메뉴 건너뛰기




Volumn 5945 LNBI, Issue , 2010, Pages 229-262

Modelling and analysis of the NF-κB pathway in Bio-PEPA

Author keywords

Analysis; Modelling; NF B pathway; Process algebras

Indexed keywords

BIOCHEMICAL SPECIES; DETERMINISTIC SIMULATION; EXPERIMENTAL DATA; EXTERNAL STIMULUS; IN-SILICO; INTERMEDIATE REPRESENTATIONS; NUCLEAR FACTORS; PROCESS ALGEBRAS; SIGNALLING PATHWAYS; SINGLE CELLS; STOCHASTIC SIMULATIONS; TIME EVOLUTIONS; TIME-DEPENDENT;

EID: 77950314677     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-11712-1_7     Document Type: Conference Paper
Times cited : (6)

References (50)
  • 1
    • 39949083374 scopus 로고    scopus 로고
    • Wires in the soup: Quantitative models of cell signalling
    • Cheong, R., Levchenko, A.: Wires in the soup: quantitative models of cell signalling. Trends in Cell Biology 18, 112-118 (2008)
    • (2008) Trends in Cell Biology , vol.18 , pp. 112-118
    • Cheong, R.1    Levchenko, A.2
  • 2
    • 38849199203 scopus 로고    scopus 로고
    • Shared principle in NF-κB Signalling
    • Hayden, M., Ghosh, S.: Shared principle in NF-κB Signalling. Cell 132, 344-362 (2008)
    • (2008) Cell , vol.132 , pp. 344-362
    • Hayden, M.1    Ghosh, S.2
  • 3
    • 0037044575 scopus 로고    scopus 로고
    • The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation
    • Hoffmann, A., Levchenko, A., Scott, M., Baltimore, D.: The IκB-NF-κB Signaling Module: Temporal Control and Selective Gene Activation. Science 298, 1241-1245 (2002)
    • (2002) Science , vol.298 , pp. 1241-1245
    • Hoffmann, A.1    Levchenko, A.2    Scott, M.3    Baltimore, D.4
  • 4
    • 0242574987 scopus 로고    scopus 로고
    • Investigations into the Analysis and the Modeling of the TNF-mediated NFκB Signaling Pathway
    • Cho, K.H., Shin, S.Y., Lee, H.W., et al.: Investigations Into the Analysis and the Modeling of the TNF-mediated NFκB Signaling Pathway. Genome Res. 13, 2413-2422 (2003)
    • (2003) Genome Res. , vol.13 , pp. 2413-2422
    • Cho, K.H.1    Shin, S.Y.2    Lee, H.W.3
  • 9
    • 17644427530 scopus 로고    scopus 로고
    • Sensitivity analysis of parameters controlling oscillatory signalling in the NF-κB pathway: The roles of IKK and IκBα
    • Ihekwaba, A., Broomhead, D., Grimley, R., Kell, D.: Sensitivity analysis of parameters controlling oscillatory signalling in the NF-κB pathway: the roles of IKK and IκBα. Systems Biology 1, 93-103 (2004)
    • (2004) Systems Biology , vol.1 , pp. 93-103
    • Ihekwaba, A.1    Broomhead, D.2    Grimley, R.3    Kell, D.4
  • 10
    • 27244454289 scopus 로고    scopus 로고
    • Synergistic control of oscillations in the NF-κB signalling pathway
    • Ihekwaba, A., Broomhead, D., Grimley, R., Kell, D.: Synergistic control of oscillations in the NF-κB signalling pathway. IEE Proc.-Syst. biol. 152, 153-160 (2005)
    • (2005) IEE Proc.-Syst. Biol. , vol.152 , pp. 153-160
    • Ihekwaba, A.1    Broomhead, D.2    Grimley, R.3    Kell, D.4
  • 11
    • 0027370376 scopus 로고
    • GEPASI: A software package for modelling the dynamics, steady states and control of biochemical and other systems
    • Mendes, P.: GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9, 563-571 (1993)
    • (1993) Comput. Appl. Biosci. , vol.9 , pp. 563-571
    • Mendes, P.1
  • 12
    • 0035888407 scopus 로고    scopus 로고
    • Application of a stochastic name-passing calculus to representation and simulation of molecular processes
    • Priami, C., Regev, A., Silverman, W., Shapiro, E.: Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80, 25-31 (2001)
    • (2001) Information Processing Letters , vol.80 , pp. 25-31
    • Priami, C.1    Regev, A.2    Silverman, W.3    Shapiro, E.4
  • 15
    • 26444448026 scopus 로고    scopus 로고
    • Beta binders for biological interactions
    • Danos, V., Schachter, V. (eds.) LNCS (LNBI), Springer, Heidelberg
    • Priami, C., Quaglia, P.: Beta binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol.3082, pp. 20-33. Springer, Heidelberg (2005)
    • (2005) CMSB 2004 , vol.3082 , pp. 20-33
    • Priami, C.1    Quaglia, P.2
  • 16
    • 38549120134 scopus 로고    scopus 로고
    • Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA
    • Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) LNCS (LNBI), Springer, Heidelberg
    • Calder, M., Gilmore, S., Hillston, J.: Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA. In: Priami, C., Ingólfsdóttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol.4230, pp. 1-23. Springer, Heidelberg (2006)
    • (2006) Transactions on Computational Systems Biology VII , vol.4230 , pp. 1-23
    • Calder, M.1    Gilmore, S.2    Hillston, J.3
  • 17
    • 77950323033 scopus 로고    scopus 로고
    • The Attributed Pi-Calculus with Priorities
    • Priami, C., et al. (eds.) LNCS (LNBI), Springer, Heidelberg
    • John, M., Lhoussaine, C., Niehren, J., Uhrmacher, A.: The Attributed Pi-Calculus with Priorities. In: Priami, C., et al. (eds.) Transactions on Computational Systems Biology XII. LNCS (LNBI), vol.5945, pp. 13-76. Springer, Heidelberg (2010)
    • (2010) Transactions on Computational Systems Biology XII , vol.5945 , pp. 13-76
    • John, M.1    Lhoussaine, C.2    Niehren, J.3    Uhrmacher, A.4
  • 21
    • 65549101937 scopus 로고    scopus 로고
    • Bio-PEPA: A Framework for the Modelling and Analysis of Biochemical Networks
    • Ciocchetta, F., Hillston, J.: Bio-PEPA: a Framework for the Modelling and Analysis of Biochemical Networks. Theoretical Computer Science 410, 3065-3084 (2009)
    • (2009) Theoretical Computer Science , vol.410 , pp. 3065-3084
    • Ciocchetta, F.1    Hillston, J.2
  • 22
    • 0034731365 scopus 로고    scopus 로고
    • Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation
    • Carlotti, F., Dower, S., Qwarnstrom, E.: Dynamic shuttling of nuclear factor kappa B between the nucleus and cytoplasm as a consequence of inhibitor dissociation. J. Biol. Chem. 275, 41028-41034 (2000)
    • (2000) J. Biol. Chem. , vol.275 , pp. 41028-41034
    • Carlotti, F.1    Dower, S.2    Qwarnstrom, E.3
  • 23
    • 0034730713 scopus 로고    scopus 로고
    • Failure to regulate TNF-induced NF-κB and cell death responses in A20-deficient mice
    • Lee, E., Boone, D., Chai, S., Libby, S., Chien, M., Lodolce, J., Ma, A.: Failure to regulate TNF-induced NF-κB and cell death responses in A20-deficient mice. Science 289, 2350-2354 (2000)
    • (2000) Science , vol.289 , pp. 2350-2354
    • Lee, E.1    Boone, D.2    Chai, S.3    Libby, S.4    Chien, M.5    Lodolce, J.6    Ma, A.7
  • 24
    • 45749113022 scopus 로고    scopus 로고
    • Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions
    • Bernardo, M., Degano, P., Zavattaro, G. (eds.) LNCS, Springer, Heidelberg
    • Degasperi, A., Gilmore, S.: Sensitivity Analysis of Stochastic Models of Bistable Biochemical Reactions. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol.5016, pp. 1-20. Springer, Heidelberg (2008)
    • (2008) SFM 2008 , vol.5016 , pp. 1-20
    • Degasperi, A.1    Gilmore, S.2
  • 25
    • 77950314874 scopus 로고    scopus 로고
    • Dizzy Edinburgh version (2009), http://homepages.inf.ed.ac.uk/stg/ software/Dizzy/
    • (2009) Dizzy Edinburgh Version
  • 26
    • 77950327762 scopus 로고    scopus 로고
    • Modelling and analysis of the NF-κB pathway in Bio-PEPA
    • Breitling, R., Gilbert, D.R., Heiner, M., Priami, C. (eds.) Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany
    • Ciocchetta, F., Degasperi, A., Heath, J., Hillston, J.: Modelling and analysis of the NF-κB pathway in Bio-PEPA. In: Breitling, R., Gilbert, D.R., Heiner, M., Priami, C. (eds.) Formal Methods in Molecular Biology, Dagstuhl, Germany. Dagstuhl Seminar Proceedings, vol.09091. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany (2009)
    • (2009) Formal Methods in Molecular Biology, Dagstuhl, Germany. Dagstuhl Seminar Proceedings , vol.9091
    • Ciocchetta, F.1    Degasperi, A.2    Heath, J.3    Hillston, J.4
  • 27
    • 0033596123 scopus 로고    scopus 로고
    • Genetic approaches in mice to understand Rel/NF-κB and IκB function: Transgenics and knockouts
    • Gerondakis, S., Grossmann, M., Nakamura, Y., Pohl, T., Grumont, R.: Genetic approaches in mice to understand Rel/NF-κB and IκB function: transgenics and knockouts. Oncogene 18, 6888-6895 (1999)
    • (1999) Oncogene , vol.18 , pp. 6888-6895
    • Gerondakis, S.1    Grossmann, M.2    Nakamura, Y.3    Pohl, T.4    Grumont, R.5
  • 28
  • 29
    • 77950312955 scopus 로고    scopus 로고
    • Technical Report TR 25/2007, The Microsoft Research-University of Trento Centre for Computational and Systems Biology
    • Larcher, R., Ihekwaba, A., Priami, C.: A BetaBW model for the NF-κB pathway. Technical Report TR 25/2007, The Microsoft Research-University of Trento Centre for Computational and Systems Biology (2007)
    • (2007) A BetaBW Model for the NF-κB Pathway
    • Larcher, R.1    Ihekwaba, A.2    Priami, C.3
  • 31
    • 70450179150 scopus 로고    scopus 로고
    • Bio-PEPA with events
    • Priami, C., Back, R.-J., Petre, I. (eds.) LNCS (LNBI), Springer, Heidelberg
    • Ciocchetta, F.: Bio-PEPA with events. In: Priami, C., Back, R.-J., Petre, I. (eds.) Transactions on Computational Systems Biology XI. LNCS (LNBI), vol.5750, pp. 45-68. Springer, Heidelberg (2009)
    • (2009) Transactions on Computational Systems Biology XI , vol.5750 , pp. 45-68
    • Ciocchetta, F.1
  • 32
    • 58149293181 scopus 로고    scopus 로고
    • Modelling Biological Compartments in Bio-PEPA
    • ENTCS
    • Ciocchetta, F., Guerriero, M.: Modelling Biological Compartments in Bio-PEPA. In: Proc. of MeCBIC 2008. ENTCS, vol.227, pp. 77-95 (2009)
    • (2009) Proc. of MeCBIC 2008 , vol.227 , pp. 77-95
    • Ciocchetta, F.1    Guerriero, M.2
  • 33
    • 77950313170 scopus 로고    scopus 로고
    • The Bio-PEPA Workbench (2009), http://www.dcs.ed.ac.uk/home/stg/software/ biopepa/about.html
    • (2009)
  • 34
    • 77950307131 scopus 로고    scopus 로고
    • Bio-PEPA (2008), http://www.biopepa.org/
    • (2008)
  • 35
    • 77950325966 scopus 로고    scopus 로고
    • MATLAB (2009), http://www.mathworks.com/products/matlab
    • (2009)
  • 36
    • 77950326555 scopus 로고    scopus 로고
    • Dizzy (2008), http://magnet.systemsbiology.net/software/Dizzy
    • (2008)
  • 37
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81, 2340-2361 (1977)
    • (1977) J. Phys. Chem. , vol.81 , pp. 2340-2361
    • Gillespie, D.1
  • 38
    • 84916436169 scopus 로고
    • Transient simulation of silicon devices and circuits
    • Bank, R., et al.: Transient simulation of silicon devices and circuits. IEEE Transactions on Electron Devices 32, 1992-2007 (1985)
    • (1985) IEEE Transactions on Electron Devices , vol.32 , pp. 1992-2007
    • Bank, R.1
  • 39
    • 0031029852 scopus 로고    scopus 로고
    • Stochastic mechanisms in gene expression
    • McAdams, H., Arkin, A.: Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA 94, 814-819 (1997)
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 814-819
    • McAdams, H.1    Arkin, A.2
  • 40
    • 33947195310 scopus 로고    scopus 로고
    • Bridging the gap between in silico and cell-based analysis of the nuclear factor κB signalling pathway by in vitro studies of IKK2
    • Ihekwaba, A., Wilkinson, S., Waithe, D., Broomhead, D., Li, P., Grimley, R., Benson, N.: Bridging the gap between in silico and cell-based analysis of the nuclear factor κB signalling pathway by in vitro studies of IKK2. FEBS Journal 274, 1678-1690 (2007)
    • (2007) FEBS Journal , vol.274 , pp. 1678-1690
    • Ihekwaba, A.1    Wilkinson, S.2    Waithe, D.3    Broomhead, D.4    Li, P.5    Grimley, R.6    Benson, N.7
  • 42
    • 29144488933 scopus 로고    scopus 로고
    • Accuracy limitations and the measurements of errors in the stochastic simulation of chemically reacting systems
    • Cao, Y., Petzold, L.: Accuracy limitations and the measurements of errors in the stochastic simulation of chemically reacting systems. J. Comput. Phys. 212, 6-24 (2006)
    • (2006) J. Comput. Phys. , vol.212 , pp. 6-24
    • Cao, Y.1    Petzold, L.2
  • 44
    • 33845200552 scopus 로고    scopus 로고
    • Stronger computational modelling of signalling pathways using both continuous and discrete-state methods
    • Priami, C. (ed.) LNCS (LNBI), Springer, Heidelberg
    • Calder, M., Duguid, A., Gilmore, S., Hillston, J.: Stronger computational modelling of signalling pathways using both continuous and discrete-state methods. In: Priami, C. (ed.) CMSB 2006. LNCS (LNBI), vol.4210, pp. 63-77. Springer, Heidelberg (2006)
    • (2006) CMSB 2006 , vol.4210 , pp. 63-77
    • Calder, M.1    Duguid, A.2    Gilmore, S.3    Hillston, J.4
  • 46
    • 34247094671 scopus 로고    scopus 로고
    • Single-cell time-lapse imaging of the dynamic control of nfκb signalling
    • Sillitoe, K., Horton, C., Spiller, D., White, M.: Single-cell time-lapse imaging of the dynamic control of nfκb signalling. Biochem. Soc. Transactions 35, 263-266 (2007)
    • (2007) Biochem. Soc. Transactions , vol.35 , pp. 263-266
    • Sillitoe, K.1    Horton, C.2    Spiller, D.3    White, M.4
  • 48
    • 77950314664 scopus 로고    scopus 로고
    • PRISM (2009), http://www.prismmodelchecker.org
    • (2009)
  • 49
    • 60449103324 scopus 로고    scopus 로고
    • Some Investigations Concerning the CTMC and the ODE Model Derived from Bio-PEPA
    • ENTCS
    • Ciocchetta, F., Degasperi, A., Hillston, J., Calder, M.: Some Investigations Concerning the CTMC and the ODE Model Derived from Bio-PEPA. In: Proc. of FBTC 2008. ENTCS, vol.209, pp. 145-163 (2009)
    • (2009) Proc. of FBTC 2008 , vol.209 , pp. 145-163
    • Ciocchetta, F.1    Degasperi, A.2    Hillston, J.3    Calder, M.4


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.