Mean-field methods in evolutionary duplication-innovation-loss models for the genome-level repertoire of protein domains

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 81, Issue 2, 2010, Pages

  Angelini, A ^a   Amato, A ^a   Bianconi, G ^b   Bassetti, B ^a   Cosentino Lagomarsino, M ^a,c  

^a UNIVERSITY OF MILAN   (Italy)

^b NORTHEASTERN UNIVERSITY   (United States)

^c CNRS   (France)

Author keywords

[No Author keywords available]

Indexed keywords

LOSS MODEL; MEAN-FIELD; MEAN-FIELD METHODS; MODEL FORMULATION; PROTEIN DOMAINS; SCALING BEHAVIOR; SIMULATION APPROACH;

PROTEINS;

GENES;

EID: 77249179783     PISSN: 15393755     EISSN: 15502376     Source Type: Journal    
DOI: 10.1103/PhysRevE.81.021919     Document Type: Article

References (35)

1. D. Tautz and M. Lassig, Trends Genet. 20, 344 (2004). 10.1016/j.tig.2004.06.002
2. M. A. Huynen and E. van Nimwegen, Mol. Biol. Evol. 15, 583 (1998).
3. J. S. Mattick, Nat. Rev. Genet. 5, 316 (2004). 10.1038/nrg1321
4. S. Maslov, S. Krishna, T. Y. Pang, and K. Sneppen, Proc. Natl. Acad. Sci. U.S.A. 106, 9743 (2009). 10.1073/pnas.0903206106
5. E. van Nimwegen, Trends Genet. 19, 479 (2003). 10.1016/S0168-9525(03) 00203-8
6. S. Itzkovitz, T. Tlusty, and U. Alon, BMC Genomics 7, 239 (2006). 10.1186/1471-2164-7-239
7. M. Lynch and J. S. Conery, Science 302, 1401 (2003). 10.1126/science. 1089370
8. E. P. Rocha, Curr. Opin. Microbiol. 11, 454 (2008). 10.1016/j.mib.2008. 09.007
9. E. V. Koonin, Int. J. Biochem. Cell Biol. 41, 298 (2009). 10.1016/j.biocel.2008.09.015
10. C. A. Orengo and J. M. Thornton, Annu. Rev. Biochem. 74, 867 (2005). 10.1146/annurev.biochem.74.082803.133029
11. C. Branden and J. Tooze, Introduction to Protein Structure (Garland, New York, 1999).
12. E. V. Koonin, Y. I. Wolf, and G. P. Karev, Nature (London) 420, 218 (2002). 10.1038/nature01256
13. J. Qian, N. M. Luscombe, and M. Gerstein, J. Mol. Biol. 313, 673 (2001). 10.1006/jmbi.2001.5079
14. G. P. Karev, Y. I. Wolf, A. Y. Rzhetsky, F. S. Berezovskaya, and E. V. Koonin, BMC Evol. Biol. 2, 18 (2002). 10.1186/1471-2148-2-18
15. V. A. Kuznetsov, in Computational and Statistical Approaches to Genomics, edited by, W. Zhang, and, I. Shmule-vich, (Kluwer, Boston, 2002), p. 125.
16. S. Abeln and C. M. Deane, Proteins 60, 690 (2005). 10.1002/prot.20506
17. N. V. Dokholyan, B. Shakhnovich, and E. I. Shakhnovich, Proc. Natl. Acad. Sci. U.S.A. 99, 14132 (2002). 10.1073/pnas.202497999
18. M. Kamal, N. Luscombe, J. Qian, and M. Gerstein, in Power Laws, Scale-Free Networks and Genome Biology, edited by, E. Koonin, Y. Wolf, and, G. Karev, (Spinger, New York, 2006), pp. 165-193. 10.1007/0-387-33916-7-10
19. R. Durrett and J. Schweinsberg, Ann. Probab. 33, 2094 (2005). 10.1214/009117905000000369
20. G. P. Karev, Y. I. Wolf, and E. V. Koonin, Bioinformatics 19, 1889 (2003). 10.1093/bioinformatics/btg351
21. G. P. Karev, Y. I. Wolf, F. S. Berezovskaya, and E. V. Koonin, BMC Evol. Biol. 4, 32 (2004). 10.1186/1471-2148-4-32
22. G. P. Karev, F. S. Berezovskaya, and E. V. Koonin, Bioinformatics 21, iii12 (2005). 10.1093/bioinformatics/bti1202
23. M. Cosentino Lagomarsino, A. L. Sellerio, P. D. Heijning, and B. Bassetti, Genome Biol. 10, R12 (2009). 10.1186/gb-2009-10-1-r12
24. J. Pitman, Notes for St. Flour Summer School (2002), 1st ed. (Springer, Berlin, 2006).
25. J. Pitman and M. Yor, Ann. Probab. 25, 855 (1997). 10.1214/aop/1024404422
26. A. L. Barabási and R. Albert, Science 286, 509 (1999). 10.1126/science.286.5439.509
27. V. Kunin and C. A. Ouzounis, Genome Res. 13, 1589 (2003). 10.1101/gr.1092603
28. C. Pal, B. Papp, and M. J. Lercher, Nat. Rev. Genet. 7, 337 (2006). 10.1038/nrg1838
29. D. Aldous, Saint-Flour Summer School XIII (1983) (Springer, Berlin, 1985).
30. J. Kingman, J. R. Stat. Soc. Ser. B (Methodol.) 37, 1 (1975).
31. Z. S. Qin, Bioinformatics 22, 1988 (2006). 10.1093/bioinformatics/btl284
32. M. Evans and T. Hanney, J. Phys. A 38, R195 (2005). 10.1088/0305-4470/38/ 19/R01
33. B. Bassetti, M. Zarei, M. Cosentino Lagomarsino, and G. Bianconi, Phys. Rev. E 80, 066118 (2009). 10.1103/PhysRevE.80.066118
34. J. C. Davis and D. A. Petrov, PLoS Biol. 2, e55 (2004). 10.1371/journal.pbio.0020055
35. See Ref.. These trends are also visible from Figs. of this work.