Kyung Hyuk Kim
Acting Assistant Professor
Not accepting graduate students
Office: Foege N410B
My research aims to engineer cellular organisms to function as a biosensor for biotoxins, disease markers, and environmental cues, and to produce useful biomass and pharmaceuticals as a cellular factory. For these aims, I am taking research approaches based on mathematical modeling, computational analysis, and experimental characterization.
RNA-based regulatory networks
Multiple time scale dynamics
Transcription and translation processes
Mutational robustness of cellular systems
My research interest is in characterizing and re-engineering complex biological systems, in particular, gene regulatory and metabolic networks in E. coli cells via mathematical modeling and in vivo experiments. In recent years, gene regulatory systems have been synthetically designed and implemented for both basic research and specific applications to understand and re-engineer functions at the cellular level. There are many important issues that need to be addressed in quantitative (computational and mathematical) ways with respect to re-engineering cellular functions, such as stochasticity, modularity, stability, and scalability. To overcome these issues, I have been pursuing my research by developing mathematical and computational analysis methods, simulating stochastic and deterministic behaviors of the systems, and constructing synthetic genetic networks in E. coli, experimentally verifying model-based theoretical predictions, and finally, proposing new theories based on experimental results. The three major research topics are
- Control of biological noise and its exploitation to design noise-induced cellular phenotypes.
- Degree of modularity in gene regulatory systems and its characterization based on stochastic measurement.
- Characterization of RNA-mediated regulatory networks via live cell imaging based on RNA aptamers.
Ph.D. (Physics), University of Washington, 2006
M.S. (Physics), University of Washington, 2001
B.S. (Physics), Seoul National University, 1998
Senior Fellow, Bioengineering, University of Washington, 2007-2012
P. Meyer, T. Cokelaer, D. Chandran, K. H. Kim, P.-R. Loh, G. Tucker, M. Lipson, B. Berger, C. Kreutz, A. Raue, B. Steiert, J. Timmer, E. Bilal, H. M. Sauro, G. Stolovitzky, J. Saez-Rodriguez. Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach. BMC Systems Biology 8:12 (2014)
K. H. Kim, D. Chandran, and H.M. Sauro. Toward Modularity in Synthetic Biology: Design Patterns and Fan-out. In Heinz Koeppl, et al, Design and Analysis of Bio-molecular Circuits. Springer-Verlag. pp117-138 (2011)