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In this paper, a new framework for target tracking in a wireless sensor network using particle filters is proposed. Under this framework, the imperfect nature of the wireless communication channels between sensors and the fusion center along with some physical layer design parameters of the network are incorporated in the tracking algorithm based on particle filters. We call this approach ldquochannel-aware particle filtering.rdquo Channel-aware particle filtering schemes are derived for different wireless channel models and receiver architectures. Furthermore, we derive the posterior Cramer-Rao lower bounds (PCRLBs) for our proposed channel-aware particle filters. Simulation results are presented to demonstrate that the tracking performance of the channel-aware particle filters can reach their theoretical performance bounds even with relatively small number of sensors and they have superior performance compared to channel-unaware particle filters.