I am pleased to offer the research community my second book-length contribution to the field of bioinformatics. My first book, Advanced Analysis of Gene Expression Microarray Data, was published in 2006 by World Scientific as part of its Science, Engineering, and Biology Informatics (SEBI) series. I first became involved in the study of bioinformatics in 1998 and, over the ensuing decade, have been struck by the enormous quantity of data being generated and the need for effective approaches to its analysis.

The analysis of protein-protein interactions (PPIs) is fundamental to the understanding of cellular organizations, processes, and functions. It has been observed that proteins seldom act as single isolated species in the performance of their functions; rather, proteins involved in the same cellular processes often interact with each other. Therefore, the functions of uncharacterized proteins can be predicted through comparison with the interactions of similar known proteins. A detailed examination of a PPI network can thus yield significant new insights into protein functions. These interactions have traditionally been examined via intensive small-scale investigations of a small set of proteins of interest, each yielding information about a limited number of PPIs. The existing databases of PPIs have been compiled from such small-scale screens, presented in individual research papers. Because these data were subject to stringent controls and evaluation in the peer-review process, they can be considered to be fairly reliable. However, each experiment observes only a few interactions and yields a data set of very limited size. Recent large-scale investigations of PPIs using such techniques as two-hybrid systems, mass spectrometry, and protein microarrays have enriched the available protein interaction data and facilitated the construction of integrated PPI networks.