Youfang Cao, Ph.D.Click here for my full CV in pdf
Visiting Research Assistant Professor
youfang AT uic DOT edu
Bioengineering Bioinformatics M/C 563
W164H, 835 S. Wolcott
Chicago, IL 60612-7340
1. Developing methods for modeling stochastic biochemical reaction systems.
Stochasticity plays critical roles in the forming of many interesting behaviors of biological systems, however, classical chemical kinetics modeling approaches based on ordinary differential equations are usually broken down in modeling these problems since they do not involve the stochasticity. We devote to develop or improve modeling methods based on chemical master equation, Langevin equation and ordinary differential equations for more efficient and/or more accurate modeling of stochastic systems.
2. Stochastic modelling of biochemical systems.
We also apply our methods to various biological systems, where stochasticity is usually significant and play important roles in the function of cellular systems.
Youfang Cao Theoretical modeling methods of stochastic biological networks and their applications (Chinese). PhD Dissertation, Shanghai Jiao Tong University Dec. 2010
Youfang Cao, Hsiao-Mei Lu and Jie Liang. Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proceedings of the National Academy of Sciences USA October 26, 2010 vol. 107 no. 43 18445-18450 Supporting Information
Youfang Cao and Jie Liang. Nonlinear Langevin model with product stochasticity for biological networks: the case of the Schnakenberg model. Journal of Systems Science and Complexity 2010, 23:896-905.
Youfang Cao and Jie Liang, Nonlinear coupling for improved stochastic network model: A study of Schnakenberg model. The Third International Symposium on Optimization and Systems Biology (OSB’09) ORSC && APORC 2009, 379-386.
Youfang Cao and Jie Liang, Optimal enumeration of state space of finitely buffered stochastic molecular networks and accurate computation of steady state landscape probability BMC Systems Biology 2008, 2:30. doi:10.1186/1752-0509-2-30.
Youfang Cao, Hsiao-Mei Lu, and Jie Liang, Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambda. Conf Proc IEEE Eng Med Biol Soc. 2008;1:611-4.
Youfang Cao and Jie Liang. An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of molecules. Conf Proc IEEE Eng Med Biol Soc. 2007, 1:4599-602.
Youfang Cao, Shi Liu, et al., Prediction of protein structural class with Rough Sets. BMC Bioinformatics 2006, 7:20. doi:10.1186/1471-2105-7-20
Youfang Cao, Lianjie Wang, et al., Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC Bioinformatics 2005, 6:190. doi:10.1186/1471-2105-6-190
Computer Culture, Flavor and Tools:
Working in Linux and editing with Vim;
Programming in C++/C, Perl, R, Fortran and Matlab;
Writting papers in LaTeX.
State space enumeration and calculation of steady state probability landscape of stochastic biological systems.
SPCR, a program for simulating polymerase chain reactions (PCR) and predicting its products.
Last updated: Sep 8, 2011