Nonequilibrium Model for Yeast Cell Cycle

  • Yuping Zhang
  • Huan Yu
  • Minghua Deng
  • Minping Qian
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4115)


In the living cells, molecules including proteins, DNAs, RNAs and so on, with interactions between them cooperate as networks that govern various cellular functions. In this paper, a stochastic model with trigger mechanism is proposed based on what are known about the genes and proteins controlling the cell cycle of budding yeast. With respect to the biological observations, it looks more natural and understandable than deterministic dynamical model and our former stochastic model. Our model vividly describes that the protein interaction network goes through the biological pathway and forms an endless loop.


Protein Interaction Network Transcriptional Regulatory Network Curr Opin Cell Biol Entropy Production Rate Yeast Cell Cycle 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.


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  1. 1.
    Zweiger, G.: Knowledge Discovery in Gene-Expression-Microarray Data: Mining the Information Output of the Genome. Trends Biotechnol. 17(11), 429–436 (1999)CrossRefGoogle Scholar
  2. 2.
    Ito, T., Chiba, T., Ozawa, R., et al.: A Comprehensive Two-hybrid Analysis to Explore the Yeast Protein Interactome. Proc. Natl. Acad. Sci. USA 98(8), 4569–4574 (2001)CrossRefGoogle Scholar
  3. 3.
    Chen, K.C., Csikasz-Nagy, A., Gyorffy, B., et al.: Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle. Mol. Biol. Cell 11(1), 369–391 (2000)Google Scholar
  4. 4.
    Cross, F.R., Archambault, V., Miller, M., et al.: Testing a Mathematical Model of the Yeast Cell Cycle. Mol. Biol. Cell 13(1), 52–70 (2002)CrossRefGoogle Scholar
  5. 5.
    Li, F., Long, T., Lu, Y., et al.: The Yeast Cell-Cycle Network is Robustly Designed. Proc. Natl. Acad. Sci. USA 101(14), 4781–4786 (2004)CrossRefGoogle Scholar
  6. 6.
    Chen, H.C., Lee, H.C., Lin, T.Y., et al.: Quantitative Characterization of the Transcriptional Regulatory Network in the Yeast Cell Cycle. Bioinformatics 20(12), 1914–1927 (2004)CrossRefGoogle Scholar
  7. 7.
    Chen, K.C., Calzone, L., Csikasz-Nagy, A., et al.: Integrative Analysis of Cell Cycle Control in Budding Yeast. Mol. Biol. Cell 15(8), 3841–3862 (2004)CrossRefGoogle Scholar
  8. 8.
    Cross, F.R., Schroeder, L., Kruse, M., et al.: Quantitative Characterization of a Mitotic Cyclin Threshold Regulating Exit from Mitosis. Mol. Biol. Cell 16(5), 2129–2138 (2005)CrossRefGoogle Scholar
  9. 9.
    Futcher, B.: Transcriptional Regulatory Networks and the Yeast Cell Cycle. Curr. Opin. Cell Biol. 14(6), 676–683 (2002)CrossRefGoogle Scholar
  10. 10.
    Murray, A.W.: Recycling the Cell Cycle: Cyclins Revisited. Cell 116(2), 221–234 (2004)CrossRefGoogle Scholar
  11. 11.
    Ingolia, N.T., Murray, A.W.: The Ups and Downs of Modeling the Cell Cycle. Curr. Biol. 14(18), R771–R777 (2004)CrossRefGoogle Scholar
  12. 12.
    Tyers, M.: Cell Cycle Goes Global. Curr. Opin. Cell Biol. 16(6), 602–613 (2004)CrossRefGoogle Scholar
  13. 13.
    Zhang, Y., Qian, M., Ouyang, Q., et al.: Stochastic Model of Yeast Cell Cycle Netwok (in appear)Google Scholar
  14. 14.
    Ao, P.: Potential in Stochastic Differential Equations: Novel Construction. Journal of Physics A: Mathematical and General (3), L25–L30 (2004)Google Scholar
  15. 15.
    Zhu, X.M., Yin, L., Hood, L., et al.: Calculating Biological Behaviors of Epigenetic States in the Phage λ Life Cycle. Funct. Integr. Genomics 4(3), 188–195 (2004)CrossRefGoogle Scholar
  16. 16.
    Albeverio, S., Feng, J., Qian, M.: Role of Noises in Neural Networks. Physical Review. E. Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics 52(6), 6593–6606 (1995)MathSciNetGoogle Scholar
  17. 17.
    Jiang, D., Qian, M.: Mathematical Theory of Nonequilibrium Steady States. Springer, Heidelberg (2004)MATHGoogle Scholar

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Yuping Zhang
    • 1
  • Huan Yu
    • 1
  • Minghua Deng
    • 1
  • Minping Qian
    • 1
  1. 1.School of Mathematical Sciences and Center for Theoretical BiologyPeking UniversityBeijingP.R. China

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