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DNA Data Bank of Japan.
Published in:
Nucleic Acids Research, 2017, v. 45, n. D1, p. D25, doi. 10.1093/nar/gkw1001
By:
- Jun Mashima;
- Yuichi Kodama;
- Takatomo Fujisawa;
- Toshiaki Katayama;
- Yoshihiro Okuda;
- Eli Kaminuma;
- Osamu Ogasawara;
- Kousaku Okubo;
- Yasukazu Nakamura;
- Toshihisa Takagi
Publication type:
Article
DNA data bank of Japan (DDBJ) progress report.
Published in:
Nucleic Acids Research, 2016, v. 44, n. 1, p. D51, doi. 10.1093/nar/gkv1105
By:
- Jun Mashima;
- Yuichi Kodama;
- Takehide Kosuge;
- Takatomo Fujisawa;
- Toshiaki Katayama;
- Hideki Nagasaki;
- Yoshihiro Okuda;
- Eli Kaminuma;
- Osamu Ogasawara;
- Kousaku Okubo;
- Yasukazu Nakamura;
- Toshihisa Takagi
Publication type:
Article
The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data.
Published in:
Nucleic Acids Research, 2015, v. 43, n. D1, p. D18, doi. 10.1093/nar/gku1120
By:
- Kodama, Yuichi;
- Mashima, Jun;
- Kosuge, Takehide;
- Katayama, Toshiaki;
- Fujisawa, Takatomo;
- Kaminuma, Eli;
- Ogasawara, Osamu;
- Okubo, Kousaku;
- Takagi, Toshihisa;
- Nakamura, Yasukazu
Publication type:
Article
TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model.
Published in:
Nucleic Acids Research, 2014, v. 42, n. W1, p. W442, doi. 10.1093/nar/gku403
By:
- Kawano, Shin;
- Watanabe, Tsutomu;
- Mizuguchi, Sohei;
- Araki, Norie;
- Katayama, Toshiaki;
- Yamaguchi, Atsuko
Publication type:
Article
CyanoBase and RhizoBase: databases of manually curated annotations for cyanobacterial and rhizobial genomes.
Published in:
Nucleic Acids Research, 2014, v. 42, n. D1, p. D666, doi. 10.1093/nar/gkt1145
By:
- Fujisawa, Takatomo;
- Okamoto, Shinobu;
- Katayama, Toshiaki;
- Nakao, Mitsuteru;
- Yoshimura, Hidehisa;
- Kajiya-Kanegae, Hiromi;
- Yamamoto, Sumiko;
- Yano, Chiyoko;
- Yanaka, Yuka;
- Maita, Hiroko;
- Kaneko, Takakazu;
- Tabata, Satoshi;
- Nakamura, Yasukazu
Publication type:
Article
KEGG OC: a large-scale automatic construction of taxonomy-based ortholog clusters.
Published in:
Nucleic Acids Research, 2013, v. 41, p. D353, doi. 10.1093/nar/gks1239
By:
- Akihiro Nakaya;
- Toshiaki Katayama;
- Masumi Itoh;
- Kazushi Hiranuka;
- Shuichi Kawashima;
- Yuki Moriya;
- Shujiro Okuda;
- Michihiro Tanaka;
- Toshiaki Tokimatsu;
- Yoshihiro Yamanishi;
- Yoshizawa, Akiyasu C.;
- Minoru Kanehisa;
- Susumu Goto
Publication type:
Article
TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services.
Published in:
Nucleic Acids Research, 2010, v. 38, n. suppl_2, p. W706, doi. 10.1093/nar/gkq386
By:
- Katayama, Toshiaki;
- Nakao, Mitsuteru;
- Takagi, Toshihisa
Publication type:
Article
Full-Malaria/Parasites and Full-Arthropods: databases of full-length cDNAs of parasites and arthropods, update 2009.
Published in:
Nucleic Acids Research, 2009, v. 37, n. suppl_1, p. D520, doi. 10.1093/nar/gkn856
By:
- Wakaguri, Hiroyuki;
- Suzuki, Yutaka;
- Katayama, Toshiaki;
- Kawashima, Shuichi;
- Kibukawa, Eri;
- Hiranuka, Kazushi;
- Sasaki, Masahide;
- Sugano, Sumio;
- Watanabe, Junichi
Publication type:
Article
KEGG Atlas mapping for global analysis of metabolic pathways.
Published in:
Nucleic Acids Research, 2008, v. 36, n. suppl_2, p. W423, doi. 10.1093/nar/gkn282
By:
- Okuda, Shujiro;
- Yamada, Takuji;
- Hamajima, Masami;
- Itoh, Masumi;
- Katayama, Toshiaki;
- Bork, Peer;
- Goto, Susumu;
- Kanehisa, Minoru
Publication type:
Article
AAindex: amino acid index database, progress report 2008.
Published in:
Nucleic Acids Research, 2008, v. 36, p. D202
By:
- Kawashima, Shuichi;
- Pokarowski, Piotr;
- Pokarowska, Maria;
- Kolinski, Andrzej;
- Katayama, Toshiaki;
- Kanehisa, Minoru
Publication type:
Article
KEGG for linking genomes to life and the environment.
Published in:
Nucleic Acids Research, 2008, v. 36, p. D480
By:
- Kanehisa, Minoru;
- Araki, Michihiro;
- Goto, Susumu;
- Hattori, Masahiro;
- Hirakawa, Mika;
- Itoh, Masumi;
- Katayama, Toshiaki;
- Kawashima, Shuichi;
- Okuda, Shujiro;
- Tokimatsu, Toshiaki;
- Yamanishi, Yoshihiro
Publication type:
Article
TogoID: an exploratory ID converter to bridge biological datasets.
Published in:
Bioinformatics, 2022, v. 38, n. 17, p. 4194, doi. 10.1093/bioinformatics/btac491
By:
- Ikeda, Shuya;
- Ono, Hiromasa;
- Ohta, Tazro;
- Chiba, Hirokazu;
- Naito, Yuki;
- Moriya, Yuki;
- Kawashima, Shuichi;
- Yamamoto, Yasunori;
- Okamoto, Shinobu;
- Goto, Susumu;
- Katayama, Toshiaki
Publication type:
Article
FALDO: a semantic standard for describing the location of nucleotide and protein feature annotation.
Published in:
Journal of Biomedical Semantics, 2016, v. 7, p. 1, doi. 10.1186/s13326-016-0067-z
By:
- Bolleman, Jerven T.;
- Mungall, Christopher J.;
- Strozzi, Francesco;
- Baran, Joachim;
- Dumontier, Michel;
- Bonnal, Raoul J. P.;
- Buels, Robert;
- Hoehndorf, Robert;
- Fujisawa, Takatomo;
- Katayama, Toshiaki;
- Cock, Peter J. A.
Publication type:
Article
Implementation of linked data in the life sciences at BioHackathon 2011.
Published in:
Journal of Biomedical Semantics, 2015, v. 6, n. 1, p. 1, doi. 10.1186/2041-1480-6-3
By:
- Aoki-Kinoshita, Kiyoko F.;
- Kinjo, Akira R.;
- Mizuki Morita;
- Yoshinobu Igarashi;
- Yi-an Chen;
- Yasumasa Shigemoto;
- Takatomo Fujisawa;
- Yukie Akune;
- Takeo Katoda;
- Anna Kokubu;
- Takaaki Mori;
- Mitsuteru Nakao;
- Shuichi Kawashima;
- Shinobu Okamoto;
- Toshiaki Katayama;
- Soichi Ogishima
Publication type:
Article
Implementation of linked data in the life sciences at BioHackathon 2011.
Published in:
Journal of Biomedical Semantics, 2015, v. 6, n. 1, p. 38, doi. 10.1186/2041-1480-6-3
By:
- Aoki-Kinoshita, Kiyoko F.;
- Kinjo, Akira R.;
- Mizuki Morita;
- Yoshinobu Igarashi;
- Yi-an Chen;
- Yasumasa Shigemoto;
- Takatomo Fujisawa;
- Yukie Akune;
- Takeo Katoda;
- Anna Kokubu;
- Takaaki Mori;
- Mitsuteru Nakao;
- Shuichi Kawashima;
- Shinobu Okamoto;
- Toshiaki Katayama;
- Soichi Ogishima
Publication type:
Article
BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains.
Published in:
Journal of Biomedical Semantics, 2014, v. 5, n. 1, p. 1, doi. 10.1186/2041-1480-5-5
By:
- Toshiaki Katayama;
- Wilkinson, Mark D.;
- Kiyoko F. Aoki-Kinoshita;
- Shuichi Kawashima;
- Yasunori Yamamoto;
- Atsuko Yamaguchi;
- Shinobu Okamoto;
- Shin Kawano;
- Jin-Dong Kim;
- Yue Wang;
- Hongyan Wu;
- Yoshinobu Kano;
- Hiromasa Ono;
- Hidemasa Bono;
- Kocbek, Simon;
- Aerts, Jan;
- Yukie Akune;
- Antezana, Erick;
- Kazuharu Arakawa;
- Aranda, Bruno
Publication type:
Article
The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies.
Published in:
Journal of Biomedical Semantics, 2013, v. 4, n. 1, p. 1, doi. 10.1186/2041-1480-4-6
By:
- Katayama, Toshiaki;
- Wilkinson, Mark D.;
- Micklem, Gos;
- Kawashima, Shuichi;
- Yamaguchi, Atsuko;
- Nakao, Mitsuteru;
- Yamamoto, Yasunori;
- Okamoto, Shinobu;
- Oouchida, Kenta;
- Hong-Woo Chun;
- Aerts, Jan;
- Afzal, Hammad;
- Antezana, Erick;
- Arakawa, Kazuharu;
- Aranda, Bruno;
- Belleau, Francois;
- Bolleman, Jerven;
- Bonnal, Raoul J. P.;
- Chapman, Brad;
- Cock, Peter J. A.
Publication type:
Article
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows.
Published in:
Journal of Biomedical Semantics, 2010, v. 1, n. 1, p. 1, doi. 10.1186/2041-1480-1-8
By:
- Katayama, Toshiaki;
- Arakawa, Kazuharu;
- Nakao, Mitsuteru;
- Ono, Keiichiro;
- Aoki-Kinoshita, Kiyoko F.;
- Yamamoto, Yasunori;
- Yamaguchi, Atsuko;
- Kawashima, Shuichi;
- Chun, Hong-Woo;
- Aerts, Jan;
- Aranda, Bruno;
- Barboza, Lord Hendrix;
- Bonnal, Raoul J. P.;
- Bruskiewich, Richard;
- Bryne, Jan C.;
- Fernández, José M.;
- Funahashi, Akira;
- Gordon, Paul M. K.;
- Goto, Naohisa;
- Groscurth, Andreas
Publication type:
Article
Novel Mitochondria-Targeted Heat-Soluble Proteins Identified in the Anhydrobiotic Tardigrade Improve Osmotic Tolerance of Human Cells.
Published in:
PLoS ONE, 2015, v. 10, n. 2, p. 1, doi. 10.1371/journal.pone.0118272
By:
- Tanaka, Sae;
- Tanaka, Junko;
- Miwa, Yoshihiro;
- Horikawa, Daiki D.;
- Katayama, Toshiaki;
- Arakawa, Kazuharu;
- Toyoda, Atsushi;
- Kubo, Takeo;
- Kunieda, Takekazu
Publication type:
Article
Analysis of DNA Repair and Protection in the Tardigrade <i>Ramazzottius varieornatus</i> and <i>Hypsibius dujardini</i> after Exposure to UVC Radiation.
Published in:
PLoS ONE, 2013, v. 8, n. 6, p. 1, doi. 10.1371/journal.pone.0064793
By:
- Horikawa, Daiki D.;
- Cumbers, John;
- Sakakibara, Iori;
- Rogoff, Dana;
- Leuko, Stefan;
- Harnoto, Raechel;
- Arakawa, Kazuharu;
- Katayama, Toshiaki;
- Kunieda, Takekazu;
- Toyoda, Atsushi;
- Fujiyama, Asao;
- Rothschild, Lynn J.
Publication type:
Article
Two Novel Heat-Soluble Protein Families Abundantly Expressed in an Anhydrobiotic Tardigrade.
Published in:
PLoS ONE, 2012, v. 7, n. 8, p. 1, doi. 10.1371/journal.pone.0044209
By:
- Yamaguchi, Ayami;
- Tanaka, Sae;
- Yamaguchi, Shiho;
- Kuwahara, Hirokazu;
- Takamura, Chizuko;
- Imajoh-Ohmi, Shinobu;
- Horikawa, Daiki D.;
- Toyoda, Atsushi;
- Katayama, Toshiaki;
- Arakawa, Kazuharu;
- Fujiyama, Asao;
- Kubo, Takeo;
- Kunieda, Takekazu;
- Battista, John R.
Publication type:
Article
An interactive gene network for securin-separase, condensin, cohesin, Dis1/Mtc1 and histones constructed by mass transformation.
Published in:
Genes to Cells, 2004, v. 9, n. 11, p. 1069, doi. 10.1111/j.1365-2443.2004.00790.x
By:
- Yuasa, Tatsuro;
- Hayashi, Takeshi;
- Ikai, Nobuyasu;
- Katayama, Toshiaki;
- Aoki, Keita;
- Obara, Takayuki;
- Toyoda, Yusuke;
- Maruyama, Takeshi;
- Kitagawa, Daisuke;
- Takahashi, Kohta;
- Nagao, Koji;
- Nakaseko, Yukinobu;
- Yanagida, Mitsuhiro
Publication type:
Article
NBDC RDF portal: a comprehensive repository for semantic data in life sciences.
Published in:
Database: The Journal of Biological Databases & Curation, 2018, v. 2018, p. 1, doi. 10.1093/database/bay123
By:
- Kawashima, Shuichi;
- Katayama, Toshiaki;
- Hatanaka, Hideki;
- Kushida, Tatsuya;
- Takagi, Toshihisa
Publication type:
Article
TogoGenome/TogoStanza: modularized Semantic Web genome database.
Published in:
Database: The Journal of Biological Databases & Curation, 2019, v. 2019, p. N.PAG, doi. 10.1093/database/bay132
By:
- Katayama, Toshiaki;
- Kawashima, Shuichi;
- Okamoto, Shinobu;
- Moriya, Yuki;
- Chiba, Hirokazu;
- Naito, Yuki;
- Fujisawa, Takatomo;
- Mori, Hiroshi;
- Takagi, Toshihisa
Publication type:
Article
The Ruby UCSC API: accessing the UCSC genome database using Ruby.
Published in:
BMC Bioinformatics, 2012, v. 13, n. 1, p. 240, doi. 10.1186/1471-2105-13-240
By:
- Mishima, Hiroyuki;
- Aerts, Jan;
- Katayama, Toshiaki;
- Bonnal, Raoul J.P.;
- Yoshiura, Koh-ichiro
Publication type:
Article
From genomics to chemical genomics: new developments in KEGG.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d354, doi. 10.1093/nar/gkj102
By:
- Kanehisa, Minoru;
- Goto, Susumu;
- Hattori, Masahiro;
- Aoki-Kinoshita, Kiyoko F.;
- Itoh, Masumi;
- Kawashima, Shuichi;
- Katayama, Toshiaki;
- Araki, Michihiro;
- Hirakawa, Mika
Publication type:
Article
ODB: a database of operons accumulating known operons across multiple genomes.
Published in:
Nucleic Acids Research, 2006, v. 34, n. suppl 1, p. d358, doi. 10.1093/nar/gkj037
By:
- Okuda, Shujiro;
- Katayama, Toshiaki;
- Kawashima, Shuichi;
- Goto, Susumu;
- Kanehisa, Minoru
Publication type:
Article
SARS-CoV-2 HaploGraph: visualization of SARS-CoV-2 haplotype spread in Japan.
Published in:
Genes & Genetic Systems, 2023, v. 98, n. 5, p. 221, doi. 10.1266/ggs.23-00085
By:
- So Nakagawa;
- Toshiaki Katayama;
- Lihua Jin;
- Jiaqi Wu;
- Kirill Kryukov;
- Rise Oyachi;
- Junko S Takeuchi;
- Takatomo Fujisawa;
- Satomi Asano;
- Momoka Komatsu;
- Jun-ichi Onami;
- Takashi Abe;
- Masanori Arita
Publication type:
Article
TogoVar: A comprehensive Japanese genetic variation database.
Published in:
Human Genome Variation, 2022, v. 9, n. 1, p. 1, doi. 10.1038/s41439-022-00222-9
By:
- Mitsuhashi, Nobutaka;
- Toyo-oka, Licht;
- Katayama, Toshiaki;
- Kawashima, Minae;
- Kawashima, Shuichi;
- Miyazaki, Kazunori;
- Takagi, Toshihisa
Publication type:
Article
Ten simple rules to run a successful BioHackathon.
Published in:
2020
By:
- Garcia, Leyla;
- Antezana, Erick;
- Garcia, Alexander;
- Bolton, Evan;
- Jimenez, Rafael;
- Prins, Pjotr;
- Banda, Juan M.;
- Katayama, Toshiaki
Publication type:
Editorial
PIERO ontology for analysis of biochemical transformations: Effective implementation of reaction information in the IUBMB enzyme list.
Published in:
Journal of Bioinformatics & Computational Biology, 2014, v. 12, n. 6, p. -1, doi. 10.1142/S0219720014420013
By:
- Kotera, Masaaki;
- Nishimura, Yosuke;
- Nakagawa, Zen-Ichi;
- Muto, Ai;
- Moriya, Yuki;
- Okamoto, Shinobu;
- Kawashima, Shuichi;
- Katayama, Toshiaki;
- Tokimatsu, Toshiaki;
- Kanehisa, Minoru;
- Goto, Susumu
Publication type:
Article
UTILIZING EVOLUTIONARY INFORMATION AND GENE EXPRESSION DATA FOR ESTIMATING GENE NETWORKS WITH BAYESIAN NETWORK MODELS.
Published in:
Journal of Bioinformatics & Computational Biology, 2005, v. 3, n. 6, p. 1295, doi. 10.1142/S0219720005001569
By:
- TAMADA, YOSHINORI;
- KANEHISA, MINORU;
- BANNAI, HIDEO;
- IMOTO, SEIYA;
- KATAYAMA, TOSHIAKI;
- MIYANO, SATORU
Publication type:
Article
SPARQL-enabled identifier conversion with Identifiers.org.
Published in:
2015
By:
- Wimalaratne, Sarala M.;
- Bolleman, Jerven;
- Juty, Nick;
- Toshiaki Katayama;
- Dumontier, Michel;
- Redaschi, Nicole;
- Le Novère, Nicolas;
- Hermjakob, Henning;
- Laibe, Camille
Publication type:
Product Review
Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics.
Published in:
Bioinformatics, 2012, v. 28, n. 7, p. 1035, doi. 10.1093/bioinformatics/bts080
By:
- Bonnal, Raoul J.P.;
- Aerts, Jan;
- Githinji, George;
- Goto, Naohisa;
- MacLean, Dan;
- Miller, Chase A.;
- Mishima, Hiroyuki;
- Pagani, Massimiliano;
- Ramirez-Gonzalez, Ricardo;
- Smant, Geert;
- Strozzi, Francesco;
- Syme, Rob;
- Vos, Rutger;
- Wennblom, Trevor J.;
- Woodcroft, Ben J.;
- Katayama, Toshiaki;
- Prins, Pjotr
Publication type:
Article
BioRuby: bioinformatics software for the Ruby programming language.
Published in:
Bioinformatics, 2010, v. 26, n. 20, p. 2617, doi. 10.1093/bioinformatics/btq475
By:
- Goto, Naohisa;
- Prins, Pjotr;
- Nakao, Mitsuteru;
- Bonnal, Raoul;
- Aerts, Jan;
- Katayama, Toshiaki
Publication type:
Article
Publishing FAIR Data: An Exemplar Methodology Utilizing PHI-Base.
Published in:
Frontiers in Plant Science, 2016, p. 1, doi. 10.3389/fpls.2016.00641
By:
- Rodríguez-Iglesias, Alejandro;
- Rodríguez-González, Alejandro;
- Irvine, Alistair G.;
- Sesma, Ane;
- Urban, Martin;
- Hammond-Kosack, Kim E.;
- Wilkinson, Mark D.;
- Toshiaki Katayama;
- Marshall, M. Scott
Publication type:
Article

Found: 36