Abstract
How can a new incoming biological node measure the degree of nodes already present in a network and thus decide, on the basis of this counting, to preferentially connect with the more connected ones? Although such explicit comparison and choice is quite plausible in the case of man-made networks, like Internet, leading the network to a scale-free topology, it is much harder to conceive for biochemical networks. The computer simulations presented in this article try to respect simple and, as far as possible, basic biological characteristics such as the heterogeneity of biological nodes, the existence of natural hubs, the way nodes bind by mutual affinity, the significance of type-based network as compared with instance-based one and the consequent importance of the nodes concentration to the selection of the partners of the incoming nodes.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Preview
Unable to display preview. Download preview PDF.
References
Barabási, A.-L., Albert, R.: Emergence of scaling in random networks. Science 286, 509–512 (1999)
Ferrer i Cancho, C., Janssen, R., Solé, R.V.: The topology of technology graphs: small world pattern in electronic circuits. Phys. Rev. E 63, 32767 (2001)
Newman, M.E.J.: The structure and function of complex networks. SIAM Review 45, 167–256 (2003)
Pastor-Satorras, R., Vespignani, A.: Evolution and structure of the Internet: A statistical physics approach. Cambridge University Press, Cambridge (2004)
Dorogovtsev, D., Mendes, J.F.F.: Evolution of networks: From biological nets to the Internet and WWW. Oxford University Press, Oxford (2003)
Solé, R.V., Pastor-Satorras, R., Smith, E., Kepler, T.: A model of large-scale proteome evolution. Adv. Complex Syst. 5, 43–54 (2002)
Strogatz, S.: Exploring Complex Networks. Nature 410, 268–276 (2001)
Barabási, L.-A., Oltvai, Z.N.: Network Biology: Understanding the cell’s functional organization. Nature Reviews Genetics 5, 101–113 (2004)
Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., Barabási, A.-L.: The large-scale organisation of metabolic networks. Nature 407, 651–654 (2000)
Uetz, P., et al.: A comprehensive analysis of protein-protein interactions in Saccharomes cerevisiaie. Nature 403, 623–627 (2000)
Vazquez, A., Flamimi, A., Maritan, A., Vespignani, A.: Modeling of Protein Interaction Networks. ComplexUs 1, 38–44 (2003)
Wagner, A., Fell, D.A.: The small world inside large metabolic networks. Proc. R. Soc. Lond. B. 268, 1803–1810 (2001)
Wagner, A.: How the global structure of protein interaction networks evolve. Proc. R. Soc. London B 270, 457–466 (2003)
Barabási, A.-L., Albert, R., Jeong, H.: Mean-field theory for scale-free random networks. Physica A 272, 173–187 (1999)
Temkin, O.N., Zeigarnik, A.V., Bonchev, D.: Chemical reaction networks: a graph-theoretical approach. CRC Press, Boca Raton (1996)
Vogelstein, B., Lane, D., Levine, A.J.: Surfing the p53 network. Nature 408, 307–310 (2000)
Bersini, H.: Immune Network and Adaptive Control. In: Proceedings of the first European Conference on Artificial Life, Toward a Practice of Autonomous Systems, Varela, Bourgine, pp. 217–225. MIT Press, Cambridge (1993)
De Boer, R.J., Perelson, A.S.: Size and Connectivity as Emergent Properties of a Developing Immune Network Journal of Theor. Biology 149, 381–424 (1991)
Detours, V., Bersini, H., Stewart, J., Varela, F.: Development of an Idiotypic Network in Shape Space. Journal of Theor. Biol. 170, 401–404 (1994)
Varela, F., Coutinho, A.: Second Generation Immune Network. Immunology Today 12(5), 159–166 (1991)
Thomas, A., Cannings, R., Monk, N.A.M., Cannings, C.: On the structure of protein interaction networks. Biochem. Soc. Trans. 31, 1491–1496 (2003)
Stumpf, M.P.H., Wiuf, C., May, R.M.: Subnets of scale-free networks are not scale-free: Sampling properties of networks. PNAS 102(12), 4221–4224 (2005)
Author information
Authors and Affiliations
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2005 Springer-Verlag Berlin Heidelberg
About this paper
Cite this paper
Bersini, H., Lenaerts, T., Santos, F.C. (2005). Growing Biochemical Networks: Identifying the Intrinsic Properties. In: Capcarrère, M.S., Freitas, A.A., Bentley, P.J., Johnson, C.G., Timmis, J. (eds) Advances in Artificial Life. ECAL 2005. Lecture Notes in Computer Science(), vol 3630. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11553090_87
Download citation
DOI: https://doi.org/10.1007/11553090_87
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28848-0
Online ISBN: 978-3-540-31816-3
eBook Packages: Computer ScienceComputer Science (R0)