The DOI matches its Crossref record; 51 of the 51 references it cites were found in a registry or an index.
Efficient modeling, simulation and coarse-graining of biological complexity with NFsim
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Citations
Cites
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
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
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
Computational systems biology.
Kitano, H. (2002) · Nature · doi:10.1038/nature01254 · Cited by 2,209
Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
Gibson, M. A., & Bruck, J. (2000) · The Journal of Physical Chemistry A · doi:10.1021/jp993732q · Cited by 1,643
Molecular Mechanisms Controlling Actin Filament Dynamics in Nonmuscle Cells
Pollard, T. D., Blanchoin, L., & Mullins, R. D. (2000) · Annual Review of Biophysics and Biomolecular Structure · doi:10.1146/annurev.biophys.29.1.545 · Cited by 1,514
Making sense of it all: bacterial chemotaxis
Wadhams, G. H., & Armitage, J. P. (2004) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1524 · Cited by 1,489
An Analytical Solution to the Kinetics of Breakable Filament Assembly
Knowles, T. P. J., Waudby, C. A., Devlin, G. L., Cohen, S. I. A., Aguzzi, A., Vendruscolo, M., Terentjev, E. M., Welland, M. E., & Dobson, C. M. (2009) · Science · doi:10.1126/science.1178250 · Cited by 1,139
Cited by
Efficient search, mapping, and optimization of multi-protein genetic systems in diverse bacteria
Farasat, I., Kushwaha, M., Collens, J., Easterbrook, M., Guido, M., & Salis, H. M. (2014) · Molecular Systems Biology · doi:10.15252/msb.20134955 · Cited by 235
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
Agent-based modelling in synthetic biology
Gorochowski, T. E. (2016) · Essays in Biochemistry · doi:10.1042/ebc20160037 · Cited by 86
A blueprint for human whole-cell modeling
Szigeti, B., Roth, Y. D., Sekar, J. A. P., Goldberg, A. P., Pochiraju, S. C., & Karr, J. R. (2018) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2017.10.005 · Cited by 72
Machines vs. Ensembles: Effective MAPK Signaling through Heterogeneous Sets of Protein Complexes
Suderman, R., & Deeds, E. J. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003278 · Cited by 52
BioNetFit: a fitting tool compatible with BioNetGen, NFsim and distributed computing environments
Thomas, B. R., Chylek, L. A., Colvin, J., Sirimulla, S., Clayton, A. H. A., Hlavacek, W. S., & Posner, R. G. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btv655 · Cited by 32
An Overview of Network-Based and -Free Approaches for Stochastic Simulation of Biochemical Systems
Gupta, A., & Mendes, P. (2018) · Computation · doi:10.3390/computation6010009 · Cited by 17
RKappa: Software for Analyzing Rule-Based Models
Sorokin, A., Sorokina, O., & Douglas Armstrong, J. (2019) · Methods in Molecular Biology · doi:10.1007/978-1-4939-9102-0_17 · Cited by 4
Metadata
- Authors
- Sneddon, M. W., Faeder, J. R., & Emonet, T.
- Venue
- Nature Methods
- Published
- 2010-12-26
- Volume
- 8
- Issue
- 2
- Pages
- 177-183
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- OpenAlex
- W2121490181
- Cited by
- 288
- References
- 51
- FWCI
- 7.92
- Type
- journal article
- Language
- en
- Open access
- closed
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Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
