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GlycoPattern: a web platform for glycan array mining

S. B. Agravat, J. H. Saltz, R. D. Cummings, D. F. Smith
2014 Bioinformatics  
GlycoPattern is Web-based bioinformatics resource to support the analysis of glycan array data for the Consortium for Functional Glycomics.  ...  This resource includes algorithms and tools to discover structural motifs, a heatmap visualization to compare multiple experiments, hierarchical clustering of Glycan Binding Proteins with respect to their  ...  it is not considered a platform for mining glycan array data.  ... 
doi:10.1093/bioinformatics/btu559 pmid:25143288 pmcid:PMC4296152 fatcat:hbfyd7rwbzgydgtsujlkyr72gy

Tools for generating and analyzing glycan microarray data

Akul Y Mehta, Jamie Heimburg-Molinaro, Richard D Cummings
2020 Beilstein Journal of Organic Chemistry  
We then highlight a number of tools for the analysis of glycan microarray data such as data repositories, data visualization and manual analysis tools, automated analysis tools and structural informatics  ...  Glycan microarrays allow a plethora of information to be obtained on protein–glycan binding interactions.  ...  Acknowledgements The authors would like to thank Zachary Klamer, Johnathan Hall and Brian Haab (MotifFinder, SignalFinder) along with Lachlan Coff and Andrew Guy (CCARL), for help with their software.  ... 
doi:10.3762/bjoc.16.187 pmid:32983270 pmcid:PMC7492694 fatcat:svk7whxb3zbo3k5egj5jybyvge

A Review of Software Applications and Databases for the Interpretation of Glycopeptide Data

Matthew P. Campbell
2017 Trends in glycoscience and glycotechnology  
Compared to proteomics, computational platforms for glycoproteomics is at an early stage and many researchers rely on the manual interpretation of large data sets to gain structural insights into the glycoproteome  ...  For a broader introduction to protein glycosylation, classes and types found in nature readers are referred to a number of comprehensive reviews (4, 5, 9-13).  ...  Acknowledgments The author acknowledges funding support from the Institute for Glycomics and Griffith University.  ... 
doi:10.4052/tigg.1601.1e fatcat:er42p3lz2fh7tda2bcawm7syem

Systems Glycobiology: Past, Present, and Future [chapter]

Songül Yaşar Yıldız
2020 Computational Biology and Chemistry [Working Title]  
Glycobiology is a glycan-based field of study that focuses on the structure, function, and biology of carbohydrates, and glycomics is a sub-study of the field of glycobiology that aims to define structure  ...  /function of glycans in living organisms.  ...  de/index.php https://acgg.asia/ http://glycosciences. de/index.php RINGS and glycomics with glycan synthesis such as A Web resource providing ggdb2 http://rings.t.soka.  ... 
doi:10.5772/intechopen.92267 fatcat:52dnyiusu5bpvbiluegofjlgpm

Databases and Associated Tools for Glycomics and Glycoproteomics [chapter]

Frederique Lisacek, Julien Mariethoz, Davide Alocci, Pauline M. Rudd, Jodie L. Abrahams, Matthew P. Campbell, Nicolle H. Packer, Jonas Ståhle, Göran Widmalm, Elaine Mullen, Barbara Adamczyk, Miguel A. Rojas-Macias (+2 others)
2016 Msphere  
The access to biodatabases for glycomics and glycoproteomics has proven to be essential for current glycobiological research.  ...  Specifi c search protocols are also provided using tools associated with experimental databases for converting primary glycoanalytical data to glycan structural information.  ...  The Japan Consortium for Glycobiology and Glycotechnology DataBase ( JCCGB ) is a metadatabase that allows one to simultaneously search in glyco related databases, www.jcggdb.jp .  ... 
doi:10.1007/978-1-4939-6493-2_18 pmid:27743371 fatcat:lqjkg2d3hrgapotei5q5ufgjci

Understanding the glycome: an interactive view of glycosylation from glycocompositions to glycoepitopes

Davide Alocci, Marie Ghraichy, Elena Barletta, Alessandra Gastaldello, Julien Mariethoz, Frederique Lisacek
2018 Glycobiology  
Glycan profile data can be imported in Glynsight, which generates a custom interactive glycan profile.  ...  The rapid growth of available glycan data accentuates the lack of innovative tools for visualizing and exploring large amount of information.  ...  Acknowledgements We thank Dr David Falk and Prof Manfred Wuhrer for helpful discussions on the genesis of Glynsight and feedback on the early prototypes.  ... 
doi:10.1093/glycob/cwy019 pmid:29518231 fatcat:tnvmhoym7bfz7cx2z37ccwe7u4

Glyco25, XXV International Symposium on Glycoconjugates

2019 Glycoconjugate Journal  
well-controlled multivalent manner on a well-defined surface.  ...  Gold nanoparticles have been explored as a tool to study the molecular interactions between S. pneumoniae polysaccharides and the human immune system.  ...  and a sialic acid rich (18%) glycan with lectins and antibodies were shown.  ... 
doi:10.1007/s10719-019-09880-4 fatcat:xdbfh5xegbfpfhugf3tgzbirq4

Program and Abstracts for the 2008 Meeting of the Society for Glycobiology

2008 Glycobiology  
The conference rate is $179 for single/double. Please refer to www.glycobiology.org for more detailed information.  ...  Therefore, the NHS-activated platform seems compatible for printing other types of glycans on the array. (Supported by NIGMS grant GM62116).  ...  Here we had established a carbohydrate membrane array platform to investigate proteincarbohydrate interactions.  ... 
doi:10.1093/glycob/cwn086 fatcat:44k7piokmrdlfa6m2xsbead62a

Heterogeneous Data Processing for Information and Knowledge Management in Glycomics and Glycoproteomics

Julien Mariethoz, Frédérique Lisacek
2022
Vincenzo Daponte, Francisco Lorenzo for the good time we shared during those last years.  ...  Finally, special thanks to my family, especially Carole, Hugo, and Alexandre, for their infinite patience and unconditional support. iv  ...  Acknowledgments We thank Kiyoko Aoki-Kinoshita, Nobuyuki Aoki and Catherine A. Hayes for fruitful discussions and valuable advice. Author Contributions Acknowledgements We thank Prof.  ... 
doi:10.13097/archive-ouverte/unige:159753 fatcat:uadamnb5yrhgfmcess2ukrh3n4

Abstracts book of the Anual International Conference of the Romanian Society for Biochemistry and Molecular Biology

Group Author
2019 Journal of Experimental and Molecular Biology  
The issues containes all the abstracts presented as lectures and posters at the Anual International Conference of the Romanian Society for Biochemistry and Molecular Biology, 26-27th September, Iasi, Romania  ...  Furthermore, we used a combined machine learning algorithm for miR targets prediction, and a clustering and topological community detection (CTCD) approach followed by gene ontology analysis to describe  ...  Abstract: Member of the miR-15 precursor family, mmu-miR-195 is a conserved small non-coding RNA known for its role in cell cycle and cell death/apoptosis regulation. miR-195 is differentially expressed  ... 
doaj:ddb59a233992453082eeba1bf81d3986 fatcat:tm6sg2npnjbsrazec7mfbq3mde