List of research products since 1998

All Kinds of Products Papers Presentations Lectures Books Reviews All Year 2010 2009 2008 2007 2006 2005 2004 2003 2002 2001 2000 1999 1998

Reviewed papers and proceedings

• Ishii, N.*, Koike, A., Yamamoto, Y. and Takagi, T.:
  Figure Classification in Biomedical Literature to Elucidate Disease Mechanisms, Based on Pathways
  Artificial Intelligence in Medicine 2009 in press
• Koike, A. and Takagi, T.:
  Classifying biomedical figures using combination of bag of keypoints and bag of keywords
  Proc. of 2nd Int. Workshop on Intell. Inform. in Biol. and Med 2009 :848-853
• Mizutani, H., Takeda, Y., Momose, A., Takeuchi, A. and Takagi, T.:
  X-ray microscopy for neural circuit reconstruction
  Journal of Physics: Conference Series 2009 , 186 :012092
• Iwasaki, W., Takagi, T.:
  Rapid Pathway Evolution Facilitated by Horizontal Gene Transfers across Prokaryotic Lineages
  PLoS Genetics 2009 , 5 (3) :e1000402
• Tatsuya Kushida, Takao Asanuma, Yoshihiro Okuda, Yo Shidahara and Toshihisa Takagi:
  Collection of Disease Networks by Hybrid Curation Method and the Application for Pathway Analysis
  Proc. of 2nd Int. Workshop on Intell. Inform. in Biol. and Med. 2009 :800-806
• Ishii, N., Koike, A., Yamamoto, Y. and Takagi, T.:
  Figure Classification in Biomedical Literature towards Figure Mining
  2008 IEEE International Conference on Bioinformatics and Biomedicine 2008 :263-269
• Otake, M., Takagi, T., and Asama, H.:
  Open Brain Simulator Estimating Internal State of Human through External Observation towards Human Biomechatronics
  Proceedings of the 2008 IEEE International Conference on Robotics and Automation 2008 :1089-1093
• Otake, M., Arai, K., Kato, M., Maeda T., Ikemoto, Y., Kawabata, K., Takagi, T. and Asama, H.:
  Experimental Analysis of the Attribution of Own Actions to the Intention of Self or Others by the multiple Forward Models.
  Journal of Robotics and Mechatronics 2007 , 19 (4) :482-488
• Otake, M., Arai, K., Kato, M., Maeda, T., Ikemoto, Y., Kawabata, K., Takagi, T. and Asama, H. :
  Experimental Analysis and Computational Simulation of the Attribution of Own Actions by the Multiple Forward Models.
  Proceedings of IEEE International Conference on Robotics and Biomimetics 2007 :1417 - 1421
• Iwasaki, W., Takagi, T.:
  Reconstruction of highly heterogeneous gene-content evolution across the three domains of life.
  Bioinformatics 2007 , 23 (13) :i230-9
• Yamamoto, Y., Takagi, T.:
  OReFiL: an online resource finder for life sciences.
  BMC Bioinformatics 2007 , 8 :287
• Kurokawa, K., Itoh, T., Kuwahara, T., Oshima, K., Toh, H., Toyoda, A., Takami, H., Morita, H., Sharma, V.K., Srivastava, T.P., Taylor, T.D., Noguchi, H., Mori, H., Ogura, Y., Ehrlich, D.S., Itoh, K., Takagi, T., Sakaki, Y., Hayashi, T., Hattori, M.:
  Comparative metagenomics revealed commonly enriched gene sets in human gut microbiomes
  DNA Res. 2007 , 14 (4) :169-81
• Sakakibara, Y., Irie, T., Suzuki, Y., Yamashita, R., Wakaguri, H., Kanai, A., Chiba, J., Takagi, T., Mizushima-Sugano, J., Hashimoto, S., Nakai, K., Sugano, S.:
  Intrinsic promoter activities of primary DNA sequences in the human genome
  DNA Res. 2007 , 14 (2) :71-77
• Yamamoto, Y., Takagi, T.:
  Biomedical knowledge navigation by literature clustering.
  Journal of Biomedical Informatics 2007 , 40 (2) :114-30
• Koike, A. and Takagi, T.:
  Knowledge discovery based on an implicit and explicit conceptual network.
  J. Am. Soc. Info. Sci. Tech. 2007 , 58 (1) :51-65
• Noguchi, H., Park, J., Takagi, T.:
  MetaGene: prokaryotic gene finding from environmental genome shotgun sequences.
  Nucleic Acids Res. 2006 , 34 (19) :5623-30
• Dohkan, S., Koike, A., Takagi, T.:
  Improving the performance of an SVM-based method for predicting protein-protein interactions.
  In Silico Biol. (Gedrukt) 2006 , 6 (6) :515-29
• Otake, M., Fukano, R., Sako, S., Sugi, M., Kotani, K., Hayashi, J., Noguchi, H., Yoneda, R., Taura, K., Otsu, N. and Sato, T.:
  Autonomous collaborative environment for project based learning
  Intelligent Autonomous Systems 9 T. Arai et al. (Eds.) IOS Press 2006 :756-763
• Otake, M.:
  From muscle to brain - modelling and control of functional materials and living systems
  Intelligent Autonomous Systems 9 T. Arai et al. (Eds.) IOS Press 2006 :1025-1032
• Kushida, T., Takagi, T., Fukuda, K.I.:
  Event ontology: a pathway-centric ontology for biological processes.
  Pacific Symposium on Biocomputing 2006 , 11 :152-63
• Otake, M. and Nakamura, Y.:
  Spinal information processing and its application to motor learning support
  Journal of Robotics and Mechatronics 2005 , 17 (6) :617-627
• Otake, M. and Nakamura, Y.:
  Anatomical model of the spinal nervous system and its application to the coordination, analysis for motor learning support system
  Proceedings of the IEEE International Conference on Robotic Systems 2005 :847-852
• Otake, M., Takagi, T.:
  Reassembly and interfacing neural models registered on biological model databases.
  Genome Informatics 2005 , 16 (2) :76-85
• Watanabe, T.K., Suzuki, M., Yamasaki, Y., Okuno, S., Hishigaki, H., Ono, T., Oga, K., Mizoguchi-Miyakita, A., Tsuji, A., Kanemoto, N., Wakitani, S., Takagi, T., Nakamura, Y., Tanigami, A.:
  Mutated G-protein-coupled receptor GPR10 is responsible for the hyperphagia/dyslipidaemia/obesity locus of Dmo1 in the OLETF rat.
  Clin. Exp. Pharmacol. Physiol. 2005 , 32 (5月6日) :355-66
• Ao, H., Takagi, T.:
  ALICE: an algorithm to extract abbreviations from MEDLINE.
  J Am Med Inform Assoc 2005 , 12 (5) :576-86
• Kushida, T., Yamamoto, S., Yamagata, Y., Asanuma, T., Hattori, E., Takagi, T. and Fukuda, K.:
  Research on bilogical pathways peculiar to woody perennial plants using a pathway database: P-INOH
  Knowledge Discovery and Data Management in Biomedical Science (KDDMBS) 2005 :56-67
• Yamamoto, Y. and Takagi, T.:
  A sentence classification system for multi-document summarization in the biomedical domain
  The proceedings of International Workshop on Biomedical Data Engineering (BMDE2005) 2005 :90-95
• Kato, K., Yamashita, R., Matoba, R., Monden, M., Noguchi, S., Takagi, T., Nakai, K.:
  Cancer gene expression database (CGED): a database for gene expression profiling with accompanying clinical information of human cancer tissues.
  Nucleic Acids Res. 2005 , 33 (Database issue) :D533-6
• Koike, A., Niwa, Y., Takagi, T.:
  Automatic extraction of gene/protein biological functions from biomedical text.
  Bioinformatics 2005 , 21 (7) :1227-36
• Koike, A., Takagi, T.:
  PRIME: automatically extracted PRotein Interactions and Molecular Information databasE.
  In Silico Biol. 2005 , 5 (1) :9月20日
• Yamamoto, S., Asanuma, T., Takagi, T. and Fukuda, K.:
  The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature
  Comparative and Functional Genomics 2004 , 5 :528-536
• Koike, A., Niwa, Y., and Takagi, T.:
  Automatic extraction of biological functions using semi-automatically gathered biological terms, Development and Applications of Ontology on OMICS Rearch
  The Third Wordshop on Ontology and Genome 2004
• Yamamoto, Y. and Takagi, T.:
  A practical partial parser for biomedical literature summarization
  Proceedings of 1st international workshop on Natural Language Understanding and Cognitive Science 2004 :75-85
• Dohkan, S., Koike, A. and Takagi, T.:
  Prediction of protein-protein interactions using Support Vector Machines
  "Proceedings of the Fourth IEEE Symposium on BioInformatics and BioEngineering (BIBE2004), Taitung, Taiwan" 2004 :576-584
• Imanishi, T., ..., Takagi, T., ..., et al.:
  Integrative annotation of 21,037 human genes validated by full-length cDNA clones.
  PLoS Biol. 2004 , 2 (6) :e162
• Koike, A., Takagi, T.:
  Prediction of protein-protein interaction sites using support vector machines.
  Protein Eng. Des. Sel. 2004 , 17 (2) :165-73
• Koike, A. and Takagi, T.:
  Gene/protein/family name recognition in biomedical literature, Linking Biological Literature, Ontologies and Databases: Tools for Users
  Workshop in conjunction with NAACL/ HLT 2004 2004 :9月16日
• Terai, G., Takagi, T.:
  Predicting rules on organization of cis-regulatory elements, taking the order of elements into account.
  Bioinformatics 2004 , 20 (7) :1119-28
• Fukuda, K. and Takagi, T.:
  A pathway editor for literature-based knowledge curation
  Conferences in Research and Practice in Information Technology 2004 , 29 :339-344
• Fukuda, K.I., Yamagata, Y., Takagi, T.:
  FREX: a query interface for biological processes with hierarchical and recursive structures.
  In Silico Biol. 2004 , 4 (1) :63-79
• Koike, A., Kobayashi, Y., Takagi, T.:
  Kinase pathway database: an integrated protein-kinase and NLP-based protein-interaction resource.
  Genome Res. 2003 , 13 (6A) :1231-43
• Poluliakh, N., Takagi, T., Nakai, K.:
  Melina: motif extraction from promoter regions of potentially co-regulated genes.
  Bioinformatics 2003 , 19 (3) :423-4
• Yada, T., Takagi, T., Totoki, Y., Sakaki, Y., Takaeda, Y.:
  DIGIT: a novel gene finding program by combining gene-finders.
  Proc. Pacific Sympo. on Biocomputing '03 2003 , 8 :375-87
• Koike, A., Nakai, K. and Takagi, T.:
  The origin and evolution of eukaryotic protein kinases
  Genome Lett. 2002 , 1 (2) :83-104
• Hirakawa, M., Tanaka, T., Hashimoto, Y., Kuroda, M., Takagi, T., Nakamura, Y.:
  JSNP: a database of common gene variations in the Japanese population.
  Nucleic Acids Res. 2002 , 30 (1) :158-62
• Okuno, S., Kondo, M., Yamasaki, Y., Miyao, H., Ono, T., Iwanaga, T., Omori, K., Okano, M., Suzuki, M., Momota, H., Hishigaki, H., Hayashi, I., Goto, Y., Shinomiya, H., Harada, Y., Hirashima, T., Kanemoto, N., Asai, T., Wakitani, S., Takagi, T., Nakamura, :
  Substitution of Dmo1 with normal alleles results in decreased manifestation of diabetes in OLETF rats.
  2002 , 4 (5) :309-18
• Watanabe, T.K., Okuno, S., Ono, T., Yamasaki, Y., Oga, K., Mizoguchi-Miyakita, A., Miyao, H., Suzuki, M., Momota, H., Goto, Y., Shinomiya, H., Hishigaki, H., Hayashi, I., Asai, T., Wakitani, S., Takagi, T., Nakamura, Y., Tanigami, A.:
  Single-allele correction of the Dmo1 locus in congenic animals substantially attenuates obesity, dyslipidaemia and diabetes phenotypes of the OLETF rat.
  Clin. Exp. Pharmacol. Physiol. 2001 , 28 (1月2日) :28-42
• Kihara, C., Tsunoda, T., Tanaka, T., Yamana, H., Furukawa, Y., Ono, K., Kitahara, O., Zembutsu, H., Yanagawa, R., Hirata, K., Takagi, T., Nakamura, Y.:
  Prediction of sensitivity of esophageal tumors to adjuvant chemotherapy by cDNA microarray analysis of gene-expression profiles.
  Cancer Res. 2001 , 61 (17) :6474-6479
• Fukuda, K., Takagi, T.:
  Knowledge representation of signal transduction pathways.
  Bioinformatics 2001 , 17 (9) :829-37
• Fukuda, K. and Takagi, T.:
  Signal transduction pathways and logical inferences
  The 2001 International Conference on Mathematics and Engineering (METMBS2001) 2001 :297-303
• Ono, T., Hishigaki, H., Tanigami, A., Takagi, T.:
  Automated extraction of information on protein-protein interactions from the biological literature.
  Bioinformatics 2001 , 17 (2) :155-61
• Okuno, S., Watanabe, T.K., Ono, T., Oga, K., Mizoguchi-Miyakita, A., Yamasaki, Y., Goto, Y., Shinomiya, H., Momota, H., Miyao, H., Hayashi, I., Asai, T., Suzuki, M., Harada, Y., Hishigaki, H., Wakitani, S., Takagi, T., Nakamura, Y., Tanigami, A.:
  Effects of Dmo1 on obesity, dyslipidaemia and hyperglycaemia in the Otsuka Long Evans Tokushima Fatty strain.
  Genet. Res. 2001 , 77 (2) :183-90
• Kitahara, O., Furukawa, Y., Tanaka, T., Kihara, C., Ono, K., Yanagawa, R., Nita, M.E., Takagi, T., Nakamura, Y., Tsunoda, T.:
  Alterations of gene expression during colorectal carcinogenesis revealed by cDNA microarrays after laser-capture microdissection of tumor tissues and normal epithelia.
  Cancer Res. 2001 , 61 (9) :3544-3549
• Hishigaki, H., Nakai, K., Ono, T., Tanigami, A., Takagi, T.:
  Assessment of prediction accuracy of protein function from protein--protein interaction data.
  Yeast 2001 , 18 (6) :523-31
• Terai, G., Takagi, T., Nakai, K.:
  Prediction of co-regulated genes in Bacillus subtilis on the basis of upstream elements conserved across three closely related species.
  Genome Biol. 2001 , 2 (11) :RESEARCH0048
• Yada, T., Totoki, Y., Takagi, T., Nakai, K.:
  A novel bacterial gene-finding system with improved accuracy in locating start codons.
  DNA Res. 2001 , 8 (3) :97-106
• Kato, M., Tsunoda, T., Takagi, T.:
  Inferring genetic networks from DNA microarray data by multiple regression analysis.
  Genome informatics. Workshop on Genome Informatics 2000 , 11 :118-28
• Ono, K., Tanaka, T., Tsunoda, T., Kitahara, O., Kihara, C., Okamoto, A., Ochiai, K., Takagi, T., Nakamura, Y.:
  Identification by cDNA microarray of genes involved in ovarian carcinogenesis.
  Cancer research 2000 , 60 (18) :5007-5011
• Hattori, M., Fujiyama, A., Taylor, T.D., Watanabe, H., Yada, T., Park, H.S., Toyoda, A., Ishii, K., Totoki, Y., Choi, D.K., Groner, Y., Soeda, E., Ohki, M., Takagi, T., Sakaki, Y., Taudien, S., Blechschmidt, K., Polley, A., Menzel, U., Delabar, J., Kumpf,:
  The DNA sequence of human chromosome 21.
  Nature 2000 , 405 (6784) :311-9
• Watanabe, T.K., Ono, T., Okuno, S., Mizoguchi-Miyakita, A., Yamasaki, Y., Kanemoto, N., Hishigaki, H., Oga, K., Takahashi, E., Irie, Y., Bihoreau, M.T., James, M.R., Lathrop, G.M., Takagi, T., Nakamura, Y., Tanigami, A.:
  Characterization of newly developed SSLP markers for the rat.
  Mammalian genome 2000 , 11 (4) :300-5
• Yoshida, M., Fukuda, K., Takagi, T.:
  PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary.
  Bioinformatics 2000 , 16 (2) :169-75
• Tsunoda, T., Fukagawa, M., and Takagi, T.:
  Time and memory efficient algorithm for extracting palindromic and repetitive subsequences in nucleic acid sequences
  Proceedings of the Pacific Symposium on Biocomputing 1999 , 4 (PSB-99) :202-213
• Tomita, H., Nagamitsu, S., Wakui, K., Fukushima, Y., Yamada, K., Sadamatsu, M., Masui, A., Konishi, T., Matsuishi, T., Aihara, M., Shimizu, K., Hashimoto, K., Mineta, M., Matsushima, M., Tsujita, T., Saito, M., Tanaka, H., Tsuji, S., Takagi, T., Nakamura,:
  Paroxysmal kinesigenic choreoathetosis locus maps to chromosome 16p11.2-q12.1.
  American journal of human genetics 1999 , 65 (6) :1688-97
• Okuno, S., Watanabe, T.K., Ono, T., Yamasaki, Y., Goto, Y., Miyao, H., Asai, T., Kanemoto, N., Oga, K., Mizoguchi-Miyakita, A., Takagi, T., Takahashi, E., Nakamura, Y., Tanigami, A.:
  Genetic determinants of plasma triglyceride levels in (OLETF x BN) x OLETF backcross rats.
  Genomics 1999 , 62 (3) :350-5
• Watanabe, T.K., Bihoreau, M.T., McCarthy, L.C., Kiguwa, S.L., Hishigaki, H., Tsuji, A., Browne, J., Yamasaki, Y., Mizoguchi-Miyakita, A., Oga, K., Ono, T., Okuno, S., Kanemoto, N., Takahashi, E., Tomita, K., Hayashi, H., Adachi, M., Webber, C., Davis, M.,:
  A radiation hybrid map of the rat genome containing 5,255 markers.
  Nature genetics 1999 , 22 (1) :27-36
• Tsunoda, T., Takagi, T.:
  Estimating transcription factor bindability on DNA.
  Bioinformatics 1999 , 15 (7月8日) :622-30
• Watanabe, T.K., Okuno, S., Oga, K., Mizoguchi-Miyakita, A., Tsuji, A., Yamasaki, Y., Hishigaki, H., Kanemoto, N., Takagi, T., Takahashi, E., Irie, Y., Nakamura, Y., Tanigami, A.:
  Genetic dissection of ""OLETF"", a rat model for non-insulin-dependent diabetes mellitus: quantitative trait locus analysis of (OLETF x BN) x OLETF.
  Genomics 1999 , 58 (3) :233-9
• Daigo, Y., Isomura, M., Nishiwaki, T., Suzuki, K., Maruyama, O., Takeuchi, K., Yamane, Y., Hayashi, R., Minami, M., Hojo, Y., Uchiyama, I., Takagi, T., Nakamura, Y.:
  Significant differences in the frequency of transcriptional units, types and numbers of repetitive elements, GC content, and the number of CpG islands between a 1010-kb G-band genomic segment on chromosome 9q31.3 and a 1200-kb R-band genomic segment on ch
  DNA research 1999 , 6 (4) :227-33
• Daigo, Y., Isomura, M., Nishiwaki, T., Tamari, M., Ishikawa, S., Kai, M., Murata, Y., Takeuchi, K., Yamane, Y., Hayashi, R., Minami, M., Fujino, M.A., Hojo, Y., Uchiyama, I., Takagi, T., Nakamura, Y.:
  Characterization of a 1200-kb genomic segment of chromosome 3p22-p21.3.
  DNA research 1999 , 6 (1) :37-44
• Murakami, K., Takagi, T.:
  Clustering and detection of 5' splice sites of mRNA by k weight-matrices model.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1999 :171-81
• Murakami, K., Takagi, T.:
  Gene recognition by combination of several gene-finding programs.
  Bioinformatics 1998 , 14 (8) :665-75
• Tsunoda, T. and Takagi, T.:
  A new cut-off estimating algorithm for transcription factor bindability on DNA
  The First International Conference on Bioinformatics of Genome Regulation and Structure 1998 :199-202
• Fukuda, K., Tsunoda, T., Tamura, A. and Takagi, T.:
  Extracting technical terms from medical and biological articles
  Transactions of Information Processing Society of Japan 1998 , 39 (8) :2421-2430
• Fukuda, K., Tamura, A., Tsunoda, T., Takagi, T.:
  Toward information extraction: identifying protein names from biological papers.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998 :707-18
• Tsunoda, T., Takagi, T.:
  Automatic extraction of position specific cooccurrence of transcription factor bindings on promoters.
  Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 1998 :252-63

Presentations

• Mizutani, H.*, Takeda, Y., Momose, A., Takeuchi, A and Takagi, T.:
  X-ray nano-tomography for neural circuit reconstruction
  36th International Congress of Physiological Sciences 2009-07-29 [Poster]
• Praneenararat, T.*, Iwasaki, W., Takagi, T.:
  Effective Multi-Scale Graph Navigation System Powered by Fast and Biologically Meaningful Hierarchical Clustering.
  The 20th International Conference on Genome Informatics 2009 [Poster]
• Koike, A.*, Ishii, N. and Takagi, T.:
  Biomedical Figure Search using Combination of Bag of Keypoints and Bag of Words
  GIW2009 2009-12-15 [Poster]
• Ishii, N.*, Koike, A. and Takagi, T.:
  Classification of Neuroimaging Figures toward Automatic Figure Annotation System
  GIW2009 2009-12-14 [Poster]
• Sakai,N*.,Sakai,S., Nakamura, H., Fukuda, K., and Takagi, T.:
  INOH Pathway Database
  GIW2009 2009-12-14 [Poster]
• Ishii, N., Koike, A., Yamamoto, Y. and Takagi, T.:
  Figure Classification in Biomedical Literature towards Figure Mining
  2008 IEEE International Conference on Bioinformatics and Biomedicine 2008 [Oral]
• Mizutani, H., Takeda, Y., Momose, A., Takeuchi, A. and Takagi, T.:
  X-ray microscopy for neural circuit reconstruction
  9th International Conference on X-Ray Microscopy 2008 [Poster]
• Iwasaki, W. and Takagi, T.:
  Reconstruction of Highly Heterogeneous Gene-Content Evolution across the Three Domains of Life.
  ISMB/ECCB 2007 [Oral and Poster]
• Fukuda, K., Yamamoto, S., Sakai, N., Nakamura, H. and Takagi, T.:
  INOH pathway database and BioPAX export
  ISMB 2007
• Demir, E., Fukuda, K., Takagi, T. and Sander, C.:
  Paxtools: A software library for accessing and analyzing biological pathway information.
  ISMB 2007
• Sakai, N., Yamamoto, S., Nakamura, H., Takagi, T. and Fukuda, K.:
  INOH Pathway Data and Ontologies
  JSBi 2007
• Iwasaki, W. and Takagi, T.:
  Maximum Likelihood Estimation of Ancestral Gene Content over the Universal Tree of Life.
  PSB 2007
• Fukagawa, H., Iwasaki, W. and Takagi, T.:
  A Prototype Platform for Flexible Comparison Analyses of Interactions and Pathways.
  ISMB/ECCB 2007
• Mizutani, H., Takeda, Y., Takeuchi, A., Momose, A. and Takagi, T.:
  3D reconstruction of neuronal circuits by using synchrotron radiation X-ray micro-tomography.
  Fall 2007 Janelia Conference: Neural Circuit Reconstruction 2007
• Ishii, N., Koike, A., Yamamoto, Y. and Takagi, T.:
  Classification of Figures in Biomedical Literature toward a Figure Finding System
  GIW 2006
• Iwasaki, W. and Takagi, T.:
  An Expectation-Maximization Algorithm for Reconstructing Heterogeneous Gene-Content
  GIW 2006
• Park, J., Noguchi, H., and Takagi, T.:
  Gene Finding for Microbial Metagenomics
  GIW 2006
• Yamaguchi, D., Koike, A., Yamamoto, Y. and Takagi, T.:
  A Gene Annotation Tool Based on Sequence Similarity and Biomedical Text
  GIW 2006
• 進化の非一様性を考慮した遺伝子セット進化史の再構築法の開発.:
  岩崎　渉, 高木　利久.
  日本分子生物学会 2006
• Dohkan, S., Koike, A. and Takagi, T.:
  Towards in silico prediction of protein-protein interaction maps
  Interactome Networks 2006
• Koike, A. and Takagi, T.:
  Semi-automatic interpretation of experimental results based on conceptual network << best poster award >>
  CBI 2005
• Koike, A. and Takagi, A.:
  Knowledge discovery using cross database search
  GIW 2005
• Kushida, T., Yamagata, Y., Yamamoto, S., Asanuma, T. and Sekiguchi, A.:
  Pathway analysis of phytohormones in trees using a bioinformatics tool
  IUFRO World Congress 2005
• Koike, A. and Takagi, T.:
  Knowledge discovery based on conceptual network
  GIW 2004
• Kouji, T., Koike, A. and Takagi, T.:
  Question Answering System in Biomedical Domain
  GIW 2004
• Kushida, T., Yamagata, Y., Yamamoto, S., Asanuma, T., Sekiguchi. A., Takagi, T. and Fukuda, K.:
  Research on Cellular Pathways Peculiar to Trees in the Pathway Database
  Functional genomics of environmental adaptation in Populus 2004
• Koike, A., Niwa, Y. and Takagi, T.:
  Automatic Extraction of Protein Interactions and Biological Functions from Text
  ISMB 2004
• Yamamoto, Y. and Takagi, T.:
  TextLens/SeC: A Sentence Classification System for Abstracts of Biomedical Literature
  ISMB 2004
• Koike, A, Kobayashi, Y. and Takagi, T.:
  PRIME:automatically extracted PRotein Interactions and Molecular Information DatabasE
  PSB 2004
• Ao, H. and Takagi,T.:
  A simple method to extract information about interactions of UV-regulated genes from MEDLINE
  PSB 2004
• Yamamoto, Y. and Takagi, T.:
  Extracting Main Idea from Title and Abstract
  PSB 2004
• Ao, H. and Takagi,T:
  An algorithm to identify abbreviations from MEDLINE
  GIW 2003
• Koike, A. and Takagi, T.:
  Prediction of Protein interaction sites and protein-protein interaction pairs
  GIW 2003
• Dohkan, S., Koike, A. and Takagi,T.:
  Support Vector Machines for Predicting Protein-Protein Interactions
  GIW 2003
• Yamamoto, Y. and Takagi, T.:
  Evaluation System for Information Retrieval in Biomedical Field
  GIW 2003
• Ao, H., Yamamoto, Y. and Takagi, T.:
  A method to retrieve papers from MEDLINE: PETER system
  TREC 2003
• Ao, H. and Takagi, T.:
  An algorithm to select abstracts from MEDLINE concerning UV-regulated genes
  ISMB 2003
• Koike, A., Kobayashi, Y. and Takagi, T.:
  PRIME:automatically extracted PRotein Interactions and Molecular Information DatabasE
  ISMB 2003
• Koike, A. and Takagi, T.:
  The analysis and prediction of protein-protein interataction sites
  ISMB 2003
• Yamamoto, Y., Ao, H., and Takagi, T.:
  TextLens: A Fast and Practical Partial Parser for Biomedical Literature
  ISMB 2003
• Koike, A., Kobayashi, Y., Takagi, T.:
  Kinase Pathway Database: An Integrated Resource of Automatically Extracted Information and Sequence Analysis
  GIW 2002
• Terai, G., Yamazaki, M., Sugiyama, Y., Ao, H., Inoue, S. and Takagi, T:
  Database of Human UV-regulated Genes
  GIW 2002
• Yamazaki, M., Ao, H., Kitamura, N. and Takagi, T.:
  Database for Human UV-regulated Genes
  GIW 2001
• Koike, A. and Takagi, T.:
  The origin and evolution of eukaryotic protein kinases
  GIW 2001

Survey papers

• Takai-Igarashi, T., Takagi, T., Michael, H. and Wingender, E.
  Third ""Ontology Workshop on Ontology and Genomes"" -Preface-
  In Silico Biology 2004 , 5 :1