{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,26]],"date-time":"2025-03-26T11:39:04Z","timestamp":1742989144790,"version":"3.40.3"},"publisher-location":"Berlin, Heidelberg","reference-count":50,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"type":"print","value":"9783642117114"},{"type":"electronic","value":"9783642117121"}],"license":[{"start":{"date-parts":[[2010,1,1]],"date-time":"2010-01-01T00:00:00Z","timestamp":1262304000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2010]]},"DOI":"10.1007\/978-3-642-11712-1_7","type":"book-chapter","created":{"date-parts":[[2010,2,11]],"date-time":"2010-02-11T20:48:43Z","timestamp":1265921323000},"page":"229-262","source":"Crossref","is-referenced-by-count":7,"title":["Modelling and Analysis of the NF-\u03baB Pathway in Bio-PEPA"],"prefix":"10.1007","author":[{"given":"Federica","family":"Ciocchetta","sequence":"first","affiliation":[]},{"given":"Andrea","family":"Degasperi","sequence":"additional","affiliation":[]},{"given":"John K.","family":"Heath","sequence":"additional","affiliation":[]},{"given":"Jane","family":"Hillston","sequence":"additional","affiliation":[]}],"member":"297","reference":[{"key":"7_CR1","doi-asserted-by":"publisher","first-page":"112","DOI":"10.1016\/j.tcb.2008.01.005","volume":"18","author":"R. Cheong","year":"2008","unstructured":"Cheong, R., Levchenko, A.: Wires in the soup: quantitative models of cell signalling. Trends in Cell Biology\u00a018, 112\u2013118 (2008)","journal-title":"Trends in Cell Biology"},{"key":"7_CR2","doi-asserted-by":"publisher","first-page":"344","DOI":"10.1016\/j.cell.2008.01.020","volume":"132","author":"M. Hayden","year":"2008","unstructured":"Hayden, M., Ghosh, S.: Shared principle in NF-\u03baB Signalling. Cell\u00a0132, 344\u2013362 (2008)","journal-title":"Cell"},{"key":"7_CR3","doi-asserted-by":"publisher","first-page":"1241","DOI":"10.1126\/science.1071914","volume":"298","author":"A. Hoffmann","year":"2002","unstructured":"Hoffmann, A., Levchenko, A., Scott, M., Baltimore, D.: The I\u03baB\u2013NF-\u03baB Signaling Module: Temporal Control and Selective Gene Activation. Science\u00a0298, 1241\u20131245 (2002)","journal-title":"Science"},{"key":"7_CR4","doi-asserted-by":"publisher","first-page":"2413","DOI":"10.1101\/gr.1195703","volume":"13","author":"K.H. Cho","year":"2003","unstructured":"Cho, K.H., Shin, S.Y., Lee, H.W., et al.: Investigations Into the Analysis and the Modeling of the TNF-mediated NF\u03baB Signaling Pathway. Genome Res.\u00a013, 2413\u20132422 (2003)","journal-title":"Genome Res."},{"key":"7_CR5","doi-asserted-by":"publisher","first-page":"195","DOI":"10.1016\/j.jtbi.2004.01.001","volume":"228","author":"T. Lipniacki","year":"2004","unstructured":"Lipniacki, T., Paszek, P., Brasier, A., Luxon, B., Kimmel, M.: Mathematical model of NF-\u03baB regulatory module. Journal of Theoretical Biology\u00a0228, 195\u2013215 (2004)","journal-title":"Journal of Theoretical Biology"},{"key":"7_CR6","doi-asserted-by":"publisher","first-page":"725","DOI":"10.1529\/biophysj.104.056754","volume":"90","author":"T. Lipniacki","year":"2006","unstructured":"Lipniacki, T., Paszek, P., Brasier, A., Luxon, B., Kimmel, M.: Stochastic Regulation in Early Immune Response. Biophysical Journal\u00a090, 725\u2013742 (2006)","journal-title":"Biophysical Journal"},{"key":"7_CR7","doi-asserted-by":"publisher","first-page":"704","DOI":"10.1126\/science.1099962","volume":"306","author":"D. Nelson","year":"2004","unstructured":"Nelson, D., Ihekwaba, A., Elliott, M., Johnson, J., Gibney, C., Foreman, B., Nelson, G., See, V., Horton, C., Spiller, D.G., Edwards, S., McDowell, H., Unitt, J.F., Sullivan, E., Grimley, R., Benson, N., Broomhead, D.S., Kell, D., White, M.: Oscillations in NF-\u03baB Signalling Control the Dynamics of Gene Expression. Science\u00a0306, 704\u2013708 (2004)","journal-title":"Science"},{"key":"7_CR8","doi-asserted-by":"publisher","first-page":"242","DOI":"10.1126\/science.1164860","volume":"324","author":"L. Ashall","year":"2009","unstructured":"Ashall, L., Horton, C., Nelson, D., Paszek, P., Harper, C., Sillitoe, K., Ryan, S., Spiller, D.G., Unitt, J.F., Broomhead, D., Kell, D., Rand, A., S\u00e9e, V., White, M.: Pulsatile Stimulation Determines Timing and Specificity of NF-\u03baB\u2013Dependent Transcription. Science\u00a0324, 242\u2013246 (2009)","journal-title":"Science"},{"key":"7_CR9","doi-asserted-by":"publisher","first-page":"93","DOI":"10.1049\/sb:20045009","volume":"1","author":"A. Ihekwaba","year":"2004","unstructured":"Ihekwaba, A., Broomhead, D., Grimley, R., Kell, D.: Sensitivity analysis of parameters controlling oscillatory signalling in the NF-\u03baB pathway: the roles of IKK and I\u03baB\u03b1. Systems Biology\u00a01, 93\u2013103 (2004)","journal-title":"Systems Biology"},{"key":"7_CR10","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1049\/ip-syb:20050050","volume":"152","author":"A. Ihekwaba","year":"2005","unstructured":"Ihekwaba, A., Broomhead, D., Grimley, R., Kell, D.: Synergistic control of oscillations in the NF-\u03baB signalling pathway. IEE Proc.-Syst. biol.\u00a0152, 153\u2013160 (2005)","journal-title":"IEE Proc.-Syst. biol."},{"key":"7_CR11","first-page":"563","volume":"9","author":"P. Mendes","year":"1993","unstructured":"Mendes, P.: GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci.\u00a09, 563\u2013571 (1993)","journal-title":"Comput. Appl. Biosci."},{"key":"7_CR12","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1016\/S0020-0190(01)00214-9","volume":"80","author":"C. Priami","year":"2001","unstructured":"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\u00a080, 25\u201331 (2001)","journal-title":"Information Processing Letters"},{"key":"7_CR13","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.tcs.2004.03.066","volume":"325","author":"M. Curti","year":"2004","unstructured":"Curti, M., Degano, P., Priami, C., Baldari, C.: Modelling biochemical pathways through enhanced \u03c0-calculus. Theoretical Computer Science\u00a0325, 111\u2013140 (2004)","journal-title":"Theoretical Computer Science"},{"key":"7_CR14","doi-asserted-by":"publisher","first-page":"141","DOI":"10.1016\/j.tcs.2004.03.061","volume":"325","author":"A. Regev","year":"2004","unstructured":"Regev, A., Panina, E., Silverman, W., Cardelli, L., Shapiro, E.: BioAmbients: an Abstraction for Biological Compartments. Theoretical Computer Science\u00a0325, 141\u2013167 (2004)","journal-title":"Theoretical Computer Science"},{"key":"7_CR15","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"20","DOI":"10.1007\/978-3-540-25974-9_3","volume-title":"Computational Methods in Systems Biology","author":"C. Priami","year":"2005","unstructured":"Priami, C., Quaglia, P.: Beta binders for biological interactions. In: Danos, V., Schachter, V. (eds.) CMSB 2004. LNCS (LNBI), vol.\u00a03082, pp. 20\u201333. Springer, Heidelberg (2005)"},{"key":"7_CR16","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/11905455_1","volume-title":"Transactions on Computational Systems Biology VII","author":"M. Calder","year":"2006","unstructured":"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., Ing\u00f3lfsd\u00f3ttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol.\u00a04230, pp. 1\u201323. Springer, Heidelberg (2006)"},{"key":"7_CR17","series-title":"LNBI","doi-asserted-by":"publisher","first-page":"13","DOI":"10.1007\/978-3-642-11712-1_2","volume-title":"Transactions on Computational Systems Biology XII","author":"M. John","year":"2010","unstructured":"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.\u00a05945, pp. 13\u201376. Springer, Heidelberg (2010)"},{"doi-asserted-by":"crossref","unstructured":"Priami, C.: Algorithmic systems biology. Communications of the ACM\u00a052 (2009)","key":"7_CR18","DOI":"10.1145\/1506409.1506427"},{"key":"7_CR19","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1038\/nbt1356","volume":"25","author":"J. Fisher","year":"2007","unstructured":"Fisher, J., Henzinger, T.: Executable cell biology. Nature Biotechnology\u00a025, 1239\u20131249 (2007)","journal-title":"Nature Biotechnology"},{"unstructured":"Ciocchetta, F., Hillston, J.: Bio-PEPA: a framework for the modelling and analysis of biological systems. School of Informatics University of Edinburgh Technical Report EDI-INF-RR-1231 (2008)","key":"7_CR20"},{"key":"7_CR21","doi-asserted-by":"publisher","first-page":"3065","DOI":"10.1016\/j.tcs.2009.02.037","volume":"410","author":"F. Ciocchetta","year":"2009","unstructured":"Ciocchetta, F., Hillston, J.: Bio-PEPA: a Framework for the Modelling and Analysis of Biochemical Networks. Theoretical Computer Science\u00a0410, 3065\u20133084 (2009)","journal-title":"Theoretical Computer Science"},{"key":"7_CR22","doi-asserted-by":"publisher","first-page":"41028","DOI":"10.1074\/jbc.M006179200","volume":"275","author":"F. Carlotti","year":"2000","unstructured":"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.\u00a0275, 41028\u201341034 (2000)","journal-title":"J. Biol. Chem."},{"key":"7_CR23","doi-asserted-by":"publisher","first-page":"2350","DOI":"10.1126\/science.289.5488.2350","volume":"289","author":"E. Lee","year":"2000","unstructured":"Lee, E., Boone, D., Chai, S., Libby, S., Chien, M., Lodolce, J., Ma, A.: Failure to regulate TNF-induced NF-\u03baB and cell death responses in A20-deficient mice. Science\u00a0289, 2350\u20132354 (2000)","journal-title":"Science"},{"key":"7_CR24","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/978-3-540-68894-5_1","volume-title":"Formal Methods for Computational Systems Biology","author":"A. Degasperi","year":"2008","unstructured":"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.\u00a05016, pp. 1\u201320. Springer, Heidelberg (2008)"},{"unstructured":"Dizzy Edinburgh version (2009), \n                  \n                    http:\/\/homepages.inf.ed.ac.uk\/stg\/software\/Dizzy\/","key":"7_CR25"},{"key":"7_CR26","series-title":"Dagstuhl Seminar Proceedings","volume-title":"Formal Methods in Molecular Biology","author":"F. Ciocchetta","year":"2009","unstructured":"Ciocchetta, F., Degasperi, A., Heath, J., Hillston, J.: Modelling and analysis of the NF-\u03baB 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.\u00a009091. Schloss Dagstuhl - Leibniz-Zentrum fuer Informatik, Germany (2009)"},{"key":"7_CR27","doi-asserted-by":"publisher","first-page":"6888","DOI":"10.1038\/sj.onc.1203236","volume":"18","author":"S. Gerondakis","year":"1999","unstructured":"Gerondakis, S., Grossmann, M., Nakamura, Y., Pohl, T., Grumont, R.: Genetic approaches in mice to understand Rel\/NF-\u03baB and I\u03baB function: transgenics and knockouts. Oncogene\u00a018, 6888\u20136895 (1999)","journal-title":"Oncogene"},{"doi-asserted-by":"crossref","unstructured":"Hillston, J., Duguid, A.: Deriving Differential Equations from Process Algebra Models in Reagent-Centric Style. In: Algorithmic Bioprocesses. Natural Computing Series. LNCS (2009)","key":"7_CR28","DOI":"10.1007\/978-3-540-88869-7_24"},{"unstructured":"Larcher, R., Ihekwaba, A., Priami, C.: A BetaBW model for the NF-\u03baB pathway. Technical Report TR 25\/2007, The Microsoft Research-University of Trento Centre for Computational and Systems Biology (2007)","key":"7_CR29"},{"key":"7_CR30","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511569951","volume-title":"A Compositional Approach to Performance Modelling","author":"J. Hillston","year":"1996","unstructured":"Hillston, J.: A Compositional Approach to Performance Modelling. Cambridge University Press, Cambridge (1996)"},{"key":"7_CR31","series-title":"LNBI","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1007\/978-3-642-04186-0_3","volume-title":"Transactions on Computational Systems Biology XI","author":"F. Ciocchetta","year":"2009","unstructured":"Ciocchetta, F.: Bio-PEPA with events. In: Priami, C., Back, R.-J., Petre, I. (eds.) Transactions on Computational Systems Biology XI. LNCS (LNBI), vol.\u00a05750, pp. 45\u201368. Springer, Heidelberg (2009)"},{"doi-asserted-by":"crossref","unstructured":"Ciocchetta, F., Guerriero, M.: Modelling Biological Compartments in Bio-PEPA. In: Proc. of MeCBIC 2008. ENTCS, vol.\u00a0227, pp. 77\u201395 (2009)","key":"7_CR32","DOI":"10.1016\/j.entcs.2008.12.105"},{"unstructured":"The Bio-PEPA Workbench (2009), \n                  \n                    http:\/\/www.dcs.ed.ac.uk\/home\/stg\/software\/biopepa\/about.html","key":"7_CR33"},{"unstructured":"Bio-PEPA (2008), \n                  \n                    http:\/\/www.biopepa.org\/","key":"7_CR34"},{"unstructured":"MATLAB (2009), \n                  \n                    http:\/\/www.mathworks.com\/products\/matlab\/","key":"7_CR35"},{"unstructured":"Dizzy (2008), \n                  \n                    http:\/\/magnet.systemsbiology.net\/software\/Dizzy","key":"7_CR36"},{"key":"7_CR37","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"D. Gillespie","year":"1977","unstructured":"Gillespie, D.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem.\u00a081, 2340\u20132361 (1977)","journal-title":"J. Phys. Chem."},{"key":"7_CR38","doi-asserted-by":"publisher","first-page":"1992","DOI":"10.1109\/T-ED.1985.22232","volume":"32","author":"R. Bank","year":"1985","unstructured":"Bank, R., et al.: Transient simulation of silicon devices and circuits. IEEE Transactions on Electron Devices\u00a032, 1992\u20132007 (1985)","journal-title":"IEEE Transactions on Electron Devices"},{"key":"7_CR39","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1073\/pnas.94.3.814","volume":"94","author":"H. McAdams","year":"1997","unstructured":"McAdams, H., Arkin, A.: Stochastic mechanisms in gene expression. Proc. Natl. Acad. Sci. USA\u00a094, 814\u2013819 (1997)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"7_CR40","doi-asserted-by":"publisher","first-page":"1678","DOI":"10.1111\/j.1742-4658.2007.05713.x","volume":"274","author":"A. Ihekwaba","year":"2007","unstructured":"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 \u03baB signalling pathway by in vitro studies of IKK2. FEBS Journal\u00a0274, 1678\u20131690 (2007)","journal-title":"FEBS Journal"},{"key":"7_CR41","volume-title":"Sensitivity Analysis","author":"A. Saltelli","year":"2000","unstructured":"Saltelli, A., Chan, K., Scott, E.: Sensitivity Analysis. Wiley, Chichester (2000)"},{"key":"7_CR42","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1016\/j.jcp.2005.06.012","volume":"212","author":"Y. Cao","year":"2006","unstructured":"Cao, Y., Petzold, L.: Accuracy limitations and the measurements of errors in the stochastic simulation of chemically reacting systems. J. Comput. Phys.\u00a0212, 6\u201324 (2006)","journal-title":"J. Comput. Phys."},{"doi-asserted-by":"crossref","unstructured":"Ciocchetta, F., Duguid, A., Gilmore, S., Guerriero, M., Hillston, J.: The Bio-PEPA Tool Suite. In: Proceedings of the 6th International Conference on Quantitative Evaluation of SysTems (QEST 2009), Budapest, Hungary, pp. 309\u2013310 (2009)","key":"7_CR43","DOI":"10.1109\/QEST.2009.27"},{"key":"7_CR44","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"63","DOI":"10.1007\/11885191_5","volume-title":"Computational Methods in Systems Biology","author":"M. Calder","year":"2006","unstructured":"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.\u00a04210, pp. 63\u201377. Springer, Heidelberg (2006)"},{"key":"7_CR45","doi-asserted-by":"publisher","first-page":"375","DOI":"10.1016\/j.copbio.2008.07.001","volume":"19","author":"J. Ankers","year":"2008","unstructured":"Ankers, J., Spiller, D., White, M., Harper, C.: Spatio-temporal protein dynamics in single living cells. Curr. Opin. Biotechnology\u00a019, 375\u2013380 (2008)","journal-title":"Curr. Opin. Biotechnology"},{"key":"7_CR46","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1042\/BST0350263","volume":"35","author":"K. Sillitoe","year":"2007","unstructured":"Sillitoe, K., Horton, C., Spiller, D., White, M.: Single-cell time-lapse imaging of the dynamic control of nf\u03bab signalling. Biochem. Soc. Transactions\u00a035, 263\u2013266 (2007)","journal-title":"Biochem. Soc. Transactions"},{"doi-asserted-by":"crossref","unstructured":"Kwiatkowska, M., Norman, G., Parker, D.: Prism: Probabilistic model checking for performance and reliability analysis. ACM SIGMETRICS Performance Evaluation Review (2009)","key":"7_CR47","DOI":"10.1145\/1530873.1530882"},{"unstructured":"PRISM (2009), \n                  \n                    http:\/\/www.prismmodelchecker.org","key":"7_CR48"},{"doi-asserted-by":"crossref","unstructured":"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.\u00a0209, pp. 145\u2013163 (2009)","key":"7_CR49","DOI":"10.1016\/j.entcs.2009.02.010"},{"doi-asserted-by":"crossref","unstructured":"Gerhart, J., Kirshner, M.: The theory of facilitated variation. PNAS (2007)","key":"7_CR50","DOI":"10.1073\/pnas.0701035104"}],"container-title":["Lecture Notes in Computer Science","Transactions on Computational Systems Biology XII"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-642-11712-1_7","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,3,12]],"date-time":"2019-03-12T05:52:36Z","timestamp":1552369956000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-642-11712-1_7"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010]]},"ISBN":["9783642117114","9783642117121"],"references-count":50,"URL":"https:\/\/doi.org\/10.1007\/978-3-642-11712-1_7","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2010]]}}}