A5042183447- Glycosylation and Glycoproteins Research
- Genomics and Phylogenetic Studies
- Biomedical Text Mining and Ontologies
- Carbohydrate Chemistry and Synthesis
- Advanced Proteomics Techniques and Applications
- Enzyme Production and Characterization
- Genetics, Bioinformatics, and Biomedical Research
- Scientific Computing and Data Management
- Enzyme Structure and Function
- Research Data Management Practices
- Monoclonal and Polyclonal Antibodies Research
- Proteoglycans and glycosaminoglycans research
Soka University
2010-2024
University of Georgia
2014-2021
Soka University of America
2019-2020
Justus-Liebig-Universität Gießen
2014
Macquarie University
2014
Niigata University
2014
National Institute of Advanced Industrial Science and Technology
2013-2014
Noguchi Institute
2014
Research Organization of Information and Systems
2014
Rapid and continued growth in the generation of glycomic data has revealed need for enhanced development basic infrastructure presenting interpreting these datasets a manner that engages broader biomedical research community. Early their growth, genomic proteomic fields implemented mechanisms assigning unique gene protein identifiers were essential organizing presentation enhancing bioinformatic approaches to extracting knowledge. Similar are currently absent from data. In order facilitate...
Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover surfaces many cells, serving 'face' whereby other biomolecules viruses interact. The structure glycans, however, differs greatly from proteins in that they branched, opposed linear sequences amino acids or nucleotides. Therefore, storage glycan information databases, let alone their curation, has been a difficult problem. This caused duplicated efforts when integration is attempted between...
Abstract Glycans serve important roles in signaling events and cell-cell communication, they are recognized by lectins, viruses bacteria, playing a variety of many biological processes. However, there was no system to organize the plethora glycan-related data literature. Thus GlyTouCan (https://glytoucan.org) developed as international glycan repository, allowing researchers assign accession numbers glycans. This also aided integration across various databases. assigns glycans which defined...
Abstract Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created released to public. Unfortunately, there is no common standard in representation of stored information or a machine-readable interface allowing groups easily extract cross-reference information. Results: An international group experts field glycomics worked together create Resource Description Framework (RDF) for data, focused on glycan sequences related biological...
Lectin microarray (LMA) is a high-sensitive profiling method of protein glycosylation. The increasing use this in many studies has led to growing demand for repository system that meets the FAIR data principles (Findable, Accessible, Interoperable, and Reusable). Herein, we present novel system, "LM-GlycoRepo," lectin-based multimodal (LM) data, including LMA accordance with international guideline MIRAGE (Minimum Information Required Glycomics Experiment). As first step our efforts provide...
In the bioinformatics field, many computer algorithmic and data mining technologies have been developed for gene prediction, protein-protein interaction analysis, sequence protein folding predictions, to name a few. This kind of research has branched off from genomics creating transcriptomics, proteomics, metabolomics, glycomics areas in postgenomic age. given complexity glycan structures with their branches monosaccharides various conformations, new methods an attempt gain better...
Abstract Background Glycoscience is a research field focusing on complex carbohydrates (otherwise known as glycans) , which can, for example, serve “switches” that toggle between different functions of glycoprotein or glycolipid. Due to the advancement glycomics technologies are used characterize glycan structures, many databases now publicly available and provide useful information glycoscience research. However, these have almost no link other life science databases. Results In order...
GlyTouCan version 1.0 was released in 2015 as the international glycan structure repository, and a new sequence format called WURCS (Web3 Unique Representation of Carbohydrate Structures) proposed during early stages project. uses its base representation for glycans because existing formats were insufficient their flexibility to represent any all universally. Therefore, order obtain strings or structures, conversion tools editors that can export became necessary. GlycanBuilder an obvious...
Glycan-binding protein (GBP) interaction experiments, such as glycan microarrays, are often used to understand recognition patterns. However, oftentimes the interpretation of array experimental data makes it difficult identify discrete GBP binding patterns due their ambiguity. It is known that lectins, for example, non-specific in affinities; same lectin can bind different monosaccharides or even structures. In bioinformatics, several tools mine generated from these sorts experiments have...
Abstract Recent years have seen great advances in the development of glycoproteomics protocols and methods resulting a sustainable increase reporting proteins, their attached glycans glycosylation sites. However, only very few these reports find way into databases or data repositories. One major reasons is absence digital standard to represent glycoproteins challenging annotations with glycans. Depending on experimental method, such must be able as complete structures compositions, store not...
Kiyoko FAoki-Kinoshita1, Hiromichi Sawaki2, Hyun Joo An3, Matthew Campbell4, Qichen Cao5, Richard Cummings6, Daniel K Hsu7, Masaki Kato8, Toshisuke Kawasaki9, Kay-Hooi Khoo7, Jaehan Kim3, Kolarich10, Xianyu Li5, Mingqi Liu11, Masaaki Matsubara12, Shujiro Okuda9,13, Nicolle H Packer4, Rene Ranzinger14, Huali Shen11, Toshihide Shikanai2, Daisuke Shinmachi2, Philip Toukach15, Issaku Yamada12, Yoshiki Yamaguchi8, Pengyuan Yang11, Wantao Ying5, Jong Shin Yoo16, Yan Zhang17, Yang Zhang11, and...
<ns3:p>We report on the activities of 2015 edition BioHackathon, an annual event that brings together researchers and developers from around world to develop tools technologies promote reusability biological data. We discuss issues surrounding representation, publication, integration, mining reuse data metadata across a wide range biomedical types relevance for life sciences, including chemistry, genotypes phenotypes, orthology phylogeny, proteomics, genomics, glycomics, metabolomics....
ABSTRACT Glycomics targets released glycans from proteins, lipids and proteoglycans. High throughput glycomics is based on mass spectrometry (MS) that increasingly depends exchange of data with databases the use software. This requires an agreed format for accurately recording experiments, developing consistent storage modules granting public access to glycomic MS data. The introduction MIRAGE (Mimimum Requirement A Experiment) reporting standards was first step towards automating recording....
The Integrated Life Science Database Project of Japan funded a group glycoscientists to carry out project integrate glycoscience databases using Semantic Web technologies. As continuation the previous period, Consortium for Glycobiology and Glycotechnology (JCGGDB) developed several glycoscience-related databases. GlycoProtDB database is among those being integrated, providing an important resource understand protein glycosylation. Another integrated GlycoEpitope, comprehensive carbohydrate...
<ns3:p>Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize syntactic and semantic interoperability of open data life sciences. Here we report advancements made 6th 7th annual BioHackathons which were held Tokyo Miyagi respectively. This review consists two major sections covering: 1) improvement utilization RDF various domains sciences 2) meta-data about these data, resources that store them, service quality SPARQL Protocol Query...