A5090788230- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Cancer Genomics and Diagnostics
- Gene Regulatory Network Analysis
- Genomics and Phylogenetic Studies
- COVID-19 Clinical Research Studies
- Gut microbiota and health
- Cancer-related molecular mechanisms research
- Genetic factors in colorectal cancer
- SARS-CoV-2 and COVID-19 Research
- COVID-19 epidemiological studies
- Genomics and Chromatin Dynamics
- Long-Term Effects of COVID-19
- Cancer Cells and Metastasis
- Acute Myeloid Leukemia Research
- Epigenetics and DNA Methylation
- SARS-CoV-2 detection and testing
- Cancer Immunotherapy and Biomarkers
- RNA modifications and cancer
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- Machine Learning in Bioinformatics
- Cancer-related gene regulation
- Traditional Chinese Medicine Studies
- Computational Drug Discovery Methods
The University of Tokyo
2016-2025
Tokyo University of Science
2014-2025
National Institute of Advanced Industrial Science and Technology
2024
Osaka University
2011-2024
Teikyo University
2013-2024
Bunkyo University
2024
Caris Life Sciences (United States)
2023
Tokyo Seitoku University
2022
Shiga University of Medical Science Hospital
2022
Aichi Cancer Center
2021
The functional impact of recently discovered long noncoding RNAs (ncRNAs) in human cancer remains to be clarified. One ncRNA which has attracted attention is the Hox transcript antisense intergenic RNA termed HOTAIR, a expressed from developmental HOXC locus located on chromosome 12q13.13. In cooperation with Polycomb complex PRC2, HOTAIR reported reprogram chromatin organization and promote breast metastasis. this study, we examined status function patients stage IV colorectal (CRC) who...
Triple negative breast cancer (TNBC) has a poor outcome due to the lack of beneficial therapeutic targets. To clarify molecular mechanisms involved in carcinogenesis TNBC and identify target molecules for novel anticancer drugs, we analyzed gene expression profiles 30 TNBCs as well 13 normal epithelial ductal cells that were purified by laser-microbeam microdissection. We identified 301 321 transcripts significantly upregulated downregulated TNBC, respectively. In particular, profile...
The gut microbiota is reported to be related obesity, and visceral fat strongly associated with cardiovascular disease overall mortality. However, the association between obesity has mainly been studied using body mass index (BMI) as a proxy for obesity. We investigated relationship of both BMI stratified by sex in population-based cross-sectional study Japanese men women 20-76 years age (n = 1001). Women higher area (VFA) harboured relative abundance Firmicutes phylum (P trend <0.001) lower...
Removal of senescent cells (senolysis) has been proposed to be beneficial for improving age-associated pathologies, but the molecular pathways such senolytic activity have not yet emerged. Here, we identified glutaminase 1 (GLS1) as an essential gene survival human cells. The intracellular pH in was lowered by lysosomal membrane damage, and this induced kidney-type (KGA) expression. resulting enhanced glutaminolysis ammonia production, which neutralized lower improved Inhibition...
Esophageal squamous cell carcinoma (ESCC) is the predominant form of esophageal cancer in Japan. Smoking and drinking alcohol are environmental risk factors for ESCC, whereas single nucleotide polymorphisms ADH1B ALDH2, which increase harmful intermediates produced by alcohol, genetic factors. We conducted a large-scale genomic analysis ESCCs from patients Japan to determine mutational landscape this cancer.
Circulating tumor cells (CTC) in blood have attracted attention both as potential seeds for metastasis and biomarkers. However, most CTC detection systems might miss epithelial-mesenchymal transition (EMT)-induced metastatic because is based on epithelial markers. First, to discover novel markers capable of detecting CTCs which EMT has not been repressed, microarray analysis 132 colorectal cancers (CRC) from Japanese patients was conducted, 2,969 genes were detected that overexpressed...
Antimicrobial peptides (AMPs) are short that play crucial roles in diverse biological processes and have various functional activities against target organisms. Due to the abuse of chemical antibiotics microbial pathogens' increasing resistance antibiotics, AMPs potential be alternatives antibiotics. As such, identification has become a widely discussed topic. A variety computational approaches been developed identify based on machine learning algorithms. However, most them not capable...
Most of the conventional feature selection algorithms have a drawback whereby weakly ranked gene that could perform well in terms classification accuracy with an appropriate subset genes will be left out selection. Considering this shortcoming, we propose algorithm expression data analysis sample classifications. The proposed first divides into subsets, sizes which are relatively small (roughly size h), then selects informative smaller subsets (of r < h) from and merges chosen another r) to...
We present a statistical method for estimating gene networks and detecting promoter elements simultaneously. When network from expression data alone, common problem is that the number of microarrays limited compared to variables in model, making accurate estimation difficult task. Our overcomes this by integrating microarray DNA sequence information into Bayesian model. The basic idea our that, if parent transcription factor, its children may share consensus motif their regions sequences....
Purpose To identify stage I lung adenocarcinoma patients with a poor prognosis who will benefit from adjuvant therapy. Patients and Methods Whole gene expression profiles were obtained at 19 time points over 48-hour course human primary epithelial cells that stimulated epidermal growth factor (EGF) in the presence or absence of clinically used EGF receptor tyrosine kinase (RTK)-specific inhibitor, gefitinib. The data subjected to mathematical simulation using State Space Model (SSM)....
Allogeneic hematopoietic stem cell transplantation (HSCT) is one of curative treatment options for patients with hematologic malignancies. Although GVHD mediated by the donor’s T lymphocytes remains most challenging toxicity allo-HSCT, graft-versus-leukemia (GVL) effect targeting leukemic cells, has an important role in affecting overall outcome AML. Here we comprehensively characterized TCR repertoire who underwent matched donor or haplo-cord HSCT using next-generation sequencing approach....
Immune checkpoint inhibitors and adoptive transfer of gene-engineered T cells have emerged as novel therapeutic modalities for hard-to-treat solid tumors; however, many patients are refractory to these immunotherapies, the mechanisms underlying tumor immune resistance not been fully elucidated. By comparing microenvironment inhibition–sensitive –resistant murine tumors, we observed that resistant tumors had low immunogenicity. We identified antigen presentation by CD11b+F4/80+...
Microsatellites are repeats of 1- to 6-bp units, and approximately 10 million microsatellites have been identified across the human genome. vulnerable DNA mismatch errors thus used detect cancers with repair deficiency. To reveal mutational landscape microsatellite repeat regions at genome level, we analyzed 20.1 billion in 2717 whole genomes pan-cancer samples 21 tissue types. First, developed a new insertion deletion caller (MIMcall) that takes into consideration error patterns different...
The tumor microenvironment can be classified into immunologically active "inflamed" tumors and inactive "non-inflamed" based on the infiltration of cytotoxic immune cells. Previous studies liver cancer have reported a superior prognosis for inflamed compared to non-inflamed tumors. However, is highly heterogeneous genetically, finer classification may improve our understanding its immunological diversity response therapy.We characterized gene signatures 234 primary cancers, mainly...
Chronic inflammation is a hallmark of HIV infection and associated with the development progression age-related comorbidities. Although gastrointestinal tract major site replication CD4 + T-cell depletion, role HIV-associated imbalance gut microbiome in chronic unclear.
We aimed to elucidate differences in the characteristics of patients with coronavirus disease 2019 (COVID-19) requiring hospitalization Japan, by COVID-19 waves, from conventional strains Delta variant.We used secondary data a database and performed retrospective cohort study that included 3261 aged ≥ 18 years enrolled 78 hospitals participated Japan Task Force between February 2020 September 2021.Patients hospitalized during second (mean age, 53.2 [standard deviation {SD}, ± 18.9]) fifth...
The rapid accumulation of high-throughput sequence data demands the development effective and efficient data-driven computational methods to functionally annotate proteins. However, most current approaches used for functional annotation simply focus on use protein-level information but ignore inter-relationships among annotations.Here, we established PFresGO, an attention-based deep-learning approach that incorporates hierarchical structures in Gene Ontology (GO) graphs advances natural...