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1,755 results
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Payao: a community platform for SBML pathway model curation.
Matsuoka Y, Ghosh S, Kikuchi N, Kitano H. Matsuoka Y, et al. Bioinformatics. 2010 May 15;26(10):1381-3. doi: 10.1093/bioinformatics/btq143. Epub 2010 Apr 5. Bioinformatics. 2010. PMID: 20371497 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: matsuoka y. Bioinformatics. 2012 Aug 1;28(15):2016-21. doi: 10.1093/bioinformatics/bts270. Epub 2012 May 10. Bioinformatics. 2012. PMID: 22581176 Free PMC article.
BioPAX support in CellDesigner.
Mi H, Muruganujan A, Demir E, Matsuoka Y, Funahashi A, Kitano H, Thomas PD. Mi H, et al. Among authors: matsuoka y. Bioinformatics. 2011 Dec 15;27(24):3437-8. doi: 10.1093/bioinformatics/btr586. Epub 2011 Oct 21. Bioinformatics. 2011. PMID: 22021903 Free PMC article.
PathText: a text mining integrator for biological pathway visualizations.
Kemper B, Matsuzaki T, Matsuoka Y, Tsuruoka Y, Kitano H, Ananiadou S, Tsujii J. Kemper B, et al. Among authors: matsuoka y. Bioinformatics. 2010 Jun 15;26(12):i374-81. doi: 10.1093/bioinformatics/btq221. Bioinformatics. 2010. PMID: 20529930 Free PMC article.
Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.
Lopes TJ, Schaefer M, Shoemaker J, Matsuoka Y, Fontaine JF, Neumann G, Andrade-Navarro MA, Kawaoka Y, Kitano H. Lopes TJ, et al. Among authors: matsuoka y. Bioinformatics. 2011 Sep 1;27(17):2414-21. doi: 10.1093/bioinformatics/btr414. Epub 2011 Jul 28. Bioinformatics. 2011. PMID: 21798963
Social engineering for virtual 'big science' in systems biology.
Kitano H, Ghosh S, Matsuoka Y. Kitano H, et al. Among authors: matsuoka y. Nat Chem Biol. 2011 Jun;7(6):323-6. doi: 10.1038/nchembio.574. Nat Chem Biol. 2011. PMID: 21587248 No abstract available.
Modeling and simulation using CellDesigner.
Matsuoka Y, Funahashi A, Ghosh S, Kitano H. Matsuoka Y, et al. Methods Mol Biol. 2014;1164:121-45. doi: 10.1007/978-1-4939-0805-9_11. Methods Mol Biol. 2014. PMID: 24927840
Software for systems biology: from tools to integrated platforms.
Ghosh S, Matsuoka Y, Asai Y, Hsin KY, Kitano H. Ghosh S, et al. Among authors: matsuoka y. Nat Rev Genet. 2011 Nov 3;12(12):821-32. doi: 10.1038/nrg3096. Nat Rev Genet. 2011. PMID: 22048662 Review.
Consistent design schematics for biological systems: standardization of representation in biological engineering.
Matsuoka Y, Ghosh S, Kitano H. Matsuoka Y, et al. J R Soc Interface. 2009 Aug 6;6 Suppl 4(Suppl 4):S393-404. doi: 10.1098/rsif.2009.0046.focus. Epub 2009 Jun 3. J R Soc Interface. 2009. PMID: 19493898 Free PMC article. Review.
Integration of CellDesigner and SABIO-RK.
Funahashi A, Jouraku A, Matsuoka Y, Kitano H. Funahashi A, et al. Among authors: matsuoka y. In Silico Biol. 2007;7(2 Suppl):S81-90. In Silico Biol. 2007. PMID: 17822394
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