References

Begitt, Andreas, Thomas Meyer, Mathias van Rossum, and Uwe Vinkemeier. 2000. “Nucleocytoplasmic Translocation of Stat1 Is Regulated by a Leucine-Rich Export Signal in the Coiled-Coil Domain.” Proceedings of the National Academy of Sciences of the USA 97 (19): 10418–23. https://doi.org/10.1073/pnas.190318397.

Blinov, Michael L., James R. Faeder, Byron Goldstein, and William S. Hlavacek. 2004. “BioNetGen: Software for Rule-Based Modeling of Signal Transduction Based on the Interactions of Molecular Domains.” Bioinformatics 20 (17): 3289–91. https://doi.org/10.1093/bioinformatics/bth378.

Borghans, J. A. M., R. J. de Boer, and L. A. Segel. 1996. “Extending the Quasi-Steady State Approximation by Changing Variables.” Bulletin of Mathematical Biology 58 (1): 43–63. https://doi.org/10.1007/BF02458281.

Bouhaddou, Mehdi, Anne Marie Barrette, Alan D. Stern, et al. 2018. “A Mechanistic Pan-Cancer Pathway Model Informed by Multi-Omics Data Interprets Stochastic Cell Fate Responses to Drugs and Mitogens.” PLoS Computational Biology 14 (3): e1005985. https://doi.org/10.1371/journal.pcbi.1005985.

Chylek, Lily A., Vyacheslav Akimov, Jörn Dengjel, et al. 2014. “Phosphorylation Site Dynamics of Early T-Cell Receptor Signaling.” PLoS ONE 9 (8): e104240. https://doi.org/10.1371/journal.pone.0104240.

Colvin, Joshua, Michael I. Monine, Ryan N. Gutenkunst, William S. Hlavacek, Daniel D. Von Hoff, and Richard G. Posner. 2010. “RuleMonkey: Software for Stochastic Simulation of Rule-Based Models.” BMC Bioinformatics 11: 404. https://doi.org/10.1186/1471-2105-11-404.

Creamer, Matthew S., Edward C. Stites, Meraj Aziz, et al. 2012. “Specification, Annotation, Visualization and Simulation of a Large Rule-Based Model for ERBB Receptor Signaling.” BMC Systems Biology 6: 107. https://doi.org/10.1186/1752-0509-6-107.

Danos, Vincent, Jérôme Feret, Walter Fontana, Russell Harmer, and Jean Krivine. 2007. “Rule-Based Modelling of Cellular Signalling.” CONCUR 2007 – Concurrency Theory, Lecture notes in computer science, 17–41. https://doi.org/10.1007/978-3-540-74407-8_3.

Danos, Vincent, Jérôme Feret, Walter Fontana, and Jean Krivine. 2007. “Scalable Simulation of Cellular Signaling Networks.” Programming Languages and Systems (APLAS 2007), Lecture notes in computer science, 139–57. https://doi.org/10.1007/978-3-540-76637-7_10.

Elowitz, Michael B., Arnold J. Levine, Eric D. Siggia, and Peter S. Swain. 2002. “Stochastic Gene Expression in a Single Cell.” Science 297 (5584): 1183–86. https://doi.org/10.1126/science.1070919.

Faeder, James R., Michael L. Blinov, and William S. Hlavacek. 2009. “Rule-Based Modeling of Biochemical Systems with BioNetGen.” Methods in Molecular Biology 500: 113–67. https://doi.org/10.1007/978-1-59745-525-1_5.

Feret, Jérôme, Vincent Danos, Jean Krivine, Russ Harmer, and Walter Fontana. 2009. “Internal Coarse-Graining of Molecular Systems.” Proceedings of the National Academy of Sciences of the United States of America 106 (16): 6453–58. https://doi.org/10.1073/pnas.0809908106.

Ferrell, James E., and Eric M. Machleder. 1998. “The Biochemical Basis of an All-or-None Cell Fate Switch in Xenopus Oocytes.” Science 280 (5365): 895–98. https://doi.org/10.1126/science.280.5365.895.

Garcia, Guadalupe C., Kavya Gupta, Thomas M. Bartol, Terrence J. Sejnowski, and Padmini Rangamani. 2023. “Mitochondrial Morphology Governs ATP Production Rate.” Journal of General Physiology 155 (9): e202213263. https://doi.org/10.1085/jgp.202213263.

Gillespie, Daniel T. 2007. “Stochastic Simulation of Chemical Kinetics.” Annual Review of Physical Chemistry 58: 35–55. https://doi.org/10.1146/annurev.physchem.58.032806.104637.

Goldstein, Byron, and Alan S. Perelson. 1984. “Equilibrium Theory for the Clustering of Bivalent Cell Surface Receptors by Trivalent Ligands. Application to Histamine Release from Basophils.” Biophysical Journal 45 (6): 1109–23. https://doi.org/10.1016/S0006-3495(84)84259-9.

Harris, Leonard A., Justin S. Hogg, and James R. Faeder. 2009. “Compartmental Rule-Based Modeling of Biochemical Systems.” Proceedings of the 2009 Winter Simulation Conference, 908–19. https://doi.org/10.1109/WSC.2009.5429719.

Harris, Leonard A., Justin S. Hogg, José-Juan Tapia, et al. 2016. “BioNetGen 2.2: Advances in Rule-Based Modeling.” Bioinformatics 32 (21): 3366–68. https://doi.org/10.1093/bioinformatics/btw469.

Heinrich, Reinhart, and Tom A. Rapoport. 1974. “A Linear Steady-State Treatment of Enzymatic Chains. General Properties, Control and Effector Strength.” European Journal of Biochemistry 42 (1): 89–95. https://doi.org/10.1111/j.1432-1033.1974.tb03318.x.

Hlavacek, William S., James R. Faeder, Michael L. Blinov, Alan S. Perelson, and Byron Goldstein. 2003. “The Complexity of Complexes in Signal Transduction.” Biotechnology and Bioengineering 84 (7): 783–94. https://doi.org/10.1002/bit.10842.

Hlavacek, William S., James R. Faeder, Michael L. Blinov, Richard G. Posner, Michael Hucka, and Walter Fontana. 2006. “Rules for Modeling Signal-Transduction Systems.” Science’s STKE 2006 (344): re6. https://doi.org/10.1126/stke.3442006re6.

Hoeve, Johanna ten, Maria de Jesus Ibarra-Sanchez, Yubin Fu, et al. 2002. “Identification of a Nuclear Stat1 Protein Tyrosine Phosphatase.” Molecular and Cellular Biology 22 (16): 5662–68. https://doi.org/10.1128/MCB.22.16.5662-5668.2002.

Husar, Adam, Mariam Ordyan, Guadalupe C. Garcia, et al. 2024. “MCell4 with BioNetGen: A Monte Carlo Simulator of Rule-Based Reaction-Diffusion Systems with Python Interface.” PLOS Computational Biology 20 (4): e1011800. https://doi.org/10.1371/journal.pcbi.1011800.

Lauffenburger, Douglas A., and Jennifer J. Linderman. 1993. Receptors: Models for Binding, Trafficking, and Signaling. Oxford University Press.

Lin, Yen Ting, Song Feng, and William S. Hlavacek. 2019. “Scaling Methods for Accelerating Kinetic Monte Carlo Simulations of Chemical Reaction Networks.” The Journal of Chemical Physics 150 (24): 244101. https://doi.org/10.1063/1.5096774.

Mitra, Eshan D., Ryan Suderman, Joshua Colvin, et al. 2019. “PyBioNetFit and the Biological Property Specification Language.” iScience 19: 1012–36. https://doi.org/10.1016/j.isci.2019.08.045.

Monine, Michael I., Richard G. Posner, Paul B. Savage, James R. Faeder, and William S. Hlavacek. 2010. “Modeling Multivalent Ligand-Receptor Interactions with Steric Constraints on Configurations of Cell-Surface Receptor Aggregates.” Biophysical Journal 98 (1): 48–56. https://doi.org/10.1016/j.bpj.2009.09.043.

Peccoud, Jean, and Bernard Ycart. 1995. “Markovian Modeling of Gene-Product Synthesis.” Theoretical Population Biology 48 (2): 222–34. https://doi.org/10.1006/tpbi.1995.1027.

Poulikakos, Poulikos I., Chao Zhang, Gideon Bollag, Kevan M. Shokat, and Neal Rosen. 2010. “RAF Inhibitors Transactivate RAF Dimers and ERK Signalling in Cells with Wild-Type BRAF.” Nature 464 (7287): 427–30. https://doi.org/10.1038/nature08902.

Raj, Arjun, and Alexander van Oudenaarden. 2008. “Nature, Nurture, or Chance: Stochastic Gene Expression and Its Consequences.” Cell 135 (2): 216–26. https://doi.org/10.1016/j.cell.2008.09.050.

Reich, Nancy C., and Ling Liu. 2006. “Tracking STAT Nuclear Traffic.” Nature Reviews Immunology 6 (8): 602–12. https://doi.org/10.1038/nri1885.

Sekar, John A. P., and James R. Faeder. 2012. “Rule-Based Modeling of Signal Transduction: A Primer.” Methods in Molecular Biology 880: 139–218. https://doi.org/10.1007/978-1-61779-833-7_9.

Sekar, John A. P., Justin S. Hogg, and James R. Faeder. 2016. “Energy-Based Modeling in BioNetGen.” 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 1460–67. https://doi.org/10.1109/BIBM.2016.7822739.

Sekar, John Arul Prakash, Jose-Juan Tapia, and James R. Faeder. 2017. “Automated Visualization of Rule-Based Models.” PLOS Computational Biology 13 (11): e1005857. https://doi.org/10.1371/journal.pcbi.1005857.

Sneddon, Michael W., James R. Faeder, and Thierry Emonet. 2011. “Efficient Modeling, Simulation and Coarse-Graining of Biological Complexity with NFsim.” Nature Methods 8 (2): 177–83. https://doi.org/10.1038/nmeth.1546.

Thomas, Brandon R., Lily A. Chylek, Joshua Colvin, et al. 2016. “BioNetFit: A Fitting Tool Compatible with BioNetGen, NFsim and Distributed Computing Environments.” Bioinformatics 32 (5): 798–800. https://doi.org/10.1093/bioinformatics/btv655.

Tyson, John J., Katherine C. Chen, and Béla Novák. 2003. “Sniffers, Buzzers, Toggles and Blinkers: Dynamics of Regulatory and Signaling Pathways in the Cell.” Current Opinion in Cell Biology 15 (2): 221–31. https://doi.org/10.1016/S0955-0674(03)00017-6.

Tyson, John J., and Béla Novák. 2010. “Functional Motifs in Biochemical Reaction Networks.” Annual Review of Physical Chemistry 61: 219–40. https://doi.org/10.1146/annurev.physchem.012809.103457.

Tzafriri, A. R. 2003. “Michaelis–Menten Kinetics at High Enzyme Concentrations.” Bulletin of Mathematical Biology 65 (6): 1111–29. https://doi.org/10.1016/S0092-8240(03)00059-4.

Xiong, Wen, and James E. Ferrell. 2003. “A Positive-Feedback-Based Bistable ‘Memory Module’ That Governs a Cell Fate Decision.” Nature 426 (6965): 460–65. https://doi.org/10.1038/nature02089.

Xu, Wen, Adam M. Smith, James R. Faeder, and G. Elisabeta Marai. 2011. “RuleBender: A Visual Interface for Rule-Based Modeling.” Bioinformatics 27 (12): 1721–22. https://doi.org/10.1093/bioinformatics/btr197.

Yang, Jin, Michael I. Monine, James R. Faeder, and William S. Hlavacek. 2008. “Kinetic Monte Carlo Method for Rule-Based Modeling of Biochemical Networks.” Physical Review E 78 (3): 031910. https://doi.org/10.1103/PhysRevE.78.031910.