A5068753999- Glycosylation and Glycoproteins Research
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Biomedical Text Mining and Ontologies
- Genetics, Bioinformatics, and Biomedical Research
- Advanced Proteomics Techniques and Applications
- Microbial Metabolites in Food Biotechnology
- Enzyme Structure and Function
- Bayesian Modeling and Causal Inference
- Scientific Computing and Data Management
- Proteoglycans and glycosaminoglycans research
- Data Management and Algorithms
- Microbial Metabolic Engineering and Bioproduction
- Protein Structure and Dynamics
- Enzyme Production and Characterization
- Machine Learning in Bioinformatics
- Advanced Text Analysis Techniques
- Semantic Web and Ontologies
- Enzyme Catalysis and Immobilization
- Microbial Community Ecology and Physiology
- Probiotics and Fermented Foods
- Galectins and Cancer Biology
- Cell Image Analysis Techniques
- Microbial Natural Products and Biosynthesis
- Data Mining Algorithms and Applications
University of Georgia
2015-2025
Justus-Liebig-Universität Gießen
2014
Macquarie University
2014
Niigata University
2014
National Institute of Advanced Industrial Science and Technology
2014
Noguchi Institute
2014
Research Organization of Information and Systems
2010-2014
Soka University
2014
German Cancer Research Center
2007-2010
Heidelberg University
2007-2010
Abstract The Symbol Nomenclature for Glycans (SNFG) is a community-curated standard the depiction of monosaccharides and complex glycans using various colored-coded, geometric shapes, along with defined text additions. It hosted by National Center Biotechnology Information (NCBI) at NCBI-Glycans Page (www.ncbi.nlm.nih.gov/glycans/snfg.html). Several changes have been made to SNFG page in past year update rules depicting SNFG, include more examples use, particularly non-mammalian organisms,...
The diversity of three major classes mammalian carbohydrates, mainly glycolipids and O- N-linked glycans, deposited in the databank GLYCOSCIENCES.de was subjected to statistical analyses. Size, chain length, branching complexity were accessed revealed that average oligosaccharide is composed about eight monosaccharide units. About a quarter all oligosaccharides are strictly linear, remainder branched at least once. Glucosamine, galactose, mannose dominating comprise ~75% monosaccharides...
During the EUROCarbDB project our group developed GlycanBuilder and GlycoWorkbench glycoinformatics tools. This short communication summarizes capabilities of these two tools updates which have been made since original publications in 2007 2008. is a tool that allows for fast intuitive drawing glycan structures; this can be used standalone, embedded web pages also integrated into other programs. has designed to semi-automatically annotate glycomics data. mass spectrometry (MS) MS/MS spectra...
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...
The MIRAGE (minimum information required for a glycomics experiment) initiative was founded in Seattle, WA, November 2011 order to develop guidelines reporting the qualitative and quantitative results obtained by diverse types of analyses, including conditions techniques that were applied prepare glycans analysis generate primary data along with tools parameters used process annotate this data. These must address broad range issues, as are inherently complex generated using methods, mass...
The MIRAGE guidelines are being developed in response to a critical need the glycobiology community clarify glycoanalytic results so that they more readily evaluated (in terms of their scope and depth) facilitate reproduction important laboratory. molecular biological complexity glycosylation process makes thorough reporting glycomics experiment highly challenging endeavor. resulting data specify identity quantity complex structures, precise features which sometimes inferred using prior...
There are considerable differences between bacterial and mammalian glycans. In contrast to most eukaryotic carbohydrates, glycans often composed of repeating units with diverse functions ranging from structural reinforcement adhesion, colonization camouflage. Since typically displayed at the cell surface, they can interact environment and, therefore, have significant biomedical importance. The sequence characteristics (monosaccharide composition, modifications, linkage patterns) for higher...
Abstract Mass spectrometric techniques are the key technology for rapid and reliable glycan analysis. However, lack of robust, dependable, freely available software (semi‐) automatic annotation mass spectra is still a severe bottleneck that hampers their interpretation. In this article “ Glyco‐Peakfinder ” web‐service described allowing de novo determination compositions from signals. Starting basic set mandatory masses components, calculation can be performed without any knowledge...
The EUROCarbDB project is a design study for technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology glycomic research. relational database containing glycan structures, their biological context and, when available, primary interpreted analytical data from high-performance liquid chromatography, mass spectrometry nuclear magnetic resonance experiments. Database content can be accessed via web-based user...
GlycomeDB integrates the structural and taxonomic data of all major public carbohydrate databases, as well carbohydrates contained in Protein Data Bank, which renders database currently most comprehensive unified resource for structures worldwide. retains links to original databases is updated at weekly intervals with newest available from source databases. The complete can be downloaded freely or accessed through a Web-interface ( www.glycome-db.org ) that provides flexible powerful search...
Recent progress in method development for characterising the branched structures of complex carbohydrates has now enabled higher throughput technology. Automation structure analysis then calls software since adding meaning to large data collections reasonable time requires corresponding bioinformatics methods and tools. Current glycobioinformatics resources do cover information on function glycans, their interaction with proteins or enzymatic synthesis. However, this is partial, scattered...
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...
The minimum information required for a glycomics experiment (MIRAGE) project was established in 2011 to provide guidelines aid data reporting from all types of experiments research including mass spectrometry (MS), liquid chromatography, glycan arrays, handling and sample preparation. MIRAGE is concerted effort the wider community that considers adaptation as an important step towards critical evaluation dissemination datasets well broadening experimental techniques worldwide. Commission...
Although carbohydrates are the third major class of biological macromolecules, after proteins and DNA, there is neither a comprehensive database for carbohydrate structures nor an established universal structure encoding scheme computational purposes. Funding further development Complex Carbohydrate Structure Database (CCSD or CarbBank) ceased in 1997, since then several initiatives have developed independent databases with partially overlapping foci. For each database, different schemes...
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...
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...
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...
Abstract Nonulosonic acids or non-2-ulosonic (NulOs) are an ancient family of 2-ketoaldonic (α-ketoaldonic acids) with a 9-carbon backbone. In nature, these monosaccharides occur either in 3-deoxy form (referred to as “sialic acids”) 3,9-dideoxy “sialic-acid-like” form. The former sialic most common the deuterostome lineage, including vertebrates, and mimicked by some their pathogens. latter sialic-acid-like molecules found bacteria archaea. NulOs often prominently positioned at outermost...
Glycosphingolipids are essential components of all eukaryotic cells and play a major role in broad range cellular biological processes, including growth, cell signaling, survival, differentiation, disease. Glycosphingolipid structural diversity arises from heterogeneity both the glycan lipid moieties. Most currently available computational tools for annotating mass-spectrometry data glycosphingolipids primarily concentrate on analysis structure, not intact glycosphingolipid. Such...
Journal Article Accepted manuscript Meeting report of the GlySpace alliance and GaLSIC symposium Get access Kiyoko F Aoki-Kinoshita, Aoki-Kinoshita Glycan Life Systems Integration Center (GaLSIC), Soka University, Tokyo 192-8677, Japan Search for other works by this author on: Oxford Academic PubMed Google Scholar Frederique Lisacek, Lisacek SIB Swiss Institute Bioinformatics & Computer Science Department, University Geneva, Switzerland Raja Mazumder, Mazumder The Department Biochemistry...