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We propose a novel subchannel and transmission power allocation scheme for multi-cell orthogonal frequency-division multiple access (OFDMA) networks with cognitive radio (CR) functionality. The multi-cell CR-OFDMA network not only has to control the interference to the primary users (PUs) but also has to coordinate inter-cell interference in itself. The proposed scheme allocates the subchannels to the cells in a way to maximize the system capacity, while at the same time limiting the transmission power on the subchannels on which the PUs are active. We formulate this joint subchannel and transmission power allocation problem as an optimization problem. To efficiently solve the problem, we divide it into multiple subproblems by using the dual decomposition method, and present the algorithms to solve these subproblems. The resulting scheme efficiently allocates the subchannels and the transmission power in a distributed way. The simulation results show that the proposed scheme provides significant improvement over the traditional fixed subchannel allocation scheme in terms of system throughput.