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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: faeder jr. 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.
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: faeder jr. Bioinformatics. 2009 Apr 1;25(7):910-7. doi: 10.1093/bioinformatics/btp066. Epub 2009 Feb 11. Bioinformatics. 2009. PMID: 19213740 Free PMC article.
GetBonNie for building, analyzing and sharing rule-based models.
Hu B, Matthew Fricke G, Faeder JR, Posner RG, Hlavacek WS. Hu B, et al. Among authors: faeder jr. Bioinformatics. 2009 Jun 1;25(11):1457-60. doi: 10.1093/bioinformatics/btp173. Epub 2009 Mar 25. Bioinformatics. 2009. PMID: 19321734 Free PMC article.
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: faeder jr. Mol Biosyst. 2011 Oct;7(10):2779-95. doi: 10.1039/c1mb05077j. Epub 2011 Jun 7. Mol Biosyst. 2011. PMID: 21647530 Free PMC article.
83 results