Modularity
in gene regulatory networks

  • Applied the engineering concept of fan-out to gene regulatory networks for quantifying the degree of modularity (J. Biol. EngIEEE CDC 2012).
  • Proposed an experimental method for measuring fan-out and retroactivity based on gene expression noise (Biophys. JIEEE 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 BiologyMathematical 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).


Metabolic networks

  • Extended the metabolic control analysis (MCA) to the stochastic regime (PLoS Computational BiologyMathematical 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 EPhysical Review Letters)
  • One-dimension stochastic flow (two-species asymmetric exclusion process) and its universal scaling behaviors (critical phenomena) and phase transition (Phys. Rev. E)