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List of works by Kenji Mizuguchi

A combined proteomics and computational approach provides a better understanding of HCV-induced liver disease.

scientific article

A family of proteins related to Spätzle, the toll receptor ligand, are encoded in the Drosophila genome.

scientific article published on October 2001

A model of a transmembrane drug-efflux pump from Gram-negative bacteria

scientific article published in December 2004

A novel superfamily of enzymes that catalyze the modification of guanidino groups.

scientific article published on August 2001

A phylogenomic profile of hemerythrins, the nonheme diiron binding respiratory proteins

scientific article

A prospective compound screening contest identified broader inhibitors for Sirtuin 1

scientific article published on 20 December 2019

A six-stranded double-psi beta barrel is shared by several protein superfamilies.

scientific article

A structural dissection of amino acid substitutions in helical transmembrane proteins

scientific article

A third fibronectin type III domain in the extracellular region of the insulin receptor family

scientific article published on 01 December 1998

A-kinase anchoring protein BIG3 coordinates oestrogen signalling in breast cancer cells.

scientific article

Actin Cytoskeletal Reorganization Function of JRAB/MICAL-L2 Is Fine-tuned by Intramolecular Interaction between First LIM Zinc Finger and C-terminal Coiled-coil Domains

scientific article published on 05 September 2019

Altered Actions of Memantine and NMDA-Induced Currents in a New Grid2-Deleted Mouse Line

scientific article

An Antigen-Free, Plasmacytoid Dendritic Cell-Targeting Immunotherapy To Bolster Memory CD8+ T Cells in Nonhuman Primates.

scientific article published on 5 February 2018

An integrative data analysis platform for gene set analysis and knowledge discovery in a data warehouse framework

scientific article

An iterative structure-assisted approach to sequence alignment and comparative modeling.

scientific article published in January 1999

Analysis of oral microbiota in Japanese oral cancer patients using 16S rRNA sequencing

scientific article published on 16 May 2019

Applying the Naïve Bayes classifier with kernel density estimation to the prediction of protein-protein interaction sites.

scientific article published on 6 June 2010

Assessing drug target suitability using TargetMine

scientific article published on 28 February 2019

B cell-intrinsic MyD88 signaling controls IFN-γ-mediated early IgG2c class switching in mice in response to a particulate adjuvant

scientific article published on 21 May 2019

BIG3 Inhibits the Estrogen-Dependent Nuclear Translocation of PHB2 via Multiple Karyopherin-Alpha Proteins in Breast Cancer Cells

scientific article published on 8 June 2015

Bioinformatics Approaches for Analysis of Protein-Ligand Interactions

Blockade of TLR3 protects mice from lethal radiation-induced gastrointestinal syndrome

scientific article published on 18 March 2014

Brefeldin A-inhibited guanine nucleotide-exchange protein 3 (BIG3) is predicted to interact with its partner through an ARM-type α-helical structure

scientific article

CAMPASS: a database of structurally aligned protein superfamilies ⬇️

scientific article published on September 15, 1998

CCRXP: exploring clusters of conserved residues in protein structures

scientific article

CLINE: a web-tool for the comparison of biological dendrogram structures

scientific article published on 28 October 2019

Categorization of the Ocular Microbiome in Japanese Stevens-Johnson Syndrome Patients With Severe Ocular Complications

scientific article published on 19 November 2021

Classification of idiopathic interstitial pneumonias using anti-myxovirus resistance-protein 1 autoantibody.

scientific article published on 23 February 2017

Co-expression analysis to identify key modules and hub genes associated with COVID-19 in platelets

scientific article published on 14 April 2022

Collective motions in proteins investigated by X-ray diffuse scattering

scientific article published on 01 January 1994

Comparison of spatial arrangements of secondary structural elements in proteins.

scientific article

Comprehensive analysis of gut microbiota of a healthy population and covariates affecting microbial variation in two large Japanese cohorts

scientific article published on 20 May 2021

Computational Model To Predict the Fraction of Unbound Drug in the Brain

scientific article published on 11 July 2019

Computational design, construction, and characterization of a set of specificity determining residues in protein-protein interactions

scientific article published on 10 July 2012

Computational systems biology for drug discovery: from molecules, structures to networks

scientific article published on 01 January 2017

Conformational changes in DNA-binding proteins: Relationships with precomplex features and contributions to specificity and stability

scholarly article by Munazah Andrabi published in November 2013

Constructing an In Silico Three-Class Predictor of Human Intestinal Absorption With Caco-2 Permeability and Dried-DMSO Solubility

scientific article published on 25 July 2019

Correction: Pathway-Based Analysis of Genome-Wide siRNA Screens Reveals the Regulatory Landscape of App Processing

scientific article published on June 2015

Creation of lysine-deficient mutant lymphotoxin-alpha with receptor selectivity by using a phage display system

scientific article

Crystal structure of FtsA from Staphylococcus aureus

scientific article

Data Curation can Improve the Prediction Accuracy of Metabolic Intrinsic Clearance

scientific article published on 24 September 2018

Data Warehousing with TargetMine for Omics Data Analysis

scientific article published on 01 January 2019

Detecting subtle functional differences in ketopantoate reductase and related enzymes using a rule-based approach with sequence-structure homology recognition scores.

scientific article published on 27 September 2010

Developing a Kinase-Specific Target Selection Method Using a Structure-Based Machine Learning Approach

scientific article published on 02 December 2020

Development of Simplified in Vitro P-Glycoprotein Substrate Assay and in Silico Prediction Models To Evaluate Transport Potential of P-Glycoprotein

scientific article published on 16 April 2019

Development of an in silico prediction system of human renal excretion and clearance from chemical structure information incorporating fraction unbound in plasma as a descriptor

scientific article published on 11 December 2019

Dextran sulfate-resistant A/Puerto Rico/8/34 influenza virus is associated with the emergence of specific mutations in the neuraminidase glycoprotein.

scientific article published on 16 September 2014

Dietary Vitamin B1 Intake Influences Gut Microbial Community and the Consequent Production of Short-Chain Fatty Acids

scientific article published on 16 May 2022

Disrupted in Schizophrenia 1 Interactome: evidence for the close connectivity of risk genes and a potential synaptic basis for schizophrenia

scientific article

Distinct protein interfaces in transmembrane domains suggest an in vivo folding model.

scientific article published in November 2004

Docking of cytochrome c6 and plastocyanin to the aa3-type cytochrome c oxidase in the cyanobacterium Phormidium laminosum

scientific article published on 29 September 2008

Double deletion of tetraspanins CD9 and CD81 in mice leads to a syndrome resembling accelerated aging.

scientific article published on 23 March 2018

Drosophila neurotrophins reveal a common mechanism for nervous system formation

scientific article

Editorial-Sequences and topology.

scientific article published on 3 June 2017

Environment specific substitution tables for thermophilic proteins

scientific article

Essential Role of CARD14 in Murine Experimental Psoriasis

scientific article published on 17 November 2017

Exploring ligand recognition and ion flow in comparative models of the human GABA type A receptor

scientific article published on 3 May 2007

Expression, purification, crystallization and preliminary crystallographic study of FtsA from methicillin-resistant Staphylococcus aureus

scientific article published on 27 July 2013

FlyMine: an integrated database for Drosophila and Anopheles genomics

scientific article published on January 2007

Functional restraints on the patterns of amino acid substitutions: Application to sequence-structure homology recognition

scientific article published on 01 December 2005

Getting knotted: a model for the structure and activation of Spätzle.

scientific article

HOMSTRAD: a database of protein structure alignments for homologous families

scientific article

HOMSTRAD: adding sequence information to structure-based alignments of homologous protein families.

scientific article published in August 2001

HOMSTRAD: recent developments of the Homologous Protein Structure Alignment Database.

scientific article published on January 2004

High-Contrast Facile Imaging with Target-Directing Fluorescent Molecular Rotors, the N3-Modified Thioflavin T Derivatives

scientific article published on 07 January 2019

Homology-based prediction of interactions between proteins using Averaged One-Dependence Estimators.

scientific article

Identification and classification of bacterial Type III toxin-antitoxin systems encoded in chromosomal and plasmid genomes.

scientific article

Identification of potential inhibitors based on compound proposal contest: Tyrosine-protein kinase Yes as a target

scientific article

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

scientific article published on 15 November 2019

Improved pose and affinity predictions using different protocols tailored on the basis of data availability

scientific article

Inhibitory roles of signal transducer and activator of transcription 3 in antitumor immunity during carcinogen-induced lung tumorigenesis.

scientific article

Integrated pathway clusters with coherent biological themes for target prioritisation

scientific article

Integrated prediction of one-dimensional structural features and their relationships with conformational flexibility in helical membrane proteins.

scientific article

Integrating sequence and gene expression information predicts genome-wide DNA-binding proteins and suggests a cooperative mechanism.

scientific article published on 25 November 2017

Integration of Ligand and Structure Based Approaches for CSAR-2014.

scientific article

Interactive Toxicogenomics: Gene set discovery, clustering and analysis in Toxygates

scientific article

JOY: protein sequence-structure representation and analysis.

scientific article

Ligand-induced Ordering of the C-terminal Tail Primes STING for Phosphorylation by TBK1

scientific article published on June 2016

Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data

scientific article

Lipophobicity and the residue environments of the transmembrane alpha-helical bundle

scientific article published in January 2009

MANTA, an integrative database and analysis platform that relates microbiome and phenotypic data

scientific article published on 04 December 2020

Metabolomic analysis of fibrotic mice combined with public RNA-seq human lung data reveal potential diagnostic biomarker candidates for lung fibrosis

scientific article published on 22 September 2020

Method for preparing DNA from feces in guanidine thiocyanate solution affects 16S rRNA-based profiling of human microbiota diversity.

scientific article

Molecular basis for SUMOylation-dependent regulation of DNA binding activity of heat shock factor 2.

scientific article published on 18 November 2008

Network analysis and in silico prediction of protein-protein interactions with applications in drug discovery.

scientific article published on 29 March 2017

Novel anti-flavivirus drugs targeting the nucleolar distribution of core protein

scientific article published on 29 November 2019

On nucleotide solvent accessibility in RNA structure

scientific article published on 12 May 2010

Organic anion transporting polypeptides of the OATP/SLCO superfamily: identification of new members in nonmammalian species, comparative modeling and a potential transport mode.

scientific article published in December 2005

Partner-Aware Prediction of Interacting Residues in Protein-Protein Complexes from Sequence Data ⬇️

scientific article published on December 14, 2011

Pathway-based analysis of genome-wide siRNA screens reveals the regulatory landscape of APP processing

scientific article published on 27 February 2015

PoSSuM v.2.0: data update and a new function for investigating ligand analogs and target proteins of small-molecule drugs.

scientific article

Predicting Fraction Unbound in Human Plasma from Chemical Structure: Improved Accuracy in the Low Value Ranges

scientific article published on 27 September 2018

Predicting conformational ensembles and genome-wide transcription factor binding sites from DNA sequences.

scientific article

Prediction and experimental validation of a putative non-consensus binding site for transcription factor STAT3 in serum amyloid A gene promoter

article

Prediction of detailed enzyme functions and identification of specificity determining residues by random forests.

scientific article published on 8 January 2014

Prediction of dinucleotide-specific RNA-binding sites in proteins

scientific article

Prediction of mono- and di-nucleotide-specific DNA-binding sites in proteins using neural networks

scientific article

Profiles of microRNA networks in intestinal epithelial cells in a mouse model of colitis

scientific article

Quantifying the relative immune cell activation from whole tissue/organ-derived differentially expressed gene data

scientific article published on 9 October 2017

Relationships between barley consumption and gut microbiome characteristics in a healthy Japanese population: a cross-sectional study

scientific article published on 14 March 2022

Retinoblastoma-binding Protein 4-regulated Classical Nuclear Transport Is Involved in Cellular Senescence

scientific article

Sagace: A web-based search engine for biomedical databases in Japan ⬇️

scientific article published on October 31, 2012

Seeking significance in three-dimensional protein structure comparisons.

scientific article

Sequence-structure homology recognition by iterative alignment refinement and comparative modeling.

scientific article

Syndecan-4 as a biomarker to predict clinical outcome for glioblastoma multiforme treated with WT1 peptide vaccine.

scientific article published on 03 October 2016

Systems Biology Approaches to a Rational Drug Discovery Paradigm

scientific article published on 26 August 2015

TargetMine, an integrated data warehouse for candidate gene prioritisation and target discovery

scientific article

Targeting BIG3-PHB2 interaction to overcome tamoxifen resistance in breast cancer cells

scientific article published on January 2013

The SWIB and the MDM2 domains are homologous and share a common fold

scientific article (publication date: April 2002)

The TargetMine Data Warehouse: Enhancement and Updates

scientific article published on 09 October 2019

The chemotherapeutic agent DMXAA as a unique IRF3-dependent type-2 vaccine adjuvant

scientific article

The common phospholipid-binding activity of the N-terminal domains of PEX1 and VCP/p97.

scientific article

The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.

scientific article published on 8 January 2016

The guanidino-group modifying enzymes: structural basis for their diversity and commonality

scientific article published on 01 September 2006

The insulin receptor: from protein sequence to structure.

scientific article

Toxygates: interactive toxicity analysis on a hybrid microarray and linked data platform

scientific article

Two distinct effector memory cell populations of WT1 (Wilms' tumor gene 1)-specific cytotoxic T lymphocytes in acute myeloid leukemia patients.

scientific article published on 3 April 2015

Using knowledge of protein structural constraints to predict the evolution of HIV-1.

scientific article

[An informatic perspective on structural proteomics]

scientific article published on 01 June 2002

[Genome analysis on the basis of protein structures]

scientific article published on 01 August 2001

beta 3: an additional auxiliary subunit of the voltage-sensitive sodium channel that modulates channel gating with distinct kinetics

scientific article

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