| 1. |
- Bimbot, F, et al.
(författare)
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An overview of the PICASSO project research activities in speaker verification for telephone applications
- 1999
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Konferensbidrag (refereegranskat)abstract
- This paper presents a general overview of the current research activities in the European PICASSO project on speaker verification for telephone applications. First, the general formalism used by the project is described. Then the scientific issues under focus are discussed in detail. Finally, the paper briefly describes the Picassoft research platform. Along the article, entry points to more specific work also published in the Eurospeech’99 proceedings are given.
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| 2. |
- Gotz, L., et al.
(författare)
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GlycoDigest: a tool for the targeted use of exoglycosidase digestions in glycan structure determination
- 2014
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Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 30:21, s. 3131-3133
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Tidskriftsartikel (refereegranskat)abstract
- Sequencing oligosaccharides by exoglycosidases, either sequentially or in an array format, is a powerful tool to unambiguously determine the structure of complex N- and O-link glycans. Here, we introduce GlycoDigest, a tool that simulates exoglycosidase digestion, based on controlled rules acquired from expert knowledge and experimental evidence available in GlycoBase. The tool allows the targeted design of glycosidase enzyme mixtures by allowing researchers to model the action of exoglycosidases, thereby validating and improving the efficiency and accuracy of glycan analysis.
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| 3. |
- Lisacek, F., et al.
(författare)
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Databases and associated tools for glycomics and glycoproteomics
- 2017
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Ingår i: High-Throughput Glycomics and Glycoproteomics. Eds: Gordan Lauc & Manfred Wuhrer. - New York : Springer. - 1064-3745. - 9781493964932 - 9781493964918 ; , s. 235-264
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research. This chapter presents available databases that are devoted to different aspects of glycobioinformatics. This includes oligosaccharide sequence databases, experimental databases, 3D structure databases (of both glycans and glycorelated proteins) and association of glycans with tissue, disease, and proteins. Specific search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information. In particular, researchers using glycoanalysis methods by U/HPLC (GlycoBase), MS (GlycoWorkbench, UniCarb-DB, GlycoDigest), and NMR (CASPER) will benefit from this chapter. In addition we also include information on how to utilize glycan structural information to query databases that associate glycans with proteins (UniCarbKB) and with interactions with pathogens (Sugar Bind). © Springer Science+Business Media New York 2017.
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| 4. |
- Alocci, D., et al.
(författare)
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GlyConnect: Glycoproteomics Goes Visual, Interactive, and Analytical
- 2019
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Ingår i: Journal of Proteome Research. - : American Chemical Society (ACS). - 1535-3893 .- 1535-3907. ; 18:2, s. 664-677
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Tidskriftsartikel (refereegranskat)abstract
- Knowledge of glycoproteins, their site-specific glycosylation patterns, and the glycan structures that they present to their recognition partners in health and disease is gradually being built on using a range of experimental approaches. The data from these analyses are increasingly being standardized and presented in various sources, from supplemental tables in publications to localized servers in investigator laboratories. Bioinformatics tools are now needed to collect these data and enable the user to search, display, and connect glycomics and glycoproteomics to other sources of related proteomics, genomics, and interactomics information. We here introduce GlyConnect (https://glyconnect.expasy.org/), the central platform of the Glycomics@ExPASy portal for glycoinformatics. GlyConnect has been developed to gather, monitor, integrate, and visualize data in a user-friendly way to facilitate the interpretation of collected glycoscience data. GlyConnect is designed to accommodate and integrate multiple data types as they are increasingly produced.
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| 5. |
- Mariethoz, J., et al.
(författare)
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An Interactive View of Glycosylation
- 2022
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Ingår i: Glycosylation. Methods and Protocols. Gavin P. Davey (red.). - New York, NY : Springer. - 1064-3745. - 9781071616857 ; , s. 41-65
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- The present chapter focuses on the interactive and explorative aspects of bioinformatics resources that have been recently released in glycobiology. The comparative analysis of data in a field where knowledge is scattered, incomplete, and disconnected from main biology requires efficient visualization, integration, and interactive tools that are currently only partially implemented. This overview highlights converging efforts toward building a consistent picture of protein glycosylation. © 2022, Springer Science+Business Media, LLC, part of Springer Nature.
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| 6. |
- Mariethoz, J., et al.
(författare)
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Glycomics@ExPASy: Bridging the gap
- 2018
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Ingår i: Molecular and Cellular Proteomics. - 1535-9476. ; 17:11, s. 2164-2176
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Tidskriftsartikel (refereegranskat)abstract
- Glycomics@ExPASy (https://www.expasy.org/glycomics) is the glycomics tab of ExPASy, the server of SIB Swiss Institute of Bioinformatics. It was created in 2016 to centralize web-based glycoinformatics resources developed within an international network of glycoscientists. The hosted collection currently includes mainly databases and tools created and maintained at SIB but also links to a range of reference resources popular in the glycomics community. The philosophy of our toolbox is that it should be {glycoscientist AND protein scientist}-friendly with the aim of (1) popularizing the use of bioinformatics in glycobiology and (2) emphasizing the relationship between glycobiology and protein-oriented bioinformatics resources. The scarcity of data bridging these two disciplines led us to design tools as interactive as possible based on database connectivity to facilitate data exploration and support hypothesis building. Glycomics@ExPASy was designed, and is developed, with a long-term vision in close collaboration with glycoscientists to meet as closely as possible the growing needs of the community for glycoinformatics. © 2018 Mariethoz et al.
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| 7. |
- Rojas-Macias, Miguel A., 1979, et al.
(författare)
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Towards a standardized bioinformatics infrastructure for N- and O-glycomics
- 2019
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Ingår i: Nature Communications. - : Springer Science and Business Media LLC. - 2041-1723. ; 10
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Tidskriftsartikel (refereegranskat)abstract
- The mass spectrometry (MS)-based analysis of free polysaccharides and glycans released from proteins, lipids and proteoglycans increasingly relies on databases and software. Here, we review progress in the bioinformatics analysis of protein-released N- and O-linked glycans (N-and O-glycomics) and propose an e-infrastructure to overcome current deficits in data and experimental transparency. This workflow enables the standardized submission of MS-based glycomics information into the public repository UniCarb-DR. It implements the MIRAGE (Minimum Requirement for A Glycomics Experiment) reporting guidelines, storage of unprocessed MS data in the GlycoPOST repository and glycan structure registration using the GlyTouCan registry, thereby supporting the development and extension of a glycan structure knowledgebase.
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