A5075761706- Computational Drug Discovery Methods
- Interstitial Lung Diseases and Idiopathic Pulmonary Fibrosis
- Bioinformatics and Genomic Networks
- Extracellular vesicles in disease
- Pulmonary Hypertension Research and Treatments
- Pharmacogenetics and Drug Metabolism
- Analytical Chemistry and Chromatography
- Metabolomics and Mass Spectrometry Studies
- Gut microbiota and health
- Gene expression and cancer classification
- Lung Cancer Treatments and Mutations
- RNA modifications and cancer
- Microbial Metabolic Engineering and Bioproduction
- RNA Research and Splicing
- Biomedical Text Mining and Ontologies
- Genomics and Chromatin Dynamics
- Clostridium difficile and Clostridium perfringens research
- Pharmacological Effects of Natural Compounds
- Protein Interaction Studies and Fluorescence Analysis
- Plant Gene Expression Analysis
- Bacterial biofilms and quorum sensing
- Psoriasis: Treatment and Pathogenesis
- vaccines and immunoinformatics approaches
- Research Data Management Practices
- Cancer, Hypoxia, and Metabolism
National Institute of Biomedical Innovation, Health and Nutrition
2017-2025
Tokushima University
2022-2025
Protein Research Foundation
2025
Osaka University
2024
Shiga University
2020
Japan Science and Technology Agency
2011-2016
Kyoto University Institute for Chemical Research
2011
Kyoto University
2011
Abstract The gut microbiome is an important determinant in various diseases. Here we perform a cross-sectional study of Japanese adults and identify the Blautia genus, especially B. wexlerae , as commensal bacterium that inversely correlated with obesity type 2 diabetes mellitus. Oral administration to mice induce metabolic changes anti-inflammatory effects decrease both high-fat diet–induced diabetes. beneficial are unique amino-acid metabolism produce S-adenosylmethionine, acetylcholine, l...
Predicting the fraction unbound in plasma provides a good understanding of pharmacokinetic properties drug to assist candidate selection early stages discovery. It is also an effective tool mitigate risk late-stage attrition and optimize further screening. In this study, we built silico prediction models human with freely available software, aiming specifically improve accuracy low value ranges. We employed several machine learning techniques trained on largest ever data set 2738...
Metagenomic analysis based on the 16S rRNA gene is generally performed to examine diversity and abundance of commensal bacteria in feces, which now recognized be associated with human health diseases. Guanidine thiocyanate (GuSCN) solution used as a less onerous way compared frozen method transport stock fecal samples at room temperature for DNA analysis; however, optimal methods measure bacterial composition GuSCN remain investigated. Here, we examined influence various factors such...
Abstract Prediction of pharmacokinetic profiles new chemical entities is essential in drug development to minimize the risks potential withdrawals. The excretion unchanged compounds by kidney constitutes a major route elimination and plays an important role pharmacokinetics. Herein, we created silico prediction models fraction excreted urine ( f e ) renal clearance CL r ), with datasets 411 401 using freely available software; notably, all require structure information alone. binary...
Developing in silico models to predict the brain penetration of drugs remains a challenge owing intricate involvement multiple transport systems blood barrier, and necessity consider combination pharmacokinetic parameters. P-glycoprotein (P-gp) is one most important transporters affecting drugs. Here, we developed an prediction model for P-gp efflux potential capillary endothelial cells (BCEC). Using representative values net ratio BCEC, proposed novel system brain-to-plasma concentration...
We developed a novel drug metabolism and pharmacokinetics (DMPK) analysis platform named DruMAP. This consists of database for DMPK parameters programs that can predict many based on the chemical structure compound. The DruMAP includes curated from public sources in-house experimental data obtained under standardized conditions; it also stores predicted produced by our prediction programs. Users several simultaneously compounds not found in database. Furthermore, highly flexible search...
Abstract Idiopathic pulmonary fibrosis (IPF) is a progressive disease characterized by severe lung and poor prognosis. Although the biomolecules related to IPF have been extensively studied, molecular mechanisms of pathogenesis their association with serum biomarkers clinical findings not fully elucidated. We constructed Bayesian network using multimodal data consisting proteome dataset from extracellular vesicles, laboratory examinations, 206 patients 36 controls. Differential protein...
Progressive pulmonary fibrosis (PPF), defined as the worsening of various interstitial lung diseases (ILDs), currently lacks useful biomarkers. To identify novel biomarkers for early detection patients at risk PPF, we performed a proteomic analysis serum extracellular vesicles (EVs). Notably, identified candidate were enriched lung-derived proteins participating in fibrosis-related pathways. Among them, surfactant-associated protein B (SFTPB) EVs could predict ILD progression better than...
Abstract Caspase recruitment domain family member 14 (CARD14) was recently identified as a psoriasis-susceptibility gene, but its immunological role in the pathogenesis of psoriasis vivo remains unclear. In this study, we examined CARD14 murine experimental models induced by either imiquimod (IMQ) cream or recombinant IL-23 injection. all tested, psoriasiform skin inflammation abrogated Card14−/− mice. Comparison early gene signature between IMQ-cream–treated mice and Tlr7−/−Tlr9−/− revealed...
Abstract A key consideration at the screening stages of drug discovery is in vitro metabolic stability, often measured human liver microsomes. Computational prediction models can be built using a large quantity experimental data available from public databases, but these databases typically contain various protocols different laboratories, raising issue quality. In this study, we retrieved intrinsic clearance ( CL int ) measurements an open database and performed extensive manual curation....
Knowing the value of unbound drug fraction in brain (fu,brain) is essential estimating its effects and toxicity on central nervous system (CNS); however, no model to predict fu,brain without experimental procedures publicly available. In this study, we collected 253 measurements from literature an open database built silico models using only freely available software. By selecting appropriate descriptors, training, evaluation, our showed acceptable performance a test data set (R2 = 0.630,...
Abstract Purpose We aimed to identify computed tomography (CT) radiomics features that are associated with cellular infiltration and construct CT models predictive of in patients fibrotic ILD. Materials methods images ILD who underwent surgical lung biopsy (SLB) were analyzed. Radiomics extracted using artificial intelligence-based software PyRadiomics. constructed a model predicting cell counts histological specimens, another two classifications higher or lower cellularity. tested these...
Abstract This study presents “mouse tissue glycome atlas” representing the profiles of major N -glycans mouse glycoproteins that may define their essential functions in surface glycocalyx organs/tissues and serum-derived extracellular vesicles (exosomes). Cell composed a variety attached covalently to membrane proteins, notably characteristic “ -glycosylation patterns” glycocalyx, plays critical role for regulation cell differentiation, adhesion, homeostatic immune response, biodistribution...
N-terminal tails of H2A, H2B, H3 and H4 histone families are subjected to posttranslational modifications that take part in transcriptional regulation mechanisms, such as transcription factor binding gene expression. Regulation mechanisms under control modification important but remain largely unclear, despite emerging datasets for comprehensive analysis modification. In this paper, we focus on what call genetic harmonious units (GHUs), which co-occurring patterns among binding, expression...
Four different histones (H2A, H2B, H3, and H4; two subunits each) constitute a histone octamer, around which DNA wraps to form histone-DNA complexes called nucleosomes. Amino acid residues in each are occasionally modified, resulting several biological effects, including differential regulation of transcription. Core promoters that encompass the transcription start site have well-conserved motifs, initiator (Inr), TATA box, DPE, collectively core promoter elements (CPEs). In this study, we...
Abstract Toxygates was originally released as a user-friendly interface to enhance the accessibility of large-scale toxicogenomics database, Open TG-GATEs, generated by Japanese Toxicogenomics Project. Since original release, significant new functionality has been added enable users perform sophisticated computational analysis with only modest bioinformatics skills. The features include an orthologous mode for data comparison among different species, interactive clustering and heatmap...
Adjuvants are important vaccine components, composed of a variety chemical and biological materials that enhance the antigen-specific immune responses by stimulating innate cells in both direct indirect manners to produce cytokines, chemokines, growth factors. It has been developed empirical methods for decades considered difficult choose single screening method an ideal adjuvant, due their diverse biochemical characteristics, complex mechanisms of, species specificity adjuvanticity. We...
The priming, boosting, and restoration of memory cytotoxic CD8+ T lymphocytes by vaccination or immunotherapy in vivo is an area active research. Particularly, nucleic acid-based compounds have attracted attention due to their ability elicit strong Ag-specific CTL responses as a vaccine adjuvant. Nucleic been shown act anticancer monotherapeutic agents even without coadministration cancer Ag(s); however, so far they lacked efficacy clinical trials. We recently developed second-generation...
With an ever-increasing interest in understanding the relationships between microbiota and host, more tools to map, analyze interpret these have been developed. Most of tools, however, focus on taxonomic profiling comparative analysis among groups, with very few analytical designed correlate host phenotypic data. We developed a software program for creating web-based integrative database platform called MANTA (Microbiota And pheNoType correlation Analysis platform). In addition storing data,...
The contribution ratio of metabolic enzymes such as cytochrome P450 to in vivo clearance (fraction metabolized: fm) is a pharmacokinetic index that particularly important for the quantitative evaluation drug–drug interactions. Since obtaining experimental fm values challenging, those derived from vitro experiments have often been used alternatively. This study aimed explore possibility constructing machine learning models predicting using chemical structure information alone. We collected...
Multi-omics analyses, combining transcriptomics, genomics, proteomics, and so on, have led to important insights in many areas of biology medicine. To support these software that can handle the difficulties associated with multi-omics datasets is crucial. Here, we describe Panomicon, a web-based, interactive analysis environment for data. Building on Toxygates, tool previously created study single-omics data features clustering, heatmaps, user uploads, Panomicon introduces improvements...