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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.
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.
Rule-based modeling of signal transduction: a primer.
Sekar JA, Faeder JR. Sekar JA, et al. Among authors: faeder jr. Methods Mol Biol. 2012;880:139-218. doi: 10.1007/978-1-61779-833-7_9. Methods Mol Biol. 2012. PMID: 23361986 Review.
'On-the-fly' or 'generate-first' modeling?
Blinov ML, Faeder JR, Yang J, Goldstein B, Hlavacek WS. Blinov ML, et al. Among authors: faeder jr. Nat Biotechnol. 2005 Nov;23(11):1344-5; author reply 1345. doi: 10.1038/nbt1105-1344. Nat Biotechnol. 2005. PMID: 16273053 No abstract available.
MCell-R: A Particle-Resolution Network-Free Spatial Modeling Framework.
Tapia JJ, Saglam AS, Czech J, Kuczewski R, Bartol TM, Sejnowski TJ, Faeder JR. Tapia JJ, et al. Among authors: faeder jr. Methods Mol Biol. 2019;1945:203-229. doi: 10.1007/978-1-4939-9102-0_9. Methods Mol Biol. 2019. PMID: 30945248 Free PMC article.
83 results