Duplication Models for Biological Networks

Journal of Computational Biology

Volumn 10, Issue 5, 2003, Pages 677-687

  Chung, Fan ^a   Lu, Linyuan ^a   Dewey, T Gregory ^b   Galas, David J ^b  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b KECK GRADUATE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGY; EVOLUTION; GENE CONTROL; GENOME; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; REVIEW;

INTERNET; MODELS, BIOLOGICAL; NEURAL NETWORKS (COMPUTER); PROBABILITY; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 0242692460     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652703322539024     Document Type: Review

References (31)

1. Aiello, W., Chung, F., and Lu, L. 2000. A random graph model for massive graphs. Proc. 32nd Annual ACM Symposium on Theory of Computing, 171-180.
2. Albert, R., and Barabasi, A.-L. 2002. Statistical mechanics of complex networks. Rev. Mod. Phys. 74, 47.
3. Albert, R., Jeong, H., and Barabasi, A.-L. 1999. Diameter of the world wide web. Nature 401, 130-131.
4. Barabasi, A.-L., and Albert, R. 1999. Emergence of scaling in random networks. Science 286, 509-512.
5. Barabasi, A.-L., Albert, R., and Jeong, H. 1999. Scale-free characteristics of random networks: The topology of the world-wide web. Physics A. 272, 173-187.
6. Bhan, A., Galas, D., and Dewey, D.G. 2002. A duplication growth model of gene expression networks. Bioinformatics 18, 1486-1493.
7. Dehal, P., Predki, P., Olsen, A.S., Kobayashi, A., Folta, P., Lucas, S., Land, M., Terry, A., et al. 2001. Human chromosome 19 and related regions in mouse: Conservative and lineage-specific evolution. Science 293, 104-111.
8. Dewey, T.G., and Galas, D. 2001. Dynamic models of gene expression and classification. Func. Integr. Genomics 1, 269-278.
9. Dorogovtsev, S.N., and Mendes, J.F.F. 2001. Scaling properties of scale-free, evolving networks: Continuous approach. Phys. Rev. E. 63, 056125, 1-18.
10. Friedman, R., and Hughes, A. 2002. Gene duplication and the structure of eukaryotic genomes. Genome Res. 11, 373-381.
11. Gu, Z., Cavalcanti, A., Chen, F.-C., Bouman, P., and Li, W.-H. 2002. Extent of gene duplication in the genomes of drosophila, nematode, and yeast. Mol. Biol. Evol. 19, 256-262.
12. International Human Genome Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409, 860-921.
13. Ito, T., Chiba, T., Ozawa, R., Toshida, M., Hattori, M., and Sakaki, Y. 2001. A comprehensive two-hybrid analysis to explore the yeast protein interactome. Proc. Natl. Acad. Sci. USA 98, 4569-4574.
14. Jeong, H., Tombor, B., Albert, R., Oltvai, Z.N., and Barabasi, A.-L. 2002. The large scale organization of metabolic networks. Nature 407, 651-654.
15. Kleinberg, J., Kumar, S.R., Raghavan, P., Rajagopalan, S., and Tompins, A. 1999. The web as a graph: Measurements, models and methods. Proc. Int. Conf. on Combinatorics and Computing, 1-18.
16. Krapivsky, P.L., Redner, S., and Leyvraz, F. 2000. Phys. Rev. Lett. 85, 4629-4632.
17. Lu, L. 2001. The diameter of random massive graphs. Proc 12th ACMMMM-SIAM Symposium on Discrete Algorithms (SODA 2001), 912-921.
18. Ohno, S. 1970. Evolution by Gene Duplication, Springer Verlag, New York.
19. Rzhetsky, A., and Gomez, S.M. 2001. Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics 17, 988-996.
20. Seioghe, C., and Wolfe, K.H. 1999. Updated map of duplicated regions in the yeast genome. Gene 238, 253-261.
21. Sidow, A. 1996. Gen(om)e duplications in the evolution of early vertebrates. Curr. Opin. Genet. Dev. 6, 715-722.
22. Snel, B., Bork, P., and Huynen, M.A. 2002. The identification of functional modules from the genomic association of genes. Proc. Natl. Acad. Sci. USA 99, 5890-5895.
23. Strogatz, S. 2001. Exploring random networks. Nature 410, 268-276.
24. Stubbs, L. 2002. Genome comparison techniques, in D. Galas and S. McCormack, eds., Genomic Technologies: Present and Future, Caister Academic Press.
25. Uetz, P., Giot, L., Cagney, G., Mansfield, T., Judson, R., Knight, J., Lockshon, D., et al. 2000. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature 403, 623-627.
26. Venter, J.C. et al. 2001. The sequence of the human genome. Science 291, 1304-1351.
27. Von Dassow, G., Meir, E., Munro, E.M., and Odell, G.M. 2000. The segment polarity network is a robust developmental module. Nature 406, 188-192.
28. Wagner, A. 1994. Evolution of gene networks by gene duplications: A mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. USA 91, 4387-4391.
29. Wagner, A. 2001. Mol. Biol. Evol. 18, 1283-1292.
30. Wagner, A., and Fell, D. 2001. The small world inside large metabolic networks. Proc. Roy. Soc. London Ser. B. 268, 1803-1810.
31. Wolfe, K.H., and Shields, D.C. 1997. Molecular evidence for an ancient duplication of the entire yeast genome. Nature 387, 708-713.