(Selected from over 40 publications)

Full publication list

Computational Systems Biology:

1. J. Liang, Y. Cao, G. Gursoy, H. Naveed, A. Terebus and J. Zhao, Multiscale modeling of cellular epigenetic states: stochasticity in molecular networks, chromatin folding in cell nuclei, and tissue pattern formation of cells. Critical Reviews in Biomedical Engineering In press (2016).

2. Y. Cao, A. Terebus and J. Liang, Modeling stochastic gene regulatory networks using direct solutions of chemical master equation and rare event sampling. Emerging Research in the Analysis and Modeling of Gene Regulatory Networks. IGI Global (2016).

3. Y. Cao, A. Terebus and J. Liang, State space truncation with quantified errors for accurate solutions to discrete Chemical Master Equation. Bulletin of Mathematical Biology. 78:617–661 (2016).

4. Y. Cao, A. Terebus and J. Liang, (2016). Accurate Chemical Master Equation solution method with multi-finite buffers for time-evolving and steady state probability landscapes and first passage times. SIAM: Multiscale Modeling and Simulation. 14(2):923–963 (2016).

5. A. Ismael, W. Tian, N. Waszczak, X. Wang, Y. Cao, D. Suchkov, Eli Bar, M. V. Metodiev, J. Liang, R. Arkowitz, and D. E. Stone. Gβ promotes receptor polarization and chemotropism by inhibiting receptor phosphorylation. Science Signaling. 9(423): ra38. (2016).

6. Sëma Kachalo, Hammad Naveed, Youfang Cao, Jieling Zhao, Jie Liang (2015). Mechanical Model of Geometric Cell and Topological Algorithm for Cell Dynamics from Single-Cell to Formation of Monolayered Tissues with Pattern. PLoS One 10(5):e0126484.

7. Youfang Cao and Jie Liang (2013). Adaptively biased sequential importance sampling for rare events in reaction networks with comparison with exact solutions from finite buffer dCME method. Journal of Chemical Physics 139, 025101.

8. Youfang Cao, Hammad Naveed, Claire Liang and Jie Liang (2013). Modeling spatial population dynamics of stem cell lineage in wound healing and cancerogenesisConf Proc IEEE Eng Med Biol Soc. 5550-5553.

9. Youfang Cao, Claire Liang, Hammad Naveed, Yingzi Li, Meng Chen and Qing Nie (2012). Modeling spatial population dynamics of stem cell lineage in tissue growthConf Proc IEEE Eng Med Biol Soc. 5502–5505.

10. Xiaojun Zhang, Siqing Yue, Huihui Zhong, Weiying Hua, Ruijia Chen, Youfang Cao, Liping Zhao (2011). A diverse bacterial community in an anoxic quinoline-degrading bioreactor determined by using pyrosequencing and clone library analysisApplied Microbiology and Biotechnology 1–10.

11. Chenhong Zhang, Menghui Zhang, Shengyue Wang, Ruijun Han, Youfang Cao, Weiying Hua, Yuejian Mao, Xiaojun Zhang, Xiaoyan Pang, Chaochun Wei, Guoping Zhao, Yan Chen and Liping Zhao (2010). Interactions between gut microbiota, host genetics and diet relevant to development of metabolic syndromes in miceThe ISME Journal 4:232–241.

12. Youfang Cao, Hsiao-Mei Lu and Jie Liang (2010). Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambdaProceedings of the National Academy of Sciences USA, 107(43), 18445–18450.

13. Youfang Cao and Jie Liang (2010). Nonlinear Langevin model with product stochasticity for biological networks: the case of the Schnakenberg model. Journal of Systems Science and Complexity, 23:896–905.

14. Youfang Cao and Jie Liang (2009). Nonlinear coupling for improved stochastic network model: A study of Schnakenberg modelThe Third International Symposium on Optimization and Systems Biology (OSB’09) ORSC & APORC 379–386.

15. Youfang Cao, Hsiao-Mei Lu, and Jie Liang (2008). Stochastic probability landscape model for switching efficiency, robustness, and differential threshold for induction of genetic circuit in phage lambdaConf Proc IEEE Eng Med Biol Soc. 1:611–614.

16. Youfang Cao and Jie Liang (2008). Optimal enumeration of state space of finitely buffered stochastic molecular networks and accurate computation of steady state landscape probability. BMC Systems Biology 2:30. 

17. Youfang Cao and Jie Liang (2007). An optimal algorithm for enumerating state space of stochastic molecular networks with small copy numbers of moleculesConf Proc IEEE Eng Med Biol Soc. 1:4599-4602.

Bioinformatics (2004-2006):

18. Youfang Cao, Shi Liu, Lida Zhang, Jie Qin, Jiang Wang and Kexuan Tang (2006). Prediction of protein structural class with Rough SetsBMC Bioinformatics 7:20.

19. Yidong Zhang, Zeyun Wang, Lida Zhang, Youfang Cao, Danfeng Huang, Kexuan Tang (2006). Molecular cloning and stress-dependent regulation of potassium channel gene in Chinese cabbage (Brassica rapa ssp. Pekinensis). Journal of Plant Physiology 163(9):968–978.

20. Jiang Wang, Lida Zhang, Kaijing Zuo, Hongmei Qian, Youfang Cao, Kexuan Tang (2006). Cloning and Expressional Studies of the Voltage-dependent Anion Channel Gene from Brassica rapa L. Journal of Integrative Plant Biology 48(2):197-203.

21. Jie Qin, Kaijing Zuo, Jingya Zhao, Hua Ling, Youfang Cao, Chengxiang Qiu, Fupeng Li, Xiaofen Sun and Kexuan Tang (2006). Overexpression of GbERF confers alteration of ethylene-responsive gene expression and enhanced resistance to Pseudomonas syringae in transgenic tobacco. Journal of Biosciences 31(2):255–263.

22. Youfang Cao, Lianjie Wang, Kexue Xu, Chunhai Kou, Yulei Zhang, Guifang Wei, Junjian He, Yunfang Wang and Liping Zhao (2005). Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC Bioinformatics 6:190.

23. Jie Qin, Jingya Zhao, Kaijing Zuo, Youfang Cao, Hua Ling, Xiaofen Sun, Kexuan Tang (2004). Isolation and characterization of an ERF-like gene from Gossypium barbadense. Plant Science 167(6):1383–1389.

24. Dongqin Tang, Hongmei Qian, Shunwu Yu, Youfang Cao, Zhihua Liao, Lingxia Zhao, Xiaofen Sun, Danfeng Huang, Kexuan Tang (2004). cDNA cloning and characterization of a new stress-responsive gene BoRS1 from Brassica oleracea var. acephala. Physiologia Plantarum 121(4):578-585.