{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T05:32:01Z","timestamp":1740634321556,"version":"3.38.0"},"publisher-location":"London","reference-count":42,"publisher":"Springer London","isbn-type":[{"type":"print","value":"9781849964739"},{"type":"electronic","value":"9781849964746"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2011]]},"DOI":"10.1007\/978-1-84996-474-6_6","type":"book-chapter","created":{"date-parts":[[2010,10,21]],"date-time":"2010-10-21T07:58:41Z","timestamp":1287647921000},"page":"101-120","source":"Crossref","is-referenced-by-count":1,"title":["Hybrid Functional Petri Net with Extension for\u00a0Dynamic Pathway Modeling"],"prefix":"10.1007","author":[{"given":"Ayumu","family":"Saito","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Masao","family":"Nagasaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroshi","family":"Matsuno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Satoru","family":"Miyano","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","reference":[{"key":"6_CR10","first-page":"159","volume":"8","author":"H. Alla","year":"1998","unstructured":"Alla, H., David, R.: Continuous and hybrid Petri nets. JCSC 8, 159\u2013188 (1998)","journal-title":"JCSC"},{"key":"6_CR59","unstructured":"Cell Illustrator Online 4.0: http:\/\/cionline.hgc.jp\/"},{"key":"6_CR61","unstructured":"Cell System Markup Language: http:\/\/www.csml.org\/"},{"key":"6_CR62","doi-asserted-by":"publisher","first-page":"785","DOI":"10.1038\/nature02752","volume":"430","author":"S. Chang","year":"2004","unstructured":"Chang, S., Johnston, R.J.Jr., Frokjaer-Jensen, C., Lockery, S., Hobert, O.: MicroRNAs act sequentially and asymmetrically to control chemosensory laterality in the nematode. Nature 430, 785\u2013789 (2004)","journal-title":"Nature"},{"issue":"3","key":"6_CR94","first-page":"185","volume":"2","author":"A. Doi","year":"2003","unstructured":"Doi, A., Nagasaki, M., Fujita, S., Matsuno, H., Miyano, S.: Abstract Genomic Object Net: II. Modelling biopathways by hybrid functional Petri net with extension. Appl. Bioinform. 2(3), 185\u2013188 (2003)","journal-title":"Appl. Bioinform."},{"issue":"3","key":"6_CR95","doi-asserted-by":"crossref","first-page":"271","DOI":"10.3233\/ISB-00133","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. In Silico Biol. 4(3), 271\u2013291 (2004)","journal-title":"In Silico Biol."},{"issue":"1\u20132","key":"6_CR96","doi-asserted-by":"crossref","first-page":"1","DOI":"10.3233\/ISB-00216","volume":"6","author":"A. Doi","year":"2006","unstructured":"Doi, A., Nagasaki, M., Matsuno, H., Miyano, S.: Simulation based validation of the p53 transcriptional activity with hybrid functional Petri net. In Silico Biol. 6(1\u20132), 1\u201313 (2006)","journal-title":"In Silico Biol."},{"issue":"1","key":"6_CR97","first-page":"112","volume":"17","author":"A. Doi","year":"2006","unstructured":"Doi, A., Nagasaki, M., Ueno, K., Matsuno, H., Miyano, S.: A combined pathway to simulate CDK-dependent phosphorylation and ARF-dependent stabilization for p53 transcriptional activity. Genome Inform. 17(1), 112\u2013123 (2006)","journal-title":"Genome Inform."},{"key":"6_CR99","first-page":"437","volume-title":"Proc. 3rd International Conference on Automation of Mixed Processes: Hybrid Dynamical Systems (ADPM)","author":"R. Drath","year":"1998","unstructured":"Drath, R.: Hybrid object nets: an object oriented concept for modeling complex hybrid systems. In: Proc. 3rd International Conference on Automation of Mixed Processes: Hybrid Dynamical Systems (ADPM), pp. 437\u2013442. Shaker Verlag, Aachen (1998)"},{"issue":"12","key":"6_CR140","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. 95(12), 6750\u20136755 (1998)","journal-title":"Proc. Natl. Acad. Sci. USA."},{"issue":"2","key":"6_CR147","doi-asserted-by":"publisher","first-page":"189","DOI":"10.1016\/j.biosystems.2008.02.005","volume":"92","author":"S. Grunwald","year":"2008","unstructured":"Grunwald, S., Speer, A., Ackermann, J., Koch, I.: Petri net modelling of gene regulation of the Duchenne muscular dystrophy. Biosystems 92(2), 189\u2013205 (2008)","journal-title":"Biosystems"},{"issue":"2","key":"6_CR162","first-page":"113","volume":"16","author":"R. Hofest\u00e4dt","year":"1994","unstructured":"Hofest\u00e4dt, R.: A petri net application to model metabolic processes. Syst. Anal. Mod. Simul. 16(2), 113\u2013122 (1994)","journal-title":"Syst. Anal. Mod. Simul."},{"key":"6_CR163","doi-asserted-by":"crossref","first-page":"39","DOI":"10.3233\/ISB-00006","volume":"1","author":"R. Hofest\u00e4dt","year":"1998","unstructured":"Hofest\u00e4dt, R., Thelen, S.: Quantitative modeling of biochemical networks. In Silico Biol. 1, 39\u201353 (1998)","journal-title":"In Silico Biol."},{"issue":"6","key":"6_CR171","doi-asserted-by":"crossref","first-page":"623","DOI":"10.3233\/ISI-2007-00335","volume":"7","author":"E. Jeong","year":"2007","unstructured":"Jeong, E., Nagasaki, M., Saito, A., Miyano, S.: Cell system ontology: representation for modeling, visualizing, and simulating biological pathways. In Silico Biol. 7(6), 623\u2013638 (2007)","journal-title":"In Silico Biol."},{"key":"6_CR172","doi-asserted-by":"publisher","first-page":"845","DOI":"10.1038\/nature02255","volume":"426","author":"R.J.Jr. Johnston","year":"2003","unstructured":"Johnston, R.J.Jr., Hobert, O.: A microRNA controlling left\/right neuronal asymmetry in Caenorhabditis elegans. Nature 426, 845\u2013849 (2003)","journal-title":"Nature"},{"issue":"24","key":"6_CR173","doi-asserted-by":"publisher","first-page":"5451","DOI":"10.1242\/dev.02163","volume":"132","author":"R.J.Jr. Johnston","year":"2005","unstructured":"Johnston, R.J.Jr., Hobert, O.: A novel C. elegans zinc finger transcription factor, lsy-2, required for the cell type-specific expression of the lsy-6 microRNA. Development 132(24), 5451\u20135460 (2005)","journal-title":"Development"},{"issue":"35","key":"6_CR174","doi-asserted-by":"publisher","first-page":"12449","DOI":"10.1073\/pnas.0505530102","volume":"102","author":"R.J.Jr. Johnston","year":"2005","unstructured":"Johnston, R.J.Jr., Chang, S., Etchberger, J.F., Ortiz, C.O., Hobert, O.: MicroRNAs acting in a double-negative feedback loop to control a neuronal cell fate decision. Proc. Natl. Acad. Sci. USA 102(35), 12449\u201312454 (2005)","journal-title":"Proc. Natl. Acad. Sci. USA"},{"issue":"2","key":"6_CR210","first-page":"129","volume":"5","author":"I. Koch","year":"2005","unstructured":"Koch, I., Sch\u00fcler, M., Heiner, M.: STEPP\u2014search tool for exploration of Petri net paths: a new tool for Petri net-based path analysis in biochemical networks. In Silico Biol. 5(2), 129\u2013137 (2005)","journal-title":"In Silico Biol."},{"issue":"7","key":"6_CR211","doi-asserted-by":"publisher","first-page":"1219","DOI":"10.1093\/bioinformatics\/bti145","volume":"21","author":"I. Koch","year":"2005","unstructured":"Koch, I., Junker, B.H., Heiner, M.: Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber. Bioinformatics 21(7), 1219\u20131226 (2005)","journal-title":"Bioinformatics"},{"key":"6_CR215","doi-asserted-by":"publisher","first-page":"D546","DOI":"10.1093\/nar\/gkj107","volume":"34","author":"M. Krull","year":"2006","unstructured":"Krull, M., Pistor, S., Voss, N., Kel, A., Reuter, I., Kronenberg, D., Michael, H., Schwarzer, K., Potapov, A., Choi, C., Kel-Margoulis, O., Wingender, E.: TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations. Nucleic Acids Res. 34, D546\u2013D551 (2006)","journal-title":"Nucleic Acids Res."},{"issue":"5","key":"6_CR230","doi-asserted-by":"publisher","first-page":"1119","DOI":"10.1142\/S021972000600234X","volume":"4","author":"C. Li","year":"2006","unstructured":"Li, C., Suzuki, S., Ge, Q.-W., Nakata, M., Matsuno, H., Miyano, S.: Structural modeling and analysis of signaling pathways based on Petri nets. J. Bioinf. Comput. Biol. 4(5), 1119\u20131140 (2006)","journal-title":"J. Bioinf. Comput. Biol."},{"key":"6_CR231","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1186\/1752-0509-3-42","volume":"3","author":"C. Li","year":"2009","unstructured":"Li, C., Nagasaki, M., Ueno, K., Miyano, S.: Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension. BMC Syst. Biol. 3, 42 (2009)","journal-title":"BMC Syst. Biol."},{"key":"6_CR248","first-page":"341","volume":"5","author":"H. Matsuno","year":"2000","unstructured":"Matsuno, H., Doi, A., Nagasaki, M., Miyano, S.: Hybrid Petri net representation of gene regulatory network. Proc. Pac. Symp. Biocomput. 5, 341\u2013352 (2000)","journal-title":"Proc. Pac. Symp. Biocomput."},{"key":"6_CR250","first-page":"152","volume":"8","author":"H. Matsuno","year":"2003","unstructured":"Matsuno, H., Murakami, R., Yamane, R., Yamasaki, N., Fujita, S., Yoshimori, H., Miyano, S.: Boundary formation by notch signaling in Drosophila multicellular systems: experimental observations and gene network modeling by Genomic Object Net. Pac. Symp. Biocomput. 8, 152\u2013163 (2003)","journal-title":"Pac. Symp. Biocomput."},{"issue":"3","key":"6_CR251","first-page":"389","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. In Silico Biol. 3(3), 389\u2013404 (2003)","journal-title":"In Silico Biol."},{"issue":"1","key":"6_CR255","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1142\/S021972000600176X","volume":"4","author":"H. Matsuno","year":"2006","unstructured":"Matsuno, H., Inouye, S.-I.T., Okitsu, Y., Fujii, Y., Miyano, S.: A new regulatory interaction suggested by simulations for circadian genetic control mechanism in mammals. J. Bioinf. Comput. Biol. 4(1), 139\u2013153 (2006)","journal-title":"J. Bioinf. Comput. Biol."},{"key":"6_CR266","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1142\/9781848163324_0018","volume":"21","author":"N. Mito","year":"2008","unstructured":"Mito, N., Ikegami, Y., Matsuno, H., Miyano, S., Inouye, S.: Simulation analysis for the effect of light-dark cycle on the entrainment in circadian rhythm. Genome Inform. 21, 212\u2013223 (2008)","journal-title":"Genome Inform."},{"issue":"3","key":"6_CR274","first-page":"181","volume":"2","author":"M. Nagasaki","year":"2003","unstructured":"Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Genomic object net: I, a platform for modeling and simulating biopathways. Appl. Bioinform. 2(3), 181\u2013184 (2003)","journal-title":"Appl. Bioinform."},{"issue":"1","key":"6_CR275","first-page":"180","volume":"15","author":"M. Nagasaki","year":"2004","unstructured":"Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: A versatile Petri net based architecture for modeling and simulation of complex biological processes. Genome Inform. 15(1), 180\u2013197 (2004)","journal-title":"Genome Inform."},{"key":"6_CR277","doi-asserted-by":"publisher","first-page":"179","DOI":"10.1007\/3-540-26888-X_7","volume-title":"Bioinformatics Technologies","author":"M. Nagasaki","year":"2005","unstructured":"Nagasaki, M., Doi, A., Matsuno, H., Miyano, S.: Computational modeling of biological processes with Petri net based architecture. In: Chen, Y.P. (ed.) Bioinformatics Technologies, pp. 179\u2013243. Springer, Berlin (2005)"},{"issue":"1","key":"6_CR278","first-page":"46","volume":"17","author":"M. Nagasaki","year":"2006","unstructured":"Nagasaki, M., Yamaguchi, R., Yoshida, R., Imoto, S., Doi, A., Tamada, Y., Matsuno, H., Miyano, S., Higuchi, T.: Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data. Genome Inform. 17(1), 46\u201361 (2006)","journal-title":"Genome Inform."},{"key":"6_CR279","doi-asserted-by":"publisher","first-page":"53","DOI":"10.1186\/1752-0509-2-53","volume":"2","author":"M. Nagasaki","year":"2008","unstructured":"Nagasaki, M., Saito, A., Li, C., Jeong, E., Miyano, S.: Systematic reconstruction of TRANSPATH data into Cell System Markup Language. BMC Syst. Biol. 2, 53 (2008)","journal-title":"BMC Syst. Biol."},{"key":"6_CR280","doi-asserted-by":"publisher","DOI":"10.1007\/978-1-84882-023-4","volume-title":"Foundations of Systems Biology\u2014Using Cell Illustrator and Pathway Databases","author":"M. Nagasaki","year":"2009","unstructured":"Nagasaki, M., Saito, A., Doi, A., Matsuno, H., Miyano, S.: Foundations of Systems Biology\u2014Using Cell Illustrator and Pathway Databases. Springer, Berlin (2009)"},{"key":"6_CR281","first-page":"227","volume":"14","author":"K. Nakamura","year":"2009","unstructured":"Nakamura, K., Yoshida, R., Nagasaki, M., Miyano, S., Higuchi, T.: Parameter estimation of in silico biological pathways with particle filtering towards a petascale computing. Pac. Symp. Biocomput. 14, 227\u2013238 (2009)","journal-title":"Pac. Symp. Biocomput."},{"key":"6_CR314","first-page":"328","volume-title":"Proc. Int. Conf. Intell. Syst. Mol. Biol.","author":"V.N. Reddy","year":"1993","unstructured":"Reddy, V.N., Mavrovouniotis, M.L., Liebman, M.N.: Petri net representation in metabolic pathways. In: Proc. Int. Conf. Intell. Syst. Mol. Biol., vol. 1, pp. 328\u2013336. MIT Press, Cambridge (1993)"},{"key":"6_CR319","series-title":"LNCS","volume-title":"Lectures on Petri Nets I: Basic Models","year":"1998","unstructured":"Reisig, W., Rozenberg, G. (eds.): Lectures on Petri Nets I: Basic Models. LNCS, vol.\u00a01491. Springer, Berlin (1998)"},{"issue":"1","key":"6_CR331","first-page":"100","volume":"17","author":"A. Saito","year":"2006","unstructured":"Saito, A., Nagasaki, M., Doi, A., Ueno, K., Miyano, S.: Cell fate simulation model of gustatory neurons with microRNAs double-negative feedback loops by hybrid functional Petri net with extension. Genome Inform. 17(1), 100\u2013111 (2006)","journal-title":"Genome Inform."},{"key":"6_CR338","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1186\/1752-0509-3-23","volume":"3","author":"Y. Sato","year":"2009","unstructured":"Sato, Y., Hashiguchi, Y., Nishida, M.: Evolution of multiple phosphodiesterase isoforms in stickleback involved in cAMP signal transduction pathway. BMC Syst. Biol. 3, 23 (2009)","journal-title":"BMC Syst. Biol."},{"issue":"2","key":"6_CR386","first-page":"226","volume":"17","author":"S. Tasaki","year":"2006","unstructured":"Tasaki, S., Nagasaki, M., Oyama, M., Hata, H., Ueno, K., Yoshida, R., Higuchi, T., Sugano,\u00a0S., Miyano, S.: Modeling and estimation of dynamic EGFR pathway by data assimilation approach using time series proteomic data. Genome Inform. 17(2), 226\u2013238 (2006)","journal-title":"Genome Inform."},{"key":"6_CR398","first-page":"427","volume":"11","author":"S. Troncale","year":"2006","unstructured":"Troncale, S., Tahi, F., Campard, D., Vannier, J.-P., Guespin, J.: Modeling and simulation with hybrid functional Petri nets of the role of interleukin-6 in human early haematopoiesis. Pac. Symp. Biocomput. 11, 427\u2013438 (2006)","journal-title":"Pac. Symp. Biocomput."},{"key":"6_CR407","first-page":"367","volume":"3","author":"K. Voss","year":"2003","unstructured":"Voss, K., Heiner, M., Koch, I.: Steady state analysis of metabolic pathways using Petri nets. In Silico Biol. 3, 367\u2013387 (2003)","journal-title":"In Silico Biol."},{"key":"6_CR418","unstructured":"WormBase: http:\/\/www.wormbase.org\/db\/gene\/variation?name=pas40332;class=Variation"}],"container-title":["Computational Biology","Modeling in Systems Biology"],"original-title":[],"link":[{"URL":"http:\/\/link.springer.com\/content\/pdf\/10.1007\/978-1-84996-474-6_6","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,27]],"date-time":"2025-02-27T00:32:21Z","timestamp":1740616341000},"score":1,"resource":{"primary":{"URL":"http:\/\/link.springer.com\/10.1007\/978-1-84996-474-6_6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2011]]},"ISBN":["9781849964739","9781849964746"],"references-count":42,"URL":"https:\/\/doi.org\/10.1007\/978-1-84996-474-6_6","relation":{},"ISSN":["1568-2684"],"issn-type":[{"type":"print","value":"1568-2684"}],"subject":[],"published":{"date-parts":[[2011]]}}}