GlycoBioinformatics
Editors:
Prof. Kiyoko F. Aoki-Kinoshita, Soka University
Dr. Frédérique Lisacek, Swiss Institute of Bioinformatics, Geneva
Dr. Niclas Karlsson, University of Gothenburg
Dr. Daniel Kolarich, Griffith University
Prof. Nicolle Packer, Macquarie University, Sydney
Prof. Kiyoko F. Aoki-Kinoshita, Soka University
Dr. Frédérique Lisacek, Swiss Institute of Bioinformatics, Geneva
Dr. Niclas Karlsson, University of Gothenburg
Dr. Daniel Kolarich, Griffith University
Prof. Nicolle Packer, Macquarie University, Sydney
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.
GlycoBioinformatics
- Kiyoko F. Aoki-Kinoshita,
- Frédérique Lisacek,
- Niclas Karlsson,
- Daniel Kolarich and
- Nicolle H. Packer
Beilstein J. Org. Chem. 2021, 17, 2726–2728, doi:10.3762/bjoc.17.184
How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates
- Carl A. Fogarty,
- Aoife M. Harbison,
- Amy R. Dugdale and
- Elisa Fadda
Beilstein J. Org. Chem. 2020, 16, 2046–2056, doi:10.3762/bjoc.16.171
Clustering and curation of electropherograms: an efficient method for analyzing large cohorts of capillary electrophoresis glycomic profiles for bioprocessing operations
- Ian Walsh,
- Matthew S. F. Choo,
- Sim Lyn Chiin,
- Amelia Mak,
- Shi Jie Tay,
- Pauline M. Rudd,
- Yang Yuansheng,
- Andre Choo,
- Ho Ying Swan and
- Terry Nguyen-Khuong
Beilstein J. Org. Chem. 2020, 16, 2087–2099, doi:10.3762/bjoc.16.176
GlypNirO: An automated workflow for quantitative N- and O-linked glycoproteomic data analysis
- Toan K. Phung,
- Cassandra L. Pegg and
- Benjamin L. Schulz
Beilstein J. Org. Chem. 2020, 16, 2127–2135, doi:10.3762/bjoc.16.180
Tools for generating and analyzing glycan microarray data
- Akul Y. Mehta,
- Jamie Heimburg-Molinaro and
- Richard D. Cummings
Beilstein J. Org. Chem. 2020, 16, 2260–2271, doi:10.3762/bjoc.16.187
Computational tools for drawing, building and displaying carbohydrates: a visual guide
- Kanhaya Lal,
- Rafael Bermeo and
- Serge Perez
Beilstein J. Org. Chem. 2020, 16, 2448–2468, doi:10.3762/bjoc.16.199
Leveraging glycomics data in glycoprotein 3D structure validation with Privateer
- Haroldas Bagdonas,
- Daniel Ungar and
- Jon Agirre
Beilstein J. Org. Chem. 2020, 16, 2523–2533, doi:10.3762/bjoc.16.204
Comparative ligand structural analytics illustrated on variably glycosylated MUC1 antigen–antibody binding
- Christopher B. Barnett,
- Tharindu Senapathi and
- Kevin J. Naidoo
Beilstein J. Org. Chem. 2020, 16, 2540–2550, doi:10.3762/bjoc.16.206
A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR)
- Benjamin P. Kellman,
- Yujie Zhang,
- Emma Logomasini,
- Eric Meinhardt,
- Karla P. Godinez-Macias,
- Austin W. T. Chiang,
- James T. Sorrentino,
- Chenguang Liang,
- Bokan Bao,
- Yusen Zhou,
- Sachiko Akase,
- Isami Sogabe,
- Thukaa Kouka,
- Elizabeth A. Winzeler,
- Iain B. H. Wilson,
- Matthew P. Campbell,
- Sriram Neelamegham,
- Frederick J. Krambeck,
- Kiyoko F. Aoki-Kinoshita and
- Nathan E. Lewis
Beilstein J. Org. Chem. 2020, 16, 2645–2662, doi:10.3762/bjoc.16.215
Semiautomated glycoproteomics data analysis workflow for maximized glycopeptide identification and reliable quantification
- Steffen Lippold,
- Arnoud H. de Ru,
- Jan Nouta,
- Peter A. van Veelen,
- Magnus Palmblad,
- Manfred Wuhrer and
- Noortje de Haan
Beilstein J. Org. Chem. 2020, 16, 3038–3051, doi:10.3762/bjoc.16.253
Simulating the enzymes of ganglioside biosynthesis with Glycologue
- Andrew G. McDonald and
- Gavin P. Davey
Beilstein J. Org. Chem. 2021, 17, 739–748, doi:10.3762/bjoc.17.64
A systems-based framework to computationally describe putative transcription factors and signaling pathways regulating glycan biosynthesis
- Theodore Groth,
- Rudiyanto Gunawan and
- Sriram Neelamegham
Beilstein J. Org. Chem. 2021, 17, 1712–1724, doi:10.3762/bjoc.17.119
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