GlycoBioinformatics
The glycosylation of proteins, lipids, proteoglycans, and lipopolysaccharides is becoming increasingly recognized as being critical to the function of cells in health and disease. To understand the roles of these glycoconjugates, it is crucial to be able to analyze the corresponding structure and function and to relate these to other -omics knowledge. The current perception is that the analysis of glycosylation is too hard. As in the growth of the other -omics analyses, the analysis of glycoconjugates and function is dependent on the development of easy-to-use and accurate bioinformatic databases and tools that can be readily accessed by the research community. This volume describes state-of-the art developments in the area of glyco-bioinformatics as it continues to develop and be made publicly available.
- Full Research Paper
- Published 21 Aug 2020
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Figure 1: Representative structures of the plant N-glycans studied in this work with corresponding nomenclatu...
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Figure 2: A representative structure of the non-galactosylated N-glycan with α(1-3)-linked core fucose (ngf) ...
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Figure 3: β-D-xylose ring pucker analysis over 3 μs of cumulative MD sampling of the ngx N-glycan. The two sn...
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Figure 4: Comparison of the different conformational equilibria of the (1-6) arm in a core α(1-3)-Fuc β(1-2)-...
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Figure 5: Conformational analysis of the (1-6) arm in four hybrid N-glycoforms, β(1-2)-xylosylated A2G2 (top-...
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Figure 6: Conformational equilibrium of the (1-6) arm in terms of phi/psi torsion angle values for the α(1-3)...
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Figure 7: List of 3D structural units of monosaccharides (glycoblocks) that regulate the 3D architecture and ...
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- Full Research Paper
- Published 27 Aug 2020
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Figure 1: A single bioreactor run with defined culture conditions for twelve days. (A to B) batch GU calculat...
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Figure 2: Problems when integrating poorly resolved peaks using FA1/FA2G2S1/A2 and M5 peaks as an example. (A...
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Figure 3: The clustering function allowed grouping of similar electropherograms and therefore clean the Happy...
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Figure 4: Comparison of the performance of the automated peak picking and semi-automated clustering and Happy...
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Figure 5: Glycans identified in anti-HER-2 samples using UPLC-MS and CE. (A) the UPLC chromatogram confirmed ...
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Figure 6: Boxplots showing the quantitation of the 11 different bioreactor conditions. The boxplots show the ...
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- Full Research Paper
- Published 01 Sep 2020
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Figure 1: Evaluation of GlypNirO site-specific N-glycosylation profiling. Site-specific relative glycoform ab...
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Figure 2: N-Glycoproteome profiling with GlypNirO. Volcano plots of site-specific N-glycoform relative abunda...
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Figure 3: Site-specific N-glycopeptide profiling with GlypNirO. Site-specific relative glycoform abundance in...
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Figure 4: O-Glycoproteome profiling with GlypNirO. Volcano plots of site-specific O-glycoform relative abunda...
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Figure 5: Peptide-specific O-glycosylation profiling with GlypNirO. Peptide-specific relative glycoform abund...
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- Review
- Published 10 Sep 2020
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Figure 1: Overview of a typical glycan microarray workflow, beginning with the obtention of glycans to analys...
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Figure 2: A decision tree to determine which type of surface to use depending on glycoconjugate and linker ty...
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Figure 3: Screenshot of microarray databases: (A) Screenshot of an example of CFG glycan array data; (B) scre...
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Figure 4: A demonstration of glycan array data visualization with GLAD. The dataset used is from Byrd-Leotis ...
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- Review
- Published 02 Oct 2020
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Figure 1: Levels of representation of glycans: from sketching to virtual reality.
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Figure 2: Depiction of lactose by various glycan sketching tools.
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Figure 3: Examples of different glycan structure text formats for the same glycan. Data in these formats are ...
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Figure 4: From top to bottom: SugarSketcher [36] interface with a glycan structure drawn using the “Quick Mode”. ...
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Figure 5: GlyTouCan [38] interface allows to search for glycans structures in the database. Data contained in Gly...
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Figure 6: From top to bottom: GlycanBuilder2 [46] interface with a glycan image in SNFG notation. Original Glycan...
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Figure 7: From top to bottom: DrawGlycan-SNFG [51] web interface with a glycan text input and the resulting image...
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Figure 8: From top to bottom: Glyco.me SugarBuilder [56] interface with a glycan structure showing options to def...
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Figure 9: From top to bottom: Sweet II [62] web-interface with a text input to generate a 3D model. GLYCAM Carboh...
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Figure 10: PolysGlycanBuilder [77] interface illustrating glycan drawing using SNFG symbols. The glycan can be fur...
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Figure 11: From top to bottom: 3D-SNFG representation of glycan using 3D-SNFG script integrated VMD [79]. LiteMol [80]...
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- Full Research Paper
- Published 09 Oct 2020
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Figure 1: Comparison of the glycan features in electron density maps over a range of resolutions from selecte...
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Figure 2: A roadmap of the software development project that allows structural biologists to quickly obtain d...
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Figure 3: N-Linked glycans in Epstein Barr virus major envelope glycoprotein (PDB entry: 2H6O [66]). A) A selecti...
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Figure 4: An N-linked glycan attached to Asn35 of human Toll-like receptor 4 (A: PDB entry 2z62 [68]). Model iter...
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- Full Research Paper
- Published 13 Oct 2020
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Figure 1: A representation of mucin glycopeptide bound to AR20.5 antibody. Chain A is represented as a molecu...
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Figure 2: A comparison of root mean analyses for the antigen and Tn-antigen in solution (unbound) and in anti...
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Figure 3: End-to-end time series and histogram for the antigen and Tn-antigen in solution (A, B) and the anti...
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Figure 4: A comparison of Ramachandran analyses for two key amino acids, Asp3 and Thr4. The first row (A–D) i...
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Figure 5: Distribution of clusters, found using TTClust, for the antigen and Tn-antigen in solution (A, B) an...
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- Commentary
- Published 27 Oct 2020
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Figure 1: Common terminology and anatomy of a theoretical glycan, (KJ(IH)GF(D(E)(C)B)A. In this figure, we de...
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Figure 2: Monosaccharide reachability analysis. (A) Clusters contain monosaccharides with highly similar ster...
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- Full Research Paper
- Published 11 Dec 2020
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Figure 1: Integration of automated glycopeptide identification by Byonic and GlycopeptideGraphMS (aided by Op...
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Figure 2: Representative IgG and IgA glycopeptide clusters detected by GlycopeptideGraphMS.
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Figure 3: Representative GlycopeptideGraphMS output for peptides of interest. Assigned compositions were iden...
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Figure 4: Comparison of quantification results obtained by manual integration of EICs in Skyline (black), aut...
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- Full Research Paper
- Published 23 Mar 2021
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Figure 1: Chemical structure of ganglioside GM1a (a β-ᴅ-galactosyl-(1→3)-N-acetyl-β-ᴅ-galactosaminyl-(1→4)-[α-...
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Figure 2: Construction of the Svennerholm name GP1cα from its Glycologue structure identifier. At each step o...
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Figure 3: Ganglioside carbohydrates predicted by the model. All structures are linked to ceramide at the base...
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Figure 4: Ganglioside biosynthetic reaction network predicted by the Glycologue enzyme simulator. Starting fr...
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Figure 5: Predicted effects on the pathways of ganglioside biosynthesis when individual enzyme activities are...
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- Full Research Paper
- Published 22 Jul 2021
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Figure 1: A systems glycobiology framework to link multi-OMICs data. a) Cell signaling proceeds to trigger TF...
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Figure 2: Analysis workflow: ChiP-Seq provides evidence of TF binding to promoter regions with 0 ≤ RP ≤ 1, qu...
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Figure 3: Summary of TFs enriched to glycosylation pathways for luminal and basal breast cancer: The TFs foun...
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Figure 4: Luminal breast cancer signaling pathway enrichment and glycogene connections. a) TF-to-glycogene co...
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Figure 5: Basal breast cancer signaling pathway enrichments and glycogene connections. a) TF-to-glycogene com...
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Figure 6: Summary of TF–glycopathway enrichments across all cancer types: TF enrichments to glycopathways acr...
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