Several strains of endophytic fungi have been shown to directly convert lignocellulosic biomass to a wide range of compounds, including ketones, ethers, and terpenoids, that could serve as potential biofuels. This discovery could potentially eliminate an expensive decomposition step required in most conventional lignocellulosic biofuel production processes. Understanding the combustion chemistry of these compounds is key to providing fuel target recommendations for synthetic biologists to optimize and scale-up these fungi metabolic pathways. A coupling of combustion experiments validated by kinetic modeling through automatic mechanism generation is used to screen and recommend viable fuel candidates. Current modeling efforts are targeted towards branched ketones such as di-isopropyl ketone, as well as cyclic ethers such as cineole.