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Kinetic Monte Carlo method for rule-based modeling of biochemical networks.
Yang J, Monine MI, Faeder JR, Hlavacek WS. Yang J, et al. Among authors: hlavacek ws. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 1):031910. doi: 10.1103/PhysRevE.78.031910. Epub 2008 Sep 10. Phys Rev E Stat Nonlin Soft Matter Phys. 2008. PMID: 18851068 Free PMC article.
On imposing detailed balance in complex reaction mechanisms.
Yang J, Bruno WJ, Hlavacek WS, Pearson JE. Yang J, et al. Among authors: hlavacek ws. Biophys J. 2006 Aug 1;91(3):1136-41. doi: 10.1529/biophysj.105.071852. Epub 2006 May 12. Biophys J. 2006. PMID: 16698778 Free PMC article. No abstract available.
Guidelines for visualizing and annotating rule-based models.
Chylek LA, Hu B, Blinov ML, Emonet T, Faeder JR, Goldstein B, Gutenkunst RN, Haugh JM, Lipniacki T, Posner RG, Yang J, Hlavacek WS. Chylek LA, et al. Among authors: hlavacek ws. Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7. Mol Biosyst. 2011. PMID: 21647530 Free PMC article.
'On-the-fly' or 'generate-first' modeling?
Blinov ML, Faeder JR, Yang J, Goldstein B, Hlavacek WS. Blinov ML, et al. Among authors: hlavacek ws. Nat Biotechnol. 2005 Nov;23(11):1344-5; author reply 1345. doi: 10.1038/nbt1105-1344. Nat Biotechnol. 2005. PMID: 16273053 No abstract available.
Rule-based modeling of biochemical systems with BioNetGen.
Faeder JR, Blinov ML, Hlavacek WS. Faeder JR, et al. Among authors: hlavacek ws. Methods Mol Biol. 2009;500:113-67. doi: 10.1007/978-1-59745-525-1_5. Methods Mol Biol. 2009. PMID: 19399430 Free article.
Depicting signaling cascades.
Blinov ML, Yang J, Faeder JR, Hlavacek WS. Blinov ML, et al. Among authors: hlavacek ws. Nat Biotechnol. 2006 Feb;24(2):137-8; author reply 138. doi: 10.1038/nbt0206-137. Nat Biotechnol. 2006. PMID: 16465147 No abstract available.
Simulation of large-scale rule-based models.
Colvin J, Monine MI, Faeder JR, Hlavacek WS, Von Hoff DD, Posner RG. Colvin J, et al. Among authors: hlavacek ws. Bioinformatics. 2009 Apr 1;25(7):910-7. doi: 10.1093/bioinformatics/btp066. Epub 2009 Feb 11. Bioinformatics. 2009. PMID: 19213740 Free PMC article.
114 results