Tetsuro Toyoda

According to our database, Tetsuro Toyoda authored at least 31 papers between 2003 and 2014.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

2014

A promoter-level mammalian expression atlas.

The 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, Masayoshi Itoh, Robin Andersson, Christopher J. Mungall, Terrence F. Meehan, Sebastian Schmeier, Nicolas Bertin, Mette Jørgensen, Emmanuel Dimont, Erik Arner, Christian Schmidl, Ulf Schaefer, Yulia A. Medvedeva, Charles Plessy, Morana Vitezic, Jessica Severin, Colin A. M. Semple, Yuri Ishizu, Robert S. Young, Margherita Francescatto, Intikhab Alam, Davide Albanese, Gabriel M. Altschuler, Takahiro Arakawa, John A. C. Archer, Peter Arner, Magda Babina, Sarah Rennie, Piotr J. Balwierz, Anthony G. Beckhouse, Swati Pradhan-Bhatt, Judith A. Blake, Antje Blumenthal, Beatrice Bodega, Alessandro Bonetti, James Briggs, Frank Brombacher, A. Maxwell Burroughs, Andrea Califano, Carlo V. Cannistraci, Daniel Carbajo, Yun Chen, Marco Chierici, Yari Ciani, Hans Clevers, Emiliano Dalla, Carrie A. Davis, Michael Detmar, Alexander D. Diehl, Taeko Dohi, Finn Drabløs, Albert S. B. Edge, Matthias Edinger, Karl Ekwall, Mitsuhiro Endoh, Hideki Enomoto, Michela Fagiolini, Lynsey Fairbairn, Hai Fang, Mary C. Farach-Carson, Geoffrey J. Faulkner, Alexander V. Favorov, Malcolm E. Fisher, Martin C. Frith, Rie Fujita, Shiro Fukuda, Cesare Furlanello, Masaaki Furuno, Jun-ichi Furusawa, Teunis B. Geijtenbeek, Andrew P. Gibson, Thomas R. Gingeras, Daniel Goldowitz, Julian Gough, Sven Guhl, Reto Guler, Stefano Gustincich, Thomas J. Ha, Masahide Hamaguchi, Mitsuko Hara, Matthias Harbers, Jayson Harshbarger, Akira Hasegawa, Yuki Hasegawa, Takehiro Hashimoto, Meenhard Herlyn, Kelly J. Hitchens, Shannan J. Ho Sui, Oliver M. Hofmann, Ilka Hoof, Fumi Hori, Lukasz Huminiecki, Kei Iida, Tomokatsu Ikawa, Boris R. Jankovic, Hui Jia, Anagha Joshi, Giuseppe Jurman, Bogumil Kaczkowski, Chieko Kai, Kaoru Kaida, Ai Kaiho, Kazuhiro Kajiyama, Mutsumi Kanamori-Katayama, Artem S. Kasianov, Takeya Kasukawa, Shintaro Katayama, Sachi Kato, Shuji Kawaguchi, Hiroshi Kawamoto, Yuki I. Kawamura, Tsugumi Kawashima, Judith S. Kempfle, Tony J. Kenna, Juha Kere, Levon M. Khachigian, Toshio Kitamura, S. Peter Klinken, Alan J. Knox, Miki Kojima, Soichi Kojima, Naoto Kondo, Haruhiko Koseki, Shigeo Koyasu, Sarah Krampitz, Atsutaka Kubosaki, Andrew T. Kwon, Jeroen F. J. Laros, Weonju Lee, Andreas Lennartsson, Kang Li, Berit Lilje, Leonard Lipovich, Alan Mackay-Sim, Ri-ichiroh Manabe, Jessica Cara Mar, Benoit Marchand, Anthony Mathelier, Niklas Mejhert, Alison M. Meynert, Yosuke Mizuno, David A. de Lima Morais, Hiromasa Morikawa, Mitsuru Morimoto, Kazuyo Moro, Efthymios Motakis, Hozumi Motohashi, Christine Mummery, Mitsuyoshi Murata, Sayaka Nagao-Sato, Yutaka Nakachi, Fumio Nakahara, Toshiyuki Nakamura, Yukio Nakamura, Kenichi Nakazato, Erik van Nimwegen, Noriko Ninomiya, Hiromi Nishiyori, Shohei Noma, Tadasuke Nozaki, Soichi Ogishima, Naganari Ohkura, Hiroko Ohmiya, Hiroshi Ohno, Mitsuhiro Ohshima, Mariko Okada-Hatakeyama, Yasushi Okazaki, Valerio Orlando, Dmitry A. Ovchinnikov, Arnab Pain, Robert Passier, Margaret Patrikakis, Helena Persson, Silvano Piazza, James G. D. Prendergast, Owen J. L. Rackham, Jordan A. Ramilowski, Mamoon Rashid, Timothy Ravasi, Patrizia Rizzu, Marco Roncador, Sugata Roy, Morten B. Rye, Eri Saijyo, Antti Sajantila, Akiko Saka, Shimon Sakaguchi, Mizuho Sakai, Hiroki Sato, Hironori Sato, Suzana Savvi, Alka Saxena, Claudio Schneider, Erik A. Schultes, Gundula G. Schulze-Tanzil, Anita Schwegmann, Thierry Sengstag, Guojun Sheng, Hisashi Shimoji, Yishai Shimoni, Jay W. Shin, Christophe Simon, Daisuke Sugiyama, Takaaki Sugiyama, Masanori Suzuki, Naoko Suzuki, Rolf K. Swoboda, Peter A. C. 't Hoen, Michihira Tagami, Naoko Takahashi, Jun Takai, Hiroshi Tanaka, Hideki Tatsukawa, Zuotian Tatum, Mark Thompson, Hiroo Toyoda, Tetsuro Toyoda, Eivind Valen, Marc van de Wetering, Linda M. van den Berg, Roberto Verardo, Dipti Vijayan, Ilya E. Vorontsov, Wyeth W. Wasserman, Shoko Watanabe, Christine A. Wells, Louise N. Winteringham, Ernst Wolvetang, Emily J. Wood, Yoko Yamaguchi, Masayuki Yamamoto, Misako Yoneda, Yohei Yonekura, Shigehiro Yoshida, Susan E. Zabierowski, Peter G. Zhang, Xiaobei Zhao, Silvia Zucchelli, Kim M. Summers, Harukazu Suzuki, Carsten O. Daub, Jun Kawai, Peter Heutink, Winston Hide, Tom C. Freeman, Boris Lenhard, Vladimir B. Bajic, Martin S. Taylor, Vsevolod J. Makeev, Albin Sandelin, David A. Hume, Piero Carninci, Yoshihide Hayashizaki

Nat., 2014

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, Hajime Watabe, Hiroshi Masuya, Tetsuro Toyoda

Nucleic Acids Res., 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: 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, Terue Takatsuki, Hiroshi Masuya, Tetsuro Toyoda

Proceedings of the 6th International Workshop on Semantic Web Applications and Tools for Life Sciences, 2013

Organizing Scientific Competitions on the Semantic Web.

Sayoko Shimoyama, Robert Sidney Cox III, David Gifford, Tetsuro Toyoda

Proceedings of the Database and Expert Systems Applications, 2013

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

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

Proceedings of the Semantic Technology, Second Joint International Conference, 2012

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, Satoshi Takahashi, Atsushi Hijikata, Kouji Kozaki, Teiichi Furuichi, Hideya Kawaji, Shigeharu Wakana, Yukio Nakamura, Atsushi Yoshiki, Takehide Murata, Kaoru Fukami-Kobayashi, S. Sujatha Mohan, Osamu Ohara, Yoshihide Hayashizaki, Riichiro Mizoguchi, Yuichi Obata, Tetsuro Toyoda

Nucleic Acids Res., 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

BioLOD.org: ontology-based integration of biological linked open data.

Koro Nishikata, Tetsuro Toyoda

Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2011

BioSPARQL: ontology-based smart building of SPARQL queries for biological linked open data.

Norio Kobayashi, Tetsuro Toyoda

Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2011

LinkData.org supports Japan's LOD challenge.

David Gifford, Tetsuro Toyoda

Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2011

Genome design with the semantic web.

Robert Sidney Cox III, Tetsuro Toyoda

Proceedings of the 4th International Workshop on Semantic Web Applications and Tools for the Life Sciences, 2011

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, Riichiro Mizoguchi

Proceedings of the 2nd International Conference on Biomedical Ontology, 2011

2010

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

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

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

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

Statistical search on the Semantic Web.

Norio Kobayashi, Tetsuro Toyoda

Bioinform., 2008

Penta and Hexa Statements are Suitable for Representing Omics Knowledge on the Semantic Web.

Norio Kobayashi, Tetsuro Toyoda

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

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, Takashi Kuromori, Kazuo Shinozaki, Tetsuro Toyoda

Proceedings of the Workshop on Semantic Web Applications and Tools for Life Sciences ( SWAT4LS ) Edinburgh, 2008

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

OmicBrowse: a browser of multidimensional omics annotations.

Tetsuro Toyoda, Yoshiki Mochizuki, Keith Player, Naohiko Heida, Norio Kobayashi, Yoshiyuki Sakaki

Bioinform., 2007

2006

Erratum: "<i>In Silico</i> 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

2005

RARGE: a large-scale database of RIKEN <i>Arabidopsis</i> 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

<i>in Silico</i> 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

Three-dimensional Definition of Leaf Morphological Traits of <i>arabidopsis in Silico</i> Phenotypic Analysis.

Eli Kaminuma, Naohiko Heida, Yuko Tsumoto, Miki Nakazawa, Nobuharu Goto, Akihiko Konagaya, Minami Matsui, Tetsuro Toyoda

J. Bioinform. Comput. Biol., 2005

2004

Omic space: coordinate-based integration and analysis of genomic phenomic interactions.

Tetsuro Toyoda, Akiyoshi Wada

Bioinform., 2004

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

Proceedings of the Proceedings Twelfth International Conference on Intelligent Systems for Molecular Biology/Third European Conference on Computational Biology 2004, 2004

2003

GSCope: a clipped fisheye viewer effective for highly complicated biomolecular network graphs.

Tetsuro Toyoda, Yoshiki Mochizuki, Akihiko Konagaya

Bioinform., 2003

KnowledgeEditor: a new tool for interactive modeling and analyzing biological pathways based on microarray data.

Tetsuro Toyoda, Akihiko Konagaya

Bioinform., 2003