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The markup is the model: reasoning about systems biology models in the Semantic Web era.

Kell DB, Mendes P. Kell DB, et al. Among authors: mendes p. J Theor Biol. 2008 Jun 7;252(3):538-43. doi: 10.1016/j.jtbi.2007.10.023. Epub 2007 Dec 3. J Theor Biol. 2008. PMID: 18054049 Review.

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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: mendes p. Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015. Bioinformatics. 2003. PMID: 12611808

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MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems.

Mendes P, Kell DB. Mendes P, et al. Bioinformatics. 2001 Mar;17(3):288-9. doi: 10.1093/bioinformatics/17.3.288. Bioinformatics. 2001. PMID: 11294797

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Condor-COPASI: high-throughput computing for biochemical networks.

Kent E, Hoops S, Mendes P. Kent E, et al. Among authors: mendes p. BMC Syst Biol. 2012 Jul 26;6:91. doi: 10.1186/1752-0509-6-91. BMC Syst Biol. 2012. PMID: 22834945 Free PMC article.

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Path2Models: large-scale generation of computational models from biochemical pathway maps.

Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M, van Iersel M, Keating S, Rall M, Wybrow M, Hermjakob H, Hucka M, Kell DB, Müller W, Mendes P, Zell A, Chaouiya C, Saez-Rodriguez J, Schreiber F, Laibe C, Dräger A, Le Novère N. Büchel F, et al. Among authors: mendes p. BMC Syst Biol. 2013 Nov 1;7:116. doi: 10.1186/1752-0509-7-116. BMC Syst Biol. 2013. PMID: 24180668 Free PMC article.

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COMODI: an ontology to characterise differences in versions of computational models in biology.

Scharm M, Waltemath D, Mendes P, Wolkenhauer O. Scharm M, et al. Among authors: mendes p. J Biomed Semantics. 2016 Jul 11;7(1):46. doi: 10.1186/s13326-016-0080-2. J Biomed Semantics. 2016. PMID: 27401413 Free PMC article.

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Systematic construction of kinetic models from genome-scale metabolic networks.

Stanford NJ, Lubitz T, Smallbone K, Klipp E, Mendes P, Liebermeister W. Stanford NJ, et al. Among authors: mendes p. PLoS One. 2013 Nov 14;8(11):e79195. doi: 10.1371/journal.pone.0079195. eCollection 2013. PLoS One. 2013. PMID: 24324546 Free PMC article.

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What can we learn from global sensitivity analysis of biochemical systems?

Kent E, Neumann S, Kummer U, Mendes P. Kent E, et al. Among authors: mendes p. PLoS One. 2013 Nov 14;8(11):e79244. doi: 10.1371/journal.pone.0079244. eCollection 2013. PLoS One. 2013. PMID: 24244458 Free PMC article.

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A method for comparing multivariate time series with different dimensions.

Tapinos A, Mendes P. Tapinos A, et al. Among authors: mendes p. PLoS One. 2013;8(2):e54201. doi: 10.1371/journal.pone.0054201. Epub 2013 Feb 5. PLoS One. 2013. PMID: 23393554 Free PMC article.

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A model of yeast glycolysis based on a consistent kinetic characterisation of all its enzymes.

Smallbone K, Messiha HL, Carroll KM, Winder CL, Malys N, Dunn WB, Murabito E, Swainston N, Dada JO, Khan F, Pir P, Simeonidis E, Spasić I, Wishart J, Weichart D, Hayes NW, Jameson D, Broomhead DS, Oliver SG, Gaskell SJ, McCarthy JE, Paton NW, Westerhoff HV, Kell DB, Mendes P. Smallbone K, et al. Among authors: mendes p. FEBS Lett. 2013 Sep 2;587(17):2832-41. doi: 10.1016/j.febslet.2013.06.043. Epub 2013 Jul 4. FEBS Lett. 2013. PMID: 23831062 Free PMC article.

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