Modeling Biological Reaction Networks for Therapeutics.

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Cells respond to environmental signals, make stochastic decisions, and cooperate with one another to control and perform tissue functions. At the heart of cell and tissue behavior controls are networks of biochemical reactions occurring at both intracellular and extracellular compartments. Dysregulated reactions in these networks cause diseases and developmental defects in human. By targeting key reactions in these networks with drugs, we can control cell and tissue behavior, thereby treat and cure diseases. However, understanding the control mechanism and identifying key reactions from these complex networks are challenging tasks. Innovative mathematical methods coupled to biological theories and state-of-the-art computational algorithms and tools are needed. My research goal is to develop those methods and apply them to model biological reaction networks and understand control mechanisms and identify key reactions to design better therapeutic strategies for human diseases. My current focus is centered on HIV infection and immune responses.

In collaboration with Dr. Jie Liang at the University of Illinois at Chicago, I have developed an innovative mathematical and computational methods, namely the Accurate Chemical Master Equation (ACME) method for accurately modeling cell fate determination controlled by stochastic and multiscale intracellular biological reaction networks. In collaboration with Dr. Alan Perelson at the Los Alamos National Laboratory, I have applied the ACME to characterize the control of HIV latency, and identified novel therapeutic targets for reversing HIV latency, and developed nonlinear viral dynamic models to characterize the role of immune response in controlling viral infections. In collaboration Dr. Jie Liang and Dr. Luisa DiPietro at the Center for Wound Healing and Tissue Regeneration at the University of Illinois at Chicago, I have developed multiscale spatio-temporal models to simulate the emergent tissue pattern formation during wound healing.