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Over the past 7 years, the US Department of Energy’s Office of Biological and Environmental Research has funded three Bioenergy Research Centers (BRCs). These centers have developed complementary and collaborative research portfolios that address the key technical and economic challenges in biofuel production from lignocellulosic biomass. All three centers have established a close, productive relationship with DOE’s Joint Genome Institute (JGI). This special issue of Bioenergy Research samples the breadth of basic science and engineering work required to underpin a diverse, sustainable, and robust biofuel industry. In this report, which was collaboratively produced by all three BRCs, we discuss the BRC contributions over their first 7 years to the development of renewable transportation fuels. We also highlight the BRC research published in the current issue and discuss technical challenges in light of recent progress.