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Bridging the gaps in systems biology.
Cvijovic M, Almquist J, Hagmar J, Hohmann S, Kaltenbach HM, Klipp E, Krantz M, Mendes P, Nelander S, Nielsen J, Pagnani A, Przulj N, Raue A, Stelling J, Stoma S, Tobin F, Wodke JA, Zecchina R, Jirstrand M. Cvijovic M, et al. Among authors: mendes p. Mol Genet Genomics. 2014 Oct;289(5):727-34. doi: 10.1007/s00438-014-0843-3. Epub 2014 Apr 13. Mol Genet Genomics. 2014. PMID: 24728588 Review.
A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.
Herrgård MJ, Swainston N, Dobson P, Dunn WB, Arga KY, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M, Hucka M, Le Novère N, Li P, Liebermeister W, Mo ML, Oliveira AP, Petranovic D, Pettifer S, Simeonidis E, Smallbone K, Spasić I, Weichart D, Brent R, Broomhead DS, Westerhoff HV, Kirdar B, Penttilä M, Klipp E, Palsson BØ, Sauer U, Oliver SG, Mendes P, Nielsen J, Kell DB. Herrgård MJ, et al. Among authors: mendes p. Nat Biotechnol. 2008 Oct;26(10):1155-60. doi: 10.1038/nbt1492. Nat Biotechnol. 2008. PMID: 18846089 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. Mol Syst Biol. 2020 Aug;16(8):e9110. doi: 10.15252/msb.20199110. Mol Syst Biol. 2020. PMID: 32845085 Free PMC article. Review.
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
Minimum information requested in the annotation of biochemical models (MIRIAM).
Le Novère N, Finney A, Hucka M, Bhalla US, Campagne F, Collado-Vides J, Crampin EJ, Halstead M, Klipp E, Mendes P, Nielsen P, Sauro H, Shapiro B, Snoep JL, Spence HD, Wanner BL. Le Novère N, et al. Among authors: mendes p. Nat Biotechnol. 2005 Dec;23(12):1509-15. doi: 10.1038/nbt1156. Nat Biotechnol. 2005. PMID: 16333295
Multi-scale modelling and simulation in systems biology.
Dada JO, Mendes P. Dada JO, et al. Among authors: mendes p. Integr Biol (Camb). 2011 Feb;3(2):86-96. doi: 10.1039/c0ib00075b. Epub 2011 Jan 6. Integr Biol (Camb). 2011. PMID: 21212881 Review.
Controlled vocabularies and semantics in systems biology.
Courtot M, Juty N, Knüpfer C, Waltemath D, Zhukova A, Dräger A, Dumontier M, Finney A, Golebiewski M, Hastings J, Hoops S, Keating S, Kell DB, Kerrien S, Lawson J, Lister A, Lu J, Machne R, Mendes P, Pocock M, Rodriguez N, Villeger A, Wilkinson DJ, Wimalaratne S, Laibe C, Hucka M, Le Novère N. Courtot M, et al. Among authors: mendes p. Mol Syst Biol. 2011 Oct 25;7:543. doi: 10.1038/msb.2011.77. Mol Syst Biol. 2011. PMID: 22027554 Free PMC article.
528 results