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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: kummer u. Bioinformatics. 2003 Mar 1;19(4):524-31. doi: 10.1093/bioinformatics/btg015. Bioinformatics. 2003. PMID: 12611808
COPASI--a COmplex PAthway SImulator.
Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, Singhal M, Xu L, Mendes P, Kummer U. Hoops S, et al. Among authors: kummer u. Bioinformatics. 2006 Dec 15;22(24):3067-74. doi: 10.1093/bioinformatics/btl485. Epub 2006 Oct 10. Bioinformatics. 2006. PMID: 17032683
A new strategy for assessing sensitivities in biochemical models.
Sahle S, Mendes P, Hoops S, Kummer U. Sahle S, et al. Among authors: kummer u. Philos Trans A Math Phys Eng Sci. 2008 Oct 13;366(1880):3619-31. doi: 10.1098/rsta.2008.0108. Philos Trans A Math Phys Eng Sci. 2008. PMID: 18632455 Free PMC article.
SYCAMORE--a systems biology computational analysis and modeling research environment.
Weidemann A, Richter S, Stein M, Sahle S, Gauges R, Gabdoulline R, Surovtsova I, Semmelrock N, Besson B, Rojas I, Wade R, Kummer U. Weidemann A, et al. Among authors: kummer u. Bioinformatics. 2008 Jun 15;24(12):1463-4. doi: 10.1093/bioinformatics/btn207. Epub 2008 May 7. Bioinformatics. 2008. PMID: 18463116
COPASI and its applications in biotechnology.
Bergmann FT, Hoops S, Klahn B, Kummer U, Mendes P, Pahle J, Sahle S. Bergmann FT, et al. Among authors: kummer u. J Biotechnol. 2017 Nov 10;261:215-220. doi: 10.1016/j.jbiotec.2017.06.1200. Epub 2017 Jun 24. J Biotechnol. 2017. PMID: 28655634 Free PMC article. Review.
Strategies for structuring interdisciplinary education in Systems Biology: an European perspective.
Cvijovic M, Höfer T, Aćimović J, Alberghina L, Almaas E, Besozzi D, Blomberg A, Bretschneider T, Cascante M, Collin O, de Atauri P, Depner C, Dickinson R, Dobrzynski M, Fleck C, Garcia-Ojalvo J, Gonze D, Hahn J, Hess HM, Hollmann S, Krantz M, Kummer U, Lundh T, Martial G, Dos Santos VM, Mauer-Oberthür A, Regierer B, Skene B, Stalidzans E, Stelling J, Teusink B, Workman CT, Hohmann S. Cvijovic M, et al. Among authors: kummer u. NPJ Syst Biol Appl. 2016 May 26;2:16011. doi: 10.1038/npjsba.2016.11. eCollection 2016. NPJ Syst Biol Appl. 2016. PMID: 28725471 Free PMC article.
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