메뉴 건너뛰기




Volumn 108, Issue 2, 2012, Pages 750-759

Numerical framework to model temporally resolved multi-stage dynamic systems

Author keywords

Androgen; Chemical kinetics; LabVIEW; MWC; Signaling; Simulation

Indexed keywords

ANDROGEN; BIOCHEMICAL MODEL; BIOCHEMICAL PATHWAY; CHEMICAL SYSTEMS; COREGULATORS; DATA COLLECTION; DNA BINDING; ESTIMATE MODEL; LABVIEW; LIGAND BINDING; MULTI-STAGE; MULTI-STAGE MODELS; MWC; NATIONAL INSTRUMENTS; NONLINEAR DIFFERENTIAL EQUATION; PROTEIN COMPLEXES; SIMULATION; SOFTWARE MODULES; SOFTWARE TOOLKITS; SPATIO-TEMPORAL COORDINATION; STEROID HORMONE; TEMPORALLY RESOLVED; TRANSCRIPTIONAL ACTIVITY; VIRTUAL INSTRUMENTATION;

EID: 84867401904     PISSN: 01692607     EISSN: 18727565     Source Type: Journal    
DOI: 10.1016/j.cmpb.2012.04.010     Document Type: Article
Times cited : (2)

References (42)
  • 1
    • 0020740241 scopus 로고
    • Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM - a flexible, portable system
    • Barshop B.A., Wrenn R.F., Frieden C. Analysis of numerical methods for computer simulation of kinetic processes: development of KINSIM - a flexible, portable system. Analytical Biochemistry 1983, 130:134-145.
    • (1983) Analytical Biochemistry , vol.130 , pp. 134-145
    • Barshop, B.A.1    Wrenn, R.F.2    Frieden, C.3
  • 3
    • 0037461036 scopus 로고    scopus 로고
    • Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations
    • (Oxford, England)
    • Shapiro B.E., Levchenko A., Meyerowitz E.M., Wold B.J., Mjolsness E.D. Cellerator: extending a computer algebra system to include biochemical arrows for signal transduction simulations. Bioinformatics 2003, 19:677-678. (Oxford, England).
    • (2003) Bioinformatics , vol.19 , pp. 677-678
    • Shapiro, B.E.1    Levchenko, A.2    Meyerowitz, E.M.3    Wold, B.J.4    Mjolsness, E.D.5
  • 4
    • 34447551397 scopus 로고    scopus 로고
    • Structural and functional analysis of cellular networks with CellNetAnalyzer
    • Klamt S., Saez-Rodriguez J., Gilles E.D. Structural and functional analysis of cellular networks with CellNetAnalyzer. BMC Systems Biology 2007, 1:2.
    • (2007) BMC Systems Biology , vol.1 , pp. 2
    • Klamt, S.1    Saez-Rodriguez, J.2    Gilles, E.D.3
  • 7
    • 56249084597 scopus 로고    scopus 로고
    • Androgen receptor functional analyses by high throughput imaging: determination of ligand, cell cycle, and mutation-specific effects
    • Szafran A.T., Szwarc M., Marcelli M., Mancini M.A. Androgen receptor functional analyses by high throughput imaging: determination of ligand, cell cycle, and mutation-specific effects. PLoS One 2008, 3:e3605.
    • (2008) PLoS One , vol.3
    • Szafran, A.T.1    Szwarc, M.2    Marcelli, M.3    Mancini, M.A.4
  • 8
  • 9
    • 0013196886 scopus 로고    scopus 로고
    • Kinetic investigation of the photocatalytic reduction of nitric oxide by carbon monoxide at low pressure on silica-supported molybdenum oxide
    • Lisachenko A.A., Chikhachev K.S., Zakharov M.N., Basov L.L., Shelimov B.N., Subbotina I.R., et al. Kinetic investigation of the photocatalytic reduction of nitric oxide by carbon monoxide at low pressure on silica-supported molybdenum oxide. Topics in Catalysis 2002, 20:119-128.
    • (2002) Topics in Catalysis , vol.20 , pp. 119-128
    • Lisachenko, A.A.1    Chikhachev, K.S.2    Zakharov, M.N.3    Basov, L.L.4    Shelimov, B.N.5    Subbotina, I.R.6
  • 10
    • 0001519679 scopus 로고
    • Some general implicit processes for the numerical solution of differential equations
    • Rosenbrock H.H. Some general implicit processes for the numerical solution of differential equations. The Computer Journal 1963, 5:329-330.
    • (1963) The Computer Journal , vol.5 , pp. 329-330
    • Rosenbrock, H.H.1
  • 11
    • 0000873069 scopus 로고
    • A method for the solution of certain problems in least squares
    • Levenberg K. A method for the solution of certain problems in least squares. Quarterly of Applied Mathematics 1944, 2:164-168.
    • (1944) Quarterly of Applied Mathematics , vol.2 , pp. 164-168
    • Levenberg, K.1
  • 12
    • 0000169232 scopus 로고
    • An algorithm for least-squares estimation of nonlinear parameters
    • Marquardt D. An algorithm for least-squares estimation of nonlinear parameters. SIAM Journal of Applied Mathematics 1963, 11:431-441.
    • (1963) SIAM Journal of Applied Mathematics , vol.11 , pp. 431-441
    • Marquardt, D.1
  • 13
    • 84867401455 scopus 로고    scopus 로고
    • Waptia - Genetic Optimization Algorithm
    • W. Golebiowski, Waptia - Genetic Optimization Algorithm, 2011.
    • (2011)
    • Golebiowski, W.1
  • 14
    • 84867396857 scopus 로고    scopus 로고
    • Release Notes for PIKAIA 1.2, National Center for Atmospheric Research Technical Note
    • P. Charbonneau, Release Notes for PIKAIA 1.2, National Center for Atmospheric Research Technical Note, 2002, 451.
    • (2002) , pp. 451
    • Charbonneau, P.1
  • 15
    • 0037342537 scopus 로고    scopus 로고
    • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models
    • (Oxford, England)
    • Hucka M., Finney A., Sauro H.M., Bolouri H., Doyle J.C., Kitano H., et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 2003, 19:524-531. (Oxford, England).
    • (2003) Bioinformatics , vol.19 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 16
    • 0000481011 scopus 로고
    • Sensitivity analysis of complex kinetic systems. Tools and applications
    • Turányi T. Sensitivity analysis of complex kinetic systems. Tools and applications. Journal of Mathematical Chemistry 1990, 5:203-248.
    • (1990) Journal of Mathematical Chemistry , vol.5 , pp. 203-248
    • Turányi, T.1
  • 17
    • 33845410054 scopus 로고    scopus 로고
    • Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments
    • van Riel N.A. Dynamic modelling and analysis of biochemical networks: mechanism-based models and model-based experiments. Briefings in Bioinformatics 2006, 7:364-374.
    • (2006) Briefings in Bioinformatics , vol.7 , pp. 364-374
    • van Riel, N.A.1
  • 20
    • 0024204442 scopus 로고
    • The rat androgen receptor: primary structure, autoregulation of its messenger ribonucleic acid, and immunocytochemical localization of the receptor protein
    • (Baltimore, MD)
    • Tan J.A., Joseph D.R., Quarmby V.E., Lubahn D.B., Sar M., French F.S., et al. The rat androgen receptor: primary structure, autoregulation of its messenger ribonucleic acid, and immunocytochemical localization of the receptor protein. Molecular Endocrinology 1988, 2:1276-1285. (Baltimore, MD).
    • (1988) Molecular Endocrinology , vol.2 , pp. 1276-1285
    • Tan, J.A.1    Joseph, D.R.2    Quarmby, V.E.3    Lubahn, D.B.4    Sar, M.5    French, F.S.6
  • 23
    • 0025935923 scopus 로고
    • Domains of the human androgen receptor involved in steroid binding, transcriptional activation, and subcellular localization
    • (Baltimore, MD)
    • Jenster G., van der Korput H.A., van Vroonhoven C., van der Kwast T.H., Trapman J., Brinkmann A.O. Domains of the human androgen receptor involved in steroid binding, transcriptional activation, and subcellular localization. Molecular Endocrinology 1991, 5:1396-1404. (Baltimore, MD).
    • (1991) Molecular Endocrinology , vol.5 , pp. 1396-1404
    • Jenster, G.1    van der Korput, H.A.2    van Vroonhoven, C.3    van der Kwast, T.H.4    Trapman, J.5    Brinkmann, A.O.6
  • 26
    • 0034714276 scopus 로고    scopus 로고
    • Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations
    • Matias P.M., Donner P., Coelho R., Thomaz M., Peixoto C., Macedo S., et al. Structural evidence for ligand specificity in the binding domain of the human androgen receptor. Implications for pathogenic gene mutations. The Journal of Biological Chemistry 2000, 275:26164-26171.
    • (2000) The Journal of Biological Chemistry , vol.275 , pp. 26164-26171
    • Matias, P.M.1    Donner, P.2    Coelho, R.3    Thomaz, M.4    Peixoto, C.5    Macedo, S.6
  • 28
    • 0028891989 scopus 로고
    • Ligand-induced conformational alterations of the androgen receptor analyzed by limited trypsinization. Studies on the mechanism of antiandrogen action
    • Kuil C.W., Berrevoets C.A., Mulder E. Ligand-induced conformational alterations of the androgen receptor analyzed by limited trypsinization. Studies on the mechanism of antiandrogen action. The Journal of Biological Chemistry 1995, 270:27569-27576.
    • (1995) The Journal of Biological Chemistry , vol.270 , pp. 27569-27576
    • Kuil, C.W.1    Berrevoets, C.A.2    Mulder, E.3
  • 29
    • 0027161982 scopus 로고
    • Steroid requirement for androgen receptor dimerization and DNA binding. Modulation by intramolecular interactions between the NH2-terminal and steroid-binding domains
    • Wong C.I., Zhou Z.X., Sar M., Wilson E.M. Steroid requirement for androgen receptor dimerization and DNA binding. Modulation by intramolecular interactions between the NH2-terminal and steroid-binding domains. The Journal of Biological Chemistry 1993, 268:19004-19012.
    • (1993) The Journal of Biological Chemistry , vol.268 , pp. 19004-19012
    • Wong, C.I.1    Zhou, Z.X.2    Sar, M.3    Wilson, E.M.4
  • 32
    • 8344226282 scopus 로고    scopus 로고
    • Structural basis for androgen receptor interdomain and coactivator interactions suggests a transition in nuclear receptor activation function dominance
    • He B., Gampe R.T., Kole A.J., Hnat A.T., Stanley T.B., An G., et al. Structural basis for androgen receptor interdomain and coactivator interactions suggests a transition in nuclear receptor activation function dominance. Molecular Cell 2004, 16:425-438.
    • (2004) Molecular Cell , vol.16 , pp. 425-438
    • He, B.1    Gampe, R.T.2    Kole, A.J.3    Hnat, A.T.4    Stanley, T.B.5    An, G.6
  • 33
    • 33744489573 scopus 로고    scopus 로고
    • Linking ligand-induced alterations in androgen receptor structure to differential gene expression: a first step in the rational design of selective androgen receptor modulators
    • (Baltimore, MD)
    • Kazmin D., Prytkova T., Cook C.E., Wolfinger R., Chu T.M., Beratan D., et al. Linking ligand-induced alterations in androgen receptor structure to differential gene expression: a first step in the rational design of selective androgen receptor modulators. Molecular Endocrinology 2006, 20:1201-1217. (Baltimore, MD).
    • (2006) Molecular Endocrinology , vol.20 , pp. 1201-1217
    • Kazmin, D.1    Prytkova, T.2    Cook, C.E.3    Wolfinger, R.4    Chu, T.M.5    Beratan, D.6
  • 34
    • 77949520128 scopus 로고    scopus 로고
    • Androgen receptor mutations associated with androgen insensitivity syndrome: a high content analysis approach leading to personalized medicine
    • Szafran A.T., Hartig S., Sun H., Uray I.P., Szwarc M., Shen Y., et al. Androgen receptor mutations associated with androgen insensitivity syndrome: a high content analysis approach leading to personalized medicine. PLoS One 2009, 4:e8179.
    • (2009) PLoS One , vol.4
    • Szafran, A.T.1    Hartig, S.2    Sun, H.3    Uray, I.P.4    Szwarc, M.5    Shen, Y.6
  • 35
    • 33846347711 scopus 로고    scopus 로고
    • The androgen receptor T877A mutant recruits LXXLL and FXXLF peptides differently than wild-type androgen receptor in a time-resolved fluorescence resonance energy transfer assay
    • Ozers M.S., Marks B.D., Gowda K., Kupcho K.R., Ervin K.M., De Rosier T., et al. The androgen receptor T877A mutant recruits LXXLL and FXXLF peptides differently than wild-type androgen receptor in a time-resolved fluorescence resonance energy transfer assay. Biochemistry 2007, 46:683-695.
    • (2007) Biochemistry , vol.46 , pp. 683-695
    • Ozers, M.S.1    Marks, B.D.2    Gowda, K.3    Kupcho, K.R.4    Ervin, K.M.5    De Rosier, T.6
  • 37
    • 0033609474 scopus 로고    scopus 로고
    • Redox-dependent DNA binding of the purified androgen receptor: evidence for disulfide-linked androgen receptor dimers
    • Liao M., Zhou Z., Wilson E.M. Redox-dependent DNA binding of the purified androgen receptor: evidence for disulfide-linked androgen receptor dimers. Biochemistry 1999, 38:9718-9727.
    • (1999) Biochemistry , vol.38 , pp. 9718-9727
    • Liao, M.1    Zhou, Z.2    Wilson, E.M.3
  • 39
    • 20344370764 scopus 로고    scopus 로고
    • Allosteric mechanisms of signal transduction
    • (New York, NY)
    • Changeux J.P., Edelstein S.J. Allosteric mechanisms of signal transduction. Science 2005, 308:1424-1428. (New York, NY).
    • (2005) Science , vol.308 , pp. 1424-1428
    • Changeux, J.P.1    Edelstein, S.J.2
  • 40
    • 0004280513 scopus 로고
    • Cambridge University Press, Cambridge Cambridgeshire, New York.
    • Imai K. Allosteric Effects in Haemoglobin 1982, Cambridge University Press, Cambridge Cambridgeshire, New York, p. 275.
    • (1982) Allosteric Effects in Haemoglobin , pp. 275
    • Imai, K.1
  • 41
    • 0015937135 scopus 로고
    • Analyses of oxygen equilibria of native and chemically modified human adult hemoglobins on the basis of Adair's stepwise oxygenation theory and the allosteric model of Monod, Wyman, and Changeux
    • Imai K. Analyses of oxygen equilibria of native and chemically modified human adult hemoglobins on the basis of Adair's stepwise oxygenation theory and the allosteric model of Monod, Wyman, and Changeux. Biochemistry 1973, 12:798-808.
    • (1973) Biochemistry , vol.12 , pp. 798-808
    • Imai, K.1
  • 42
    • 0030907624 scopus 로고    scopus 로고
    • Can a two-state MWC allosteric model explain hemoglobin kinetics?
    • Henry E.R., Jones C.M., Hofrichter J., Eaton W.A. Can a two-state MWC allosteric model explain hemoglobin kinetics?. Biochemistry 1997, 36:6511-6528.
    • (1997) Biochemistry , vol.36 , pp. 6511-6528
    • Henry, E.R.1    Jones, C.M.2    Hofrichter, J.3    Eaton, W.A.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.