Modelling Biological Networks via Tailored Random Graphs [chapter]

Anthony C. C. Coolen, Franca Fraternali, Alessia Annibale, Luis Fernandes, Jens Kleinjung
2011 Handbook of Statistical Systems Biology  
Conzelmann H and Gilles ED 2008 Dynamic pathway modeling of signal transduction networks: a domain-oriented approach. Methods Mol. Biol. 484, 559-578. Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD and Posner RG 2009 Simulation of large-scale rule-based models. Bioinformatics 25, 910-917. Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD and Posner RG 2010 RuleMonkey: software for stochastic simulation of rule-based models. BMC Bioinformatics 11, 404. Czech J, Dittrich M
more » ... Stiles JR 2009 Rapid creation, Monte Carlo simulation, and visualization of realistic 3D cell models. Methods Mol. Biol. 500, 237-287. Danos V, Feret J, Fontana W and Krivine J 2007 Scalable simulation of cellular signaling networks. Lect. Notes Comput. Sci. 4807, 139-157. Danos V, Feret J, Fontana W, Harmer R and Krivine J 2009 Rule-based modelling and model perturbation. Lect. Notes Comput. Sci. 5750, 116-137. Deininger M, Buchdunger E and Druker BJ 2005 The development of imatinib as a therapeutic agent for chronic myeloid leukemia. Blood 105, 2640-2653. Dinkel H, Chica C, Via A, Gould CM, Jensen LJ, Gibson TJ and Diella F 2011 Phopho.ELM: a database of phosphorylation sites-update 2011. Nucleic Acids Res. 39, D261-D267. Ederer M and Gilles ED 2007 Thermodynamically feasible kinetic models of reaction networks. Biophys. J. 92, 1846-1857. Ederer M and Gilles ED 2008 Thermodynamic constraints in kinetic modeling: thermodynamic-kinetic modeling in comparison to other approaches. Eng. Life Sci. 8, 467-476. Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I and Wall ME 2007 q-bio 2007: a watershed moment in modern biology. Mol. Syst. Biol. 3, 148. Endy D and Brent R 2001 Modelling cellular behaviour. Nature 409, 391-395. Faeder JR, Blinov ML, Goldstein B and Hlavacek WS 2005 Rule-based modeling of biochemical networks. Complexity 10, 22-41. Faeder JR, Blinov ML and Hlavacek WS 2009 Rule-based modeling of biochemical systems with BioNetGen.
doi:10.1002/9781119970606.ch15 fatcat:mo56h5qfkvbsrgpy2bs72nja3u