Kathy Chen

Retired 4724 Knights Arm Drive Durham, NC 27707 Email: kchen@vt.edu
chuankaichen@gmail.com
Tel: 540-553-4673 or 919-928-3906

Link to Profile in LinkedIn
Profile in ResearchGate
Previous position at VT: Research Scientist, 1994-2015.

Research Pages: Tyson Lab Budding Yeast Cell Cycle Model Generic Cell Cycle Model JigCell

Current Research Interests

The control of cell division cycle in eukaryotes is a complicated and vital process. The molecular network is known in most detail in budding yeast among all eukaryotes, and recently a consensus picture has emerged from such studies. To know if this picture gives a consistent result against all available experimental data, we build a mathematical model of the yeast cell cycle control.

The model successfully describes the phenotypes of more than 100 mutants with deletions or over-expressions of the basic genetic components in various combinations. The broad ranging success of the model confirms the basic accuracy of the consensus mechanism, although some modifications are needed.

As experimental characterization of cell-cycle control continues to grow, the model must grow as well. We are refining the model to describe more accurately the roles of Cdc5 polo kinase, FEAR pathway and the MEN pathway in driving Cdc14 release and mitotic exit. Also the regulation of Start transition is refined to take into account of the effect Whi5 (its phosphorylation state and its nuclear localization) on SBF activation.

Education

Ph.D. 1979 Purdue University, Developmental Biology.
M.S. 1971 University of Maryland, Biophysics.
B.S. 1966 National Taiwan University, Taipei, Taiwan, Physics.

Publications

Laomettachit, T., Chen, K.C., Baumann, W.T., and Tyson, J.J. (2016). A model of yeast cell-cycle regulation based on a standard component modeling strategy for protein regulatory networks. PLoS One 11 (5): e0153738.
[Abstract] [Article]
Laomettachit, T., Chen, K.C., Baumann, W.T., and Tyson, J.J. (2016). A model of yeast cell-cycle regulation based on a standard component modeling strategy for protein regulatory networks. PLoS One 11 (5): e0153738.
[Abstract] [Article]
Adames, N.R., Schuck, P.L., Chen, K.C., Murali, T.M., Tyson, J.J., and Peccoud, J. (2015). Experimental testing of a new integrated model of the budding yeast Start transition. Mol. Biol. Cell 26:3966-3984.
[Abstract] [Article]
Kraikivski, P., Chen, K.C., Laomettachit, T., Murali, T.M., and Tyson, J.J. (2015). From START to FINISH: computational analysis of cell cycle control in budding yeast. NPJ Syst. Biol. Appl. 1: 15016.
[Abstract] [Article]
Oguz, C., Teeraphan, L., Chen, K.C., Watson, L.T., Baumann, W.T., and Tyson, J.J. (2013). Optimization and model reduction in the high dimensional parameter space of a budding yeast cell cycle model. BMC Systems Biology 7:53.
[Abstract] [Article]
Poirel, C.L., Rodrigues, R.R., Chen, K.C., Tyson, J.J., and Murali, T.M. (2013). Top-down network analysis to drive bottom-up modeling of physiological processes. J Comput Biol 20: 409-418.
[Abstract] [Article]
Ball, D.A., Ahn, T.-H., Wang, P., Chen, K.C., Cao, Y., Tyson, J.J., Peccoud, J., and Baumann, W.T. (2011). Stochastic exit from mitosis in budding yeast: model predictions and experimental observations. Cell Cycle 10: 999-1009.
[Abstract]
Ball, D.A., Marehand, J., Poulet, M., Baumann, W.T., Chen, K.C., Tyson, J.J., and Peccoud, J. (2011). Oscillatory dynamics of cell cycle proteins in single yeast cells analyzed by imaging cytometry. PLoS ONE 5, e26272.
[Abstract] [Article]
Panning, T.D., Watson, L.T., Allen, N.A., Chen, K.C., Shaffer, C.A., and Tyson, J.J. (2008). Deterministic parallel global parameter estimation for a model of the budding yeast cell cycle. J Glob Optim 40:719-738.
[Abstract] [Article]
Allen, N. A., Chen, K. C., Shaffer, C. A., Tyson, J. J. and Watson, L. T. (2006). Computer evaluation of network dynamics models with application to cell cycle control in budding yeast. IEE Proc Syst Biol (Stevenage) 153:13-21.
[Abstract]
Csikasz-Nagy, A., Battogtokh, D., Chen, K. C., Novak, B. and Tyson, J. J. (2006). Analysis of a generic model of eukaryotic cell cycle regulation. Biophys. J. 90:4361-4379.
[Abstract] [Article]
Cross, F.R., Schroeder, L., Kruse, M. and Chen, K.C. (2005). Quantitative characterization of a mitotic cyclin threshold regulating exit from mitosis. Mol. Biol. Cell 16:2129-2138.
[Abstract] [Article]
Novak, B., Chen, K.C. and Tyson, J.J. (2005). Systems biology of the yeast cell cycle engine. In Topics in Current Genetics, Vol. 13. Systems Biology: Definitions and Perspectives. L. Alberghina and H. V. Westerhoff eds. (Springer, Berlin /Heidelberg) pp. 305-324.
[Abstract]
Chen, K.C., Calzone, L., Csikasz-Nagy, A., Cross, F.R., Novak, B. and Tyson, J.J. (2004). Integrative analysis of cell cycle control in budding yeast. Mol. Biol. Cell 15:3841-3862.
[Abstract] [Article]
Thornton, B. R., Chen, K.C., Cross, F.R., Tyson, J.J., and Toczyski, D.P. (2004). Cycling without the cyclosome: modeling a yeast strain lacking the APC. Cell Cycle 3: 629-633.
[Abstract] [Article]
Allen, N.A., Calzone, L., Chen, K.C., Ciliberto, A., Ramakrishnan, N., Shaffer, C.A., Sible, J.C., Tyson, J.J., Vass, M.T., Watson, L.T. and Zwolak, J.W. (2003). Modeling regulatory networks at Virginia Tech. OMICS 7:285-299.
[Abstract] [Article]
Sha, W., Moore, J., Chen, K., Lassaletta, A.D., Yi, C.-S., Tyson, J.J. and Sible, J.C. (2003). Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proc. Natl. Acad. Sci. USA 100:975-980.
[Abstract] [Article]
Tyson, J.J., Chen, K.C. and Novak, B. (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15:221-231.
[Abstract] [Article]
Tyson, J.J., Chen, K. and Novak, B. (2001). Network dynamics and cell physiology. Nat. Rev. Mol. Cell Biol. 2:908-916.
[Abstract] [Article]
Chen, K.C., Csikasz-Nagy, A., Gyorffy, B., Val, J., Novak, B. and Tyson, J.J. (2000). Kinetic analysis of a molecular model of the budding yeast cell cycle. Mol. Biol. Cell 11:369-391.
[Abstract] [Article]
Tyson, J.J., Borisuk, M.T., Chen, K., and Novak, B. (2000). Analysis of complex dynamics in cell cycle regulation, in Computational Modeling of Genetic and Biochemical Networks, (J.M. Bower, and H. Bolouri,Eds), pp. 287-305 (Cambridge, MA, MIT Press).
[Abstract]
Novak, B., Csikasz-Nagy, A., Gyorffy, B., Chen, K. and Tyson, J.J. (1998). Mathematical model of the fission yeast cell cycle with checkpoint controls at the G1/S, G2/M and metaphase/anaphase transitions Biophys. Chem. 72:185-200.
[Abstract] [Article]
Tyson, J.J., Chen, K.C. and Novak, B. (1997). The eukaryotic cell cycle: molecules, mechanisms and mathematical models, in Case Studies in Mathematical Modeling: Ecology, Physiology and Cell Biology. (H. G. Othmer, F. R. Adler, M. A. Lewis and J. C. Dallon Eds.) pp. 127-147 (Prentice Hall, Upper Saddle River).
[Abstract]
Tyson, J.J., Novak, B., Odell, G.M., Chen, K. and Thron, C.D. (1996). Chemical kinetic theory: understanding cell-cycle regulation. Trends Biochem. Sci. 21:89-96.
[Abstract] [Article]
Tyson, J. J., Novak, B., Chen, K. and Val, J. (1995). Checkpoints in the cell cycle from a modeler's perspective. Prog. Cell Cycle Res.1:1-8.
[Abstract]
Tyson, J.J., Chen, K.C., Lederman M., and Bates, R.C. (1990). Analysis of the kinetic hairpin transfer model for parvoviral DNA replication. J. Theor. Biol. 144:155-169.
[Abstract] [Article]
Chen, K.C., Tyson, J.J., Lederman, M., Stout E.R., and Bates, R.C. (1989). A kinetic hairpin transfer model for parvoviral DNA replication. J. Molec. Biol. 208:283-296.
[Abstract] [Article]
Diffoot, N., Shull, B. C., Chen, K. C., Stout, E. R., Lederman, M. and Bates, R. C. (1989). Identical ends are not required for the equal encapsidation of plus- and minus- strand parvovirus LuIII DNA. J. Virology 63:3180-3184.
[Abstract] [Article]
Chen, K. C., Shull, B. C., Lederman, M., Stout, E. R. and Bates, R. C. (1988). Analysis of the termini of the DNA of bovine parvovirus: demonstration of sequence inversion at the left terminus and its implication for the replication model. J. Virology 62:3807-3813.
[Abstract] [Article]
Shull, B. C., Chen, K. C., Lederman, M., Stout, E. R. and Bates, R. C. (1988). Genomic clones of bovine parvovirus: construction and effect of deletions and terminal sequence inversions on infectivity. J. Virology 62:417-426.
[Abstract] [Article]
Chen, K. C., Shull, B. C., Moses, E. A., Lederman, M., Stout, E. R., and Bates, R. C. (1986). Complete nucleotide sequence and genome organization of bovine parvovirus. J. Virology 60:1085-1097.
[Abstract] [Article]
Chen, K. C., Chen, J. S., and Johnson, J. L. (1986). Structural features of multiple nifH-like sequences and very biased codon usage in nitrogenase genes of Clostridium pasteurianum. J. Bacteriol. 166:162-172.
[Abstract] [Article]

Personal

Kathy retires with her husband Jiann-Shin in Durham, NC. She has one son Eric and two grandchildren Avery and Everett. Eric is practicing Family Medicine (with specialty in Obstetrics) in Carilion Clinics in Roanoke, VA. Avery was born on June 8, 2009, and Everett on January 20, 2014. Kathy and Jiann-Shin are proud and doting grandparents. Kathy's hobbies are cooking, gardening, working on photo albums, and reading about nature and animal behaviors.