Modularity in gene regulatory networks
- Applied the engineering concept of fan-out to gene regulatory networks for quantifying the degree of modularity (J. Biol. Eng, IEEE CDC 2012).
- Proposed an experimental method for measuring fan-out and retroactivity based on gene expression noise (Biophys. J, IEEE CDC 2012 ).
- Gene circuit analysis by mapping between gene regulatory networks and analog electrical circuits (J. Biol. Eng).
- Experimental verification of fan-out and retroactivity (in progress)
Stochasticity in gene regulatory networks
- "Stochastic Control Analysis" (SCA): Developed a sensitivity analysis method for adjusting phenotypes by noise control (PLoS Computational Biology, Mathematical Biosciences).
- SCA application to noise control in E. coli (in progress).
- Analyzed noise propagation and its effect on system sensitivities in reaction networks (Journal of Chemical Physics 2013).
- Application of SCA to real biological systems such as stochastic switching in the HIV-1 long terminal repeat (LTR) promoter activity (future work).
Nonlinearity in gene regulatory networks
- Novel way to control cell-to-cell variability (in the aim to design noise-induced phenotypes in E. coli; Journal of Chemical Physics 2013) (in progress).
- Interaction between stochasticity and nonlinearity (Hill coefficient) (in progress).
- Extended the metabolic control analysis (MCA) to the stochastic regime (PLoS Computational Biology, Mathematical Biosciences).
- Visualization of signal propagation in biological networks.
- Metabolic flux optimization under the constraint of the total enzyme mass (Bio.
Circuit Stability in gene regulatory networks
- Circuit stability in synthetic genetic circuits: designing fitness landscapes for gene regulatory networks (future work).
- Inter-cellular interactions and cellular communities: mathematical modeling and analysis of co-operative synthetic yeast strains in collaboration with Prof. Shou at the Fred Hutchinson Cancer Research Center (reference).
Non-equilibrium statistical physics (Jarzynski equality and fluctuation theorem; Ph.D. thesis)
- Extended the Jarzynski equality and the fluctuation theorems for feed-back control systems (Physical Review E, Physical Review Letters)
- One-dimension stochastic flow (two-species asymmetric exclusion process) and its universal scaling behaviors (critical phenomena) and phase transition (Phys. Rev. E)