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This handbook brings together recent advances in the areas of supply chain optimization, supply chain management, and life-cycle cost analysis of bioenergy. These topics are important for the development and long-term sustainability of the bioenergy industry. The increasing interest in bioenergy has been motivated by its potential to become a key future energy source. The opportunities and challenges that this industry has been facing have been the motivation for a number of optimization-related works on bioenergy. Practitioners and academicians agree that the two major barriers of further investments in this industry are biomass supply uncertainty and costs. The goal of this handbook is to present several cutting-edge developments and tools to help the industry overcome these supply chain and economic challenges. Case studies highlighting the problems faced by investors in the US and Europe illustrate the impact of certain tools in making bioenergy an economically viable energy option.