Spontaneous evolution of modularity and network motifs

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 39, 2005, Pages 13773-13778

  Kashtan, Nadav ^a   Alon, Uri ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; EVOLUTION; NERVE CELL NETWORK; PRIORITY JOURNAL; PROTEIN ENGINEERING; PROTEIN MOTIF; PROTEIN STABILITY; PROTEIN STRUCTURE; STRUCTURE ANALYSIS;

ALGORITHMS; COMPUTER SIMULATION; EVOLUTION; NEURAL NETWORKS (COMPUTER);

EID: 25444448797     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0503610102     Document Type: Article

References (46)

1. Koza, J. (1992) Genetic Programming: On the Programming of Computers by Means of Natural Selection (MIT Press, Cambridge, MA).
2. Simon, H. A. (1996) The Sciences of the Artificial (MIT Press, Cambridge, MA).
3. Hartwell, L. H., Hopfield, J. J., Leibler, S. & Murray, A. W. (1999) Nature 402, C47-C52.
4. Schlosser, G. & Wagner, G. (2004) Modularity in Development und Evolution (Chicago Univ. Press. Chicago).
5. Wagner, G. P. & Altenberg, L. (1996) Evolution 50, 967-976.
6. Shen-Orr, S., Milo, R., Mangan, S. & Alon, U. (2002) Nat. Genet. 31, 64-68.
7. Milo, R., Shen-Orr, S., Itzkovitz, S., Kashtan, N., Chklovskii, D. & Alon, U. (2002) Science 298, 824-827.
8. Milo, R., Itzkovitz, S., Kashtan, N., Levitt, R., Shen-Orr, S., Ayzenshtat, I., Sheffer, M. & Alon, U. (2004) Science 303, 1538-1542.
9. Conant, G. C. & Wagner, A. (2003) Nat. Genet. 34, 264-266.
10. Mangan, S. & Alon, U. (2003) Proc. Natl. Acad. Sci. USA 100, 11980-11985.
11. Kalir, S., Mangan, S. & Alon, U. (2005) Mol. Syst. Biol. 1, msb4100010-E1-msb4100010-E6.
12. Lenski, R. E., Ofria, C., Pennock, R. T. & Adami, C. (2003) Nature 423, 139-144.
13. Holland, J. (1975) Adaptation in Natural and Artificial Systems (Univ. of Michigan Press. Ann Arbor).
14. Goldberg, D. (1989) Genetic Algorithms in Search, Optimization, and Machine Learning (Addison-Wesley, Reading. MA).
15. Mitchell, M. (1996) An Introduction to Genetic Algorithms (MIT Press, Cambridge, MA).
16. Thompson, A. (1998) Hardware Evolution: Automatic Design of Electronic Circuits in Reconfigurable Hardware by Artificial Evolution (Springer, New York).
17. Raichman, N., Segev, R. & Ben-Jacob, E. (2003) Physica A 326, 265-285.
18. Wilkins, A. (2002) The Evolution of Developmental Pathways (Sinauer, Sunderland, MA).
19. Alon, U. (2003) Science 301, 1866-1867.
20. Vassilev, V., Job, D. & Miller, J. (2000) in Proceedings of the Second NASA/DoD Workshop on Evolvable Hardware (IEEE Computer Society. Washington, DC), pp. 151-160.
21. Hornby, G., Lipson, H. & Pollack, J. B. (2001) in IEEE Conference on Robotics and Automation ICRA, (IEEE Computer Society. Washington, DC), Vol. 4. pp. 4146-4151
22. Angeline, P. & Pollack, J. (1993) in Proceedings of the Second Annual Conference on Evolutionary Programming, eds. Fogel, D. & Almar, W. (Evolutionary Programming Society, La Jolla, CA). pp. 154-163.
23. Koza, J. (1994) Genetic Programming II: Automatic Discovery of Reusable Programs (MIT Press, Cambridge. MA).
24. Calabretta, R., Nolfi, S., Parisi, D. & Wagner, G. P. (1998) in Proceedings of the Sixth International Conference on Artificial Life, eds. Adami, C., Belew, R., Kitano, H. & Taylor, C. E. (MIT Press, Cambridge. MA), pp. 275-2S4.
25. Variano, E. A., McCoy, J. H. & Lipson, H. (2004) Phys. Rev. Lett. 92, 188701.
26. Thompson, A. & Layzeii, P. (2000) in Evolvable Systems: From Biology to Hardware. Third International Conference, ICES 2000, eds. Miller, J. F., Thompson, A., Thomson, P. & Fogarty, T. C. (Springer. New York), pp. 218-228.
27. Lipson, H., Pollack, J. B. & Suh, N. P. (2002) Evolution 56, 1549-1556.
28. Vasconcelos, J. A., Ramirez, J. A., Takahashi, R. H. C. & Saldanha, R. R. (2001) IEEE Trans. Magnetics 37, 3414-3418.
29. Yao, X. (1992) A Review of Evolutionary Artificial Neural Networks (Commonwealth Scientific and Industrial Research Organization, Victoria, Australia).
30. Haykin, S. (1999) Neural Networks: A Comprehensive Foundation (Macmillan. New York).
31. Newman, M. E. J. (2004) Phys. Rev. E 69, 066133.
32. Newman, M. E. J. & Girvan, M. (2004) Phys. Rev. E 69, 026113.
33. Guimera, R. & Nunes Amaral, L. A. (2005) Nature 433, 895-900.
34. Itzkovitz, S., Levitt, R., Kashtan, N., Milo, R., Itzkovitz, M. & Alon, U. (2005) Phys. Rev. E 71, 016127.
35. Miller, J. F., Thomson, P. & Fogarty, T. (1997) in Genetic Algorithms and Evolution Strategies in Engineering and Computer Science: Recent Advancements and Industrial Applications, eds. Quagliarella, D., Periaux, J., Poloni, C. & Winter, G. (Wiley, New York), pp. 103-131.
36. Kashtan, N., Itzkovitz, S., Milo, R. & Alon, U. (2004) Phys. Rev. E 70, 031909.
37. Hansen, M. C., Yaclin, H. & Haves, J. P. (1999) IEEE Design Test 16, 72-80.
38. Ripley, B. D. (1996) Pattern Recognition and Neural Networks (Cambridge Univ. Press, Cambridge, U.K.).
39. Kashtan, N., Itzkovitz, S., Milo, R. & Alon, U. (2004) Bioinformatics 20, 1746-1758.
40. Bray, D. (1995) Nature 376, 307-312.
41. Bhalla, U. S. & Iyengar, R. (1999) Science 283, 381-387.
42. Itzkovitz, S., Milo, R., Kashtan, N., Ziv, G. & Alon, U. (2003) Phys. Rev. E 68, 026127.
43. Berg, H. C. & Brown, D. A. (1972) Nature 239, 500-504.
44. Eisenbach, M., Lengeier, J. W., Varon, M., Gutnick, D., Meili, R., Firtel, R. A., Segall, J. E., Omann, G. M., Tamada, A. & Murakami, F. (2004) Chemotaxis (World Scientific, Teancck, NJ).
45. Schaeffer, H. J. & Weber, M. J. (1999) Mol. Cell. Biol. 19, 2435-2444.
46. Park, S. H., Zarrinpar, A. & Lim, W. A. (2003) Science 299, 1061-1064.