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Topological aspects of protein networks

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Emergent Intelligence of Networked Agents

Part of the book series: Studies in Computational Intelligence ((SCI,volume 56))

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References

  1. Albert R, Jeong H and Barabási A-L (2000) Error and attack tolerance of complex networks Nature 406:378-382.

    Article  Google Scholar 

  2. Barabási A-L and Albert R (1999) Emergence of scaling in random networks. Science 286:509-512.

    Article  MathSciNet  Google Scholar 

  3. Barrat A, Barthelemy M, Pastor-Satorras R and Vespignani A (2004) The architecture of complex weigthed networks. Proc. Natl. Acad. Sci. USA 101 (11):3747-3752.

    Article  Google Scholar 

  4. Barabási A-L and Oltvai Z N (2004) Network biology: Understanding the cell’s functional organization. Nature Reviews Genetics 5:101-113.

    Article  Google Scholar 

  5. Erdös P and Rényi A (1960) Random Graphs. Publ. Math. Inst. Hung. Acad. Sci. 5:17-63.

    MATH  Google Scholar 

  6. Doolittle R F (1995) The multiplicity of domains in proteins. Ann. Rev. Biochem. 64:287-314.

    Article  Google Scholar 

  7. Deng M, Mehta S, Sun F and Chen T (2002) Inferring domain-domain interactions from protein-protein interactions. Genome Research 12:1540-1548.

    Article  Google Scholar 

  8. Dorogovtsev S N and Mendes J F F (2003) Evolution of Networks: From Biological Nets to the Internet and WWW, Oxford University Press, Oxford.

    MATH  Google Scholar 

  9. Furusawa C and Kaneko K (2003) Zipf ’s law in gene expression. Phys. Rev. Lett. 90:008102(1-4).

    Google Scholar 

  10. Hayashida M, Ueda N and Akutsu T (2003) Inferring strengths of proteinprotein interactions from experimental data using linear programming. Bioinformatics 19(2):58–65.

    Google Scholar 

  11. Jeong H, Mason S, Barabási A-L and Oltvai Z N (2001) Lethality and centrality in protein networks. Nature 411:41-42.

    Article  Google Scholar 

  12. Jeong H, Tombor B, Albert R, Oltvai Z N and Barabási A-L (2000) The largescale organization of metabolic networks. Nature 407:651-654.

    Article  Google Scholar 

  13. Kuznetsov V A, Knott G D and Bonner R F (2002) General statistics of stochastic process of gene expression in eukaryotic cells. Genetics 161:1321–1332.

    Google Scholar 

  14. Nacher J C, Hayashida M and Akutsu T (2006) Physica A, in press.

    Google Scholar 

  15. Nacher J C, Hayashida M and Akutsu T In preparation.

    Google Scholar 

  16. Pastor-Satorras R and Vespignani A (2004) Evolution and Structure of the Internet: A Statistical Physics Approach, Cambridge University Press, Cambridge.

    Google Scholar 

  17. Qian J, Luscombe N M and Gerstein M (2001) Protein-fold occurrence in genomes: power-law behaviour and evolutionary model. Journal of Molecular Biology 313:673-681.

    Article  Google Scholar 

  18. Ueda H R, et al. (2004) Universality and flexibility in gene expression from bacteria to human. Proc. Natl. Acad. Sci. USA 101(11):3765-3769.

    Article  Google Scholar 

  19. Watts D J and Strogatz S H (1998) Collective dynamics of “small-world ” networks. Nature 393:440-442.

    Article  Google Scholar 

  20. Wuchty S (2001) Scale-free behavior in protein domain networks. Mol. Biol. Evol. 18(9):1694-1702.

    Google Scholar 

  21. Yook S H, Oltvai Z N and Barabási A-L (2004) Functional and topological characterization of protein interaction networks. Proteomics 4:928-942.

    Article  Google Scholar 

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Nacher, J.C., Hayashida, M., Akutsu, T. (2007). Topological aspects of protein networks. In: Namatame, A., Kurihara, S., Nakashima, H. (eds) Emergent Intelligence of Networked Agents. Studies in Computational Intelligence, vol 56. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-71075-2_12

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  • DOI: https://doi.org/10.1007/978-3-540-71075-2_12

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-71073-8

  • Online ISBN: 978-3-540-71075-2

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