{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,9,11]],"date-time":"2024-09-11T07:16:40Z","timestamp":1726039000060},"publisher-location":"Cham","reference-count":29,"publisher":"Springer International Publishing","isbn-type":[{"type":"print","value":"9783030280413"},{"type":"electronic","value":"9783030280420"}],"license":[{"start":{"date-parts":[[2019,1,1]],"date-time":"2019-01-01T00:00:00Z","timestamp":1546300800000},"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":[[2019]]},"DOI":"10.1007\/978-3-030-28042-0_4","type":"book-chapter","created":{"date-parts":[[2019,8,1]],"date-time":"2019-08-01T01:03:46Z","timestamp":1564621426000},"page":"45-62","update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Fixed-Point Computation of Equilibria in Biochemical Regulatory Networks"],"prefix":"10.1007","author":[{"given":"Isabel Cristina","family":"P\u00e9rez-Verona","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mirco","family":"Tribastone","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Max","family":"Tschaikowski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,8,1]]},"reference":[{"issue":"4","key":"4_CR1","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1007\/s00285-009-0309-0","volume":"61","author":"D Angeli","year":"2010","unstructured":"Angeli, D., De Leenheer, P., Sontag, E.: Graph-theoretic characterizations of monotonicity of chemical networks in reaction coordinates. J. Math. Biol. 61(4), 581\u2013616 (2010)","journal-title":"J. Math. Biol."},{"issue":"7","key":"4_CR2","doi-asserted-by":"publisher","first-page":"1822","DOI":"10.1073\/pnas.0308265100","volume":"101","author":"D Angeli","year":"2004","unstructured":"Angeli, D., Ferrell, J.E., Sontag, E.D.: Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems. Proc. Natl. Acad. Sci. 101(7), 1822\u20131827 (2004)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"3\u20134","key":"4_CR3","doi-asserted-by":"publisher","first-page":"185","DOI":"10.1016\/j.sysconle.2003.08.003","volume":"51","author":"D Angeli","year":"2004","unstructured":"Angeli, D., Sontag, E.D.: Multi-stability in monotone input\/output systems. Syst. Control Lett. 51(3\u20134), 185\u2013202 (2004)","journal-title":"Syst. Control Lett."},{"issue":"1","key":"4_CR4","doi-asserted-by":"publisher","first-page":"142","DOI":"10.1016\/j.biotechadv.2011.05.010","volume":"30","author":"F Bianconi","year":"2012","unstructured":"Bianconi, F., Baldelli, E., Ludovini, V., Crin\u00f2, L., Flacco, A., Valigi, P.: Computational model of EGFR and IGF1R pathways in lung cancer: a systems biology approach for translational oncology. Biotechnol. Adv. 30(1), 142\u2013153 (2012)","journal-title":"Biotechnol. Adv."},{"issue":"3","key":"4_CR5","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 (2004)","journal-title":"Phys. Biol."},{"issue":"1","key":"4_CR6","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":"4_CR7","doi-asserted-by":"crossref","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: Forward and backward bisimulations for chemical reaction networks. In: CONCUR, pp. 226\u2013239 (2015)","DOI":"10.1145\/2933575.2935318"},{"key":"4_CR8","doi-asserted-by":"crossref","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: Comparing chemical reaction networks: a categorical and algorithmic perspective. In: LICS, pp. 485\u2013494 (2016)","DOI":"10.1145\/2933575.2935318"},{"key":"4_CR9","doi-asserted-by":"crossref","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: Symbolic computation of differential equivalences. In: POPL, pp. 137\u2013150 (2016)","DOI":"10.1145\/2914770.2837649"},{"issue":"38","key":"4_CR10","doi-asserted-by":"publisher","first-page":"10029","DOI":"10.1073\/pnas.1702697114","volume":"114","author":"L Cardelli","year":"2017","unstructured":"Cardelli, L., Tribastone, M., Tschaikowski, M., Vandin, A.: Maximal aggregation of polynomial dynamical systems. Proc. Natl. Acad. Sci. (PNAS) 114(38), 10029\u201310034 (2017)","journal-title":"Proc. Natl. Acad. Sci. (PNAS)"},{"key":"4_CR11","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"134","DOI":"10.1007\/978-3-642-18275-4_11","volume-title":"Verification, Model Checking, and Abstract Interpretation","author":"B Cook","year":"2011","unstructured":"Cook, B., Fisher, J., Krepska, E., Piterman, N.: Proving stabilization of biological systems. In: Jhala, R., Schmidt, D. (eds.) VMCAI 2011. LNCS, vol. 6538, pp. 134\u2013149. Springer, Heidelberg (2011). https:\/\/doi.org\/10.1007\/978-3-642-18275-4_11"},{"key":"4_CR12","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: LICS, pp. 362\u2013381 (2010)","DOI":"10.1109\/LICS.2010.44"},{"issue":"1","key":"4_CR13","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1016\/j.jde.2005.05.007","volume":"224","author":"G Enciso","year":"2006","unstructured":"Enciso, G., Smith, H., Sontag, E.: Nonmonotone systems decomposable into monotone systems with negative feedback. J. Differ. Equ. 224(1), 205\u2013227 (2006)","journal-title":"J. Differ. Equ."},{"issue":"16","key":"4_CR14","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. Natl. Acad. Sci. 106(16), 6453\u20136458 (2009)","journal-title":"Proc. Natl. Acad. Sci."},{"issue":"5495","key":"4_CR15","doi-asserted-by":"publisher","first-page":"1358","DOI":"10.1126\/science.290.5495.1358","volume":"290","author":"GF Fussmann","year":"2000","unstructured":"Fussmann, G.F., Ellner, S.P., Shertzer, K.W., Hairston Jr., N.G.: Crossing the Hopf bifurcation in a live predator-prey system. Science 290(5495), 1358\u20131360 (2000)","journal-title":"Science"},{"issue":"4","key":"4_CR16","doi-asserted-by":"publisher","first-page":"339","DOI":"10.1093\/bib\/bbl043","volume":"7","author":"D Gilbert","year":"2006","unstructured":"Gilbert, D., et al.: Computational methodologies for modelling, analysis and simulation of signalling networks. Brief. Bioinform. 7(4), 339\u2013353 (2006)","journal-title":"Brief. Bioinform."},{"key":"4_CR17","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"396","DOI":"10.1007\/978-3-642-22110-1_31","volume-title":"Computer Aided Verification","author":"R Grosu","year":"2011","unstructured":"Grosu, R., et al.: From cardiac cells to genetic regulatory networks. In: Gopalakrishnan, G., Qadeer, S. (eds.) CAV 2011. LNCS, vol. 6806, pp. 396\u2013411. Springer, Heidelberg (2011). https:\/\/doi.org\/10.1007\/978-3-642-22110-1_31"},{"issue":"6","key":"4_CR18","doi-asserted-by":"publisher","first-page":"1583","DOI":"10.1046\/j.1432-1327.2000.01197.x","volume":"267","author":"BN Kholodenko","year":"2000","unstructured":"Kholodenko, B.N.: Negative feedback and ultrasensitivity can bring about oscillations in the mitogen-activated protein kinase cascades. Eur. J. Biochem. 267(6), 1583\u20131588 (2000)","journal-title":"Eur. J. Biochem."},{"key":"4_CR19","doi-asserted-by":"publisher","first-page":"826","DOI":"10.1038\/nrg1471","volume":"5","author":"H Kitano","year":"2004","unstructured":"Kitano, H.: Biological robustness. Nat. Rev. Genet. 5, 826 (2004)","journal-title":"Nat. Rev. Genet."},{"issue":"2","key":"4_CR20","doi-asserted-by":"publisher","first-page":"357","DOI":"10.1016\/j.jcp.2003.08.010","volume":"193","author":"D Knoll","year":"2004","unstructured":"Knoll, D., Keyes, D.: Jacobian-free Newton-Krylov methods: a survey of approaches and applications. J. Comput. Phys. 193(2), 357\u2013397 (2004)","journal-title":"J. Comput. Phys."},{"issue":"3","key":"4_CR21","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1083\/jcb.200308060","volume":"164","author":"NI Markevich","year":"2004","unstructured":"Markevich, N.I., Hoek, J.B., Kholodenko, B.N.: Signaling switches and bistability arising from multisite phosphorylation in protein kinase cascades. J. Cell Biol. 164(3), 353\u2013359 (2004)","journal-title":"J. Cell Biol."},{"issue":"1","key":"4_CR22","doi-asserted-by":"publisher","first-page":"100","DOI":"10.1186\/1752-0509-3-100","volume":"3","author":"RJ Orton","year":"2009","unstructured":"Orton, R.J., Adriaens, M.E., Gormand, A., Sturm, O.E., Kolch, W., Gilbert, D.R.: Computational modelling of cancerous mutations in the EGFR\/ERK signalling pathway. BMC Syst. Biol. 3(1), 100 (2009)","journal-title":"BMC Syst. Biol."},{"issue":"2","key":"4_CR23","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1042\/BJ20050908","volume":"392","author":"RJ Orton","year":"2005","unstructured":"Orton, R.J., Sturm, O.E., Vyshemirsky, V., Calder, M., Gilbert, D.R., Kolch, W.: Computational modelling of the receptor-tyrosine-kinase-activated MAPK pathway. Biochem. J. 392(2), 249\u2013261 (2005)","journal-title":"Biochem. J."},{"issue":"3","key":"4_CR24","doi-asserted-by":"publisher","first-page":"e0152104","DOI":"10.1371\/journal.pone.0152104","volume":"11","author":"F Pappalardo","year":"2016","unstructured":"Pappalardo, F., et al.: Computational modeling of PI3K\/AKT and MAPK signaling pathways in melanoma cancer. PLoS ONE 11(3), e0152104 (2016)","journal-title":"PLoS ONE"},{"issue":"22","key":"4_CR25","doi-asserted-by":"publisher","first-page":"2874","DOI":"10.1093\/bioinformatics\/btq517","volume":"26","author":"N Radde","year":"2010","unstructured":"Radde, N.: Fixed point characterization of biological networks with complex graph topology. Bioinformatics 26(22), 2874\u20132880 (2010)","journal-title":"Bioinformatics"},{"issue":"1","key":"4_CR26","doi-asserted-by":"publisher","first-page":"57","DOI":"10.1186\/1752-0509-6-57","volume":"6","author":"N Radde","year":"2012","unstructured":"Radde, N.: Analyzing fixed points of intracellular regulation networks with interrelated feedback topology. BMC Syst. Biol. 6(1), 57 (2012)","journal-title":"BMC Syst. Biol."},{"issue":"1","key":"4_CR27","doi-asserted-by":"publisher","first-page":"219","DOI":"10.1146\/annurev.physchem.012809.103457","volume":"61","author":"JJ Tyson","year":"2010","unstructured":"Tyson, J.J., Nov\u00e1k, B.: Functional motifs in biochemical reaction networks. Annu. Rev. Phys. Chem. 61(1), 219\u2013240 (2010). pMID: 20055671","journal-title":"Annu. Rev. Phys. Chem."},{"issue":"5573","key":"4_CR28","doi-asserted-by":"publisher","first-page":"1648","DOI":"10.1126\/science.1071552","volume":"296","author":"D Vaudry","year":"2002","unstructured":"Vaudry, D., Stork, P., Lazarovici, P., Eiden, L.: Signaling pathways for PC12 cell differentiation: making the right connections. Science 296(5573), 1648\u20131649 (2002)","journal-title":"Science"},{"issue":"8","key":"4_CR29","doi-asserted-by":"publisher","first-page":"a009043","DOI":"10.1101\/cshperspect.a009043","volume":"5","author":"N Volinsky","year":"2013","unstructured":"Volinsky, N., Kholodenko, B.N.: Complexity of receptor tyrosine kinase signal processing. Cold Spring Harb. Perspect. Biol. 5(8), a009043 (2013)","journal-title":"Cold Spring Harb. Perspect. Biol."}],"container-title":["Lecture Notes in Computer Science","Hybrid Systems Biology"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-3-030-28042-0_4","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,9,25]],"date-time":"2022-09-25T00:00:54Z","timestamp":1664064054000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-3-030-28042-0_4"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019]]},"ISBN":["9783030280413","9783030280420"],"references-count":29,"URL":"https:\/\/doi.org\/10.1007\/978-3-030-28042-0_4","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"type":"print","value":"0302-9743"},{"type":"electronic","value":"1611-3349"}],"subject":[],"published":{"date-parts":[[2019]]},"assertion":[{"value":"1 August 2019","order":1,"name":"first_online","label":"First Online","group":{"name":"ChapterHistory","label":"Chapter History"}},{"value":"HSB","order":1,"name":"conference_acronym","label":"Conference Acronym","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"International Workshop on Hybrid Systems Biology","order":2,"name":"conference_name","label":"Conference Name","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Prague","order":3,"name":"conference_city","label":"Conference City","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"Czech Republic","order":4,"name":"conference_country","label":"Conference Country","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"2019","order":5,"name":"conference_year","label":"Conference Year","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6 April 2019","order":7,"name":"conference_start_date","label":"Conference Start Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"7 April 2019","order":8,"name":"conference_end_date","label":"Conference End Date","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"6","order":9,"name":"conference_number","label":"Conference Number","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"hsb2019","order":10,"name":"conference_id","label":"Conference ID","group":{"name":"ConferenceInfo","label":"Conference Information"}},{"value":"http:\/\/hsb2019.fit.vutbr.cz","order":11,"name":"conference_url","label":"Conference URL","group":{"name":"ConferenceInfo","label":"Conference Information"}}]}}