Many natural and man-made systems, ranging from thenervous system to power and transportation grids to societies, exhibitdynamic behaviors that evolve over a sparse and complex network. This networked aspect raises significant challenges and opportunities for the identification, analysis, and control of such dynamic behaviors. While some of these challenges emanate from the networked aspect \emph{per se} (such as the sparsity of connections between system components and the interplay between nodal \emph{communication} and network dynamics), various challenges arise from the specific application areas (such as privacy concerns in cyber-physical systems or the need for \emph{scalable} algorithm designs due to the large size of various biological and engineered networks). On the other hand, networked systems provide significant opportunities and allow for performance and robustness levels that are far beyond reach for centralized systems, with examples ranging from the Internet (of Things) to the smart grid and the brain. This dissertation aims to address several of these challenges and harness these opportunities. The dissertation is divided into three parts. In the first part, we study privacy concerns whose resolution is vital for the utility of networked cyber-physical systems. We study the problems of average consensus and convex optimization as two principal distributed computations occurring over networks and design algorithm with rigorous privacy guarantees that provide a \emph{best achievable} tradeoff between network utility and privacy. In the second part, we analyze networks with resource constraints. More specifically, we study three problems of stabilization under communication (bandwidth and latency) limitations in sensing and actuation, optimal time-varying control scheduling problem under limited number of actuators and control energy, and the structure identification problem of under-sensed networks (i.e., networks with latent nodes). Finally in the last part, we focus on the intersection of networked dynamical systems and neuroscience and draw connections between brain network dynamics and two extensively studied but yet not fully understood neuro-cognitive phenomena: goal-driven selective attention and neural oscillations. Using a novel axiomatic approach, we establish these connections in the form of necessary and/or sufficient conditions on the network structure that match the network output trajectories with experimentally observed brain activity
