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Journal Articles
- 2023
[j24]Kyohei Koyama, Kosuke Hashimoto, Chioko Nagao, Kenji Mizuguchi:
Attention network for predicting T-cell receptor-peptide binding can associate attention with interpretable protein structural properties. Frontiers Bioinform. 3 (2023)- 2022
- [j23]Yi-An Chen, Rodolfo S. Allendes Osorio
, Kenji Mizuguchi:
TargetMine 2022: a new vision into drug target analysis. Bioinform. 38(18): 4454-4456 (2022) - [j22]Attayeb Mohsen, Yi-An Chen, Rodolfo S. Allendes Osorio, Chihiro Higuchi, Kenji Mizuguchi:
Snaq: A Dynamic Snakemake Pipeline for Microbiome Data Analysis With QIIME2. Frontiers Bioinform. 2 (2022) - [j21]Saransh Gupta, Haswanth Vundavilli, Rodolfo S. Allendes Osorio, Mari N. Itoh, Attayeb Mohsen, Aniruddha Datta, Kenji Mizuguchi, Lokesh P. Tripathi:
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 26(9): 4785-4793 (2022) - 2019
- [j20]Rodolfo S. Allendes Osorio, Lokesh P. Tripathi, Kenji Mizuguchi:
CLINE: a web-tool for the comparison of biological dendrogram structures. BMC Bioinform. 20(1): 528:1-528:12 (2019) - [j19]Attayeb Mohsen, Jonguk Park, Yi-An Chen, Hitoshi Kawashima, Kenji Mizuguchi:
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. 20(1): 581:1-581:10 (2019) - [j18]Tsuyoshi Esaki, Rikiya Ohashi, Reiko Watanabe, Yayoi Natsume-Kitatani, Hitoshi Kawashima, Chioko Nagao, Kenji Mizuguchi:
Computational Model To Predict the Fraction of Unbound Drug in the Brain. J. Chem. Inf. Model. 59(7): 3251-3261 (2019) - 2016
- [j17]Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi:
An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework. Database J. Biol. Databases Curation 2016 (2016) - [j16]Philip Prathipati, Chioko Nagao, Shandar Ahmad, Kenji Mizuguchi:
Improved pose and affinity predictions using different protocols tailored on the basis of data availability. J. Comput. Aided Mol. Des. 30(9): 817-828 (2016) - [j15]Philip Prathipati, Kenji Mizuguchi:
Integration of Ligand and Structure Based Approaches for CSAR-2014. J. Chem. Inf. Model. 56(6): 974-987 (2016) - 2015
- [j14]Jun-Ichi Ito, Kazuyoshi Ikeda, Kazunori D. Yamada, Kenji Mizuguchi, Kentaro Tomii:
PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs. Nucleic Acids Res. 43(Database-Issue): 392-398 (2015) - 2014
- [j13]Yoichi Murakami, Kenji Mizuguchi:
Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators. BMC Bioinform. 15: 213 (2014) - 2013
- [j12]Johan Nyström-Persson, Yoshinobu Igarashi, Maori Ito, Mizuki Morita, Noriyuki Nakatsu, Hiroshi Yamada, Kenji Mizuguchi:
Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform. Bioinform. 29(23): 3080-3086 (2013) - 2011
- [j11]Michael Fernández, Yutaro Kumagai, Daron M. Standley, Akinori Sarai, Kenji Mizuguchi, Shandar Ahmad:
Prediction of dinucleotide-specific RNA-binding sites in proteins. BMC Bioinform. 12(S-13): S5 (2011) - 2010
- [j10]Yoichi Murakami, Kenji Mizuguchi:
Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites. Bioinform. 26(15): 1841-1848 (2010) - [j9]Shandar Ahmad, Yumlembam Hemjit Singh, Yogesh Paudel, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi:
Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins. BMC Bioinform. 11: 533 (2010) - [j8]Shandar Ahmad, Ozlem Keskin, Kenji Mizuguchi, Akinori Sarai, Ruth Nussinov:
CCRXP: exploring clusters of conserved residues in protein structures. Nucleic Acids Res. 38(Web-Server-Issue): 398-401 (2010) - 2007
- [j7]Kenji Mizuguchi, M. Sele, Maria Vittoria Cubellis:
Environment specific substitution tables for thermophilic proteins. BMC Bioinform. 8(S-1) (2007) - 2005
- [j6]Younes Mokrab, Kenji Mizuguchi:
Amino-Acid Substitutions In Membrane Proteins: Applications To Homology Recognition And Comparative Modelling. BMC Bioinform. 6(S-3) (2005) - 2004
- [j5]Lucy A. Stebbings, Kenji Mizuguchi:
HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database. Nucleic Acids Res. 32(Database-Issue): 203-207 (2004) - 2002
- [j4]Riccardo Bennett-Lovsey, Sarah E. Hart, Hiroki Shirai, Kenji Mizuguchi:
The SWIB and the MDM2 domains are homologous and share a common fold. Bioinform. 18(4): 626-630 (2002) - 2001
- [j3]Paul I. W. de Bakker, Alex Bateman, David F. Burke, Ricardo Núñez Miguel, Kenji Mizuguchi, Jiye Shi, Hiroki Shirai, Tom L. Blundell:
HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families. Bioinform. 17(8): 748-749 (2001) - 2000
- [j2]Kenji Mizuguchi, Tom L. Blundell:
Analysis of conservation and substitutions of secondary structure elements within protein superfamilies. Bioinform. 16(12): 1111-1119 (2000) - 1998
- [j1]Kenji Mizuguchi, Charlotte M. Deane, Tom L. Blundell, Mark S. Johnson, John P. Overington:
JOY: protein sequence-structure representation and analysis. Bioinform. 14(7): 617-623 (1998)
Conference and Workshop Papers
- 2023
- [c3]Chihiro Higuchi, Agustin Martin-Morales, Ai Oya, Mai Inoue, Misako Ikkai, Kenji Mizuguchi, Michihiro Araki:
Toward the Construction of a Knowledge Graph from Japanese Food Ontology for the Prevention of Frailty. IJCKG (Workshop/Poster/Demo) 2023: 1-4 - 2015
- [c2]Maori Ito, Shin-ichi Nakagawa, Kenji Mizuguchi, Takashi Okumura:
Integration of Disease Entries Across OMIM, Orphanet, and a Proprietary Knowledge Base. IEA/AIE 2015: 120-130 - 2012
- [c1]Gabriel Keeble-Gagnère, Johan Nyström-Persson, Matthew I. Bellgard, Kenji Mizuguchi:
An Open Framework for Extensible Multi-stage Bioinformatics Software. PRIB 2012: 106-117
Reference Works
- 2019
- [r3]Lokesh P. Tripathi, Tsuyoshi Esaki, Mari N. Itoh, Yi-An Chen, Kenji Mizuguchi:
Integrative Analysis of Multi-Omics Data. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 194-199 - [r2]Lokesh P. Tripathi, Yi-An Chen, Kenji Mizuguchi, Yoichi Murakami:
Network-Based Analysis for Biological Discovery. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 283-291 - [r1]Lokesh P. Tripathi, Yi-An Chen, Kenji Mizuguchi, Eiji Morita:
Network-Based Analysis of Host-Pathogen Interactions. Encyclopedia of Bioinformatics and Computational Biology (3) 2019: 932-937
Informal and Other Publications
- 2019
- [i2]Yi-An Chen, Erika Yogo, Naoko Kurihara, Tomoshige Ohno, Chihiro Higuchi, Masatomo Rokushima, Kenji Mizuguchi:
Assessing drug target suitability using TargetMine. F1000Research 8: 233 (2019) - 2012
- [i1]Gabriel Keeble-Gagnère, Johan Nyström-Persson, Matthew I. Bellgard, Kenji Mizuguchi:
An Open Framework for Extensible Multi-Stage Bioinformatics Software. CoRR abs/1208.4436 (2012)
Coauthor Index
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