Three topics concerning the coordination in supply chains are discussed in the book. Firstly, we consider the integration of production and transportation logistics at the operational level. Our method allows the optimization model to reconcile the viewpoints from transportation and production planning. Secondly, an auction theoretic model for production coordination is discussed. Motivated by the increasing needs to coordinate diverse decision processes and systems, we investigate an auction-theoretic mechanism for production coordination in a supply chain. Our efforts focuses on an iterative auction mechanism wherein agents compete based on their local utilities, announced conflict pricing, and production targets. Thirdly, a bargaining model for the supplier-buyer coordination is introduced. We show that in subgame perfect equilibrium, the channel coordinated optimal quantity is also optimal for the players, but the players must negotiate the surplus generated by the contract in a bargaining game. The model allows us to predict the negotiation outcome between a pair of buyer and supplier.