems that can be solved by methods from linear and mixed-integer linear programming.