A5084380350- Glycosylation and Glycoproteins Research
- Genomics and Phylogenetic Studies
- Carbohydrate Chemistry and Synthesis
- Biomedical Text Mining and Ontologies
- Advanced Proteomics Techniques and Applications
- Advanced Battery Technologies Research
- Advanced Battery Materials and Technologies
- Machine Learning in Bioinformatics
- Monoclonal and Polyclonal Antibodies Research
- Bioinformatics and Genomic Networks
- Regulation of Appetite and Obesity
- Microbial Metabolites in Food Biotechnology
- Solid-state spectroscopy and crystallography
- Advancements in Battery Materials
- Cryptographic Implementations and Security
- Microbial Metabolic Engineering and Bioproduction
- Thermodynamic properties of mixtures
- Chaos-based Image/Signal Encryption
- Phase Equilibria and Thermodynamics
- Advanced Malware Detection Techniques
- Security and Verification in Computing
- Enzyme Structure and Function
- Physiological and biochemical adaptations
- Viral Infectious Diseases and Gene Expression in Insects
- Proteoglycans and glycosaminoglycans research
National University of Ireland, Maynooth
2024-2025
University of Geneva
2021-2024
SIB Swiss Institute of Bioinformatics
2011-2024
University of Gothenburg
2011-2018
University of Vermont
2013
National Institute for Bioprocessing Research and Training
2011
University College Dublin
2011
Macquarie University
2011
National University of Ireland
2011
Ollscoil na Gaillimhe – University of Galway
2009
The Human Proteome Organisation Disease Glycomics/Proteome Initiative recently coordinated a multi-institutional study that evaluated methodologies are widely used for defining the N-glycan content in glycoproteins. convincingly endorsed mass spectrometry as technique of choice glycomic profiling discovery phase diagnostic research. present reports extension Initiative's activities to an assessment currently O-glycan analysis. Three samples IgA1 isolated from serum patients with multiple...
Abstract Summary: Glycosylation is one of the most important post-translational modifications proteins, known to be involved in pathogen recognition, innate immune response and protection epithelial membranes. However, when compared tools databases available for processing high-throughput proteomic data, glycomic domain severely lacking. While assist analysis mass spectrometry (MS) HPLC are continuously improving, there few resources support liquid chromatography (LC)–MS/MS techniques glycan...
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...
Abstract Despite the success of several international initiatives glycosciences still lack a managed infrastructure that contributes to advancement research through provision comprehensive structural and experimental glycan data collections. UniCarbKB is an initiative aims promote creation online information storage search platform for glycomics glycobiology research. The knowledgebase will offer freely accessible information‐rich resource supported by querying interfaces, annotation...
One of the hallmarks severe pneumonia and associated acute lung injury is neutrophil recruitment to lung. Leptin thought be up-regulated in following exert diverse effects on leukocytes, influencing both chemotaxis survival. We hypothesized that pulmonary leptin contributes directly development neutrophilia during injury.Controlled human murine vivo ex experimental studies.Research laboratory a university hospital.Healthy volunteers subjects hospitalized with bacterial H1N1 pneumonia....
Maybe we need to think more about non-cryptographic hash functions.
Abstract The SIB Swiss Institute of Bioinformatics (https://www.sib.swiss/) is a federation bioinformatics research and service groups. international life science community in academia industry has been accessing the freely available databases provided by since its inception 1998. In this paper we present 11 which currently offer semantically enriched data accordance with FAIR principles (Findable, Accessible, Interoperable, Reusable), as well Personalized Health Network initiative (SPHN)...
Abstract Dynamic changes in protein glycosylation impact human health and disease progression. However, current resources that capture phenotype information focus primarily on the macromolecules within central dogma of molecular biology (DNA, RNA, proteins). To gain a better understanding organisms, there is need to functional glycans biological processes. A workshop titled “Functional their curation” was held conjunction with 16th Annual International Biocuration Conference discuss ongoing...
Abstract Motivation: Glycosylation is one of the most important post-translational modifications proteins and explains some aspects diversification higher organisms not explained by template-driven synthesis. For glycomics to mature as much genomics proteomics, necessary tools need be developed tested. Liquid chromatography-mass spectrometry gold standards for oligosaccharide analysis leads large amounts data, easily interpreted manually. We present a study on testing validation statistical...
Collision induced dissociation (CID) fragmentation was compared between reducing and reduced sulfated, sialylated, neutral O-linked oligosaccharides. It found that of the [M - H](-) ions aldoses with acidic residues gave unique Z-fragmentation end GalNAc containing C-6 branch, where entire C-3 branch lost. This pathway, which is not seen in alditols, showed process involved charge remote catalyzed by a anomeric proton. With structures sialic acid on both were dominated loss acid. pathway...
The availability of specific exoglycosidases alongside a spectral library O-linked oligosaccharide collision induced dissociation (CID) MS fragments, UniCarb-DB, provides pathway to make the elucidation oligosaccharides more efficient. Here, we advise an approach exoglycosidase-digestion mixtures, for structures that do not provide confirmative spectra. combination exoglycosidase digestion and MS2 matching products with from allowed assignment unknown structures. This was illustrated by...
Sulfation is the final decoration of mucin-type O-linked oligosaccharides before mucins are released into lumen gastrointestinal, respiratory, and genital tracts. Because only a fraction undergo this type modifications in Golgi apparatus, sometimes also by dedicated cells, glycobiology these low abundant sulfated often overlooked. At same time, technology to consistently identify characterize them has been lagging. We adopted higher energy collisional dissociation from porcine gastric human...
The level of ambiguity in describing glycan structure has significantly increased with the upsurge large-scale glycomics and glycoproteomics experiments. Consequently, an ontology-based model appears as appropriate solution for navigating these data. However, navigation is not sufficient should also enable advanced search comparison. A new ontology a tree logical introduced to represent structures irrespective precision molecular details. heavily relies on GlycoCT encoding structures. Its...
The research area of glycomics is maturing and it realized that as difficult to identify the relevance glycosylation amongst biological house-keeping with any other omics techniques. This review focuses on sulfoglycomics N-linked O-linked oligosaccharides relevant questions. describes how sulfated have been analyzed in past, focus MS its current application using ESI MALDI. Also included are particular issues sample preparation oligosaccharides, including enrichment separation capillary nano...
Abstract Recent technological advances in glycobiology have resulted a large influx of data and the publication many papers describing discoveries glycoscience. However, terms used glycan structural features are not standardized, making it difficult to harmonize across biomolecular databases, hampering harvesting information studies hindering text mining curation efforts. To address this shortcoming, Glycan Structure Dictionary has been developed as reference dictionary provide standardized...
Although cryptographic and non-cryptographic hash functions are everywhere, there seems to be a gap in how they designed. Lots of criteria exist for hashes motivated by various security requirements, but on the side is certain amount folklore that, despite long history functions, has not been fully explored. While targeting uniform distribution makes lot sense real-world datasets, it can challenge when confronted dataset with particular patterns.
Abstract MatrixDB, a member of the International Molecular Exchange consortium (IMEx), is curated interaction database focused on interactions established by extracellular matrix (ECM) constituents including proteins, proteoglycans, glycosaminoglycans and ECM bioactive fragments. The architecture MatrixDB was upgraded to ease data export, allow versioning programmatic access ensure sustainability. new version includes more than twice number manually experimentally-supported interactions....