Abstract
One of major challenges for post-genomic biology is to understand how molecules dynamically interact to form networks which facilitate sophisticated biological functions. Instead of analyzing individual molecules, systems biology is to study dynamical networks of interacting molecules which give rise to life. In recent years, many progress have been made in systematic approaches and high-throughput technologies for systematic studying complex molecular networks. Analyzing these networks provides novel insights in understanding not only complicated cellular phenomena but also the essential principles or fundamental mechanisms behind the phenomena at system level. This paper presents a brief survey on recent developments on modeling and analyzing complex molecular networks mainly from global and dynamical properties of complex molecular networks. Some recent developments and perspectives of analysis on molecular networks are also discussed.
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References
Kitano, H.: Systems biology: toward system-level understanding of biological systems. In: Kitano, H. (ed.) Foundations of systems biology, pp. 1–36. MIT Press, Cambridge (2001)
Yeung, M.K.S., Tegner, J., Collins, J.J.: Reverse engineering gene networks using singular value decomposition and robust regression. Proc. Natl. Acad. Sci. 99, 6163–6168 (2002)
Andrec, M., Kholodenko, B.N., Levy, R.M., Sontag, E.: Inference of signaling and gene regulatory networks by steady-state perturbation experiments: structure and accuracy. J. Theor. Biol. 232, 427–441 (2005)
Wang, Y., Joshi, T., Zhang, S.-X., Xu, D., Chen, L.: Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics 22, 2413–2420 (2006)
Zhao, X.-M., Wang, Y., Chen, L., Aihara, K.: Protein domain annotation with integration of heterogeneous information sources. Proteins: Structure, Function, and Bioinformatics 72, 461–473 (2008)
Tegner, J., Yeung, M.K.S., Hasty, J., Collins, J.J.: Reverse engineering gene networks: Integrating genetic perturbations with dynamical modeling. Proc. Natl. Acad. Sci. 100, 5944–5949 (2003)
Barabasi, A., Oltvai, Z.N.: Network biology: Understanding the cell’s functional organization. Nat. Rev. Genet. 5, 101–113 (2004)
Buchler, N.E., Gerland, U., Hwa, T.: Nonlinear protein degradation and the function of genetic circuits. Proc. Natl. Acad. Sci. 102, 9559–9564 (2005)
Kramer, B.P., Fussenegger, M.: Hysteresis in a synthetic mammalian gene network. Proc. Natl. Acad. Sci. 102, 9517–9522 (2005)
Stelling, J., Gilles, E.D., Doyle III, F.J.: Robustness properties of circadian clock architectures. Proc. Natl. Acad. Sci. 101, 13210–13215 (2004)
Wang, R., Jing, Z., Chen, L.: Modelling periodic oscillation in gene regulatory networks by cyclic feedback systems. Bull. Math. Biol. 67, 339–367 (2005)
Kobayashi, T., Chen, L., Aihara, K.: Modelling genetic switches with positive feedback loops. J. Theor. Biol. 221, 379–399 (2003)
Chen, L., Wang, R.: Designing gene regulatory networks with specified functions. IEEE Trans. Circuits Syst. I 53, 2444–2450 (2006)
Wang, R., Chen, L., Aihara, K.: Construction of genetic oscillators with interlocked feedback networks. J. Theor. Biol. 242, 454–463 (2006)
Wang, R., Zhou, T., Jing, Z., Chen, L.: Modelling periodic oscillation of biological systems with multiple time scale networks. Syst. Biol. 1, 71–84 (2004)
Wang, R., Chen, L.: Synchronizing genetic oscillators by signaling molecules. J. Biol. Rhythms 20, 257–269 (2005)
McMillen, D., Kopell, N., Hasty, J., Collins, J.J.: Synchronizing genetic relaxation oscillators by intercell signaling. Proc. Natl. Acad. Sci. 99, 679–684 (2002)
Wang, R., Chen, L., Aihara, K.: Synchronizing a multicellular system by external input: An artificial control strategy. Bioinformatics 22, 1775–1781 (2006)
Chen, L., Wang, R., Zhou, T., Aihara, K.: Noise-induced cooperative behavior in a multicell system. Bioinformatics 21, 2722–2729 (2005)
Li, C., Chen, L., Aihara, K.: Stochastic synchronization of genetic oscillator networks. BMC Systems Biology 1, article no. 6 (2007), doi:10.1186/1752-0509-1-6
Garcia-Ojalvo, J., Elowitz, M., Strogatz, S.H.: Modeling a synthetic multicellular clock: Repressilators coupled by quorum sensing. Proc. Natl. Acad. Sci. 101, 10955–10960 (2004)
de Jong, H.: Modeling and simulation of genetic regulatory systems: A iiterature review. J. Comput. Biol. 7, 67–103 (2002)
Wang, R., Li, C., Chen, L., Aihara, K.: Modeling and analyzing biological oscillations in molecular networks. Proceedings of the IEEE 96, 1361–1385 (2008)
Tyson, J.J., Csikasz-Nagy, A., Novak, B.: The dynamics of cell cycle regulation. BioEssays 24, 1095–1109 (2002)
Leloup, J.-C., Goldbeter, A.: Chaos and birhythmicity in a model for circadian oscillations of the PER and TIM proteins in Drosophila. J. Theor. Biol. 198, 445–459 (1999)
Ma, L., Iglesias, P.A.: Quantifying robustness of biochemical network models. BMC Bioinformatics 3, 1–13 (2002)
Li, C., Chen, L., Aihara, K.: Stability of genetic networks with SUM regulatory logic: Lur’e system and LMI approach. IEEE Trans. Circuits Syst. I 53, 2451–2458 (2006)
Smith, H.: Monotone Dynamical Systems 41. American Mathematical Society, Providence (1995)
Angeli, D., Sontag, E.: Monotone control systems. IEEE Trans. Auto Cont. 48, 1684–1698 (2003)
Angeli, D., Ferrell, J., Sontag, E.: Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Nat. Acad. Sci. 101, 1822–1827 (2004)
Yi, T., Huang, Y., Simon, M.I., Doyle, J.: Robust perfect adaptation in bacterial chemotaxis through integral feedback control. Proc. Nat. Acad. Sci. 97, 4649–4653 (2000)
Tyson, J.J., Chen, K.C., Novak, B.: Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221–231 (2003)
Dunlap, J.C.: Molecular bases for circadian clocks. Cell 96, 271–290 (1999)
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., Barabási, A.-L.: The large-scale organization of metabolic networks. Nature 407, 651–654 (2000)
Zhao, D., Liu, Z., Wang, J.: Dupication: a mechanism producing disassortative mixing networks in biology. Chinese Phys. Lett. 24, 2766–2768 (2007)
Jordan, I. K., Marin̋o-Rami̋rez L., Wolf, Y. I., and Koonin, E. V.: Conservation and co-evolution in the scale-free human gene coexpression network. Mol. Biol. Evol. 21, 2058-2070 (2004)
Gonze, D., Halloy, J., Gaspard, P.: Biochemical clocks and molecular noise: Theoretical study of robustness factors. J. Chem. Phys. 116, 10997–11010 (2006)
Hasty, J., Pradines, J., Dolnik, M., Collins, J.J.: Noise-based switches and amplifiers for gene expression. Proc. Natl. Acad. Sci. 97, 2075–2080 (2000)
Paulsson, J., Berg, O.G., Ehrenberg, M.: Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. 97, 7148–7153 (2000)
Stelling, J., Sauer, U., Szallasi, Z., Doyle III, F.J., Doyle, J.: Robustness of cellular functions. Cell 118, 675–685 (2004)
Barkai, N., Leibler, S.: Biological rhythms: Circadian clocks limited by noise. Nature 403, 267–268 (1999)
Gonze, D., Halloy, J., Goldbeter, A.: Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. 99, 673–678 (2002)
Wagner, A.: Circuit topology and the evolution of robustness in two-gene circadian oscillators. Proc. Natl. Acad. Sci. 102, 11775–11780 (2005)
Bagley, R.J., Farmer, J.D., Kauffman, S.A., Packard, N.H., Perelson, A.S., Stadnyk, I.M.: Modeling adaptive biological systems. BioSystems 23, 113–138 (1989)
Zhao, X.-M., Wang, R., Chen, L., Aihara, K.: Uncovering signal transduction networks from high-throughput data by integer linear programming. Nucl. Acids Res. 36, e48 (2008)
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© 2009 ICST Institute for Computer Science, Social Informatics and Telecommunications Engineering
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Wang, R., Zhao, XM., Liu, Z. (2009). Modeling and Dynamical Analysis of Molecular Networks. In: Zhou, J. (eds) Complex Sciences. Complex 2009. Lecture Notes of the Institute for Computer Sciences, Social Informatics and Telecommunications Engineering, vol 5. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-02469-6_90
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DOI: https://doi.org/10.1007/978-3-642-02469-6_90
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