GlycoBioinformatics

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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
 
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.
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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

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Editorial
Published 09 Nov 2021

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

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Published 21 Aug 2020

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

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Published 27 Aug 2020

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

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Published 01 Sep 2020

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

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Review
Published 10 Sep 2020

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

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Published 02 Oct 2020

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

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Published 09 Oct 2020

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

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Published 13 Oct 2020

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

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Commentary
Published 27 Oct 2020

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

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Published 11 Dec 2020

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

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Published 23 Mar 2021

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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Published 22 Jul 2021
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