A5086059561- Scientific Computing and Data Management
- Genomics and Phylogenetic Studies
- Research Data Management Practices
- Ion channel regulation and function
- Biomedical Text Mining and Ontologies
- Ion Channels and Receptors
- Gene expression and cancer classification
- Molecular Biology Techniques and Applications
- Neuroscience and Neuropharmacology Research
- Distributed and Parallel Computing Systems
- Neuropeptides and Animal Physiology
- Neurobiology and Insect Physiology Research
- Genomics and Chromatin Dynamics
- Neuroscience of respiration and sleep
- Epigenetics and DNA Methylation
- RNA modifications and cancer
- Bioinformatics and Genomic Networks
- Genetic Associations and Epidemiology
- Amino Acid Enzymes and Metabolism
- Cancer Genomics and Diagnostics
- Genetics, Bioinformatics, and Biomedical Research
- Semantic Web and Ontologies
- Genomic variations and chromosomal abnormalities
- Nitric Oxide and Endothelin Effects
- Advanced Manufacturing and Logistics Optimization
Chiba University
2023-2025
Research Organization of Information and Systems
2016-2025
Tottori University
2009-2022
The University of Tokyo
1989-2022
Gifu University
2021-2022
Miyazaki Agricultural Research Institute
2021
RIKEN Center for Integrative Medical Sciences
2020
Kitami Institute of Technology
2016
Hokkaido University
1994-2010
Osaka University
1992-2009
Resource9 November 2018Open Access Transparent process ChIP-Atlas: a data-mining suite powered by full integration of public ChIP-seq data Shinya Oki Corresponding Author [email protected] orcid.org/0000-0002-4767-3259 Department Developmental Biology, Graduate School Medical Sciences, Kyushu University, Fukuoka, Japan Search for more papers this author Tazro Ohta orcid.org/0000-0003-3777-5945 Database Center Life Science, Joint-Support Data Science Research, Research Organization...
ChIP-Atlas (https://chip-atlas.org) is a web service providing both GUI- and API-based data-mining tools to reveal the architecture of transcription regulatory landscape. powered by comprehensively integrating all data sets from high-throughput ChIP-seq DNase-seq, method for profiling chromatin regions accessible DNase. In this update, we further collected ATAC-seq whole-genome bisulfite-seq six model organisms (human, mouse, rat, fruit fly, nematode, budding yeast) with latest genome...
Abstract ChIP-Atlas (https://chip-atlas.org/) presents a suite of data-mining tools for analyzing epigenomic landscapes, powered by the comprehensive integration over 376 000 public ChIP-seq, ATAC-seq, DNase-seq and Bisulfite-seq experiments from six representative model organisms. To unravel intricacies chromatin architecture that mediates regulome-initiated generation transcriptional phenotypic diversity within cells, we report 3.0 enhances clarity incorporating additional tracks genomic...
The first BioHackrXiv preprint was published in 2020, using a platform based on the idea of Markdown, and just weeks ago, their 100th preprint. Machine-readable etadata added to Markdown that is includes title, keywords, author names, affiliations, details about Biohackathon event related to. metadata 2000 already supported listing ORCID identifier authors, but this not list generated PDF. This report describes two improvements platform: visualization identifiers PDF support for Research...
Abstract Mosaic loss of chromosome Y (mLOY) is frequently observed in the leukocytes ageing men. However, genetic architecture and biological mechanisms underlying mLOY are not fully understood. In a cohort 95,380 Japanese men, we identify 50 independent markers 46 loci associated with at genome-wide significant level, 35 which unreported. Lead overlap enhancer marks hematopoietic stem cells (HSCs, P ≤ 1.0 × 10 −6 ). association study signals exhibit polygenic demonstrate strong heritability...
Recording the provenance of scientific computation results is key to support traceability, reproducibility and quality assessment data products. Several models have been explored address this need, providing representations workflow plans their executions as well means packaging resulting information for archiving sharing. However, existing approaches tend lack interoperable adoption across management systems. In work we present Workflow Run RO-Crate, an extension RO-Crate (Research Object...
Regulation of D-glucose transport in the porcine kidney epithelial cell line LLC-PK1 was examined. To identify sodium-coupled glucose transporter (SGLT), we cloned and sequenced several partial cDNAs homologous to SGLT1 from rabbit small intestine (M. A. Hediger, M. J. Coady, T. S. Ikeda, E. Wright, Nature (London) 330:379-381, 1987). The extensive homology two sequences leads us suggest that high-affinity SGLT expressed by cells is SGLT1. mRNA levels were highest when concentration culture...
<ns3:p>The increased demand for efficient computation in data analysis encourages researchers biomedical science to use workflow systems. Workflow systems, or so-called languages, are used the description and execution of a set steps. systems increase productivity researchers, specifically fields that high-throughput DNA sequencing applications, where scalable is required. As have improved portability workflows, research communities able share workflows reduce cost building ordinary...
TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases. With its ability obtain related in different semantic relationships, a user-friendly web interface, and regular automatic data update system, has been valuable tool for bioinformatics. We have recently expanded TogoID's represent semantics between datasets, enabling it handle multiple relationships within dataset pairs. This enhancement...
BioSample is a comprehensive repository of experimental sample metadata, playing crucial role in providing archive and enabling experiment searches regardless type. However, the difficulty comprehensively defining rules for describing metadata limited user awareness best practices have resulted substantial variability depending on submitter. This inconsistency poses significant challenges to findability reusability data. Given vast scale BioSample, which hosts over 40 million records, manual...
In this paper, we present the work executed on re-architecting BioHackrXiv during international ELIXIR BioHackathon Europe 2023 in Barcelona, Spain. is a scholarly publication service for biohackathons and codefests that target biology biomedical sciences spirit of pre-publishing platforms.
Abstract The 2024 Noto-Hanto earthquake with a magnitude of 7.6 occurred in the Noto Peninsula on January 1, 2024. mainshock had reverse fault focal solution and direction compression axis was northwest–southeast. In Peninsula, swarms have been observed since December 2020. contrast to this swarm activity, extending marine area. Therefore, we performed rapid response seafloor seismic observation source region its vicinity. We deployed 34 free-fall pop-up type ocean bottom seismometers (OBSs)...
To provide information regarding the cause of muscle rigidity in malignant hyperthermia-susceptible (MHS) pigs, Ca-induced Ca-release mechanism sarcoplasmic reticulum (SR), Ca uptake by SR, and Ca-activated tension production contractile system were examined skinned skeletal fibers from MHS normal pigs. In muscles rate release was significantly higher than muscle. The potentiation effect on halothane caffeine did not differ appreciably between fibers. SR sensitivity different those fibers,...
Adenosine and inosine accumulate extracellularly during hypoxia/ischaemia in the brain may act as neuroprotectants. In spinal cord, there is pharmacological evidence for increases extracellular adenosine hypoxia, but no direct measurements of purine release. Furthermore, efflux pathways origin purines are not defined. To characterize hypoxia-evoked accumulation, we examined effect acute hypoxia on levels isolated cords from rats.Extracellular concentrations were assayed an vitro preparation...
TRPA1 is a Ca-permeable nonselective cation channel expressed in sensory neurons and acts as nocisensor. Recent reports show that some monoterpenes, group of naturally occurring organic compounds, modulate TRP activity. Here, we report limonene, being contained citrus fruits mushrooms, shows unique bimodal action on channel.We examine the effects limonene from wild-type, TRPV1- TRPA1-gene-deficient mice heterologously channels vitro. Molecular determinants were identified with using mutated...
High-throughput sequencing technology, also called next-generation (NGS), has the potential to revolutionize whole process of genome sequencing, transcriptomics, and epigenetics. Sequencing data is captured in a public primary archive, Sequence Read Archive (SRA). As January 2013, from more than 14,000 projects have been submitted SRA, which double that previous year. Researchers can download raw sequence SRA website perform further analyses compare with their own data. However, it extremely...
<ns4:p>The taxon Elasmobranchii (sharks and rays) contains one of the long-established evolutionary lineages vertebrates with a tantalizing collection species occupying critical aquatic habitats. To overcome current limitation in molecular resources, we launched Squalomix Consortium 2020 to promote genome-wide array approaches, specifically targeting shark ray species. Among various bottlenecks working elasmobranchs are their elusiveness low fecundity as well large highly repetitive genomes....
Predicting responsible transcription regulators on the basis of transcriptome data is one most promising computational approaches to understanding cellular processes and characteristics. Here, we present a novel method employing vast amounts chromatin immunoprecipitation (ChIP) experimental address this issue. Global high-throughput ChIP was collected construct comprehensive database, containing 8 578 738 binding interactions 454 regulators. To incorporate information about heterogeneous...
1. Effects of apamin on electrical and mechanical activities cyclic nucleotide accumulation in response to vasoactive intestinal peptide (VIP) intramural nerve stimulation were investigated isolated circular strips the rat stomach presence atropine guanethidine. 2. Circular muscles generated rhythmic contractions slow waves antrum but not fundus. Intramural VIP caused frequency‐ dose‐dependent relaxation fundic inhibition spontaneous antral strips. Apamin partly reduced responses those VIP....
Abstract Motivation Understanding life cannot be accomplished without making full use of biological data, which are scattered across databases diverse categories in sciences. To connect such data seamlessly, identifier (ID) conversion plays a key role. However, existing ID services have disadvantages, as covering only limited range databases, not keeping up with the updates original and outputs being hard to interpret context relations, especially when converting IDs multiple steps. Results...