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We consider cooperative relay networks with multiple stochastically varying end-to-end flows. For such networks, we study throughput optimal network control policies which stabilize the network's queues for any arrival rate in its stability region. In earlier work, we have developed such a policy for a simple four-node parallel relay network. In this paper, we show that this policy can be generalized to a much larger class of cooperative relay networks with various types of two-hop "cooperative links".