Hideo Matsuda
A5007909918- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Machine Learning in Bioinformatics
- RNA and protein synthesis mechanisms
- Distributed and Parallel Computing Systems
- Cell Image Analysis Techniques
- Algorithms and Data Compression
- Single-cell and spatial transcriptomics
- Gene Regulatory Network Analysis
- Microbial Metabolic Engineering and Bioproduction
- RNA Research and Splicing
- Genomics and Chromatin Dynamics
- Scientific Computing and Data Management
- Molecular Biology Techniques and Applications
- RNA modifications and cancer
- Cancer-related molecular mechanisms research
- Parallel Computing and Optimization Techniques
- Genetic diversity and population structure
- Bacterial Genetics and Biotechnology
- Silicon Carbide Semiconductor Technologies
- Protein Structure and Dynamics
- Genetics, Bioinformatics, and Biomedical Research
- Computational Drug Discovery Methods
- DNA and Biological Computing
Osaka University
2016-2025
Ube Frontier University
2014
The University of Tokyo
2002-2009
Osaka Health Science University
2002-2006
Toshiba (South Korea)
1998-2005
Polytechnic University
1999-2004
Toshiba (Japan)
2000-2003
Hachinohe National College of Technology
2003
Kobe University
1986-2002
Tokyo Polytechnic University
2002
This study describes comprehensive polling of transcription start and termination sites analysis previously unidentified full-length complementary DNAs derived from the mouse genome. We identify 5' 3' boundaries 181,047 transcripts with extensive variation in arising alternative promoter usage, splicing, polyadenylation. There are 16,247 new protein-coding transcripts, including 5154 encoding proteins. Genomic mapping transcriptome reveals transcriptional forests, overlapping on both...
<h3>Importance</h3> Application of deep learning algorithms to whole-slide pathology images can potentially improve diagnostic accuracy and efficiency. <h3>Objective</h3> Assess the performance automated at detecting metastases in hematoxylin eosin–stained tissue sections lymph nodes women with breast cancer compare it pathologists' diagnoses a setting. <h3>Design, Setting, Participants</h3> Researcher challenge competition (CAMELYON16) develop solutions for node (November 2015-November...
Only a small proportion of the mouse genome is transcribed into mature messenger RNA transcripts. There an international collaborative effort to identify all full-length mRNA transcripts from mouse, and ensure that each represented in physical collection clones. Here we report manual annotation 60,770 complementary DNA sequences. These are clustered 33,409 'transcriptional units', contributing 90.1% newly established transcriptome database. Of these transcriptional units, 4,258 new...
We have developed a new tool, called fastDNAml, for constructing phylogenetic trees from DNA sequences. The program can be run on wide variety of computers ranging Unix workstations to massively parallel systems, and is available the Ribosomal Database Project (RDP) by anonymous FTP. Our uses maximum likelihood approach based version 3.3 Felsenstein's dnaml program. Several enhancements, including algorithmic changes, significantly improve performance reduce memory usage, making it feasible...
The human genome sequence defines our inherent biological potential; the realization of biology encoded therein requires knowledge function each gene. Currently, in this area is still limited. Several lines investigation have been used to elucidate structure and genes genome. Even so, gene prediction remains a difficult task, as varieties transcripts may vary great extent. We thus performed an exhaustive integrative characterization 41,118 full-length cDNAs that capture complete functional...
Bone homeostasis is regulated by communication between bone-forming mature osteoblasts (mOBs) and bone-resorptive osteoclasts (mOCs). However, the spatial-temporal relationship mode of interaction in vivo remain elusive. Here we show, using an intravital imaging technique, that mOB mOC functions are via direct cell-cell contact these cell types. The mOBs mOCs mainly occupy discrete territories steady state, although detected spatiotemporally limited areas. In addition, a pH-sensing...
Genome reduction by removing dispensable genomic sequences in bacteria is commonly used both fundamental and applied studies to determine the minimal genetic requirements for a living system or develop highly efficient bioreactors. Nevertheless, whether how accumulative loss of disturbs bacterial growth remains unclear. To investigate relationship between genome growth, series Escherichia coli strains carrying genomes reduced stepwise manner were used. Intensive analyses revealed that...
Abstract Bone morphogenetic protein (BMP)-2 plays a central role in bone-tissue engineering because of its potent bone-induction ability. However, the process BMP-induced bone formation vivo remains poorly elucidated. Here, we aimed to establish method for intravital imaging entire BMP-2-induced ectopic formation. Using multicolor transgenic mice, visualized spatiotemporal induction, including appearance and motility osteoblasts osteoclasts, angiogenesis, collagen-fiber formation,...
A general overview of the protein sequence set for mouse transcriptome produced during FANTOM2 sequencing project is presented here. We applied different algorithms to characterize sequences derived from a nonredundant representative (RPS) and variant (VPS) transcriptome. The functional characterization assignment Gene Ontology terms was done by analysis proteome using InterPro. Superfamily database analyses gave detailed structural classification according SCOP provide additional evidence...
Obesity causes excess fat accumulation in white adipose tissues (WAT) and also other insulin-responsive organs such as the skeletal muscle, increasing risk for insulin resistance, which can lead to obesity-related metabolic disorders. Peroxisome proliferator-activated receptor-α (PPARα) is a master regulator of fatty acid oxidation whose activator known improve hyperlipidemia. However, molecular mechanisms underlying PPARα activator-mediated reduction adiposity improvement disorders are...
In vivo two-photon fluorescence imaging is a powerful modality to monitor cell dynamics in biomedical studies. To detect protein functions living animals real-time, fluorescent probes must show quick response the target function specific tissues. Here, we developed rhodamine-based small-molecule probe called Red-pHocas (red pH-activatable for osteoclast activity sensing) reversibly acidic environments spatiotemporal analysis of proton pumps. The introduction electron-withdrawing N-alkyl...
Osteoclastic bone resorption and osteoblastic formation/replenishment are closely coupled in metabolism. Anabolic parathyroid hormone (PTH), which is commonly used for treating osteoporosis, shifts the balance from osteoclastic to osteoblastic, although it unclear how these cells coordinately regulated by PTH. Here, we identify a serine protease inhibitor, secretory leukocyte inhibitor (SLPI), as critical mediator that involved PTH-mediated shift phase. Slpi highly upregulated osteoblasts...
PURPOSE: Breast cancer tumors frequently have intratumor heterogeneity. Tumors with high heterogeneity caused therapeutic resistance and human epidermal growth factor receptor 2 (HER2) in response to HER2-targeted therapies. This study aimed investigate whether HER2 levels were clinically related poor prognosis for adjuvant therapies primary breast cancers.
 METHODS: included patients (n = 251) treated was manifested by the shape of fluorescence situ hybridization amplification (FISH)...
Breast cancer tumors frequently have intratumoral heterogeneity (ITH). Tumors with high ITH cause therapeutic resistance and human epidermal growth factor receptor 2 (HER2) in response to HER2-targeted therapies. This study aimed investigate whether HER2 levels were clinically related a poor prognosis for adjuvant therapy primary breast cancers. included patients (n = 251) treated was manifested by the shape of fluorescence situ hybridization amplification (FISH) distributed histograms gene...
Femoral condyle geometry was evaluated in 30 normal and varus knees using magnetic resonance imaging. In the sagittal view, distal part of medial deformed knees, but there no significant difference posterior between knees. transverse transepicondylar axis(a reliable rotational landmark) showed approximately 6° external rotation relative to condylar axis The results this study suggest that hypoplasia exists at addition, may be a landmark is internal when total knee arthroplasty performed.
Both large deletions in genome and heat shock stress would lead to alterations the gene expression profile; however, whether there is any potential linkage between these disturbances transcriptome have not been discovered. Here, relationship genomic environmental contributions was analyzed by comparing transcriptomes of bacterium Escherichia coli (strain MG1655 its extensive deletion derivative, MDS42) grown regular transient conditions.The analysis showed following: (i) a reorganization...