{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,7]],"date-time":"2025-11-07T13:29:20Z","timestamp":1762522160902,"version":"3.37.3"},"reference-count":29,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2018,6,14]],"date-time":"2018-06-14T00:00:00Z","timestamp":1528934400000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Investissements d'Avenir Bio-informatique programme under project RESET","award":["ANR-11-BINF-0005"],"award-info":[{"award-number":["ANR-11-BINF-0005"]}]},{"name":"Conseil R\u00e9gional PACA"},{"name":"Program LABEX SIGNALIFE","award":["NR-11-LABX-0028-01"],"award-info":[{"award-number":["NR-11-LABX-0028-01"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["BMC Syst Biol"],"published-print":{"date-parts":[[2018,12]]},"DOI":"10.1186\/s12918-018-0586-6","type":"journal-article","created":{"date-parts":[[2018,6,13]],"date-time":"2018-06-13T19:21:20Z","timestamp":1528917680000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Principal process analysis of biological models"],"prefix":"10.1186","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-7652-727X","authenticated-orcid":false,"given":"Stefano","family":"Casagranda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suzanne","family":"Touzeau","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Delphine","family":"Ropers","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-Luc","family":"Gouz\u00e9","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2018,6,14]]},"reference":[{"issue":"5","key":"586_CR1","doi-asserted-by":"publisher","first-page":"2578","DOI":"10.1074\/jbc.M508090200","volume":"281","author":"K Bettenbrock","year":"2006","unstructured":"Bettenbrock K, Fischer S, Kremling A, Jahreis K, Sauter T, Gilles E-D. A quantitative approach to catabolite repression in Escherichia coli. J Biol Chem. 2006; 281(5):2578\u201384.","journal-title":"J Biol Chem"},{"issue":"9","key":"586_CR2","doi-asserted-by":"publisher","first-page":"1001","DOI":"10.1038\/nbt1330","volume":"25","author":"L Kuepfer","year":"2007","unstructured":"Kuepfer L, Peter M, Sauer U, Stelling J. Ensemble modeling for analysis of cell signaling dynamics. Nat Biotechnol. 2007; 25(9):1001\u20136.","journal-title":"Nat Biotechnol"},{"issue":"7","key":"586_CR3","doi-asserted-by":"publisher","first-page":"1449","DOI":"10.1007\/s11538-017-0277-2","volume":"79","author":"TJ Snowden","year":"2017","unstructured":"Snowden TJ, van der Graaf PH, Tindall MJ. Methods of model reduction for large-scale biological systems: a survey of current methods and trends. Bull Math Biol. 2017; 79(7):1449\u201386.","journal-title":"Bull Math Biol"},{"key":"586_CR4","doi-asserted-by":"publisher","first-page":"16","DOI":"10.1016\/j.jtbi.2012.03.019","volume":"304","author":"M Apri","year":"2012","unstructured":"Apri M, de Gee M, Molenaar J. Complexity reduction preserving dynamical behavior of biochemical networks. J Theor Biol. 2012; 304:16\u201326.","journal-title":"J Theor Biol"},{"issue":"4","key":"586_CR5","doi-asserted-by":"publisher","first-page":"869","DOI":"10.1002\/aic.690450418","volume":"45","author":"L Petzold","year":"1999","unstructured":"Petzold L, Zhu W. Model reduction for chemical kinetics: An optimization approach. AIChE J. 1999; 45(4):869\u201386.","journal-title":"AIChE J"},{"issue":"1","key":"586_CR6","doi-asserted-by":"publisher","first-page":"140","DOI":"10.1186\/1752-0509-5-140","volume":"5","author":"M Sunn\u00e5ker","year":"2011","unstructured":"Sunn\u00e5ker M, Cedersund G, Jirstrand M. A method for zooming of nonlinear models of biochemical systems. BMC Syst Biol. 2011; 5(1):140.","journal-title":"BMC Syst Biol"},{"issue":"21","key":"586_CR7","doi-asserted-by":"publisher","first-page":"4751","DOI":"10.1016\/j.ces.2002.12.001","volume":"58","author":"AN Gorban","year":"2003","unstructured":"Gorban AN, Karlin IV. Method of invariant manifold for chemical kinetics. Chem Eng Sci. 2003; 58(21):4751\u201368.","journal-title":"Chem Eng Sci"},{"issue":"6","key":"586_CR8","doi-asserted-by":"publisher","first-page":"1165","DOI":"10.1016\/j.automatica.2011.03.010","volume":"47","author":"J Anderson","year":"2011","unstructured":"Anderson J, Chang Y-C, Papachristodoulou A. Model decomposition and reduction tools for large-scale networks in systems biology. Automatica. 2011; 47(6):1165\u201374.","journal-title":"Automatica"},{"key":"586_CR9","volume-title":"Control Conference (ECC), 2013 European","author":"KM Hangos","year":"2013","unstructured":"Hangos KM, G\u00e1bor A, Szederk\u00e9nyi G. Model reduction in bio-chemical reaction networks with Michaelis-Menten kinetics. In: Control Conference (ECC), 2013 European. Z\u00fcrich: IEEE: 2013. p. 4478\u20134483."},{"issue":"3","key":"586_CR10","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1137\/1031091","volume":"31","author":"LA Segel","year":"1989","unstructured":"Segel LA, Slemrod M. The quasi-steady-state assumption: a case study in perturbation. SIAM Rev. 1989; 31(3):446\u201377.","journal-title":"SIAM Rev"},{"issue":"2","key":"586_CR11","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1016\/j.bulm.2003.08.010","volume":"66","author":"H de Jong","year":"2004","unstructured":"de Jong H, Gouz\u00e9 J-L, Hernandez C, Page M, Sari T, Geiselmann J. Qualitative simulation of genetic regulatory networks using piecewise-linear models. Bull Math Biol. 2004; 66(2):301\u201340.","journal-title":"Bull Math Biol"},{"issue":"6","key":"586_CR12","doi-asserted-by":"publisher","first-page":"1000812","DOI":"10.1371\/journal.pcbi.1000812","volume":"6","author":"V Baldazzi","year":"2010","unstructured":"Baldazzi V, Ropers D, Markowicz Y, Kahn D, Geiselmann J, de Jong H. The carbon assimilation network in Escherichia coli is densely connected and largely sign-determined by directions of metabolic fluxes. PLoS Comput Biol. 2010; 6(6):1000812.","journal-title":"PLoS Comput Biol"},{"issue":"3","key":"586_CR13","doi-asserted-by":"publisher","first-page":"191","DOI":"10.1016\/S0010-2180(03)00159-7","volume":"135","author":"B Bhattacharjee","year":"2003","unstructured":"Bhattacharjee B, Schwer DA, Barton PI, Green WH. Optimally-reduced kinetic models: reaction elimination in large-scale kinetic mechanisms. Combust Flame. 2003; 135(3):191\u2013208.","journal-title":"Combust Flame"},{"key":"586_CR14","volume-title":"2015 23rd Mediterranean Conference on Control and Automation (MED)","author":"S Casagranda","year":"2015","unstructured":"Casagranda S, Ropers D, Gouz\u00e9 J-L. Model reduction and process analysis of biological models. In: 2015 23rd Mediterranean Conference on Control and Automation (MED). Torremolinos: IEEE: 2015. p. 1132\u20139."},{"issue":"1","key":"586_CR15","doi-asserted-by":"publisher","first-page":"70","DOI":"10.1177\/074873098128999934","volume":"13","author":"J-C Leloup","year":"1998","unstructured":"Leloup J-C, Goldbeter A. A model for circadian rhythms in Drosophila incorporating the formation of a complex between the PER and TIM proteins. J Biol Rhythm. 1998; 13(1):70\u201387.","journal-title":"J Biol Rhythm"},{"key":"586_CR16","volume-title":"Computational Methods in Systems Biology","author":"C Kwang-Hyun","year":"2003","unstructured":"Kwang-Hyun C, Sung-Young S, Hyun-Woo K, Wolkenhauer O, McFerran B, Kolch W. Mathematical modeling of the influence of RKIP on the ERK signaling pathway In: Priami C, editor. Computational Methods in Systems Biology. Rovereto: Springer: 2003. p. 127\u201341."},{"issue":"4","key":"586_CR17","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1016\/j.jtbi.2004.04.040","volume":"230","author":"J-C Leloup","year":"2004","unstructured":"Leloup J-C, Goldbeter A. Modeling the mammalian circadian clock: sensitivity analysis and multiplicity of oscillatory mechanisms. J Theor Biol. 2004; 230(4):541\u201362.","journal-title":"J Theor Biol"},{"key":"586_CR18","volume-title":"Nonlinear Systems, Second edn","author":"HK Khalil","year":"1996","unstructured":"Khalil HK. Nonlinear Systems, Second edn. New Jersey: Prentice Hall; 1996."},{"issue":"12","key":"586_CR19","doi-asserted-by":"publisher","first-page":"7051","DOI":"10.1073\/pnas.1132112100","volume":"100","author":"J-C Leloup","year":"2003","unstructured":"Leloup J-C, Goldbeter A. Toward a detailed computational model for the mammalian circadian clock. Proc Natl Acad Sci. 2003; 100(12):7051\u20136.","journal-title":"Proc Natl Acad Sci"},{"issue":"7","key":"586_CR20","doi-asserted-by":"publisher","first-page":"881","DOI":"10.1109\/TPAMI.2002.1017616","volume":"24","author":"T Kanungo","year":"2002","unstructured":"Kanungo T, Mount DM, Netanyahu NS, Piatko CD, Silverman R, Wu AY. An efficient k-means clustering algorithm: Analysis and implementation. IEEE Trans Pattern Anal Mach Intell. 2002; 24(7):881\u201392.","journal-title":"IEEE Trans Pattern Anal Mach Intell"},{"issue":"1","key":"586_CR21","doi-asserted-by":"publisher","first-page":"12661","DOI":"10.1016\/j.ifacol.2017.08.2241","volume":"50","author":"S Casagranda","year":"2017","unstructured":"Casagranda S, Gouz\u00e9 J-L. Principal Process Analysis and reduction of biological models with order of magnitude. IFAC-PapersOnLine. 2017; 50(1):12661\u20136.","journal-title":"IFAC-PapersOnLine"},{"key":"586_CR22","doi-asserted-by":"publisher","first-page":"311","DOI":"10.1016\/j.csda.2016.09.003","volume":"113","author":"A Kobilinsky","year":"2017","unstructured":"Kobilinsky A, Monod H, Bailey RA. Automatic generation of generalised regular factorial designs. Comput Stat Data Anal. 2017; 113:311\u201329.","journal-title":"Comput Stat Data Anal"},{"issue":"4","key":"586_CR23","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1016\/j.ress.2010.12.002","volume":"96","author":"M Lamboni","year":"2011","unstructured":"Lamboni M, Monod H, Makowski D. Multivariate sensitivity analysis to measure global contribution of input factors in dynamic models. Reliab Eng Syst Saf. 2011; 96(4):450\u20139.","journal-title":"Reliab Eng Syst Saf"},{"issue":"3","key":"586_CR24","first-page":"311","volume":"3","author":"GE Box","year":"1961","unstructured":"Box GE, Hunter JS. The 2 k-p fractional factorial designs. Technometrics. 1961; 3(3):311\u201351.","journal-title":"Technometrics"},{"issue":"5","key":"586_CR25","doi-asserted-by":"publisher","first-page":"683","DOI":"10.1016\/S0092-8674(01)00380-4","volume":"105","author":"B Zheng","year":"2001","unstructured":"Zheng B, Albrecht U, Kaasik K, Sage M, Lu W, Vaishnav S, Li Q, Sun ZS, Eichele G, Bradley A, et al. Nonredundant roles of the mPer1 and mPer2 genes in the mammalian circadian clock. Cell. 2001; 105(5):683\u201394.","journal-title":"Cell"},{"issue":"6728","key":"586_CR26","doi-asserted-by":"publisher","first-page":"627","DOI":"10.1038\/19323","volume":"398","author":"GT Van Der Horst","year":"1999","unstructured":"Van Der Horst GT, Muijtjens M, Kobayashi K, Takano R, Kanno S-i, Takao M, de Wit J, Verkerk A, Eker AP, van Leenen D, et al. Mammalian Cry1 and Cry2 are essential for maintenance of circadian rhythms. Nature. 1999; 398(6728):627\u2013630.","journal-title":"Nature"},{"issue":"5","key":"586_CR27","doi-asserted-by":"publisher","first-page":"2411","DOI":"10.1016\/S0006-3495(99)77078-5","volume":"77","author":"JJ Tyson","year":"1999","unstructured":"Tyson JJ, Hong CI, Thron CD, Novak B. A simple model of circadian rhythms based on dimerization and proteolysis of PER and TIM. Biophys J. 1999; 77(5):2411\u20137.","journal-title":"Biophys J"},{"key":"586_CR28","doi-asserted-by":"publisher","first-page":"349","DOI":"10.1016\/j.soilbio.2016.09.014","volume":"103","author":"H Pagel","year":"2016","unstructured":"Pagel H, Poll C, Ingwersen J, Kandeler E, Streck T. Modeling coupled pesticide degradation and organic matter turnover: From gene abundance to process rates. Soil Biol Biochem. 2016; 103:349\u201364.","journal-title":"Soil Biol Biochem"},{"key":"586_CR29","volume-title":"2016 24th Mediterranean Conference on Control and Automation (MED)","author":"C Robles-Rodriguez","year":"2016","unstructured":"Robles-Rodriguez C, Bideaux C, Guillouet S, Gorret N, Roux G, Molina-Jouve C, Aceves-Lara C. Multi-objective particle swarm optimization (MOPSO) of lipid accumulation in fed-batch cultures. In: 2016 24th Mediterranean Conference on Control and Automation (MED). Athens: IEEE: 2016. p. 979\u2013984."}],"container-title":["BMC Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0586-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/article\/10.1186\/s12918-018-0586-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1186\/s12918-018-0586-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,6,13]],"date-time":"2019-06-13T19:13:49Z","timestamp":1560453229000},"score":1,"resource":{"primary":{"URL":"https:\/\/bmcsystbiol.biomedcentral.com\/articles\/10.1186\/s12918-018-0586-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2018,6,14]]},"references-count":29,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2018,12]]}},"alternative-id":["586"],"URL":"https:\/\/doi.org\/10.1186\/s12918-018-0586-6","relation":{},"ISSN":["1752-0509"],"issn-type":[{"type":"electronic","value":"1752-0509"}],"subject":[],"published":{"date-parts":[[2018,6,14]]},"assertion":[{"value":"4 December 2017","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 May 2018","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"14 June 2018","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"The authors declare that they have no competing interests.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Publisher\u2019s Note"}}],"article-number":"68"}}