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The ideas of wireless network coding at the physical layer promise high throughput gains in wireless systems with relays and multi--way traffic flows. This gain can be ascribed to two principles: (1) joint transmission of multiple communication flows and (2) usage of a priori information to cancel the interference. In this paper we use these principles to devise new transmission schemes in wireless cellular systems that feature both users served directly by the base stations (direct users) and users served through relays (relayed users). We present four different schemes for coordinated transmission of uplink and downlink traffic in which one direct and one relayed user are served. These schemes are then used as building blocks in multi--user scenarios, where we present several schemes for scheduling pairs of users for coordinated transmissions. The optimal scheme involves exhaustive search of the best user pair in terms of overall rate. We propose several suboptimal scheduling schemes, which perform closely to the optimal scheme. The numerical results show a substantial increase in the system--level rate with respect to the systems with non--coordinated transmissions.