Publications
7 results found
Akune Y, Arpinar S, Silva LM, et al., 2022, CarbArrayART-An update on the software tool for carbohydrate microarray data, storage, processing, presentation and reporting, Glycobiology, Vol: 30, Pages: 1031-1031, ISSN: 0959-6658
Glycan microarrays are essential tools in glycobiology and are being widely used for assignment of glycan ligands in diverse glycan recognition systems. We have developed a new software, called Carbohydrate microArray Analysis and Reporting Tool (CarbArrayART), to address the need for a distributable application for glycan microarray data management. The main features of CarbArrayART include: (i) Storage of quantified array data from different array layouts with scan data and array-specific metadata, such as lists of arrayed glycans, array geometry, information on glycan-binding samples, and experimental protocols. (ii) Presentation of microarray data as charts, tables, and heatmaps derived from the average fluorescence intensity values that are calculated based on the imaging scan data and array geometry, as well as filtering and sorting functions according to monosaccharide content and glycan sequences. (iii) Data export for reporting in Word, PDF, and Excel formats, together with metadata that are compliant with the guidelines of MIRAGE (Minimum Information Required for A Glycomics Experiment). CarbArrayART is designed for routine use in recording, storage, and management of any slide-based glycan microarray experiment. In conjunction with the MIRAGE guidelines, CarbArrayART addresses issues that are critical for glycobiology, namely, clarity of data for evaluation of reproducibility and validity.
Bonnardel F, Haslam SM, Dell A, et al., 2021, Proteome-wide prediction of bacterial carbohydrate-binding proteins as a tool for understanding commensal and pathogen colonisation of the vaginal microbiome, npj Biofilms and Microbiomes, Vol: 7, Pages: 1-10, ISSN: 2055-5008
Bacteria use carbohydrate-binding proteins (CBPs), such as lectins and carbohydrate-binding modules (CBMs), to anchor to specific sugars on host surfaces. CBPs in the gut microbiome are well studied, but their roles in the vagina microbiome and involvement in sexually transmitted infections, cervical cancer and preterm birth are largely unknown. We established a classification system for lectins and designed Hidden Markov Model (HMM) profiles for data mining of bacterial genomes, resulting in identification of >100,000 predicted bacterial lectins available at unilectin.eu/bacteria. Genome screening of 90 isolates from 21 vaginal bacterial species shows that those associated with infection and inflammation produce a larger CBPs repertoire, thus enabling them to potentially bind a wider array of glycans in the vagina. Both the number of predicted bacterial CBPs and their specificities correlated with pathogenicity. This study provides new insights into potential mechanisms of colonisation by commensals and potential pathogens of the reproductive tract that underpin health and disease states.
Aoki-Kinoshita KF, Kinjo AR, Morita M, et al., 2015, Implementation of linked data in the life sciences at BioHackathon 2011, Journal of Biomedical Semantics, Vol: 6
Katayama T, Wilkinson MD, Aoki-Kinoshita KF, et al., 2014, BioHackathon series in 2011 and 2012: penetration of ontology and linked data in life science domains, Journal of Biomedical Semantics, Vol: 5, Pages: 5-5, ISSN: 2041-1480
Campbell MP, Ranzinger R, Luetteke T, et al., 2014, Toolboxes for a standardised and systematic study of glycans, BMC BIOINFORMATICS, Vol: 15, ISSN: 1471-2105
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Campbell MP, Peterson R, Mariethoz J, et al., 2014, UniCarbKB: building a knowledge platform for glycoproteomics, Nucleic Acids Research, Vol: 42, Pages: D215-D221, ISSN: 0305-1048
Akune Y, Hosoda M, Kaiya S, et al., 2010, The RINGS Resource for Glycome Informatics Analysis and Data Mining on the Web, OMICS: A Journal of Integrative Biology, Vol: 14, Pages: 475-486, ISSN: 1536-2310
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