An Approximation Algorithm for the Minimum Common Supertree Problem. - Atsuko Yamaguchi; Koji Nakano; Satoru Miyano (Nord. J. Comput., 1997)

An Approximation Algorithm for the Two-Layered Graph Drawing Problem. - Atsuko Yamaguchi; Akihiro Sugimoto (COCOON, 1999)

Finding the Maximum Common Subgraph of a Partial k-Tree and a Graph with a Polynomially Bounded Number of Spanning Trees. - Atsuko Yamaguchi; Hiroshi Mamitsuka (ISAAC, 2003)

Mining biologically active patterns in metabolic pathways using microarray expression profiles. - Hiroshi Mamitsuka; Yasushi Okuno; Atsuko Yamaguchi (SIGKDD Explor., 2003)

Application of a new probabilistic model for recognizing complex patterns in glycans. - Kiyoko F. Aoki; Nobuhisa Ueda; Atsuko Yamaguchi; Minoru Kanehisa; Tatsuya Akutsu; Hiroshi Mamitsuka (ISMB/ECCB (Supplement of Bioinformatics), 2004)

Finding the maximum common subgraph of a partial k-tree and a graph with a polynomially bounded number of spanning trees. - Atsuko Yamaguchi; Kiyoko F. Aoki; Hiroshi Mamitsuka (Inf. Process. Lett., 2004)

KCaM (KEGG Carbohydrate Matcher): a software tool for analyzing the structures of carbohydrate sugar chains. - Kiyoko F. Aoki; Atsuko Yamaguchi; Nobuhisa Ueda; Tatsuya Akutsu; Hiroshi Mamitsuka; Susumu Goto; Minoru Kanehisa (Nucleic Acids Res., 2004)

Managing and Analyzing Carbohydrate Data. - Kiyoko F. Aoki; Nobuhisa Ueda; Atsuko Yamaguchi; Tatsuya Akutsu; Minoru Kanehisa; Hiroshi Mamitsuka (SIGMOD Rec., 2004)

A Probabilistic Model for Mining Labeled Ordered Trees: Capturing Patterns in Carbohydrate Sugar Chains. - Nobuhisa Ueda; Kiyoko F. Aoki-Kinoshita; Atsuko Yamaguchi; Tatsuya Akutsu; Hiroshi Mamitsuka (IEEE Trans. Knowl. Data Eng., 2005)

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)

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)

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)

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)

Building linked open data using approximate string matching methods and domain specific resources. - Yasunori Yamamoto; Atsuko Yamaguchi; Akinori Yonezawa (SWAT4LS, 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)

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)

Building Linked Open Data towards integration of biomedical scientific literature with DBpedia. - Yasunori Yamamoto; Atsuko Yamaguchi; Akinori Yonezawa (J. Biomed. Semant., 2013)

An Intelligent SPARQL Query Builder for Exploration of Various Life-science Databases. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Hongyan Wu; Norio Kobayashi (IESD@ISWC, 2014)

Prototype Implementation of SPARQL Builder for Life-science Databases by Intelligent Schema Analysis on RDF datasets. - Norio Kobayashi; Kai Lenz; Hongyan Wu; Kouji Kozaki; Atsuko Yamaguchi (SWAT4LS, 2014)

BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains. - Toshiaki Katayama; Mark D. Wilkinson; Kiyoko F. Aoki-Kinoshita; Shuichi Kawashima; Yasunori Yamamoto; Atsuko Yamaguchi; Shinobu Okamoto; Shin Kawano; Jin-Dong Kim; Yue Wang 040; Hongyan Wu; Yoshinobu Kano; et al. (J. Biomed. Semant., 2014)

BioBenchmark Toyama 2012: an evaluation of the performance of triple stores on biological data. - Hongyan Wu; Toyofumi Fujiwara; Yasunori Yamamoto; Jerven T. Bolleman; Atsuko Yamaguchi (J. Biomed. Semant., 2014)

TogoTable: cross-database annotation system using the Resource Description Framework (RDF) data model. - Shin Kawano; Tsutomu Watanabe; Sohei Mizuguchi; Norie Araki; Toshiaki Katayama; Atsuko Yamaguchi (Nucleic Acids Res., 2014)

Efficiently Finding Paths Between Classes to Build a SPARQL Query for Life-Science Databases. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Hongyan Wu; Yasunori Yamamoto; Norio Kobayashi (JIST, 2015)

Dynamic Join Order Optimization for SPARQL Endpoint Federation. - Hongyan Wu; Atsuko Yamaguchi; Jin-Dong Kim (SSWS@ISWC, 2015)

RDF-Based Integration with SPARQL Building System for Life Science Database Archive. - Atsuko Yamaguchi; Katsuhiko Okubo; Norio Kobayashi; Kouji Kozaki; Sadahiro Kumagai; Kai Lenz; Tomoe Nobusada; Hongyan Wu; Yasunori Yamamoto; Hideki Hatanaka (SWAT4LS, 2015)

Semantic Data Acquisition by Traversing Class-Class Relationships Over Linked Open Data. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (JIST, 2016)

SPARQL Builder: Constructing SPARQL Query by Traversing Class-Class Relationships for Life Science Databases. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (JIST (Workshops & Posters), 2016)

Umaka-Yummy Data: Where Providers and Consumers in Life Sciences Communicate with Each Other. - Yasunori Yamamoto; Atsuko Yamaguchi; Andrea Splendiani (JIST (Workshops & Posters), 2016)

Data Acquisition by Traversing Class-Class Relationships over the Linked Open Data. - Atsuko Yamaguchi; Kouji Kozaki; Kai Lenz; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (ISWC (Posters & Demos), 2016)

SPARQL Query Construction with Monitoring Service for Endpoints. - Atsuko Yamaguchi; Yasunori Yamamoto; Kouji Kozaki; Kai Lenz; Hiroshi Masuya; Norio Kobayashi (SWAT4LS, 2016)

Umaka-Yummy Data: A Place to Facilitate Communication between Data Providers and Consumers. - Yasunori Yamamoto; Atsuko Yamaguchi; Andrea Splendiani (SWAT4LS, 2016)

Semantic Graph Analysis for Federated LOD Surfing in Life Sciences. - Atsuko Yamaguchi; Kouji Kozaki; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (JIST, 2017)

LOD Surfer API: Web API for LOD Surfing Using Class-Class Relationships in Life Sciences. - Atsuko Yamaguchi; Kouji Kozaki; Yasunori Yamamoto; Hiroshi Masuya; Norio Kobayashi (SWAT4LS, 2017)

Implementing LOD Surfer as a Search System for the Annotation of Multiple Protein Sequence Alignment. - Atsuko Yamaguchi; Hiroyuki Toh (JIST, 2018)

YummyData: providing high-quality open life science data. - Yasunori Yamamoto; Atsuko Yamaguchi; Andrea Splendiani (Database J. Biol. Databases Curation, 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)

Investigating Schema Definitions Using RDFS and OWL 2 for RDF Databases in Life Sciences. - Atsuko Yamaguchi; Tatsuya Kushida; Yasunori Yamamoto; Kouji Kozaki (JIST (2), 2019)

UmakaData Extension: Toward Realization of a Practical SPARQL Endpoint Discovery Service for Life Sciences. - Norio Kobayashi; Yasunori Yamamoto; Atsuko Yamaguchi (SWAT4HCLS, 2019)

Semantic Integration of Intrinsically Disordered Proteins and Existing DBs. - Atsuko Yamaguchi; Hideki Hatanaka; Satoshi Fukuchi; Motonori Ota (SWAT4HCLS, 2019)

Finding RDF Data you need by Umaka Suite. - Yasunori Yamamoto; Atsuko Yamaguchi (SWAT4HCLS, 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)

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)

Gene Ranking based on Paths from Phenotypes to Genes on Knowledge Graph. - Atsuko Yamaguchi; Jae-Moon Shin; Toyofumi Fujiwara (IJCKG, 2021)

A Comparative Study on Storing and Retrieval of URIs for Life Sciences Databases. - Atsuko Yamaguchi; Yasunori Yamamoto (IJCKG (Workshop/Poster/Demo), 2023)

Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases. - Jae-Moon Shin; Toyofumi Fujiwara; Atsuko Yamaguchi (SWAT4HCLS, 2023)

Extracting Long COVID Knowledge from LitCovid: A Glossary-Based Approach. - Atsuko Yamaguchi; Reo Takeda; Yuka Tateisi (IIAI-AAI, 2024)

A semantic design for the biological processes associated with intrinsically disordered proteins. - Atsuko Yamaguchi; Yumiko Kado; Shigetaka Sakamoto; Satoshi Fukuchi; Motonori Ota (SWAT4HCLS, 2024)

Ontology-based expansion of virtual gene panels to improve diagnostic efficiency for rare genetic diseases. - Jae-Moon Shin; Toyofumi Fujiwara; Hirotomo Saitsu; Atsuko Yamaguchi (BMC Medical Informatics Decis. Mak., 2025)