JOY: protein sequence-structure representation and analysis. - Kenji Mizuguchi; Charlotte M. Deane; Tom L. Blundell; Mark S. Johnson; John P. Overington (Bioinform., 1998)

Analysis of conservation and substitutions of secondary structure elements within protein superfamilies. - Kenji Mizuguchi; Tom L. Blundell (Bioinform., 2000)

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. - Paul I. W. de Bakker; Alex Bateman; David F. Burke; Ricardo Núñez Miguel; Kenji Mizuguchi; Jiye Shi; Hiroki Shirai; Tom L. Blundell (Bioinform., 2001)

The SWIB and the MDM2 domains are homologous and share a common fold. - Riccardo Bennett-Lovsey; Sarah E. Hart; Hiroki Shirai; Kenji Mizuguchi (Bioinform., 2002)

HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. - Lucy A. Stebbings; Kenji Mizuguchi (Nucleic Acids Res., 2004)

Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling. - Younes Mokrab; Kenji Mizuguchi (BMC Bioinform., 2005)

Environment specific substitution tables for thermophilic proteins. - Kenji Mizuguchi; M. Sele; Maria Vittoria Cubellis (BMC Bioinform., 2007)

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. - Yoichi Murakami; Kenji Mizuguchi (Bioinform., 2010)

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. - Shandar Ahmad; Yumlembam Hemjit Singh; Yogesh Paudel; Takaharu Mori; Yuji Sugita; Kenji Mizuguchi (BMC Bioinform., 2010)

CCRXP: exploring clusters of conserved residues in protein structures. - Shandar Ahmad; Ozlem Keskin; Kenji Mizuguchi; Akinori Sarai; Ruth Nussinov (Nucleic Acids Res., 2010)

Prediction of dinucleotide-specific RNA-binding sites in proteins. - Michael Fernández; Yutaro Kumagai; Daron M. Standley; Akinori Sarai; Kenji Mizuguchi; Shandar Ahmad (BMC Bioinform., 2011)

An Open Framework for Extensible Multi-stage Bioinformatics Software. - Gabriel Keeble-Gagnère; Johan Nyström-Persson; Matthew I. Bellgard; Kenji Mizuguchi (PRIB, 2012)

Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform. - Johan Nyström-Persson; Yoshinobu Igarashi; Maori Ito; Mizuki Morita; Noriyuki Nakatsu; Hiroshi Yamada; Kenji Mizuguchi (Bioinform., 2013)

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. - Yoichi Murakami; Kenji Mizuguchi (BMC Bioinform., 2014)

Integration of Disease Entries Across OMIM, Orphanet, and a Proprietary Knowledge Base. - Maori Ito; Shin-ichi Nakagawa; Kenji Mizuguchi; Takashi Okumura (IEA/AIE, 2015)

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. - Jun-Ichi Ito; Kazuyoshi Ikeda; Kazunori D. Yamada; Kenji Mizuguchi; Kentaro Tomii (Nucleic Acids Res., 2015)

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. - Yi-An Chen; Lokesh P. Tripathi; Kenji Mizuguchi (Database J. Biol. Databases Curation, 2016)

Improved pose and affinity predictions using different protocols tailored on the basis of data availability. - Philip Prathipati; Chioko Nagao; Shandar Ahmad; Kenji Mizuguchi (J. Comput. Aided Mol. Des., 2016)

Integration of Ligand and Structure Based Approaches for CSAR-2014. - Philip Prathipati; Kenji Mizuguchi (J. Chem. Inf. Model., 2016)

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks. - Attayeb Mohsen; Jonguk Park; Yi-An Chen; Hitoshi Kawashima; Kenji Mizuguchi (BMC Bioinform., 2019)

CLINE: a web-tool for the comparison of biological dendrogram structures. - Rodolfo S. Allendes Osorio; Lokesh P. Tripathi; Kenji Mizuguchi (BMC Bioinform., 2019)

Assessing drug target suitability using TargetMine. - Yi-An Chen; Erika Yogo; Naoko Kurihara; Tomoshige Ohno; Chihiro Higuchi; Masatomo Rokushima; Kenji Mizuguchi (F1000Research, 2019)

Computational Model To Predict the Fraction of Unbound Drug in the Brain. - Tsuyoshi Esaki; Rikiya Ohashi; Reiko Watanabe; Yayoi Natsume-Kitatani; Hitoshi Kawashima; Chioko Nagao; Kenji Mizuguchi (J. Chem. Inf. Model., 2019)

Network-Based Analysis for Biological Discovery. - Lokesh P. Tripathi; Yi-An Chen; Kenji Mizuguchi; Yoichi Murakami (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Network-Based Analysis of Host-Pathogen Interactions. - Lokesh P. Tripathi; Yi-An Chen; Kenji Mizuguchi; Eiji Morita (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

Integrative Analysis of Multi-Omics Data. - Lokesh P. Tripathi; Tsuyoshi Esaki; Mari N. Itoh; Yi-An Chen; Kenji Mizuguchi (Encyclopedia of Bioinformatics and Computational Biology (3), 2019)

TargetMine 2022: a new vision into drug target analysis. - Yi-An Chen; Rodolfo S. Allendes Osorio; Kenji Mizuguchi (Bioinform., 2022)

Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2. - Attayeb Mohsen; Yi-An Chen; Rodolfo S. Allendes Osorio; Chihiro Higuchi; Kenji Mizuguchi (Frontiers Bioinform., 2022)

Integrative Network Modeling Highlights the Crucial Roles of Rho-GDI Signaling Pathway in the Progression of non-Small Cell Lung Cancer. - Saransh Gupta; Haswanth Vundavilli; Rodolfo S. Allendes Osorio; Mari N. Itoh; Attayeb Mohsen; Aniruddha Datta; Kenji Mizuguchi; Lokesh P. Tripathi (IEEE J. Biomed. Health Informatics, 2022)

Toward the Construction of a Knowledge Graph from Japanese Food Ontology for the Prevention of Frailty. - Chihiro Higuchi; Agustin Martin-Morales; Ai Oya; Mai Inoue; Misako Ikkai; Kenji Mizuguchi; Michihiro Araki (IJCKG (Workshop/Poster/Demo), 2023)

Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties. - Kyohei Koyama; Kosuke Hashimoto; Chioko Nagao; Kenji Mizuguchi (Frontiers Bioinform., 2023)

Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning. - Yosui Nojima; Kenji Mizuguchi (Comput. Biol. Chem., 2025)

Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning. - Elpri Eka Permadi; Reiko Watanabe; Kenji Mizuguchi (J. Cheminformatics, 2025)