Since the 1950s, we have developed mature theories of modern control theory and computational neuroscience with almost no interaction between these disciplines. With the advent of computationally efficient nonlinear Kalman filtering techniques, along with improved neuroscience models that provide increasingly accurate reconstruction of dynamics in a variety of important normal and disease states in the brain, the prospects for a synergistic interaction between these fields are now strong. I show recent examples of the use of nonlinear control theory for the assimilation and control of single neuron dynamics, the modulation of oscillatory wave dynamics in brain cortex, a control framework for Parkinsonian dynamics and seizures, and the use of optimized parameter model networks to assimilate complex network data - the `consensus set'.