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The number of independent input pins used to control the electrodes in digital microfluidic “biochips” is an important cost-driver in the emerging market place, especially for disposable PCB devices that are being developed for clinical and point-of-care diagnostics. However, most prior work on pin-constrained biochip design considers droplet routing and the assignment of pins to electrodes as independent problems. In this paper, we propose optimization methods to solve the droplet routing and pin-constrained design problems concurrently. First, we formulate the co-optimization problem involving droplet routing and pin-mapping. Next, we present an integer linear programming-based optimization method to solve the droplet-routing and the pin-mapping design problems concurrently. The proposed co-optimization method minimizes the number of control pins. We also present an efficient heuristic approach to tackle the co-optimization problem. These methods overcome a major drawback of a recently proposed method, which leads to infeasible solutions involving conflicts in the mapping of pins to electrodes in different droplet-routing stages. The effectiveness of the proposed co-optimization method is demonstrated for two commercial biochips and an experimental university chip for multiplexed in-vitro diagnostics.