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BioHackathon 2015: Semantics of data for life sciences and reproducible research.
Vos RA, Katayama T, Mishima H, Kawano S, Kawashima S, Kim JD, Moriya Y, Tokimatsu T, Yamaguchi A, Yamamoto Y, Wu H, Amstutz P, Antezana E, Aoki NP, Arakawa K, Bolleman JT, Bolton E, Bonnal RJP, Bono H, Burger K, Chiba H, Cohen KB, Deutsch EW, Fernández-Breis JT, Fu G, Fujisawa T, Fukushima A, García A, Goto N, Groza T, Hercus C, Hoehndorf R, Itaya K, Juty N, Kawashima T, Kim JH, Kinjo AR, Kotera M, Kozaki K, Kumagai S, Kushida T, Lütteke T, Matsubara M, Miyamoto J, Mohsen A, Mori H, Naito Y, Nakazato T, Nguyen-Xuan J, Nishida K, Nishida N, Nishide H, Ogishima S, Ohta T, Okuda S, Paten B, Perret JL, Prathipati P, Prins P, Queralt-Rosinach N, Shinmachi D, Suzuki S, Tabata T, Takatsuki T, Taylor K, Thompson M, Uchiyama I, Vieira B, Wei CH, Wilkinson M, Yamada I, Yamanaka R, Yoshitake K, Yoshizawa AC, Dumontier M, Kosaki K, Takagi T. Vos RA, et al. Among authors: katayama t. F1000Res. 2020 Feb 24;9:136. doi: 10.12688/f1000research.18236.1. eCollection 2020. F1000Res. 2020. PMID: 32308977 Free PMC article.
KEGG for linking genomes to life and the environment.
Kanehisa M, Araki M, Goto S, Hattori M, Hirakawa M, Itoh M, Katayama T, Kawashima S, Okuda S, Tokimatsu T, Yamanishi Y. Kanehisa M, et al. Among authors: katayama t. Nucleic Acids Res. 2008 Jan;36(Database issue):D480-4. doi: 10.1093/nar/gkm882. Epub 2007 Dec 12. Nucleic Acids Res. 2008. PMID: 18077471 Free PMC article.
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.
Katayama T, Arakawa K, Nakao M, Ono K, Aoki-Kinoshita KF, Yamamoto Y, Yamaguchi A, Kawashima S, Chun HW, Aerts J, Aranda B, Barboza LH, Bonnal RJ, Bruskiewich R, Bryne JC, Fernández JM, Funahashi A, Gordon PM, Goto N, Groscurth A, Gutteridge A, Holland R, Kano Y, Kawas EA, Kerhornou A, Kibukawa E, Kinjo AR, Kuhn M, Lapp H, Lehvaslaiho H, Nakamura H, Nakamura Y, Nishizawa T, Nobata C, Noguchi T, Oinn TM, Okamoto S, Owen S, Pafilis E, Pocock M, Prins P, Ranzinger R, Reisinger F, Salwinski L, Schreiber M, Senger M, Shigemoto Y, Standley DM, Sugawara H, Tashiro T, Trelles O, Vos RA, Wilkinson MD, York W, Zmasek CM, Asai K, Takagi T. Katayama T, et al. J Biomed Semantics. 2010 Aug 21;1(1):8. doi: 10.1186/2041-1480-1-8. J Biomed Semantics. 2010. PMID: 20727200 Free PMC article.
BioRuby: bioinformatics software for the Ruby programming language.
Goto N, Prins P, Nakao M, Bonnal R, Aerts J, Katayama T. Goto N, et al. Among authors: katayama t. Bioinformatics. 2010 Oct 15;26(20):2617-9. doi: 10.1093/bioinformatics/btq475. Epub 2010 Aug 25. Bioinformatics. 2010. PMID: 20739307 Free PMC article.
The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications.
Katayama T, Wilkinson MD, Vos R, Kawashima T, Kawashima S, Nakao M, Yamamoto Y, Chun HW, Yamaguchi A, Kawano S, Aerts J, Aoki-Kinoshita KF, Arakawa K, Aranda B, Bonnal RJ, Fernández JM, Fujisawa T, Gordon PM, Goto N, Haider S, Harris T, Hatakeyama T, Ho I, Itoh M, Kasprzyk A, Kido N, Kim YJ, Kinjo AR, Konishi F, Kovarskaya Y, von Kuster G, Labarga A, Limviphuvadh V, McCarthy L, Nakamura Y, Nam Y, Nishida K, Nishimura K, Nishizawa T, Ogishima S, Oinn T, Okamoto S, Okuda S, Ono K, Oshita K, Park KJ, Putnam N, Senger M, Severin J, Shigemoto Y, Sugawara H, Taylor J, Trelles O, Yamasaki C, Yamashita R, Satoh N, Takagi T. Katayama T, et al. J Biomed Semantics. 2011 Aug 2;2:4. doi: 10.1186/2041-1480-2-4. J Biomed Semantics. 2011. PMID: 21806842 Free PMC article.
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.
Bonnal RJ, Aerts J, Githinji G, Goto N, MacLean D, Miller CA, Mishima H, Pagani M, Ramirez-Gonzalez R, Smant G, Strozzi F, Syme R, Vos R, Wennblom TJ, Woodcroft BJ, Katayama T, Prins P. Bonnal RJ, et al. Among authors: katayama t. Bioinformatics. 2012 Apr 1;28(7):1035-7. doi: 10.1093/bioinformatics/bts080. Epub 2012 Feb 12. Bioinformatics. 2012. PMID: 22332238 Free PMC article.
The Ruby UCSC API: accessing the UCSC genome database using Ruby.
Mishima H, Aerts J, Katayama T, Bonnal RJ, Yoshiura K. Mishima H, et al. Among authors: katayama t. BMC Bioinformatics. 2012 Sep 21;13:240. doi: 10.1186/1471-2105-13-240. BMC Bioinformatics. 2012. PMID: 22994508 Free PMC article.
1,755 results