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Volumn 223, Issue 1, 2010, Pages 1-11

Stochastic and delayed stochastic models of gene expression and regulation

Author keywords

Gene expression; Gene regulatory network; Stochastic; Time delay

Indexed keywords

DELAYED MODELS; GENE NETWORKS; GENE REGULATORY NETWORKS; IN-CELL; POST-TRANSCRIPTIONAL REGULATIONS; REVERSIBLE PHOSPHORYLATION; RNA MOLECULES; RNA POLYMERASE; SINGLE NUCLEOTIDES; STOCHASTIC; STOCHASTIC TIME DELAY; STOCHASTICITY; TRANSCRIPTION INITIATION;

EID: 72449206548     PISSN: 00255564     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.mbs.2009.10.007     Document Type: Review
Times cited : (60)

References (119)
  • 2
  • 3
    • 25444468618 scopus 로고    scopus 로고
    • Noise in gene expression: origins, consequences, and control
    • Raser J., and O'Shea E. Noise in gene expression: origins, consequences, and control. Science 309 (2005) 2010
    • (2005) Science , vol.309 , pp. 2010
    • Raser, J.1    O'Shea, E.2
  • 4
    • 34147131574 scopus 로고    scopus 로고
    • From fluctuations to phenotypes: the physiology of noise
    • Samoilov M., Price G., and Arkin A. From fluctuations to phenotypes: the physiology of noise. Sci. STKE 366 (2006) re17
    • (2006) Sci. STKE , vol.366
    • Samoilov, M.1    Price, G.2    Arkin, A.3
  • 5
  • 7
    • 41349119880 scopus 로고    scopus 로고
    • Stochastic switching as a survival strategy in fluctuating environments
    • Acar M., Mettetal J., and van Oudenaarden A. Stochastic switching as a survival strategy in fluctuating environments. Nat. Genet. 40 (2008) 471
    • (2008) Nat. Genet. , vol.40 , pp. 471
    • Acar, M.1    Mettetal, J.2    van Oudenaarden, A.3
  • 8
    • 33645293152 scopus 로고    scopus 로고
    • An excitable gene regulatory circuit induces transient cellular differentiation
    • Suel G., Garcia-Ojalvo J., Liberman L., and Elowitz M. An excitable gene regulatory circuit induces transient cellular differentiation. Nature 440 (2006) 545
    • (2006) Nature , vol.440 , pp. 545
    • Suel, G.1    Garcia-Ojalvo, J.2    Liberman, L.3    Elowitz, M.4
  • 9
    • 44349162752 scopus 로고    scopus 로고
    • Transcriptome-wide noise controls lineage choice in mammalian progenitor cells
    • Chang H., Hemberg M., Barahona M., Ingber D., and Huang S. Transcriptome-wide noise controls lineage choice in mammalian progenitor cells. Nature 453 (2008) 544
    • (2008) Nature , vol.453 , pp. 544
    • Chang, H.1    Hemberg, M.2    Barahona, M.3    Ingber, D.4    Huang, S.5
  • 10
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz M., Levine A., Siggia E., and Swain P. Stochastic gene expression in a single cell. Science 297 (2002) 1183
    • (2002) Science , vol.297 , pp. 1183
    • Elowitz, M.1    Levine, A.2    Siggia, E.3    Swain, P.4
  • 11
    • 28944434119 scopus 로고    scopus 로고
    • Real-time kinetics of gene activity in individual bacteria
    • Golding I., Paulsson J., Zawilski S., and Cox E. Real-time kinetics of gene activity in individual bacteria. Cell 123 (2005) 1025
    • (2005) Cell , vol.123 , pp. 1025
    • Golding, I.1    Paulsson, J.2    Zawilski, S.3    Cox, E.4
  • 12
    • 33748994704 scopus 로고    scopus 로고
    • Stochastic mRNA synthesis in mammalian cells
    • Raj A., et al. Stochastic mRNA synthesis in mammalian cells. PLoS Biol. 4 (2006) e309
    • (2006) PLoS Biol. , vol.4
    • Raj, A.1
  • 13
    • 33645027986 scopus 로고    scopus 로고
    • Stochastic protein expression in individual cells at the single molecule level
    • Cai L., Friedman N., and Xie X. Stochastic protein expression in individual cells at the single molecule level. Nature 440 (2006) 358
    • (2006) Nature , vol.440 , pp. 358
    • Cai, L.1    Friedman, N.2    Xie, X.3
  • 14
    • 33645033645 scopus 로고    scopus 로고
    • Probing gene expression in live cells, one protein molecule at a time
    • Yu J., Xiao J., Ren X., Lao K., and Xie S. Probing gene expression in live cells, one protein molecule at a time. Science 311 1600-1603 (2006) 597
    • (2006) Science , vol.311 , Issue.1600-1603 , pp. 597
    • Yu, J.1    Xiao, J.2    Ren, X.3    Lao, K.4    Xie, S.5
  • 15
    • 19544379881 scopus 로고    scopus 로고
    • Stochasticity in gene expression: from theories to phenotypes
    • Kaern M., Elston T., Blake W., and Collins J.J. Stochasticity in gene expression: from theories to phenotypes. Nat. Rev. Genet. 6 (2005) 451
    • (2005) Nat. Rev. Genet. , vol.6 , pp. 451
    • Kaern, M.1    Elston, T.2    Blake, W.3    Collins, J.J.4
  • 16
    • 56749102636 scopus 로고    scopus 로고
    • Regulatory activity revealed by dynamic correlations in gene expression noise
    • Dunlop M., Cox R., Levine A., Murray R., and Elowitz M. Regulatory activity revealed by dynamic correlations in gene expression noise. Nat. Genet. 40 (2008) 1493
    • (2008) Nat. Genet. , vol.40 , pp. 1493
    • Dunlop, M.1    Cox, R.2    Levine, A.3    Murray, R.4    Elowitz, M.5
  • 17
    • 20344389483 scopus 로고    scopus 로고
    • Models of stochastic gene expression
    • Paulsson J. Models of stochastic gene expression. Phys. Life Rev. 2 (2005) 157
    • (2005) Phys. Life Rev. , vol.2 , pp. 157
    • Paulsson, J.1
  • 18
    • 0014945080 scopus 로고
    • Immunity phase-shift in defective lysogens: non-mutational hereditary change of early regulation of lambda prophage
    • Neubauerz Z., and Calef E. Immunity phase-shift in defective lysogens: non-mutational hereditary change of early regulation of lambda prophage. J. Mol. Biol. 51 (1970) 1
    • (1970) J. Mol. Biol. , vol.51 , pp. 1
    • Neubauerz, Z.1    Calef, E.2
  • 19
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells
    • Arkin A., Ross J., and McAdams H. Stochastic kinetic analysis of developmental pathway bifurcation in phage λ-infected Escherichia coli cells. Genetics 149 (1998) 1633
    • (1998) Genetics , vol.149 , pp. 1633
    • Arkin, A.1    Ross, J.2    McAdams, H.3
  • 20
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie D. Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81 (1977) 2340
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340
    • Gillespie, D.1
  • 22
    • 34249950625 scopus 로고    scopus 로고
    • Stochastic simulation of chemical kinetics
    • Gillespie D. Stochastic simulation of chemical kinetics. Annu. Rev. Phys. Chem. 58 (2007) 35
    • (2007) Annu. Rev. Phys. Chem. , vol.58 , pp. 35
    • Gillespie, D.1
  • 24
    • 0041677612 scopus 로고    scopus 로고
    • Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator
    • Lewis J. Autoinhibition with transcriptional delay: a simple mechanism for the zebrafish somitogenesis oscillator. Curr. Biol. 13 (2003) 1398
    • (2003) Curr. Biol. , vol.13 , pp. 1398
    • Lewis, J.1
  • 25
    • 0043180477 scopus 로고    scopus 로고
    • Oscillatory expression of Hes1, p53, and NF-kB driven by transcriptional time delays
    • Monk N. Oscillatory expression of Hes1, p53, and NF-kB driven by transcriptional time delays. Curr. Biol. 13 (2003) 1409
    • (2003) Curr. Biol. , vol.13 , pp. 1409
    • Monk, N.1
  • 27
    • 33749336242 scopus 로고    scopus 로고
    • Oscillatory regulation of Hes1: discrete stochastic delay modelling and simulation
    • Barrio M., Burrage K., Leier A., and Tian T. Oscillatory regulation of Hes1: discrete stochastic delay modelling and simulation. PLoS Comput. Biol. 2 (2006) e117
    • (2006) PLoS Comput. Biol. , vol.2
    • Barrio, M.1    Burrage, K.2    Leier, A.3    Tian, T.4
  • 28
    • 34247550417 scopus 로고    scopus 로고
    • Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression
    • Roussel M., and Zhu R. Validation of an algorithm for delay stochastic simulation of transcription and translation in prokaryotic gene expression. Phys. Biol. 3 (2006) 274
    • (2006) Phys. Biol. , vol.3 , pp. 274
    • Roussel, M.1    Zhu, R.2
  • 29
    • 33845369407 scopus 로고    scopus 로고
    • A general modeling strategy for gene regulatory networks with stochastic dynamics
    • Ribeiro A.S., Zhu R., and Kauffman S. A general modeling strategy for gene regulatory networks with stochastic dynamics. J. Comput. Biol. 13 (2006) 1630
    • (2006) J. Comput. Biol. , vol.13 , pp. 1630
    • Ribeiro, A.S.1    Zhu, R.2    Kauffman, S.3
  • 30
    • 34248147640 scopus 로고    scopus 로고
    • Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models
    • Zhu R., Ribeiro A.S., Salahub D., and Kauffman S.A. Studying genetic regulatory networks at the molecular level: delayed reaction stochastic models. J. Theor. Biol. 246 (2007) 725
    • (2007) J. Theor. Biol. , vol.246 , pp. 725
    • Zhu, R.1    Ribeiro, A.S.2    Salahub, D.3    Kauffman, S.A.4
  • 31
    • 48749114725 scopus 로고    scopus 로고
    • Delay stochastic simulation of single-gene expression reveals a detailed relationship between protein noise and mean abundance
    • Zhu R., and Salahub D. Delay stochastic simulation of single-gene expression reveals a detailed relationship between protein noise and mean abundance. FEBS Lett. 582 (2008) 2905
    • (2008) FEBS Lett. , vol.582 , pp. 2905
    • Zhu, R.1    Salahub, D.2
  • 33
    • 1842383693 scopus 로고
    • Rate-limiting steps in RNA chain initiation
    • McClure W. Rate-limiting steps in RNA chain initiation. Proc. Natl. Acad. Sci. USA 77 (1980) 5634
    • (1980) Proc. Natl. Acad. Sci. USA , vol.77 , pp. 5634
    • McClure, W.1
  • 34
    • 0035883859 scopus 로고    scopus 로고
    • Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator
    • Lutz R., Lozinski T., Ellinger T., and Bujard H. Dissecting the functional program of Escherichia coli promoters: the combined mode of action of Lac repressor and AraC activator. Nucleic Acids Res. 29 (2001) 3873
    • (2001) Nucleic Acids Res. , vol.29 , pp. 3873
    • Lutz, R.1    Lozinski, T.2    Ellinger, T.3    Bujard, H.4
  • 35
  • 37
  • 38
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson M., and Bruck J. Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. A 104 (2000) 1876
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1876
    • Gibson, M.1    Bruck, J.2
  • 39
    • 2942718723 scopus 로고    scopus 로고
    • Control of stochasticity in eukaryotic gene expression
    • Raser J., and O'Shea E. Control of stochasticity in eukaryotic gene expression. Science 304 (2004) 1811
    • (2004) Science , vol.304 , pp. 1811
    • Raser, J.1    O'Shea, E.2
  • 40
    • 33746596624 scopus 로고    scopus 로고
    • Gene expression time delays and turing pattern formation systems
    • Gaffney E., and Monk N. Gene expression time delays and turing pattern formation systems. Bull. Math. Biol. 68 (2006) 99
    • (2006) Bull. Math. Biol. , vol.68 , pp. 99
    • Gaffney, E.1    Monk, N.2
  • 41
    • 33748691544 scopus 로고    scopus 로고
    • Comprehensive analysis of delay in transcriptional regulation using expression profiles
    • Ota K., et al. Comprehensive analysis of delay in transcriptional regulation using expression profiles. Genome Inform. 14 (2003) 302
    • (2003) Genome Inform. , vol.14 , pp. 302
    • Ota, K.1
  • 42
    • 0034737593 scopus 로고    scopus 로고
    • Single-molecule study of transcriptional pausing and arrest by E. coli rna polymerase
    • Davenport R., White G., Landick R., and Bustamante C. Single-molecule study of transcriptional pausing and arrest by E. coli rna polymerase. Science 287 (2000) 2497
    • (2000) Science , vol.287 , pp. 2497
    • Davenport, R.1    White, G.2    Landick, R.3    Bustamante, C.4
  • 43
    • 36249008660 scopus 로고    scopus 로고
    • Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks
    • Ribeiro A.S. Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks. Phys. Rev. E 76 (2007) 051915
    • (2007) Phys. Rev. E , vol.76 , pp. 051915
    • Ribeiro, A.S.1
  • 44
    • 0035896577 scopus 로고    scopus 로고
    • The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression
    • Kierzek A., Zaim J., and Zielenkiewicz P. The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J. Biol. Chem. 276 (2001) 8165
    • (2001) J. Biol. Chem. , vol.276 , pp. 8165
    • Kierzek, A.1    Zaim, J.2    Zielenkiewicz, P.3
  • 46
    • 57349199452 scopus 로고    scopus 로고
    • Analysis of RNA polymerase-promoter complex formation
    • Ross W., and Gourse R. Analysis of RNA polymerase-promoter complex formation. Methods 47 (2009) 13
    • (2009) Methods , vol.47 , pp. 13
    • Ross, W.1    Gourse, R.2
  • 47
    • 34147106039 scopus 로고    scopus 로고
    • SGN Sim, a stochastic genetic networks simulator
    • Ribeiro A.S., and Lloyd-Price J. SGN Sim, a stochastic genetic networks simulator. Bioinformatics 23 (2007) 777
    • (2007) Bioinformatics , vol.23 , pp. 777
    • Ribeiro, A.S.1    Lloyd-Price, J.2
  • 48
    • 17644396339 scopus 로고    scopus 로고
    • Dizzy: stochastic simulation of large-scale genetic regulatory networks
    • Ramsey S., Orrell D., and Bolouri H. Dizzy: stochastic simulation of large-scale genetic regulatory networks. J. Bioinform. Comput. Biol. 3 (2005) 415
    • (2005) J. Bioinform. Comput. Biol. , vol.3 , pp. 415
    • Ramsey, S.1    Orrell, D.2    Bolouri, H.3
  • 49
    • 0017780941 scopus 로고
    • Stochastic model of linear, continuous protein-synthesis in bacterial populations
    • Rigney D., and Schieve W. Stochastic model of linear, continuous protein-synthesis in bacterial populations. J. Theor. Biol. 69 (1977) 761
    • (1977) J. Theor. Biol. , vol.69 , pp. 761
    • Rigney, D.1    Schieve, W.2
  • 50
    • 0842277514 scopus 로고
    • A model for statistical fluctuations of protein numbers in a microbial-population
    • Berg O. A model for statistical fluctuations of protein numbers in a microbial-population. J. Theor. Biol. 73 (1978) 307
    • (1978) J. Theor. Biol. , vol.73 , pp. 307
    • Berg, O.1
  • 51
    • 0034691214 scopus 로고    scopus 로고
    • Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation
    • Paulsson J., Berg O., and Ehrenberg M. Stochastic focusing: fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. USA 97 (2000) 7148
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 7148
    • Paulsson, J.1    Berg, O.2    Ehrenberg, M.3
  • 53
    • 0036790975 scopus 로고    scopus 로고
    • Intrinsic and extrinsic contributions to stochasticity in gene expression
    • Swain P., Elowitz M., and Siggia E. Intrinsic and extrinsic contributions to stochasticity in gene expression. Proc. Natl. Acad. Sci. USA 99 (2002) 12795
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 12795
    • Swain, P.1    Elowitz, M.2    Siggia, E.3
  • 54
    • 0014489272 scopus 로고
    • Metabolic stability and epigenesis in randomly constructed genetic nets
    • Kauffman S.A. Metabolic stability and epigenesis in randomly constructed genetic nets. J. Theor. Biol. 22 (1969) 437
    • (1969) J. Theor. Biol. , vol.22 , pp. 437
    • Kauffman, S.A.1
  • 55
    • 0141903547 scopus 로고    scopus 로고
    • Boolean dynamics of networks with scale-free topology
    • Aldana M. Boolean dynamics of networks with scale-free topology. Physica D 185 (2003) 45
    • (2003) Physica D , vol.185 , pp. 45
    • Aldana, M.1
  • 56
    • 0028844979 scopus 로고
    • A mathematical framework for describing and analyzing gene regulatory networks
    • Mestl T., Plahte E., and Omholt S. A mathematical framework for describing and analyzing gene regulatory networks. J. Theor. Biol. 176 (1995) 291
    • (1995) J. Theor. Biol. , vol.176 , pp. 291
    • Mestl, T.1    Plahte, E.2    Omholt, S.3
  • 57
    • 0016758861 scopus 로고
    • Classification of biological networks by their qualitative dynamics
    • Glass L. Classification of biological networks by their qualitative dynamics. J. Theor. Biol. 54 (1975) 85
    • (1975) J. Theor. Biol. , vol.54 , pp. 85
    • Glass, L.1
  • 58
    • 4444311806 scopus 로고    scopus 로고
    • A proposal for using the ensemble approach to understand genetic regulatory networks
    • Kauffman S.A. A proposal for using the ensemble approach to understand genetic regulatory networks. J. Theor. Biol. 230 (2004) 581
    • (2004) J. Theor. Biol. , vol.230 , pp. 581
    • Kauffman, S.A.1
  • 59
    • 14644407528 scopus 로고    scopus 로고
    • Thinking quantitatively about transcriptional regulation
    • Greive S., and von Hippel P. Thinking quantitatively about transcriptional regulation. Nat. Rev. Mol. Cell Biol. 6 (2005) 221
    • (2005) Nat. Rev. Mol. Cell Biol. , vol.6 , pp. 221
    • Greive, S.1    von Hippel, P.2
  • 60
    • 0032584643 scopus 로고    scopus 로고
    • An integrated model of the transcription complex in elongation, termination, and editing
    • von Hippel P. An integrated model of the transcription complex in elongation, termination, and editing. Science 281 (1998) 661
    • (1998) Science , vol.281 , pp. 661
    • von Hippel, P.1
  • 61
    • 33846914726 scopus 로고    scopus 로고
    • The regulatory roles and mechanism of transcriptional pausing
    • Landick R. The regulatory roles and mechanism of transcriptional pausing. Biochem. Soc. Trans. 34 (2006) 1062
    • (2006) Biochem. Soc. Trans. , vol.34 , pp. 1062
    • Landick, R.1
  • 62
    • 0031008221 scopus 로고    scopus 로고
    • Basic mechanisms of transcript elongation and its regulation
    • Uptain S., Kane C., and Chamberlin M. Basic mechanisms of transcript elongation and its regulation. Annu. Rev. Biochem. 66 (1997) 117
    • (1997) Annu. Rev. Biochem. , vol.66 , pp. 117
    • Uptain, S.1    Kane, C.2    Chamberlin, M.3
  • 63
    • 62449302589 scopus 로고    scopus 로고
    • Elongation dynamics shape bursty transcription and translation
    • Dobrzyński M., and Bruggeman F. Elongation dynamics shape bursty transcription and translation. Proc. Natl. Acad. Sci. USA 106 (2009) 2583
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 2583
    • Dobrzyński, M.1    Bruggeman, F.2
  • 64
    • 0034688174 scopus 로고    scopus 로고
    • Construction of a genetic toggle switch in Escherichia coli
    • Gardner T., Cantor C., and Collins J.J. Construction of a genetic toggle switch in Escherichia coli. Nature 403 (2000) 339
    • (2000) Nature , vol.403 , pp. 339
    • Gardner, T.1    Cantor, C.2    Collins, J.J.3
  • 65
    • 0242416539 scopus 로고    scopus 로고
    • Noise in eukaryotic gene expression
    • Blake W., Kaern M., Cantor C., and Collins J. Noise in eukaryotic gene expression. Nature 422 (2003) 633
    • (2003) Nature , vol.422 , pp. 633
    • Blake, W.1    Kaern, M.2    Cantor, C.3    Collins, J.4
  • 66
    • 22744441386 scopus 로고    scopus 로고
    • Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity
    • Weinberger L., Burnett J., Toettcher J., Arkin A., and Schaffer D. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122 (2005) 169
    • (2005) Cell , vol.122 , pp. 169
    • Weinberger, L.1    Burnett, J.2    Toettcher, J.3    Arkin, A.4    Schaffer, D.5
  • 67
    • 73049167504 scopus 로고
    • Teleonomic mechanisms in cellular metabolism, growth, and differentiation
    • Monod J., and Jacob F. Teleonomic mechanisms in cellular metabolism, growth, and differentiation. Cold Spring Harb. Symp. Quant. Biol. 26 (1961) 389
    • (1961) Cold Spring Harb. Symp. Quant. Biol. , vol.26 , pp. 389
    • Monod, J.1    Jacob, F.2
  • 68
    • 33645097646 scopus 로고    scopus 로고
    • Multistable and multistep dynamics in neutrophil differentiation
    • Chang H., Oh P., Ingber D., and Huang S. Multistable and multistep dynamics in neutrophil differentiation. BMC Cell Biol. 7 (2006) 11
    • (2006) BMC Cell Biol. , vol.7 , pp. 11
    • Chang, H.1    Oh, P.2    Ingber, D.3    Huang, S.4
  • 69
    • 66149145491 scopus 로고    scopus 로고
    • Bistable switches control memory and plasticity in cellular differentiation
    • Wang L., et al. Bistable switches control memory and plasticity in cellular differentiation. Proc. Natl. Acad. Sci. USA 106 (2009) 6638
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 6638
    • Wang, L.1
  • 70
    • 34447548696 scopus 로고    scopus 로고
    • Noisy attractors and ergodic sets in models of gene regulatory networks
    • Ribeiro A.S., and Kauffman S.A. Noisy attractors and ergodic sets in models of gene regulatory networks. J. Theor. Biol. 247 (2007) 743
    • (2007) J. Theor. Biol. , vol.247 , pp. 743
    • Ribeiro, A.S.1    Kauffman, S.A.2
  • 71
    • 2342464752 scopus 로고    scopus 로고
    • Enhancement of the stability of genetic switches by overlapping upstream regulatory domains
    • Warren P., and Wolde P. Enhancement of the stability of genetic switches by overlapping upstream regulatory domains. Phys. Rev. Lett. 92 (2004) 128101
    • (2004) Phys. Rev. Lett. , vol.92 , pp. 128101
    • Warren, P.1    Wolde, P.2
  • 72
    • 57549084860 scopus 로고    scopus 로고
    • Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments
    • Ribeiro A.S. Dynamics and evolution of stochastic bistable gene networks with sensing in fluctuating environments. Phys. Rev. E 78 (2008) 061902
    • (2008) Phys. Rev. E , vol.78 , pp. 061902
    • Ribeiro, A.S.1
  • 73
    • 67949123162 scopus 로고    scopus 로고
    • Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch
    • Ribeiro A.S., Dai X., and Yli-Harja O. Variability of the distribution of differentiation pathway choices regulated by a multipotent delayed stochastic switch. J. Theor. Biol. 260 (2009) 66
    • (2009) J. Theor. Biol. , vol.260 , pp. 66
    • Ribeiro, A.S.1    Dai, X.2    Yli-Harja, O.3
  • 77
    • 28844465824 scopus 로고    scopus 로고
    • Stable and unstable attractors in Boolean networks
    • Klemm K., and Bornholdt S. Stable and unstable attractors in Boolean networks. Phys. Rev. E 72 (2005) 055101
    • (2005) Phys. Rev. E , vol.72 , pp. 055101
    • Klemm, K.1    Bornholdt, S.2
  • 78
    • 27144548324 scopus 로고    scopus 로고
    • Dynamics of critical Kauffman networks under asynchronous stochastic update
    • Greil F., and Drossel B. Dynamics of critical Kauffman networks under asynchronous stochastic update. Phys. Rev. Lett. 95 (2005) 048701
    • (2005) Phys. Rev. Lett. , vol.95 , pp. 048701
    • Greil, F.1    Drossel, B.2
  • 79
    • 69849099365 scopus 로고    scopus 로고
    • Determining noisy attractors of delayed stochastic Gene Regulatory Networks from multiple data sources
    • Dai X., Yli-Harja O., and Ribeiro A.S. Determining noisy attractors of delayed stochastic Gene Regulatory Networks from multiple data sources. Bioinformatics 25 (2009) 2362
    • (2009) Bioinformatics , vol.25 , pp. 2362
    • Dai, X.1    Yli-Harja, O.2    Ribeiro, A.S.3
  • 80
    • 0034614490 scopus 로고    scopus 로고
    • Signaling - 2000 and beyond
    • Hunter T. Signaling - 2000 and beyond. Cell 100 (2000) 113
    • (2000) Cell , vol.100 , pp. 113
    • Hunter, T.1
  • 81
    • 0036901003 scopus 로고    scopus 로고
    • Multisite phosphorylation provides sophisticated regulation of transcription factors
    • Holmberg C., Tran S., Eriksson J., and Sistonen L. Multisite phosphorylation provides sophisticated regulation of transcription factors. Trends Biochem. Sci. 27 (2002)
    • (2002) Trends Biochem. Sci. , vol.27
    • Holmberg, C.1    Tran, S.2    Eriksson, J.3    Sistonen, L.4
  • 82
    • 0033020147 scopus 로고    scopus 로고
    • Regulation of p53 function and stability by phosphorylation
    • Ashcroft M., Kubbutat M., and Vousden K. Regulation of p53 function and stability by phosphorylation. Mol. Cell. Biol. 19 (1999) 1751
    • (1999) Mol. Cell. Biol. , vol.19 , pp. 1751
    • Ashcroft, M.1    Kubbutat, M.2    Vousden, K.3
  • 83
    • 0029670589 scopus 로고    scopus 로고
    • p53 in signalling checkpoint arrest or apoptosis
    • Bates S., and Vousden K. p53 in signalling checkpoint arrest or apoptosis. Curr. Opin. Genet. Dev. 6 (1996) 1
    • (1996) Curr. Opin. Genet. Dev. , vol.6 , pp. 1
    • Bates, S.1    Vousden, K.2
  • 84
    • 34047136657 scopus 로고    scopus 로고
    • Exact stochastic simulation of coupled chemical reactions with delays
    • Cai X. Exact stochastic simulation of coupled chemical reactions with delays. J. Chem. Phys. 126 (2007) 124108
    • (2007) J. Chem. Phys. , vol.126 , pp. 124108
    • Cai, X.1
  • 85
    • 44049103351 scopus 로고    scopus 로고
    • Internal noise-sustained circadian rhythms in a Drosophila model
    • Li O., and Lang X. Internal noise-sustained circadian rhythms in a Drosophila model. Biophys. J. 94 (2008) 1983
    • (2008) Biophys. J. , vol.94 , pp. 1983
    • Li, O.1    Lang, X.2
  • 86
    • 36549005051 scopus 로고    scopus 로고
    • Stochastic simulations of the repressilator circuit
    • Loinger A., and Biham O. Stochastic simulations of the repressilator circuit. Phys. Rev. E 76 (2007) 051917
    • (2007) Phys. Rev. E , vol.76 , pp. 051917
    • Loinger, A.1    Biham, O.2
  • 87
    • 0034688173 scopus 로고    scopus 로고
    • A synthetic oscillatory network of transcriptional regulators
    • Elowitz M., and Leibler S. A synthetic oscillatory network of transcriptional regulators. Nature 403 (2000) 335
    • (2000) Nature , vol.403 , pp. 335
    • Elowitz, M.1    Leibler, S.2
  • 88
    • 33747078457 scopus 로고    scopus 로고
    • Identifying transcription factor functions and targets by phenotypic activation
    • Chua G., et al. Identifying transcription factor functions and targets by phenotypic activation. Proc. Natl. Acad. Sci. USA 103 (2006) 12045
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 12045
    • Chua, G.1
  • 89
    • 66149084052 scopus 로고    scopus 로고
    • Exploring the roles of noise in the eukaryotic cell cycle
    • Kara S., et al. Exploring the roles of noise in the eukaryotic cell cycle. Proc. Natl. Acad. Sci. USA 106 (2009) 6471
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 6471
    • Kara, S.1
  • 90
    • 67049134207 scopus 로고    scopus 로고
    • Computational models of the notch network elucidate mechanisms of context-dependent signaling
    • Agrawal S., Archer C., and Schaffer D. Computational models of the notch network elucidate mechanisms of context-dependent signaling. PLOS Comput. Biol. 5 (2009) e1000390
    • (2009) PLOS Comput. Biol. , vol.5
    • Agrawal, S.1    Archer, C.2    Schaffer, D.3
  • 91
    • 39649083113 scopus 로고    scopus 로고
    • Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity Island 1
    • Temme K., et al. Induction and relaxation dynamics of the regulatory network controlling the type III secretion system encoded within Salmonella pathogenicity Island 1. J. Mol. Biol. 377 (2008) 47
    • (2008) J. Mol. Biol. , vol.377 , pp. 47
    • Temme, K.1
  • 92
    • 74049102425 scopus 로고    scopus 로고
    • Stochastic kinetic modeling of vesicular stomatitis virus intracellular growth
    • Hensel S., Rawlings J., and Yin J. Stochastic kinetic modeling of vesicular stomatitis virus intracellular growth. Bull. Math. Biol. 71 (2009) 1671
    • (2009) Bull. Math. Biol. , vol.71 , pp. 1671
    • Hensel, S.1    Rawlings, J.2    Yin, J.3
  • 93
    • 60849119860 scopus 로고    scopus 로고
    • Biochemical simulations: stochastic, approximate stochastic and hybrid approaches
    • Pahle J. Biochemical simulations: stochastic, approximate stochastic and hybrid approaches. Brief. Bioinform. 10 (2009) 53
    • (2009) Brief. Bioinform. , vol.10 , pp. 53
    • Pahle, J.1
  • 94
    • 34248158654 scopus 로고    scopus 로고
    • Spurious oscillation in a uniform Euler discretisation of linear stochastic differential equations with vanishing delay
    • Appleby J., and Kelly C. Spurious oscillation in a uniform Euler discretisation of linear stochastic differential equations with vanishing delay. J. Comput. Appl. Math. 205 (2007) 923
    • (2007) J. Comput. Appl. Math. , vol.205 , pp. 923
    • Appleby, J.1    Kelly, C.2
  • 95
    • 57149091743 scopus 로고    scopus 로고
    • Multistable decision switches for flexible control of epigenetic differentiation
    • Guantes R., and Poyatos J.F. Multistable decision switches for flexible control of epigenetic differentiation. PLoS Comput. Biol. 4 11 (2008) e1000235
    • (2008) PLoS Comput. Biol. , vol.4 , Issue.11
    • Guantes, R.1    Poyatos, J.F.2
  • 96
    • 49549101799 scopus 로고    scopus 로고
    • A delay stochastic process with applications in molecular biology
    • Schlicht R., and Winkler S. A delay stochastic process with applications in molecular biology. J. Math. Biol. 57 (2008) 613
    • (2008) J. Math. Biol. , vol.57 , pp. 613
    • Schlicht, R.1    Winkler, S.2
  • 97
    • 70049108481 scopus 로고    scopus 로고
    • A model of sequential branching in hierarchical cell fate determination
    • Foster D., et al. A model of sequential branching in hierarchical cell fate determination. J. Theor. Biol. 260 4 (2009) 589
    • (2009) J. Theor. Biol. , vol.260 , Issue.4 , pp. 589
    • Foster, D.1
  • 98
  • 99
    • 22744441386 scopus 로고    scopus 로고
    • Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity
    • Weinberger L.S., Burnett J.C., Toettcher J.E., Arkin A.P., and Schaffer D.V. Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity. Cell 122 (2005) 169
    • (2005) Cell , vol.122 , pp. 169
    • Weinberger, L.S.1    Burnett, J.C.2    Toettcher, J.E.3    Arkin, A.P.4    Schaffer, D.V.5
  • 100
    • 0043180477 scopus 로고    scopus 로고
    • Oscillatory expression of Hes1, p53, and NF-kB driven by transcriptional time delays
    • Monk N.A.M. Oscillatory expression of Hes1, p53, and NF-kB driven by transcriptional time delays. Curr. Biol. 13 (2003) 1409
    • (2003) Curr. Biol. , vol.13 , pp. 1409
    • Monk, N.A.M.1
  • 101
    • 33745041963 scopus 로고    scopus 로고
    • Single molecule analysis of RNA polymerase transcription
    • Bai L., et al. Single molecule analysis of RNA polymerase transcription. Annu. Rev. Biophys. Biomol. Struct. 35 (2006) 343
    • (2006) Annu. Rev. Biophys. Biomol. Struct. , vol.35 , pp. 343
    • Bai, L.1
  • 102
    • 0025031912 scopus 로고
    • Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences
    • Lee D., Phung L., Stewart J., and Landick R. Transcription pausing by Escherichia coli RNA polymerase is modulated by downstream DNA sequences. J. Biol. Chem. 265 (1990) 15145
    • (1990) J. Biol. Chem. , vol.265 , pp. 15145
    • Lee, D.1    Phung, L.2    Stewart, J.3    Landick, R.4
  • 103
    • 13444293395 scopus 로고    scopus 로고
    • A method to estimate stochastic noise in large genetic regulatory networks
    • Orrell D., Ramsey S., deAtauri P., and Bolouri H. A method to estimate stochastic noise in large genetic regulatory networks. Bioinformatics 21 (2005) 208
    • (2005) Bioinformatics , vol.21 , pp. 208
    • Orrell, D.1    Ramsey, S.2    deAtauri, P.3    Bolouri, H.4
  • 104
    • 17644396339 scopus 로고    scopus 로고
    • Dizzy: stochastic simulation of large-scale genetic regulatory networks
    • Ramsey S., Orrell D., and Bolouri H. Dizzy: stochastic simulation of large-scale genetic regulatory networks. J. Bioinform. Comput. Biol. 3 2 (2005) 415
    • (2005) J. Bioinform. Comput. Biol. , vol.3 , Issue.2 , pp. 415
    • Ramsey, S.1    Orrell, D.2    Bolouri, H.3
  • 105
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie D.T. Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115 (2001) 1716
    • (2001) J. Chem. Phys. , vol.115 , pp. 1716
    • Gillespie, D.T.1
  • 106
    • 0942279178 scopus 로고    scopus 로고
    • Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method
    • Rathinam M., Petzold L., Cao Y., and Gillespie D. Stiffness in stochastic chemically reacting systems: the implicit tau-leaping method. J. Chem. Phys. 119 (2003) 12784
    • (2003) J. Chem. Phys. , vol.119 , pp. 12784
    • Rathinam, M.1    Petzold, L.2    Cao, Y.3    Gillespie, D.4
  • 107
    • 0242425970 scopus 로고    scopus 로고
    • Improved leap-size selection for accelerated stochastic simulation
    • Gillespie D.T., and Petzold L.R. Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys. 119 (2004) 8229
    • (2004) J. Chem. Phys. , vol.119 , pp. 8229
    • Gillespie, D.T.1    Petzold, L.R.2
  • 108
    • 3042595010 scopus 로고    scopus 로고
    • Cellware - a multi-algorithmic software for computational systems biology
    • Dhar P., et al. Cellware - a multi-algorithmic software for computational systems biology. Bioinformatics 20 (2004) 1319
    • (2004) Bioinformatics , vol.20 , pp. 1319
    • Dhar, P.1
  • 109
    • 0032825010 scopus 로고    scopus 로고
    • Mathematical simulation and analysis of cellular metabolism and regulation
    • Goryanin I., Hodgman T.C., and Selkov E. Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15 (1999) 749
    • (1999) Bioinformatics , vol.15 , pp. 749
    • Goryanin, I.1    Hodgman, T.C.2    Selkov, E.3
  • 110
    • 0030921160 scopus 로고    scopus 로고
    • Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3
    • Mendes P. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22 (1997) 361
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 361
    • Mendes, P.1
  • 111
    • 0030792287 scopus 로고    scopus 로고
    • New pc versions of the kinetic-simulation and fitting programs, kinsim and fitsim
    • Dang Q., and Frieden C. New pc versions of the kinetic-simulation and fitting programs, kinsim and fitsim. Trends Biochem. Sci. 22 (1997) 317
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 317
    • Dang, Q.1    Frieden, C.2
  • 112
    • 42449102270 scopus 로고    scopus 로고
    • Unbiased tau-leap methods for stochastic simulation of chemically reacting systems
    • Xu Z., and Cai X. Unbiased tau-leap methods for stochastic simulation of chemically reacting systems. J. Chem. Phys. 128 (2008) 54112
    • (2008) J. Chem. Phys. , vol.128 , pp. 54112
    • Xu, Z.1    Cai, X.2
  • 113
    • 44449148341 scopus 로고    scopus 로고
    • Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise
    • Leier A., Marquez-Lago T., and Burrage K. Generalized binomial τ-leap method for biochemical kinetics incorporating both delay and intrinsic noise. J. Chem. Phys. 128 (2008) 205107
    • (2008) J. Chem. Phys. , vol.128 , pp. 205107
    • Leier, A.1    Marquez-Lago, T.2    Burrage, K.3
  • 114
    • 52949098296 scopus 로고    scopus 로고
    • Frequency-modulated nuclear localization bursts coordinate gene regulation
    • Cai L., Dalal C.K., and Elowitz M.B. Frequency-modulated nuclear localization bursts coordinate gene regulation. Nature 455 (2008) 485
    • (2008) Nature , vol.455 , pp. 485
    • Cai, L.1    Dalal, C.K.2    Elowitz, M.B.3
  • 115
    • 33748520215 scopus 로고    scopus 로고
    • Stochastic simulation of chemical reactions with spatial resolution and single molecule detail
    • Andrews S., and Bray D. Stochastic simulation of chemical reactions with spatial resolution and single molecule detail. Phys. Biol. 1 (2004) 137
    • (2004) Phys. Biol. , vol.1 , pp. 137
    • Andrews, S.1    Bray, D.2
  • 116
    • 0035455635 scopus 로고    scopus 로고
    • Distributing MCell simulations on the grid
    • Casanova H., et al. Distributing MCell simulations on the grid. Int. J. High Perform. Comput. Appl. 15 (2001) 243
    • (2001) Int. J. High Perform. Comput. Appl. , vol.15 , pp. 243
    • Casanova, H.1
  • 117
    • 0035789518 scopus 로고    scopus 로고
    • Gromacs 3.0: a package for molecular simulation and trajectory analysis
    • Lindahl E., Hess B., and van der Spoel D. Gromacs 3.0: a package for molecular simulation and trajectory analysis. J. Mol. Model. 7 (2001) 306
    • (2001) J. Mol. Model. , vol.7 , pp. 306
    • Lindahl, E.1    Hess, B.2    van der Spoel, D.3
  • 118
    • 29244454300 scopus 로고    scopus 로고
    • Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space
    • van Zon J., and Wolde P. Green's-function reaction dynamics: a particle-based approach for simulating biochemical networks in time and space. J. Chem. Phys. 123 (2005) 1
    • (2005) J. Chem. Phys. , vol.123 , pp. 1
    • van Zon, J.1    Wolde, P.2
  • 119
    • 34548141875 scopus 로고    scopus 로고
    • Computational methods for diffusion-influenced biochemical reactions
    • Dobrzynski M., Rodriguez J., Kaandorp J., and Blom J. Computational methods for diffusion-influenced biochemical reactions. Bioinformatics 23 (2007) 1969
    • (2007) Bioinformatics , vol.23 , pp. 1969
    • Dobrzynski, M.1    Rodriguez, J.2    Kaandorp, J.3    Blom, J.4


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