Complexity and modularity of intracellular networks: A systematic approach for modelling and simulation

IET Systems Biology

Volumn 2, Issue 5, 2008, Pages 363-368

  Blinov, M L ^a   Ruebenacker, O ^a   Moraru, I I ^a  

^a UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

FISCHER-TROPSCH SYNTHESIS; FLOW INTERACTIONS; MOLECULAR STRUCTURE; NETWORK PROTOCOLS; ONTOLOGY; PHOSPHORYLATION; SENSOR NETWORKS;

AUTOMATIC EXTRACTIONS; CHEMICAL SPECIES; COMBINATORIAL COMPLEXITIES; COMPLEX NETWORKS; INTRACELLULAR NETWORKS; KINETIC MODELS; MODEL COMPONENTS; MODEL ELEMENTS; MODELLING AND SIMULATIONS; MODULARITY; MOLECULAR SPECIES; ORDERS OF MAGNITUDES; PHOSPHORYLATION SITES; PROTEIN COMPLEXES; QUANTITATIVE MATHEMATICAL MODELS; QUANTITATIVE MODELS; REACTION NETWORKS; SEMI-AUTOMATIC; SIGNALLING MOLECULES; SIMULATING; SYSTEMATIC APPROACHES; TIME COURSES; VIRTUAL CELLS; VISUALISATION;

MATHEMATICAL MODELS;

BIOLOGICAL MODEL; COMPUTER ANALYSIS; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFERENCE PAPER; DATA BASE; INFORMATION PROCESSING; MATHEMATICAL MODEL; MOLECULAR DYNAMICS; MOLECULAR INTERACTION; PHOSPHORYLATION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; WEB BROWSER;

COMPUTER SIMULATION; GENE EXPRESSION REGULATION; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PROTEOME; SIGNAL TRANSDUCTION;

EID: 54049090016     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb:20080092     Document Type: Conference Paper

References (25)

1. Moraru, I.I., and LoSw, L.M.: 'Intracellular signaling: spatial and temporal control', Physiology, 2005, 20, p. 169-179
2. Ravasz, E., Somera, A.L., Mongru, D.A., Oltvai, Z.N., and Barabasi, A.L.: 'Hierarchical organization of modularity in metabolic networks', Science, 2002, 297, p. 1551-1555 0036-8075
3. Pawson, T., and Nash, P.: 'Assembly of cell regulatory systems through protein interaction domains', Science, 2003, 300, p. 445-452 0036-8075
4. Blinov, M.L., Faeder, J.R., Goldstein, B., and Hlavacek, W.S.: 'A network model of early events in epidermal growth factor receptor signaling that accounts for combinatorial complexity', Biosystems, 2006, 83, p. 136-151
5. Kholodenko, B.N., Demin, O.V., Moehren, G., and Hoek, J.B.: 'Quantification of short term signaling by the epidermal growth factor receptor', J. Biol. Chem., 1999, 274, (42), p. 30169-30181
6. Li, Q.J., Dinner, A.R., and Qi, S.: Et al. 'CD4 enhances T cell sensitivity to antigen by coordinating Lck accumulation at the immunological synapse', Nat. Immunol., 2004, 5, (8), p. 791-799
7. Schoeberl, B., Eichler-Jonsson, C., Gilles, E.D., and Müller, G.: 'Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors', Nat. Biotechnol., 2002, 20, (4), p. 370-375
8. Luciano, J.S.: 'PAX of mind for pathway researchers', Drug Discov. Today, 2005, 10, p. 937-942
9. Hlavacek, W.S., Faeder, J.R., Blinov, M.L., Posner, R.G., Hucka, M., and Fontana, W.: 'Rules for modeling signal-transduction systems', Sci. STKE, 2006, 344, p. re6
10. Blinov, M.L., Faeder, J.R., Goldstein, B., and Hlavacek, W.S.: 'BioNetGen: Software for rule-based modeling of signal transduction based on the interactions of molecular domains', Bioinformatics, 2004, 20, p. 3289-3291
11. Loew, L.M., aAd Schaff, J.C.: 'The virtual cell: a software environment for computational cell biology', Trends Biotechnol., 2001, 19, p. 401-406
12. Moraru, I.I., Schaff, J.C., and Loew, L.M.: 'Think simulation - think experiment: The virtual cell paradigm', Perrone, L.F., Wieland, F.P., Liu, J., Lawson, B.G., Nicol, D.M., Fujimoto, R.M., Proc. 2006 Winter Simulation Conf., p. 1713-1719
13. Hucka, M., Finney, A., and Sauro, H.M.: Et al. 'The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models', Bioinformatics, 2003, 19, p. 524-531
14. Vastrik, I.,AD'Eustachio, P., and Schmidt, E.: Et al. 'Reactome: a knowledge base of biologic pathways and processes', Genome Biol., 2007, 8, (3), p. R39
15. Le Novère, N., Bornstein, B., and Broicher, A.: Et al. 'Biomodels database: A free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems', Nucleic Acids Res., 2006, 34, (database issue), p. D689-D691
16. Laibe, C., anT Le Novere, N.: 'MIRIAM resources: tools to generate and resolve robust cross-references in systems biology', BMC Syst. Biol., 2007, 1, (1), p. 58
17. Karp, P.D., Ouzounis, C.A., and Moore-Kochlacs, C.: Et al. 'Expansion of the BioCyc collection of pathway/genome databases to 160 genomes', Nucleic Acids Res., 2005, 33, (19), p. 6083-6089
18. Ruebenacker, O., Moraru, I.I., Schaff, J.C., and Blinov, M.L.: 'Kinetic modeling using BioPAX ontology', Proc. 2007 IEEE Int. Conf. Bioinformatics and Biomedicine, 2007, p. 339-348
19. Shannon, P., Aarkiel, A., and Ozier, O.: Et al. 'Cytoscape: a software environment for integrated models of biomolecular interaction networks', Genome Res., 2003, 13, (11), p. 2498-2504
20. Faeder, J.R., Hlavacek, W.S., and Reischl, I.: Et al. 'Investigation of early events in Fc epsilon RI-mediated signaling using a detailed mathematical model', J. Immunol., 2003, 170, (7), p. 3769-3781
21. Barua, D., Faeder, J.R., and Haugh, J.M.: 'Structure-based kinetic models of modular signaling protein function: Focus on Shp2', Biophys. J., 2007, 92, (7), p. 2290-2230 0006-3495
22. Bhattacharyya, R.P., Reményi, A., Yeh, B.J., and Lim, W.A.: 'Domains, motifs, and scaffolds: The role of modular interactions in the evolution and wiring of cell signaling circuits', Annu. Rev. Biochem., 2006, 75, p. 655-680
23. Lok, L., and Brent, R.: 'Automatic generation of cellular reaction networks with moleculizer 1.0', Nat. Biotechnol., 2005, 23, (1), p. 131-136
24. Faeder, J.R., Blinov, M.L., and Hlavacek, W.S.: 'Rule-based modeling of biochemical networks', Complexity, 2005, 10, p. 22-41 10.1002/cplx.20074 1076-2787
25. Blinov, M.L., and Moraru, I.I.: 'XML encoding of features describing rule-based modeling of reaction networks with multi-component molecular complexes', Proc. 7th IEEE Int. Conf. Bioinformatics and Bioengineering, 2007, p. 987-994