GENAS: a database system for nucleic acid sequence analysis. - Satoru Kuhara; Fumihiro Matsuo; Syoichi Futamura; Atsushi Fujita; Takeshi Shinohara; Toshihisa Takagi; Yoshiyuki Sakaki (Nucleic Acids Res., 1984)

Implementation of Inferential Relational Database System. - Toshihisa Takagi; Fumihiro Matsuo; Shouichi Futamura; Kazuo Ushijima (FODO, 1985)

A Matching Tree Oriented Abstract Machine for Prolog. - Neng-Fa Zhou; Toshihisa Takagi; Kazuo Ushijima (ICLP, 1990)

Bidirectional inference of mode information for logic programs. - Neng-Fa Zhou; Kazuo Ushijima; Toshihisa Takagi (Syst. Comput. Jpn., 1991)

Evaluation of a deductive database system for CAD applications. - Toshihisa Takagi; Takahiko Suzuki; Susumu Goto; Kazuo Ushijima (Syst. Comput. Jpn., 1992)

Object-Oriented Database with Rule-Based Query Interface for Genomic Computation. - Susumu Goto; Norihiro Sakamoto; Toshihisa Takagi (DASFAA, 1993)

Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome. - Norihiro Sakamoto; Toshihisa Takagi; Yasubumi Sakaki (Comput. Appl. Biosci., 1993)

A deductive database system PACADE for analyzing 3-D and secondary structures of protein. - Kenji Satou; Emiko Furuichi; Kyoko Takiguchi; Toshihisa Takagi; Satoru Kuhara (Comput. Appl. Biosci., 1993)

A Deductive Object-Oriented Language for Integrated Genome Databaser. - Susumu Goto; Norihiro Sakamoto; Toshihisa Takagi (HICSS (5), 1994)

Application of a Deductive Database System PACADE toward Discovery of Clusters of Similar Structures in Proteins. - Kenji Satou; Emiko Furuichi; Kyoko Takiguchi; Satoru Kuhara; Toshihisa Takagi (HICSS (5), 1994)

Development of an integrated Database for Genome Mapping and Nucleotide Sequences. - Takahiko Suzuki; Toshihisa Takagi; Satoru Kuhara; Minoru Kanehisa (HICSS (5), 1994)

Automatic Construction of Knowledge Base from Biological Papers. - Yoshihiro Ohta; Yasunori Yamamoto; Tomoko Okazaki; Ikuo Uchiyama; Toshihisa Takagi (ISMB, 1997)

Extraction of Substructures of Proteins Essential to their Biological Functions by a Data Mining Technique. - Kenji Satou; Toshihide Ono; Yoshihisa Yamamura; Emiko Furuichi; Satoru Kuhara; Toshihisa Takagi (ISMB, 1997)

Application of a deductive database system to search for topological and similar three-dimensional structures in protein. - Y. Tsukamoto; Kyoko Takiguchi; Kenji Satou; Emiko Furuichi; Toshihisa Takagi; Satoru Kuhara (Comput. Appl. Biosci., 1997)

Gene recognition by combination of several gene-finding programs. - Katsuhiko Murakami; Toshihisa Takagi (Bioinform., 1998)

Clustering and Detection of 5' Splice Sites of mRNA by k Weight-Matrices Model. - Katsuhiko Murakami; Toshihisa Takagi (Pacific Symposium on Biocomputing, 1999)

Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences. - Tatsuhiko Tsunoda; Masao Fukagawa; Toshihisa Takagi (Pacific Symposium on Biocomputing, 1999)

Estimating transcription factor bindability on DNA. - Tatsuhiko Tsunoda; Toshihisa Takagi (Bioinform., 1999)

PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary. - Mikio Yoshida; Ken-ichiro Fukuda; Toshihisa Takagi (Bioinform., 2000)

Ontology and functional genomics. - Takako Takai-Igarashi; Toshihisa Takagi (German Conference on Bioinformatics, 2001)

Knowledge representation of signal transduction pathways. - Ken-ichiro Fukuda; Toshihisa Takagi (Bioinform., 2001)

Automated extraction of information on protein-protein interactions from the biological literature. - Toshihide Ono; Haretsugu Hishigaki; Akira Tanigami; Toshihisa Takagi (Bioinform., 2001)

JSNP: a database of common gene variations in the Japanese population. - Mika Hirakawa; Toshihiro Tanaka; Yoichi Hashimoto; Masako Kuroda; Toshihisa Takagi; Yusuke Nakamura (Nucleic Acids Res., 2002)

DIGIT: A Novel Gene Finding Program by Combining Gene-Finders. - Tetsushi Yada; Yasushi Totoki; Y. Takaeda; Yasubumi Sakaki; Toshihisa Takagi (Pacific Symposium on Biocomputing, 2003)

A Method to Retrieve Papers from MEDLINE: PETER System. - Hiroko Ao; Yasunori Yamamoto; Toshihisa Takagi (TREC, 2003)

MELINA: motif extraction from promoter regions of potentially co-regulated genes. - Natalia V. Poluliakh; Toshihisa Takagi; Kenta Nakai (Bioinform., 2003)

FREX: A query interface for biological processes with hierarchical and recursive structures. - Ken-ichiro Fukuda; Yuki Yamagata; Toshihisa Takagi (Silico Biol., 2003)

Preface: The Second Workshop on Ontology and Genome. - Takako Takai-Igarashi; Toshihisa Takagi; Edgar Wingender (Silico Biol., 2003)

A Pathway Editor for Literature-based Knowledge Curation. - Ken-ichiro Fukuda; Toshihisa Takagi (APBC, 2004)

Prediction of Protein-Protein Interactions Using Support Vector Machines. - Shinsuke Dohkan; Asako Koike; Toshihisa Takagi (BIBE, 2004)

A Practical Partial Parser for Biomedical Literature Summarization. - Yasunori Yamamoto; Toshihisa Takagi (NLUCS, 2004)

Predicting rules on organization of cis-regulatory elements, taking the order of elements into account. - Goro Terai; Toshihisa Takagi (Bioinform., 2004)

PRIME: automatically extracted PRotein Interactions and Molecular Information databas. - Asako Koike; Toshihisa Takagi (Silico Biol., 2004)

Large-scale collection and characterization of promoters of human and mouse genes. - Yutaka Suzuki; Riu Yamashita; Matsuyuki Shirota; Yuta Sakakibara; Joe Chiba; Junko Mizushima-Sugano; Alexander E. Kel; Takahiro Arakawa; Piero Carninci; Jun Kawai; Yoshihide Hayashizaki; Toshihisa Takagi; et al. (Silico Biol., 2004)

Preface - Third "Ontology Workshop on Ontology and Genomes". - Takako Takai-Igarashi; Toshihisa Takagi; Holger Michael; Edgar Wingender (Silico Biol., 2004)

A Sentence Classification System for Multi Biomedical Literature Summarization. - Yasunori Yamamoto; Toshihisa Takagi (ICDE Workshops, 2005)

Automatic extraction of gene/protein biological functions from biomedical text. - Asako Koike; Yoshiki Niwa; Toshihisa Takagi (Bioinform., 2005)

Research Paper: ALICE: An Algorithm to Extract Abbreviations from MEDLINE. - Hiroko Ao; Toshihisa Takagi (J. Am. Medical Informatics Assoc., 2005)

Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. - Kikuya Kato; Riu Yamashita; Ryo Matoba; Morito Monden; Shinzaburo Noguchi; Toshihisa Takagi; Kenta Nakai (Nucleic Acids Res., 2005)

Event Ontology: A Pathway-Centric Ontology for Biological Processes. - Tatsuya Kushida; Toshihisa Takagi; Ken-ichiro Fukuda (Pacific Symposium on Biocomputing, 2006)

Improving the Performance of an SVM-Based Method for Predicting Protein-Protein Interactions. - Shinsuke Dohkan; Asako Koike; Toshihisa Takagi (Silico Biol., 2006)

Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. - Wataru Iwasaki 001; Toshihisa Takagi (ISMB/ECCB (Supplement of Bioinformatics), 2007)

Experimental analysis and computational simulation of the attribution of own actions by the multiple forward models. - Mihoko Otake; Kohei Arai; Motoichiro Kato; Takaki Maeda; Yusuke Ikemoto; Kuniaki Kawabata; Toshihisa Takagi; Hajime Asama (ROBIO, 2007)

OReFiL: an online resource finder for life sciences. - Yasunori Yamamoto; Toshihisa Takagi (BMC Bioinform., 2007)

Knowledge discovery based on an implicit and explicit conceptual network. - Asako Koike; Toshihisa Takagi (J. Assoc. Inf. Sci. Technol., 2007)

Biomedical knowledge navigation by literature clustering. - Yasunori Yamamoto; Toshihisa Takagi (J. Biomed. Informatics, 2007)

Experimental Analysis of the Attribution of Own Actions to the Intention of Self or Others by the Multiple Forward Models. - Mihoko Otake; Kohei Arai; Motoichiro Kato; Takaki Maeda; Yusuke Ikemoto; Kuniaki Kawabata; Toshihisa Takagi; Hajime Asama (J. Robotics Mechatronics, 2007)

Figure Classification in Biomedical Literature towards Figure Mining. - Natsu Ishii; Asako Koike; Yasunori Yamamoto; Toshihisa Takagi (BIBM, 2008)

Prediction of Protein Sub-cellular Localization using Information from Texts and Sequences. - Hong-Woo Chun; Chisato Yamasaki; Naomi Saichi; Masayuki Tanaka 009; Teruyoshi Hishiki; Tadashi Imanishi; Takashi Gojobori; Jin-Dong Kim; Jun'ichi Tsujii; Toshihisa Takagi (BioNLP, 2008)

On-line discovery of temporal-difference networks. - Takaki Makino; Toshihisa Takagi (ICML, 2008)

Open brain simulator estimating internal state of human through external observation towards human biomechatronics. - Mihoko Otake; Toshihisa Takagi; Hajime Asama (ICRA, 2008)

A Markov Logic Approach to Bio-Molecular Event Extraction. - Sebastian Riedel 001; Hong-Woo Chun; Toshihisa Takagi; Jun'ichi Tsujii (BioNLP@HLT-NAACL (Shared Task), 2009)

Classifying Biomedical Figures Using Combination of Bag of Keypoints and Bag of Words. - Asako Koike; Toshihisa Takagi (CISIS, 2009)

Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis. - Tatsuya Kushida; Takao Asanuma; Yoshihiro Okuda; Yo Shidahara; Toshihisa Takagi (CISIS, 2009)

Coimagination Method: Communication Support System with Collected Images and Its Evaluation via Memory Task. - Mihoko Otake; Motoichiro Kato; Toshihisa Takagi; Hajime Asama (HCI (5), 2009)

GuideLink: A Corpus Annotation System that Integrates the Management of Annotation Guidelines. - Kenta Oouchida; Jin-Dong Kim; Toshihisa Takagi; Jun'ichi Tsujii (PACLIC, 2009)

Development of coimagination method towards cognitive enhancement via image based interactive communication. - Mihoko Otake; Motoichiro Kato; Toshihisa Takagi; Hajime Asama (RO-MAN, 2009)

BodyParts3D: 3D structure database for anatomical concepts. - Nobutaka Mitsuhashi; Kaori Fujieda; Takuro Tamura; Shoko Kawamoto; Toshihisa Takagi; Kousaku Okubo (Nucleic Acids Res., 2009)

Gendoo: Functional profiling of gene and disease features using MeSH vocabulary. - Takeru Nakazato; Hidemasa Bono; Hideo Matsuda; Toshihisa Takagi (Nucleic Acids Res., 2009)

Natural Language Query Processing for Life Science Knowledge - Position Paper. - Jin-Dong Kim; Yasunori Yamamoto; Atsuko Yamaguchi; Mitsuteru Nakao; Kenta Oouchida; Hong-Woo Chun; Toshihisa Takagi (AMT, 2010)

Literature-Based Knowledge Discovery from Relationship Associations Based on a DL Ontology Created from MeSH. - Steven B. Kraines; Weisen Guo; Daisuke Hoshiyama; Takaki Makino; Haruo Mizutani; Yoshihiro Okuda; Yo Shidahara; Toshihisa Takagi (IC3K, 2010)

Generating Literature-based Knowledge Discoveries in Life Sciences using Relationship Associations. - Steven B. Kraines; Weisen Guo; Daisuke Hoshiyama; Haruo Mizutani; Toshihisa Takagi (KDIR, 2010)

Bridging the Knowledge Gap between Research and Education through Textbooks. - Steven B. Kraines; Takaki Makino; Weisen Guo; Haruo Mizutani; Toshihisa Takagi (ICWL, 2010)

Authoring Computer-Understandable Semantic Summaries of Life Science Articles Optimized for Knowledge Mining. - Steven B. Kraines; Weisen Guo; Toshihisa Takagi (ICDM (Workshops), 2010)

Multiscale Service Design Method and Its Application to Sustainable Service for Prevention and Recovery from Dementia. - Mihoko Otake; Motoichiro Kato; Toshihisa Takagi; Shuichi Iwata; Hajime Asama; Jun Ota 001 (JSAI-isAI Workshops, 2010)

Figure classification in biomedical literature to elucidate disease mechanisms, based on pathways. - Natsu Ishii; Asako Koike; Yasunori Yamamoto; Toshihisa Takagi (Artif. Intell. Medicine, 2010)

Ligand-binding site prediction of proteins based on known fragment-fragment interactions. - Kota Kasahara; Kengo Kinoshita; Toshihisa Takagi (Bioinform., 2010)

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. - 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 H. Barboza; et al. (J. Biomed. Semant., 2010)

DDBJ launches a new archive database with analytical tools for next-generation sequence data. - Eli Kaminuma; Jun Mashima; Yuichi Kodama; Takashi Gojobori; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura (Nucleic Acids Res., 2010)

TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. - Toshiaki Katayama; Mitsuteru Nakao; Toshihisa Takagi (Nucleic Acids Res., 2010)

Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering. - Atsuko Yamaguchi; Yasunori Yamamoto; Jin-Dong Kim; Toshihisa Takagi; Akinori Yonezawa (BIBM, 2011)

Overview of Genia Event Task in BioNLP Shared Task 2011. - Jin-Dong Kim; Yue Wang 040; Toshihisa Takagi; Akinori Yonezawa (BioNLP@ACL (Shared Task), 2011)

Discriminative Optimization of String Similarity and Its Application to Biomedical Abbreviation Clustering. - Atsuko Yamaguchi; Yasunori Yamamoto; Jin-Dong Kim; Toshihisa Takagi; Akinori Yonezawa (ICMLA (2), 2011)

INOH: ontology-based highly structured database of signal transduction pathways. - Satoko Yamamoto; Noriko Sakai; Hiromi Nakamura; Hiroshi Fukagawa; Ken Fukuda; Toshihisa Takagi (Database J. Biol. Databases Curation, 2011)

Allie: a database and a search service of abbreviations and long forms. - Yasunori Yamamoto; Atsuko Yamaguchi; Hidemasa Bono; Toshihisa Takagi (Database J. Biol. Databases Curation, 2011)

Interactive, multiscale navigation of large and complicated biological networks. - Thanet Praneenararat; Toshihisa Takagi; Wataru Iwasaki 001 (Bioinform., 2011)

The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. - Toshiaki Katayama; Mark D. Wilkinson; Rutger A. Vos; Takeshi Kawashima; Shuichi Kawashima; Mitsuteru Nakao; Yasunori Yamamoto; Hong-Woo Chun; Atsuko Yamaguchi; Shin Kawano; Jan Aerts; Kiyoko F. Aoki-Kinoshita; et al. (J. Biomed. Semant., 2011)

Bio-molecular Event Extraction with Markov Logic. - Sebastian Riedel 001; Rune Sætre; Hong-Woo Chun; Toshihisa Takagi; Jun'ichi Tsujii (Comput. Intell., 2011)

DDBJ progress report. - Eli Kaminuma; Takehide Kosuge; Yuichi Kodama; Hideo Aono; Jun Mashima; Takashi Gojobori; Hideaki Sugawara; Osamu Ogasawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura (Nucleic Acids Res., 2011)

Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. - Shin Kawano; Hiromasa Ono; Toshihisa Takagi; Hidemasa Bono (Briefings Bioinform., 2012)

The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. - Jin-Dong Kim; Ngan L. T. Nguyen; Yue Wang 040; Jun'ichi Tsujii; Toshihisa Takagi; Akinori Yonezawa (BMC Bioinform., 2012)

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; Yasukazu Nakamura (Nucleic Acids Res., 2012)

DDBJ new system and service refactoring. - Osamu Ogasawara; Jun Mashima; Yuichi Kodama; Eli Kaminuma; Yasukazu Nakamura; Kousaku Okubo; Toshihisa Takagi (Nucleic Acids Res., 2013)

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; Yasukazu Nakamura (Nucleic Acids Res., 2014)

The DDBJ Japanese Genotype-phenotype Archive for genetic and phenotypic human data. - Yuichi Kodama; Jun Mashima; Takehide Kosuge; Toshiaki Katayama; Takatomo Fujisawa; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Toshihisa Takagi; Yasukazu Nakamura (Nucleic Acids Res., 2015)

DNA data bank of Japan (DDBJ) progress report. - Jun Mashima; Yuichi Kodama; Takehide Kosuge; Takatomo Fujisawa; Toshiaki Katayama; Hideki Nagasaki; Yoshihiro Okuda; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Yasukazu Nakamura; Toshihisa Takagi (Nucleic Acids Res., 2016)

Efficient Construction of a New Ontology for Life Sciences by Sub-classifying Related Terms in the Japan Science, Technology Agency Thesaurus. - Tatsuya Kushida; Kouji Kozaki; Yuka Tateisi; Katsutaro Watanabe; Takeshi Masuda; Katsuji Matsumura; Takahiro Kawamura; Toshihisa Takagi (ICBO, 2017)

Refined JST Thesaurus Extended with Data from Other Open Life Science Data Sources. - Tatsuya Kushida; Yuka Tateisi; Takeshi Masuda; Katsutaro Watanabe; Katsuji Matsumura; Takahiro Kawamura; Kouji Kozaki; Toshihisa Takagi (JIST, 2017)

DrG at NTCIR-13: MedWeb Task. - Morita Kazui; Toshihisa Takagi (NTCIR, 2017)

DNA Data Bank of Japan. - Jun Mashima; Yuichi Kodama; Takatomo Fujisawa; Toshiaki Katayama; Yoshihiro Okuda; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Yasukazu Nakamura; Toshihisa Takagi (Nucleic Acids Res., 2017)

A Quantitative Evaluation of Natural Language Question Interpretation for Question Answering Systems. - Takuto Asakura; Jin-Dong Kim; Yasunori Yamamoto; Yuka Tateisi; Toshihisa Takagi (JIST, 2018)

Inference of Functions, Roles, and Applications of Chemicals Using Linked Open Data and Ontologies. - Tatsuya Kushida; Kouji Kozaki; Takahiro Kawamura; Yuka Tateisi; Yasunori Yamamoto; Toshihisa Takagi (JIST, 2018)

NBDC RDF portal: a comprehensive repository for semantic data in life sciences. - Shuichi Kawashima; Toshiaki Katayama; Hideki Hatanaka; Tatsuya Kushida; Toshihisa Takagi (Database J. Biol. Databases Curation, 2018)

The international nucleotide sequence database collaboration. - Ilene Karsch-Mizrachi; Toshihisa Takagi; Guy Cochrane (Nucleic Acids Res., 2018)

DNA Data Bank of Japan: 30th anniversary. - Yuichi Kodama; Jun Mashima; Takehide Kosuge; Eli Kaminuma; Osamu Ogasawara; Kousaku Okubo; Yasukazu Nakamura; Toshihisa Takagi (Nucleic Acids Res., 2018)

Reconstruction of Hierarchical Structures in a Thesaurus-based Ontology through Curation by Domain Experts. - Tatsuya Kushida; Kouji Kozaki; Yasunori Yamamoto; Atsuko Yamaguchi; Takahiro Kawamura; Takako Nakagawa; Yuka Tateisi; Toshihisa Takagi (ICBO, 2019)

Building Knowledge Graph Across Different Subdomains Using Interlinking Ontology for Biomedical Concepts. - Kouji Kozaki; Tatsuya Kushida; Yasunori Yamamoto; Toshihisa Takagi (JIST (2), 2019)

TogoGenome/TogoStanza: modularized Semantic Web genome database. - Toshiaki Katayama; Shuichi Kawashima; Shinobu Okamoto; Yuki Moriya; Hirokazu Chiba; Yuki Naito; Takatomo Fujisawa; Hiroshi Mori; Toshihisa Takagi (Database J. Biol. Databases Curation, 2019)

BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services. - Toshiaki Katayama; Shuichi Kawashima; Gos Micklem; Shin Kawano; Jin-Dong Kim; Simon Kocbek; Shinobu Okamoto; Yue Wang 040; Hongyan Wu; Atsuko Yamaguchi; Yasunori Yamamoto; Erick Antezana; et al. (F1000Research, 2019)

Interconnection of Biological Knowledge Using NikkajiRDF and Interlinking Ontology for Biological Concepts. - Tatsuya Kushida; Kouji Kozaki; Takahiro Kawamura; Yuka Tateisi; Yasunori Yamamoto; Toshihisa Takagi (New Gener. Comput., 2019)

BioHackathon 2015: Semantics of data for life sciences and reproducible research. - Rutger A. Vos; Toshiaki Katayama; Hiroyuki Mishima; Shin Kawano; Shuichi Kawashima; Jin-Dong Kim; Yuki Moriya; Toshiaki Tokimatsu; Atsuko Yamaguchi; Yasunori Yamamoto; Hongyan Wu; Peter Amstutz; et al. (F1000Research, 2020)