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Parameter inference for stochastic kinetic models of bacterial gene regulation: A Bayesian approach to systems biology. In: Bernardo JM, Bayarri MJ, amd A P Dawid JOB, Heckerman D, Smith AFM, West M, editors. Proc. of 9th Valencia Int. Meet. (Bayesian Statistics 9), Valencia, Spain. Oxford University Press; 2010. p. 679\u2013705.","DOI":"10.1093\/acprof:oso\/9780199694587.003.0023"},{"issue":"1","key":"ref7","doi-asserted-by":"crossref","first-page":"104","DOI":"10.1093\/bioinformatics\/btp619","article-title":"Simulation-based model selection for dynamical systems in systems and population biology","volume":"26","author":"T Toni","year":"2010","journal-title":"Bioinf"},{"key":"ref8","article-title":"Inference for diffusion processes with applications in life sciences","author":"C Fuchs","year":"2013"},{"key":"ref9","doi-asserted-by":"crossref","unstructured":"Mikeev L, Wolf V. Parameter estimation for stochastic hybrid models of biochemical reaction networks. In: Proc. of the 15th ACM International Conference on Hybrid Systems: Computation and Control. New York, NY, USA: ACM; 2012. p. 155\u2013166.","DOI":"10.1145\/2185632.2185657"},{"issue":"2","key":"ref10","doi-asserted-by":"crossref","first-page":"287","DOI":"10.1007\/s11222-011-9310-8","article-title":"Moment closure based parameter inference of stochastic kinetic models","volume":"23","author":"P Milner","year":"2013","journal-title":"Stat Comp"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1038\/nmeth.2794","article-title":"Scalable inference of heterogeneous reaction kinetics from pooled single-cell recordings","volume":"11","author":"C Zechner","year":"2014","journal-title":"Nat Meth"},{"issue":"3","key":"ref12","doi-asserted-by":"crossref","first-page":"e1003359","DOI":"10.1371\/journal.pcbi.1003359","article-title":"Direct solution of the Chemical Master Equation using quantized tensor trains","volume":"10","author":"V Kazeev","year":"2014","journal-title":"PLoS Comput Biol"},{"key":"ref13","first-page":"52","article-title":"Computational Methods in Systems Biology. vol. 9308 of Lecture Notes in Computer Science","author":"C Loos","year":"2015"},{"issue":"6","key":"ref14","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1049\/iet-syb.2010.0013","article-title":"Identification from stochastic cell-to-cell variation: a genetic switch case study","volume":"4","author":"B Munsky","year":"2010","journal-title":"IET Syst Biol"},{"key":"ref15","unstructured":"N\u00fcesch T. Finite state projection-based parameter estimation algorithms for stochastic chemical kinetics [Master Thesis]. Swiss Federal Institute of Technology, Z\u00fcrich; 2010."},{"key":"ref16","unstructured":"Hasenauer J, Radde N, Doszczak M, Scheurich P, Allg\u00f6wer F. Parameter estimation for the CME from noisy binned snapshot data: Formulation as maximum likelihood problem; 2011. Extended abstract at <italic>Conf. of Stoch. Syst. Biol<\/italic>., Monte Verita, Switzerland."},{"issue":"21","key":"ref17","doi-asserted-by":"crossref","first-page":"8340","DOI":"10.1073\/pnas.1200161109","article-title":"Moment-based inference predicts bimodality in transient gene expression","volume":"109","author":"C Zechner","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref18","unstructured":"Kazeroonian A, Hasenauer J, Theis FJ. Parameter estimation for stochastic biochemical processes: A comparison of moment equation and finite state projection. In: Autio R, Shmulevich I, Strimmer K, Wiuf C, Sarbu S, Yli-Harja O, editors. Proceedings of 10th International Workshop on Computational Systems Biology. Tampere, Finland: Tampere International Center for Signal Processing; 2013. p. 66\u201373."},{"issue":"18","key":"ref19","doi-asserted-by":"crossref","first-page":"2311","DOI":"10.1093\/bioinformatics\/btt380","article-title":"The signal within the noise: efficient inference of stochastic gene regulation models using fluorescence histograms and stochastic simulations","volume":"29","author":"G Lillacci","year":"2013","journal-title":"Bioinf"},{"issue":"6119","key":"ref20","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1126\/science.1231456","article-title":"Systematic identification of signal-activated stochastic gene regulation","volume":"339","author":"G Neuert","year":"2013","journal-title":"Science"},{"issue":"25","key":"ref21","doi-asserted-by":"crossref","first-page":"2340","DOI":"10.1021\/j100540a008","article-title":"Exact stochastic simulation of coupled chemical reactions","volume":"81","author":"DT Gillespie","year":"1977","journal-title":"J Phys Chem"},{"issue":"4","key":"ref22","doi-asserted-by":"crossref","first-page":"044104","DOI":"10.1063\/1.2145882","article-title":"The finite state projection algorithm for the solution of the chemical master equation","volume":"124","author":"B Munsky","year":"2006","journal-title":"J Chem Phys"},{"issue":"15","key":"ref23","doi-asserted-by":"crossref","first-page":"154105","DOI":"10.1063\/1.3702848","article-title":"A study of the accuracy of moment-closure approximations for stochastic chemical kinetics","volume":"136","author":"R Grima","year":"2012","journal-title":"J Chem Phys"},{"key":"ref24","article-title":"Stochastic processes in physics and chemistry","author":"NG van Kampen","year":"2007"},{"issue":"4","key":"ref25","doi-asserted-by":"crossref","first-page":"2025","DOI":"10.1093\/genetics\/162.4.2025","article-title":"Approximate Bayesian Computation in population genetics","volume":"162","author":"MA Beaumont","year":"2002","journal-title":"Genetics"},{"issue":"37","key":"ref26","doi-asserted-by":"crossref","first-page":"15112","DOI":"10.1073\/pnas.1102900108","article-title":"Lack of confidence in Approximate Bayesian Computation model choice","volume":"108","author":"CP Robert","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"6","key":"ref27","doi-asserted-by":"crossref","first-page":"441","DOI":"10.1049\/iet-syb.2010.0005","article-title":"Fast adaptive uniformisation of the chemical master equation","volume":"4","author":"M Mateescu","year":"2010","journal-title":"IET Syst Biol"},{"issue":"1","key":"ref28","doi-asserted-by":"crossref","first-page":"1579","DOI":"10.1016\/j.procs.2010.04.177","article-title":"An optimal Finite State Projection method","volume":"1","author":"V Sunkara","year":"2010","journal-title":"Procedia Computer Science"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"498","DOI":"10.1016\/j.amc.2005.12.032","article-title":"Computing the moments of high dimensional solutions of the master equation","volume":"180","author":"S Engblom","year":"2006","journal-title":"Appl Math Comp"},{"issue":"13","key":"ref30","doi-asserted-by":"crossref","first-page":"134107","DOI":"10.1063\/1.3103264","article-title":"A moment closure method for stochastic reaction networks","volume":"130","author":"CH Lee","year":"2009","journal-title":"J Chem Phys"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"52","DOI":"10.1049\/iet-syb:20070031","article-title":"Moment-closure approximations for mass-action models","volume":"3","author":"CS Gillespie","year":"2009","journal-title":"IET Syst Biol"},{"issue":"17","key":"ref32","doi-asserted-by":"crossref","first-page":"174101","DOI":"10.1063\/1.4802475","article-title":"A general moment expansion method for stochastic kinetic models","volume":"138","author":"A Ale","year":"2013","journal-title":"J Chem Phys"},{"issue":"18","key":"ref33","doi-asserted-by":"crossref","DOI":"10.1063\/1.4934990","article-title":"Comparison of different moment-closure approximations for stochastic chemical kinetics","volume":"143","author":"D Schnoerr","year":"2015","journal-title":"The Journal of Chemical Physics"},{"issue":"2","key":"ref34","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1111\/j.2517-6161.1957.tb00263.x","article-title":"On the use of the normal approximation in the treatment of stochastic processes","volume":"19","author":"P Whittle","year":"1957","journal-title":"J R Stat Soc B"},{"key":"ref35","doi-asserted-by":"crossref","unstructured":"Singh A, Hespanha JP. 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(CDC); 2006. p. 2063\u20132068.","DOI":"10.1109\/CDC.2006.376994"},{"issue":"035101","key":"ref36","article-title":"An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions","volume":"133","author":"R Grima","year":"2010","journal-title":"J Chem Phys"},{"issue":"5 Pt 2","key":"ref37","doi-asserted-by":"crossref","first-page":"056109","DOI":"10.1103\/PhysRevE.84.056109","article-title":"Construction and accuracy of partial differential equation approximations to the chemical master equation","volume":"84","author":"R Grima","year":"2011","journal-title":"Physical Review E"},{"issue":"8","key":"ref38","doi-asserted-by":"crossref","first-page":"084103","DOI":"10.1063\/1.4892838","article-title":"Validity conditions for moment closure approximations in stochastic chemical kinetics","volume":"141","author":"D Schnoerr","year":"2014","journal-title":"J Chem 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in systems biology","volume":"8","author":"A Raue","year":"2013","journal-title":"PLoS ONE"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"042124","DOI":"10.1103\/PhysRevE.92.042124","article-title":"Linear-noise approximation and the chemical master equation agree up to second-order moments for a class of chemical systems","volume":"92","author":"R Grima","year":"2015","journal-title":"Phys Rev E"},{"issue":"779","key":"ref44","article-title":"Discreteness-induced concentration inversion in mesoscopic chemical systems","volume":"3","author":"R Ramaswamy","year":"2012","journal-title":"Nat Comm"},{"issue":"Suppl 4","key":"ref45","doi-asserted-by":"crossref","first-page":"S5","DOI":"10.1186\/1471-2164-14-S4-S5","article-title":"How reliable is the linear noise approximation of gene regulatory networks?","volume":"14","author":"P Thomas","year":"2013","journal-title":"BMC Genomics"},{"issue":"1","key":"ref46","doi-asserted-by":"crossref","first-page":"e0146732","DOI":"10.1371\/journal.pone.0146732","article-title":"CERENA: ChEmical REaction Network Analyzer\u2014A Toolbox for the Simulation and Analysis of Stochastic Chemical Kinetics","volume":"11","author":"A Kazeroonian","year":"2016","journal-title":"PLoS ONE"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"2475","DOI":"10.1101\/gr.1196503","article-title":"Fast evaluation of fluctuations in biochemical networks with the linear noise approximation","volume":"13","author":"J Elf","year":"2003","journal-title":"Genome Res"},{"issue":"2","key":"ref48","doi-asserted-by":"crossref","first-page":"8","DOI":"10.1145\/2688906","article-title":"Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks","volume":"25","author":"J Ruess","year":"2015","journal-title":"ACM Transactions on Modeling and Computer Simulation (TOMACS)"},{"key":"ref49","first-page":"1","article-title":"On the convergence of reflective Newton Methods for large-scale nonlinear minimization subject to bounds","author":"TF Coleman","year":"1992","journal-title":"Math Prog"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1137\/0806023","article-title":"An interior trust region approach for nonlinear minimization subject to bounds","volume":"6","author":"TF Coleman","year":"1996","journal-title":"SIAM J Optim"},{"issue":"3","key":"ref51","doi-asserted-by":"crossref","first-page":"363","DOI":"10.1145\/1089014.1089020","article-title":"SUNDIALS: Suite of Nonlinear and Differential\/Algebraic Equation Solvers","volume":"31","author":"AC Hindmarsh","year":"2005","journal-title":"ACM T Math Software"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1007\/BFb0067700","article-title":"The Levenberg-Marquardt algorithm: Implementation and theory","volume":"630","author":"JJ More","year":"1978","journal-title":"Lecture Notes in Mathematics"},{"issue":"25","key":"ref53","doi-asserted-by":"crossref","first-page":"1923","DOI":"10.1093\/bioinformatics\/btp358","article-title":"Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood","volume":"25","author":"A Raue","year":"2009","journal-title":"Bioinf"},{"issue":"450","key":"ref54","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1080\/01621459.2000.10474219","article-title":"On profile likelihood","volume":"95","author":"SA Murphy","year":"2000","journal-title":"J Am Stat Assoc"},{"issue":"1984","key":"ref55","doi-asserted-by":"crossref","DOI":"10.1098\/rsta.2011.0544","article-title":"Joining forces of Bayesian and frequentist methodology: A study for inference in the presence of non-identifiability","volume":"371","author":"A Raue","year":"2013","journal-title":"Phil Trans Royal Soc A"},{"issue":"2","key":"ref56","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1093\/bib\/bbm007","article-title":"Bayesian methods in bioinformatics and computational systems biology","volume":"8","author":"DJ Wilkinson","year":"2007","journal-title":"Briefings in Bioinf"},{"issue":"2","key":"ref57","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1111\/j.1467-9868.2010.00765.x","article-title":"Riemann manifold Langevin and Hamiltonian Monte Carlo methods","volume":"73","author":"M Girolami","year":"2011","journal-title":"J R Statist Soc B"},{"issue":"1","key":"ref58","doi-asserted-by":"crossref","first-page":"87","DOI":"10.2307\/2347496","article-title":"A Method for Computing Profile-Likelihood Based Confidence Intervals","volume":"37","author":"D Venzon","year":"1988","journal-title":"Applied Statistics"},{"key":"ref59","doi-asserted-by":"crossref","unstructured":"Fr\u00f6hlich F, Theis FJ, Hasenauer J. Uncertainty analysis for non-identifiable dynamical systems: Profile likelihoods, bootstrapping and more. In: Mendes P, Dada JO, Smallbone KO, editors. Proceedings of the 12th International Conference on Computational Methods in Systems Biology (CMSB 2014), Manchester, UK. Lecture Notes in Bioinformatics. Springer International Publishing Switzerland; 2014. p. 61\u201372.","DOI":"10.1007\/978-3-319-12982-2_5"},{"issue":"4","key":"ref60","doi-asserted-by":"crossref","first-page":"339","DOI":"10.1007\/s11222-006-9438-0","article-title":"DRAM: Efficient adaptive MCMC","volume":"16","author":"H Haario","year":"2006","journal-title":"Stat Comp"},{"issue":"3\/4","key":"ref61","doi-asserted-by":"crossref","first-page":"217","DOI":"10.2307\/2988185","article-title":"On the likelihood of a time series model","volume":"27","author":"H Akaike","year":"1978","journal-title":"The Statistician"},{"issue":"2","key":"ref62","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1214\/aos\/1176344136","article-title":"Estimating the dimension of a model","volume":"6","author":"G Schwarz","year":"1978","journal-title":"Ann Statist"},{"key":"ref63","article-title":"Statistics for Industry and Technology","author":"C Huber-Carol","year":"2002"},{"key":"ref64","doi-asserted-by":"crossref","first-page":"813","DOI":"10.1038\/nrm2030","article-title":"Linking data to models: Data regression","volume":"7","author":"K Jaqaman","year":"2006","journal-title":"Nature Reviews Molecular Cell Biology"},{"key":"ref65","article-title":"Probability, Random Variables, and Stochastic Processes","author":"A Papoulis","year":"2002"},{"key":"ref66","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-662-03976-2","article-title":"Parameter estimation and hypothesis testing in linear models","author":"KR Koch","year":"1999"},{"issue":"3","key":"ref67","doi-asserted-by":"crossref","first-page":"1028","DOI":"10.1073\/pnas.0237333100","article-title":"Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling","volume":"100","author":"I Swameye","year":"2003","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"Pt 8","key":"ref68","doi-asserted-by":"crossref","first-page":"1281","DOI":"10.1242\/jcs.00963","article-title":"The JAK\/STAT signaling pathway","volume":"117","author":"JS Rawlings","year":"2004","journal-title":"J Cell Sci"},{"issue":"Suppl 1","key":"ref69","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1634\/theoncologist.2009-S1-43","article-title":"Anemia management in oncology and hematology","volume":"14","author":"JL Spivak","year":"2009","journal-title":"Oncologist"},{"issue":"19","key":"ref70","doi-asserted-by":"crossref","first-page":"6151","DOI":"10.1158\/1078-0432.CCR-10-3298","article-title":"Recombinant human erythropoietin in combination with chemotherapy increases breast cancer metastasis in preclinical mouse models","volume":"17","author":"BD Hedley","year":"2011","journal-title":"Clin Cancer Res"},{"issue":"7","key":"ref71","article-title":"Division of labor by dual feedback regulators controls JAK2\/STAT5 signaling over broad ligand range","volume":"516","author":"J Bachmann","year":"2011","journal-title":"Mol Syst Biol"},{"issue":"108","key":"ref72","doi-asserted-by":"crossref","DOI":"10.1098\/rsif.2015.0233","article-title":"Tensor methods for parameter estimation and bifurcation analysis of stochastic reaction networks","volume":"12","author":"S Liao","year":"2015","journal-title":"Journal of The Royal Society Interface"},{"issue":"8","key":"ref73","doi-asserted-by":"crossref","first-page":"e43001","DOI":"10.1371\/journal.pone.0043001","article-title":"Moment fitting for parameter inference in repeatedly and partially observed stochastic biological models","volume":"7","author":"P K\u00fcgler","year":"2012","journal-title":"PloS one"},{"issue":"5092","key":"ref74","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1126\/science.8421783","article-title":"Regulation of heat shock factor trimer formation: role of a conserved leucine zipper","volume":"259","author":"S Rabindran","year":"1993","journal-title":"Science"},{"issue":"1","key":"ref75","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1016\/S0896-6273(00)80284-6","article-title":"Heteromultimerization and NMDA Receptor-Clustering Activity of Chapsyn-110, a Member of the PSD-95 Family of Proteins","volume":"17","author":"E Kim","year":"1996","journal-title":"Neuron"},{"issue":"6","key":"ref76","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1016\/j.cell.2005.09.031","article-title":"Real-time kinetics of gene activity in individual bacteria","volume":"123","author":"I Golding","year":"2005","journal-title":"Cell"},{"key":"ref77","doi-asserted-by":"crossref","unstructured":"Thomas P, Matuschek H, Grima R. Computation of biochemical pathway fluctuations beyond the linear noise approximation using iNA. IEEE International Conference on Bioinformatics and Biomedicine; 2012;p. 192\u2013196.","DOI":"10.1109\/BIBM.2012.6392668"},{"issue":"2","key":"ref78","doi-asserted-by":"crossref","first-page":"222","DOI":"10.1006\/tpbi.1995.1027","article-title":"Markovian modelling of gene product synthesis","volume":"48","author":"J Peccoud","year":"1995","journal-title":"Theor Popul Biol"},{"issue":"16","key":"ref79","doi-asserted-by":"crossref","first-page":"168302","DOI":"10.1103\/PhysRevLett.97.168302","article-title":"Linking stochastic dynamics to population distribution: an analytical framework of gene expression","volume":"97","author":"N Friedman","year":"2006","journal-title":"Phys Rev Lett"},{"issue":"45","key":"ref80","doi-asserted-by":"crossref","first-page":"17256","DOI":"10.1073\/pnas.0803850105","article-title":"Analytical distributions for stochastic gene expression","volume":"105","author":"V Shahrezaei","year":"2008","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref81","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.copbio.2014.10.010","article-title":"Computational and experimental single cell biology techniques for the definition of cell type heterogeneity, interplay and intracellular dynamics","volume":"34","author":"L De Vargas Roditi","year":"2015","journal-title":"Curr Opin Biotechnol"},{"issue":"1","key":"ref82","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nrg2484","article-title":"RNA-Seq: a revolutionary tool for transcriptomics","volume":"10","author":"Z Wang","year":"2009","journal-title":"Nat Rev Gen"},{"issue":"22","key":"ref83","doi-asserted-by":"crossref","first-page":"3743","DOI":"10.1242\/jcs.087486","article-title":"Getting the whole picture: combining throughput with content in microscopy","volume":"124","author":"N Rimon","year":"2011","journal-title":"J Cell Sci"},{"issue":"9","key":"ref84","doi-asserted-by":"crossref","first-page":"858","DOI":"10.1038\/nbt.2317","article-title":"Multiplexed mass cytometry profiling of cellular states perturbed by small-molecule regulators","volume":"30","author":"B Bodenmiller","year":"2012","journal-title":"Nat Biotechnol"},{"issue":"012120","key":"ref85","article-title":"Approximate distributions of the Master equation","volume":"92","author":"P Thomas","year":"2015","journal-title":"Physical Review E"},{"issue":"2","key":"ref86","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1016\/j.mbs.2013.04.002","article-title":"High-dimensional Bayesian parameter estimation: Case study for a model of JAK2\/STAT5 signaling","volume":"246","author":"S Hug","year":"2013","journal-title":"Math Biosci"},{"issue":"8","key":"ref87","doi-asserted-by":"crossref","first-page":"1490","DOI":"10.1016\/j.jprocont.2012.01.017","article-title":"Dynamical optimization using reduced order models: A method to guarantee performance","volume":"22","author":"J Hasenauer","year":"2012","journal-title":"Journal of Process Control"},{"key":"ref88","doi-asserted-by":"crossref","unstructured":"Dihlmann M, Haasdonk B. Certified nonlinear parameter optimization with reduced basis surrogate models. In: Cvetkovi\u0107 L, Atanackovi\u0107 T, Kosti\u0107 V, editors. Proceedings of Applied Mathematics and Mechanics (PAMM). vol. 13; 2013. p. 3\u20136.","DOI":"10.1002\/pamm.201310002"},{"key":"ref89","article-title":"Probabilistic solution of differential equations for Bayesian uncertainty quantification and inference","author":"OA Chkrebtii","year":"2013"},{"key":"ref90","unstructured":"Chkrebtii OA, Campbell DA, Girolami MA, Calderhead B. Bayesian uncertainty quantification for differential equations. arXiv:13062365 [statME]; 2014;."},{"issue":"3","key":"ref91","doi-asserted-by":"crossref","first-page":"687","DOI":"10.1007\/s00285-013-0711-5","article-title":"Method of conditional moments (MCM) for the chemical master equation","volume":"69","author":"J Hasenauer","year":"2014","journal-title":"Journal of Mathematical Biology"},{"issue":"19","key":"ref92","doi-asserted-by":"crossref","first-page":"6994","DOI":"10.1073\/pnas.1400049111","article-title":"Phenotypic switching in gene regulatory networks","volume":"111","author":"P Thomas","year":"2014","journal-title":"Proc Natl Acad Sci U S A"},{"issue":"7","key":"ref93","doi-asserted-by":"crossref","first-page":"e1003686","DOI":"10.1371\/journal.pcbi.1003686","article-title":"ODE constrained mixture modelling: A method for unraveling subpopulation structures and dynamics","volume":"10","author":"J Hasenauer","year":"2014","journal-title":"PLoS Comput Biol"},{"issue":"4","key":"ref94","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1038\/nmeth.1577","article-title":"Long-term single-cell imaging of mammalian stem cells","volume":"8","author":"T Schroeder","year":"2011","journal-title":"Nat Methods"},{"issue":"7","key":"ref95","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1038\/nmeth.1338","article-title":"Quantitative analysis of gene expression in a single cell by qPCR","volume":"6","author":"K Taniguchi","year":"2009","journal-title":"Nature Methods"},{"issue":"6080","key":"ref96","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1126\/science.1222161","article-title":"Using cell-to-cell variability\u2013A new era in molecular biology","volume":"336","author":"L Pelkmans","year":"2012","journal-title":"Science"},{"issue":"6078","key":"ref97","doi-asserted-by":"crossref","first-page":"183","DOI":"10.1126\/science.1216379","article-title":"Using gene expression noise to understand gene regulation","volume":"336","author":"B Munsky","year":"2012","journal-title":"Science"}],"container-title":["PLOS Computational Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005030","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,6,18]],"date-time":"2024-06-18T11:32:19Z","timestamp":1718710339000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pcbi.1005030"}},"subtitle":[],"editor":[{"given":"Daniel A","family":"Beard","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2016,7,22]]},"references-count":97,"journal-issue":{"issue":"7","published-online":{"date-parts":[[2016,7,22]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pcbi.1005030","relation":{},"ISSN":["1553-7358"],"issn-type":[{"value":"1553-7358","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,7,22]]}}}