Chisato Yamasaki
A5014486236- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Bioinformatics and Genomic Networks
- Biomedical Text Mining and Ontologies
- Ethics in Clinical Research
- Chromosomal and Genetic Variations
- Marine Ecology and Invasive Species
- Scientific Computing and Data Management
- Escherichia coli research studies
- Marine Biology and Environmental Chemistry
- RNA and protein synthesis mechanisms
- Genomics and Rare Diseases
- RNA Research and Splicing
- Marine Biology and Ecology Research
- RNA modifications and cancer
- Semantic Web and Ontologies
- Viral gastroenteritis research and epidemiology
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Health Systems, Economic Evaluations, Quality of Life
- Mental Health and Patient Involvement
- Transgenic Plants and Applications
- Underground infrastructure and sustainability
- Coagulation, Bradykinin, Polyphosphates, and Angioedema
- BRCA gene mutations in cancer
Saitama Prefectural University
2023
National Institute of Biomedical Innovation, Health and Nutrition
2023
Osaka University
2020-2021
National Institute of Advanced Industrial Science and Technology
2003-2016
Research Organization of Information and Systems
2011-2013
Japan Biological Informatics Consortium
2007-2011
United States National Library of Medicine
2010
National Institutes of Health
2010
The Nature Conservancy
2009
Saitama International Medical Center
1999-2004
The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of International Genome Sequencing (IRGSP), manually curated annotation sequence, and other genomics information that could be useful for comprehensive understanding rice biology. Since last publication RAP-DB, IRGSP has been revised reassembled. In addition, a large number rice-expressed tags have released, functional resources produced worldwide. Thus, we thoroughly updated our by manual...
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...
We present here the annotation of complete genome rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions identified or inferred in 19,969 (70%) proteins, 131 possible npRNAs (including 58 antisense transcripts) found. Almost 5000 annotated protein-coding genes found to be disrupted insertional mutant lines, which will accelerate future experimental validation annotations....
Infection with Shiga toxin (Stx)-producing Escherichia coli O157:H7, which causes diarrhea and hemorrhagic colitis in humans, often results fatal systemic complications, such as neurological damage hemolytic-uremic syndrome. Because Stx circulating the blood is a major causative factor of these development neutralizer that functions circulation holds promise viable therapy. Here we developed series carbosilane dendrimers, trisaccharides globotriaosyl ceramide, receptor for Stx, were...
Human biomedical datasets that are critical for research and clinical studies to benefit human health also often contain sensitive or potentially identifying information of individual participants. Thus, care must be taken when they processed made available comply with ethical regulatory frameworks informed consent data conditions. To enable streamline access these datasets, the Global Alliance Genomics Health (GA4GH) Data Use Researcher Identities (DURI) work stream developed approved...
ABSTRACT We sequenced the genome of Theileria orientalis , a tick-borne apicomplexan protozoan parasite cattle. The focus this study was comparative analysis T . relative to other highly pathogenic species, parva and annulata induce transformation infected cells lymphocyte or macrophage/monocyte lineages; in contrast, does not uncontrolled proliferation leukocytes multiplies predominantly within erythrocytes. While synteny across homologous chromosomes three species found be well conserved...
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
Stx1 and Stx2 produced by Shiga toxin‐producing Escherichia coli are cytotoxic due to their N ‐glycosidase activity on 28S rRNA. In this study, we have shown that proinflammatory cytokine mRNAs, especially IL‐8, were induced in Caco‐2 cells. A non‐toxic mutant of which lacks did not induce mRNAs. IL‐8 production at the protein level was enhanced Stx2, but Stx1. These results demonstrate toxins expression synthesis cytokines cells is essential for induction.
Here we report the new features and improvements in our latest release of H-Invitational Database (H-InvDB; http://www.h-invitational.jp/ ), a comprehensive annotation resource for human genes transcripts. H-InvDB, originally developed as an integrated database transcriptome based on extensive large sets full-length cDNA (FLcDNA) clones, now provides 120 558 mRNAs extracted from International Nucleotide Sequence Databases (INSD), addition to 54 978 FLcDNAs, H-InvDB_4.6. We mapped those...
We report the extended database and data mining resources newly released in H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). H-InvDB is a comprehensive annotation resource of human genes transcripts, consists two main views six sub-databases. The latest release (release 6.2) provides for 219,765 transcripts 43,159 gene clusters based on full-length cDNAs mRNAs. now several new features, such as mapping microarray probes, models, relation to known ncRNAs information from...
BioHackathon 2010 was the third in a series of meetings hosted by Database Center for Life Sciences (DBCLS) Tokyo, Japan. The overall goal is to improve quality and accessibility life science research data on Web bringing together representatives from public databases, analytical tool providers, cyber-infrastructure researchers jointly tackle important challenges area silico biological research. theme 'Semantic Web', all attendees gathered with shared producing Semantic their respective...
Selective deep neck flexor muscle activation through craniocervical flexion exercises has been considered to be different from cervical retraction exercises.To compare the immediate analgesic effect of versus in individuals with nonacute, directional preference (DP) for or extension.A two-arm, assessor-blinded, pretest-posttest randomized experiment was conducted. Participants were randomly assigned either and those who confirmed at post-intervention examination have a DP extension analyzed....
H-InvDB (http://www.h-invitational.jp/) is a comprehensive human gene database started in 2004. In the latest version, 8.0, total of 244 709 complementary DNA was mapped onto hg19 reference genome and 43 829 loci, including nonprotein-coding ones, were identified. Of these 35 631 identified as potential protein-coding genes, 22 898 identical to known genes. our analysis, 19 309 annotated genes specific not found RefSeq Ensembl. fact, 233 turned out have protein functions this version...
Abstract Background The role of patients in medical research is changing, as more emphasis being placed on patient involvement, and reported outcomes are increasingly contributing to clinical decision-making. Information communication technology provides new opportunities for actively become involved research. These trends particularly noticeable Europe the US, but less obvious Japan. aim this study was investigate practice active involvement Japan by utilizing a digital platform, analyze...
The interaction between biological researchers and the bioinformatics tools they use is still hampered by incomplete interoperability such tools. To ensure initiatives are effectively deployed, end-user applications need to be aware of, support, best practices standards. Here, we report on an initiative in which software developers genome biologists came together explore raise awareness of these issues: BioHackathon 2009.Developers attendance from diverse backgrounds, with experts Web...
Hereditary angioedema (HAE) adversely affects patients’ social and daily life significantly, the disease burden is high. We recruited study participants from a patient-participatory registry, Rare Undiagnosed Diseases Study (RUDY) Japan, to better understand broader effect of HAE on lives. Thirteen patients with who registered between January 2019 March 2021 completed an online questionnaire record details episodes quality (AE-QoL) questionnaire, in which they described degree QoL was...
H-Invitational Database (H-InvDB; http://hinv.jp/) is an integrated database of all human genes and transcripts that started in international collaborative research project for establishing a functional annotation full-length cDNAs. Because H-InvDB contains abundance information transcripts, including not only well-characterized protein-coding but also those without experimental evidence at the protein level, this will be useful resource identifying novel uncharacterized proteins (so-called...
CIPRO database (http://cipro.ibio.jp/2.5) is an integrated protein for a tunicate species Ciona intestinalis that part of the Urochordata. Although provides proteomic and transcriptomic data on single species, animal considered unique in evolutionary tree, representing possible origin vertebrates good model understanding chordate evolution, including human evolution. Furthermore, C. has been one favorites developmental biologists; therefore, lot amount accumulated knowledge its development,...
Abstract H-Invitational Database (H-InvDB; "http://www.h-invitational.jp/":http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses all transcripts, we provide curated annotations transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, domains, sub-cellular localizations, metabolic pathways, 3D structure, genetic polymorphisms, relation with diseases, expression profiling,...