| Published Papers |
| No. | Ｔitle | Journal | Vol | No | Start Page | End Page | Publication date | DOI | Referee |
| 1 | Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases | CEUR Workshop Proceedings | 3415 | | 87 | 91 | 2023 | | Refereed |
| 2 | Advances in the development of PubCaseFinder, including the new application programming interface and matching algorithm. | Human mutation | | | | | Feb. 10, 2022 | https://doi.org/10.1002/humu.243411 | Refereed |
| 3 | Gene Ranking based on Paths from Phenotypes to Genes on Knowledge Graph.  | IJCKG 21 | | | 131 | 134 | Dec. 2021 | https://doi.org/10.1145/3502223.35022401 | Refereed |
| 4 | O-JMeSH: creating a bilingual English-Japanese controlled vocabulary of MeSH UIDs through machine translation and mutual information | Genomics & Informatics | | | | | Sep. 30, 2021 | https://doi.org/10.5808/gi.210141 | Refereed |
| 5 | Constructing Japanese MeSH term dictionaries related to the COVID-19 literature | Genomics & Informatics | | | | | Sep. 30, 2021 | https://doi.org/10.5808/gi.210121 | Refereed |
| 6 | A proof-of-concept study of extracting patient histories for rare/intractable diseases from social media. | Genomics & informatics | 18 | 2 | | | Jun. 30, 2020 | https://doi.org/10.5808/gi.2020.18.2.e171 | Refereed |
| 7 | Investigating schema definitions using RDFS and OWL 2 for RDF databases in life sciences | Communications in Computer and Information Science | 1157 CCIS | | 137 | 144 | 2020 | https://doi.org/10.1007/978-981-15-3412-6_141 | Refereed |
| 8 | BioHackathon 2015: Semantics of data for life sciences and reproducible research | F1000Research | 9 | | | | 2020 | https://doi.org/10.12688/f1000research.18236.11 | Refereed |
| 9 | BioHackathon series in 2013 and 2014: improvements of semantic interoperability in life science data and services | F1000Research | 8 | | | | Sep. 2019 | https://doi.org/10.12688/f1000research.18238.11 | Refereed |
| 10 | Semantic Integration of Intrinsically Disordered Proteins and Existing DBs. | SWAT4HCLS 2019 | | | 147 | 148 | 2019 | | Refereed |
| 11 | Reconstruction of Hierarchical Structures in a Thesaurus-based Ontology through Curation by Domain Experts. | ICBO 2019 | | | 1 | 1 | 2019 | | Refereed |
| 12 | Split4Blank: Maintaining consistency while improving efficiency of loading RDF data with blank nodes | PLoS ONE | 14 | 6 | e0217852 | | 2019 | https://doi.org/10.1371/journal.pone.02178521 | Refereed |
| 13 | UmakaData Extension: Toward Realization of a Practical SPARQL Endpoint Discovery Service for Life Sciences. | SWAT4HCLS 2019 | | | 151 | 152 | 2019 | | Refereed |
| 14 | Finding RDF Data you need by Umaka Suite. | SWAT4HCLS 2019 | | | 157 | 158 | 2019 | | Refereed |
| 15 | Implementing LOD surfer as a search system for the annotation of multiple protein sequence alignment | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 11341 LNCS | | 418 | 426 | 2018 | https://doi.org/10.1007/978-3-030-04284-4_291 | Refereed |
| 16 | YummyData: Providing high-quality open life science data | Database | 2018 | 2018 | | 022 | 2018 | https://doi.org/10.1093/database/bay0221 | Refereed |
| 17 | LOD Surfer API: A Web API for LOD Surfing Using Class-Class Relationships in Life Sciences | CEUR Workshop Proceedings | 2042 | | | | 2017 | | Refereed |
| 18 | Semantic graph analysis for federated LOD surfing in life sciences | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 10675 | | 268 | 276 | 2017 | https://doi.org/10.1007/978-3-319-70682-5_181 | Refereed |
| 19 | The health care and life sciences community profile for dataset descriptions | PEERJ | 4 | 8 | | | Aug. 2016 | https://doi.org/10.7717/peerj.23311 | Refereed |
| 20 | SPARQL query construction with monitoring service for endpoints | CEUR Workshop Proceedings | 1795 | | | | 2016 | | Refereed |
| 21 | Efficiently finding paths between classes to build a SPARQL query for life-science databases | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 9544 | | 321 | 330 | 2016 | https://doi.org/10.1007/978-3-319-31676-5_241 | Refereed |
| 22 | Umaka-Yummy Data: Where providers and consumers in life sciences communicate with each other | CEUR Workshop Proceedings | 1741 | | 50 | 53 | 2016 | | Refereed |
| 23 | Data acquisition by traversing class-class relationships over the linked open data | CEUR Workshop Proceedings | 1690 | | | | 2016 | | Refereed |
| 24 | Umaka-Yummy data: A place to facilitate communication between data providers and consumers | CEUR Workshop Proceedings | 1795 | | | | 2016 | | Refereed |
| 25 | Semantic data acquisition by traversing class–class relationships over linked open data | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 10055 | | 136 | 151 | 2016 | https://doi.org/10.1007/978-3-319-50112-3_111 | Refereed |
| 26 | SPARQL builder: Constructing SPARQL query by traversing class{Class relationships for life science databases | CEUR Workshop Proceedings | 1741 | | 58 | 61 | 2016 | | Refereed |
| 27 | Dynamic join order optimization for SPARQL endpoint federation | CEUR Workshop Proceedings | 1457 | | 48 | 62 | 2015 | | Refereed |
| 28 | RDF-based integration with SPARQL building system for Life Science Database Archive | CEUR Workshop Proceedings | 1546 | | 195 | 196 | 2015 | | Refereed |
| 29 | An intelligent SPARQL query builder for exploration of various life-science databases | CEUR Workshop Proceedings | 1279 | | | | 2015 | | Refereed |
| 30 | Semantic Web technologies for the big data in life sciences | BIOSCIENCE TRENDS | 8 | 4 | 192 | 201 | Aug. 2014 | https://doi.org/10.5582/bst.2014.010481 | Refereed |
| 31 | Semantic Web technologies for the big data in life sciences | BIOSCIENCE TRENDS | 8 | 4 | 192 | 201 | Aug. 2014 | https://doi.org/10.5582/bst.2014.010481 | Refereed |
| 32 | BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data | JOURNAL OF BIOMEDICAL SEMANTICS | 5 | 1 | | | Jul. 2014 | https://doi.org/10.1186/2041-1480-5-321 | Refereed |
| 33 | TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model | NUCLEIC ACIDS RESEARCH | 42 | W1 | W442 | W448 | Jul. 2014 | https://doi.org/10.1093/nar/gku4031 | Refereed |
| 34 | BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. | Journal of biomedical semantics | 5 | 1 | | | 2014 | https://doi.org/10.1186/2041-1480-5-51 | Refereed |
| 35 | Prototype implementation of SPARQL Builder for Life-science Databases by intelligent schema analysis on RDF datasets | CEUR Workshop Proceedings | 1320 | | | | 2014 | | Refereed |
| 36 | Chemical compound complexity in biological pathways | Quantitative Graph Theory: Mathematical Foundations and Applications | | | 471 | 492 | 2014 | https://doi.org/10.1201/b176451 | Refereed |
| 37 | Building Linked Open Data towards integration of biomedical scientific literature with DBpedia | JOURNAL OF BIOMEDICAL SEMANTICS | 4 | 1 | | | Mar. 2013 | https://doi.org/10.1186/2041-1480-4-81 | Refereed |
| 38 | The 3rd DBCLS BioHackathon: improving life science data integration with Semantic Web technologies | JOURNAL OF BIOMEDICAL SEMANTICS | 4 | 1 | | | Feb. 2013 | https://doi.org/10.1186/2041-1480-4-61 | Refereed |
| 39 | Discriminative application of string similarity methods to chemical and non-chemical names for biomedical abbreviation clustering | BMC GENOMICS | 13 | | | | Jun. 2012 | https://doi.org/10.1186/1471-2164-13-S3-S81 | Refereed |
| 40 | Building linked open data using approximate string matching methods and domain specific resources | ACM International Conference Proceeding Series | | | 121 | 122 | 2012 | https://doi.org/10.1145/2166896.21669271 | Refereed |
| 41 | The 2nd DBCLS BioHackathon: interoperable bioinformatics Web services for integrated applications. | Journal of biomedical semantics | 2 | 1 | 4 | 4 | Aug. 2, 2011 | https://doi.org/10.1186/2041-1480-2-41 | Refereed |
| 42 | Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering | 2011 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM 2011) | | | 544 | 549 | 2011 | https://doi.org/10.1109/BIBM.2011.981 | Refereed |
| 43 | Discriminative Application of String Similarity Methods to Chemical and Non-chemical Names for Biomedical Abbreviation Clustering | 2011 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE (BIBM 2011) | 13 Suppl 3 | | 544 | 549 | 2011 | https://doi.org/10.1109/BIBM.2011.981 | Refereed |
| 44 | Discriminative optimization of string similarity and its application to biomedical abbreviation clustering | Proceedings - 10th International Conference on Machine Learning and Applications, ICMLA 2011 | 2 | | 72 | 77 | 2011 | https://doi.org/10.1109/ICMLA.2011.581 | Refereed |
| 45 | Allie: A database and a search service of abbreviations and long forms | Database | 2011 | | | | 2011 | https://doi.org/10.1093/database/bar0131 | Refereed |
| 46 | The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. | Journal of biomedical semantics | 1 | 1 | 1 | 19 | Dec. 2010 | | Refereed |
| 47 | The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*. | Journal of biomedical semantics | 1 | 1 | 8 | 8 | Aug. 21, 2010 | https://doi.org/10.1186/2041-1480-1-81 | Refereed |
| 48 | Natural Language Query Processing for Life Science Knowledge Position Paper | ACTIVE MEDIA TECHNOLOGY | 6335 | | 158 | + | 2010 | https://doi.org/10.1007/978-3-642-15470-6_171 | Refereed |
| 49 | Visualization of Genetic Networks: Edge Crossing Minimization of a Graph Drawing with Vertex Pairs | Res. Commun. Biochem. Cell & Mol. Biol. | 14 | | 5 | 14 | 2009 | | Refereed |
| 50 | A probabilistic model for mining labeled ordered trees: Capturing patterns in carbohydrate sugar chains | IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING | 17 | 8 | 1051 | 1064 | Aug. 2005 | https://doi.org/10.1109/TKDE.2005.1171 | Refereed |
| 51 | Finding the maximum common subgraph of a partial k-tree and a graph with a polynomially bounded number of spanning trees | INFORMATION PROCESSING LETTERS | 92 | 2 | 57 | 63 | Oct. 2004 | https://doi.org/10.1016/j.ipl.2004.06.0191 | Refereed |
| 52 | Application of a new probabilistic model for recognizing complex patterns in glycans | BIOINFORMATICS | 20 | SUPPL. 1 | 6 | 14 | Aug. 2004 | https://doi.org/10.1093/bioinformatics/bth9161 | Refereed |
| 53 | KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains | NUCLEIC ACIDS RESEARCH | 32 | WEB SERVER ISS. | W267 | W272 | Jul. 2004 | https://doi.org/10.1093/nar/gkh4731 | Refereed |
| 54 | Managing and analyzing carbohydrate data | SIGMOD RECORD | 33 | 2 | 33 | 38 | Jun. 2004 | | Refereed |
| 55 | Efficient tree-matching methods for accurate carbohydrate database queries. | Genome informatics. International Conference on Genome Informatics | 14 | | 134 | 143 | 2003 | | Refereed |
| 56 | Statistical Significance of Tree Similarity Scores | GI | 14 | | 579 | 580 | 2003 | https://doi.org/10.11234/gi1990.14.5791 | |
| 57 | Finding the maximum common subgraph of a partial k-tree and a graph with a polynomially bounded number of spanning trees | ALGORITHMS AND COMPUTATION, PROCEEDINGS | 2906 | | 58 | 67 | 2003 | | Refereed |
| 58 | Mining biologically active patterns in metabolic pathways using microarray expression profiles. | SIGKDD Explor. | 5 | 2 | 113 | 121 | 2003 | https://doi.org/10.1145/980972.9809861 | |
| 59 | An approximation algorithm for the two-layered graph drawing problem | Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | 1627 | | 81 | 91 | 1999 | https://doi.org/10.1007/3-540-48686-0_81 | Refereed |
