Modeling genome evolution with a diffusion approximation of a birth-and-death process

Bioinformatics

Volumn 21, Issue SUPPL. 3, 2005, Pages

  Karev, Georgy P ^a   Berezovskaya, Faina S ^b   Koonin, Eugene V ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

^b HOWARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIRTH; DATA ANALYSIS; DEATH; DYNAMICS; GENE AMPLIFICATION; GENOME; MOLECULAR EVOLUTION; MULTIGENE FAMILY; PARALOGY; PRIORITY JOURNAL; STATISTICAL MODEL;

EID: 28944434433     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/bti1202     Document Type: Article

References (24)

1. Abramovitz,M. and Stegun,I.A. (1970) Handbook of Mathematical Functions. Dover, New York.
2. Barabasi,A.L. and Oltvai,Z.N. (2004) Network biology: Understanding the cell's functional oranization. Nat. Rev. Genet., 5, 101-113.
3. Berezovskaya,FS. and Karev,G.P. (2005) Bifurcations of self-similar solution of the Fokker-Plank Equation. Discrete and Continuous Dynamical Systems, Supplement Volume 2005 (in press).
4. Bhattacharya,R. and Waymire,E. (1990) Stochastic Processes with Applications. Wiley, New York.
5. Eldredge,N. and Gould.S.J. (1997) On punctuated equilibria. Science, 276, 338-341.
6. Gardiner,CM. (2004) Handbook of Stochostic Models for Physics, Chemistry and the Natural Sciences, 3rd edn. Springer, Berlin.
7. Gisiger,T. (2001) Scale invariance in biology: Coincidence or footprint of a universal mechanism? Biol Rev. Camb. Philos. Soc., 76, 161-209.
8. Gould,S.J. (2002) The Structure of Evolutionary Theory. Harvard University Press, Cambridige, MA.
9. Gurney,W.S.C., and Nisbet,,R.M. (1998) Ecological Dynamics. Oxford University Press, Oxford.
10. Hughes,B.D. (1995) Random Walks and Random Environmens. Oxford University Press, Oxford.
11. Huynen,M.A., and Bork,P, (1998) Measuring, genome evolution, Proc., Natl Acad. Sci. USA, 95, 5849-5856.
12. Huynen,M.A. and van Nimwegen,E. (1998) The finquency distribution of gene family sizes in complete genomes. Mol. Biol, Evol., 15, 583-589.
13. Karev,G.P., Wolf,Y.I. and Koonin,E.V, (2002a) In Galperin,M.Y., Koonin,E.V. (eds), Computational Genomics: From Sequence to Function. Horizon Amsterdam, Vol. 3, pp 216-314.
14. Karev,G.P.,et al (2002b) Birth and death of protein domains: A simple model of evolution: Explains power law behavior. BMC Evol. Biol., 2, 18.
15. Karev,G.P. et al. (2003) Simple stochastic birth and death models of genome evolution: Was there enough time for us to evolve? Bioinformatics. 19, 1889-1900.
16. Karev,G.P. et, al. (2004) Gene family evolution: An in-depth theoretical and simulation. analysis of non-linear birth-death-innovation models. BMC Evol. Biol., 4, 32.
17. Koonin,E.V. et al. (2002) The structure of the protein universe and genome evolution. Nature, 420. 218-223.
18. Koonin,E.V., Wolf,Y.I. and Karev,G.P. (eds) (2005) Power Laws, Scalefree Networks, and Genome Biology. Landes Bioscience, Georgetown, TX.
19. Kuznetsov,V.A. (2001) Distribution associated with stochostic processes of gene expression in a single eukariotic cell. EUROSIP J. Appl. Signal Process. 4, 285-296.
20. Luscombe,N, et al. (2002) The dominance of the population by a selected few: Power-law behavior applies to a wide variety of genemic, properties. Genome Biol. 3, research0040.0041-0040.0047.
21. Lynch,M. and Coney,J.S. (2000) The evolutionary fate and consequences of duplicate genes. Science, 290, 1151-1155.
22. Reed,W.J. and Hughes,B.D. (2004) A model explaining the size distribution of gene and protein families. Math. Biosci., 189, 97-102.
23. Rzhetsky,A. and Gomez,S.M. (2001) Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics, 17, 988-996.
24. Van Kempen,N.G.(1981) Stochastic Processes in Physics and Chemistry. North-Holland Publishing Company, Amsterdam, New York, Oxford.