Modularity in gene regulatory networks
 Applied the engineering concept of fanout to gene regulatory networks for quantifying the degree of modularity (J. Biol. Eng, IEEE CDC 2012).
 Proposed an experimental method for measuring fanout 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 fanout 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 HIV1 long terminal repeat (LTR) promoter activity (future work).
Nonlinearity in gene regulatory networks  Novel way to control celltocell variability (in the aim to design noiseinduced phenotypes in E. coli; Journal of Chemical Physics 2013) (in progress).
 Interaction between stochasticity and nonlinearity (Hill coefficient) (in progress).
Metabolic networks 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).
 Intercellular interactions and cellular communities: mathematical modeling and analysis of cooperative synthetic yeast strains in collaboration with Prof. Shou at the Fred Hutchinson Cancer Research Center (reference).
Nonequilibrium statistical physics (Jarzynski equality and fluctuation theorem; Ph.D. thesis) Extended the Jarzynski equality and the fluctuation theorems for feedback control systems (Physical Review E, Physical Review Letters)
 Onedimension stochastic flow (twospecies asymmetric exclusion process) and its universal scaling behaviors (critical phenomena) and phase transition (Phys. Rev. E)
