Multi-state modeling of biomolecules (English Wikipedia)

Analysis of information sources in references of the Wikipedia article "Multi-state modeling of biomolecules" in English language version.

refsWebsite

Global rank English rank

75nih.gov

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55doi.org

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17harvard.edu

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14semanticscholar.org

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4psu.edu

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2arxiv.org

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1ed.ac.uk

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1handle.net

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1sbml.org

low place

1unt.edu

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arxiv.org

Yang J, Meng X, Hlavacek WS (November 2010). "Rule-based modelling and simulation of biochemical systems with molecular finite automata". IET Systems Biology. 4 (6): 453–66. arXiv:1007.1315. doi:10.1049/iet-syb.2010.0015. PMC 3070173. PMID 21073243.
Yang J, Monine MI, Faeder JR, Hlavacek WS (September 2008). "Kinetic Monte Carlo method for rule-based modeling of biochemical networks". Physical Review E. 78 (3 Pt 1): 031910. arXiv:0712.3773. Bibcode:2008PhRvE..78c1910Y. doi:10.1103/PhysRevE.78.031910. PMC 2652652. PMID 18851068.

doi.org

Danos V, Laneve C (2004). "Formal molecular biology". Theoretical Computer Science. 325: 69–110. doi:10.1016/j.tcs.2004.03.065.
Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (November 2004). "BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains". Bioinformatics. 20 (17): 3289–91. doi:10.1093/bioinformatics/bth378. PMID 15217809.
Faeder JR, Blinov ML, Goldstein B, Hlavacek WS (2005). "Rule-Based Modeling of Biochemical Networks". Complexity. 10 (4): 22–41. Bibcode:2005Cmplx..10d..22F. doi:10.1002/cplx.20074. S2CID 9307441.
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (July 2006). "Rules for modeling signal-transduction systems". Science's STKE. 2006 (344): re6. CiteSeerX 10.1.1.83.1561. doi:10.1126/stke.3442006re6. PMID 16849649. S2CID 1816082.
Faeder JR, Blinov ML, Hlavacek WS (2009). "Rule-Based Modeling of Biochemical Systems with BioNetGen". Systems Biology. Methods in Molecular Biology. Vol. 500. Totowa, NJ: Humana Press. pp. 113–67. CiteSeerX 10.1.1.323.9577. doi:10.1007/978-1-59745-525-1_5. ISBN 978-1-934115-64-0. PMID 19399430.
Ollivier JF, Shahrezaei V, Swain PS (November 2010). "Scalable rule-based modelling of allosteric proteins and biochemical networks". PLOS Computational Biology. 6 (11): e1000975. Bibcode:2010PLSCB...6E0975O. doi:10.1371/journal.pcbi.1000975. PMC 2973810. PMID 21079669.
Lok L, Brent R (January 2005). "Automatic generation of cellular reaction networks with Moleculizer 1.0". Nature Biotechnology. 23 (1): 131–6. doi:10.1038/nbt1054. PMID 15637632. S2CID 23696958.
Yang J, Meng X, Hlavacek WS (November 2010). "Rule-based modelling and simulation of biochemical systems with molecular finite automata". IET Systems Biology. 4 (6): 453–66. arXiv:1007.1315. doi:10.1049/iet-syb.2010.0015. PMC 3070173. PMID 21073243.
Yang J, Monine MI, Faeder JR, Hlavacek WS (September 2008). "Kinetic Monte Carlo method for rule-based modeling of biochemical networks". Physical Review E. 78 (3 Pt 1): 031910. arXiv:0712.3773. Bibcode:2008PhRvE..78c1910Y. doi:10.1103/PhysRevE.78.031910. PMC 2652652. PMID 18851068.
Le Novère N, Shimizu TS (June 2001). "STOCHSIM: modelling of stochastic biomolecular processes". Bioinformatics. 17 (6): 575–6. doi:10.1093/bioinformatics/17.6.575. PMID 11395441.
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG (April 2009). "Simulation of large-scale rule-based models". Bioinformatics. 25 (7): 910–7. doi:10.1093/bioinformatics/btp066. PMC 2660871. PMID 19213740.
Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG (July 2010). "RuleMonkey: software for stochastic simulation of rule-based models". BMC Bioinformatics. 11: 404. doi:10.1186/1471-2105-11-404. PMC 2921409. PMID 20673321.
Sneddon MW, Faeder JR, Emonet T (February 2011). "Efficient modeling, simulation and coarse-graining of biological complexity with NFsim". Nature Methods. 8 (2): 177–83. doi:10.1038/nmeth.1546. PMID 21186362. S2CID 5412795.
Schöneberg J, Ullrich A, Noé F (2014-10-24). "Simulation tools for particle-based reaction-diffusion dynamics in continuous space". BMC Biophysics. 7 (1): 11. doi:10.1186/s13628-014-0011-5. PMC 4347613. PMID 25737778.
Tolle DP, Le Novère N (March 2010). "Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes". BMC Systems Biology. 4: 24. doi:10.1186/1752-0509-4-24. PMC 2848630. PMID 20233406.
Gruenert G, Ibrahim B, Lenser T, Lohel M, Hinze T, Dittrich P (June 2010). "Rule-based spatial modeling with diffusing, geometrically constrained molecules". BMC Bioinformatics. 11: 307. doi:10.1186/1471-2105-11-307. PMC 2911456. PMID 20529264.
Grunert G, Dittrich P (2011). "Using the SRSim Software for Spatial and Rule-Based Modeling of Combinatorially Complex Biochemical Reaction Systems". Membrane Computing. Lecture Notes in Computer Science. Vol. 6501. pp. 240–256. doi:10.1007/978-3-642-18123-8_19. ISBN 978-3-642-18122-1.
Stiles JR, Van Helden D, Bartol TM, Salpeter EE, Salpeter MM (June 1996). "Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle". Proceedings of the National Academy of Sciences of the United States of America. 93 (12): 5747–52. Bibcode:1996PNAS...93.5747S. doi:10.1073/pnas.93.12.5747. PMC 39132. PMID 8650164.
Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, et al. (October 2008). "Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces". SIAM Journal on Scientific Computing. 30 (6): 3126–3149. Bibcode:2008SJSC...30.3126K. doi:10.1137/070692017. PMC 2819163. PMID 20151023.
Bray D (July 1995). "Protein molecules as computational elements in living cells". Nature. 376 (6538): 307–12. Bibcode:1995Natur.376..307B. doi:10.1038/376307a0. PMID 7630396. S2CID 4326068.
Endy D, Brent R (January 2001). "Modelling cellular behaviour". Nature. 409 (6818): 391–5. Bibcode:2001Natur.409..391E. doi:10.1038/35053181. PMID 11201753. S2CID 480515.
Bray D (February 2003). "Genomics. Molecular prodigality". Science. 299 (5610): 1189–90. doi:10.1126/science.1080010. PMID 12595679. S2CID 34035288.
Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (December 2003). "The complexity of complexes in signal transduction". Biotechnology and Bioengineering. 84 (7): 783–94. doi:10.1002/bit.10842. PMID 14708119. S2CID 9092264.
Bennett MK, Erondu NE, Kennedy MB (October 1983). "Purification and characterization of a calmodulin-dependent protein kinase that is highly concentrated in brain". The Journal of Biological Chemistry. 258 (20): 12735–44. doi:10.1016/S0021-9258(17)44239-6. PMID 6313675.
Rosenberg OS, Deindl S, Sung RJ, Nairn AC, Kuriyan J (December 2005). "Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme". Cell. 123 (5): 849–60. doi:10.1016/j.cell.2005.10.029. PMID 16325579. S2CID 2654357.
Stefan MI, Marshall DP, Le Novère N (2012). "Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII". PLOS ONE. 7 (1): e29406. Bibcode:2012PLoSO...729406S. doi:10.1371/journal.pone.0029406. PMC 3261145. PMID 22279535.
Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, et al. (August 2012). "Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling". BMC Systems Biology. 6: 107. doi:10.1186/1752-0509-6-107. PMC 3485121. PMID 22913808.
Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (May 2013). "Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits". BMC Systems Biology. 7: 42. doi:10.1186/1752-0509-7-42. PMC 3680069. PMID 23705868.
Feret J, Danos V, Krivine J, Harmer R, Fontana W (April 2009). "Internal coarse-graining of molecular systems". Proceedings of the National Academy of Sciences of the United States of America. 106 (16): 6453–8. Bibcode:2009PNAS..106.6453F. doi:10.1073/pnas.0809908106. PMC 2672529. PMID 19346467.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. (March 2003). "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models". Bioinformatics. 19 (4): 524–31. doi:10.1093/bioinformatics/btg015. PMID 12611808.
Finney A, Hucka M (December 2003). "Systems biology markup language: Level 2 and beyond". Biochemical Society Transactions. 31 (Pt 6): 1472–3. CiteSeerX 10.1.1.466.8001. doi:10.1042/bst0311472. PMID 14641091.
Monod J, Wyman J, Changeux JP (May 1965). "On the nature of allosteric transitions: A plausible model". Journal of Molecular Biology. 12: 88–118. doi:10.1016/S0022-2836(65)80285-6. PMID 14343300.
Colquhoun D, Dowsland KA, Beato M, Plested AJ (June 2004). "How to impose microscopic reversibility in complex reaction mechanisms". Biophysical Journal. 86 (6): 3510–8. Bibcode:2004BpJ....86.3510C. doi:10.1529/biophysj.103.038679. PMC 1304255. PMID 15189850.
Priami C (1995). "Stochastic π-calculus". The Computer Journal. 38 (7): 578–589. doi:10.1093/comjnl/38.7.578.
Gillespie DT (1977). "Exact Stochastic Simulation of Coupled Chemical Reactions". J Phys Chem. 81 (25): 2340–2361. CiteSeerX 10.1.1.704.7634. doi:10.1021/j100540a008. S2CID 2606191.
Maus C, Rybacki S, Uhrmacher AM (October 2011). "Rule-based multi-level modeling of cell biological systems". BMC Systems Biology. 5: 166. doi:10.1186/1752-0509-5-166. PMC 3306009. PMID 22005019.
Oury N, Plotkin G (2013). "Multi-level modelling via stochastic multi-level multiset rewriting" (PDF). Mathematical Structures in Computer Science. 23 (2): 471–503. doi:10.1017/s0960129512000199. hdl:20.500.11820/2c05ac75-14eb-4939-bf71-5e76b9a942ef. S2CID 702281.
Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN (July 2006). "Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method". PLOS Computational Biology. 2 (7): e82. Bibcode:2006PLSCB...2...82M. doi:10.1371/journal.pcbi.0020082. PMC 1513273. PMID 16854213.
Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M (January 2012). "Computational modeling of cellular signaling processes embedded into dynamic spatial contexts". Nature Methods. 9 (3): 283–9. doi:10.1038/nmeth.1861. PMC 3448286. PMID 22286385.
Lis M, Artyomov MN, Devadas S, Chakraborty AK (September 2009). "Efficient stochastic simulation of reaction-diffusion processes via direct compilation". Bioinformatics. 25 (17): 2289–91. doi:10.1093/bioinformatics/btp387. PMC 2734316. PMID 19578038.
Lopez CF, Muhlich JL, Bachman JA, Sorger PK (2013). "Programming biological models in Python using PySB". Molecular Systems Biology. 9: 646. doi:10.1038/msb.2013.1. PMC 3588907. PMID 23423320.
Tolle DP, Le Novère N (2006). "Particle-Based Stochastic Simulation in Systems Biology". Curr. Bioinform. 1 (3): 315–320. doi:10.2174/157489306777827964. S2CID 41366617.
Michalski PJ, Loew LM (June 2012). "CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation". Physical Biology. 9 (3): 036010. Bibcode:2012PhBio...9c6010M. doi:10.1088/1478-3975/9/3/036010. PMC 3507550. PMID 22683827.
Mogilner A, Allard J, Wollman R (April 2012). "Cell polarity: quantitative modeling as a tool in cell biology". Science. 336 (6078): 175–9. Bibcode:2012Sci...336..175M. doi:10.1126/science.1216380. PMID 22499937. S2CID 10491696.
Levin MD, Shimizu TS, Bray D (April 2002). "Binding and diffusion of CheR molecules within a cluster of membrane receptors". Biophysical Journal. 82 (4): 1809–17. Bibcode:2002BpJ....82.1809L. doi:10.1016/S0006-3495(02)75531-8. PMC 1301978. PMID 11916840.
Yang J, Hlavacek WS (October 2011). "The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems". Physical Biology. 8 (5): 055009. Bibcode:2011PhBio...8e5009Y. doi:10.1088/1478-3975/8/5/055009. PMC 3168694. PMID 21832806.
Kinney JP, Spacek J, Bartol TM, Bajaj CL, Harris KM, Sejnowski TJ (February 2013). "Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil". The Journal of Comparative Neurology. 521 (2): 448–64. doi:10.1002/cne.23181. PMC 3540825. PMID 22740128.
Plimpton S (March 1995). "Fast parallel algorithms for short-range molecular dynamics". Journal of Computational Physics. 117 (1): 1–9. Bibcode:1995JCoPh.117....1P. doi:10.1006/jcph.1995.1039. S2CID 15881414.
Tschernyschkow S, Herda S, Gruenert G, Döring V, Görlich D, Hofmeister A, et al. (September 2013). "Rule-based modeling and simulations of the inner kinetochore structure". Progress in Biophysics and Molecular Biology. 113 (1): 33–45. doi:10.1016/j.pbiomolbio.2013.03.010. PMID 23562479.
Shimizu TS, Aksenov SV, Bray D (May 2003). "A spatially extended stochastic model of the bacterial chemotaxis signalling pathway". Journal of Molecular Biology. 329 (2): 291–309. doi:10.1016/s0022-2836(03)00437-6. PMID 12758077.
Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED (March 2009). "PROMOT: modular modeling for systems biology". Bioinformatics. 25 (5): 687–9. doi:10.1093/bioinformatics/btp029. PMC 2647835. PMID 19147665.
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, et al. (December 2006). "COPASI--a COmplex PAthway SImulator". Bioinformatics. 22 (24): 3067–74. doi:10.1093/bioinformatics/btl485. PMID 17032683.
Aitken S, Alexander RD, Beggs JD (September 2013). "A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation". Journal of the Royal Society, Interface. 10 (86): 20130438. doi:10.1098/rsif.2013.0438. PMC 3730697. PMID 23804443.
Artyomov MN, Lis M, Devadas S, Davis MM, Chakraborty AK (September 2010). "CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery". Proceedings of the National Academy of Sciences of the United States of America. 107 (39): 16916–21. Bibcode:2010PNAS..10716916A. doi:10.1073/pnas.1010568107. PMC 2947881. PMID 20837541.
Ibrahim B, Henze R, Gruenert G, Egbert M, Huwald J, Dittrich P (July 2013). "Spatial rule-based modeling: a method and its application to the human mitotic kinetochore". Cells. 2 (3): 506–44. doi:10.3390/cells2030506. PMC 3972674. PMID 24709796.

ed.ac.uk

pure.ed.ac.uk

Oury N, Plotkin G (2013). "Multi-level modelling via stochastic multi-level multiset rewriting" (PDF). Mathematical Structures in Computer Science. 23 (2): 471–503. doi:10.1017/s0960129512000199. hdl:20.500.11820/2c05ac75-14eb-4939-bf71-5e76b9a942ef. S2CID 702281.

handle.net

hdl.handle.net

Oury N, Plotkin G (2013). "Multi-level modelling via stochastic multi-level multiset rewriting" (PDF). Mathematical Structures in Computer Science. 23 (2): 471–503. doi:10.1017/s0960129512000199. hdl:20.500.11820/2c05ac75-14eb-4939-bf71-5e76b9a942ef. S2CID 702281.

harvard.edu

ui.adsabs.harvard.edu

Faeder JR, Blinov ML, Goldstein B, Hlavacek WS (2005). "Rule-Based Modeling of Biochemical Networks". Complexity. 10 (4): 22–41. Bibcode:2005Cmplx..10d..22F. doi:10.1002/cplx.20074. S2CID 9307441.
Ollivier JF, Shahrezaei V, Swain PS (November 2010). "Scalable rule-based modelling of allosteric proteins and biochemical networks". PLOS Computational Biology. 6 (11): e1000975. Bibcode:2010PLSCB...6E0975O. doi:10.1371/journal.pcbi.1000975. PMC 2973810. PMID 21079669.
Yang J, Monine MI, Faeder JR, Hlavacek WS (September 2008). "Kinetic Monte Carlo method for rule-based modeling of biochemical networks". Physical Review E. 78 (3 Pt 1): 031910. arXiv:0712.3773. Bibcode:2008PhRvE..78c1910Y. doi:10.1103/PhysRevE.78.031910. PMC 2652652. PMID 18851068.
Stiles JR, Van Helden D, Bartol TM, Salpeter EE, Salpeter MM (June 1996). "Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle". Proceedings of the National Academy of Sciences of the United States of America. 93 (12): 5747–52. Bibcode:1996PNAS...93.5747S. doi:10.1073/pnas.93.12.5747. PMC 39132. PMID 8650164.
Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, et al. (October 2008). "Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces". SIAM Journal on Scientific Computing. 30 (6): 3126–3149. Bibcode:2008SJSC...30.3126K. doi:10.1137/070692017. PMC 2819163. PMID 20151023.
Bray D (July 1995). "Protein molecules as computational elements in living cells". Nature. 376 (6538): 307–12. Bibcode:1995Natur.376..307B. doi:10.1038/376307a0. PMID 7630396. S2CID 4326068.
Endy D, Brent R (January 2001). "Modelling cellular behaviour". Nature. 409 (6818): 391–5. Bibcode:2001Natur.409..391E. doi:10.1038/35053181. PMID 11201753. S2CID 480515.
Stefan MI, Marshall DP, Le Novère N (2012). "Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII". PLOS ONE. 7 (1): e29406. Bibcode:2012PLoSO...729406S. doi:10.1371/journal.pone.0029406. PMC 3261145. PMID 22279535.
Feret J, Danos V, Krivine J, Harmer R, Fontana W (April 2009). "Internal coarse-graining of molecular systems". Proceedings of the National Academy of Sciences of the United States of America. 106 (16): 6453–8. Bibcode:2009PNAS..106.6453F. doi:10.1073/pnas.0809908106. PMC 2672529. PMID 19346467.
Colquhoun D, Dowsland KA, Beato M, Plested AJ (June 2004). "How to impose microscopic reversibility in complex reaction mechanisms". Biophysical Journal. 86 (6): 3510–8. Bibcode:2004BpJ....86.3510C. doi:10.1529/biophysj.103.038679. PMC 1304255. PMID 15189850.
Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN (July 2006). "Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method". PLOS Computational Biology. 2 (7): e82. Bibcode:2006PLSCB...2...82M. doi:10.1371/journal.pcbi.0020082. PMC 1513273. PMID 16854213.
Michalski PJ, Loew LM (June 2012). "CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation". Physical Biology. 9 (3): 036010. Bibcode:2012PhBio...9c6010M. doi:10.1088/1478-3975/9/3/036010. PMC 3507550. PMID 22683827.
Mogilner A, Allard J, Wollman R (April 2012). "Cell polarity: quantitative modeling as a tool in cell biology". Science. 336 (6078): 175–9. Bibcode:2012Sci...336..175M. doi:10.1126/science.1216380. PMID 22499937. S2CID 10491696.
Levin MD, Shimizu TS, Bray D (April 2002). "Binding and diffusion of CheR molecules within a cluster of membrane receptors". Biophysical Journal. 82 (4): 1809–17. Bibcode:2002BpJ....82.1809L. doi:10.1016/S0006-3495(02)75531-8. PMC 1301978. PMID 11916840.
Yang J, Hlavacek WS (October 2011). "The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems". Physical Biology. 8 (5): 055009. Bibcode:2011PhBio...8e5009Y. doi:10.1088/1478-3975/8/5/055009. PMC 3168694. PMID 21832806.
Plimpton S (March 1995). "Fast parallel algorithms for short-range molecular dynamics". Journal of Computational Physics. 117 (1): 1–9. Bibcode:1995JCoPh.117....1P. doi:10.1006/jcph.1995.1039. S2CID 15881414.
Artyomov MN, Lis M, Devadas S, Davis MM, Chakraborty AK (September 2010). "CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery". Proceedings of the National Academy of Sciences of the United States of America. 107 (39): 16916–21. Bibcode:2010PNAS..10716916A. doi:10.1073/pnas.1010568107. PMC 2947881. PMID 20837541.

nih.gov

pubmed.ncbi.nlm.nih.gov

Blinov ML, Faeder JR, Goldstein B, Hlavacek WS (November 2004). "BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains". Bioinformatics. 20 (17): 3289–91. doi:10.1093/bioinformatics/bth378. PMID 15217809.
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (July 2006). "Rules for modeling signal-transduction systems". Science's STKE. 2006 (344): re6. CiteSeerX 10.1.1.83.1561. doi:10.1126/stke.3442006re6. PMID 16849649. S2CID 1816082.
Faeder JR, Blinov ML, Hlavacek WS (2009). "Rule-Based Modeling of Biochemical Systems with BioNetGen". Systems Biology. Methods in Molecular Biology. Vol. 500. Totowa, NJ: Humana Press. pp. 113–67. CiteSeerX 10.1.1.323.9577. doi:10.1007/978-1-59745-525-1_5. ISBN 978-1-934115-64-0. PMID 19399430.
Ollivier JF, Shahrezaei V, Swain PS (November 2010). "Scalable rule-based modelling of allosteric proteins and biochemical networks". PLOS Computational Biology. 6 (11): e1000975. Bibcode:2010PLSCB...6E0975O. doi:10.1371/journal.pcbi.1000975. PMC 2973810. PMID 21079669.
Lok L, Brent R (January 2005). "Automatic generation of cellular reaction networks with Moleculizer 1.0". Nature Biotechnology. 23 (1): 131–6. doi:10.1038/nbt1054. PMID 15637632. S2CID 23696958.
Yang J, Meng X, Hlavacek WS (November 2010). "Rule-based modelling and simulation of biochemical systems with molecular finite automata". IET Systems Biology. 4 (6): 453–66. arXiv:1007.1315. doi:10.1049/iet-syb.2010.0015. PMC 3070173. PMID 21073243.
Yang J, Monine MI, Faeder JR, Hlavacek WS (September 2008). "Kinetic Monte Carlo method for rule-based modeling of biochemical networks". Physical Review E. 78 (3 Pt 1): 031910. arXiv:0712.3773. Bibcode:2008PhRvE..78c1910Y. doi:10.1103/PhysRevE.78.031910. PMC 2652652. PMID 18851068.
Le Novère N, Shimizu TS (June 2001). "STOCHSIM: modelling of stochastic biomolecular processes". Bioinformatics. 17 (6): 575–6. doi:10.1093/bioinformatics/17.6.575. PMID 11395441.
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG (April 2009). "Simulation of large-scale rule-based models". Bioinformatics. 25 (7): 910–7. doi:10.1093/bioinformatics/btp066. PMC 2660871. PMID 19213740.
Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG (July 2010). "RuleMonkey: software for stochastic simulation of rule-based models". BMC Bioinformatics. 11: 404. doi:10.1186/1471-2105-11-404. PMC 2921409. PMID 20673321.
Sneddon MW, Faeder JR, Emonet T (February 2011). "Efficient modeling, simulation and coarse-graining of biological complexity with NFsim". Nature Methods. 8 (2): 177–83. doi:10.1038/nmeth.1546. PMID 21186362. S2CID 5412795.
Schöneberg J, Ullrich A, Noé F (2014-10-24). "Simulation tools for particle-based reaction-diffusion dynamics in continuous space". BMC Biophysics. 7 (1): 11. doi:10.1186/s13628-014-0011-5. PMC 4347613. PMID 25737778.
Tolle DP, Le Novère N (March 2010). "Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes". BMC Systems Biology. 4: 24. doi:10.1186/1752-0509-4-24. PMC 2848630. PMID 20233406.
Gruenert G, Ibrahim B, Lenser T, Lohel M, Hinze T, Dittrich P (June 2010). "Rule-based spatial modeling with diffusing, geometrically constrained molecules". BMC Bioinformatics. 11: 307. doi:10.1186/1471-2105-11-307. PMC 2911456. PMID 20529264.
Stiles JR, Van Helden D, Bartol TM, Salpeter EE, Salpeter MM (June 1996). "Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle". Proceedings of the National Academy of Sciences of the United States of America. 93 (12): 5747–52. Bibcode:1996PNAS...93.5747S. doi:10.1073/pnas.93.12.5747. PMC 39132. PMID 8650164.
Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, et al. (October 2008). "Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces". SIAM Journal on Scientific Computing. 30 (6): 3126–3149. Bibcode:2008SJSC...30.3126K. doi:10.1137/070692017. PMC 2819163. PMID 20151023.
Bray D (July 1995). "Protein molecules as computational elements in living cells". Nature. 376 (6538): 307–12. Bibcode:1995Natur.376..307B. doi:10.1038/376307a0. PMID 7630396. S2CID 4326068.
Endy D, Brent R (January 2001). "Modelling cellular behaviour". Nature. 409 (6818): 391–5. Bibcode:2001Natur.409..391E. doi:10.1038/35053181. PMID 11201753. S2CID 480515.
Bray D (February 2003). "Genomics. Molecular prodigality". Science. 299 (5610): 1189–90. doi:10.1126/science.1080010. PMID 12595679. S2CID 34035288.
Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (December 2003). "The complexity of complexes in signal transduction". Biotechnology and Bioengineering. 84 (7): 783–94. doi:10.1002/bit.10842. PMID 14708119. S2CID 9092264.
Bennett MK, Erondu NE, Kennedy MB (October 1983). "Purification and characterization of a calmodulin-dependent protein kinase that is highly concentrated in brain". The Journal of Biological Chemistry. 258 (20): 12735–44. doi:10.1016/S0021-9258(17)44239-6. PMID 6313675.
Rosenberg OS, Deindl S, Sung RJ, Nairn AC, Kuriyan J (December 2005). "Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme". Cell. 123 (5): 849–60. doi:10.1016/j.cell.2005.10.029. PMID 16325579. S2CID 2654357.
Stefan MI, Marshall DP, Le Novère N (2012). "Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII". PLOS ONE. 7 (1): e29406. Bibcode:2012PLoSO...729406S. doi:10.1371/journal.pone.0029406. PMC 3261145. PMID 22279535.
Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, et al. (August 2012). "Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling". BMC Systems Biology. 6: 107. doi:10.1186/1752-0509-6-107. PMC 3485121. PMID 22913808.
Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (May 2013). "Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits". BMC Systems Biology. 7: 42. doi:10.1186/1752-0509-7-42. PMC 3680069. PMID 23705868.
Feret J, Danos V, Krivine J, Harmer R, Fontana W (April 2009). "Internal coarse-graining of molecular systems". Proceedings of the National Academy of Sciences of the United States of America. 106 (16): 6453–8. Bibcode:2009PNAS..106.6453F. doi:10.1073/pnas.0809908106. PMC 2672529. PMID 19346467.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, et al. (March 2003). "The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models". Bioinformatics. 19 (4): 524–31. doi:10.1093/bioinformatics/btg015. PMID 12611808.
Finney A, Hucka M (December 2003). "Systems biology markup language: Level 2 and beyond". Biochemical Society Transactions. 31 (Pt 6): 1472–3. CiteSeerX 10.1.1.466.8001. doi:10.1042/bst0311472. PMID 14641091.
Monod J, Wyman J, Changeux JP (May 1965). "On the nature of allosteric transitions: A plausible model". Journal of Molecular Biology. 12: 88–118. doi:10.1016/S0022-2836(65)80285-6. PMID 14343300.
Colquhoun D, Dowsland KA, Beato M, Plested AJ (June 2004). "How to impose microscopic reversibility in complex reaction mechanisms". Biophysical Journal. 86 (6): 3510–8. Bibcode:2004BpJ....86.3510C. doi:10.1529/biophysj.103.038679. PMC 1304255. PMID 15189850.
Maus C, Rybacki S, Uhrmacher AM (October 2011). "Rule-based multi-level modeling of cell biological systems". BMC Systems Biology. 5: 166. doi:10.1186/1752-0509-5-166. PMC 3306009. PMID 22005019.
Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN (July 2006). "Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method". PLOS Computational Biology. 2 (7): e82. Bibcode:2006PLSCB...2...82M. doi:10.1371/journal.pcbi.0020082. PMC 1513273. PMID 16854213.
Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M (January 2012). "Computational modeling of cellular signaling processes embedded into dynamic spatial contexts". Nature Methods. 9 (3): 283–9. doi:10.1038/nmeth.1861. PMC 3448286. PMID 22286385.
Lis M, Artyomov MN, Devadas S, Chakraborty AK (September 2009). "Efficient stochastic simulation of reaction-diffusion processes via direct compilation". Bioinformatics. 25 (17): 2289–91. doi:10.1093/bioinformatics/btp387. PMC 2734316. PMID 19578038.
Lopez CF, Muhlich JL, Bachman JA, Sorger PK (2013). "Programming biological models in Python using PySB". Molecular Systems Biology. 9: 646. doi:10.1038/msb.2013.1. PMC 3588907. PMID 23423320.
Michalski PJ, Loew LM (June 2012). "CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation". Physical Biology. 9 (3): 036010. Bibcode:2012PhBio...9c6010M. doi:10.1088/1478-3975/9/3/036010. PMC 3507550. PMID 22683827.
Mogilner A, Allard J, Wollman R (April 2012). "Cell polarity: quantitative modeling as a tool in cell biology". Science. 336 (6078): 175–9. Bibcode:2012Sci...336..175M. doi:10.1126/science.1216380. PMID 22499937. S2CID 10491696.
Levin MD, Shimizu TS, Bray D (April 2002). "Binding and diffusion of CheR molecules within a cluster of membrane receptors". Biophysical Journal. 82 (4): 1809–17. Bibcode:2002BpJ....82.1809L. doi:10.1016/S0006-3495(02)75531-8. PMC 1301978. PMID 11916840.
Yang J, Hlavacek WS (October 2011). "The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems". Physical Biology. 8 (5): 055009. Bibcode:2011PhBio...8e5009Y. doi:10.1088/1478-3975/8/5/055009. PMC 3168694. PMID 21832806.
Kinney JP, Spacek J, Bartol TM, Bajaj CL, Harris KM, Sejnowski TJ (February 2013). "Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil". The Journal of Comparative Neurology. 521 (2): 448–64. doi:10.1002/cne.23181. PMC 3540825. PMID 22740128.
Tschernyschkow S, Herda S, Gruenert G, Döring V, Görlich D, Hofmeister A, et al. (September 2013). "Rule-based modeling and simulations of the inner kinetochore structure". Progress in Biophysics and Molecular Biology. 113 (1): 33–45. doi:10.1016/j.pbiomolbio.2013.03.010. PMID 23562479.
Shimizu TS, Aksenov SV, Bray D (May 2003). "A spatially extended stochastic model of the bacterial chemotaxis signalling pathway". Journal of Molecular Biology. 329 (2): 291–309. doi:10.1016/s0022-2836(03)00437-6. PMID 12758077.
Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED (March 2009). "PROMOT: modular modeling for systems biology". Bioinformatics. 25 (5): 687–9. doi:10.1093/bioinformatics/btp029. PMC 2647835. PMID 19147665.
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, et al. (December 2006). "COPASI--a COmplex PAthway SImulator". Bioinformatics. 22 (24): 3067–74. doi:10.1093/bioinformatics/btl485. PMID 17032683.
Aitken S, Alexander RD, Beggs JD (September 2013). "A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation". Journal of the Royal Society, Interface. 10 (86): 20130438. doi:10.1098/rsif.2013.0438. PMC 3730697. PMID 23804443.
Artyomov MN, Lis M, Devadas S, Davis MM, Chakraborty AK (September 2010). "CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery". Proceedings of the National Academy of Sciences of the United States of America. 107 (39): 16916–21. Bibcode:2010PNAS..10716916A. doi:10.1073/pnas.1010568107. PMC 2947881. PMID 20837541.
Ibrahim B, Henze R, Gruenert G, Egbert M, Huwald J, Dittrich P (July 2013). "Spatial rule-based modeling: a method and its application to the human mitotic kinetochore". Cells. 2 (3): 506–44. doi:10.3390/cells2030506. PMC 3972674. PMID 24709796.

ncbi.nlm.nih.gov

Ollivier JF, Shahrezaei V, Swain PS (November 2010). "Scalable rule-based modelling of allosteric proteins and biochemical networks". PLOS Computational Biology. 6 (11): e1000975. Bibcode:2010PLSCB...6E0975O. doi:10.1371/journal.pcbi.1000975. PMC 2973810. PMID 21079669.
Yang J, Meng X, Hlavacek WS (November 2010). "Rule-based modelling and simulation of biochemical systems with molecular finite automata". IET Systems Biology. 4 (6): 453–66. arXiv:1007.1315. doi:10.1049/iet-syb.2010.0015. PMC 3070173. PMID 21073243.
Yang J, Monine MI, Faeder JR, Hlavacek WS (September 2008). "Kinetic Monte Carlo method for rule-based modeling of biochemical networks". Physical Review E. 78 (3 Pt 1): 031910. arXiv:0712.3773. Bibcode:2008PhRvE..78c1910Y. doi:10.1103/PhysRevE.78.031910. PMC 2652652. PMID 18851068.
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG (April 2009). "Simulation of large-scale rule-based models". Bioinformatics. 25 (7): 910–7. doi:10.1093/bioinformatics/btp066. PMC 2660871. PMID 19213740.
Colvin J, Monine MI, Gutenkunst RN, Hlavacek WS, Von Hoff DD, Posner RG (July 2010). "RuleMonkey: software for stochastic simulation of rule-based models". BMC Bioinformatics. 11: 404. doi:10.1186/1471-2105-11-404. PMC 2921409. PMID 20673321.
Schöneberg J, Ullrich A, Noé F (2014-10-24). "Simulation tools for particle-based reaction-diffusion dynamics in continuous space". BMC Biophysics. 7 (1): 11. doi:10.1186/s13628-014-0011-5. PMC 4347613. PMID 25737778.
Tolle DP, Le Novère N (March 2010). "Meredys, a multi-compartment reaction-diffusion simulator using multistate realistic molecular complexes". BMC Systems Biology. 4: 24. doi:10.1186/1752-0509-4-24. PMC 2848630. PMID 20233406.
Gruenert G, Ibrahim B, Lenser T, Lohel M, Hinze T, Dittrich P (June 2010). "Rule-based spatial modeling with diffusing, geometrically constrained molecules". BMC Bioinformatics. 11: 307. doi:10.1186/1471-2105-11-307. PMC 2911456. PMID 20529264.
Stiles JR, Van Helden D, Bartol TM, Salpeter EE, Salpeter MM (June 1996). "Miniature endplate current rise times less than 100 microseconds from improved dual recordings can be modeled with passive acetylcholine diffusion from a synaptic vesicle". Proceedings of the National Academy of Sciences of the United States of America. 93 (12): 5747–52. Bibcode:1996PNAS...93.5747S. doi:10.1073/pnas.93.12.5747. PMC 39132. PMID 8650164.
Kerr RA, Bartol TM, Kaminsky B, Dittrich M, Chang JC, Baden SB, et al. (October 2008). "Fast Monte Carlo Simulation Methods for Biological Reaction-Diffusion Systems in Solution and on Surfaces". SIAM Journal on Scientific Computing. 30 (6): 3126–3149. Bibcode:2008SJSC...30.3126K. doi:10.1137/070692017. PMC 2819163. PMID 20151023.
Stefan MI, Marshall DP, Le Novère N (2012). "Structural analysis and stochastic modelling suggest a mechanism for calmodulin trapping by CaMKII". PLOS ONE. 7 (1): e29406. Bibcode:2012PLoSO...729406S. doi:10.1371/journal.pone.0029406. PMC 3261145. PMID 22279535.
Creamer MS, Stites EC, Aziz M, Cahill JA, Tan CW, Berens ME, et al. (August 2012). "Specification, annotation, visualization and simulation of a large rule-based model for ERBB receptor signaling". BMC Systems Biology. 6: 107. doi:10.1186/1752-0509-6-107. PMC 3485121. PMID 22913808.
Marchisio MA, Colaiacovo M, Whitehead E, Stelling J (May 2013). "Modular, rule-based modeling for the design of eukaryotic synthetic gene circuits". BMC Systems Biology. 7: 42. doi:10.1186/1752-0509-7-42. PMC 3680069. PMID 23705868.
Feret J, Danos V, Krivine J, Harmer R, Fontana W (April 2009). "Internal coarse-graining of molecular systems". Proceedings of the National Academy of Sciences of the United States of America. 106 (16): 6453–8. Bibcode:2009PNAS..106.6453F. doi:10.1073/pnas.0809908106. PMC 2672529. PMID 19346467.
Colquhoun D, Dowsland KA, Beato M, Plested AJ (June 2004). "How to impose microscopic reversibility in complex reaction mechanisms". Biophysical Journal. 86 (6): 3510–8. Bibcode:2004BpJ....86.3510C. doi:10.1529/biophysj.103.038679. PMC 1304255. PMID 15189850.
Maus C, Rybacki S, Uhrmacher AM (October 2011). "Rule-based multi-level modeling of cell biological systems". BMC Systems Biology. 5: 166. doi:10.1186/1752-0509-5-166. PMC 3306009. PMID 22005019.
Meier-Schellersheim M, Xu X, Angermann B, Kunkel EJ, Jin T, Germain RN (July 2006). "Key role of local regulation in chemosensing revealed by a new molecular interaction-based modeling method". PLOS Computational Biology. 2 (7): e82. Bibcode:2006PLSCB...2...82M. doi:10.1371/journal.pcbi.0020082. PMC 1513273. PMID 16854213.
Angermann BR, Klauschen F, Garcia AD, Prustel T, Zhang F, Germain RN, Meier-Schellersheim M (January 2012). "Computational modeling of cellular signaling processes embedded into dynamic spatial contexts". Nature Methods. 9 (3): 283–9. doi:10.1038/nmeth.1861. PMC 3448286. PMID 22286385.
Lis M, Artyomov MN, Devadas S, Chakraborty AK (September 2009). "Efficient stochastic simulation of reaction-diffusion processes via direct compilation". Bioinformatics. 25 (17): 2289–91. doi:10.1093/bioinformatics/btp387. PMC 2734316. PMID 19578038.
Lopez CF, Muhlich JL, Bachman JA, Sorger PK (2013). "Programming biological models in Python using PySB". Molecular Systems Biology. 9: 646. doi:10.1038/msb.2013.1. PMC 3588907. PMID 23423320.
Michalski PJ, Loew LM (June 2012). "CaMKII activation and dynamics are independent of the holoenzyme structure: an infinite subunit holoenzyme approximation". Physical Biology. 9 (3): 036010. Bibcode:2012PhBio...9c6010M. doi:10.1088/1478-3975/9/3/036010. PMC 3507550. PMID 22683827.
Levin MD, Shimizu TS, Bray D (April 2002). "Binding and diffusion of CheR molecules within a cluster of membrane receptors". Biophysical Journal. 82 (4): 1809–17. Bibcode:2002BpJ....82.1809L. doi:10.1016/S0006-3495(02)75531-8. PMC 1301978. PMID 11916840.
Yang J, Hlavacek WS (October 2011). "The efficiency of reactant site sampling in network-free simulation of rule-based models for biochemical systems". Physical Biology. 8 (5): 055009. Bibcode:2011PhBio...8e5009Y. doi:10.1088/1478-3975/8/5/055009. PMC 3168694. PMID 21832806.
Kinney JP, Spacek J, Bartol TM, Bajaj CL, Harris KM, Sejnowski TJ (February 2013). "Extracellular sheets and tunnels modulate glutamate diffusion in hippocampal neuropil". The Journal of Comparative Neurology. 521 (2): 448–64. doi:10.1002/cne.23181. PMC 3540825. PMID 22740128.
Mirschel S, Steinmetz K, Rempel M, Ginkel M, Gilles ED (March 2009). "PROMOT: modular modeling for systems biology". Bioinformatics. 25 (5): 687–9. doi:10.1093/bioinformatics/btp029. PMC 2647835. PMID 19147665.
Aitken S, Alexander RD, Beggs JD (September 2013). "A rule-based kinetic model of RNA polymerase II C-terminal domain phosphorylation". Journal of the Royal Society, Interface. 10 (86): 20130438. doi:10.1098/rsif.2013.0438. PMC 3730697. PMID 23804443.
Artyomov MN, Lis M, Devadas S, Davis MM, Chakraborty AK (September 2010). "CD4 and CD8 binding to MHC molecules primarily acts to enhance Lck delivery". Proceedings of the National Academy of Sciences of the United States of America. 107 (39): 16916–21. Bibcode:2010PNAS..10716916A. doi:10.1073/pnas.1010568107. PMC 2947881. PMID 20837541.
Ibrahim B, Henze R, Gruenert G, Egbert M, Huwald J, Dittrich P (July 2013). "Spatial rule-based modeling: a method and its application to the human mitotic kinetochore". Cells. 2 (3): 506–44. doi:10.3390/cells2030506. PMC 3972674. PMID 24709796.

psu.edu

citeseerx.ist.psu.edu

Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (July 2006). "Rules for modeling signal-transduction systems". Science's STKE. 2006 (344): re6. CiteSeerX 10.1.1.83.1561. doi:10.1126/stke.3442006re6. PMID 16849649. S2CID 1816082.
Faeder JR, Blinov ML, Hlavacek WS (2009). "Rule-Based Modeling of Biochemical Systems with BioNetGen". Systems Biology. Methods in Molecular Biology. Vol. 500. Totowa, NJ: Humana Press. pp. 113–67. CiteSeerX 10.1.1.323.9577. doi:10.1007/978-1-59745-525-1_5. ISBN 978-1-934115-64-0. PMID 19399430.
Finney A, Hucka M (December 2003). "Systems biology markup language: Level 2 and beyond". Biochemical Society Transactions. 31 (Pt 6): 1472–3. CiteSeerX 10.1.1.466.8001. doi:10.1042/bst0311472. PMID 14641091.
Gillespie DT (1977). "Exact Stochastic Simulation of Coupled Chemical Reactions". J Phys Chem. 81 (25): 2340–2361. CiteSeerX 10.1.1.704.7634. doi:10.1021/j100540a008. S2CID 2606191.

sbml.org

Zhang F, Meier-Schellersheim M (2013). "SBML Level 3 Package Specification: Multistate, Multicomponent and Multicompartment Species Package for SBML Level 3 (Multi). Version 1, Release 01 (Draft, Rev 369)".

semanticscholar.org

api.semanticscholar.org

Faeder JR, Blinov ML, Goldstein B, Hlavacek WS (2005). "Rule-Based Modeling of Biochemical Networks". Complexity. 10 (4): 22–41. Bibcode:2005Cmplx..10d..22F. doi:10.1002/cplx.20074. S2CID 9307441.
Hlavacek WS, Faeder JR, Blinov ML, Posner RG, Hucka M, Fontana W (July 2006). "Rules for modeling signal-transduction systems". Science's STKE. 2006 (344): re6. CiteSeerX 10.1.1.83.1561. doi:10.1126/stke.3442006re6. PMID 16849649. S2CID 1816082.
Lok L, Brent R (January 2005). "Automatic generation of cellular reaction networks with Moleculizer 1.0". Nature Biotechnology. 23 (1): 131–6. doi:10.1038/nbt1054. PMID 15637632. S2CID 23696958.
Sneddon MW, Faeder JR, Emonet T (February 2011). "Efficient modeling, simulation and coarse-graining of biological complexity with NFsim". Nature Methods. 8 (2): 177–83. doi:10.1038/nmeth.1546. PMID 21186362. S2CID 5412795.
Bray D (July 1995). "Protein molecules as computational elements in living cells". Nature. 376 (6538): 307–12. Bibcode:1995Natur.376..307B. doi:10.1038/376307a0. PMID 7630396. S2CID 4326068.
Endy D, Brent R (January 2001). "Modelling cellular behaviour". Nature. 409 (6818): 391–5. Bibcode:2001Natur.409..391E. doi:10.1038/35053181. PMID 11201753. S2CID 480515.
Bray D (February 2003). "Genomics. Molecular prodigality". Science. 299 (5610): 1189–90. doi:10.1126/science.1080010. PMID 12595679. S2CID 34035288.
Hlavacek WS, Faeder JR, Blinov ML, Perelson AS, Goldstein B (December 2003). "The complexity of complexes in signal transduction". Biotechnology and Bioengineering. 84 (7): 783–94. doi:10.1002/bit.10842. PMID 14708119. S2CID 9092264.
Rosenberg OS, Deindl S, Sung RJ, Nairn AC, Kuriyan J (December 2005). "Structure of the autoinhibited kinase domain of CaMKII and SAXS analysis of the holoenzyme". Cell. 123 (5): 849–60. doi:10.1016/j.cell.2005.10.029. PMID 16325579. S2CID 2654357.
Gillespie DT (1977). "Exact Stochastic Simulation of Coupled Chemical Reactions". J Phys Chem. 81 (25): 2340–2361. CiteSeerX 10.1.1.704.7634. doi:10.1021/j100540a008. S2CID 2606191.
Oury N, Plotkin G (2013). "Multi-level modelling via stochastic multi-level multiset rewriting" (PDF). Mathematical Structures in Computer Science. 23 (2): 471–503. doi:10.1017/s0960129512000199. hdl:20.500.11820/2c05ac75-14eb-4939-bf71-5e76b9a942ef. S2CID 702281.
Tolle DP, Le Novère N (2006). "Particle-Based Stochastic Simulation in Systems Biology". Curr. Bioinform. 1 (3): 315–320. doi:10.2174/157489306777827964. S2CID 41366617.
Mogilner A, Allard J, Wollman R (April 2012). "Cell polarity: quantitative modeling as a tool in cell biology". Science. 336 (6078): 175–9. Bibcode:2012Sci...336..175M. doi:10.1126/science.1216380. PMID 22499937. S2CID 10491696.
Plimpton S (March 1995). "Fast parallel algorithms for short-range molecular dynamics". Journal of Computational Physics. 117 (1): 1–9. Bibcode:1995JCoPh.117....1P. doi:10.1006/jcph.1995.1039. S2CID 15881414.

unt.edu

digital.library.unt.edu

Plimpton S (March 1995). "Fast parallel algorithms for short-range molecular dynamics". Journal of Computational Physics. 117 (1): 1–9. Bibcode:1995JCoPh.117....1P. doi:10.1006/jcph.1995.1039. S2CID 15881414.