Before revision: Motivation: Recent advances in experimental techniques have generated large amounts of protein interaction data, producing networks containing large numbers of cellular proteins. Mathematically sound and robust foundations are needed for extensive, context-specific exploration of networks, integrating knowledge from different specializations and facilitating biological discovery.
After revision: In our previous publication, a framework for information flow in interaction networks based on random walks with damping was formulated with two fundamental modes: emitting and absorbing. While many other network analysis methods based on random walks or equivalent notions have been developed before and after our earlier work, one can show that they can all be mapped to one of the two modes. In addition to these two fundamental modes, a major strength of our earlier formalism was its accommodation of context-specific exploration of networks, integrating knowledge from different specializations and facilitating biological discovery.