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The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.
Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, Stelling J, Takahashi K, Tomita M, Wagner J, Wang J; SBML Forum. Hucka M, et al. Among authors: doyle jc. Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015. Bioinformatics. 2003. PMID: 12611808
MathSBML: a package for manipulating SBML-based biological models.
Shapiro BE, Hucka M, Finney A, Doyle J. Shapiro BE, et al. Among authors: doyle j. Bioinformatics. 2004 Nov 1;20(16):2829-31. doi: 10.1093/bioinformatics/bth271. Epub 2004 Apr 15. Bioinformatics. 2004. PMID: 15087311 Free PMC article.
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Keating SM, Waltemath D, König M, Zhang F, Dräger A, Chaouiya C, Bergmann FT, Finney A, Gillespie CS, Helikar T, Hoops S, Malik-Sheriff RS, Moodie SL, Moraru II, Myers CJ, Naldi A, Olivier BG, Sahle S, Schaff JC, Smith LP, Swat MJ, Thieffry D, Watanabe L, Wilkinson DJ, Blinov ML, Begley K, Faeder JR, Gómez HF, Hamm TM, Inagaki Y, Liebermeister W, Lister AL, Lucio D, Mjolsness E, Proctor CJ, Raman K, Rodriguez N, Shaffer CA, Shapiro BE, Stelling J, Swainston N, Tanimura N, Wagner J, Meier-Schellersheim M, Sauro HM, Palsson B, Bolouri H, Kitano H, Funahashi A, Hermjakob H, Doyle JC, Hucka M; SBML Level 3 Community members. Keating SM, et al. Among authors: doyle jc. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
Metabolic syndrome and robustness tradeoffs.
Kitano H, Oda K, Kimura T, Matsuoka Y, Csete M, Doyle J, Muramatsu M. Kitano H, et al. Among authors: doyle j. Diabetes. 2004 Dec;53 Suppl 3:S6-S15. doi: 10.2337/diabetes.53.suppl_3.s6. Diabetes. 2004. PMID: 15561923 Review.
Architecture, constraints, and behavior.
Doyle JC, Csete M. Doyle JC, et al. Proc Natl Acad Sci U S A. 2011 Sep 13;108 Suppl 3(Suppl 3):15624-30. doi: 10.1073/pnas.1103557108. Epub 2011 Jul 25. Proc Natl Acad Sci U S A. 2011. PMID: 21788505 Free PMC article. Review.
2,207 results