{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,10]],"date-time":"2024-09-10T17:11:07Z","timestamp":1725988267233},"publisher-location":"Cham","reference-count":43,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319994284"},{"type":"electronic","value":"9783319994291"}],"license":[{"start":{"date-parts":[[2018,1,1]],"date-time":"2018-01-01T00:00:00Z","timestamp":1514764800000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2018]]},"DOI":"10.1007\/978-3-319-99429-1_9","type":"book-chapter","created":{"date-parts":[[2018,8,23]],"date-time":"2018-08-23T13:45:12Z","timestamp":1535031912000},"page":"146-164","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":3,"title":["Stochastic Rate Parameter Inference Using the Cross-Entropy Method"],"prefix":"10.1007","author":[{"given":"Jeremy","family":"Revell","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paolo","family":"Zuliani","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,8,24]]},"reference":[{"issue":"1","key":"9_CR1","doi-asserted-by":"publisher","first-page":"26","DOI":"10.1186\/s12918-017-0406-4","volume":"11","author":"LU Aguilera","year":"2017","unstructured":"Aguilera, L.U., Zimmer, C., Kummer, U.: A new efficient approach to fit stochastic models on the basis of high-throughput experimental data using a model of IRF7 gene expression as case study. BMC Syst. Biol. 11(1), 26 (2017)","journal-title":"BMC Syst. Biol."},{"key":"9_CR2","unstructured":"Andersen, J.B., Sternberg, C., Poulsen, L.K., Bj\u00f8rn, S.P., Givskov, M., Molin, S.: New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl. Environ. Microbiol. 64(6), 2240\u20132246 (1998)"},{"key":"9_CR3","doi-asserted-by":"crossref","unstructured":"Andreychenko, A., Mikeev, L., Spieler, D., Wolf, V.: Approximate maximum likelihood estimation for stochastic chemical kinetics. EURASIP J. Bioinform. Syst. Biol. 2012(1), 9 (2012)","DOI":"10.1186\/1687-4153-2012-9"},{"issue":"6932","key":"9_CR4","doi-asserted-by":"publisher","first-page":"633","DOI":"10.1038\/nature01546","volume":"422","author":"WJ Blake","year":"2003","unstructured":"Blake, W.J., KAErn, M., Cantor, C.R., Collins, J.J.: Noise in eukaryotic gene expression. Nature 422(6932), 633\u2013637 (2003)","journal-title":"Nature"},{"key":"9_CR5","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1007\/s11222-007-9043-x","volume":"18","author":"R Boys","year":"2008","unstructured":"Boys, R., Wilkinson, D., Kirkwood, T.: Bayesian inference for a discretely observed stochastic kinetic model. Stat. Comput. 18, 125\u2013135 (2008)","journal-title":"Stat. Comput."},{"issue":"5","key":"9_CR6","doi-asserted-by":"publisher","first-page":"573","DOI":"10.1016\/j.orl.2006.11.005","volume":"35","author":"A Costa","year":"2007","unstructured":"Costa, A., Jones, O.D., Kroese, D.: Convergence properties of the cross-entropy method for discrete optimization. Oper. Res. Lett. 35(5), 573\u2013580 (2007)","journal-title":"Oper. Res. Lett."},{"issue":"4","key":"9_CR7","doi-asserted-by":"publisher","first-page":"044110","DOI":"10.1063\/1.3522769","volume":"134","author":"BJ Daigle","year":"2011","unstructured":"Daigle, B.J., Roh, M.K., Gillespie, D.T., Petzold, L.R.: Automated estimation of rare event probabilities in biochemical systems. J. Chem. Phys. 134(4), 044110 (2011)","journal-title":"J. Chem. Phys."},{"issue":"1","key":"9_CR8","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1186\/1471-2105-13-68","volume":"13","author":"BJ Daigle","year":"2012","unstructured":"Daigle, B.J., Roh, M.K., Petzold, L.R., Niemi, J.: Accelerated maximum likelihood parameter estimation for stochastic biochemical systems. BMC Bioinform. 13(1), 68 (2012)","journal-title":"BMC Bioinform."},{"issue":"11","key":"9_CR9","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1000985","volume":"6","author":"SH Dandach","year":"2010","unstructured":"Dandach, S.H., Khammash, M.: Analysis of stochastic strategies in bacterial competence: a master equation approach. PLoS Comput. Biol. 6(11), 1\u201311 (2010)","journal-title":"PLoS Comput. Biol."},{"issue":"2","key":"9_CR10","first-page":"498","volume":"180","author":"S Engblom","year":"2006","unstructured":"Engblom, S.: Computing the moments of high dimensional solutions of the master equation. Appl. Math. Comput. 180(2), 498\u2013515 (2006)","journal-title":"Appl. Math. Comput."},{"issue":"7","key":"9_CR11","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1371\/journal.pcbi.1005030","volume":"12","author":"F Fr\u00f6hlich","year":"2016","unstructured":"Fr\u00f6hlich, F., Thomas, P., Kazeroonian, A., Theis, F.J., Grima, R., Hasenauer, J.: Inference for stochastic chemical kinetics using moment equations and system size expansion. PLoS Comput. Biol. 12(7), 1\u201328 (2016)","journal-title":"PLoS Comput. Biol."},{"issue":"6767","key":"9_CR12","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1038\/35002131","volume":"403","author":"TS Gardner","year":"2000","unstructured":"Gardner, T.S., Cantor, C.R., Collins, J.J.: Construction of a genetic toggle switch in Escherichia coli. Nature 403(6767), 339\u2013342 (2000)","journal-title":"Nature"},{"issue":"4","key":"9_CR13","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/0021-9991(76)90041-3","volume":"22","author":"DT Gillespie","year":"1976","unstructured":"Gillespie, D.T.: A general method for numerically simulating the stochastic time evolution of coupled chemical reactions. J. Comput. Phys. 22(4), 403\u2013434 (1976)","journal-title":"J. Comput. Phys."},{"issue":"25","key":"9_CR14","doi-asserted-by":"publisher","first-page":"2340","DOI":"10.1021\/j100540a008","volume":"81","author":"DT Gillespie","year":"1977","unstructured":"Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. J. Phys. Chem. 81(25), 2340\u20132361 (1977)","journal-title":"J. Phys. Chem."},{"issue":"4","key":"9_CR15","doi-asserted-by":"publisher","first-page":"1716","DOI":"10.1063\/1.1378322","volume":"115","author":"DT Gillespie","year":"2001","unstructured":"Gillespie, D.T.: Approximate accelerated stochastic simulation of chemically reacting systems. J. Chem. Phys. 115(4), 1716\u20131733 (2001)","journal-title":"J. Chem. Phys."},{"issue":"3","key":"9_CR16","doi-asserted-by":"publisher","first-page":"687","DOI":"10.1007\/s00285-013-0711-5","volume":"69","author":"J Hasenauer","year":"2014","unstructured":"Hasenauer, J., Wolf, V., Kazeroonian, A., Theis, F.J.: Method of conditional moments (MCM) for the chemical master equation. J. Math. Biol. 69(3), 687\u2013735 (2014)","journal-title":"J. Math. Biol."},{"issue":"24","key":"9_CR17","doi-asserted-by":"publisher","first-page":"3067","DOI":"10.1093\/bioinformatics\/btl485","volume":"22","author":"S Hoops","year":"2006","unstructured":"Hoops, S., et al.: COPASI - a complex pathway simulator. Bioinformatics 22(24), 3067\u20133074 (2006)","journal-title":"Bioinformatics"},{"key":"9_CR18","doi-asserted-by":"crossref","unstructured":"Horv\u00e1th, A., Martini, D.: Parameter estimation of kinetic rates in stochastic reaction networks by the EM method. In: BMEI, pp. 713\u2013717. IEEE (2008)","DOI":"10.1109\/BMEI.2008.237"},{"issue":"1","key":"9_CR19","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1186\/1471-2105-10-343","volume":"10","author":"M Komorowski","year":"2009","unstructured":"Komorowski, M., Finkenst\u00e4dt, B., Harper, C.V., Rand, D.A.: Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinform. 10(1), 343 (2009)","journal-title":"BMC Bioinform."},{"issue":"1","key":"9_CR20","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1214\/aoms\/1177729694","volume":"22","author":"S Kullback","year":"1951","unstructured":"Kullback, S., Leibler, R.A.: On information and sufficiency. Ann. Math. Stat. 22(1), 79\u201386 (1951)","journal-title":"Ann. Math. Stat."},{"key":"9_CR21","unstructured":"Leon, M.: Computational design and characterisation of synthetic genetic switches. Ph.D. thesis, University College London, UK (2017). http:\/\/discovery.ucl.ac.uk\/1546318\/1\/Leon_Miriam_thesis_final.pdf"},{"issue":"108","key":"9_CR22","doi-asserted-by":"publisher","first-page":"20150233","DOI":"10.1098\/rsif.2015.0233","volume":"12","author":"S Liao","year":"2015","unstructured":"Liao, S., Vejchodsk\u00fd, T., Erban, R.: Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks. J. Roy. Soc. Interface 12(108), 20150233 (2015)","journal-title":"J. Roy. Soc. Interface"},{"issue":"3","key":"9_CR23","doi-asserted-by":"publisher","first-page":"814","DOI":"10.1073\/pnas.94.3.814","volume":"94","author":"HH McAdams","year":"1997","unstructured":"McAdams, H.H., Arkin, A.: Stochastic mechanisms in gene expression. PNAS 94(3), 814\u2013819 (1997)","journal-title":"PNAS"},{"issue":"1","key":"9_CR24","doi-asserted-by":"publisher","first-page":"111","DOI":"10.1016\/j.jtbi.2003.08.008","volume":"226","author":"JR Pirone","year":"2004","unstructured":"Pirone, J.R., Elston, T.C.: Fluctuations in transcription factor binding can explain the graded and binary responses observed in inducible gene expression. J. Theoret. Biol. 226(1), 111\u2013112 (2004)","journal-title":"J. Theoret. Biol."},{"issue":"4","key":"9_CR25","doi-asserted-by":"publisher","first-page":"168","DOI":"10.1049\/ip-syb:20050105","volume":"153","author":"S Reinker","year":"2006","unstructured":"Reinker, S., Altman, R.M., Timmer, J.: Parameter estimation in stochastic biochemical reactions. IEE Proc. - Syst. Biol. 153(4), 168\u2013178 (2006)","journal-title":"IEE Proc. - Syst. Biol."},{"key":"9_CR26","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4757-4145-2","volume-title":"Monte Carlo Statistical Methods","author":"C Robert","year":"2004","unstructured":"Robert, C., Casella, G.: Monte Carlo Statistical Methods. Springer, Heidelberg (2004). https:\/\/doi.org\/10.1007\/978-1-4757-4145-2"},{"issue":"1","key":"9_CR27","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1016\/S0377-2217(96)00385-2","volume":"99","author":"RY Rubinstein","year":"1997","unstructured":"Rubinstein, R.Y.: Optimization of computer simulation models with rare events. Eur. J. Oper. Res. 99(1), 89\u2013112 (1997)","journal-title":"Eur. J. Oper. Res."},{"issue":"2","key":"9_CR28","doi-asserted-by":"publisher","first-page":"127","DOI":"10.1023\/A:1010091220143","volume":"1","author":"RY Rubinstein","year":"1999","unstructured":"Rubinstein, R.Y.: The cross-entropy method for combinatorial and continuous optimization. Methodol. Comput. Appl. Prob. 1(2), 127\u2013190 (1999)","journal-title":"Methodol. Comput. Appl. Prob."},{"key":"9_CR29","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-4757-4321-0","volume-title":"The Cross-Entropy Method","author":"RY Rubinstein","year":"2004","unstructured":"Rubinstein, R.Y., Kroese, D.P.: The Cross-Entropy Method. Springer, Heidelberg (2004)"},{"issue":"2","key":"9_CR30","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1007\/BF01379769","volume":"253","author":"F Schl\u00f6gl","year":"1972","unstructured":"Schl\u00f6gl, F.: Chemical reaction models for non-equilibrium phase transitions. Zeitschrift f\u00fcr physik 253(2), 147\u2013161 (1972)","journal-title":"Zeitschrift f\u00fcr physik"},{"key":"9_CR31","doi-asserted-by":"publisher","first-page":"1567","DOI":"10.1038\/nbt1037","volume":"22","author":"NC Shaner","year":"2004","unstructured":"Shaner, N.C., Campbell, R.E., Steinbach, P.A., Giepmans, B.N.G., Palmer, A.E., Tsien, R.Y.: Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat. Biotechnol. 22, 1567\u20131572 (2004)","journal-title":"Nat. Biotechnol."},{"issue":"6","key":"9_CR32","doi-asserted-by":"publisher","first-page":"1760","DOI":"10.1073\/pnas.0607208104","volume":"104","author":"SA Sisson","year":"2007","unstructured":"Sisson, S.A., Fan, Y., Tanaka, M.M.: Sequential Monte Carlo without likelihoods. PNAS 104(6), 1760\u20135 (2007)","journal-title":"PNAS"},{"issue":"4","key":"9_CR33","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/0041-5553(67)90144-9","volume":"7","author":"IM Sobol\u2019","year":"1967","unstructured":"Sobol\u2019, I.M.: On the distribution of points in a cube and the approximate evaluation of integrals. USSR Comput. Math. Math. Phys. 7(4), 86\u2013112 (1967)","journal-title":"USSR Comput. Math. Math. Phys."},{"issue":"1","key":"9_CR34","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1093\/bioinformatics\/btl552","volume":"23","author":"T Tian","year":"2007","unstructured":"Tian, T., Xu, S., Gao, J., Burrage, K.: Simulated maximum likelihood method for estimating kinetic rates in gene expression. Bioinformatics 23(1), 84\u201391 (2007)","journal-title":"Bioinformatics"},{"issue":"31","key":"9_CR35","doi-asserted-by":"publisher","first-page":"187","DOI":"10.1098\/rsif.2008.0172","volume":"6","author":"T Toni","year":"2009","unstructured":"Toni, T., Welch, D., Strelkowa, N., Ipsen, A., Stumpf, M.P.H.: Approximate Bayesian computation scheme for parameter inference and model selection in dynamical systems. J. Roy. Soc. Interface 6(31), 187\u2013202 (2009)","journal-title":"J. Roy. Soc. Interface"},{"issue":"1","key":"9_CR36","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12918-017-0484-3","volume":"12","author":"I Vernon","year":"2018","unstructured":"Vernon, I., Liu, J., Goldstein, M., Rowe, J., Topping, J., Lindsey, K.: Bayesian uncertainty analysis for complex systems biology models: emulation, global parameter searches and evaluation of gene functions. BMC Syst. Biol. 12(1), 1 (2018)","journal-title":"BMC Syst. Biol."},{"issue":"91","key":"9_CR37","doi-asserted-by":"publisher","first-page":"20130505","DOI":"10.1098\/rsif.2013.0505","volume":"11","author":"AF Villaverde","year":"2013","unstructured":"Villaverde, A.F., Banga, J.R.: Reverse engineering and identification in systems biology: strategies, perspectives and challenges. J. Roy. Soc. Interface 11(91), 20130505 (2013)","journal-title":"J. Roy. Soc. Interface"},{"issue":"6","key":"9_CR38","doi-asserted-by":"publisher","first-page":"e1391","DOI":"10.1002\/wics.1391","volume":"9","author":"EO Voit","year":"2017","unstructured":"Voit, E.O.: The best models of metabolism. Wiley Interdisc. Rev.: Syst. Biol. Med. 9(6), e1391 (2017)","journal-title":"Wiley Interdisc. Rev.: Syst. Biol. Med."},{"issue":"1","key":"9_CR39","doi-asserted-by":"publisher","first-page":"99","DOI":"10.1186\/1752-0509-4-99","volume":"4","author":"Y Wang","year":"2010","unstructured":"Wang, Y., Christley, S., Mjolsness, E., Xie, X.: Parameter inference for discretely observed stochastic kinetic models using stochastic gradient descent. BMC Syst. Biol. 4(1), 99 (2010)","journal-title":"BMC Syst. Biol."},{"issue":"2","key":"9_CR40","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/nrg2509","volume":"10","author":"DJ Wilkinson","year":"2009","unstructured":"Wilkinson, D.J.: Stochastic modelling for quantitative description of heterogeneous biological systems. Nat. Rev. Genet. 10(2), 122\u2013133 (2009)","journal-title":"Nat. Rev. Genet."},{"key":"9_CR41","unstructured":"Wilkinson, D.J.: Stochastic Modelling for Systems Biology. CRC Press, Boca Raton (2012)"},{"issue":"1","key":"9_CR42","first-page":"11","volume":"6","author":"C Zimmer","year":"2012","unstructured":"Zimmer, C., Sahle, S.: Parameter estimation for stochastic models of biochemical reactions. J. Comput. Sci. Syst. Biol. 6(1), 11\u201321 (2012)","journal-title":"J. Comput. Sci. Syst. Biol."},{"key":"9_CR43","doi-asserted-by":"publisher","first-page":"181","DOI":"10.1049\/iet-syb.2014.0020","volume":"9","author":"C Zimmer","year":"2015","unstructured":"Zimmer, C., Sahle, S.: Deterministic inference for stochastic systems using multiple shooting and a linear noise approximation for the transition probabilities. IET Syst. Biol. 9, 181\u2013192 (2015)","journal-title":"IET Syst. Biol."}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-99429-1_9","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,10,22]],"date-time":"2019-10-22T20:56:42Z","timestamp":1571777802000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-99429-1_9"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018]]},"ISBN":["9783319994284","9783319994291"],"references-count":43,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-99429-1_9","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2018]]}}}