Graphs as models of large-scale biochemical organization

Complexity in Chemistry, Biology, and Ecology

Volumn , Issue , 2005, Pages 155-189

  Fernández, Pau ^a   Solé, Ricard V ^a,b  

^a UNIVERSITAT POMPEU FABRA   (Spain)

^b SANTA FE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 34250841962     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1007/0-387-25871-X_4     Document Type: Chapter

References (34)

1. R. V. Solé, R. Ferrer, J. M. Montoya and S. Valverde, Complexity 8, 20-33 (2002).
2. B. Bollobás, Random Graphs, 2nd edition, Cambridge University Press, Cambridge, UK (2001).
3. M. E. J. Newman, Random Graphs as Models of Networks, in Handbook of Graphs and Networks, S Bornholdt and HG Schuster (eds.), John Wiley-VCH, Berlin (2002) pp. 147-169.
4. D. Watts and S. H. Strogatz, Nature 393, 440-442 (1998).
5. B. Alberts, A. Johnson, J. Lewis, M. Raff, K. Roberts, and P.Walter, Molecular Biology of the Cell, 4th edition, Garland Science, New York (2002).
6. A. M. Gutin, V. I. Abkevich, and E. I. Shakhnovich, PNAS 92, 1282-1286 (1995).
7. J. Espadaler, N. Fernández-Fuentes, A. Hermoso, E. Querol, F. X. Aviles, M. J. Sternberg, and B. Oliva, Archdb, Nucl. Acids. Res, 32D, 185-188 (2004).
8. L. W. Ancel and W. Fontana, , J. Exp. Zool. 288, 242-283 (2000).
9. G. von Dassow, E. Meir, E. Munro and G. M. Odell, Nature 406, 188-192 (2000).
10. G. von Dassow and E. Munro, J. Exp. Zool. 406, 188-192 (1999).
11. R. V. Solé, I. Salazar-Ciudad, and S. A. Newman, Trends Ecol. Evol. 15, 479-480 (2000).
12. G. P. Wagner, Am. Zool. 36, 36-43 (1996).
13. G. P. Wagner and L. Altenberg, Evolution 50, 967-976 (1996).
14. N. M. Stadler, P. F. Stadler, G. P.Wagner, andW. Fontana, J. Theor. Biol. 213, 241-274 (2001).
15. E. Ravasz, A. L. Somera, D. A. Mongru, Z. N. Oltvai, and A. L. Barabási, Science 297, 1551-1555 (2002).
16. R. Albert and A. L. Barabási, Rev. Mod. Phys. 74, 47-97 (2002).
17. S. N. Dorogovtsev and J. F. F. Mendes, Evolution of Networks. From Biological Nets to Internet and WWW, Oxford University Press, Oxford (2003).
18. T. Ito, T. Chiba, R. Ozawa, M. Yoshida, M. Hattori and Y. Sakaki, PNAS 98, 4569-4574 (2001).
19. S. Li, C. M. Armstrong, N. Bertin, H. Ge, S. Milstein, M. Boxem, P. O. Vidalain, J. D. Han, A.Chesneau, T. Hao, D. S. Goldberg, N. Li, M. Martinez, J. F. Rual, P. Lamesch, L. Xu, M. Tewari, S. L.Wong, L. V. Zhang, G. F. Berriz, L. Jacotot, P. Vaglio, J. Reboul, T. Hirozane-Kishikawa, Q. Li, H. W. Gabel, A. Elewa, B. Baumgartner, D. J. Rose, H. Yu, S. Bosak, R. Sequerra, A. Fraser, S. E. Mango, W. M. Saxton, S. Strome, S. Van Den Heuvel, F. Piano, J. Vandenhaute, C. Sardet, M. Gerstein, L. Doucette-Stamm, K. C. Gunsalus, J. W. Harper, M. E. Cusick, F. P. Roth, D. E. Hill, and M. Vidal. Science 303, 540-543 (2004).
20. M. E. .J. Newman, Phys. Rev. Lett. 89, 208701 (2002).
21. S. Maslov and K. Sneppen, Science 296, 910-913 (2002).
22. M. Maslov, K. Sneppen and U. Alon, Correlation Profiles and Circuit Motifs in Complex Networks,S. Bornholdt and H. G. Schuster (eds.), Handbook of Graphs and Networks, John Wiley-VCH, Berlin (2002) pp. 168-198.
23. R. V. Solé, R. Pastor-Satorras, E. Smithm and T. Kepler, Adv. Complex Systems 5, 43-54 (2002).
24. A. Vázquez, Phys. Rev. E. 67, 056104 (2003).
25. A.Vázquez, A. Flammini, A. Maritan, and A.Vespigniani, ComPlexUs 1, 38-44 (2003).
26. S. A. Kauffman, J. Theor. Biol. 22, 437-467 (1969).
27. R. Albert and H. G. Othmer, J. Theor. Biol. 223, 1-18 (2003).
28. R. V. Solé, P. Fernández, and S. A. Kauffman, IJDB 47, 685-693 (2003).
29. S. A. Kauffman, The Origins of Order, Oxford U. Press, New York (1993).
30. M. Aldana-González, S. Coppersmith, and L. P. Kadanoff, Boolean Dynamics with Random Couplings, in Perspectives and Problems in Nonlinear Science, A Celebratory Volume in Honor of Lawrence Sirovich, E. Kaplan, J. E. Marsden, and K. R. Sreenivasan (eds.), Applied Mathematical Sciences, Springer, New York (2002).
31. A. H. Tong, G. Lesage, G. D. Bader, H. Ding, H. Xu, X. Xin, J. Young, G. F. Berriz, R. L. Brost, M. Chang, Y. Chen, X. Cheng, G. Chua, H. Friesen, D. S. Goldberg, J. Haynes, C. Humphries, G. He, S. Hussein, L. Ke, N. Krogan, Z. Li, J. N, Levinson. H, Lu, P. Menard, C. Munyana, A. B. Parsons, O. Ryan, R. Tonikian, T. Roberts, A. M. Sdicu, J. Shapiro, B. Sheikh, B. Suter, S. L. Wong, L. V. Zhang, H. Zhu, C. G. Burd, S. Munro, C. Sander, J. Rine, J. Greenblatt, M. Peter, A. Bretscher, G. Bell, F. P. Roth, G. W. Brown, B. Andrews, H. Bussey, and C. Boone Science 303, 808-813 (2004).
32. D. E. Featherstone and K. Broadie, BioEssays 24, 267-274 (2002).
33. M. Aldana, Physica D 185, 45-66 (2003).
34. M. Aldana and P. Cluzel, PNAS 100, 8710-8714 (2003).