Project Description

Acting Assistant Professor

Not accepting graduate students
Phone: (206)543-8321
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.

Synthetic biology
Systems biology
Stochastic processes
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

  1. Control of biological noise and its exploitation to design noise-induced cellular phenotypes.
  2. Degree of modularity in gene regulatory systems and its characterization based on stochastic measurement.
  3. 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, H. Qian, and H. M. Sauro. Nonlinear Biochemical Signal Processing via Noise Propagation. Journal of Chemical Physics 139:144108 (2013)

H. M. Sauro and K. H. Kim. It’s an analog world. Nature 497:572 (2013)

K. H. Kim and H. M. Sauro. In Search of Noise-Induced Bimodality. BMC Biology 10:89 (2012)

K. H. Kim and H. M. Sauro. Measuring the degree of modularity in gene regulatory networks from the relaxation of finite perturbations. Proc. IEEE Conf. on Decision and Control (Invited Paper) (2012)

W. B. Copeland, D. Chandran, B. A. Bartley, M. Galdzicki, K. H. Kim, C. Maranas, S. C. Sleight, and H. M. Sauro. Computational Tools for Metabolic Engineering. Metabolic Engineering 14:270-280 (2012)

K. H. Kim, and H. M. Sauro.  Adjusting Phenotypes by Noise Control. PLoS Computational Biology 8:e1002344 (2012)

K. H. Kim, and H. M. Sauro. Measuring Retroactivity from Noise in Gene Regulatory Networks. Biophysical Journal 100:1167-1177 (2011)

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)

K. H. Kim, and H. M. Sauro. Fan-out in Gene Regulatory Networks. Journal of Biological Engineering 4:16 (2010)

K. H. Kim, and H. M. Sauro. Sensitivity Summation Theorems for Stochastic Biochemical Reaction Systems. Mathematical Biosciences 226:109 (2010)

K. H. Kim, and H. M. Sauro. Stochastic Control Analysis for Biochemical Reaction Systems. arXiv:0904.3124 [q-bio.QM] (2009)

K. H. Kim and M. den Nijs. Dynamic Screening in a Two-species Asymmetric Exclusion Process. Phys. Rev. E 76, 021107 (2007)

K. H. Kim and H. Qian. Fluctuation Theorems of a Molecular Refrigerator. Phys. Rev. E 75, 022102 (2007)

K. H. Kim and H. Qian. Entropy Production of Brownian Macromolecules with Inertia. Phys. Rev. Lett. 93, 120602 (2004)

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