Cyber-Physical Systems (CPS), the amalgamation of sophisticated sensing, communication, and computing technologies, applied to physical spaces, have become intrinsically linked to society's critical infrastructures. This monograph provides a comprehensive survey of intelligent tools for analysis and design that take fundamental steps towards achieving resilient operation in CPS. The authors investigate the challenges of achieving reliable control and estimation over networks, particularly in the face of uncertainty and resource constraints. The threat of bad actors, formulating realistic models to characterize adversaries as well as systematic tools to detect and respond to attacks is covered before finishing with a brief introduction to the problem of privacy in CPS, providing both measures to describe and techniques to preserve the confidentiality of sensitive information. This monograph is the first comprehensive survey of the increasingly important topic of Cyber-Physical Systems. It provides researchers and students with a concise overview of the state-of-the-art of the field in a systems and control framework.