{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,2]],"date-time":"2026-01-02T07:51:30Z","timestamp":1767340290498,"version":"3.40.3"},"publisher-location":"Cham","reference-count":36,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783031150333"},{"type":"electronic","value":"9783031150340"}],"license":[{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"},{"start":{"date-parts":[[2022,1,1]],"date-time":"2022-01-01T00:00:00Z","timestamp":1640995200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/www.springer.com\/tdm"}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022]]},"DOI":"10.1007\/978-3-031-15034-0_10","type":"book-chapter","created":{"date-parts":[[2022,8,18]],"date-time":"2022-08-18T19:03:08Z","timestamp":1660849388000},"page":"198-216","update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":7,"title":["Exact Linear Reduction for\u00a0Rational Dynamical Systems"],"prefix":"10.1007","author":[{"given":"Antonio","family":"Jim\u00e9nez-Pastor","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua Paul","family":"Jacob","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gleb","family":"Pogudin","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2022,8,19]]},"reference":[{"doi-asserted-by":"crossref","unstructured":"Antoulas, A.: Approximation of large-scale dynamical systems. Advance in Design and Control, SIAM (2005)","key":"10_CR1","DOI":"10.1137\/1.9780898718713"},{"issue":"4","key":"10_CR2","doi-asserted-by":"publisher","first-page":"e1000364","DOI":"10.1371\/journal.pcbi.1000364","volume":"5","author":"D Barua","year":"2009","unstructured":"Barua, D., Faeder, J.R., Haugh, J.M.: A bipolar clamp mechanism for activation of Jak-family protein tyrosine kinases. PLoS Comput. Biol. 5(4), e1000364 (2009). https:\/\/doi.org\/10.1371\/journal.pcbi.1000364","journal-title":"PLoS Comput. Biol."},{"issue":"3","key":"10_CR3","doi-asserted-by":"publisher","first-page":"317","DOI":"10.1016\/0304-3975(83)90110-X","volume":"22","author":"W Baur","year":"1983","unstructured":"Baur, W., Strassen, V.: The complexity of partial derivatives. Theoret. Comput. Sci. 22(3), 317\u2013330 (1983). https:\/\/doi.org\/10.1016\/0304-3975(83)90110-X","journal-title":"Theoret. Comput. Sci."},{"unstructured":"Baydin, A.G., Pearlmutter, B.A., Radul, A.A., Siskind, J.M.: Automatic differentiation in machine learning: a survey. J. Mach. Learn. Res. 18(153), 1\u201343 (2018). https:\/\/jmlr.org\/papers\/v18\/17-468.html","key":"10_CR4"},{"issue":"2","key":"10_CR5","doi-asserted-by":"publisher","first-page":"951","DOI":"10.1529\/biophysj.105.060533","volume":"89","author":"N Borisov","year":"2005","unstructured":"Borisov, N., Markevich, N., Hoek, J., Kholodenko, B.: Signaling through receptors and scaffolds: independent interactions reduce combinatorial complexity. Biophys. J. 89(2), 951\u2013966 (2005). https:\/\/doi.org\/10.1529\/biophysj.105.060533","journal-title":"Biophys. J."},{"issue":"5","key":"10_CR6","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1049\/iet-syb:20070081","volume":"2","author":"N Borisov","year":"2008","unstructured":"Borisov, N., Kholodenko, B., Faeder, J., Chistopolsky, A.: Domain-oriented reduction of rule-based network models. IET Syst. Biol. 2(5), 342\u2013351 (2008). https:\/\/doi.org\/10.1049\/iet-syb:20070081","journal-title":"IET Syst. Biol."},{"issue":"14","key":"10_CR7","doi-asserted-by":"publisher","first-page":"9867","DOI":"10.1074\/jbc.m112.432062","volume":"288","author":"C Br\u00e4nnmark","year":"2013","unstructured":"Br\u00e4nnmark, C., et al.: Insulin signaling in type 2 diabetes. J. Biol. Chem. 288(14), 9867\u20139880 (2013). https:\/\/doi.org\/10.1074\/jbc.m112.432062","journal-title":"J. Biol. Chem."},{"issue":"3","key":"10_CR8","doi-asserted-by":"publisher","first-page":"184","DOI":"10.1088\/1478-3967\/1\/3\/006","volume":"1","author":"KS Brown","year":"2004","unstructured":"Brown, K.S., et al.: The statistical mechanics of complex signaling networks: nerve growth factor signaling. Phys. Biol. 1(3), 184\u2013195 (2004). https:\/\/doi.org\/10.1088\/1478-3967\/1\/3\/006","journal-title":"Phys. Biol."},{"key":"10_CR9","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"310","DOI":"10.1007\/978-3-662-54580-5_19","volume-title":"Tools and Algorithms for the Construction and Analysis of Systems","author":"L Cardelli","year":"2017","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: ERODE: a tool for the evaluation and reduction of ordinary differential equations. In: Legay, A., Margaria, T. (eds.) TACAS 2017. LNCS, vol. 10206, pp. 310\u2013328. Springer, Heidelberg (2017). https:\/\/doi.org\/10.1007\/978-3-662-54580-5_19"},{"doi-asserted-by":"crossref","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: Maximal aggregation of polynomial dynamical systems. Proc. National Acad. Sci. 114(38), 10029\u201310034 (2017). https:\/\/www.pnas.org\/content\/114\/38\/10029","key":"10_CR10","DOI":"10.1073\/pnas.1702697114"},{"key":"10_CR11","doi-asserted-by":"publisher","first-page":"132","DOI":"10.1016\/j.tcs.2019.03.018","volume":"777","author":"L Cardelli","year":"2019","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: Symbolic computation of differential equivalences. Theoret. Comput. Sci. 777, 132\u2013154 (2019). https:\/\/doi.org\/10.1016\/j.tcs.2019.03.018","journal-title":"Theoret. Comput. Sci."},{"doi-asserted-by":"crossref","unstructured":"Chou, T.C., Talalay, P.: A simple generalized equation for the analysis of multiple inhibitions of Michaelis-Menten kinetic systems. J. Biol. Chem. 252, 6438\u20136442 (1977). https:\/\/www.jbc.org\/article\/S0021-9258(17)39978--7\/pdf","key":"10_CR12","DOI":"10.1016\/S0021-9258(17)39978-7"},{"issue":"1","key":"10_CR13","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1186\/1752-0509-2-78","volume":"2","author":"H Conzelmann","year":"2008","unstructured":"Conzelmann, H., Fey, D., Gilles, E.: Exact model reduction of combinatorial reaction networks. BMC Syst. Biol. 2(1), 78 (2008). https:\/\/doi.org\/10.1186\/1752-0509-2-78","journal-title":"BMC Syst. Biol."},{"issue":"3","key":"10_CR14","doi-asserted-by":"publisher","first-page":"257","DOI":"10.1016\/0301-4622(92)80018-z","volume":"42","author":"G Dupont","year":"1992","unstructured":"Dupont, G., Goldbeter, A.: Protein phosphorylation driven by intracellular calcium oscillations: a kinetic analysis. Biophys. Chem. 42(3), 257\u2013270 (1992). https:\/\/doi.org\/10.1016\/0301-4622(92)80018-z","journal-title":"Biophys. Chem."},{"doi-asserted-by":"crossref","unstructured":"Elliott, C.: Beautiful differentiation. In: International Conference on Functional Programming (ICFP) (2009). http:\/\/conal.net\/papers\/beautiful-differentiation","key":"10_CR15","DOI":"10.1145\/1596550.1596579"},{"issue":"7","key":"10_CR16","doi-asserted-by":"publisher","first-page":"3769","DOI":"10.4049\/jimmunol.170.7.3769","volume":"170","author":"JR Faeder","year":"2003","unstructured":"Faeder, J.R., et al.: Investigation of early events in fc$$\\varepsilon $$RI-mediated signaling using a detailed mathematical model. J. Immunol. 170(7), 3769\u20133781 (2003). https:\/\/doi.org\/10.4049\/jimmunol.170.7.3769","journal-title":"J. Immunol."},{"issue":"16","key":"10_CR17","doi-asserted-by":"publisher","first-page":"6453","DOI":"10.1073\/pnas.0809908106","volume":"106","author":"J Feret","year":"2009","unstructured":"Feret, J., Danos, V., Krivine, J., Harmer, R., Fontana, W.: Internal coarse-graining of molecular systems. Proc. National Acad. Sci. 106(16), 6453\u20136458 (2009). https:\/\/doi.org\/10.1073\/pnas.0809908106","journal-title":"Proc. National Acad. Sci."},{"key":"10_CR18","doi-asserted-by":"publisher","first-page":"775","DOI":"10.1007\/s11075-015-0067-6","volume":"72","author":"PH Hoffmann","year":"2016","unstructured":"Hoffmann, P.H.: A Hitchhiker\u2019s guide to automatic differentiation. Numer. Algorithms 72, 775\u2013811 (2016). https:\/\/doi.org\/10.1007\/s11075-015-0067-6","journal-title":"Numer. Algorithms"},{"issue":"316","key":"10_CR19","doi-asserted-by":"publisher","first-page":"ra23","DOI":"10.1126\/scisignal.2004738","volume":"7","author":"SM Kallenberger","year":"2014","unstructured":"Kallenberger, S.M., et al.: Intra- and interdimeric caspase-8 self-cleavage controls strength and timing of CD95-induced apoptosis. Sci. Signal. 7(316), ra23 (2014). https:\/\/doi.org\/10.1126\/scisignal.2004738","journal-title":"Sci. Signal."},{"issue":"6","key":"10_CR20","doi-asserted-by":"publisher","first-page":"1413","DOI":"10.1016\/0009-2509(89)85014-6","volume":"44","author":"G Li","year":"1989","unstructured":"Li, G., Rabitz, H.: A general analysis of exact lumping in chemical kinetics. Chem. Eng. Sci. 44(6), 1413\u20131430 (1989). https:\/\/doi.org\/10.1016\/0009-2509(89)85014-6","journal-title":"Chem. Eng. Sci."},{"issue":"1","key":"10_CR21","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1038\/msb4100107","volume":"2","author":"J Li","year":"2006","unstructured":"Li, J., et al.: A stochastic model ofEscherichia coliAI-2 quorum signal circuit reveals alternative synthesis pathways. Mol. Syst. Biol. 2(1), 67 (2006). https:\/\/doi.org\/10.1038\/msb4100107","journal-title":"Mol. Syst. Biol."},{"issue":"D1","key":"10_CR22","doi-asserted-by":"publisher","first-page":"D407","DOI":"10.1093\/nar\/gkz1055","volume":"48","author":"RS Malik-Sheriff","year":"2020","unstructured":"Malik-Sheriff, R.S., et al.: BioModels - 15 years of sharing computational models in life science. Nucleic Acids Res. 48(D1), D407\u2013D415 (2020). https:\/\/doi.org\/10.1093\/nar\/gkz1055","journal-title":"Nucleic Acids Res."},{"issue":"4","key":"10_CR23","doi-asserted-by":"publisher","first-page":"666","DOI":"10.1016\/j.cell.2008.04.025","volume":"133","author":"SR Neves","year":"2008","unstructured":"Neves, S.R., et al.: Cell shape and negative links in regulatory motifs together control spatial information flow in signaling networks. Cell 133(4), 666\u2013680 (2008). https:\/\/doi.org\/10.1016\/j.cell.2008.04.025","journal-title":"Cell"},{"issue":"98","key":"10_CR24","doi-asserted-by":"publisher","first-page":"391","DOI":"10.1021\/cr950223l","volume":"2","author":"M Okino","year":"1998","unstructured":"Okino, M., Mavrovouniotis, M.: Simplification of mathematical models of chemical reaction systems. Chem. Rev. 2(98), 391\u2013408 (1998). https:\/\/doi.org\/10.1021\/cr950223l","journal-title":"Chem. Rev."},{"issue":"19","key":"10_CR25","doi-asserted-by":"publisher","first-page":"3385","DOI":"10.1093\/bioinformatics\/btab258","volume":"37","author":"A Ovchinnikov","year":"2021","unstructured":"Ovchinnikov, A., P\u00e9rez Verona, I., Pogudin, G., Tribastone, M.: CLUE: exact maximal reduction of kinetic models by constrained lumping of differential equations. Bioinformatics 37(19), 3385\u20133385 (2021). https:\/\/doi.org\/10.1093\/bioinformatics\/btab258","journal-title":"Bioinformatics"},{"issue":"2","key":"10_CR26","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1000675","volume":"6","author":"S Pepke","year":"2010","unstructured":"Pepke, S., Kinzer-Ursem, T., Mihalas, S., Kennedy, M.B.: A dynamic model of interactions of Ca$$^{2+}$$, calmodulin, and catalytic subunits of Ca$$^{2+}$$\/calmodulin-dependent protein kinase II. PLoS Comput. Biol. 6(2), e1000675 (2010). https:\/\/doi.org\/10.1371\/journal.pcbi.1000675","journal-title":"PLoS Comput. Biol."},{"key":"10_CR27","doi-asserted-by":"publisher","first-page":"41","DOI":"10.1016\/j.tcs.2021.06.026","volume":"893","author":"IC Perez-Verona","year":"2021","unstructured":"Perez-Verona, I.C., Tribastone, M., Vandin, A.: A large-scale assessment of exact lumping of quantitative models in the BioModels repository. Theoret. Comput. Sci. 893, 41\u201359 (2021). https:\/\/doi.org\/10.1016\/j.tcs.2021.06.026","journal-title":"Theoret. Comput. Sci."},{"issue":"400","key":"10_CR28","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1093\/jxb\/erh090","volume":"55","author":"MG Poolman","year":"2004","unstructured":"Poolman, M.G., Assmus, H.E., Fell, D.A.: Applications of metabolic modelling to plant metabolism. J. Exp. Bot. 55(400), 1177\u20131186 (2004). https:\/\/doi.org\/10.1093\/jxb\/erh090","journal-title":"J. Exp. Bot."},{"issue":"3","key":"10_CR29","doi-asserted-by":"publisher","first-page":"693","DOI":"10.1158\/0008-5472.can-10-2987","volume":"71","author":"V Raia","year":"2010","unstructured":"Raia, V., et al.: Dynamic mathematical modeling of IL13-induced signaling in hodgkin and primary mediastinal b-cell lymphoma allows prediction of therapeutic targets. Can. Res. 71(3), 693\u2013704 (2010). https:\/\/doi.org\/10.1158\/0008-5472.can-10-2987","journal-title":"Can. Res."},{"issue":"2","key":"10_CR30","doi-asserted-by":"publisher","first-page":"437","DOI":"10.1042\/bj3580437","volume":"358","author":"JM Rohwer","year":"2001","unstructured":"Rohwer, J.M., Botha, F.C.: Analysis of sucrose accumulation in the sugar cane culm on the basis of in vitro kinetic data. Biochem. J. 358(2), 437\u2013445 (2001). https:\/\/doi.org\/10.1042\/bj3580437","journal-title":"Biochem. J."},{"issue":"1\/2","key":"10_CR31","doi-asserted-by":"publisher","first-page":"155","DOI":"10.1023\/a:1019139423811","volume":"27","author":"S Schnell","year":"2000","unstructured":"Schnell, S., Mendoza, C.: Enzyme kinetics of multiple alternative substrates. J. Math. Chem. 27(1\/2), 155\u2013170 (2000). https:\/\/doi.org\/10.1023\/a:1019139423811","journal-title":"J. Math. Chem."},{"issue":"2","key":"10_CR32","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1038\/nmeth.1546","volume":"8","author":"MW Sneddon","year":"2010","unstructured":"Sneddon, M.W., Faeder, J.R., Emonet, T.: Efficient modeling, simulation and coarse-graining of biological complexity with NFsim. Nat. Meth. 8(2), 177\u2013183 (2010). https:\/\/doi.org\/10.1038\/nmeth.1546","journal-title":"Nat. Meth."},{"doi-asserted-by":"publisher","unstructured":"Warner, F.W.: Foundations of Differentiable Manifolds and Lie Groups. Springer, New York, NY (1983). https:\/\/doi.org\/10.1007\/978-1-4757-1799-0","key":"10_CR33","DOI":"10.1007\/978-1-4757-1799-0"},{"issue":"9","key":"10_CR34","doi-asserted-by":"publisher","first-page":"E1038","DOI":"10.1073\/pnas.1416533112","volume":"112","author":"AY Wei\u00dfe","year":"2015","unstructured":"Wei\u00dfe, A.Y., Oyarz\u00fan, D.A., Danos, V., Swain, P.S.: Mechanistic links between cellular trade-offs, gene expression, and growth. Proc. Natl. Acad. Sci. 112(9), E1038\u2013E1047 (2015). https:\/\/doi.org\/10.1073\/pnas.1416533112","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"8","key":"10_CR35","doi-asserted-by":"publisher","first-page":"463","DOI":"10.1145\/355586.364791","volume":"7","author":"RE Wengert","year":"1964","unstructured":"Wengert, R.E.: A simple automatic derivative evaluation program. Commun. ACM 7(8), 463\u2013464 (1964). https:\/\/doi.org\/10.1145\/355586.364791","journal-title":"Commun. ACM"},{"doi-asserted-by":"publisher","unstructured":"Zippel, R.: Effective Polynomial Computation. Springer (1993). https:\/\/doi.org\/10.1007\/978-1-4615-3188-3","key":"10_CR36","DOI":"10.1007\/978-1-4615-3188-3"}],"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\/978-3-031-15034-0_10","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,6]],"date-time":"2022-09-06T23:04:24Z","timestamp":1662505464000},"score":1,"resource":{"primary":{"URL":"https:\/\/link.springer.com\/10.1007\/978-3-031-15034-0_10"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022]]},"ISBN":["9783031150333","9783031150340"],"references-count":36,"URL":"https:\/\/doi.org\/10.1007\/978-3-031-15034-0_10","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2022]]},"assertion":[{"value":"19 August 2022","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"CMSB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Conference on Computational Methods in Systems Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Bucharest","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Romania","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2022","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"14 September 2022","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"16 September 2022","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"20","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"cmsb2022","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"https:\/\/fmi.unibuc.ro\/en\/cmsb-2022\/","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Single-blind","order":1,"name":"type","label":"Type","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"EasyChair","order":2,"name":"conference_management_system","label":"Conference Management System","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"43","order":3,"name":"number_of_submissions_sent_for_review","label":"Number of Submissions Sent for Review","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"13","order":4,"name":"number_of_full_papers_accepted","label":"Number of Full Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"0","order":5,"name":"number_of_short_papers_accepted","label":"Number of Short Papers Accepted","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"30% - The value is computed by the equation \"Number of Full Papers Accepted \/ Number of Submissions Sent for Review * 100\" and then rounded to a whole number.","order":6,"name":"acceptance_rate_of_full_papers","label":"Acceptance Rate of Full Papers","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"3","order":7,"name":"average_number_of_reviews_per_paper","label":"Average Number of Reviews per Paper","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"2","order":8,"name":"average_number_of_papers_per_reviewer","label":"Average Number of Papers per Reviewer","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}},{"value":"Yes","order":9,"name":"external_reviewers_involved","label":"External Reviewers Involved","group":{"name":"ConfEventPeerReviewInformation","label":"Peer Review Information (provided by the conference organizers)"}}]}}