메뉴 건너뛰기




Volumn 4, Issue 3, 2004, Pages 293-309

Modeling and simulation of biological systems with stochasticity

Author keywords

Gene regulation; Gillespie algorithms; In silico biology; Noise; Pathway modeling; Signal transduction; Stochastic focusing; Stochastic resonance

Indexed keywords

ACCURACY; ARTICLE; BIOLOGICAL MODEL; CELLULAR PARAMETERS; COMPUTER MODEL; COMPUTER PROGRAM; COMPUTER SIMULATION; ESCHERICHIA COLI; GENE CONTROL; GENE EXPRESSION; GENETIC ALGORITHM; GENETIC VARIABILITY; MATHEMATICAL MODEL; METABOLISM; NONHUMAN; PHENOTYPE; SIGNAL TRANSDUCTION; STOCHASTIC MODEL;

EID: 10044260032     PISSN: 13866338     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Article
Times cited : (99)

References (62)
  • 1
    • 0030065744 scopus 로고    scopus 로고
    • Evidence that hematopoiesis may be a stochastic process in vivo
    • Abkowitz, J., Catlin, S. and Guttorp, P. (1996). Evidence that hematopoiesis may be a stochastic process in vivo. Nat. Med. 2, 190-197.
    • (1996) Nat. Med. , vol.2 , pp. 190-197
    • Abkowitz, J.1    Catlin, S.2    Guttorp, P.3
  • 2
    • 10044257345 scopus 로고    scopus 로고
    • Kinsolver: A simulator for biochemical and gene regulatory networks
    • Aleman-Meza, B., Schuttler, H.B., Arnold, J. and Taha, T.R. (2002). Kinsolver: A simulator for biochemical and gene regulatory networks. http://webster.cs.uga.edu/boanerg/mams.
    • (2002)
    • Aleman-Meza, B.1    Schuttler, H.B.2    Arnold, J.3    Taha, T.R.4
  • 4
    • 0031879114 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells
    • Arkin, A., Ross, J. and McAdams, H.H. (1998). Stochastic kinetic analysis of developmental pathway bifurcation in phage lambda-infected escherichia coli cells. Genetics 4, 1633-1648.
    • (1998) Genetics , vol.4 , pp. 1633-1648
    • Arkin, A.1    Ross, J.2    McAdams, H.H.3
  • 5
    • 0034688220 scopus 로고    scopus 로고
    • Circadian clocks limited by noise
    • Barkai, N. and Leibler, S. (2000). Circadian clocks limited by noise. Nature 403, 267-268.
    • (2000) Nature , vol.403 , pp. 267-268
    • Barkai, N.1    Leibler, S.2
  • 6
    • 10044224247 scopus 로고    scopus 로고
    • M-cell
    • Bartol, T.M. and Stiles, J.R. (2002). M-cell. http://www.MCell.cnl.salk.edu.
    • (2002)
    • Bartol, T.M.1    Stiles, J.R.2
  • 7
    • 0028465092 scopus 로고
    • Counting polymers moving through a single ion channel
    • Bezrukov, S.M., Vodyanoy, I. and Parsegian, V.A. (1994). Counting polymers moving through a single ion channel. Nature 370, 279-281.
    • (1994) Nature , vol.370 , pp. 279-281
    • Bezrukov, S.M.1    Vodyanoy, I.2    Parsegian, V.A.3
  • 9
    • 84888265913 scopus 로고    scopus 로고
    • Using hybrid concurrent constraint programming to model dynamic biological systems
    • Copenhagen, July 2002. Springer, LNCS
    • Bockmayr, A. and Courtois, A. (2002). Using hybrid concurrent constraint programming to model dynamic biological systems. 18th International Conference on Logic Programming, ICLP'02, Copenhagen, July 2002. Springer, LNCS 2401, 85-99.
    • (2002) 18th International Conference on Logic Programming, ICLP'02 , vol.2401 , pp. 85-99
    • Bockmayr, A.1    Courtois, A.2
  • 10
    • 0037339442 scopus 로고    scopus 로고
    • Fluctuations and slow variables in genetic networks
    • Bundschuh, R., Hayot, F. and Javaprakash, C. (2003). Fluctuations and slow variables in genetic networks. Biophys. J. 84, 1606-1615.
    • (2003) Biophys. J. , vol.84 , pp. 1606-1615
    • Bundschuh, R.1    Hayot, F.2    Javaprakash, C.3
  • 11
    • 0020338594 scopus 로고
    • Expression of malT, the regulator gene of the maltose region in Escherichia coli, is limited both at transcription and translation
    • Chapon, C. (1982). Expression of malT, the regulator gene of the maltose region in Escherichia coli, is limited both at transcription and translation. EMBO J. 1, 369-374.
    • (1982) EMBO J. , vol.1 , pp. 369-374
    • Chapon, C.1
  • 12
    • 0026023024 scopus 로고
    • Metamodel: A program for modling and control analysis of metabolic pathways on the ibm pc and compatibles
    • Cornish-Bowden, A. and Hofmeyr, J.-H.S. (1991). Metamodel: A program for modling and control analysis of metabolic pathways on the ibm pc and compatibles. Comput. Applic. Biosci. 7, 89-93.
    • (1991) Comput. Applic. Biosci. , vol.7 , pp. 89-93
    • Cornish-Bowden, A.1    Hofmeyr, J.-H.S.2
  • 13
    • 0030792287 scopus 로고    scopus 로고
    • New pc versions of the kinetic-simulation and fitting programs, kinsim and fitsim
    • Dang, Q. and Frieden, C. (1997). New pc versions of the kinetic-simulation and fitting programs, kinsim and fitsim. Trends Biochem. Sci. 22, 317.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 317
    • Dang, Q.1    Frieden, C.2
  • 14
    • 10044231353 scopus 로고    scopus 로고
    • Cellware
    • Dhar, P. 2003. Cellware. http://www.bii.a-star.edu.sg/sbg/cellware.
    • (2003)
    • Dhar, P.1
  • 16
    • 0027485141 scopus 로고
    • Stochastic resonance: Noise-enhanced information transfer in crayfish mechanoreceptors
    • Douglass, J.K., Wilkens, L., Pantazelou, E. amnd Moss, F. (1993). Stochastic resonance: Noise-enhanced information transfer in crayfish mechanoreceptors. Nature 36, 337-340.
    • (1993) Nature , vol.36 , pp. 337-340
    • Douglass, J.K.1    Wilkens, L.2    Pantazelou, E.3    Moss, F.4
  • 17
    • 0029073341 scopus 로고
    • Mist: A user-friendly metabolic simulator
    • Ehlde, M. and Zacchi, G. (1995). Mist: A user-friendly metabolic simulator. Comput. Applic. Biosci. 11, 201-207.
    • (1995) Comput. Applic. Biosci. , vol.11 , pp. 201-207
    • Ehlde, M.1    Zacchi, G.2
  • 18
    • 0041324718 scopus 로고    scopus 로고
    • Mesoscopic reaction-diffusion in intracellular signaling
    • Elf, J., Doncic, A. and Ehrenberg, M. (2003). Mesoscopic reaction-diffusion in intracellular signaling. Proceedings of SPIE 5110, 114-124.
    • (2003) Proceedings of SPIE , vol.5110 , pp. 114-124
    • Elf, J.1    Doncic, A.2    Ehrenberg, M.3
  • 19
    • 0037119587 scopus 로고    scopus 로고
    • Stochastic gene expression in a single cell
    • Elowitz, M.B., Levine, A., Siggia, E. and Swain, P. (2002). Stochastic gene expression in a single cell. Science 297, 1183-1186.
    • (2002) Science , vol.297 , pp. 1183-1186
    • Elowitz, M.B.1    Levine, A.2    Siggia, E.3    Swain, P.4
  • 21
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson, M.A. and Bruck, J. (2000). Efficient exact stochastic simulation of chemical systems with many species and many channels. J. Phys. Chem. 104, 1876-1889.
    • (2000) J. Phys. Chem. , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 22
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.T. (1977). Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361.
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.T.1
  • 23
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie, D.T. (2001). Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115, 1716-1733.
    • (2001) J. Chem. Phys. , vol.115 , pp. 1716-1733
    • Gillespie, D.T.1
  • 24
    • 0242425970 scopus 로고    scopus 로고
    • Improved leap-size selection for accelerated stochastic simulation
    • Gillespie, D.T. and Petzold, L.R. (2004). Improved leap-size selection for accelerated stochastic simulation. J. Chem. Phys. 119, 8229-8234.
    • (2004) J. Chem. Phys. , vol.119 , pp. 8229-8234
    • Gillespie, D.T.1    Petzold, L.R.2
  • 25
    • 0037154231 scopus 로고    scopus 로고
    • Robustness of circadian rhythms with respect to molecular noise
    • Gonze, D., Halloy, J. and Goldbeter, A. (2002). Robustness of circadian rhythms with respect to molecular noise. Proc. Natl. Acad. Sci. USA 99, 673-678.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 673-678
    • Gonze, D.1    Halloy, J.2    Goldbeter, A.3
  • 26
    • 0032825010 scopus 로고    scopus 로고
    • Mathematical simulation and analysis of cellular metabolism and regulation
    • Goryanin, I., Hodgman, T.C. and Selkov, E. (1999). Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics 15, 749-758.
    • (1999) Bioinformatics , vol.15 , pp. 749-758
    • Goryanin, I.1    Hodgman, T.C.2    Selkov, E.3
  • 27
    • 0037109565 scopus 로고    scopus 로고
    • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    • Haseltine, E.L. and Rawlings, J.B. (2002). Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics. J. Chem. Phys. 117, 6959-6969.
    • (2002) J. Chem. Phys. , vol.117 , pp. 6959-6969
    • Haseltine, E.L.1    Rawlings, J.B.2
  • 28
    • 0036578786 scopus 로고    scopus 로고
    • Translating the noise
    • Hasty, J. and Collins, J.J. (2002). Translating the noise. Nat. Genet. 31, 13-14.
    • (2002) Nat. Genet. , vol.31 , pp. 13-14
    • Hasty, J.1    Collins, J.J.2
  • 29
    • 0006092502 scopus 로고    scopus 로고
    • Designer gene networks: Towards fundamental cellular control
    • Hasty, J. and Issacs, F. (2001). Designer gene networks: Towards fundamental cellular control. CHAOS 11, 207-220.
    • (2001) CHAOS , vol.11 , pp. 207-220
    • Hasty, J.1    Issacs, F.2
  • 31
    • 0034307684 scopus 로고    scopus 로고
    • Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression
    • Hume, D.A. (2000). Probability in transcriptional regulation and its implications for leukocyte differentiation and inducible gene expression. Blood 96, 2323-2328.
    • (2000) Blood , vol.96 , pp. 2323-2328
    • Hume, D.A.1
  • 32
    • 0036207347 scopus 로고    scopus 로고
    • Modeling and simulation of genetic regulatory systems: A literature review, journal of computational biology
    • de Jong, H. (2002). Modeling and simulation of genetic regulatory systems: A literature review, journal of computational biology. J. Comput. Biol. 9, 67-103.
    • (2002) J. Comput. Biol. , vol.9 , pp. 67-103
    • de Jong, H.1
  • 33
    • 0036607108 scopus 로고    scopus 로고
    • Modeling a hox gene network in silico using a stochastic simulation algorithm
    • Kastner, J., Solomon, J., and Fraser, S. (2002). modeling a hox gene network in silico using a stochastic simulation algorithm. Developmental Biology 246, 122-131.
    • (2002) Developmental Biology , vol.246 , pp. 122-131
    • Kastner, J.1    Solomon, J.2    Fraser, S.3
  • 35
    • 0035896577 scopus 로고    scopus 로고
    • The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression
    • Kierzek, A.M., Zaim, J. and Zielenkiewicz, P. (2001). The effect of transcription and translation initiation frequencies on the stochastic fluctuations in prokaryotic gene expression. J. Biol. Chem. 276, 8165-8172.
    • (2001) J. Biol. Chem. , vol.276 , pp. 8165-8172
    • Kierzek, A.M.1    Zaim, J.2    Zielenkiewicz, P.3
  • 36
    • 0029978336 scopus 로고    scopus 로고
    • Broadband neural encoding in the cricket cercal sensory system enhanced by stochastic resonance
    • Levin, J.E. and Miller, J.P. (1996). Broadband neural encoding in the cricket cercal sensory system enhanced by stochastic resonance. Nature 380, 165-168.
    • (1996) Nature , vol.380 , pp. 165-168
    • Levin, J.E.1    Miller, J.P.2
  • 37
    • 0142039003 scopus 로고    scopus 로고
    • Noise in gene expression as the source of non-genetic individuality in the chemotactic response of Escherichia coli
    • Levin, M.D. (2003). Noise in gene expression as the source of non-genetic individuality in the chemotactic response of Escherichia coli. FEBS Lett. 550, 135-138.
    • (2003) FEBS Lett. , vol.550 , pp. 135-138
    • Levin, M.D.1
  • 38
    • 0033648431 scopus 로고    scopus 로고
    • Hybrid petri net representations of gene regulatory networks
    • Matsuno, H., Doi, A., Nagasaki, M. and Miyano, S. (2000). Hybrid petri net representations of gene regulatory networks. Pac. Symp. Biocomput. 5, 333-349.
    • (2000) Pac. Symp. Biocomput. , vol.5 , pp. 333-349
    • Matsuno, H.1    Doi, A.2    Nagasaki, M.3    Miyano, S.4
  • 39
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • McAdams, H.H. and Arkin, A. (1997). Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA 94, 814-819.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 814-819
    • McAdams, H.H.1    Arkin, A.2
  • 40
    • 0030921160 scopus 로고    scopus 로고
    • Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3
    • Mendes, P. (1997). Biochemistry by numbers: Simulation of biochemical pathways with Gepasi 3. Trends Biochem. Sci. 22, 361-363.
    • (1997) Trends Biochem. Sci. , vol.22 , pp. 361-363
    • Mendes, P.1
  • 42
    • 0032492834 scopus 로고    scopus 로고
    • Predicting temporal fluctuations in an intracellular signaling pathway
    • Morton-Firth, C.J. and Bray, D. (1998). Predicting temporal fluctuations in an intracellular signaling pathway. J. Theor. Biol. 192, 117-128.
    • (1998) J. Theor. Biol. , vol.192 , pp. 117-128
    • Morton-Firth, C.J.1    Bray, D.2
  • 44
    • 0034691214 scopus 로고    scopus 로고
    • Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation
    • Paulsson, J., Berg, O.G., and Ehrenberg, M. (2000). Stochastic focusing: Fluctuation-enhanced sensitivity of intracellular regulation. Proc. Natl. Acad. Sci. USA 97, 7148-7153.
    • (2000) Proc. Natl. Acad. Sci. USA , vol.97 , pp. 7148-7153
    • Paulsson, J.1    Berg, O.G.2    Ehrenberg, M.3
  • 45
    • 1542345686 scopus 로고    scopus 로고
    • Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
    • Puchalka, J. and Kierzek, A.M. (2004). Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophys. J. 86, 1357-1372.
    • (2004) Biophys. J. , vol.86 , pp. 1357-1372
    • Puchalka, J.1    Kierzek, A.M.2
  • 46
    • 0028328719 scopus 로고
    • Transcription of individual genes in eukaryotic cells occurs randomly and infrequently
    • Ross, I.L., Browne, C.M., and Hume, D.A. (1994). Transcription of individual genes in eukaryotic cells occurs randomly and infrequently. Immunol. Cell Biol. 72, 177-185.
    • (1994) Immunol. Cell Biol. , vol.72 , pp. 177-185
    • Ross, I.L.1    Browne, C.M.2    Hume, D.A.3
  • 48
    • 10044262905 scopus 로고
    • Use of the theories of multi-criteria optimization and of linear inequality systems for the steady-state modeling of biochemical systems
    • Schuster, S. and Heinrich, R. (1995). Use of the theories of multi-criteria optimization and of linear inequality systems for the steady-state modeling of biochemical systems. Mathematical Population Dynamics: Analysis of Heterogeneity 2, 35-48.
    • (1995) Mathematical Population Dynamics: Analysis of Heterogeneity , vol.2 , pp. 35-48
    • Schuster, S.1    Heinrich, R.2
  • 49
    • 17644426906 scopus 로고    scopus 로고
    • Parallel stochastic simulation of whole-cell models
    • Omnipress
    • Schwehm, M. (1996). Parallel stochastic simulation of whole-cell models. Proc. 2nd Int. Conf Systems Biology (ICSB 2001), Omnipress, pp. 333-341.
    • (1996) Proc. 2nd Int. Conf Systems Biology (ICSB 2001) , pp. 333-341
    • Schwehm, M.1
  • 51
    • 10044276143 scopus 로고    scopus 로고
    • The spatial organisation of cell signaling pathways - A computer based study
    • Ph. D. thesis, University of Cambridge, Cambridge, UK
    • Shimizu, T.S. (2002). The spatial organisation of cell signaling pathways - a computer based study. Ph. D. thesis, University of Cambridge, Cambridge, UK.
    • (2002)
    • Shimizu, T.S.1
  • 52
    • 0033782304 scopus 로고    scopus 로고
    • Modeling transcriptional control in gene networks-methods, recent results, and future directions
    • Smolen, P., Baxter, D. and Byrne, J. (2000). Modeling transcriptional control in gene networks-methods, recent results, and future directions. Bull. Math. Biol. 62, 247-292.
    • (2000) Bull. Math. Biol. , vol.62 , pp. 247-292
    • Smolen, P.1    Baxter, D.2    Byrne, J.3
  • 54
    • 0030211187 scopus 로고    scopus 로고
    • Stochastic simulation of coupled reaction-diffusion processes
    • Stundzia, A.B. and Lumsden, C.J. (1996). Stochastic simulation of coupled reaction-diffusion processes. J. Comput. Phys. 127, 196-207.
    • (1996) J. Comput. Phys. , vol.127 , pp. 196-207
    • Stundzia, A.B.1    Lumsden, C.J.2
  • 56
    • 78651158197 scopus 로고
    • A stochastic model of stem cell proliferation based on the growth of spleen colony-forming cells
    • Till, J.E., McCulloch, E. and Siminovitch, L. (1964). A stochastic model of stem cell proliferation based on the growth of spleen colony-forming cells. Proc. Natl. Acad. Sci. USA 51, 29-36.
    • (1964) Proc. Natl. Acad. Sci. USA , vol.51 , pp. 29-36
    • Till, J.E.1    McCulloch, E.2    Siminovitch, L.3
  • 58
    • 0026438799 scopus 로고
    • DNA inversions in phages and bacteria
    • van de Putte, P. and Goosen, N. (1992). DNA inversions in phages and bacteria. Trends Genet. 8, 457-462.
    • (1992) Trends Genet. , vol.8 , pp. 457-462
    • van de Putte, P.1    Goosen, N.2
  • 61
    • 0000860515 scopus 로고    scopus 로고
    • Minireview of stochastic resonance
    • Wiesenfeld, K. and Jaramillo, F. (1998). Minireview of stochastic resonance. Chaos 8, 539-548.
    • (1998) Chaos , vol.8 , pp. 539-548
    • Wiesenfeld, K.1    Jaramillo, F.2
  • 62
    • 0026663105 scopus 로고
    • Interdependence of translation, transcription and mRNA degradation in the lacZ gene
    • Yarchuk, O., Jacques, N., Guillerez, J. and Dreyfus, M. (1992). Interdependence of translation, transcription and mRNA degradation in the lacZ gene. J. Mol. Biol. 226, 581-596.
    • (1992) J. Mol. Biol. , vol.226 , pp. 581-596
    • Yarchuk, O.1    Jacques, N.2    Guillerez, J.3    Dreyfus, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.