KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data. - Tetsuro Toyoda; Akihiko Konagaya (Bioinform., 2003)

GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs. - Tetsuro Toyoda; Yoshiki Mochizuki; Akihiko Konagaya (Bioinform., 2003)

TraitMap: an XML-based genetic-map database combining multigenic loci and biomolecular networks. - Naohiko Heida; Yoshikazu Hasegawa; Yoshiki Mochizuki; Katsura Hirosawa; Akihiko Konagaya; Tetsuro Toyoda (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Omic space: coordinate-based integration and analysis of genomic phenomic interactions. - Tetsuro Toyoda; Akiyoshi Wada (Bioinform., 2004)

Three-dimensional Definition of Leaf Morphological Traits of arabidopsis in Silico Phenotypic Analysis. - Eli Kaminuma; Naohiko Heida; Yuko Tsumoto; Miki Nakazawa; Nobuharu Goto; Akihiko Konagaya; Minami Matsui; Tetsuro Toyoda (J. Bioinform. Comput. Biol., 2005)

in Silico Phenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples. - Eli Kaminuma; Naohiko Heida; Takeshi Yoshizumi; Miki Nakazawa; Minami Matsui; Tetsuro Toyoda (J. Bioinform. Comput. Biol., 2005)

RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome. - Tetsuya Sakurai; Masakazu Satou; Kenji Akiyama; Kei Iida; Motoaki Seki; Takashi Kuromori; Takuya Ito; Akihiko Konagaya; Tetsuro Toyoda; Kazuo Shinozaki (Nucleic Acids Res., 2005)

Erratum: "In Silico Phenotypic Screening Method of Mutants Based on Statistical Modeling of Genetically Mixed Samples". - Eli Kaminuma; Naohiko Heida; Takeshi Yoshizumi; Miki Nakazawa; Minami Matsui; Tetsuro Toyoda (J. Bioinform. Comput. Biol., 2006)

OmicBrowse: a browser of multidimensional omics annotations. - Tetsuro Toyoda; Yoshiki Mochizuki; Keith Player; Naohiko Heida; Norio Kobayashi; Yoshiyuki Sakaki (Bioinform., 2007)

Phenosite: a Web Database Integrating the mouse phenotyping Platform and the Experimental Procedures in mice. - Hiroshi Masuya; Sumi Yoshikawa; Naohiko Heida; Tetsuro Toyoda; Shigeharu Wakana; Toshihiko Shiroishi (J. Bioinform. Comput. Biol., 2007)

A Secure Data Repository Integrating Huge Volumes of Digital Contents as a Semantic Web. - Norio Kobayashi; Yuko Makita; Eli Kaminuma; Shuji Kawaguchi; Yuko Yoshida; Yoshiki Mochizuki; Akihiro Matsushima; Manabu Ishii; Ryo Umetsu; Satomi Asano; Naohiko Heida; Tetsuya Sakurai; et al. (SWAT4LS, 2008)

Penta and Hexa Statements are Suitable for Representing Omics Knowledge on the Semantic Web. - Norio Kobayashi; Tetsuro Toyoda (SWAT4LS, 2008)

Statistical search on the Semantic Web. - Norio Kobayashi; Tetsuro Toyoda (Bioinform., 2008)

Objective Evaluation Measures of Genetic Marker Selection in Large-Scale SNP genotyping. - Eli Kaminuma; Hiroshi Masuya; Ikuo Miura; Hiromi Motegi; Kenzi R. Takahasi; Miki Nakazawa; Minami Matsui; Yoichi Gondo; Tetsuo Noda; Toshihiko Shiroishi; Shigeharu Wakana; Tetsuro Toyoda (J. Bioinform. Comput. Biol., 2008)

OmicBrowse: a Flash-based high-performance graphics interface for genomic resources. - Akihiro Matsushima; Norio Kobayashi; Yoshiki Mochizuki; Manabu Ishii; Shuji Kawaguchi; Takaho A. Endo; Ryo Umetsu; Yuko Makita; Tetsuro Toyoda (Nucleic Acids Res., 2009)

PosMed (Positional Medline): prioritizing genes with an artificial neural network comprising medical documents to accelerate positional cloning. - Yuko Yoshida; Yuko Makita; Naohiko Heida; Satomi Asano; Akihiro Matsushima; Manabu Ishii; Yoshiki Mochizuki; Hiroshi Masuya; Shigeharu Wakana; Norio Kobayashi; Tetsuro Toyoda (Nucleic Acids Res., 2009)

sORF finder: a program package to identify small open reading frames with high coding potential. - Kousuke Hanada; Kenji Akiyama; Tetsuya Sakurai; Tetsuro Toyoda; Kazuo Shinozaki; Shin-Han Shiu (Bioinform., 2010)

An Advanced Strategy for Integration of Biological Measurement Data. - Hiroshi Masuya; Georgios V. Gkoutos; Nobuhiko Tanaka; Kazunori Waki; Yoshihiro Okuda; Tatsuya Kushida; Norio Kobayashi; Koji Doi; Kouji Kozaki; Robert Hoehndorf; Shigeharu Wakana; Tetsuro Toyoda; et al. (ICBO, 2011)

Genome design with the semantic web. - Robert Sidney Cox III; Tetsuro Toyoda (SWAT4LS, 2011)

LinkData.org supports Japan's LOD challenge. - David Gifford 002; Tetsuro Toyoda (SWAT4LS, 2011)

BioSPARQL: ontology-based smart building of SPARQL queries for biological linked open data. - Norio Kobayashi; Tetsuro Toyoda (SWAT4LS, 2011)

BioLOD.org: ontology-based integration of biological linked open data. - Koro Nishikata; Tetsuro Toyoda (SWAT4LS, 2011)

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases. - Norio Kobayashi; Manabu Ishii; Satoshi Takahashi; Yoshiki Mochizuki; Akihiro Matsushima; Tetsuro Toyoda (Nucleic Acids Res., 2011)

The RIKEN integrated database of mammals. - Hiroshi Masuya; Yuko Makita; Norio Kobayashi; Koro Nishikata; Yuko Yoshida; Yoshiki Mochizuki; Koji Doi; Terue Takatsuki; Kazunori Waki; Nobuhiko Tanaka; Manabu Ishii; Akihiro Matsushima; et al. (Nucleic Acids Res., 2011)

Development of Linked Open Data for Bioresources. - Hiroshi Masuya; Terue Takatsuki; Yuko Makita; Yuko Yoshida; Yoshiki Mochizuki; Norio Kobayashi; Atsushi Yoshiki; Yukio Nakamura; Tetsuro Toyoda; Yuichi Obata (JIST, 2012)

Positional correlation analysis improves reconstruction of full-length transcripts and alternative isoforms from noisy array signals or short reads. - Shuji Kawaguchi; Kei Iida; Erimi Harada; Kousuke Hanada; Akihiro Matsui; Masanori Okamoto; Kazuo Shinozaki; Motoaki Seki; Tetsuro Toyoda (Bioinform., 2012)

Organizing Scientific Competitions on the Semantic Web. - Sayoko Shimoyama; Robert Sidney Cox III; David Gifford 002; Tetsuro Toyoda (DEXA (1), 2013)

PosMed: A Biomedical Entity Prioritisation Tool Based on Statistical Inference over Literature and the Semantic Web. - Norio Kobayashi; Yuko Makita; Manabu Ishii; Akihiro Matsushima; Yoshiki Mochizuki; Koji Doi; Koro Nishikata; David Gifford 002; Terue Takatsuki; Hiroshi Masuya; Tetsuro Toyoda (SWAT4LS, 2013)

PromoterCAD: data-driven design of plant regulatory DNA. - Robert Sidney Cox III; Koro Nishikata; Sayoko Shimoyama; Yuko Yoshida; Minami Matsui; Yuko Makita; Tetsuro Toyoda (Nucleic Acids Res., 2013)

PosMed: ranking genes and bioresources based on Semantic Web Association Study. - Yuko Makita; Norio Kobayashi; Yuko Yoshida; Koji Doi; Yoshiki Mochizuki; Koro Nishikata; Akihiro Matsushima; Satoshi Takahashi; Manabu Ishii; Terue Takatsuki; Rinki Bhatia; Zolzaya Khadbaatar; et al. (Nucleic Acids Res., 2013)

A promoter-level mammalian expression atlas. - Fantom Consortium; RIKEN PMII; RIKEN CLST (DGT); Alistair R. R. Forrest; Hideya Kawaji; Michael Rehli; J. Kenneth Baillie; Michiel J. L. de Hoon; Vanja Haberle; Timo Lassmann; Ivan V. Kulakovskiy; Marina Lizio; et al. (Nat., 2014)