Land and other resource constraints currently limit the portion of transportation energy that can be derived from biofuels. Next generation biofuels, such as those made from lignocellulosic or algal biomass feedstocks, could in principle provide a significant portion of transportation fuel in the U.S. and China. Advanced biofuels development and deployment can be accelerated by linking biotechnology to combustion process and exhaust aftertreatment design, optimization and control.