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The systems biology simulation core algorithm.
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H, Zell A, Dräger A. Keller R, et al. Among authors: funahashi a. BMC Syst Biol. 2013 Jul 5;7:55. doi: 10.1186/1752-0509-7-55. BMC Syst Biol. 2013. PMID: 23826941 Free PMC article.
The Systems Biology Graphical Notation.
Le Novère N, Hucka M, Mi H, Moodie S, Schreiber F, Sorokin A, Demir E, Wegner K, Aladjem MI, Wimalaratne SM, Bergman FT, Gauges R, Ghazal P, Kawaji H, Li L, Matsuoka Y, Villéger A, Boyd SE, Calzone L, Courtot M, Dogrusoz U, Freeman TC, Funahashi A, Ghosh S, Jouraku A, Kim S, Kolpakov F, Luna A, Sahle S, Schmidt E, Watterson S, Wu G, Goryanin I, Kell DB, Sander C, Sauro H, Snoep JL, Kohn K, Kitano H. Le Novère N, et al. Among authors: funahashi a. Nat Biotechnol. 2009 Aug;27(8):735-41. doi: 10.1038/nbt.1558. Epub 2009 Aug 7. Nat Biotechnol. 2009. PMID: 19668183 Free article.
Physiological environment induces quick response - slow exhaustion reactions.
Hiroi N, Lu J, Iba K, Tabira A, Yamashita S, Okada Y, Flamm C, Oka K, Köhler G, Funahashi A. Hiroi N, et al. Among authors: funahashi a. Front Physiol. 2011 Sep 21;2:50. doi: 10.3389/fphys.2011.00050. eCollection 2011. Front Physiol. 2011. PMID: 21960972 Free PMC article.
Software support for SBGN maps: SBGN-ML and LibSBGN.
van Iersel MP, Villéger AC, Czauderna T, Boyd SE, Bergmann FT, Luna A, Demir E, Sorokin A, Dogrusoz U, Matsuoka Y, Funahashi A, Aladjem MI, Mi H, Moodie SL, Kitano H, Le Novère N, Schreiber F. van Iersel MP, et al. Among authors: funahashi a. Bioinformatics. 2012 Aug 1;28(15):2016-21. doi: 10.1093/bioinformatics/bts270. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581176 Free PMC article.
From microscopy data to in silico environments for in vivo-oriented simulations.
Hiroi1 N, Klann M, Iba K, Heras Ciechomski Pd, Yamashita S, Tabira A, Okuhara T, Kubojima T, Okada Y, Oka K, Mange R, Unger M, Funahashi A, Koeppl H. Hiroi1 N, et al. Among authors: funahashi a. EURASIP J Bioinform Syst Biol. 2012 Jun 26;2012(1):7. doi: 10.1186/1687-4153-2012-7. EURASIP J Bioinform Syst Biol. 2012. PMID: 22734658 Free PMC article.
120 results