Last updated:2014.5.30.

DDBJ activity publications

| 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007 | 2006 | 2005 | 2004 | 2003 | 2002 | 2001 | 2000 | 1999 | 1998 | 1997 |

2014

"Toward richer metadata for microbial sequences: replacing strain-level NCBI taxonomy taxids with BioProject, BioSample and Assembly records"
Scott Federhen, Karen Clark, Tanya Barrett, Helen Parkinson, James Ostell, Yuichi Kodama, Jun Mashima, Yasukazu Nakamura, Guy Cochrane, Ilene Karsch-Mizrachi
Stand. Genomic Sci. 2014 9(3): doi:10.4056/sigs.4851102.
"DDBJ progress report: a new submission system for leading to a correct annotation"
Takehide Kosuge, Jun Mashima, Yuichi Kodama, Takatomo Fujisawa, Eli Kaminuma, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi and Yasukazu Nakamura
Nucleic Acids Res. 2014, 42 Database issue: D44-D49.

2013

"DDBJ new system and service refactoring"
Osamu Ogasawara, Jun Mashima, Yuichi Kodama, Eli Kaminuma, Yasukazu Nakamura, Kousaku Okubo and Toshihisa Takagi
Nucleic Acids Res. 2013, 41 Database issue: D25-D29.
"The International Nucleotide Sequence Database Collaboration"
Yasukazu Nakamura,Guy Cochrane and Ilene Karsch-Mizrachi on behalf of the International Nucleotide Sequence Database: Collaboration
Nucleic Acids Res. 2013, 41 Database issue: D21-D24.

2012

"The International Nucleotide Sequence Database Collaboration"
Ilene Karsch-Mizrachi, Yasukazu Nakamura, and Guy Cochrane on behalf of the International Nucleotide Sequence Database Collaboration
Nucleic Acids Res. 2012, 40, Database issue: D33-D37; doi:10.1093/nar/gkr1006.
"The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments"
Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, and Yasukazu Nakamura
Nucleic Acids Res. 2012, 40 Database issue: D38-D42; doi:10.1093/nar/gkr994.
"The sequence read archive: explosive growth of sequencing data"
Yuichi Kodama, Martin Shumway, and Rasko Leinonen on behalf of the International Nucleotide Sequence Database Collaboration
Nucleic Acids Res. 2012, 40 Database issue: D54-D56; doi:10.1093/nar/gkr854.

2011

"The International Nucleotide Sequence Database Collaboration"
Guy Cochrane, Ilene Karsch-Mizrachi, and Yasukazu Nakamura on behalf of the International Nucleotide Sequence Database Collaboration.
Nucleic Acids Research, 2011, 39 Database issue: D15-D18
"The Sequence Read Archive"
Rasko Leinonen, Hideaki Sugawara, and Martin Shumway on behalf of the International Nucleotide Sequence Database Collaboration.
Nucleic Acids Research, 2011, 39 Database issue: D19-D21
"DDBJ progress report"
Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, and Yasukazu Nakamura.
Nucleic Acids Research, 2011, 39 Database issue: D22-D27

2010

"Biological databases at DNA Data Bank of Japan in the era of next-generation sequencing technologies"
Kodama Y, Kaminuma E, Saruhashi S, Ikeo K, Sugawara H, Tateno Y, Nakamura Y.
Advances in Experimental Medicine and Biology, 2010, 680 Part 1: 125-135
"DDBJ launches a new archive database with analytical tools for next-generation sequence data"
Kaminuma E, Mashima J, Kodama Y, Gojobori T, Ogasawara O, Okubo K, Takagi T and Nakamura Y.
Nucleic Acids Res., 2010, 38 Database issue: D33-D38
"Archiving next generation sequencing data"
Shumway M, Cochrane G and Sugawara H.
Nucleic Acids Res., 2010, 38 Database issue: D870-D871

2009

"DDBJ dealing with mass data produced by the second generation sequencer"
Sugawara H, Ikeo K, Fukuchi S, Gojobori T and Tateno Y.
Nucleic Acids Res., 2009, 37 Database issue: D16-D18
"Web API for biology with a workflow navigation system"
Kwon Y, Shigemoto Y, Kuwana Y and Sugawara H.
Nucleic Acids Res., 2009, 37 No. suppl_2: W11-W16

2008

"DDBJ with new system and face"
Sugawara H, Ogasawara O, Okubo K, Gojobori T and Tateno Y.
Nucleic Acids Res., 2008, 36 Database issue: D22-D24
"The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts"
Genome Information Integration Project And H-Invitation 2 (From DDBJ, Okido T, Mashima J, Lee K-B, Nozaki A, Sakai K, Suzuki Y, Ikeo K, Saitou N, Sugawara H, Fukuchi S, Tateno Y, Gojobori T.)
Nucleic Acids Res., 2008, 36 Database issue: D793-D799

2007

"DDBJ working on evaluation and classification of bacterial genes in INSDC"
Sugawara H, Abe T, Gojobori T and Tateno Y.
Nucleic Acids Res., 2007, 35 Database issue: D13-D15

2006

"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.
DNA Res. 2006, 13(6): 245-54. Epub 2006, Dec. 13
"DDBJ in preparation for overview of research activities behind data submissions"
Okubo K, Sugawara H, Gojobori T and Tateno Y.
Nucleic Acids Res., 2006, 34 Database issue: D6-D9
"Evidence standards in experimental and inferential INSDC Third Party Annotation data"
Cochrane G, Bates K, Apweiler R, Tateno Y, Mashima J, Kosuge T, Mizrachi IK, Schafer S, Fetchko M.
OMICS, 2006, 10(2): 105-13

2005

"DDBJ in collaboration with mass-sequencing teams on annotation"
Tateno Y, Saitou N, Okubo K, Sugawara H and Gojobori T.
Nucleic Acids Res., 2005, 33 Database issue: D25-D28

2004

"DDBJ in the stream of various biological data"
Miyazaki S, Sugawara H, Ikeo K, Gojobori T and Tateno Y.
Nucleic Acids Res., 2004, 32, Database issue D31-D34
"Submission of microarray data to public repositories"
Ball CA, Brazma A, Causton H, Chervitz S, Edgar R, Hingamp P, Matese JC, Parkinson H, Quackenbush J, Ringwald M, Sansone SA, Sherlock G, Spellman P, Stoeckert C, Tateno Y, Taylor R, White J, Winegarden N.
PLoS Biol. 2004, 2(9): E317. Epub 2004, Aug. 31

2003

"CIBEX: center for information biology gene expression database"
Ikeo K, Ishi-i J, Tamura T, Gojobori T, Tateno Y.
C R Biol. 2003, 326(10-11): 1079-1082
"Populations and Genetics, Legal and Socio-Ethical Perspectives"
Edited by Bartha Maria Knoppers. Martinus Nijhoff Publishers.
ISBN: 90-04-13678-9. Miyazaki S, Tateno Y : DNA Data Bank of Japan as an Indispensable Public Database (115-121).

2002

"Genome Information Broker (GIB): data retrieval and comparative analysis system for completed microbial genomes and more"
Fumoto M, Miyazaki S and Sugawara H.
Nucleic Acids Res., 2002, 30(1): 66-68
"GTOP : A database of protein structures predicted from genome sequences"
Kawabata T, Fukuchi S, Homma K, Ota M, Araki J, Ito T, Ichiyoshi N and Nishikawa K.
Nucleic Acids Res., 2002, 30(1): 294-298
"DNA Data Bank of Japan (DDBJ) for genome scale research in life science"
Tateno Y, Imanishi T, Miyazaki S, Fukami-Kobayashi K, Saitou N, Sugawara H and Gojobori T.
Nucleic Acids Res., 2002, 30(1): 27-30

2001

"CAMUS DB for amino acid sequence data"
Misu S, Iizuka T, Kawanishi Y, Fukami K and Saitou N.
Genome Informatics, 2001: 502-503

2000

"Quality control in data banks for molecular biology"
Abola E.E, Bairoch A, Baker W.C, Beck S, Benson D.A, Berman H, Cameron G, Cantor C, Doubet S, Hubbbard T.J.P, Jones T.A, Kleywegt G.J. Kolaskar A.S, Kuik Van A, Lesk A.M, Mews H.-W, Neuhaus D, Pfeiffer F, TenEyck L.F, Simpson R.J, Stosser G, Sussman J.L, Tateno Y, Tsugita H, Ulrich E.L, and Viegenthart J.F.G.
BioEssays, 22: 1024-1034
"A new file format and tools for the large-scale data submission to DNA Data Bank of Japan (DDBJ)"
Miyazaki S, Hashimoto H, Shimada A, Tateno Y and Sugawara H.
Currents in Computational Molecular Biology, pp. 60-61
"CAMUS DB:Development of structural database for homology search"
Kikuchi M, Misu S, Imanishi T, and Saitou N. In Miyano S, Shamir R and Takagi T. (eds.)
Currents in Computational Molecular Biology, Universal Academy Press, Tokyo, pp. 80-81
"DNA data bank of Japan (DDBJ) in collaboration with mass sequencing teams"
Tateno Y, Miyazaki S, Ota M, Sugawara H. and Gojobori T.
Nucleic Acids Res., 2000, 28(1): 24-26

1999

"Reconstruction of large-scale phylogentic trees: Problems and solutions"
Miyazaki S and Sugawara H.
Amino Acids,(1999) 17 (1): 119
"DNA Data Bank of Japan dealing with large-scale data submission"
Sugawara H, Miyazaki S, Gojobori T and Tateno Y.
Nucleic Acids Res., 1999, 27(1): 25-28

1998

"Codon usage tabulated from the international DNA sequence databases"
Nakamura Y, Gojobori T and Ikemura T.
Nucleic Acids Res., 1998, 26(1): 334
"Formal design and implementation of an improved DDBJ DNA database with a new schema and object oriented library"
Okayama T, Tamura T, Gojobori T, Tateno Y, Ikeo K, Miyazaki S, Fukami-Kobayashi K and Sugawara H.
Bioinformatics, 1998, 14(6): 472-478
"DNA Data Bank of Japan at work on genome sequence data"
Tateno Y, Fukami-Kobayashi K, Miyazaki S, Sugawara H and Gojobori T.
Nucleic Acids Res., 1998, 26(1): 16-20

1997

"International DNA databanking activities at the National Institute of Genetics"
Gojobori T and Tateno Y.
Japanese Science Monthly, 1997, 50: 352-367
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