The development of autonomous cyber-physical systems (CPS) and advances towards the fifth generation (5G) of wireless technology is promising to revolutionize many industry verticals such as Healthcare, Transportation, Energy, Retail Services, Building Automation, Education, etc., leading to the realization of the smart city paradigm. The Internet of Things (IoT), enables powerful and unprecedented capabilities for intelligent and autonomous operation. We leverage ideas from Network Science, Optimization & Decision Theory, Incentive Mechanism Design, and Data Science/Machine Learning to achieve key design goals, in IoT-enabled urban systems, such as efficiency, security & resilience, and economics.