Over the past decades, a large number of algorithms and methods have been developed in bioinformatics to process and analyze biological data generated in the research of molecular biology. Complex interactions often exist in biological systems and accurate analysis of these interactions is crucial for the understanding of these systems. This book, therefore, provides a new perspective to integrating the interactions in a biological system into the algorithms and methods developed to analyze it, which is supplemental to the more traditional algorithms and methods that most researchers in bioinformatics currently use. Specifically, parameters are introduced into the models for a few biological systems and parameterized methods are developed to study and solve four problems with fundamental importance in bioinformatics. The development and analysis of these methods should help shed some light on this newly emerged and exciting area, and should be especially useful to researchers and professionals in Bioinformatics, Computational Biology and Computer Science, or anyone else who may be considering utilizing parameterized methods for the study and analysis of complex biological systems