{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,27]],"date-time":"2025-03-27T19:32:46Z","timestamp":1743103966088,"version":"3.40.3"},"publisher-location":"Cham","reference-count":36,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319269153"},{"type":"electronic","value":"9783319269160"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"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":[[2015]]},"DOI":"10.1007\/978-3-319-26916-0_1","type":"book-chapter","created":{"date-parts":[[2016,1,9]],"date-time":"2016-01-09T05:44:21Z","timestamp":1452318261000},"page":"3-19","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":1,"title":["Reconstructing Statistics of Promoter Switching from Reporter Protein Population Snapshot Data"],"prefix":"10.1007","author":[{"given":"Eugenio","family":"Cinquemani","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2016,1,10]]},"reference":[{"key":"1_CR1","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1038\/msb4100120","volume":"3","author":"M Bansal","year":"2007","unstructured":"Bansal, M., Belcastro, V., Ambesi-Impiombato, A., di Bernardo, D.: How to infer gene networks from expression profiles. Mol. Syst. Biol. 3, 78 (2007)","journal-title":"Mol. Syst. Biol."},{"issue":"3","key":"1_CR2","doi-asserted-by":"publisher","first-page":"e1002965","DOI":"10.1371\/journal.pcbi.1002965","volume":"9","author":"CG Bowsher","year":"2013","unstructured":"Bowsher, C.G., Voliotis, M., Swain, P.S.: The fidelity of dynamic signaling by noisy biomolecular networks. PLoS Comput. Biol. 9(3), e1002965 (2013)","journal-title":"PLoS Comput. Biol."},{"key":"1_CR3","doi-asserted-by":"crossref","unstructured":"Cinquemani, E.: Reconstruction of promoter activity statistics from reporter protein population snapshot data. In: Accepted for the 54th IEEE Conference on Decision and Control (2015)","DOI":"10.1109\/CDC.2015.7402418"},{"key":"1_CR4","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1007\/978-3-642-00602-9_8","volume-title":"Hybrid Systems: Computation and Control","author":"E Cinquemani","year":"2009","unstructured":"Cinquemani, E., Milias-Argeitis, A., Summers, S., Lygeros, J.: Local identification of piecewise deterministic models of genetic networks. In: Majumdar, R., Tabuada, P. (eds.) HSCC 2009. LNCS, vol. 5469, pp. 105\u2013119. Springer, Heidelberg (2009)"},{"key":"1_CR5","unstructured":"Cox, D., Isham, V.: Point Processes. Chapman & Hall\/CRC Monographs on Statistics & Applied Probability, Taylor & Francis (1980)"},{"issue":"24","key":"1_CR6","doi-asserted-by":"publisher","first-page":"2901","DOI":"10.1093\/bioinformatics\/btn562","volume":"24","author":"B Finkenst\u00e4dt","year":"2008","unstructured":"Finkenst\u00e4dt, B., Heron, E.A., Komorowski, M., Edwards, K., Tang, S., Harper, C.V., Davis, J.R.E., White, M.R.H., Millar, A.J., Rand, D.A.: Reconstruction of transcriptional dynamics from gene reporter data using differential equations. Bioinformatics 24(24), 2901\u20132907 (2008)","journal-title":"Bioinformatics"},{"key":"1_CR7","doi-asserted-by":"publisher","first-page":"168302","DOI":"10.1103\/PhysRevLett.97.168302","volume":"97","author":"N Friedman","year":"2006","unstructured":"Friedman, N., Cai, L., Xie, X.S.: Linking stochastic dynamics to population distribution: An analytical framework of gene expression. Phys. Rev. Lett. 97, 168302 (2006)","journal-title":"Phys. Rev. Lett."},{"key":"1_CR8","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1063\/1.481811","volume":"113","author":"DT Gillespie","year":"2000","unstructured":"Gillespie, D.T.: The chemical Langevin equation. J. Chem. Phys. 113, 297\u2013306 (2000)","journal-title":"J. Chem. Phys."},{"issue":"1","key":"1_CR9","doi-asserted-by":"publisher","first-page":"125","DOI":"10.1186\/1471-2105-12-125","volume":"12","author":"J Hasenauer","year":"2011","unstructured":"Hasenauer, J., Waldherr, S., Doszczak, M., Radde, N., Scheurich, P., Allgower, F.: Identification of models of heterogeneous cell populations from population snapshot data. BMC Bioinf. 12(1), 125 (2011)","journal-title":"BMC Bioinf."},{"issue":"5","key":"1_CR10","doi-asserted-by":"publisher","first-page":"520","DOI":"10.1049\/ip-cta:20050088","volume":"153","author":"J Hespanha","year":"2006","unstructured":"Hespanha, J.: Modelling and analysis of stochastic hybrid systems. IEE Proc. Control Theory Appl. 153(5), 520\u2013535 (2006)","journal-title":"IEE Proc. Control Theory Appl."},{"issue":"1","key":"1_CR11","doi-asserted-by":"publisher","first-page":"55","DOI":"10.1186\/1752-0509-4-55","volume":"4","author":"H Jong de","year":"2010","unstructured":"de Jong, H., Ranquet, C., Ropers, D., Pinel, C., Geiselmann, J.: Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria. BMC Syst. Biol. 4(1), 55 (2010)","journal-title":"BMC Syst. Biol."},{"key":"1_CR12","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/nrg1615","volume":"6","author":"M Kaern","year":"2005","unstructured":"Kaern, M., Elston, T.C., Blake, W.J., Collins, J.J.: Stochasticity in gene expression: From theories to phenotypes. Nat. Rev. Gen. 6, 451\u2013464 (2005)","journal-title":"Nat. Rev. Gen."},{"issue":"1","key":"1_CR13","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., Rand, D.: Bayesian inference of biochemical kinetic parameters using the linear noise approximation. BMC Bioinf. 10(1), 343 (2009)","journal-title":"BMC Bioinf."},{"issue":"18","key":"1_CR14","doi-asserted-by":"publisher","first-page":"2311","DOI":"10.1093\/bioinformatics\/btt380","volume":"29","author":"G Lillacci","year":"2013","unstructured":"Lillacci, G., Khammash, M.: The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations. Bioinformatics 29(18), 2311\u20132319 (2013)","journal-title":"Bioinformatics"},{"key":"1_CR15","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-662-45750-4","volume-title":"Linear Stochastic Systems - A Geometric Approach to Modeling, Estimation and Identification","author":"A Lindquist","year":"2015","unstructured":"Lindquist, A., Picci, G.: Linear Stochastic Systems - A Geometric Approach to Modeling, Estimation and Identification. Springer, Heidelberg (2015)"},{"key":"1_CR16","doi-asserted-by":"publisher","first-page":"1114","DOI":"10.1038\/nbt.2018","volume":"29","author":"A Milias-Argeitis","year":"2011","unstructured":"Milias-Argeitis, A., Stewart-Ornstein, S.S.J., Zuleta, I., Pincus, D., El-Samad, H., Khammash, M., Lygeros, J.: In silico feedback for in vivo regulation of a gene expression circuit. Nat. Biotechnol. 29, 1114\u20131116 (2011)","journal-title":"Nat. Biotechnol."},{"key":"1_CR17","doi-asserted-by":"publisher","first-page":"318","DOI":"10.1038\/msb.2009.75","volume":"5","author":"B Munsky","year":"2009","unstructured":"Munsky, B., Trinh, B., Khammash, M.: Listening to the noise: random fluctuations reveal gene network parameters. Mol. Syst. Biol. 5, 318 (2009)","journal-title":"Mol. Syst. Biol."},{"issue":"6119","key":"1_CR18","doi-asserted-by":"publisher","first-page":"584","DOI":"10.1126\/science.1231456","volume":"339","author":"G Neuert","year":"2013","unstructured":"Neuert, G., Munsky, B., Tan, R., Teytelman, L., Khammash, M., van Oudenaarden, A.: Systematic identification of signal-activated stochastic gene regulation. Science 339(6119), 584\u2013587 (2013)","journal-title":"Science"},{"issue":"12","key":"1_CR19","doi-asserted-by":"publisher","first-page":"i89","DOI":"10.1093\/bioinformatics\/btv257","volume":"31","author":"A Ocone","year":"2015","unstructured":"Ocone, A., Haghverdi, L., Mueller, N.S., Theis, F.J.: Reconstructing gene regulatory dynamics from high-dimensional single-cell snapshot data. Bioinformatics 31(12), i89\u2013i96 (2015)","journal-title":"Bioinformatics"},{"key":"1_CR20","unstructured":"Lafferty, J., Williams, C., Shawe-Taylor, J., Zemel, R., Culotta, A. (eds.) Advances in Neural Information Processing Systems 23, pp. 1831\u20131839. Curran Associates, Inc., (2010)"},{"key":"1_CR21","doi-asserted-by":"crossref","unstructured":"Parise, F., Ruess, J., Lygeros, J.: Grey-box techniques for the identification of a controlled gene expression model. In: Proceedings of the ECC (2014)","DOI":"10.1109\/ECC.2014.6862244"},{"issue":"2","key":"1_CR22","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1016\/j.plrev.2005.03.003","volume":"2","author":"J Paulsson","year":"2005","unstructured":"Paulsson, J.: Models of stochastic gene expression. Phys. Life Rev. 2(2), 157\u2013175 (2005)","journal-title":"Phys. Life Rev."},{"issue":"9","key":"1_CR23","doi-asserted-by":"publisher","first-page":"1239","DOI":"10.1093\/bioinformatics\/btq120","volume":"26","author":"R Porreca","year":"2010","unstructured":"Porreca, R., Cinquemani, E., Lygeros, J., Ferrari-Trecate, G.: Identification of genetic network dynamics with unate structure. Bioinformatics 26(9), 1239\u20131245 (2010)","journal-title":"Bioinformatics"},{"issue":"2","key":"1_CR24","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1145\/2688906","volume":"25","author":"J Ruess","year":"2015","unstructured":"Ruess, J., Lygeros, J.: Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Trans. Model. Comput. Simul. 25(2), 8 (2015)","journal-title":"ACM Trans. Model. Comput. Simul."},{"issue":"16","key":"1_CR25","doi-asserted-by":"publisher","first-page":"165102","DOI":"10.1063\/1.3654135","volume":"135","author":"J Ruess","year":"2011","unstructured":"Ruess, J., Milias-Argeitis, A., Summers, S., Lygeros, J.: Moment estimation for chemically reacting systems by extended Kalman filtering. J. Chem. Phys. 135(16), 165102 (2011)","journal-title":"J. Chem. Phys."},{"key":"1_CR26","doi-asserted-by":"publisher","first-page":"691","DOI":"10.1002\/rnc.1018","volume":"15","author":"HE Samad","year":"2005","unstructured":"Samad, H.E., Khammash, M., Petzold, L., Gillespie, D.: Stochastic modelling of gene regulatory networks. Int. J. Robust Nonlin. Contr. 15, 691\u2013711 (2005)","journal-title":"Int. J. Robust Nonlin. Contr."},{"issue":"17","key":"1_CR27","doi-asserted-by":"publisher","first-page":"2457","DOI":"10.1093\/bioinformatics\/btr401","volume":"27","author":"KR Sanft","year":"2011","unstructured":"Sanft, K.R., Wu, S., Roh, M., Fu, J., Lim, R.K., Petzold, L.R.: Stochkit2: software for discrete stochastic simulation of biochemical systems with events. Bioinformatics 27(17), 2457\u20132458 (2011)","journal-title":"Bioinformatics"},{"issue":"1","key":"1_CR28","doi-asserted-by":"publisher","first-page":"e1004028","DOI":"10.1371\/journal.pcbi.1004028","volume":"11","author":"D Stefan","year":"2015","unstructured":"Stefan, D., Pinel, C., Pinhal, S., Cinquemani, E., Geiselmann, J., de Jong, H.: Inference of quantitative models of bacterial promoters from time-series reporter gene data. PLoS Comput. Biol. 11(1), e1004028 (2015)","journal-title":"PLoS Comput. Biol."},{"key":"1_CR29","doi-asserted-by":"publisher","first-page":"472","DOI":"10.1126\/science.1198817","volume":"332","author":"DM Suter","year":"2011","unstructured":"Suter, D.M., Molina, N., Gatfield, D., Schneider, K., Schibler, U., Naef, F.: Mammalian genes are transcribed with widely different bursting kinetics. Science 332, 472\u2013474 (2011)","journal-title":"Science"},{"key":"1_CR30","doi-asserted-by":"publisher","first-page":"533","DOI":"10.1126\/science.1188308","volume":"329","author":"Y Taniguchi","year":"2010","unstructured":"Taniguchi, Y., Choi, P.J., Li, G.W., Chen, H., Babu, M., Hearn, J., Emili, A., Xie, X.S.: Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329, 533\u2013538 (2010)","journal-title":"Science"},{"issue":"15","key":"1_CR31","doi-asserted-by":"publisher","first-page":"8614","DOI":"10.1073\/pnas.151588598","volume":"98","author":"M Thattai","year":"2001","unstructured":"Thattai, M., van Oudenaarden, A.: Intrinsic noise in gene regulatory networks. PNAS 98(15), 8614\u20138619 (2001)","journal-title":"PNAS"},{"issue":"35","key":"1_CR32","doi-asserted-by":"publisher","first-page":"14271","DOI":"10.1073\/pnas.1206810109","volume":"109","author":"J Uhlendorf","year":"2012","unstructured":"Uhlendorf, J., Miermont, A., Delaveau, T., Charvin, G., Fages, F., Bottani, S., Batt, G., Hersen, P.: Long-term model predictive control of gene expression at the population and single-cell levels. PNAS 109(35), 14271\u201314276 (2012)","journal-title":"PNAS"},{"key":"1_CR33","doi-asserted-by":"crossref","unstructured":"Wahba, G.: Spline models for observational data. In: SIAM (1990)","DOI":"10.1137\/1.9781611970128"},{"issue":"109","key":"1_CR34","doi-asserted-by":"publisher","first-page":"8340","DOI":"10.1073\/pnas.1200161109","volume":"21","author":"C Zechner","year":"2012","unstructured":"Zechner, C., Ruess, J., Krenn, P., Pelet, S., Peter, M., Lygeros, J., Koeppl, H.: Moment-based inference predicts bimodality in transient gene expression. PNAS 21(109), 8340\u20138345 (2012)","journal-title":"PNAS"},{"key":"1_CR35","doi-asserted-by":"publisher","first-page":"197","DOI":"10.1038\/nmeth.2794","volume":"11","author":"C Zechner","year":"2014","unstructured":"Zechner, C., Unger, M., Pelet, S., Peter, M., Koeppl, H.: Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings. Nat. Methods 11, 197\u2013202 (2014)","journal-title":"Nat. Methods"},{"issue":"12","key":"1_CR36","doi-asserted-by":"publisher","first-page":"i71","DOI":"10.1093\/bioinformatics\/btv246","volume":"31","author":"V Zulkower","year":"2015","unstructured":"Zulkower, V., Page, M., Ropers, D., Geiselmann, J., de Jong, H.: Robust reconstruction of gene expression profiles from reporter gene data using linear inversion. Bioinformatics 31(12), i71\u2013i79 (2015)","journal-title":"Bioinformatics"}],"container-title":["Lecture Notes in Computer Science","Hybrid Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-26916-0_1","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,16]],"date-time":"2023-08-16T12:25:59Z","timestamp":1692188759000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-319-26916-0_1"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319269153","9783319269160"],"references-count":36,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-26916-0_1","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2015]]},"assertion":[{"value":"10 January 2016","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}