Research Projects



Biomedical Engineering Research Group applies a systems engineering and process controls approach to manipulating biological reaction networks in the field of Systems Biology. Mathematical modeling and system analysis techniques have been developed to study biological reaction networks for predicting how cells respond to extracellular stimuli via the interaction of hundreds of genes, enzymes, and metabolites. The developed models can be used to identify essential genes and enzymes, investigate pathway interactions, and integrate "omics" data (e.g., genomics or proteomics data). Ongoing projects center on developing models to engineer microorganisms for producing biofuels such as hydrogen and higher alcohol, and to prevent biofilm formation of pathogens that cause severe nosocomial infections in hospitalized patients




Investigating Metabolism of Disease-associated Pathogens in Biofilms

This project is about studying metabolism specific to biofilm formation of pathogens that cause severe nosocomial infections acquired by hospitalized patients. These infections can cause severe pneumonia or complications of the urinary tract, bloodstream, and other parts of the body. The biofilm can enhance the drug resistance of pathogens and allow them to survive and flourish in hostile environments. The aim of the project is to explore how individual pathogens collect into the more harmful biofilm and use the developed mathematical model to predict and prevent that transition. The developed model will be used to identify drug targets that can manipulate biofilm formation.


Engineering Microorganism E.coli for Producing Hydrogen from Waste Streams

This project involves engineering microorganisms for producing hydrogen from waste streams. Research on sustainable biogas production is increasing due to strong public interest in protecting the global climate and a growing demand for independence from scarce fossil energy sources. Hydrogen has tremendous potential because it is the most abundant element in the universe, is renewable, efficient and clean, and is utilized for fuel cells in portable electronics, power plants and internal combustion engines. The goal of this project is to use a systems biology approach to manipulate the metabolism of E.coli to improve hydrogen production such that fermentative hydrogen can be commercialized.


Developing Mathematical Models for Signal Transduction Pathways Involved in Heat Shock

Fever is one of the characteristic elements of the acute-phase response, and it can in turn lead to heat shock that regulate the dynamics of acute phase response proteins. In this project, a mathematical model will be developed to investigate the interaction between heat shock and acute phase response. The model to develop will be used as a systems platform for investigating regulation mechanisms involved in acute phase response.


Mathematical Modeling and Systems Analysis Techniques for Biological Systems

Mathematical modeling and systems analysis techniques will be developed for complex biological systems in order to acquire systems-level insight of their behavior. One on-going research topic is about developing novel sensitivity analysis approaches for investigating the impact of pathway modules on the robustness of signal transduction pathways. Robustness is the key property that assures reliable and immutable signal processing within and among cells in the tissue to variations in the components and environment of the system. This approach can be applied to any signal transduction pathway as well as traditional chemical reaction networks.