{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,8]],"date-time":"2026-02-08T00:04:06Z","timestamp":1770509046962,"version":"3.49.0"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2013,7,29]],"date-time":"2013-07-29T00:00:00Z","timestamp":1375056000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/2.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2013,12]]},"DOI":"10.1186\/1752-0509-7-71","type":"journal-article","created":{"date-parts":[[2013,7,29]],"date-time":"2013-07-29T14:14:35Z","timestamp":1375107275000},"source":"Crossref","is-referenced-by-count":13,"title":["Estimating confidence intervals in predicted responses for oscillatory biological models"],"prefix":"10.1186","volume":"7","author":[{"given":"Peter C","family":"St John","sequence":"first","affiliation":[]},{"suffix":"III","given":"Francis J","family":"Doyle","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2013,7,29]]},"reference":[{"issue":"10","key":"1116_CR1","doi-asserted-by":"publisher","first-page":"1871","DOI":"10.1371\/journal.pcbi.0030189","volume":"3","author":"RN Gutenkunst","year":"2007","unstructured":"Gutenkunst RN, Waterfall JJ, Casey FP, Brown KS, Myers CR, Sethna JP: Universally sloppy parameter sensitivities in systems biology models. PLoS Comput Biol. 2007, 3 (10): 1871-1878.","journal-title":"PLoS Comput Biol"},{"key":"1116_CR2","first-page":"3","volume-title":"System Modeling in, Cellular Biology: From Concepts to Nuts and Bolts","author":"JD Knowles","year":"2006","unstructured":"Knowles JD, Kell DB: The role of modeling in systems biology. System Modeling in, Cellular Biology: From Concepts to Nuts and Bolts. Edited by: Szallasi Z, Stelling J, Periwal V. 2006, Cambridge: MIT Press, 3-18."},{"issue":"15","key":"1116_CR3","doi-asserted-by":"publisher","first-page":"1923","DOI":"10.1093\/bioinformatics\/btp358","volume":"25","author":"A Raue","year":"2009","unstructured":"Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingm\u00fcller U, Timmer J: Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinformatics. 2009, 25 (15): 1923-1929. 10.1093\/bioinformatics\/btp358.","journal-title":"Bioinformatics"},{"issue":"12","key":"1116_CR4","doi-asserted-by":"publisher","first-page":"1831","DOI":"10.1002\/bit.260191208","volume":"19","author":"M Nihtil\u00e4","year":"1977","unstructured":"Nihtil\u00e4 M, Virkkunen J: Practical identifiability of growth and substrate consumption models. Biotechnol Bioeng. 1977, 19 (12): 1831-1850. 10.1002\/bit.260191208.","journal-title":"Biotechnol Bioeng"},{"key":"1116_CR5","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.bej.2009.01.010","volume":"45","author":"JE Jim\u00e9nez-Hornero","year":"2009","unstructured":"Jim\u00e9nez-Hornero JE, Santos-Due\u00f1as IM, Garc\u00eda-Garc\u00eda I: Optimization of biotechnological processes. The acetic acid fermentation. Part II: Practical identifiability analysis and parameter estimation. Biochem Eng J. 2009, 45: 7-21. 10.1016\/j.bej.2009.01.010.","journal-title":"Biochem Eng J"},{"key":"1116_CR6","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1016\/0025-5564(82)90061-X","volume":"62","author":"A Holmberg","year":"1982","unstructured":"Holmberg A: On the practical identifiability of microbial growth models incorporating Michaelis-Menten type nonlinearities. Math Biosci. 1982, 62: 23-43. 10.1016\/0025-5564(82)90061-X.","journal-title":"Math Biosci"},{"issue":"5","key":"1116_CR7","doi-asserted-by":"publisher","first-page":"447","DOI":"10.1016\/j.ymben.2006.04.003","volume":"8","author":"M Joshi","year":"2006","unstructured":"Joshi M, Seidel-Morgenstern A, Kremling A: Exploiting the bootstrap method for quantifying parameter confidence intervals in dynamical systems. Metab Eng. 2006, 8 (5): 447-455. 10.1016\/j.ymben.2006.04.003.","journal-title":"Metab Eng"},{"key":"1116_CR8","doi-asserted-by":"publisher","DOI":"10.1017\/CBO9780511608193","volume-title":"Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behaviour Volume 51","author":"A Goldbeter","year":"1996","unstructured":"Goldbeter A, Keizer J: Biochemical Oscillations and Cellular Rhythms: The Molecular Bases of Periodic and Chaotic Behaviour Volume 51. 1996, Cambridge: Cambridge University Press"},{"issue":"25","key":"1116_CR9","doi-asserted-by":"publisher","first-page":"14806","DOI":"10.1073\/pnas.2036281100","volume":"100","author":"DB Forger","year":"2003","unstructured":"Forger DB, Peskin CS: A detailed predictive model of the mammalian circadian clock. Proc Natl Acad Sci USA. 2003, 100 (25): 14806-14811. 10.1073\/pnas.2036281100.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"12","key":"1116_CR10","doi-asserted-by":"publisher","first-page":"7051","DOI":"10.1073\/pnas.1132112100","volume":"100","author":"JC Leloup","year":"2003","unstructured":"Leloup JC, Goldbeter A: Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci USA. 2003, 100 (12): 7051-7056. 10.1073\/pnas.1132112100.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"27","key":"1116_CR11","doi-asserted-by":"publisher","first-page":"11107","DOI":"10.1073\/pnas.0904837106","volume":"106","author":"HP Mirsky","year":"2009","unstructured":"Mirsky HP, Liu AC, Welsh DK, Kay SA, Doyle III FJ: A model of the cell-autonomous mammalian circadian clock. Proc Natl Acad Sci USA. 2009, 106 (27): 11107-11112. 10.1073\/pnas.0904837106.","journal-title":"Proc Natl Acad Sci USA"},{"issue":"4","key":"1116_CR12","doi-asserted-by":"publisher","first-page":"2706","DOI":"10.1137\/070707129","volume":"31","author":"AK Wilkins","year":"2009","unstructured":"Wilkins AK, Tidor B, White J, Barton PI: Sensitivity analysis for oscillating dynamical systems. SIAM J Sci Comput. 2009, 31 (4): 2706-2732. 10.1137\/070707129.","journal-title":"SIAM J Sci Comput"},{"issue":"6098","key":"1116_CR13","doi-asserted-by":"publisher","first-page":"1094","DOI":"10.1126\/science.1223710","volume":"337","author":"T Hirota","year":"2012","unstructured":"Hirota T, Lee JW, St. John PC, Sawa M, Iwaisako K, Noguchi T, Pongsawakul PY, Sonntag T, Welsh DK, Brenner DA, Doyle III FJ, Schultz PG, Kay SA: Identification of small molecule activators of Cryptochrome. Science. 2012, 337 (6098): 1094-1097. 10.1126\/science.1223710.","journal-title":"Science"},{"key":"1116_CR14","doi-asserted-by":"publisher","first-page":"R271","DOI":"10.1093\/hmg\/ddl207","volume":"15 Spec No 2","author":"CH Ko","year":"2006","unstructured":"Ko CH, Takahashi JS: Molecular components of the mammalian circadian clock. Hum Mol Genet. 2006, 15 Spec No 2: R271-R277.","journal-title":"Hum Mol Genet"},{"issue":"10\u201312","key":"1116_CR15","doi-asserted-by":"publisher","first-page":"1700","DOI":"10.1016\/j.compchemeng.2006.05.029","volume":"30","author":"FJ Doyle III","year":"2006","unstructured":"Doyle III FJ, Gunawan R, Bagheri N, Mirsky HP, To TL: Circadian rhythm: A natural, robust, multi-scale control system. Comput Chem Eng. 2006, 30 (10\u201312): 1700-1711.","journal-title":"Comput Chem Eng"},{"issue":"10","key":"1116_CR16","doi-asserted-by":"publisher","first-page":"790","DOI":"10.1038\/nrn2215","volume":"8","author":"ED Herzog","year":"2007","unstructured":"Herzog ED: Neurons and networks in daily rhythms. Nat Rev Neurosci. 2007, 8 (10): 790-802. 10.1038\/nrn2215.","journal-title":"Nat Rev Neurosci"},{"issue":"4","key":"1116_CR17","doi-asserted-by":"publisher","first-page":"e1000442","DOI":"10.1371\/journal.pgen.1000442","volume":"5","author":"ME Hughes","year":"2009","unstructured":"Hughes ME, DiTacchio L, Hayes KR, Vollmers C, Pulivarthy S, Baggs JE, Panda S, Hogenesch JB: Harmonics of circadian gene transcription in mammals. PLoS Genet. 2009, 5 (4): e1000442-10.1371\/journal.pgen.1000442.","journal-title":"PLoS Genet"},{"key":"1116_CR18","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1016\/j.cell.2009.08.031","volume":"139","author":"EE Zhang","year":"2009","unstructured":"Zhang EE, Liu AC, Hirota T, Miraglia LJ, Welch G, Pongsawakul PY, Liu X, Atwood A, Huss JW, Janes J, Su AI, Hogenesch JB, Kay SA: A genome-wide RNAi screen for modifiers of the circadian clock in human cells. Cell. 2009, 139: 199-210. 10.1016\/j.cell.2009.08.031.","journal-title":"Cell"},{"issue":"12","key":"1116_CR19","doi-asserted-by":"publisher","first-page":"e1000559","DOI":"10.1371\/journal.pbio.1000559","volume":"8","author":"T Hirota","year":"2010","unstructured":"Hirota T, Lee JW, Lewis WG, Zhang EE, Breton G, Liu X, Garcia M, Peters EC, Etchegaray JP, Traver D, Schultz PG, Kay SA: High-throughput chemical screen identifies a novel potent modulator of cellular circadian rhythms and reveals CKI\u03b1, as a clock regulatory kinase. PLoS Biol. 2010, 8 (12): e1000559-10.1371\/journal.pbio.1000559.","journal-title":"PLoS Biol"},{"issue":"52","key":"1116_CR20","doi-asserted-by":"publisher","first-page":"20746","DOI":"10.1073\/pnas.0811410106","volume":"105","author":"T Hirota","year":"2008","unstructured":"Hirota T, Lewis WG, Liu AC, Lee JW, Schultz PG, Kay SA: A chemical biology approach reveals period shortening of the mammalian circadian clock by specific inhibition of GSK-3beta. Proc Natl Acad Sci USA. 2008, 105 (52): 20746-20751. 10.1073\/pnas.0811410106.","journal-title":"Proc Natl Acad Sci USA"},{"key":"1116_CR21","doi-asserted-by":"publisher","DOI":"10.1137\/1.9780898719383","volume-title":"Nonlinear Programming: Concepts, Algorithms, and Applications to Chemical Processes","author":"LT Biegler","year":"2010","unstructured":"Biegler LT: Nonlinear Programming: Concepts, Algorithms, and Applications to Chemical Processes. 2010, Philidelphia: SIAM"},{"issue":"2","key":"1116_CR22","doi-asserted-by":"publisher","first-page":"376","DOI":"10.1002\/gamm.200790024","volume":"408","author":"HG Bock","year":"2007","unstructured":"Bock HG, Kostina E, Schloder JP: Numerical methods for parameter estimation in nonlinear differential algebraic equations. GAMM-\u00e2\u0102R\u0306Mitteilungen. 2007, 408 (2): 376-408.","journal-title":"GAMM-\u00e2\u0102R\u0306Mitteilungen"},{"key":"1116_CR23","first-page":"1045","volume":"7","author":"EG Bure","year":"1974","unstructured":"Bure EG, Rosenwasser E: The study of the sensitivity of oscillatory systems. Autom Rem Contr. 1974, 7: 1045-1052.","journal-title":"Autom Rem Contr"},{"issue":"5","key":"1116_CR24","doi-asserted-by":"publisher","first-page":"328","DOI":"10.1016\/0307-904X(84)90146-X","volume":"8","author":"M Kramer","year":"1984","unstructured":"Kramer M, Rabitz H, Calo J: Sensitivity analysis of oscillatory systems. Appl Math Modell. 1984, 8 (5): 328-350. 10.1016\/0307-904X(84)90146-X.","journal-title":"Appl Math Modell"},{"issue":"11","key":"1116_CR25","doi-asserted-by":"publisher","first-page":"2396","DOI":"10.1101\/gr.1198103","volume":"13","author":"DE Zak","year":"2003","unstructured":"Zak DE, Gonye GE, Schwaber JS, Doyle III FJ: Importance of input perturbations and stochastic gene expression in the reverse engineering of genetic regulatory networks: insights from an identifiability analysis of an in silico network. Genome Res. 2003, 13 (11): 2396-2405. 10.1101\/gr.1198103.","journal-title":"Genome Res"},{"issue":"7","key":"1116_CR26","doi-asserted-by":"publisher","first-page":"855","DOI":"10.1016\/S0092-8674(01)00610-9","volume":"107","author":"C Lee","year":"2001","unstructured":"Lee C, Etchegaray JP, Cagampang FR, Loudon ASI, Reppert SM: Posttranslational mechanisms regulate the mammalian circadian clock. Cell. 2001, 107 (7): 855-867. 10.1016\/S0092-8674(01)00610-9.","journal-title":"Cell"},{"key":"1116_CR27","doi-asserted-by":"publisher","first-page":"25","DOI":"10.1007\/s10107-004-0559-y","volume":"106","author":"A Wachter","year":"2006","unstructured":"Wachter A, Biegler LT: On the implementation of an interior-point filter line-search algorithm for large-scale nonlinear programming. Math Program. 2006, 106: 25-57. 10.1007\/s10107-004-0559-y.","journal-title":"Math Program"},{"key":"1116_CR28","volume-title":"Recent Advances in Algorithmic Differentiation, Lecture Notes in Computational Science and Engineering","author":"J Andersson","year":"2012","unstructured":"Andersson J, \u00c5kesson J, Diehl M: CasADi \u2013 A symbolic package for automatic differentiation and optimal control. Recent Advances in Algorithmic Differentiation, Lecture Notes in Computational Science and Engineering. Edited by: Forth S, Hovland P, Phipps E, Utke J, Walther A. 2012, Berlin: Springer"},{"issue":"3","key":"1116_CR29","doi-asserted-by":"publisher","first-page":"363","DOI":"10.1145\/1089014.1089020","volume":"31","author":"AC Hindmarsh","year":"2005","unstructured":"Hindmarsh AC, Brown PN, Grant KE, Lee SL, Serban R, Shumaker DANE, Woodward CS: SUNDIALS: Suite of nonlinear and differential \/ algebraic equation solvers. ACM T Math Softw. 2005, 31 (3): 363-396. 10.1145\/1089014.1089020.","journal-title":"ACM T Math Softw"}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-7-71.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/1752-0509-7-71\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/1752-0509-7-71.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,2,17]],"date-time":"2020-02-17T21:53:06Z","timestamp":1581976386000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/1752-0509-7-71"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2013,7,29]]},"references-count":29,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2013,12]]}},"alternative-id":["1116"],"URL":"https:\/\/doi.org\/10.1186\/1752-0509-7-71","relation":{},"ISSN":["1752-0509"],"issn-type":[{"value":"1752-0509","type":"electronic"}],"subject":[],"published":{"date-parts":[[2013,7,29]]},"article-number":"71"}}