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DDBJ new system and service refactoring.
Ogasawara O, Mashima J, Kodama Y, Kaminuma E, Nakamura Y, Okubo K, Takagi T. Ogasawara O, et al. Among authors: mashima j. Nucleic Acids Res. 2013 Jan;41(Database issue):D25-9. doi: 10.1093/nar/gks1152. Epub 2012 Nov 24. Nucleic Acids Res. 2013. PMID: 23180790 Free PMC article.
Exploration and grading of possible genes from 183 bacterial strains by a common protocol to identification of new genes: Gene Trek in Prokaryote Space (GTPS).
Kosuge T, Abe T, Okido T, Tanaka N, Hirahata M, Maruyama Y, Mashima J, Tomiki A, Kurokawa M, Himeno R, Fukuchi S, Miyazaki S, Gojobori T, Tateno Y, Sugawara H. Kosuge T, et al. Among authors: mashima j. DNA Res. 2006 Dec 31;13(6):245-54. doi: 10.1093/dnares/dsl014. Epub 2006 Dec 13. DNA Res. 2006. PMID: 17166861
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts.
Genome Information Integration Project And H-Invitational 2, Yamasaki C, Murakami K, Fujii Y, Sato Y, Harada E, Takeda J, Taniya T, Sakate R, Kikugawa S, Shimada M, Tanino M, Koyanagi KO, Barrero RA, Gough C, Chun HW, Habara T, Hanaoka H, Hayakawa Y, Hilton PB, Kaneko Y, Kanno M, Kawahara Y, Kawamura T, Matsuya A, Nagata N, Nishikata K, Noda AO, Nurimoto S, Saichi N, Sakai H, Sanbonmatsu R, Shiba R, Suzuki M, Takabayashi K, Takahashi A, Tamura T, Tanaka M, Tanaka S, Todokoro F, Yamaguchi K, Yamamoto N, Okido T, Mashima J, Hashizume A, Jin L, Lee KB, Lin YC, Nozaki A, Sakai K, Tada M, Miyazaki S, Makino T, Ohyanagi H, Osato N, Tanaka N, Suzuki Y, Ikeo K, Saitou N, Sugawara H, O'Donovan C, Kulikova T, Whitfield E, Halligan B, Shimoyama M, Twigger S, Yura K, Kimura K, Yasuda T, Nishikawa T, Akiyama Y, Motono C, Mukai Y, Nagasaki H, Suwa M, Horton P, Kikuno R, Ohara O, Lancet D, Eveno E, Graudens E, Imbeaud S, Debily MA, Hayashizaki Y, Amid C, Han M, Osanger A, Endo T, Thomas MA, Hirakawa M, Makalowski W, Nakao M, Kim NS, Yoo HS, De Souza SJ, Bonaldo Mde F, Niimura Y, Kuryshev V, Schupp I, Wiemann S, Bellgard M, Shionyu M, Jia L, Thierry-Mieg D, Thierry-Mieg J, Wagner L, Zhang Q, Go M, Minoshima S, Ohtsubo M, Hanada K, Tonellato P, Isogai T, Zhang J, Lenhard B, Kim S, Chen Z, Hinz U, Estreicher A, Nakai K, Makalowska I, Hide W, Tiffin N, Wilming L, Chakraborty R, Soares MB, Chiusano ML, Suzuki Y, Auffray C, Yamaguchi-Kabata Y, Itoh T, Hishiki T, Fukuchi S, Nishikawa K, Sugano S, Nomura N, Tateno Y, Imanishi T, Gojobori T. Genome Information Integration Project And H-Invitational 2, et al. Among authors: mashima j. Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. doi: 10.1093/nar/gkm999. Epub 2007 Dec 18. Nucleic Acids Res. 2008. PMID: 18089548 Free PMC article.
DDBJ progress report.
Kaminuma E, Kosuge T, Kodama Y, Aono H, Mashima J, Gojobori T, Sugawara H, Ogasawara O, Takagi T, Okubo K, Nakamura Y. Kaminuma E, et al. Among authors: mashima j. Nucleic Acids Res. 2011 Jan;39(Database issue):D22-7. doi: 10.1093/nar/gkq1041. Epub 2010 Nov 9. Nucleic Acids Res. 2011. PMID: 21062814 Free PMC article.
DDBJ progress report: a new submission system for leading to a correct annotation.
Kosuge T, Mashima J, Kodama Y, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y. Kosuge T, et al. Among authors: mashima j. Nucleic Acids Res. 2014 Jan;42(Database issue):D44-9. doi: 10.1093/nar/gkt1066. Epub 2013 Nov 4. Nucleic Acids Res. 2014. PMID: 24194602 Free PMC article.
Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records.
Federhen S, Clark K, Barrett T, Parkinson H, Ostell J, Kodama Y, Mashima J, Nakamura Y, Cochrane G, Karsch-Mizrachi I. Federhen S, et al. Among authors: mashima j. Stand Genomic Sci. 2014 Jan 29;9(3):1275-7. doi: 10.4056/sigs.4851102. eCollection 2014 Jun 15. Stand Genomic Sci. 2014. PMID: 25197497 Free PMC article.
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data.
Kodama Y, Mashima J, Kosuge T, Katayama T, Fujisawa T, Kaminuma E, Ogasawara O, Okubo K, Takagi T, Nakamura Y. Kodama Y, et al. Among authors: mashima j. Nucleic Acids Res. 2015 Jan;43(Database issue):D18-22. doi: 10.1093/nar/gku1120. Epub 2014 Dec 3. Nucleic Acids Res. 2015. PMID: 25477381 Free PMC article.
DNA data bank of Japan (DDBJ) progress report.
Mashima J, Kodama Y, Kosuge T, Fujisawa T, Katayama T, Nagasaki H, Okuda Y, Kaminuma E, Ogasawara O, Okubo K, Nakamura Y, Takagi T. Mashima J, et al. Nucleic Acids Res. 2016 Jan 4;44(D1):D51-7. doi: 10.1093/nar/gkv1105. Epub 2015 Nov 17. Nucleic Acids Res. 2016. PMID: 26578571 Free PMC article.
24 results