Toshihisa Takagi

Osamu Ogasawara, Jun Mashima, Yuichi Kodama, Eli Kaminuma, Yasukazu Nakamura, Kousaku Okubo, Toshihisa Takagi: DDBJ new system and service refactoring. Nucleic Acids Research 41(Database-Issue): 25-29 (2013)

Shin Kawano, Hiromasa Ono, Toshihisa Takagi, Hidemasa Bono: Tutorial videos of bioinformatics resources: online distribution trial in Japan named TogoTV. Briefings in Bioinformatics 13(2): 258-268 (2012)

Jin-Dong Kim, Ngan Nguyen, Yue Wang, Jun'ichi Tsujii, Toshihisa Takagi, Akinori Yonezawa: The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011. BMC Bioinformatics 13(S-11): S1 (2012)

Yuichi Kodama, Jun Mashima, Eli Kaminuma, Takashi Gojobori, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura: The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments. Nucleic Acids Research 40(Database-Issue): 38-42 (2012)

Thanet Praneenararat, Toshihisa Takagi, Wataru Iwasaki: Interactive, multiscale navigation of large and complicated biological networks. Bioinformatics 27(8): 1121-1127 (2011)

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, Kazuharu Arakawa, Bruno Aranda, Raoul J. P. Bonnal, José M. Fernández, Takatomo Fujisawa, Paul M. K. Gordon, Naohisa Goto, Syed Haider, Todd Harris, Takashi Hatakeyama, Isaac Ho, Masumi Itoh, Arek Kasprzyk, Nobuhiro Kido, Young-Joo Kim, Akira R. Kinjo, Fumikazu Konishi, Yulia Kovarskaya, Gregory Von Kuster, Alberto Labarga, Vachiranee Limviphuvadh, E. Luke McCarthy, Yasukazu Nakamura, Yunsun Nam, Kozo Nishida, Kunihiro Nishimura, Tatsuya Nishizawa, Soichi Ogishima, Tom Oinn, Shinobu Okamoto, Shujiro Okuda, Keiichiro Ono, Kazuki Oshita, Keun-Joon Park, Nicholas Putnam, Martin Senger, Jessica Severin, Yasumasa Shigemoto, Hideaki Sugawara, James Taylor, Oswaldo Trelles, Chisato Yamasaki, Riu Yamashita, Noriyuki Satoh, Toshihisa Takagi: The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. J. Biomedical Semantics 2: 4 (2011)

Sebastian Riedel, Rune Sætre, Hong-Woo Chun, Toshihisa Takagi, Jun'ichi Tsujii: Bio-molecular Event Extraction with Markov Logic. Computational Intelligence 27(4): 558-582 (2011)

Eli Kaminuma, Takehide Kosuge, Yuichi Kodama, Hideo Aono, Jun Mashima, Takashi Gojobori, Hideaki Sugawara, Osamu Ogasawara, Toshihisa Takagi, Kousaku Okubo, Yasukazu Nakamura: DDBJ progress report. Nucleic Acids Research 39(Database-Issue): 22-27 (2011)

Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa: Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering. BIBM 2011: 544-549

Atsuko Yamaguchi, Yasunori Yamamoto, Jin-Dong Kim, Toshihisa Takagi, Akinori Yonezawa: Discriminative Optimization of String Similarity and Its Application to Biomedical Abbreviation Clustering. ICMLA (2) 2011: 72-77

Natsu Ishii, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi: Figure classification in biomedical literature to elucidate disease mechanisms, based on pathways. Artificial Intelligence in Medicine 49(3): 135-143 (2010)

Kota Kasahara, Kengo Kinoshita, Toshihisa Takagi: Ligand-binding site prediction of proteins based on known fragment-fragment interactions. Bioinformatics 26(12): 1493-1499 (2010)

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, Raoul J. P. Bonnal, Richard M. Bruskiewich, Jan Christian Bryne, José M. Fernández, Akira Funahashi, Paul M. K. Gordon, Naohisa Goto, Andreas Groscurth, Alex Gutteridge, Richard C. G. Holland, Yoshinobu Kano, Edward A. Kawas, Arnaud Kerhornou, Eri Kibukawa, Akira R. Kinjo, Michael Kuhn, Hilmar Lapp, Heikki Lehväslaiho, Hiroyuki Nakamura, Yasukazu Nakamura, Tatsuya Nishizawa, Chikashi Nobata, Tamotsu Noguchi, Thomas M. Oinn, Shinobu Okamoto, Stuart Owen, Evangelos Pafilis, Matthew R. Pocock, Pjotr Prins, René Ranzinger, Florian Reisinger, Lukasz Salwínski, Mark J. 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: The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. J. Biomedical Semantics 1: 8 (2010)

Eli Kaminuma, Jun Mashima, Yuichi Kodama, Takashi Gojobori, Osamu Ogasawara, Kousaku Okubo, Toshihisa Takagi, Yasukazu Nakamura: DDBJ launches a new archive database with analytical tools for next-generation sequence data. Nucleic Acids Research 38(Database-Issue): 33-38 (2010)

Toshiaki Katayama, Mitsuteru Nakao, Toshihisa Takagi: TogoWS: integrated SOAP and REST APIs for interoperable bioinformatics Web services. Nucleic Acids Research 38(Web-Server-Issue): 706-711 (2010)

Jin-Dong Kim, Yasunori Yamamoto, Atsuko Yamaguchi, Mitsuteru Nakao, Kenta Oouchida, Hong-Woo Chun, Toshihisa Takagi: Natural Language Query Processing for Life Science Knowledge - Position Paper. AMT 2010: 158-165

Steven B. Kraines, Weisen Guo, Daisuke Hoshiyama, Haruo Mizutani, Toshihisa Takagi: Generating Literature-based Knowledge Discoveries in Life Sciences using Relationship Associations. KDIR 2010: 35-44

Steven B. Kraines, Takaki Makino, Weisen Guo, Haruo Mizutani, Toshihisa Takagi: Bridging the Knowledge Gap between Research and Education through Textbooks. ICWL 2010: 121-130

Steven B. Kraines, Weisen Guo, Toshihisa Takagi: Authoring Computer-Understandable Semantic Summaries of Life Science Articles Optimized for Knowledge Mining. Industrial Conference on Data Mining - Workshops 2010: 133-143

Mihoko Otake, Motoichiro Kato, Toshihisa Takagi, Shuichi Iwata, Hajime Asama, Jun Ota: Multiscale Service Design Method and Its Application to Sustainable Service for Prevention and Recovery from Dementia. JSAI-isAI Workshops 2010: 321-330

Nobutaka Mitsuhashi, Kaori Fujieda, Takuro Tamura, Shoko Kawamoto, Toshihisa Takagi, Kousaku Okubo: BodyParts3D: 3D structure database for anatomical concepts. Nucleic Acids Research 37(Database-Issue): 782-785 (2009)

Takeru Nakazato, Hidemasa Bono, Hideo Matsuda, Toshihisa Takagi: Gendoo: Functional profiling of gene and disease features using MeSH vocabulary. Nucleic Acids Research 37(Web-Server-Issue): 166-169 (2009)

Tatsuya Kushida, Takao Asanuma, Yoshihiro Okuda, Yo Shidahara, Toshihisa Takagi: Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis. CISIS 2009: 800-806

Asako Koike, Toshihisa Takagi: Classifying Biomedical Figures Using Combination of Bag of Keypoints and Bag of Words. CISIS 2009: 848-853

Mihoko Otake, Motoichiro Kato, Toshihisa Takagi, Hajime Asama: Coimagination Method: Communication Support System with Collected Images and Its Evaluation via Memory Task. HCI (5) 2009: 403-411

Kenta Oouchida, Jin-Dong Kim, Toshihisa Takagi, Jun'ichi Tsujii: GuideLink: A Corpus Annotation System that Integrates the Management of Annotation Guidelines. PACLIC 2009: 771-778

Mihoko Otake, Motoichiro Kato, Toshihisa Takagi, Hajime Asama: Development of coimagination method towards cognitive enhancement via image based interactive communication. RO-MAN 2009: 835-840

Natsu Ishii, Asako Koike, Yasunori Yamamoto, Toshihisa Takagi: Figure Classification in Biomedical Literature towards Figure Mining. BIBM 2008: 263-269

Takaki Makino, Toshihisa Takagi: On-line discovery of temporal-difference networks. ICML 2008: 632-639

Mihoko Otake, Toshihisa Takagi, Hajime Asama: Open brain simulator estimating internal state of human through external observation towards human biomechatronics. ICRA 2008: 1089-1093

Yasunori Yamamoto, Toshihisa Takagi: OReFiL: an online resource finder for life sciences. BMC Bioinformatics 8 (2007)

Asako Koike, Toshihisa Takagi: Knowledge discovery based on an implicit and explicit conceptual network. JASIST 58(1): 51-65 (2007)

Yasunori Yamamoto, Toshihisa Takagi: Biomedical knowledge navigation by literature clustering. Journal of Biomedical Informatics 40(2): 114-130 (2007)

Wataru Iwasaki, Toshihisa Takagi: Reconstruction of highly heterogeneous gene-content evolution across the three domains of life. ISMB/ECCB (Supplement of Bioinformatics) 2007: 230-239

Mihoko Otake, Kohei Arai, Motoichiro Kato, Takaki Maeda, Yusuke Ikemoto, Kuniaki Kawabata, Toshihisa Takagi, Hajime Asama: Experimental analysis and computational simulation of the attribution of own actions by the multiple forward models. ROBIO 2007: 1417-1421

Tatsuya Kushida, Toshihisa Takagi, Ken-ichiro Fukuda: Event Ontology: A Pathway-Centric Ontology for Biological Processes. Pacific Symposium on Biocomputing 2006: 152-163

Asako Koike, Yoshiki Niwa, Toshihisa Takagi: Automatic extraction of gene/protein biological functions from biomedical text. Bioinformatics 21(7): 1227-1236 (2005)

Hiroko Ao, Toshihisa Takagi: Research Paper: ALICE: An Algorithm to Extract Abbreviations from MEDLINE. JAMIA 12(5): 576-586 (2005)

Kikuya Kato, Riu Yamashita, Ryo Matoba, Morito Monden, Shinzaburo Noguchi, Toshihisa Takagi, Kenta Nakai: Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues. Nucleic Acids Research 33(Database-Issue): 533-536 (2005)

Yasunori Yamamoto, Toshihisa Takagi: A Sentence Classification System for Multi Biomedical Literature Summarization. ICDE Workshops 2005: 1163

Goro Terai, Toshihisa Takagi: Predicting rules on organization of cis-regulatory elements, taking the order of elements into account. Bioinformatics 20(7): 1119-1128 (2004)

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, Kenta Nakai, Sumio Sugano: Large-scale collection and characterization of promoters of human and mouse genes. In Silico Biology 4 (2004)

Asako Koike, Toshihisa Takagi: PRIME: automatically extracted PRotein Interactions and Molecular Information databas. In Silico Biology 5 (2004)

Takako Takai-Igarashi, Toshihisa Takagi, Holger Michael, Edgar Wingender: Preface - Third "Ontology Workshop on Ontology and Genomes". In Silico Biology 5 (2004)

Ken-ichiro Fukuda, Toshihisa Takagi: A Pathway Editor for Literature-based Knowledge Curation. APBC 2004: 339-344

Shinsuke Dohkan, Asako Koike, Toshihisa Takagi: Prediction of Protein-Protein Interactions Using Support Vector Machines. BIBE 2004: 576-586

Yasunori Yamamoto, Toshihisa Takagi: A Practical Partial Parser for Biomedical Literature Summarization. NLUCS 2004: 75-85

Natalia V. Poluliakh, Toshihisa Takagi, Kenta Nakai: MELINA: motif extraction from promoter regions of potentially co-regulated genes. Bioinformatics 19(3): 423-424 (2003)

Ken-ichiro Fukuda, Yuki Yamagata, Toshihisa Takagi: FREX: A query interface for biological processes with hierarchical and recursive structures. In Silico Biology 4 (2003)

Takako Takai-Igarashi, Toshihisa Takagi, Edgar Wingender: Preface. In Silico Biology 4 (2003)

Tetsushi Yada, Yasushi Totoki, Y. Takaeda, Yasubumi Sakaki, Toshihisa Takagi: DIGIT: A Novel Gene Finding Program by Combining Gene-Finders. Pacific Symposium on Biocomputing 2003: 375-387

Hiroko Ao, Yasunori Yamamoto, Toshihisa Takagi: A Method to Retrieve Papers from MEDLINE: PETER System. TREC 2003: 806-809

Mika Hirakawa, Toshihiro Tanaka, Yoichi Hashimoto, Masako Kuroda, Toshihisa Takagi, Yusuke Nakamura: JSNP: a database of common gene variations in the Japanese population. Nucleic Acids Research 30(1): 158-162 (2002)

Toshihide Ono, Haretsugu Hishigaki, Akira Tanigami, Toshihisa Takagi: Automated extraction of information on protein-protein interactions from the biological literature. Bioinformatics 17(1): 155-161 (2001)

Ken-ichiro Fukuda, Toshihisa Takagi: Knowledge representation of signal transduction pathways. Bioinformatics 17(9): 829-837 (2001)

Takako Takai-Igarashi, Toshihisa Takagi: Ontology and functional genomics. German Conference on Bioinformatics 2001: 46

Mikio Yoshida, Ken-ichiro Fukuda, Toshihisa Takagi: PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary. Bioinformatics 16(2): 169-175 (2000)

Tatsuhiko Tsunoda, Toshihisa Takagi: Estimating transcription factor bindability on DNA. Bioinformatics 15(7): 622-630 (1999)

Tatsuhiko Tsunoda, Masao Fukagawa, Toshihisa Takagi: Time and Memory Efficient Algorithm for Extracting Palindromic and Repetitive Subsequences in Nucleic Acid Sequences. Pacific Symposium on Biocomputing 1999: 202-213

Y. Tsukamoto, Kyoko Takiguchi, Kenji Satou, Emiko Furuichi, Toshihisa Takagi, Satoru Kuhara: Application of a deductive database system to search for topological and similar three-dimensional structures in protein. Computer Applications in the Biosciences 13(2): 183-190 (1997)

Yoshihiro Ohta, Yasunori Yamamoto, Tomoko Okazaki, Ikuo Uchiyama, Toshihisa Takagi: Automatic Construction of Knowledge Base from Biological Papers. ISMB 1997: 218-225

Kenji Satou, Toshihide Ono, Yoshihisa Yamamura, Emiko Furuichi, Satoru Kuhara, Toshihisa Takagi: Extraction of Substructures of Proteins Essential to their Biological Functions by a Data Mining Technique. ISMB 1997: 254-257

Takahiko Suzuki, Toshihisa Takagi, Satoru Kuhara, Minoru Kanehisa: Development of an integrated Database for Genome Mapping and Nucleotide Sequences. HICSS (5) 1994: 68-76

Susumu Goto, Norihiro Sakamoto, Toshihisa Takagi: A Deductive Object-Oriented Language for Integrated Genome Databaser. HICSS (5) 1994: 108-110

Kenji Satou, Emiko Furuichi, Kyoko Takiguchi, Satoru Kuhara, Toshihisa Takagi: Application of a Deductive Database System PACADE toward Discovery of Clusters of Similar Structures in Proteins. HICSS (5) 1994: 160-170

Kenji Satou, Emiko Furuichi, Kyoko Takiguchi, Toshihisa Takagi, Satoru Kuhara: A deductive database system PACADE for analyzing 3-D and secondary structures of protein. Computer Applications in the Biosciences 9(3): 259-265 (1993)

Norihiro Sakamoto, Toshihisa Takagi, Yasubumi Sakaki: Development of the Overlapping Oligonucleotide Database and its application to signal sequence search of the human genome. Computer Applications in the Biosciences 9(4): 427-434 (1993)

Susumu Goto, Norihiro Sakamoto, Toshihisa Takagi: Object-Oriented Database with Rule-Based Query Interface for Genomic Computation. DASFAA 1993: 65-72

Toshihisa Takagi, Takahiko Suzuki, Susumu Goto, Kazuo Ushijima: Evaluation of a deductive database system for CAD applications. Systems and Computers in Japan 23(13): 15-27 (1992)

Neng-Fa Zhou, Kazuo Ushijima, Toshihisa Takagi: Bidirectional inference of mode information for logic programs. Systems and Computers in Japan 22(4): 1-9 (1991)

Neng-Fa Zhou, Toshihisa Takagi, Kazuo Ushijima: A Matching Tree Oriented Abstract Machine for Prolog. ICLP 1990: 159-173

Toshihisa Takagi, Fumihiro Matsuo, Shouichi Futamura, Kazuo Ushijima: Implementation of Inferential Relational Database System. FODO 1985: 539-546

Satoru Kuhara, Fumihiro Matsuo, Shouichi Futamura, A. Fujita, Takeshi Shinohara, Toshihisa Takagi, Yasubumi Sakaki: GENAS: a database system for nucleic acid sequence analysis. Nucleic Acids Research 12(1): 89-99 (1984)