Literature DB >> 14681352

DDBJ in the stream of various biological data.

S Miyazaki1, H Sugawara, K Ikeo, T Gojobori, Y Tateno.   

Abstract

In the past year we at DDBJ (http://www.ddbj.nig. ac.jp) have made a steady increase in the number of data submissions with a 50.6% increment in the number of bases or 46.5% increment in the number of entries. Among them the genome data of man, ascidian and rice hold the top three. Our activity has extended to providing a tool that enables sequence retrieval using regular expressions, and to launching our SOAP server and web services to facilitate the acquisition of proper data and tools from a huge number of biological data resources on websites worldwide. We have also opened our public gene expression database, CIBEX.

Entities:  

Mesh：

Year:  2004        PMID： 14681352      PMCID： PMC308861          DOI： 10.1093/nar/gkh127

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  15 in total

1.  The DNA sequence of human chromosome 22.

Authors:  I Dunham; N Shimizu; B A Roe; S Chissoe; A R Hunt; J E Collins; R Bruskiewich; D M Beare; M Clamp; L J Smink; R Ainscough; J P Almeida; A Babbage; C Bagguley; J Bailey; K Barlow; K N Bates; O Beasley; C P Bird; S Blakey; A M Bridgeman; D Buck; J Burgess; W D Burrill; K P O'Brien
Journal:  Nature       Date:  1999-12-02       Impact factor: 49.962

2.  Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium.

Authors: 
Journal:  Nature       Date:  1999-10-28       Impact factor: 49.962

3.  DNA Data Bank of Japan (DDBJ) in XML.

Authors:  S Miyazaki; H Sugawara; T Gojobori; Y Tateno
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  Biological SOAP servers and web services provided by the public sequence data bank.

Authors:  H Sugawara; S Miyazaki
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

Review 5.  Ciona intestinalis: an emerging model for whole-genome analyses.

Authors:  Nori Satoh; Yutaka Satou; Brad Davidson; Michael Levine
Journal:  Trends Genet       Date:  2003-07       Impact factor: 11.639

6.  Basic local alignment search tool.

Authors:  S F Altschul; W Gish; W Miller; E W Myers; D J Lipman
Journal:  J Mol Biol       Date:  1990-10-05       Impact factor: 5.469

7.  DNA Data Bank of Japan at work on genome sequence data.

Authors:  Y Tateno; K Fukami-Kobayashi; S Miyazaki; H Sugawara; T Gojobori
Journal:  Nucleic Acids Res       Date:  1998-01-01       Impact factor: 16.971

8.  Rapid and sensitive protein similarity searches.

Authors:  D J Lipman; W R Pearson
Journal:  Science       Date:  1985-03-22       Impact factor: 47.728

9.  Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice.

Authors:  Shoshi Kikuchi; Kouji Satoh; Toshifumi Nagata; Nobuyuki Kawagashira; Koji Doi; Naoki Kishimoto; Junshi Yazaki; Masahiro Ishikawa; Hitomi Yamada; Hisako Ooka; Isamu Hotta; Keiichi Kojima; Takahiro Namiki; Eisuke Ohneda; Wataru Yahagi; Kohji Suzuki; Chao Jie Li; Kenji Ohtsuki; Toru Shishiki; Yasuhiro Otomo; Kazuo Murakami; Yoshiharu Iida; Sumio Sugano; Tatsuto Fujimura; Yutaka Suzuki; Yuki Tsunoda; Takashi Kurosaki; Takeko Kodama; Hiromi Masuda; Michie Kobayashi; Quihong Xie; Min Lu; Ryuya Narikawa; Akio Sugiyama; Kouichi Mizuno; Satoko Yokomizo; Junko Niikura; Rieko Ikeda; Junya Ishibiki; Midori Kawamata; Akemi Yoshimura; Junichirou Miura; Takahiro Kusumegi; Mitsuru Oka; Risa Ryu; Mariko Ueda; Kenichi Matsubara; Jun Kawai; Piero Carninci; Jun Adachi; Katsunori Aizawa; Takahiro Arakawa; Shiro Fukuda; Ayako Hara; Wataru Hashizume; Norihito Hayatsu; Koichi Imotani; Yoshiyuki Ishii; Masayoshi Itoh; Ikuko Kagawa; Shinji Kondo; Hideaki Konno; Ai Miyazaki; Naoki Osato; Yoshimi Ota; Rintaro Saito; Daisuke Sasaki; Kenjiro Sato; Kazuhiro Shibata; Akira Shinagawa; Toshiyuki Shiraki; Masayasu Yoshino; Yoshihide Hayashizaki; Ayako Yasunishi
Journal:  Science       Date:  2003-07-18       Impact factor: 47.728

10.  The genome sequence and structure of rice chromosome 1.

Authors:  Takuji Sasaki; Takashi Matsumoto; Kimiko Yamamoto; Katsumi Sakata; Tomoya Baba; Yuichi Katayose; Jianzhong Wu; Yoshihito Niimura; Zhukuan Cheng; Yoshiaki Nagamura; Baltazar A Antonio; Hiroyuki Kanamori; Satomi Hosokawa; Masatoshi Masukawa; Koji Arikawa; Yoshino Chiden; Mika Hayashi; Masako Okamoto; Tsuyu Ando; Hiroyoshi Aoki; Kohei Arita; Masao Hamada; Chizuko Harada; Saori Hijishita; Mikiko Honda; Yoko Ichikawa; Atsuko Idonuma; Masumi Iijima; Michiko Ikeda; Maiko Ikeno; Sachie Ito; Tomoko Ito; Yuichi Ito; Yukiyo Ito; Aki Iwabuchi; Kozue Kamiya; Wataru Karasawa; Satoshi Katagiri; Ari Kikuta; Noriko Kobayashi; Izumi Kono; Kayo Machita; Tomoko Maehara; Hiroshi Mizuno; Tatsumi Mizubayashi; Yoshiyuki Mukai; Hideki Nagasaki; Marina Nakashima; Yuko Nakama; Yumi Nakamichi; Mari Nakamura; Nobukazu Namiki; Manami Negishi; Isamu Ohta; Nozomi Ono; Shoko Saji; Kumiko Sakai; Michie Shibata; Takanori Shimokawa; Ayahiko Shomura; Jianyu Song; Yuka Takazaki; Kimihiro Terasawa; Kumiko Tsuji; Kazunori Waki; Harumi Yamagata; Hiroko Yamane; Shoji Yoshiki; Rie Yoshihara; Kazuko Yukawa; Huisun Zhong; Hisakazu Iwama; Toshinori Endo; Hidetaka Ito; Jang Ho Hahn; Ho-Il Kim; Moo-Young Eun; Masahiro Yano; Jiming Jiang; Takashi Gojobori
Journal:  Nature       Date:  2002-11-21       Impact factor: 49.962
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  32 in total

1.  IMGT/V-QUEST, an integrated software program for immunoglobulin and T cell receptor V-J and V-D-J rearrangement analysis.

Authors:  Véronique Giudicelli; Denys Chaume; Marie-Paule Lefranc
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

2.  Expression and purification of human PAG, a transmembrane adapter protein using an insect cell expression system and its structure basis.

Authors:  Satoru Takeuchi
Journal:  Protein J       Date:  2006-06       Impact factor: 2.371

3.  Molecular cloning, sequence, function and structural basis of human heart 150 kDa oxygen-regulated protein, an ER chaperone.

Authors:  Satoru Takeuchi
Journal:  Protein J       Date:  2006-12       Impact factor: 2.371

Review 4.  Genotype-phenotype databases: challenges and solutions for the post-genomic era.

Authors:  Gudmundur A Thorisson; Juha Muilu; Anthony J Brookes
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

5.  A new species of Calicotyle Diesing, 1850 (Monogenea: Monocotylidae) from the shortspine spurdog Squalus mitsukurii Jordan & Snyder and the synonymy of Gymnocalicotyle Nybelin, 1941 with this genus.

Authors:  Akiko Kitamura; Kazuo Ogawa; Toshiya Shimizu; Akira Kurashima; Nobuhiro Mano; Toru Taniuchi; Hitomi Hirose
Journal:  Syst Parasitol       Date:  2010-01-30       Impact factor: 1.431

6.  Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

Authors:  Terrence S Furey; Mark Diekhans; Yontao Lu; Tina A Graves; Lachlan Oddy; Jennifer Randall-Maher; LaDeana W Hillier; Richard K Wilson; David Haussler
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

7.  TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services.

Authors:  Toshiaki Katayama; Mitsuteru Nakao; Toshihisa Takagi
Journal:  Nucleic Acids Res       Date:  2010-05-14       Impact factor: 16.971

8.  The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.

Authors:  Toshiaki Katayama; Kazuharu Arakawa; Mitsuteru Nakao; Keiichiro Ono; Kiyoko F Aoki-Kinoshita; Yasunori Yamamoto; Atsuko Yamaguchi; Shuichi Kawashima; Hong-Woo Chun; Jan Aerts; Bruno Aranda; Lord Hendrix Barboza; Raoul Jp Bonnal; Richard Bruskiewich; Jan C Bryne; José M Fernández; Akira Funahashi; Paul Mk Gordon; Naohisa Goto; Andreas Groscurth; Alex Gutteridge; Richard Holland; Yoshinobu Kano; Edward A Kawas; Arnaud Kerhornou; Eri Kibukawa; Akira R Kinjo; Michael Kuhn; Hilmar Lapp; Heikki Lehvaslaiho; Hiroyuki Nakamura; Yasukazu Nakamura; Tatsuya Nishizawa; Chikashi Nobata; Tamotsu Noguchi; Thomas M Oinn; Shinobu Okamoto; Stuart Owen; Evangelos Pafilis; Matthew Pocock; Pjotr Prins; René Ranzinger; Florian Reisinger; Lukasz Salwinski; Mark Schreiber; Martin Senger; Yasumasa Shigemoto; Daron M Standley; Hideaki Sugawara; Toshiyuki Tashiro; Oswaldo Trelles; Rutger A Vos; Mark D Wilkinson; William York; Christian M Zmasek; Kiyoshi Asai; Toshihisa Takagi
Journal:  J Biomed Semantics       Date:  2010-08-21

9.  Bio-jETI: a framework for semantics-based service composition.

Authors:  Anna-Lena Lamprecht; Tiziana Margaria; Bernhard Steffen
Journal:  BMC Bioinformatics       Date:  2009-10-01       Impact factor: 3.307

10.  Web API for biology with a workflow navigation system.

Authors:  Yeondae Kwon; Yasumasa Shigemoto; Yoshikazu Kuwana; Hideaki Sugawara
Journal:  Nucleic Acids Res       Date:  2009-05-05       Impact factor: 16.971
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