About the Lab

 

Systems Biology, Synthetic Biology and Metabolic Engineering for Sustainability

Recent advances in experimental and computational technologies have enabled the detailed characterization of biological systems. In particular, the molecular components of these systems including the list of genes, proteins they encode, and compounds that interact with these proteins can be determined. This availability of tools to analyze system-wide changes at the level of the genes, proteins, and metabolites has created significant opportunities to understand cellular functions resulting in the emergence of systems biology. The goal of this nascent discipline is a quantitative characterization of biological systems at multiple scales from genes to physiology and to ultimately design processes in a systematic way for applications in industrial and medical biotechnology (e.g. synthetic biology, metabolic engineering, bioprocess optimization and control). The research interests of our group involve the development and utilization of dynamic mathematical models of biological systems for improved design, optimization and control.

In this process (see the figure above), the first step is to determine the list of components in the system. This is usually the list of genes, protein and other biological entities. Once this is accomplished, the next stage is to identify the interactions among the network components and the nature of their interactions (chemical/physical interaction etc…). Once the components and the interactions have been identified, and additional biological data on the strength of interaction, the next step is the development of a qualitative/quantitative model that is a predictive model and is robust to parametric changes. The model that represents most of the biological knowledge and has been validated can be used for design or for hypothesis-based discovery that leads to further model refinement. Scalable models of biological networks across different organisms will be crucial to optimize these systems in industrial biotechnology and to understand the behaviour and evolution of biological systems and their response to multiple environmental cues. Such fundamental understanding forms the basis for the design of therapeutic strategies in biomedical engineering.

The potential for this approach for design and discovery of biological processes is reflected in the diversity of the research projects in the group ranging from microbial fuel cells, biofuels, biochemicals, bioremediation and the analysis of metabolic interactions in human brain, cancer and diabetes, where we bring to bear the group’s expertise in modeling and analysis of metabolism on designing innovative solutions for these outstanding challenges.