Microalgae are terrific organisms capable of generating value added chemicals with high photosynthetic efficiency. Some key examples include biofuels, bioplastics, pharmaceuticals, and food supplements. Despite the exceptional potential, we are still at the infancy of utilizing these organisms to their full extent mostly due to lack of model organisms with complete genomic make-up. Yet, many groups worldwide, including ours, push efforts to understand the cellular and molecular mechanisms of microalgae and try to funnel this information into environmentally sustainable and economically feasible commodity products. To this extent, we utilize fundamental bioprocess engineering and systems biology tools applied to several novel microalgae and cyanobacteria species for fourth-generation biofuels and novel biochemicals production. Our projects build on understanding the fundamental biochemistry of algal species by coupling with high-throughput "OMICS" characterization tools such as next-generation DNA sequencing, metabolomics, proteomics, and bioinformatics. Most recently, we are investigating the relationship between the expression and interaction of anabolic and catabolic reactions with the goal of maximizing lipid formation in microalgae. This work presents a multidisciplinary approach to extend current understanding beyond disparate parts of lipid biosynthesis in oleaginous non-model microalgae.