Geometric robustness theory and biological networks

Theory in Biosciences

Volumn 125, Issue 2, 2007, Pages 93-121

  Ay, Nihat ^a,b   Krakauer, David C ^b  

^a MAX PLANCK INSTITUTE FOR MATHEMATICS IN THE SCIENCES   (Germany)

^b SANTA FE INSTITUTE   (United States)

Author keywords

Complexity; Information Geometry; Knockouts; Networks; Robustness

Indexed keywords

ARTICLE; CONCEPTUAL FRAMEWORK; GEOMETRY; INFORMATION SCIENCE; MATHEMATICAL ANALYSIS; NONHUMAN; THEORETICAL MODEL;

INFORMATION THEORY; MODELS, BIOLOGICAL; STOCHASTIC PROCESSES; SYSTEMS BIOLOGY;

EID: 33947723676     PISSN: 14317613     EISSN: 16117530     Source Type: Journal    
DOI: 10.1016/j.thbio.2006.06.002     Document Type: Article

References (32)

1. Albert R., Jeong H., and Barabasi A.L. Error and attack tolerance of complex networks. Nature 406 (2000) 378-382
2. Amari, S., 1985. Differential-Geometric Methods in Statistics, Lecture Notes in Statistics, vol. 28. Springer, Heidelberg.
3. Amari, S., Nagaoka, H., 2000. Methods of Information Geometry, AMS Translations of Mathematical Monographs, vol. 191. Oxford University Press, Oxford.
4. Barkai N., and Leibler S. Robustness in simple biochemical networks. Nature 376 (1997) 307-312
5. Bialek W., Nemenman I., and Tishby N. Predictability, Complexity, and Learning. Neural Comput. 13 (2001) 2409-2463
6. Callaway D.S., Newman J.E.J., Strogatz S.H., and Watts D.J. Network robustness and fragility: percolation on random graphs. Phys. Rev. Lett. 85 (2000) 5468-5471
7. Chosmky N. Principles and parameters in syntactic theory. In: Hornstein N., and Lightfoot D. (Eds). Explanations in Linguistics (1981), Longman, London
8. Cover T.M., and Thomas J.A. Elements of Information Theory (2001), Wiley, New York
9. Crutchfield J.P., and Packard N.H. Symbolic dynamics of noisy chaos. Physica D 7 (1983) 201-223
10. de Visser, J.A.G.M., Hermisson, J., Wagner, G.P., Meyers, L.A., Bagheri-Chaichian, H., Blanchard, J.L., Chao, L., Cheverud, J.M., Elena, S.F., Fontana, W., Gibson, G., Hansen, T.F., Krakauer, D., Lewontin, R.C., Ofria, C., Rice, S.H., von Dassow, G., Wagner, A., Whitlock, M.C., 2003. Evolution and detection of genetic robustness. Evolution 57, 1959-1972.
11. Dunne J.A., Williams R.J., and Martinez N.D. Networks structure and biodiversity loss in food webs: robustness increases with connectance. Ecol. Lett. 5 (2002) 558
12. Erb I., and Ay N. Multi-information in the thermodynamic limit. J. Stat. Phys. 115 (2003) 949-976
13. Flack, J., Girvan, M., de Waal, F., Krakauer, D.C., 2006. Policing stabilizes construction of social niches in primates. Nature, 439, 426-429.
14. Friedberg E.C. DNA Repair (1985), W.H. Freeman, New York
15. Grassberger P. Toward a quantitative theory of self-generated complexity. Int. J. Theor. Phys. 25 9 (1986) 907-938
16. Krakauer D.C. Genetic Redundancy, Evolution and Comparative Genomics. Encyclopedia of the human genome. Nature Publishing Group (2003), MacMillan Publishers, New York
17. Krakauer, D.C., 2004. Robustness in biological systems: a provisional taxonomy. In: T.S. Dreisboeck, J. Yasha Kresh. (Eds.), Complex Systems Science in Biomedicine, Kluwer Academic Press, Dordrecht.
18. Krakauer D.C., and Nowak M.A. Evolutionary preservation of redundant duplicated genes. Semin. Cell. Dev. Biol. 10 (1999) 555-559
19. Krakauer D.C., and Plotkin J.B. Redundancy, antiredundancy, and the robustness of genomes. Proc. Natl. Acad. Sci. USA 99 (2002) 1405-1409
20. Krakauer D.C., and Plotkin J.B. Principles and parameters of molecular robustness. In: Jen E. (Ed). Robust Design: A Repertoire for Biology, Ecology and Engineering (2004), Oxford University Press, Oxford 115-133
21. Newman M. The structure and function of complex networks. SIAM Rev. 45 (2003) 167-256
22. Pearl J. Causality (2000), Cambridge University Press, Cambridge
23. Peterson W.W., and Weldon E.J. Error Correcting Codes (1972), MIT Press, Cambridge, MA
24. Schuster, P., Fontana, W., Stadler, P.F., Hofacker, I.L., 1994. From sequences to shapes and back: a case study in RNA secondary structures. Proc. Roy. Soc. (London) B, 255, 279-284 (1994).
25. Shmulevich I., Lahdesmaki H., Dougherty E.R., and Zhang W. The role of certain postclasses in Boolean network models of genetic networks. Proc. Natl. Acad. Sci. USA 100 (2003) 10734-10739
26. Strogatz S.H. Exploring complex networks. Nature 410 (2001) 268-276
27. Tononi G., Sporns O., and Edelman G.M. A measure for brain complexity: relating functional segregation and integration in the nervous system. Proc. Natl. Acad. Sci. USA 91 (1994) 5033-5037
28. Tyson J.J., Chen K., and Novak B. Network dynamics and cell physiology. Nat. Rev. Mol. Bio. 2 (2001) 908-916
29. van Baalen M., Krivan V., van Rijn P.C.J., and Sabelis M.W. Alternative food, switching predators, and the persistence of predator-prey systems. Am. Nat. 157 (2001)
30. Wagner A. Evolution of gene networks by gene duplications: a mathematical model and its implications on genome organization. Proc. Natl. Acad. Sci. USA 91 (1994) 4387-4391
31. Wagner A. Robustness against mutations in genetic networks of yeast. Nat. Genet. 24 (2000) 355-361
32. Wagner A. Robustness and Evolvability in Living Systems (2005), Princeton University Press, Princeton, NJ