The DOI matches its Crossref record; 56 of the 56 references it cites were found in a registry or an index.
Rule-Based Modeling of Biochemical Systems with BioNetGen
Abstract
Rule-based modeling involves the representation of molecules as structured objects and molecular interactions as rules for transforming the attributes of these objects. The approach is notable in that it allows one to systematically incorporate site-specific details about protein-protein interactions into a model for the dynamics of a signal-transduction system, but the method has other applications as well, such as following the fates of individual carbon atoms in metabolic reactions. The consequences of protein-protein interactions are difficult to specify and track with a conventional modeling approach because of the large number of protein phosphoforms and protein complexes that these interactions potentially generate. Here, we focus on how a rule-based model is specified in the BioNetGen language (BNGL) and how a model specification is analyzed using the BioNetGen software tool. We also discuss new developments in rule-based modeling that should enable the construction and analyses of comprehensive models for signal transduction pathways and similarly large-scale models for other biochemical systems.
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Cites
Exact stochastic simulation of coupled chemical reactions
Gillespie, D. T. (1977) · The Journal of Physical Chemistry · doi:10.1021/j100540a008 · Cited by 10,136
Massagué, J. (1998) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.67.1.753 · Cited by 7,556
Gillespie, D. T. (1976) · Journal of Computational Physics · doi:10.1016/0021-9991(76)90041-3 · Cited by 6,029
Cellular Motility Driven by Assembly and Disassembly of Actin Filaments
Pollard, T. D., & Borisy, G. G. (2003) · Cell · doi:10.1016/s0092-8674(03)00120-x · Cited by 4,195
Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks
Olsen, J. V., Blagoev, B., Gnad, F., Macek, B., Kumar, C., Mortensen, P., & Mann, M. (2006) · Cell · doi:10.1016/j.cell.2006.09.026 · Cited by 3,499
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060
COPASI—a COmplex PAthway SImulator
Hoops, S., Sahle, S., Gauges, R., Lee, C., Pahle, J., Simus, N., Singhal, M., Xu, L., Mendes, P., & Kummer, U. (2006) · Bioinformatics · doi:10.1093/bioinformatics/btl485 · Cited by 2,618
Hunter, T. (2000) · Cell · doi:10.1016/s0092-8674(00)81688-8 · Cited by 2,586
SUNDIALS: Suite of nonlinear and differential/algebraic equation solvers
Hindmarsh, A. C., Brown, P. N., Grant, K. E., Lee, S. L., Serban, R., Shumaker, D. E., & Woodward, C. S. (2005) · ACM Transactions on Mathematical Software · doi:10.1145/1089014.1089020 · Cited by 2,556
An Algorithm for Subgraph Isomorphism
Ullmann, J. R. (1976) · Journal of the ACM · doi:10.1145/321921.321925 · Cited by 2,277
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Sneddon, M. W., Faeder, J. R., & Emonet, T. (2011) · Nature Methods · doi:10.1038/nmeth.1546 · Cited by 288
Self-citationClassic and contemporary approaches to modeling biochemical reactions
Chen, W. W., Niepel, M., & Sorger, P. K. (2010) · Genes & Development · doi:10.1101/gad.1945410 · Cited by 286
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Keating, S. M., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199110 · Cited by 285
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Artyomov, M. N., Lis, M., Devadas, S., Davis, M. M., & Chakraborty, A. K. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1010568107 · Cited by 207
The Kappa platform for rule-based modeling
Boutillier, P., Maasha, M., Li, X., Medina-Abarca, H. F., Krivine, J., Feret, J., Cristescu, I., Forbes, A. G., & Fontana, W. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty272 · Cited by 107
Metadata
- Authors
- Faeder, J. R., Blinov, M. L., & Hlavacek, W. S.
- Venue
- Methods in Molecular Biology
- Publisher
- Humana Press
- Published
- 2009
- Volume
- 500
- Pages
- 113-167
- ISSN
- 1064-3745 (ISSN-L)
- 1940-6029
- OpenAlex
- W2175715045
- Cited by
- 425
- References
- 56
- FWCI
- 35.83
- Type
- book chapter
- Language
- en
- Open access
- closed
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