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Youfang Cao

Postdoc Research Associate
Theoretical Biology and Biophysics (T-6) and Center for Nonlinear Studies (CNLS)

Stochastic multiscale modeling of complex biological networks.

Youfang Cao

Office: TA-3, Bldg 1690, Room 142
Mail Stop: B258
Phone: (505) 667-7135
Fax: (505) 665-2659
home page

 Educational Background/Employment:
  • Full CV
  • B.S. (1999) Computational Mathematics, Shanxi University, China
  • M.S. (2002) Biochemistry and Molecular Biology (Bioinformatics), Shanxi University, China
  • Ph.D. (2011) Biomedical Engineering, Shanghai Jiao Tong University
  • Employment:
    • 2002-2006 Assistant Investigator, College of Agriculture and Biology, Shanghai Jiao Tong University
    • 2006-2011 Assistant Investigator, Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University
    • 2012-2015 Research Assistant Professor, Department of Bioengineering, University of Illinois at Chicago
  • Professional Training:
    • 2011-2012 Postdoc Research Associate at Department of Bioengineering, University of Illinois at Chicago
    • 2015-present Postdoc Research Associate at Theoretical Biology and Biophysics (T-6) and Center for Nonlinear Studies (CNLS), Los Alamos National Laboratory

Research Interests:

  • HIV infection and immune system dynamics
  • Stochastic control of HIV latency and activation
  • Multiscale complex biological networks in immune responses and tissue pattern formation
  • Developing modeling methods for stochastic biological networks: discrete Chemical Master Equation
  • Stochastic control of genetic circuits in cell decision making

Selected Recent Publications:

  1. Full publication list
  2. J. B. Honeycutt, W.O. Thayer, C. E. Baker, R.M. Ribeiro, S.M. Lada, Youfang Cao, R.A. Cleary, M. G. Hudgens, D.D. Richman, and J. V. Garcia, HIV persistence in tissue macrophages of humanized myeloid only mice during antiretroviral therapy. Nature Medicine, Accepted. (2017).
  3. Jieling Zhao*, Youfang Cao*, Luisa A. DiPietro, and Jie Liang, Dynamic cellular finite element method for modeling large scale cell migration and proliferation under the control of mechanical and biochemical cues: A study of reepithelialization. Journal of the Royal Society Interface, Accepted. (2017).
  4. 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).
  5. 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).
  6. Y. Cao, A. Terebus and J. Liang, Accurate Chemical Master Equation solution method with multi-finite buffers. SIAM: Multiscale Modeling and Simulation. 14(2):923–963 (2016).
  7. 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).
  8. 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 43(4):323-346 (2015).
  9. S. Kachalo, H. Naveed, Y. Cao, J. Zhao, and J. Liang. 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. (2015).
  10. Y. Cao and J. Liang. 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. (2013).
  11. Y. Cao, H.-M. Lu and J. Liang. Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda. Proceedings of the National Academy of Sciences USA. 107(43), 18445–18450. (2010).
  12. Y. Cao and J. Liang. Optimal enumeration of state space of finitely buffered stochastic molecular networks and accurate computation of steady state landscape probability. BMC Systems Biology 2:30. (2008).
  13. Y. Cao, S. Liu, L. Zhang, J. Qin, J. Wang and K. Tang. Prediction of protein structural class with Rough Sets. BMC Bioinformatics 7:20. (2006).
  14. Y. Cao, L. Wang, K. Xu, C. Kou, Y. Zhang, G. Wei, J. He, Y. Wang and L. Zhao. Information theory-based algorithm for in silico prediction of PCR products with whole genomic sequences as templates. BMC Bioinformatics 6:190. (2005).
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