{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,2]],"date-time":"2026-10-02T11:25:15Z","timestamp":1790940315480,"version":"4.1.0"},"publisher-location":"Berlin, Heidelberg","reference-count":38,"publisher":"Springer Berlin Heidelberg","isbn-type":[{"value":"9783540488378","type":"print"},{"value":"9783540488392","type":"electronic"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006]]},"DOI":"10.1007\/11905455_3","type":"book-chapter","created":{"date-parts":[[2006,11,17]],"date-time":"2006-11-17T01:41:17Z","timestamp":1163727677000},"page":"56-72","source":"Crossref","is-referenced-by-count":24,"title":["From Logical Regulatory Graphs to Standard Petri Nets: Dynamical Roles and Functionality of Feedback Circuits"],"prefix":"10.1007","author":[{"given":"Elisabeth","family":"Remy","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul","family":"Ruet","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Luis","family":"Mendoza","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Denis","family":"Thieffry","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claudine","family":"Chaouiya","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","reference":[{"key":"3_CR1","doi-asserted-by":"publisher","first-page":"147","DOI":"10.1023\/A:1023381027062","volume":"23","author":"D. Agnello","year":"2003","unstructured":"Agnello, D., Lankford, C.S.R., Bream, J., Morinobu, A., Gadina, M., O\u2019Shea, J., Frucht, D.M.: Cytokines and transcription factors that regulate T helper cell differentiation: new players and new insights. J. Clin. Immunol.\u00a023, 147\u2013161 (2003)","journal-title":"J. Clin. Immunol."},{"key":"3_CR2","doi-asserted-by":"publisher","first-page":"159","DOI":"10.1142\/S0218126698000079","volume":"8-1","author":"H. Alla","year":"1998","unstructured":"Alla, H., David, R.: Continuous and hybrid petri nets. Journal of Circuits, Systems, and Computers\u00a08-1, 159\u2013188 (1998)","journal-title":"Journal of Circuits, Systems, and Computers"},{"key":"3_CR3","unstructured":"Aracena, J.: Mod\u00e8les math\u00e9matiques discrets associ\u00e9s \u00e0 des syst\u00e8mes biologiques. Application aux r\u00e9seaux de r\u00e9gulation g\u00e9n\u00e9tiques. Th\u00e8se de Doctorat Sp\u00e9cialit\u00e9 Math\u00e9matiques Appliqu\u00e9es, Universit\u00e9 Joseph Fourier, Grenoble (2001)"},{"key":"3_CR4","doi-asserted-by":"publisher","first-page":"405","DOI":"10.1006\/bulm.2000.0215","volume":"63","author":"C. Bergmann","year":"2001","unstructured":"Bergmann, C., Van Hemmen, J.L., Segel, L.A.: Th1 or Th2: how an appropriate T helper response can be made. Bull. Math. Biol.\u00a063, 405\u2013430 (2001)","journal-title":"Bull. Math. Biol."},{"issue":"8","key":"3_CR5","doi-asserted-by":"publisher","first-page":"677","DOI":"10.1109\/TC.1986.1676819","volume":"C-35","author":"R. Bryant","year":"1986","unstructured":"Bryant, R.: Graph-Based Algorithms for Boolean Function Manipulation. IEEE Trans. on Computers\u00a0C-35(8), 677\u2013691 (1986)","journal-title":"IEEE Trans. on Computers"},{"key":"3_CR6","first-page":"29","volume":"3","author":"M. Chen","year":"2003","unstructured":"Chen, M., Hofestaedt, R.: Quantitative Petri net model of gene regulated metabolic networks in the cell. Silico Biology\u00a03, 29 (2003)","journal-title":"Silico Biology"},{"key":"3_CR7","unstructured":"Chaouiya, C., Remy, E., Thieffry, D.: Petri Net Modelling of Biological Regulatory Networks, IML Research report 2005-20 (2005), Accessible at: http:\/\/iml.univ-mrs.fr\/editions\/preprint2005\/preprint2005.html"},{"key":"3_CR8","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"137","DOI":"10.1007\/978-3-540-27793-4_9","volume-title":"Applications and Theory of Petri Nets 2004","author":"C. Chaouiya","year":"2004","unstructured":"Chaouiya, C., Remy, E., Ruet, P., Thieffry, D.: Qualitative Modelling of Genetic Networks: From Logical Regulatory Graphs to Standard Petri Nets. In: Cortadella, J., Reisig, W. (eds.) ICATPN 2004. LNCS, vol.\u00a03099, pp. 137\u2013156. Springer, Heidelberg (2004)"},{"key":"3_CR9","doi-asserted-by":"crossref","unstructured":"Chaouiya, C., Remy, E., Moss\u00e9, B., Thieffry, D.: Qualitative analysis of regulatory graphs: a computational tool based on a discrete formal framework. In: Benvenuti, L., De Santis, A., Farina, L. (eds.) POSTA 2003. LNCIS, vol.\u00a0294, pp. 119\u2013126. Springer, Heidelberg (2003)","DOI":"10.1007\/978-3-540-44928-7_17"},{"key":"3_CR10","doi-asserted-by":"publisher","first-page":"67","DOI":"10.1089\/10665270252833208","volume":"9","author":"H. Jong de","year":"2002","unstructured":"de Jong, H.: Modeling and Simulation of Genetic Regulatory Systems: A Literature Review. J. Comp. Biol.\u00a09, 67\u2013103 (2002)","journal-title":"J. Comp. Biol."},{"key":"3_CR11","first-page":"23","volume":"4","author":"A. Doi","year":"2004","unstructured":"Doi, A., Fujita, S., Matsuno, H., Nagasaki, M., Miyano, S.: Constructing biological pathway models with hybrid functional Petri nets. Silico Biology\u00a04, 23 (2004)","journal-title":"Silico Biology"},{"key":"3_CR12","doi-asserted-by":"publisher","first-page":"103","DOI":"10.1016\/0022-5193(73)90208-7","volume":"39","author":"L. Glass","year":"1973","unstructured":"Glass, L., Kauffman, S.A.: The logical analysis of continuous, non-linear biochemical control networks. J. Theor. Biol.\u00a039, 103\u2013129 (1973)","journal-title":"J. Theor. Biol."},{"key":"3_CR13","doi-asserted-by":"publisher","first-page":"6750","DOI":"10.1073\/pnas.95.12.6750","volume":"95","author":"P.J.E. Goss","year":"1998","unstructured":"Goss, P.J.E., Peccoud, J.: Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets. Proc. Natl. Acad. Sci. USA.\u00a095, 6750\u20136755 (1998)","journal-title":"Proc. Natl. Acad. Sci. USA."},{"key":"3_CR14","doi-asserted-by":"publisher","first-page":"11","DOI":"10.1142\/S0218339098000054","volume":"6","author":"J.L. Gouz\u00e9","year":"1998","unstructured":"Gouz\u00e9, J.L.: Positive and negative circuits in dynamical systems. J. Biol. Syst.\u00a06, 11\u201315 (1998)","journal-title":"J. Biol. Syst."},{"key":"3_CR15","series-title":"Lecture Notes in Computer Science","doi-asserted-by":"publisher","first-page":"216","DOI":"10.1007\/978-3-540-27793-4_13","volume-title":"Applications and Theory of Petri Nets 2004","author":"M. Heiner","year":"2004","unstructured":"Heiner, M., Koch, I.: Petri Net Based Model Validation in Systems Biology. In: Cortadella, J., Reisig, W. (eds.) ICATPN 2004. LNCS, vol.\u00a03099, pp. 216\u2013237. Springer, Heidelberg (2004)"},{"key":"3_CR16","first-page":"39","volume":"1","author":"R. Hofest\u00e4dt","year":"1998","unstructured":"Hofest\u00e4dt, R., Thelen, S.: Quantitative Modeling of Biochemical Networks. Silico Biology\u00a01, 39\u201353 (1998)","journal-title":"Silico Biology"},{"key":"3_CR17","first-page":"365","volume":"16","author":"G.R.H. Krueger","year":"2002","unstructured":"Krueger, G.R.H., Marshall, G.R., Junker, U., Schroeder, H., Buja, L.M., Wang, G.: Growth factors, cytokines, chemokines and neuropeptides in the modeling of T-cells. Vivo\u00a016, 365\u2013386 (2002)","journal-title":"Vivo"},{"key":"3_CR18","first-page":"925","volume":"9","author":"R. K\u00fcffner","year":"2000","unstructured":"K\u00fcffner, R., Zimmer, R., Lengauer, T.: Pathway analysis in metabolic databases via differential metabolic display (DMD). Bioinformatics\u00a09, 925\u2013936 (2000)","journal-title":"Bioinformatics"},{"key":"3_CR19","unstructured":"Larrinaga, A., Naldi, A., S\u00e1nchez, L., Thieffry, D., Chaouiya, C.: GINsim: a software suite for the qualitative modelling, simulation and analysis of regulatory networks. BioSystems (in press)"},{"key":"3_CR20","first-page":"32","volume":"3","author":"H. Matsuno","year":"2003","unstructured":"Matsuno, H., Tanaka, Y., Aoshima, H., Doi, A., Matsui, M., Miyano, S.: Biopathways representation and simulation on hybrid functional Petri net. Silico Biology\u00a03, 32 (2003)","journal-title":"Silico Biology"},{"key":"3_CR21","doi-asserted-by":"crossref","unstructured":"Mendoza L.: A network model for the control of the differentiation process in Th cells. BioSystems (in press)","DOI":"10.1016\/j.biosystems.2005.10.004"},{"key":"3_CR22","doi-asserted-by":"publisher","first-page":"541","DOI":"10.1109\/5.24143","volume":"77","author":"T. Murata","year":"1989","unstructured":"Murata, T.: Petri Nets: Properties, Analysis and Applications. Proceedings of the IEEE\u00a077, 541\u2013580 (1989)","journal-title":"Proceedings of the IEEE"},{"key":"3_CR23","doi-asserted-by":"publisher","first-page":"933","DOI":"10.1038\/nri954","volume":"2","author":"K.M. Murphy","year":"2002","unstructured":"Murphy, K.M., Reiner, S.L.: The lineage decisions on helper T cells. Nat. Rev. Immunol.\u00a02, 933\u2013944 (2002)","journal-title":"Nat. Rev. Immunol."},{"key":"3_CR24","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1016\/0010-4825(95)00042-9","volume":"26","author":"V.N. Reddy","year":"1996","unstructured":"Reddy, V.N., Liebman, M.N., Mavrovouniotis, M.L.: Qualitative analysis of biochemical reaction systems. Comput. Biol. Med.\u00a026, 9\u201324 (1996)","journal-title":"Comput. Biol. Med."},{"key":"3_CR25","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1093\/bioinformatics\/btg1075","volume":"19","author":"E. Remy","year":"2003","unstructured":"Remy, E., Moss\u00e9, B., Chaouiya, C., Thieffry, D.: A description of dynamical graphs associated to elementary regulatory circuits. Bioinformatics\u00a019, ii172\u2013178 (2003)","journal-title":"Bioinformatics"},{"key":"3_CR26","doi-asserted-by":"crossref","unstructured":"Remy, E., Ruet, P., Thieffry, D.: Graphic requirement for multistability and attractive cycles in a Boolean dynamical framework, IML Research report 2005-08 (2005), Accessible at: http:\/\/iml.univ-mrs.fr\/~ruet\/papiers.html","DOI":"10.1016\/j.aam.2007.11.003"},{"key":"3_CR27","series-title":"Lecture Notes in Bioinformatics","doi-asserted-by":"publisher","first-page":"153","DOI":"10.1007\/11905455_8","volume-title":"Transactions on Computational Systems Biology VII","author":"\u00c9. Remy","year":"2006","unstructured":"Remy, \u00c9., Ruet, P.: On differentiation and homeostatic behaviours of Boolean dynamical systems. In: Priami, C., Ing\u00f3lfsd\u00f3ttir, A., Mishra, B., Riis Nielson, H. (eds.) Transactions on Computational Systems Biology VII. LNCS (LNBI), vol.\u00a04230, pp. 153\u2013162. Springer, Heidelberg (2006)"},{"key":"3_CR28","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-642-69968-9","volume-title":"Petri Nets","author":"W. Reisig","year":"1985","unstructured":"Reisig, W.: Petri Nets. Springer, Heidelberg (1985)"},{"key":"3_CR29","doi-asserted-by":"crossref","first-page":"973","DOI":"10.1007\/BF02460695","volume":"55","author":"E.H. Snoussi","year":"1993","unstructured":"Snoussi, E.H., Thomas, R.: Logical identification of all steady states: the concept of feedback loop characteristic states. Bul. Math. Biol.\u00a055, 973\u2013991 (1993)","journal-title":"Bul. Math. Biol."},{"key":"3_CR30","doi-asserted-by":"publisher","first-page":"3","DOI":"10.1142\/S0218339098000042","volume":"6","author":"E.H. Snoussi","year":"1998","unstructured":"Snoussi, E.H.: Necessary conditions for multistationatity and stable periodicity. J. Biol. Syst.\u00a06, 3\u20139 (1998)","journal-title":"J. Biol. Syst."},{"key":"3_CR31","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1159\/000076100","volume":"1","author":"C. Soul\u00e9","year":"2003","unstructured":"Soul\u00e9, C.: Graphic requirements for multistationarity. ComPlexUs\u00a01, 123\u2013133 (2003)","journal-title":"ComPlexUs"},{"key":"3_CR32","doi-asserted-by":"crossref","first-page":"1148","DOI":"10.1002\/bbpc.19940980916","volume":"98","author":"R. Thomas","year":"1994","unstructured":"Thomas, R.: The role of feedback circuits: positive feedback circuits are a necessary conditions for positive eigenvalues of the Jacobian matrix. Ber. Besenges. Phys. Chem.\u00a098, 1148\u20131151 (1994)","journal-title":"Ber. Besenges. Phys. Chem."},{"key":"3_CR33","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/BF02460618","volume":"57","author":"R. Thomas","year":"1995","unstructured":"Thomas, R., Thieffry, D., Kaufman, M.: Dynamical behaviour of biological regulatory networks\u2013I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bull. Math. Biol.\u00a057, 247\u2013276 (1995)","journal-title":"Bull. Math. Biol."},{"key":"3_CR34","doi-asserted-by":"publisher","first-page":"483","DOI":"10.1016\/S0022-5193(05)80374-1","volume":"146","author":"G. Weisbuch","year":"1990","unstructured":"Weisbuch, G., De Boer, R.J., Perelson, A.S.: Localized memories in idiotypic networks. J. Theor. Biol.\u00a0146, 483\u2013499 (1990)","journal-title":"J. Theor. Biol."},{"key":"3_CR35","doi-asserted-by":"publisher","first-page":"539","DOI":"10.1006\/jtbi.2000.2147","volume":"206","author":"A. Yates","year":"2000","unstructured":"Yates, A., Bergman, C., Van Hemmen, J.L., Stark, J., Callard, R.: Cytokine-mediated regulation of helper T cell populations. J. Theor. Biol.\u00a0206, 539\u2013560 (2000)","journal-title":"J. Theor. Biol."},{"key":"3_CR36","first-page":"29","volume":"3","author":"I. Zevedei-Oancea","year":"2003","unstructured":"Zevedei-Oancea, I., Schuster, S.: Topological analysis of metabolic networks based on Petri net theory. Silico Biology\u00a03, 29 (2003)","journal-title":"Silico Biology"},{"key":"3_CR37","unstructured":"INA: Integrated Net Analyzer, http:\/\/www.informatik.hu-berlin.de\/lehrstuehle\/automaten\/ina\/"},{"key":"3_CR38","unstructured":"GINsim: Gene Interaction Network simulation, http:\/\/www.esil.univ-mrs.fr\/~chaouiya\/GINsim"}],"container-title":["Lecture Notes in Computer Science","Transactions on Computational Systems Biology VII"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/11905455_3.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,11,17]],"date-time":"2020-11-17T14:56:58Z","timestamp":1605625018000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/11905455_3"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006]]},"ISBN":["9783540488378","9783540488392"],"references-count":38,"URL":"https:\/\/doi.org\/10.1007\/11905455_3","relation":{},"ISSN":["0302-9743","1611-3349"],"issn-type":[{"value":"0302-9743","type":"print"},{"value":"1611-3349","type":"electronic"}],"subject":[],"published":{"date-parts":[[2006]]}}}