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This paper studies the resource allocation problem for the relay-assisted orthogonal frequency-division multiple-access (OFDMA)-based multiuser system. A new transmission protocol, named hierarchical OFDMA, is proposed to support two-way communications between the base station (BS) and each mobile user (MU) with or without an assisting relay station (RS) in ldquorelayrdquo or ldquodirectrdquo mode, respectively. In particular, the recently discovered two-way relaying technology, based on the principle of network coding, is applied to MUs in relay mode with two possible relay-operations, namely, decode-and-forward (DF) and amplify-and-forward (AF). By applying convex optimization techniques, efficient algorithms are developed for optimal allocation of transmit resources such as power levels, bit rates, and OFDM subcarriers at the BS, RSs, and MUs. Simulation results show that substantial system throughput gains are achievable by the proposed two-way relaying and optimal resource allocation schemes over the traditional one-way relaying and fixed resource allocation schemes for relay-assisted OFDMA-based wireless networks.