Content-based network model with duplication and divergence

Physica A: Statistical Mechanics and its Applications

Volumn 365, Issue 2, 2006, Pages 446-462

  Şengün, Yasemin ^a   Erzan, Ayşe ^a  

^a ISTANBUL TECHNICAL UNIVERSITY   (Turkey)

Author keywords

Genomics; Networks; Scaling behavior

Indexed keywords

COMPUTATIONAL COMPLEXITY; COMPUTATIONAL METHODS; MATHEMATICAL MODELS; MUTAGENESIS; OSCILLATIONS;

CLUSTERING COEFFICIENT; DEGREE DISTRIBUTION; SCALING BEHAVIOR;

GENES;

EID: 33646109799     PISSN: 03784371     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.physa.2006.02.045     Document Type: Article

References (41)

1. Barabasi A.-L., and Albert R. Science 286 (1999) 509
2. Maslov S., and Sneppen K. Science 296 (2002) 910
3. Albert R., and Barabasi A.-L. Rev. Mod. Phys. 74 (2002) 47
4. Dorogovtsev S.N., and Mendes J.F.F. Adv. Phys. 51 (2002) 1079
5. Wagner A. Proc. Natl. Acad. Sci. 91 (1994) 4387
6. Wagner A. Mol. Biol. Evol. 18 (2001) 1283
7. Pastor-Satorras R., Smith E., and Solé R.V. J. Theor. Biol. 222 (2003) 199
8. R.V. Sole, R. Pastor-Satorras, Complex Networks in Genomics and Proteomics, in: S. Bornholdt, H.G. Schuster (Eds.), Handbook of Graphs and Networks (Wiley-VCH Verlag, Berlin 2002).
9. Watts D.J., and Strogatz S.H. Nature 393 (1998) 440
10. B. Alberts, et al., Molecular Biology of the Cell, (Garland Science, NY, 2002) (Chapter 7).
11. Lewin B. Genes (1997), Oxford University Press, Oxford (Chapter 18)
12. Teichmann S.S., and Madan Babu M. Nat. Genet. 36 (2004) 492
13. Madan Babu M., Luscombe N.M., Aravind L., Gerstein M., and Teichmann S.A. Curr. Op. Struct. Biol. 14 (2004) 283
14. Balcan D., and Erzan A. Eur. Phys. J. B 38 (2004) 253
15. Mungan M., Kabakcioglu A., Balcan D., and Erzan A. q-bio.MN/0406049, J. Phys. A, Math. Gen. 38 (2005) 9599-9620
16. Hannon G.J. Nature 418 (2002) 244-251
17. Novina C.D., and Sharp P.A. Nature 430 (2004) 161-164
18. Lee T.I., et al. Science 298 (2002) 799
19. Harbison C.T., et al. Nature 431 (2004) 99
20. Vázquez A., Flammini A., Maritan A., and Vespignani A. Nature Biotechnol. 21 (2003) 697
21. Vázquez A., Flammini A., Maritan A., and Vespignani A. Complexus 1 (2003) 38
22. Colizza V., Flammini A., Maritan A., and Vespignani A. Physica A 352 (2005) 1
23. Butland G., et al. Nature 433 (2005) 531
24. Milo R., Shen-Orr S.S., Itzkovitz S., Kashtan N., and Alon U. Science 298 (2002) 824
25. Vázquez A., Dobrin R., Sergi D., Eckmann J.-P., Oltvai Z.N., and Barabasi A.-L. Proc. Natl. Acad. Sci. 101 (2004) 17940
26. T. Reil, Dynamics of Gene Expression in an Artificial Genome, Lecture-Notes in Computer Science, vol. 1674, Proceedings of the fifth European Conference on Advances in Artificial Life, Springer, London, 1999, pp. 457-466.
27. N. Geard, J. Wiles, Structure and dynamics of a gene network model incorporating small RNAs, in: R. Sarker, R. Reynolds, H. Abbass, K.-C. Tan, R. McKay, D. Essam, T. Gedeon (Eds.), Proceedings of the 2003 Congress on Evolutionary Computation, CEC2003, IEEE Press, Piscataway, NJ, 2003, pp. 199-206.
28. Watson J., Geard N., and Wiles J. Biosystems 76 (2004) 239
29. van Noort V., Snel B., and Huynen M.A. EMBO Rep. 5 (2004) 1
30. Banzhaf W., and Kuo P.D. J. Biol. Phys. Chem. 4 (2004) 85
31. Erdös P., and Renyi A. Publ. Mat. (Debrecen) 6 (1959) 290
32. Erdös P., and Renyi A. Publ. Mat. Inst. Hung. Acad. Sci. 5 (1960) 17
33. Erdös P., and Renyi A. Bull. Inst. Int. Stat. 38 (1961) 343
34. Albert R., and Barabasi A.-L. Rev. Mod. Phys. 74 (2002) 47
35. At this Level of sophistication, we have decided we cannot very well make distinctions between transposable elements and pseudogenes. B. Alberts et al. (see Ref. [10]), p. 395.
36. 〈http://cgsigma.cshl.org/jian 〉. Also see Young Lab, 〈http://web.wi.mit.edu/young 〉.
37. A.H. Bilge, A. Erzan, D. Balcan, The Shift-match Number and String Matching Probabilities for Binary Sequences, q-bio.GN/0409023.
38. Guelzim N., Bottani S., Bourgine P., and Kepes F. Nat. Gen. 31 (2002) 61
39. S. Bergmann, J. Ihmels, N. Barkai, PloS Biol. 2 (2004) 0085. 〈http://biology.plosjournals.org 〉 (2003).
40. Dobrin R., Beg Q.K., Barabasi A.-L., and Oltvai Z.N. BMC Bioinformatics 5 (2004) 1
41. Tong A.H.Y., et al. Science 303 (2004) 808