Kenji Mizuguchi

37 papers C 1Journal 31Unranked 2
YearRankTypeTitle / Venue / Authors
2025 J jnl
Identification of the differences in molecular networks between idiopathic pulmonary fibrosis and lung squamous cell carcinoma using machine learning.
Comput. Biol. Chem.
Yosui Nojima, Kenji Mizuguchi
2025 J jnl
Improving ADME Prediction with Multitask Graph Neural Networks and Assessing Explainability in Lead Optimization.
J. Chem. Inf. Model.
Shoma Ito, Takuto Koyama, Shigeyuki Matsumoto, Ryosuke Kojima, Yuji Okamoto, Masataka Kuroda, Hitoshi Kawashima, Reiko Watanabe, Tomoki Yonezawa, Takaaki Sumiyoshi, Kazuyoshi Ikeda, Kenji Mizuguchi, Hiroaki Iwata, Yasushi Okuno
2025 J jnl
Improving the accuracy of prediction models for small datasets of Cytochrome P450 inhibition with deep learning.
J. Cheminformatics
Elpri Eka Permadi, Reiko Watanabe, Kenji Mizuguchi
2025 J jnl
Integrating a chromatin remodeling layer into single-cell gene regulatory networks.
Briefings Bioinform.
Junsoo Song, Kenji Mizuguchi
2025 J jnl
SEND: a suite of tools for the easy sharing of linked biological data.
Database J. Biol. Databases Curation
Rodolfo S. Allendes Osorio, Yi-An Chen, Kenji Mizuguchi
2023 J jnl
Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties.
Frontiers Bioinform.
Kyohei Koyama, Kosuke Hashimoto, Chioko Nagao, Kenji Mizuguchi
2023 — conf
Toward the Construction of a Knowledge Graph from Japanese Food Ontology for the Prevention of Frailty.
IJCKG (Workshop/Poster/Demo)
Chihiro Higuchi, Agustin Martin-Morales, Ai Oya, Mai Inoue, Misako Ikkai, Kenji Mizuguchi, Michihiro Araki
2022 J jnl
Integrative Network Modeling Highlights the Crucial Roles of Rho-GDI Signaling Pathway in the Progression of non-Small Cell Lung Cancer.
IEEE J. Biomed. Health Informatics
Saransh Gupta, Haswanth Vundavilli, Rodolfo S. Allendes Osorio, Mari N. Itoh, Attayeb Mohsen, Aniruddha Datta, Kenji Mizuguchi, Lokesh P. Tripathi
2022 J jnl
Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2.
Frontiers Bioinform.
Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi
2022 J jnl
TargetMine 2022: a new vision into drug target analysis.
Bioinform.
Yi-An Chen, Rodolfo S. Allendes Osorio, Kenji Mizuguchi
2019 J jnl
Assessing drug target suitability using TargetMine.
F1000Research
Yi-An Chen, Erika Yogo, Naoko Kurihara, Tomoshige Ohno, Chihiro Higuchi, Masatomo Rokushima, Kenji Mizuguchi
2019 J jnl
CLINE: a web-tool for the comparison of biological dendrogram structures.
BMC Bioinform.
Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji Mizuguchi
2019 J jnl
Computational Model To Predict the Fraction of Unbound Drug in the Brain.
J. Chem. Inf. Model.
Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Kenji Mizuguchi
2019 J jnl
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.
BMC Bioinform.
Attayeb Mohsen, Jonguk Park, Yi-An Chen, Hitoshi Kawashima, Kenji Mizuguchi
2019 — ch.
Integrative Analysis of Multi-Omics Data.
Encyclopedia of Bioinformatics and Computational Biology (3)
Lokesh P. Tripathi, Tsuyoshi Esaki, Mari N. Itoh, Yi-An Chen, Kenji Mizuguchi
2019 — ch.
Network-Based Analysis for Biological Discovery.
Encyclopedia of Bioinformatics and Computational Biology (3)
Lokesh P. Tripathi, Yi-An Chen, Kenji Mizuguchi, Yoichi Murakami
2019 — ch.
Network-Based Analysis of Host-Pathogen Interactions.
Encyclopedia of Bioinformatics and Computational Biology (3)
Lokesh P. Tripathi, Yi-An Chen, Kenji Mizuguchi, Eiji Morita
2016 J jnl
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework.
Database J. Biol. Databases Curation
Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi
2016 J jnl
Improved pose and affinity predictions using different protocols tailored on the basis of data availability.
J. Comput. Aided Mol. Des.
Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi
2016 J jnl
Integration of Ligand and Structure Based Approaches for CSAR-2014.
J. Chem. Inf. Model.
Philip Prathipati, Kenji Mizuguchi
2015 C conf
Integration of Disease Entries Across OMIM, Orphanet, and a Proprietary Knowledge Base.
IEA/AIE
Maori Ito, Shin-ichi Nakagawa, Kenji Mizuguchi, Takashi Okumura
2015 J jnl
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.
Nucleic Acids Res.
Jun-Ichi Ito, Kazuyoshi Ikeda, Kazunori D. Yamada, Kenji Mizuguchi, Kentaro Tomii
2014 J jnl
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.
BMC Bioinform.
Yoichi Murakami, Kenji Mizuguchi
2013 J jnl
Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform.
Bioinform.
Johan Nyström-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi
2012 J jnl
An Open Framework for Extensible Multi-Stage Bioinformatics Software
CoRR
Gabriel Keeble-Gagnère, Johan Nyström-Persson, Matthew I. Bellgard, Kenji Mizuguchi
2012 — conf
An Open Framework for Extensible Multi-stage Bioinformatics Software.
PRIB
Gabriel Keeble-Gagnère, Johan Nyström-Persson, Matthew I. Bellgard, Kenji Mizuguchi
2011 J jnl
Prediction of dinucleotide-specific RNA-binding sites in proteins.
BMC Bioinform.
Michael Fernández, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad
2010 J jnl
Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.
Bioinform.
Yoichi Murakami, Kenji Mizuguchi
2010 J jnl
CCRXP: exploring clusters of conserved residues in protein structures.
Nucleic Acids Res.
Shandar Ahmad, Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, Ruth Nussinov
2010 J jnl
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.
BMC Bioinform.
Shandar Ahmad, Yumlembam Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi
2007 J jnl
Environment specific substitution tables for thermophilic proteins.
BMC Bioinform.
Kenji Mizuguchi, M. Sele, Maria Vittoria Cubellis
2005 J jnl
Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling.
BMC Bioinform.
Younes Mokrab, Kenji Mizuguchi
2004 J jnl
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database.
Nucleic Acids Res.
Lucy A. Stebbings, Kenji Mizuguchi
2002 J jnl
The SWIB and the MDM2 domains are homologous and share a common fold.
Bioinform.
Riccardo Bennett-Lovsey, Sarah E. Hart, Hiroki Shirai, Kenji Mizuguchi
2001 J jnl
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.
Bioinform.
Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell
2000 J jnl
Analysis of conservation and substitutions of secondary structure elements within protein superfamilies.
Bioinform.
Kenji Mizuguchi, Tom L. Blundell
1998 J jnl
JOY: protein sequence-structure representation and analysis.
Bioinform.
Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington