Determination of critical network interactions: An augmented Boolean pseudo-dynamics approach

IET Systems Biology

Volumn 2, Issue 2, 2008, Pages 55-63

  Soni, A S ^a   Jenkins, J W ^a   Sundaram, S S ^a  

^a CFD RESEARCH CORPORATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ACIDS; DYNAMICS; ELECTRIC NETWORK TOPOLOGY; INFORMATION THEORY; PLANT SHUTDOWNS; PROBABILITY DENSITY FUNCTION; TOPOLOGY;

ABSCISIC ACIDS; BIOLOGICAL INTERACTIONS; CELLULAR PROPERTIES; DYNAMIC STATES; GUARD CELLS; IN PLANTS; INTEGRATED ANALYSIS; NETWORK FUNCTIONS; NETWORK HUBS; NETWORK INTERACTIONS; NETWORK RESPONSES; NETWORK THEORIES; NETWORK TOPOLOGIES; OBJECTIVE METHODS; REGULATORY NETWORKS; SIGNALLING NETWORKS; STRONG CORRELATIONS; TOPOLOGICAL ANALYSES;

FLOW INTERACTIONS;

ALGORITHM; ARTICLE; BOOLEAN PSEUDO DYNAMICS; CELL ACTIVITY; CELL INTERACTION; GENETIC REGULATION; HIGH THROUGHPUT SCREENING; MOLECULAR DYNAMICS; NETWORK LEARNING; NONHUMAN; PHENOTYPE; PLANT CELL; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY; ARTIFICIAL NEURAL NETWORK; BIOLOGICAL MODEL; COMPUTER SIMULATION; METABOLISM; METHODOLOGY; PHYSIOLOGY; PLANT PHYSIOLOGY; PLANT STOMA; PROTEIN ANALYSIS; SYSTEMS THEORY;

ABSCISIC ACID;

ABSCISIC ACID; ALGORITHMS; COMPUTER SIMULATION; MODELS, BIOLOGICAL; NEURAL NETWORKS (COMPUTER); PLANT PHYSIOLOGY; PLANT STOMATA; PROTEIN INTERACTION MAPPING; SIGNAL TRANSDUCTION; SYSTEMS THEORY;

EID: 47649083545     PISSN: 17518849     EISSN: None     Source Type: Journal    
DOI: 10.1049/iet-syb:20070025     Document Type: Article

References (30)

1. Arnone, M.I., and Davidson, E.H.: 'The hardwiring of development: organization and function of genomic regulatory systems', Development, 1997, 124, (10), p. 1851-1864
2. Gabor Miklos, G.L., and Rubin, G.M.: 'The role of the genome project in determining gene function insights from model organisms', Cell, 1996, 86, (4), p. 4521-4529
3. Varner, J., and Ramkrishna, D.: 'Mathematical models of metabolic pathways', Curr. Opin. Biotechnol., 1999, 10, p. 146-150
4. Bailey, J.E.: 'Complex biology with no parameters', Nat. Biotechnol., 2001, 19, (6), p. 503-504
5. Ajay, S., and Bhalla, U.: 'Synaptic plasticity in vitro and in silico: insights into an intracellular signaling maze', Physiology, 2006, 21, p. 289-296
6. Gunawan, R., and Doyle, F.: 'Phase sensitivity analysis of circadian rhythm entrainment', J. Biol. Rhythms, 2007, 22, (2), p. 180-194 10.1177/ 0748730407299194 0748-7304
7. Kemp, M., Wille, L., Lewis, C., Nicholson, L., and Lauffenburger, D.: 'Quantitative network signal combinations downstream of TCR activation can predict IL-2 production response', J. Immunol., 2007, 178, (8), p. 4984-4992
8. Von Dassow, G., Meir, E., Munro, E., and Odell, G.: 'The segment polarity network is a robust developmental module', Nature, 2000, 406, (6792), p. 131-132 0028-0836
9. Fallon, E., and Lauffenburger, D.: 'Computational model for effects of ligand/receptor binding properties on interleukin-2 trafficking dynamics and T cell proliferation response', Biotechnol. Prog., 2000, 16, (5), p. 905-916
10. Abouhamad, W., Bray, D., Schuster, M., Boesch, K., Silversmith, R., and Bourret, R.: 'Computer-aided resolution of an experimental paradox in bacterial chemotaxis', J. Bacteriol., 1998, 180, (15), p. 3757-3764
11. Endy, D., You, L., Yin, J., and Molineux, I.: 'Computation, prediction, and experimental tests of fitness for bacteriophage T7 mutants with permuted genomes', Proc. Natl. Acad. Sci. USA, 2000, 97, p. 5375-5380 0027-8424
12. Gadkar, K., Varner, J., and Doyle, F.: 'Model identification of signal transduction networks from data using a state regulator problem', IEE Proc. Syst. Biol., 2005, 2, (1), p. 17-30 10.1049/sb:20045029
13. Yao, K., Shaw, B., Kou, B., Mcauley, K., and Bacon, D.: 'Modeling ethylene/butene copolymerization with multi-site catalysts: Parameter estimability and experimental design', Polym. React. Eng., 2003, 11, p. 563-588 1054-3414
14. Thomas, R.: 'Boolean formalization of genetic control circuits', J. Theor. Biol., 1973, 42, (3), p. 563-585
15. Chaves, M., Albert, R., and Sontag, E.D.: 'Robustness and fragility of Boolean models for genetic regulatory networks', J. Theor. Biol., 2005, 235, p. 431-449
16. Albert, R., and Othmer, H.G.: 'The topology of the regulatory interactions predicts the expression pattern of the Drosophila segment polarity genes', J. Theor. Biol., 2003, 223, p. 1-18
17. Kauffman, S.: 'The origins of order', (Oxford University Press, New York 1993)
18. Kauffman, S., Peterson, C., Samuelson, B., and Troein, C.: 'Random Boolean network models and the yeast transcription network', Proc. Natl. Acad. Sci. USA, 2003, 100, (25), p. 14796-14799 0027-8424
19. Albert, R.: 'Scale-free networks in cell biology', J. Cell Sci., 2005, 118, p. 4947-4957
20. Li, S., Assmann, S., and Albert, R.: 'Predicting essential components of signal transduction networks: A dynamic model of guard cell abscisic acid signaling', PLoS Biology, 2006, 4, p. e312
21. Lahdesmaki, H., Hautaniemi, S., Shmulevich, I., and Yli-Harja, O.: 'Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks', Signal Process., 2006, 86, p. 814-834 10.1016/j.sigpro.2005.06.008 0165-1684
22. Shmulevich, I., Gluhovsky, I., Hashimoto, R.F., Dougherty, E.R., and Zhang, W.: 'Steady-state analysis of genetic regulatory networks modeled by probabilistic Boolean networks', Comp. Funct. Genomics, 2003, 4, (6), p. 601-608
23. Mason, O., and Verwoerd, M.: 'Graph theory and networks in biology', IET Syst. Biol., 2007, 1, (2), p. 89-119 10.1049/iet-syb:20060038
24. Klamt, S., Rodriguez, J., Lindqist, J., Simeoni, L., and Gilles, E.D.: 'A methodology for structural and regulatory analysis of signaling networks' BMC Bioinformatics, 2006, 7, (56)
25. Stelling, J., Klamt, S., Bettenbrock, K., Schuster, S., and Gilles, E.D.: 'Metabolic network structure determines key aspects of functionality and regulation', Nature, 2002, 420, p. 190-193 0028-0836
26. Cakir, T., Kirdar, B., and Ulgen, K.: 'Metabolic pathway analysis of yeast strengthens the bridge between transcriptomics and metabolic networks', Biotechnol. Bioeng., 2004, 86, (3), p. 251-260
27. Kauffman, S.A.: 'GeneAregulation networks: a theory for their global structure and behavior' Curr. Topics Dev. Biol., 1971, 6, p. 145-182
28. Mehra, S., Hu, W., and Karypis, G.: 'A Boolean algorithm for reconstructing the structure of regulatory networks' Metab. Eng., 2004, 6, p. 326-329
29. Chaves, M., Albert, R., and Sontag, E.D.: 'Methods of robustness analysis for Boolean models of gene control networks' IEE Proc. Syst. Biol., 2006, 153, p. 154-167 10.1049/ip-syb:20050079
30. Gupta, S., Bishta, S., Kukretia, R., Jain, S., and Brahmacharia, S.: 'Boolean network analysis of a neurotransmitter signaling pathway' J. Theor. Biol., 2007, 244, p. 463-469