This book summarizes the existing applications of pathway analysis and investigates new opportunities for drug development. It covers traditional computational methods and software for pathway analysis microarray, proteomics, and metabolomics. In addition, the book includes other aspects relevant to the pharmaceutical industry: 1) pathway reconstruction of diseases and toxic states; 2) pathway analysis for selection of drug targets, lead compound validation, and prediction of compound Absorption Distribution Metabolism Excretion and Toxicology (ADMET) properties; 3) dynamic modeling of drug responses; and 4) pathway analysis for design of selective drug mixtures and promiscuous drugs.