{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,8]],"date-time":"2026-01-08T05:38:22Z","timestamp":1767850702064,"version":"3.49.0"},"reference-count":60,"publisher":"Springer Science and Business Media LLC","issue":"1","content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2010,12]]},"abstract":"<jats:title>Abstract<\/jats:title>\n          <jats:sec>\n            <jats:title>Background<\/jats:title>\n            <jats:p>Fluorescent and luminescent reporter genes have become popular tools for the real-time monitoring of gene expression in living cells. However, mathematical models are necessary for extracting biologically meaningful quantities from the primary data.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Results<\/jats:title>\n            <jats:p>We present a rigorous method for deriving relative protein synthesis rates (mRNA concentrations) and protein concentrations by means of kinetic models of gene expression. We experimentally and computationally validate this approach in the case of the protein Fis, a global regulator of transcription in <jats:italic>Escherichia coli<\/jats:italic>. We show that the mRNA and protein concentration profiles predicted from the models agree quite well with direct measurements obtained by Northern and Western blots, respectively. Moreover, we present computational procedures for taking into account systematic biases like the folding time of the fluorescent reporter protein and differences in the half-lives of reporter and host gene products. The results show that large differences in protein half-lives, more than mRNA half-lives, may be critical for the interpretation of reporter gene data in the analysis of the dynamics of regulatory systems.<\/jats:p>\n          <\/jats:sec>\n          <jats:sec>\n            <jats:title>Conclusions<\/jats:title>\n            <jats:p>The paper contributes to the development of sound methods for the interpretation of reporter gene data, notably in the context of the reconstruction and validation of models of regulatory networks. The results have wide applicability for the analysis of gene expression in bacteria and may be extended to higher organisms.<\/jats:p>\n          <\/jats:sec>","DOI":"10.1186\/1752-0509-4-55","type":"journal-article","created":{"date-parts":[[2010,4,29]],"date-time":"2010-04-29T18:15:30Z","timestamp":1272564930000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":63,"title":["Experimental and computational validation of models of fluorescent and luminescent reporter genes in bacteria"],"prefix":"10.1186","volume":"4","author":[{"given":"Hidde","family":"de Jong","sequence":"first","affiliation":[]},{"given":"Caroline","family":"Ranquet","sequence":"additional","affiliation":[]},{"given":"Delphine","family":"Ropers","sequence":"additional","affiliation":[]},{"given":"Corinne","family":"Pinel","sequence":"additional","affiliation":[]},{"given":"Johannes","family":"Geiselmann","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2010,4,29]]},"reference":[{"issue":"5771","key":"444_CR1","doi-asserted-by":"publisher","first-page":"217","DOI":"10.1126\/science.1124618","volume":"312","author":"B Giepmans","year":"2006","unstructured":"Giepmans B, Adams S, Ellisman M, Tsien R: The fluorescent toolbox for assessing protein location and function. Science. 2006, 312 (5771): 217-224. 10.1126\/science.1124618","journal-title":"Science"},{"key":"444_CR2","doi-asserted-by":"publisher","first-page":"43","DOI":"10.1002\/bio.676","volume":"17","author":"L Greer","year":"2002","unstructured":"Greer L, Szalay A: Imaging of light emission from the expression of luciferases in living cells and organisms: A review. Luminescence. 2002, 17: 43-74. 10.1002\/bio.676","journal-title":"Luminescence"},{"key":"444_CR3","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1038\/msb4100110","volume":"2","author":"D Longo","year":"2006","unstructured":"Longo D, Hasty J: Dynamics of single-cell gene expression. Mol Syst Biol. 2006, 2: 64- 10.1038\/msb4100110","journal-title":"Mol Syst Biol"},{"issue":"10","key":"444_CR4","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1038\/nrm1494","volume":"5","author":"Y Shav-Tal","year":"2004","unstructured":"Shav-Tal Y, Singer R, Darzacq X: Imaging gene expression in single living cells. Nat Rev Mol Cell Biol. 2004, 5 (10): 855-861. 10.1038\/nrm1494","journal-title":"Nat Rev Mol Cell Biol"},{"issue":"5","key":"444_CR5","doi-asserted-by":"publisher","first-page":"1191","DOI":"10.1046\/j.1365-2958.2002.03089.x","volume":"45","author":"C Southward","year":"2002","unstructured":"Southward C, Surette M: The dynamic microbe: Green fluorescent protein brings bacteria to light. Mol Microbiol. 2002, 45 (5): 1191-1196. 10.1046\/j.1365-2958.2002.03089.x","journal-title":"Mol Microbiol"},{"issue":"6912","key":"444_CR6","doi-asserted-by":"publisher","first-page":"231","DOI":"10.1038\/nature01258","volume":"420","author":"C Rao","year":"2002","unstructured":"Rao C, Wolf D, Arkin A: Control, exploitation and tolerance of intracellular noise. Nature. 2002, 420 (6912): 231-237. 10.1038\/nature01258","journal-title":"Nature"},{"issue":"6","key":"444_CR7","doi-asserted-by":"publisher","first-page":"451","DOI":"10.1038\/nrg1615","volume":"6","author":"M Kaern","year":"2005","unstructured":"Kaern M, Elston T, Blake W, Collins J: Stochasticity in gene expression: From theories to phenotypes. Nat Rev Genet. 2005, 6 (6): 451-464. 10.1038\/nrg1615","journal-title":"Nat Rev Genet"},{"issue":"2","key":"444_CR8","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1038\/nrg2509","volume":"10","author":"D Wilkinson","year":"2009","unstructured":"Wilkinson D: Stochastic modelling for quantitative description of heterogeneous biological systems. Nat Rev Genet. 2009, 10 (2): 122-133. 10.1038\/nrg2509","journal-title":"Nat Rev Genet"},{"issue":"5","key":"444_CR9","doi-asserted-by":"publisher","first-page":"2555","DOI":"10.1073\/pnas.041620498","volume":"98","author":"T Van Dyk","year":"2001","unstructured":"Van Dyk T, Wei Y, Hanafey M, Dolan M, Reeve M, Rafalski J, Rothman-Denes L, LaRossa R: A genomic approach to gene fusion technology. Proc Natl Acad Sci USA. 2001, 98 (5): 2555-2560. 10.1073\/pnas.041620498","journal-title":"Proc Natl Acad Sci USA"},{"issue":"8","key":"444_CR10","doi-asserted-by":"publisher","first-page":"623","DOI":"10.1038\/nmeth895","volume":"3","author":"A Zaslaver","year":"2006","unstructured":"Zaslaver A, Bren A, Ronen M, Itzkovitz S, Kikoin I, Shavit S, Liebermeister W, Surette M, Alon U: A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Meth. 2006, 3 (8): 623-628. 10.1038\/nmeth895.","journal-title":"Nat Meth"},{"issue":"12","key":"444_CR11","doi-asserted-by":"publisher","first-page":"4470","DOI":"10.1073\/pnas.0500670102","volume":"102","author":"O Kobiler","year":"2005","unstructured":"Kobiler O, Rokney A, Friedman N, Court D, Stavans J, Oppenheim A: Quantitative kinetic analysis of the bacteriophage \u03bb genetic network. Proc Natl Acad Sci USA. 2005, 102 (12): 4470-4475. 10.1073\/pnas.0500670102","journal-title":"Proc Natl Acad Sci USA"},{"issue":"5","key":"444_CR12","doi-asserted-by":"publisher","first-page":"574","DOI":"10.1002\/bit.20389","volume":"89","author":"C Lu","year":"2005","unstructured":"Lu C, Albano C, Bentley W, Rao G: Quantitative and kinetic study of oxidative stress regulons using green fluorescent protein. Biotechnol Bioeng. 2005, 89 (5): 574-587. 10.1002\/bit.20389","journal-title":"Biotechnol Bioeng"},{"issue":"16","key":"444_CR13","doi-asserted-by":"publisher","first-page":"10555","DOI":"10.1073\/pnas.152046799","volume":"99","author":"M Ronen","year":"2002","unstructured":"Ronen M, Rosenberg R, Shraiman B, Alon U: Assigning numbers to the arrows: Parameterizing a gene regulation network by using accurate expression kinetics. Proc Natl Acad Sci USA. 2002, 99 (16): 10555-10560. 10.1073\/pnas.152046799","journal-title":"Proc Natl Acad Sci USA"},{"issue":"19","key":"444_CR14","doi-asserted-by":"publisher","first-page":"5496","DOI":"10.1128\/JB.183.19.5496-5505.2001","volume":"183","author":"T Van Dyk","year":"2001","unstructured":"Van Dyk T, DeRose E, Gonye G: LuxArray, a high-density, genomewide transcription analysis of Escherichia coli using bioluminescent reporter strains. J Bacteriol. 2001, 183 (19): 5496-5505. 10.1128\/JB.183.19.5496-5505.2001","journal-title":"J Bacteriol"},{"issue":"2","key":"444_CR15","doi-asserted-by":"publisher","first-page":"795","DOI":"10.1016\/j.bbrc.2004.08.236","volume":"324","author":"C Forde","year":"2004","unstructured":"Forde C, Rocco J, Fitch F, McCutchen-Maloney S: Real-time characterization of virulence factor expression in Yersinia pestis using a GFP reporter system. Biochem Biophys Res Commun. 2004, 324 (2): 795-800. 10.1016\/j.bbrc.2004.08.236","journal-title":"Biochem Biophys Res Commun"},{"issue":"13","key":"444_CR16","doi-asserted-by":"publisher","first-page":"7702","DOI":"10.1073\/pnas.1230759100","volume":"100","author":"Y Setty","year":"2003","unstructured":"Setty Y, Mayo A, Surette M, Alon U: Detailed map of a cis-regulatory input function. Proc Natl Acad Sci USA. 2003, 100 (13): 7702-7707. 10.1073\/pnas.1230759100","journal-title":"Proc Natl Acad Sci USA"},{"issue":"6767","key":"444_CR17","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/35002125","volume":"403","author":"M Elowitz","year":"2000","unstructured":"Elowitz M, Leibler S: A synthetic oscillatory network of transcriptional regulators. Nature. 2000, 403 (6767): 335-338. 10.1038\/35002125","journal-title":"Nature"},{"issue":"24","key":"444_CR18","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, Komorowski M, Edwards K, Tang S, Harper C, Davis J, White M, Millar A, Rand D: Reconstruction of transcriptional dynamics from gene reporter data using differential equations. Bioinformatics. 2008, 24 (24): 2901-2907. 10.1093\/bioinformatics\/btn562","journal-title":"Bioinformatics"},{"issue":"6","key":"444_CR19","doi-asserted-by":"publisher","first-page":"611","DOI":"10.1089\/cmb.2007.0220","volume":"15","author":"D Gold","year":"2008","unstructured":"Gold D, Mallick B, Coombes K: Real-time gene expression: Statistical challenges in design and inference. J Comput Biol. 2008, 15 (6): 611-624. 10.1089\/cmb.2007.0220","journal-title":"J Comput Biol"},{"key":"444_CR20","doi-asserted-by":"publisher","first-page":"64","DOI":"10.1186\/1752-0509-2-64","volume":"2","author":"Z Huang","year":"2008","unstructured":"Huang Z, Senocak F, Jayaraman A, Hahn J: Integrated modeling and experimental approach for determining transcription factor profiles from fluorescent reporter data. BMC Syst Biol. 2008, 2: 64- 10.1186\/1752-0509-2-64","journal-title":"BMC Syst Biol"},{"issue":"23","key":"444_CR21","doi-asserted-by":"publisher","first-page":"6752","DOI":"10.1128\/JB.183.23.6752-6762.2001","volume":"183","author":"J Leveau","year":"2001","unstructured":"Leveau J, Lindow S: Predictive and interpretive simulation of green fluorescent protein expression in reporter bacteria. J Bacteriol. 2001, 183 (23): 6752-6762. 10.1128\/JB.183.23.6752-6762.2001","journal-title":"J Bacteriol"},{"issue":"1-3","key":"444_CR22","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1016\/0168-1656(96)01536-2","volume":"49","author":"S Subramanian","year":"1996","unstructured":"Subramanian S, Srienc F: Quantitative analysis of transient gene expression in mammalian cells using the green fluorescent protein. J Biotechnol. 1996, 49 (1-3): 137-151. 10.1016\/0168-1656(96)01536-2","journal-title":"J Biotechnol"},{"issue":"6","key":"444_CR23","doi-asserted-by":"publisher","first-page":"2017","DOI":"10.1529\/biophysj.107.122200","volume":"94","author":"X Wang","year":"2008","unstructured":"Wang X, Errede B, Elston T: Mathematical analysis and quantification of fluorescent proteins as transcriptional reporters. Biophys J. 2008, 94 (6): 2017-2026. 10.1529\/biophysj.107.122200","journal-title":"Biophys J"},{"issue":"9","key":"444_CR24","doi-asserted-by":"publisher","first-page":"2922","DOI":"10.1099\/mic.0.2007\/008565-0","volume":"153","author":"M Bradley","year":"2007","unstructured":"Bradley M, Beach M, de Koning A, Pratt T, Osuna R: Effects of Fis on Escherichia coli gene expression during different growth stages. Microbiol. 2007, 153 (9): 2922-2940. 10.1099\/mic.0.2007\/008565-0.","journal-title":"Microbiol"},{"issue":"20","key":"444_CR25","doi-asserted-by":"crossref","first-page":"6361","DOI":"10.1128\/JB.181.20.6361-6370.1999","volume":"181","author":"TA Azam","year":"1999","unstructured":"Azam TA, Iwata A, Nishimura A, Ueda S, Ishihama A: Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid. J Bacteriol. 1999, 181 (20): 6361-6370.","journal-title":"J Bacteriol"},{"key":"444_CR26","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1128\/JB.186.1.122-135.2004","volume":"186","author":"P Mallik","year":"2004","unstructured":"Mallik P, Pratt T, Beach M, Bradley M, Undamatla J, Osuna R: Growth phase-dependent regulation and stringent control of fis are conserved processes in enteric bacteria and involve a single promoter (fis P) in Escherichia coli. J Bacteriol. 2004, 186: 122-135. 10.1128\/JB.186.1.122-135.2004","journal-title":"J Bacteriol"},{"issue":"3","key":"444_CR27","doi-asserted-by":"crossref","first-page":"1075","DOI":"10.1002\/j.1460-2075.1992.tb05146.x","volume":"11","author":"O Ninnemann","year":"1992","unstructured":"Ninnemann O, Koch C, Kahmann R: The E. coli fis promoter is subject to stringent control and autoregulation. EMBO J. 1992, 11 (3): 1075-1083.","journal-title":"EMBO J"},{"key":"444_CR28","volume-title":"Mol Syst Biol","author":"T Baba","year":"2006","unstructured":"Baba T, Ara T, Hasegawa M, Takai Y, Okumura Y, Baba M, Datsenko K, Tomita M, Wanner B, Mori H: Construction of Escherichia coli K-12 in-frame, single-gene knock-out mutants: The Keio collection. Mol Syst Biol. 2006, 2: 10.1038\/msb4100050. 2006.0008.,"},{"issue":"19","key":"444_CR29","doi-asserted-by":"crossref","first-page":"5449","DOI":"10.1002\/j.1460-2075.1996.tb00928.x","volume":"15","author":"S D\u00e9thiollaz","year":"1996","unstructured":"D\u00e9thiollaz S, Eichenberger P, Geiselmann J: Influence of DNA geometry on transcriptional activation in Escherichia coli. EMBO J. 1996, 15 (19): 5449-5458.","journal-title":"EMBO J"},{"key":"444_CR30","volume-title":"Experiments in Molecular Genetics","author":"J Miller","year":"1972","unstructured":"Miller J: Experiments in Molecular Genetics. 1972, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory,"},{"key":"444_CR31","volume-title":"A Practical Guide to Splines","author":"C de Boor","year":"2001","unstructured":"de Boor C: A Practical Guide to Splines. 2001, New York: Springer-Verlag, 2,","edition":"2"},{"key":"444_CR32","volume-title":"Generalized Additive Models","author":"T Hastie","year":"1999","unstructured":"Hastie T, Tibshirani R: Generalized Additive Models. 1999, Boca Raton, FL: CRC Press,"},{"issue":"8","key":"444_CR33","doi-asserted-by":"publisher","first-page":"647","DOI":"10.1080\/00949650213743","volume":"72","author":"T Lee","year":"2002","unstructured":"Lee T: On algorithms for ordinary least square regression spline fitting: A comparative study. J Stat Comput Simul. 2002, 72 (8): 647-663. 10.1080\/00949650213743.","journal-title":"J Stat Comput Simul"},{"key":"444_CR34","volume-title":"Regression with Graphics: A Second Course in Applied Statistics","author":"L Hamilton","year":"1992","unstructured":"Hamilton L: Regression with Graphics: A Second Course in Applied Statistics. 1992, Belmond, CA: Duxbury Press,"},{"issue":"7","key":"444_CR35","first-page":"36","volume":"11","author":"M Abramoff","year":"2004","unstructured":"Abramoff M, Magelhaes P, Ram S: Image processing with ImageJ. Biophoton Int. 2004, 11 (7): 36-42.","journal-title":"Biophoton Int"},{"issue":"22","key":"444_CR36","doi-asserted-by":"crossref","first-page":"11905","DOI":"10.1016\/S0021-9258(19)68491-7","volume":"256","author":"H Aiba","year":"1981","unstructured":"Aiba H, Adhya S, de Crombrugghe B: Evidence for two functional gal promoters in intact Escherichia coli cells. J Biol Chem. 1981, 256 (22): 11905-11910.","journal-title":"J Biol Chem"},{"issue":"6","key":"444_CR37","doi-asserted-by":"publisher","first-page":"1203","DOI":"10.1093\/nar\/25.6.1203","volume":"25","author":"R Lutz","year":"1997","unstructured":"Lutz R, Bujard H: Independent and tight regulation of transcriptional units in Escherichia coli via LacR\/O, the TetR\/O and AraC\/l1-l2 regulatory elements. Nucleic Acids Res. 1997, 25 (6): 1203-1210. 10.1093\/nar\/25.6.1203","journal-title":"Nucleic Acids Res"},{"issue":"6","key":"444_CR38","doi-asserted-by":"crossref","first-page":"2240","DOI":"10.1128\/AEM.64.6.2240-2246.1998","volume":"64","author":"J Andersen","year":"1998","unstructured":"Andersen J, Sternberg C, Poulsen L, Bjorn S, Givskov M, Molin S: New unstable variants of green fluorescent protein for studies of transient gene expression in bacteria. Appl Environ Microbiol. 1998, 64 (6): 2240-2246.","journal-title":"Appl Environ Microbiol"},{"key":"444_CR39","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1128\/mr.55.1.123-142.1991","volume":"55","author":"E Meighen","year":"1991","unstructured":"Meighen E: Molecular biology of bacterial bioluminescence. Microbiol Rev. 1991, 55: 123-142.","journal-title":"Microbiol Rev"},{"issue":"4","key":"444_CR40","doi-asserted-by":"crossref","first-page":"1269","DOI":"10.1128\/JB.181.4.1269-1280.1999","volume":"181","author":"K Walker","year":"1999","unstructured":"Walker K, Atkins C, Osuna R: Functional determinants of the Escherichia coli fis promoter: Roles of -35, -10, and transcription initiation regions in the response to stringent control and growth phase-dependent regulation. J Bacteriol. 1999, 181 (4): 1269-1280.","journal-title":"J Bacteriol"},{"key":"444_CR41","doi-asserted-by":"publisher","first-page":"509","DOI":"10.1146\/annurev.biochem.67.1.509","volume":"67","author":"R Tsien","year":"1998","unstructured":"Tsien R: The green fluorescent protein. Annu Rev Biochem. 1998, 67: 509-544. 10.1146\/annurev.biochem.67.1.509","journal-title":"Annu Rev Biochem"},{"key":"444_CR42","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"H de Jong","year":"2002","unstructured":"de Jong H: Modeling and simulation of genetic regulatory systems: A literature review. J Comput Biol. 2002, 9: 67-103. 10.1089\/10665270252833208","journal-title":"J Comput Biol"},{"key":"444_CR43","volume-title":"Temporal Organization in Cells","author":"B Goodwin","year":"1963","unstructured":"Goodwin B: Temporal Organization in Cells. 1963, New York, N.Y.: Academic Press,"},{"issue":"4","key":"444_CR44","doi-asserted-by":"publisher","first-page":"815","DOI":"10.1002\/bit.21065","volume":"96","author":"A Kremling","year":"2007","unstructured":"Kremling A: Comment on mathematical models which describe transcription and calculate the relationship between mRNA and protein expression ratio. Biotechnol Bioeng. 2007, 96 (4): 815-819. 10.1002\/bit.21065","journal-title":"Biotechnol Bioeng"},{"key":"444_CR45","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/B978-0-12-543105-7.50008-7","volume":"5","author":"J Tyson","year":"1978","unstructured":"Tyson J, Othmer H: The dynamics of feedback control circuits in biochemical pathways. Prog Theor Biol. 1978, 5: 1-62.","journal-title":"Prog Theor Biol"},{"issue":"7227","key":"444_CR46","doi-asserted-by":"publisher","first-page":"309","DOI":"10.1038\/nature07616","volume":"457","author":"M Tigges","year":"2009","unstructured":"Tigges M, Marquez-Lago T, Stelling J, Fussenegger M: A tunable synthetic mammalian oscillator. Nature. 2009, 457 (7227): 309-12. 10.1038\/nature07616","journal-title":"Nature"},{"issue":"3","key":"444_CR47","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1002\/bit.10475","volume":"81","author":"C Kelly","year":"2003","unstructured":"Kelly C, Hsiung CJ, Lajoie C: Kinetic analysis of bacterial bioluminescence. Biotechnol Bioengin. 2003, 81 (3): 370-378. 10.1002\/bit.10475.","journal-title":"Biotechnol Bioengin"},{"issue":"24","key":"444_CR48","doi-asserted-by":"crossref","first-page":"8043","DOI":"10.1128\/jb.174.24.8043-8056.1992","volume":"174","author":"C Ball","year":"1992","unstructured":"Ball C, Osuna R, Ferguson K, Johnson R: Dramatic changes in Fis levels upon nutrient upshift in Escherichia coli. J Bacteriol. 1992, 174 (24): 8043-8056.","journal-title":"J Bacteriol"},{"issue":"9","key":"444_CR49","doi-asserted-by":"publisher","first-page":"2758","DOI":"10.1073\/pnas.0308747101","volume":"101","author":"J Bernstein","year":"2004","unstructured":"Bernstein J, Lin PH, Cohen S, Lin-Chao S: Global analysis of Escherichia coli RNA degradosome function using DNA microarrays. Proc Natl Acad Sci USA. 2004, 101 (9): 2758-63. 10.1073\/pnas.0308747101","journal-title":"Proc Natl Acad Sci USA"},{"issue":"9","key":"444_CR50","doi-asserted-by":"publisher","first-page":"5860","DOI":"10.1073\/pnas.092538799","volume":"99","author":"Y Wang","year":"2002","unstructured":"Wang Y, Liu C, Storey J, Tibshirani R, Herschlag D, Brown P: Precision and functional specificity in mRNA decay. Proc Natl Acad Sci USA. 2002, 99 (9): 5860-5. 10.1073\/pnas.092538799","journal-title":"Proc Natl Acad Sci USA"},{"issue":"1 Spec No","key":"444_CR51","doi-asserted-by":"publisher","first-page":"33","DOI":"10.1016\/0378-1119(95)00685-0","volume":"173","author":"B Cormack","year":"1996","unstructured":"Cormack B, Valdivia R, Falkow S: FACS-optimized mutants of the green fluorescent protein (GFP). Gene. 1996, 173 (1 Spec No): 33-38. 10.1016\/0378-1119(95)00685-0","journal-title":"Gene"},{"key":"444_CR52","volume-title":"System Modeling in Cellular Biology: From Concepts to Nuts and Bolts","year":"2006","unstructured":"Szallasi Z, Periwal V, Stelling J, : System Modeling in Cellular Biology: From Concepts to Nuts and Bolts. 2006, Cambridge, MA: MIT Press,"},{"key":"444_CR53","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. 2007, 3: 78-","journal-title":"Mol Syst Biol"},{"issue":"3","key":"444_CR54","doi-asserted-by":"publisher","first-page":"149","DOI":"10.1049\/iet-syb:20060075","volume":"1","author":"KH Cho","year":"2007","unstructured":"Cho KH, Choo SM, Jung S, Kim JR, Choi HS, Kim J: Reverse engineering of gene regulatory networks. IET Syst Biol. 2007, 1 (3): 149-163. 10.1049\/iet-syb:20060075","journal-title":"IET Syst Biol"},{"key":"444_CR55","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1016\/j.plrev.2005.01.001","volume":"2","author":"T Gardner","year":"2005","unstructured":"Gardner T, Faith J: Reverse-engineering transcription control networks. Phys Life Rev. 2005, 2: 65-88. 10.1016\/j.plrev.2005.01.001.","journal-title":"Phys Life Rev"},{"issue":"Suppl 6","key":"444_CR56","doi-asserted-by":"publisher","first-page":"S5","DOI":"10.1186\/1471-2105-8-S6-S5","volume":"28","author":"F Markowetz","year":"2007","unstructured":"Markowetz F, Spang R: Inferring cellular networks: A review. BMC Bioinform. 2007, 28 (Suppl 6): S5-10.1186\/1471-2105-8-S6-S5.","journal-title":"BMC Bioinform"},{"issue":"2","key":"444_CR57","doi-asserted-by":"publisher","first-page":"718","DOI":"10.1128\/JB.01020-07","volume":"190","author":"M Buckstein","year":"2008","unstructured":"Buckstein M, He J, Rubin H: Characterization of nucleotide pools as a function of physiological state in Escherichia coli. J Bacteriol. 2008, 190 (2): 718-726. 10.1128\/JB.01020-07","journal-title":"J Bacteriol"},{"issue":"7082","key":"444_CR58","doi-asserted-by":"publisher","first-page":"358","DOI":"10.1038\/nature04599","volume":"440","author":"L Cai","year":"2006","unstructured":"Cai L, Friedman N, Xie X: Stochastic protein expression in individual cells at the single molecule level. Nature. 2006, 440 (7082): 358-362. 10.1038\/nature04599","journal-title":"Nature"},{"issue":"6","key":"444_CR59","doi-asserted-by":"publisher","first-page":"1025","DOI":"10.1016\/j.cell.2005.09.031","volume":"123","author":"I Golding","year":"2005","unstructured":"Golding I, Paulsson J, Zawilski S, Cox E: Real-time kinetics of gene activity in individual bacteria. Cell. 2005, 123 (6): 1025-1036. 10.1016\/j.cell.2005.09.031","journal-title":"Cell"},{"issue":"2","key":"444_CR60","doi-asserted-by":"publisher","first-page":"759","DOI":"10.1529\/biophysj.105.073098","volume":"91","author":"N Rosenfeld","year":"2006","unstructured":"Rosenfeld N, Perkins T, Alon U, Elowitz M, Swain P: A fluctuation method to quantify in vivo fluorescence data. Biophys J. 2006, 91 (2): 759-766. 10.1529\/biophysj.105.073098","journal-title":"Biophys J"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-4-55.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,1]],"date-time":"2021-09-01T05:08:26Z","timestamp":1630472906000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-4-55"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2010,4,29]]},"references-count":60,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2010,12]]}},"alternative-id":["444"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-4-55","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2010,4,29]]},"assertion":[{"value":"27 October 2009","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 April 2010","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"29 April 2010","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}}],"article-number":"55"}}