A survey on evolutionary analysis in PPI networks

The analysis and application of the evolutionary information, as measured by means of the conservation of protein sequences, using protein-protein interaction (PPI) networks, has become one of the central research areas in systems biology from the last decade. It provides a promising approach for better understanding the evolution of living systems, for inferring relevant biological information about proteins, and for creating powerful protein interaction and function prediction tools. The aim of this survey is to give a general overview of the relevant literature and advances in the analysis and application of evolution in PPI networks. Due to the broad scope and vast literature on this subject, the present overview will focus on a representative selection of research directions and state-of-the-art methods to be used as a solid knowledge background for guiding the development of new hypothesis and methods aiming at the extraction and exploitation of evolutionary information in PPI networks.