{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,3,25]],"date-time":"2025-03-25T19:56:19Z","timestamp":1742932579433,"version":"3.40.3"},"publisher-location":"Cham","reference-count":30,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783319234007"},{"type":"electronic","value":"9783319234014"}],"license":[{"start":{"date-parts":[[2015,1,1]],"date-time":"2015-01-01T00:00:00Z","timestamp":1420070400000},"content-version":"tdm","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\/978-3-319-23401-4_12","type":"book-chapter","created":{"date-parts":[[2015,9,1]],"date-time":"2015-09-01T10:37:23Z","timestamp":1441103843000},"page":"133-144","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":2,"title":["Structural Simplification of Chemical Reaction Networks Preserving Deterministic Semantics"],"prefix":"10.1007","author":[{"given":"Guillaume","family":"Madelaine","sequence":"first","affiliation":[]},{"given":"C\u00e9dric","family":"Lhoussaine","sequence":"additional","affiliation":[]},{"given":"Joachim","family":"Niehren","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2015,9,2]]},"reference":[{"issue":"4","key":"12_CR1","doi-asserted-by":"publisher","first-page":"886","DOI":"10.1111\/j.1742-4658.2008.06844.x","volume":"276","author":"M Ashyraliyev","year":"2009","unstructured":"Ashyraliyev, M., Fomekong-Nanfack, Y., Kaandorp, J.A., Blom, J.G.: Systems biology: parameter estimation for biochemical models. Febs J. 276(4), 886\u2013902 (2009)","journal-title":"Febs J."},{"key":"12_CR2","first-page":"202","volume-title":"Mathematical Foundations of Computer Science","author":"G Berthelot","year":"1976","unstructured":"Berthelot, G., Roucairol, G.: Reduction of petri-nets. In: Mazurkiewicz, A. (ed.) Mathematical Foundations of Computer Science, vol. 45, pp. 202\u2013209. Springer, Heidelberg (1976)"},{"issue":"329","key":"12_CR3","first-page":"0022","volume":"85","author":"M Bodenstein","year":"1913","unstructured":"Bodenstein, M.: Eine theorie der photochemischen reaktionsgeschwindigkeiten. Z. Phys. Chem. 85(329), 0022\u20133654 (1913)","journal-title":"Z. Phys. Chem."},{"issue":"1","key":"12_CR4","doi-asserted-by":"publisher","first-page":"84","DOI":"10.1186\/1752-0509-8-84","volume":"8","author":"L Cardelli","year":"2014","unstructured":"Cardelli, L.: Morphisms of reaction networks that couple structure to function. BMC Syst. Biol. 8(1), 84 (2014)","journal-title":"BMC Syst. Biol."},{"key":"12_CR5","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"65","DOI":"10.1007\/978-3-540-85101-1_6","volume-title":"Algebraic Biology","author":"L Cardelli","year":"2008","unstructured":"Cardelli, L., Zavattaro, G.: On the computational power of biochemistry. In: Horimoto, K., Regensburger, G., Rosenkranz, M., Yoshida, H. (eds.) AB 2008. LNCS, vol. 5147, pp. 65\u201380. Springer, Heidelberg (2008)"},{"key":"12_CR6","doi-asserted-by":"crossref","unstructured":"Danos, V., Feret, J., Fontana, W., Harmer, R., Krivine, J.: Abstracting the differential semantics of rule-based models: exact and automated model reduction. In: Logic In Computer Science (LICS), pp. 362\u2013381. IEEE (2010)","DOI":"10.1109\/LICS.2010.44"},{"issue":"1","key":"12_CR7","doi-asserted-by":"crossref","first-page":"69","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. 9(1), 69\u2013105 (2002)","journal-title":"J. Comput. Biol."},{"key":"12_CR8","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"370","DOI":"10.1007\/978-3-642-33636-2_23","volume-title":"Computational Methods in Systems Biology","author":"F Fages","year":"2012","unstructured":"Fages, F., Gay, S., Soliman, S.: Inferring reaction models from ODEs. In: Gilbert, D., Heiner, M. (eds.) CMSB 2012. LNCS, vol. 7605, pp. 370\u2013373. Springer, Heidelberg (2012)"},{"key":"12_CR9","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1007\/978-3-540-68894-5_3","volume-title":"Formal Methods for Computational Systems Biology","author":"F Fages","year":"2008","unstructured":"Fages, F., Soliman, S.: Formal Cell Biology in Biocham. In: Bernardo, M., Degano, P., Zavattaro, G. (eds.) SFM 2008. LNCS, vol. 5016, pp. 54\u201380. Springer, Heidelberg (2008)"},{"issue":"18","key":"12_CR10","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1093\/bioinformatics\/btq388","volume":"26","author":"S Gay","year":"2010","unstructured":"Gay, S., Soliman, S., Fages, F.: A graphical method for reducing and relating models in systems biology. Bioinformatics 26(18), 575\u2013581 (2010)","journal-title":"Bioinformatics"},{"issue":"21","key":"12_CR11","doi-asserted-by":"publisher","first-page":"4751","DOI":"10.1016\/j.ces.2002.12.001","volume":"58","author":"AN Gorban","year":"2003","unstructured":"Gorban, A.N., Karlin, I.V.: Method of invariant manifold for chemical kinetics. Chem. Eng. Sci. 58(21), 4751\u20134768 (2003)","journal-title":"Chem. Eng. Sci."},{"issue":"1","key":"12_CR12","doi-asserted-by":"publisher","first-page":"203","DOI":"10.1016\/S0377-0257(00)00135-X","volume":"96","author":"AN Gorban","year":"2001","unstructured":"Gorban, A.N., Karlin, I.V., Ilg, P., \u00d6ttinger, H.C.: Corrections and enhancements of quasi-equilibrium states. J. Non-newton. Fluid Mech. 96(1), 203\u2013219 (2001)","journal-title":"J. Non-newton. Fluid Mech."},{"issue":"12","key":"12_CR13","doi-asserted-by":"publisher","first-page":"5547","DOI":"10.1073\/pnas.89.12.5547","volume":"89","author":"M Gossen","year":"1992","unstructured":"Gossen, M., Bujard, H.: Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl. Acad. Sci. U.S.A. 89(12), 5547\u20135551 (1992)","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"issue":"5218","key":"12_CR14","doi-asserted-by":"publisher","first-page":"1766","DOI":"10.1126\/science.7792603","volume":"268","author":"M Gossen","year":"1995","unstructured":"Gossen, M., Freundlieb, S., Bender, G., M\u00fcller, G., Hillen, W., Bujard, H.: Transcriptional activation by tetracyclines in mammalian cells. Science 268(5218), 1766\u20131769 (1995)","journal-title":"Science"},{"issue":"10","key":"12_CR15","doi-asserted-by":"publisher","first-page":"1883","DOI":"10.1039\/c003229h","volume":"6","author":"Z Huang","year":"2010","unstructured":"Huang, Z., Moya, C., Jayaraman, A., Hahn, J.: Using the Tet-On system to develop a procedure for extracting transcription factor activation dynamics. Mol. BioSyst. 6(10), 1883\u20131889 (2010)","journal-title":"Mol. BioSyst."},{"key":"12_CR16","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1007\/978-3-642-19718-5_18","volume-title":"Programming Languages and Systems","author":"M John","year":"2011","unstructured":"John, M., Lhoussaine, C., Niehren, J., Versari, C.: Biochemical reaction rules with constraints. In: Barthe, G. (ed.) ESOP 2011. LNCS, vol. 6602, pp. 338\u2013357. Springer, Heidelberg (2011)"},{"issue":"10","key":"12_CR17","doi-asserted-by":"publisher","first-page":"1375","DOI":"10.1021\/j150544a010","volume":"60","author":"EL King","year":"1956","unstructured":"King, E.L., Altman, C.: A schematic method of deriving the rate laws for enzyme-catalyzed reactions. J. Phys. Chem. 60(10), 1375\u20131378 (1956)","journal-title":"J. Phys. Chem."},{"issue":"5560","key":"12_CR18","doi-asserted-by":"publisher","first-page":"1662","DOI":"10.1126\/science.1069492","volume":"295","author":"H Kitano","year":"2002","unstructured":"Kitano, H.: Systems biology: a brief overview. Science 295(5560), 1662\u20131664 (2002)","journal-title":"Science"},{"key":"12_CR19","unstructured":"Lemaire, F., Sedoglavic, A., Urguplu, A.: Moving frame based strategies for reduction of ordinary differential\/recurrence systems using their expanded lie point symmetries (2008)"},{"key":"12_CR20","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"crossref","first-page":"82","DOI":"10.1007\/978-3-319-10398-3_7","volume-title":"Formal Methods in Macro-Biology","author":"G Madelaine","year":"2014","unstructured":"Madelaine, G., Lhoussaine, C., Niehren, J.: Attractor equivalence: an observational semantics for reaction networks. In: Fages, F., Piazza, C. (eds.) FMMB 2014. LNCS, vol. 8738, pp. 82\u2013101. Springer, Heidelberg (2014)"},{"key":"12_CR21","doi-asserted-by":"publisher","first-page":"1278","DOI":"10.1093\/nar\/gkr923","volume":"40","author":"U M\u00e4der","year":"2012","unstructured":"M\u00e4der, U., Schmeisky, A.G., Fl\u00f3rez, L.A., St\u00fclke, J.: SubtiWiki-a comprehensive community resource for the model organism Bacillus subtilis. Nucleic Acids Res. 40, 1278\u20131287 (2012)","journal-title":"Nucleic Acids Res."},{"issue":"333\u2013369","key":"12_CR22","first-page":"352","volume":"49","author":"L Michaelis","year":"1913","unstructured":"Michaelis, L., Menten, M.L.: Die kinetik der invertinwirkung. Biochem. z 49(333\u2013369), 352 (1913)","journal-title":"Die kinetik der invertinwirkung. Biochem. z"},{"issue":"1","key":"12_CR23","doi-asserted-by":"publisher","first-page":"68","DOI":"10.1109\/TCS.1980.1084711","volume":"27","author":"T Murata","year":"1980","unstructured":"Murata, T., Koh, J.: Reduction and expansion of live and safe marked graphs. IEEE Trans. Circuits Syst. 27(1), 68\u201370 (1980)","journal-title":"IEEE Trans. Circuits Syst."},{"key":"12_CR24","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"378","DOI":"10.1007\/3-540-45699-6_8","volume-title":"Applied Semantics","author":"Andrew M Pitts","year":"2002","unstructured":"Pitts, Andrew M.: Operational semantics and program equivalence. In: Barthe, Gilles, Dybjer, Peter, Pinto, Lu\u00eds, Saraiva, Jo\u00e3o (eds.) APPSEM 2000. LNCS, vol. 2395, p. 378. Springer, Heidelberg (2002)"},{"issue":"6905","key":"12_CR25","doi-asserted-by":"publisher","first-page":"343","DOI":"10.1038\/419343a","volume":"419","author":"A Regev","year":"2002","unstructured":"Regev, A., Shapiro, E.: Cellular abstractions: cells as computation. Nature 419(6905), 343 (2002)","journal-title":"Nature"},{"key":"12_CR26","doi-asserted-by":"publisher","first-page":"98","DOI":"10.1016\/j.tcs.2015.02.027","volume":"577","author":"M Schmidt-Schauss","year":"2015","unstructured":"Schmidt-Schauss, M., Sabel, D., Niehren, J., Schwinghammer, J.: Observational program calculi and the correctness of translations. J. Theor. Comput. Sci.(TCS) 577, 98\u2013124 (2015)","journal-title":"J. Theor. Comput. Sci.(TCS)"},{"issue":"3","key":"12_CR27","doi-asserted-by":"publisher","first-page":"446","DOI":"10.1137\/1031091","volume":"31","author":"LA Segel","year":"1989","unstructured":"Segel, L.A., Slemrod, M.: The quasi-steady-state assumption: a case study in perturbation. SIAM Rev. 31(3), 446\u2013477 (1989)","journal-title":"SIAM Rev."},{"key":"12_CR28","doi-asserted-by":"crossref","unstructured":"Soliman, S., Fages, F., Radulescu, O., et al.: A constraint solving approach to tropical equilibration and model reduction. In: WCB-Ninth Workshop on Constraint Based Methods for Bioinformatics, Colocated with CP 2013, (2013)","DOI":"10.1186\/s13015-014-0024-2"},{"key":"12_CR29","doi-asserted-by":"crossref","unstructured":"Uhlendorf, J., Bottani, S., Fages, F., Hersen, P., Batt, G.: Towards real-time control of gene expression: controlling the hog signaling cascade. In: Pacific Symposium On Biocomputing, pp. 338\u2013349. World Scientific (2011)","DOI":"10.1142\/9789814335058_0035"},{"issue":"35","key":"12_CR30","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. Proc. Natl. Acad. Sci. 109(35), 14271\u201314276 (2012)","journal-title":"Proc. Natl. Acad. Sci."}],"container-title":["Lecture Notes in Computer Science","Computational Methods in Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-319-23401-4_12","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,2,15]],"date-time":"2023-02-15T15:42:08Z","timestamp":1676475728000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-319-23401-4_12"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2015]]},"ISBN":["9783319234007","9783319234014"],"references-count":30,"URL":"https:\/\/doi.org\/10.1007\/978-3-319-23401-4_12","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":"2 September 2015","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}}]}}