{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,16]],"date-time":"2026-02-16T18:20:45Z","timestamp":1771266045225,"version":"3.50.1"},"reference-count":17,"publisher":"Oxford University Press (OUP)","issue":"2","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2008,1,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation.<\/jats:p>\n               <jats:p>Results: This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca2+\/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.<\/jats:p>\n               <jats:p>Contact: \u00a0simon.hardy@polymtl.ca<\/jats:p>\n               <jats:p>Supplementary information: Complete data of the Petri net model of the CaMKII regulation pathway available at http:\/\/www.polymtl.ca\/rgl\/Downloads.php<\/jats:p>","DOI":"10.1093\/bioinformatics\/btm560","type":"journal-article","created":{"date-parts":[[2007,11,23]],"date-time":"2007-11-23T01:33:56Z","timestamp":1195781636000},"page":"209-217","source":"Crossref","is-referenced-by-count":32,"title":["Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways"],"prefix":"10.1093","volume":"24","author":[{"given":"Simon","family":"Hardy","sequence":"first","affiliation":[{"name":"Department of Computer Engineering, \u00c9cole Polytechnique de Montr\u00e9al, P.O. Box 6079, Station Centre-Ville, Montr\u00e9al, H3C 3A7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pierre N.","family":"Robillard","sequence":"additional","affiliation":[{"name":"Department of Computer Engineering, \u00c9cole Polytechnique de Montr\u00e9al, P.O. Box 6079, Station Centre-Ville, Montr\u00e9al, H3C 3A7, Canada"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2007,11,22]]},"reference":[{"key":"2023020209481840400_B1","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1126\/science.283.5400.381","article-title":"Emergent properties of networks of biological signaling pathways","volume":"283","author":"Bhalla","year":"1999","journal-title":"Science"},{"key":"2023020209481840400_B2","doi-asserted-by":"crossref","first-page":"1940","DOI":"10.1126\/science.280.5371.1940","article-title":"Gating of CaMKII by cAMP-regulated protein phosphatase activity during LTP","volume":"280","author":"Blitzer","year":"1998","journal-title":"Science"},{"key":"2023020209481840400_B3","doi-asserted-by":"crossref","first-page":"661","DOI":"10.1016\/j.tcb.2004.10.007","article-title":"Computational approaches for modeling regulatory cellular networks","volume":"14","author":"Eungdamrong","year":"2004","journal-title":"Trends Cell Biol."},{"key":"2023020209481840400_B4","doi-asserted-by":"crossref","first-page":"6750","DOI":"10.1073\/pnas.95.12.6750","article-title":"Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets","volume":"95","author":"Goss","year":"1998","journal-title":"Proc. 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