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
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
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
Design principles of biochemical oscillators
Novák, B., & Tyson, J. J. (2008) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2530 · Cited by 1,137
Rate constants for the reactions of ATP- and ADP-actin with the ends of actin filaments.
Pollard, T. D. (1986) · The Journal of cell biology · doi:10.1083/jcb.103.6.2747 · Cited by 858
Rao, C. V., & Arkin, A. P. (2003) · The Journal of Chemical Physics · doi:10.1063/1.1545446 · Cited by 656
Bacterial chemoreceptors: high-performance signaling in networked arrays
Hazelbauer, G. L., Falke, J. J., & Parkinson, J. S. (2008) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2007.09.014 · Cited by 632
An Ultrasensitive Bacterial Motor Revealed by Monitoring Signaling Proteins in Single Cells
Cluzel, P., Surette, M., & Leibler, S. (2000) · Science · doi:10.1126/science.287.5458.1652 · Cited by 606
Fisher, J., & Henzinger, T. A. (2007) · Nature Biotechnology · doi:10.1038/nbt1356 · Cited by 538
Schafer, D. A., Jennings, P. B., & Cooper, J. A. (1996) · The Journal of cell biology · doi:10.1083/jcb.135.1.169 · Cited by 427
Rule-Based Modeling of Biochemical Systems with BioNetGen
Faeder, J. R., Blinov, M. L., & Hlavacek, W. S. (2009) · Methods in Molecular Biology · doi:10.1007/978-1-59745-525-1_5 · Cited by 425
Self-citation(2004) · Interdisciplinary Applied Mathematics · doi:10.1007/b97701 · Cited by 405
Chen, W. W., Schoeberl, B., Jasper, P. J., Niepel, M., Nielsen, U. B., Lauffenburger, D. A., & Sorger, P. K. (2009) · Molecular Systems Biology · doi:10.1038/msb.2008.74 · Cited by 391
Rules for Modeling Signal-Transduction Systems
Hlavacek, W. S., Faeder, J. R., Blinov, M. L., Posner, R. G., Hucka, M., & Fontana, W. (2006) · Science's STKE · doi:10.1126/stke.3442006re6 · Cited by 350
Self-citationRule-Based Modelling of Cellular Signalling
Danos, V., Feret, J., Fontana, W., Harmer, R., & Krivine, J. (2007) · Lecture Notes in Computer Science · doi:10.1007/978-3-540-74407-8_3 · Cited by 320
Cellular Stoichiometry of the Components of the Chemotaxis Signaling Complex
Li, M., & Hazelbauer, G. L. (2004) · Journal of Bacteriology · doi:10.1128/jb.186.12.3687-3694.2004 · Cited by 273
Amann, K. J., & Pollard, T. D. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.211556398 · Cited by 263
DIZZY: STOCHASTIC SIMULATION OF LARGE-SCALE GENETIC REGULATORY NETWORKS
RAMSEY, S., ORRELL, D., & BOLOURI, H. (2005) · Journal of Bioinformatics and Computational Biology · doi:10.1142/s0219720005001132 · Cited by 253
Unlimited multistability in multisite phosphorylation systems
Thomson, M., & Gunawardena, J. (2009) · Nature · doi:10.1038/nature08102 · Cited by 248
Mathematical and computational models of immune-receptor signalling
Goldstein, B., Faeder, J. R., & Hlavacek, W. S. (2004) · Nature Reviews Immunology · doi:10.1038/nri1374 · Cited by 204
Self-citationScalable Simulation of Cellular Signaling Networks
Danos, V., Feret, J., Fontana, W., & Krivine, J. (2007) · Lecture Notes in Computer Science · doi:10.1007/978-3-540-76637-7_10 · Cited by 201
S toch S im: modelling of stochastic biomolecular processes
Le Novère, N., & Shimizu, T. S. (2001) · Bioinformatics · doi:10.1093/bioinformatics/17.6.575 · Cited by 198
Chemotaxis in Escherichia coli: A Molecular Model for Robust Precise Adaptation
Hansen, C. H., Endres, R. G., & Wingreen, N. S. (2008) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0040001 · Cited by 195
Investigation of Early Events in FcεRI-Mediated Signaling Using a Detailed Mathematical Model
Faeder, J. R., Hlavacek, W. S., Reischl, I., Blinov, M. L., Metzger, H., Redondo, A., Wofsy, C., & Goldstein, B. (2003) · The Journal of Immunology · doi:10.4049/jimmunol.170.7.3769 · Cited by 165
Self-citationAutomatic generation of cellular reaction networks with Moleculizer 1.0
Lok, L., & Brent, R. (2005) · Nature Biotechnology · doi:10.1038/nbt1054 · Cited by 158
Precise adaptation in bacterial chemotaxis through “assistance neighborhoods”
Endres, R. G., & Wingreen, N. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0603101103 · Cited by 154
Mello, B. A., & Tu, Y. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506961102 · Cited by 154
Towards genome-scale signalling-network reconstructions
Hyduke, D. R., & Palsson, B. Ø. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2750 · Cited by 125
A free-energy-based stochastic simulation of the tar receptor complex 1 1Edited by I. B. Holland
Morton-Firth, C. J., Shimizu, T. S., & Bray, D. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2535 · Cited by 122
Location and architecture of the Caulobacter crescentus chemoreceptor array
Briegel, A., Ding, H. J., Li, Z., Werner, J., Gitai, Z., Dias, D. P., Jensen, R. B., & Jensen, G. J. (2008) · Molecular Microbiology · doi:10.1111/j.1365-2958.2008.06219.x · Cited by 113
Kinetic Monte Carlo method for rule-based modeling of biochemical networks
Yang, J., Monine, M. I., Faeder, J. R., & Hlavacek, W. S. (2008) · Physical Review E · doi:10.1103/physreve.78.031910 · Cited by 104
Self-citationPathway of Actin Filament Branch Formation by Arp2/3 Complex*
Beltzner, C., & Pollard, T. D. (2008) · Journal of Biological Chemistry · doi:10.1074/jbc.m705894200 · Cited by 102
Capping protein binding to actin in yeast
Kim, K., Yamashita, A., Wear, M. A., Maéda, Y., & Cooper, J. A. (2004) · The Journal of Cell Biology · doi:10.1083/jcb.200308061 · Cited by 102
An overview of the CellML API and its implementation
Miller, A. K., Marsh, J., Reeve, A. M., Garny, A., Britten, R. D., Halstead, M. D. B., Cooper, J., Nickerson, D. P., & Nielsen, P. F. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-178 · Cited by 81
Roland, J., Berro, J., Michelot, A., Blanchoin, L., & Martiel, J. (2007) · Biophysical Journal · doi:10.1529/biophysj.107.121988 · Cited by 76
Khursigara, C. M., Wu, X., & Subramaniam, S. (2008) · Journal of Bacteriology · doi:10.1128/jb.00640-08 · Cited by 74
Defining the scientific method
(2009) · Nature Methods · doi:10.1038/nmeth0409-237 · Cited by 71
Global parameter estimation methods for stochastic biochemical systems
Poovathingal, S. K., & Gunawan, R. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-414 · Cited by 66
RuleMonkey: software for stochastic simulation of rule-based models
Colvin, J. C., Monine, M. I., Gutenkunst, R. N., Hlavacek, W. S., Hoff, D. D. V., & Posner, R. G. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-404 · Cited by 57
Simulation of large-scale rule-based models
Colvin, J. C., Monine, M. I., Faeder, J. R., Hlavacek, W. S., Hoff, D. D. V., & Posner, R. G. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp066 · Cited by 57
Self-citationGoldstein, B., & Perelson, A. S. (1984) · Biophysical Journal · doi:10.1016/s0006-3495(84)84259-9 · Cited by 56
Monine, M. I., Posner, R. G., Savage, P. B., Faeder, J. R., & Hlavacek, W. S. (2010) · Biophysical Journal · doi:10.1016/j.bpj.2009.09.043 · Cited by 45
Self-citationRedefining the "Scientific Method"
Spiece, K. R., & Colosi, J. C. (2000) · The American Biology Teacher · doi:10.2307/4450823 · Cited by 22
Rejection-free kinetic Monte Carlo simulation of multivalent biomolecular interactionsPreprint
Yang, J., & Hlavacek, W. S. (2008) · arXiv (Cornell University) · doi:10.48550/arxiv.0812.4619 · Cited by 3
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
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
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
Data sources
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.
