An essential idea in the area of Systems Biology is that a good understanding of interactions between components is crucial for developing deep knowledge of the functioning of the system as a whole. Network analysis is an approach uniquely suited to uncover patterns and organizing principles in a wide variety of complex systems. In this chapter, we will give a detailed description of central network concepts and their algorithmic implementation, and demonstrate how they may be applied on two biological networks: the protein-interaction network of Mus musculus and the reconstructed genome-scale metabolic network of the bacterium Yersinia pestis.