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References
C. Adami, (1998) Introduction to artificial life, Springer-Verlag, New-York.
J.O. Bishop, J.G. Morton, M. Rosbash, and M. Richardson, (1974) Three classes in Hela cell messenger RNA. Nature, 250, 199–204.
M. Yu. Borodovsky, S.M. Gusein-Zade (1989) A general rule for ranged series of codon frequencies in different genomes. J. Biomolecular Structure and Dynamics, 6, 1001–1012.
C.R. Cantor, C. L. Smith (1999) Genomics, J. Willey & Sons, Inc. New York.
J. Chelly, J.-P. Concordet, J.-C. Kaplan, A. Kahn (1989) Illegitimate transcription: Transcription of any gene in cell type. Proc. Natl. Acad. Sci. U.S.A., 86, 2617–2621.
J.-J. Chen, J. D. Rowley & S. M. Wang (2000) Generation of longer cDNA fragments from serial analysis of gene expression tags for gene identification. Proc. Natl. Acad. Sci. U.S.A., 97, 349–353.
D. L. Cook, A.N. Gerber and S.T. Tatscott (1998). Modeling stochastic gene expression: Implications for haploinsufficiency, Proc. Natl. Acad. Sci. U.S.A., 95, 15641–15646.
Caron, H., et al. (2001) The human transcriptome map: clustering of highly expressed genes in chromosomal domains. Science, 291, 1289–1292.
B.S. Croix et al. (2000) Genes expressed in human tumor endothelium. Science, 289, 1197–1202.
R. Crollius, et al. (2000) Estimate of human gene number provided by genomewide analysis using Tetraodon nigroviridis DNA sequence. Nature Genetics, 25, 235–238.
S. Douglas et al. (2001) The highly reduced genome of an enslaved aldal nucleus. Nature, 410, 1091–1096.
S.R. Eddy (2001) Non-coding RNA genes and the modern RNA world. Nature Rev. Genetics, 2, 919–928.
M. R. Emmert-Buck, et al. (2000) Molecular profiling of clinical tissue specimens: Feasibility and applications. Am. J. Pathol., 156, 1109–1115.
B. Ewing, P. Green (2000) Analysis of expressed sequence tags indicates 35,000 human genes. Nature Genetics 25, 232–234.
A.M. Femino, F.S. Fay, K. Fogarty and R.H. Singer (1998) Visualization of single RNA transcripts in situ. Science, 280, 585–590.
R.A. Fisher (1930). The genetical theory of natural selection. Oxford: Clarendon Press.
R. Friedman and A.L. Hughes (2001) Pattern and timing of gene duplication in animal genomes. Genome Res., 11, 1842–1847.
P. Guptasarma (1995) Does replication-induced transcription regulate synthesis of the myriad low number proteins of Escherichia coli? BioAssays, 17, 987–997.
J.B. Hogenesch, et al. (2001) A comparison of the Celera and Ensemble predicted gene sets reveals little overlap in novel genes. Cell, 106, 413–415.
G.A. Hollander. On the stochastic regulation of interleukin-2 transcription. Seminars in Immunology, 11, 357–367.
F. C. P. Holstege, et al. (1998) Dissecting the regulatory circuitry of a eukaryotic genome. Cell, 95, 717–728.
Huang S.-P. and Weir B. S. (2001) Estimating the total number of alleles using a sample coverage method. Genetics, 159, 1365–1373.
Hughes A.L., da Silva J., Freadman R. (2001) Ancient genome duplications did not structure the human Hox-bearing chromosomes. Genome Res., 11, 771–780.
D. A. Hume (2000) Probability in transcriptional regulation and implications for leukocyte differentiation and inducible gene expression. Blood, 96, 7, 2323–2328.
International Human Genome Sequencing Consortium (2001) Initial sequencing and analysis of the human genome. Nature, 409, 860–921.
D.A. Jackson, A. Pombo and F. Iborra (2000) The balance sheet for transcription: an analysis of nuclear RNA metabolism in mammalian cells. FASEB J., 14, 242–254.
S. A. Jelinsky and L. D. Samson (1999) Global response of Saccharomyces cerevisiae to alkylating agent. Proc. Natl. Acad. Sci. U.S.A., 96, 1486–1491.
S. A. Jelinsky, P. Estep, G.M. Church, and L. D. Samson (2000) Regulatory networks revealed by transcriptional profiling of damaged Saccharomyces cerevisiae cells: Rpn4 links base excision repair with proteasomes. Molec. and Cell. Biology, 20, 8157–8167.
H. Jeong, B. Tombor, R. Albert, Z.N. Ottval, A.-L. Barabasi (2000) The large-scale organization of metabolic networks. Nature 407, 651–654.
M. Johnson (2000) The yeast genome: on the road to the gold age. Current Opinion in Genetics and Development, 10, 617–623.
N. L. Johnson, S. Kotz, A. W. Kemp, Univariate Discrete Distributions. John Wiley & Sons, Inc., New-York, 1992.
S. A. Kauffman (1993) The origins of Order: Self-Organization and Selection in Evolution. Oxford University Press, New-York.
M.S.H. Ko (1992) Induction mechanism of a single gene molecule: stochastic or deterministic. BioAssays, 14, 341–346.
E. Koonin, L. Aravind & A. S. Kondrashov (2000). The impact of comparative genomics on our understanding of evolution. Cell, 101, 573–576.
V. A. Kuznetsov & R.F. Bonner (1999) Statistical tools for analysis of gene expression distributions with missing data. In: 3rd Annual Con-ference on Computational Genomics. Nov. 18–21. Baltimore, MD: The Institute for Genomic Research, p. 26.
V. A. Kuznetsov (2000) The genes number game in growing sample. J. Comput. Biol, 7, 642.
V. A. Kuznetsov (2001) Analysis of stochastic processes of gene expression in a single cell. In: 2001 IEEE-EURASIP Workshop on Nonlinear Signals and Image Processing, University of Delaware, Baltimore, MD, USA, June, 2001.
V. A. Kuznetsov (2001) Distribution associated with stochastic processes of gene expression in a single eukaryotic cell. EURASIP J. on Applied Signal Processing, 4, 285–296.
A. S. Lash, et al. (2000) SAGEmap: A public gene expression resource. Genome Res., 10, 1051–1060, 2000.
W, Li (1992), Random texts exhibit Zipf’s-law-like word frequency distribution, IEEE Transactions on Information Theory, 38, 1842–1845.
W. Li (1999) Statistical properties of open reading frames in complete genome sequences. Computers & Chemistry, 23, 283–301.
W.-H. Li, Z. Gu, H. Wang and A. Nekrutenko (2001) Evolutionary analyses of the human genome. Nature, 409, 847–849.
B. Mandelbrot (1982). Fractal Geometry in Nature. New York: Freeman.
H.H. McAdams and A. Arkin (1999) It’s a noisy business! Genetic regulation at the nanomolar scale. Trends in Genetics, 15, 65–69.
T. Misteli (2001) Protein dynamics: Implications for nuclear architecture and gene expression. Science, 291, 843–847.
S. Newlands, et al. (1998) Transcription occurs in pulses in muscle fibers. Genes Dev., 12, 2748–2758, 1998.
M. E. J. Newman, S.H. Strogatz and D.J. Watts (2001) Physical Rev. E., 64, 026118-1-02618-17.
E. Pennisi (2000) And the gene number is...? Science, 288, 1146–1147.
R. Ohlsson, A. Paldi, and J.A. Marshall Graves (2001) Did genomic imprinting and X chromosome inactivation arise from stochastic expression? Trends in Genetics, 17, 136–141.
S. Ohno (1970) Evolution by gene duplication. Springer Verlag, New York.
A. Pombo et al. (2000) Specialized transcription factories within mammalian nuclei. Critical Reviews in Eukaryotic Gene Expression, 10, 21–29.
J. J. Ramsden, J. Vohradsky (1998) Zipf-like behavior in prokaryotic protein expression. Phys. Review. E., 58, 7777–7780.
I. L. Ross, C. M. Browne, and D. A. Hume (1994) Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. Immunol. Cell. Biol. 72, 177–185.
G. M. Rubin et al. (2000) Comparative genomics of the Eukaryotes. Science, 287, 2204–2215.
A. Rzhetsky and S. M. Gomez (2001) Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinformatics, 17, 988–996.
Y. Sano et al. (2001) Random monoallelic expression of three genes clustered within 60 kb of mouse t complex genomic DNA. Genome Res., 11, 1833–1841.
I. Shmulevich, E.R. Dougherty, S. Kim, and W. Zhang (2002) Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks Bioinformatics, 18 (in press).
M.J. Shulman & G.E. Wu, (1999) Hypothesis: genes which function in a stochastic linagecommitment process are subject to monoallelic expression. Seminars in Immunology, 11, 369–371.
H.A. Simon & T.A. Van Wormer (1963). Some Monte-Carlo estimates of the Yule distribution, Behavior Science, 8, 203–210.
H.E. Stanley, et al. (1999) Scaling features of noncoding DNA. Phys. Review. E, 273, 1–18.
H.G. Sutherland, et al. (2000) Reactivation of heritably silenced gene expression in mice. Mammalian Genome, 11, 347–355.
D. Thieffry, A.M. Huerta, E. Perez-Rueda and J. Collado-Vides (1998) From specific gene regulation to genomic networks: a global analysis of transcriptional regulation in Escherichia coli. BioEssays, 20, 433–440.
J.E. Till, E.A. McCulloch, L. Siminovish (1964) A stochastic model of stem cell proliferation, based on the growth of spleen colony-forming cells. Proc. Natl. Acad. Sci. U.S.A., 51, 29–38.
V. E. Velculescu, et al. (1997) Characterization of yeast transcriptome. Cell, 88, 243–251.
V. E. Velculescu, et al. (1999) Analysis of human transcriptomes. Nat. Genet., 23, 387–388.
J.C. Venter, J.C., et al. (2001) The sequence of the human genome. Science, 291, 1304–1351.
T.J. Vision, D.G. Brown and S.D. Tanksley (2000) The origins of genome duplications in Arabidopsis. Science, 290, 2114–2117.
J. Vohradsky and J.J. Ramsden. (2001) Genome resource utilization during prokaryotic development. FASEB J. (express article 10.1096/fj.00-0889fje).
M.C. Walters, et al. (1995) Enhancers increase the probability but not the level of gene expression. Proc. Natl. Acad. Sci. U.S.A., 92, 7125–7129.
H. Weintraub (1988) Formation of stabletranscription complexes as assayed by analysis of individual templates. Proc. Natl. Acad. Sci. U.S.A., 85, 5819–5823.
S. Wuchty (2001) Scale-free behavior in protein domain networks. Molec. Biol. Evol., 18, 1694–1702.
G.U. Yule (1924) A mathematical theory of evolution, based on the conclusions of Dr. J.C. Willis, F.R.S. Philosophical Transactions of the Royal Society of London. Ser. B., 213, 21–87.
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Kuznetsov, V.A. (2003). Statistics of the Numbers of Transcripts and Protein Sequences Encoded in the Genome. In: Zhang, W., Shmulevich, I. (eds) Computational and Statistical Approaches to Genomics. Springer, Boston, MA. https://doi.org/10.1007/0-306-47825-0_9
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