Literature DB >> 23230149

Glycosylation Network Analysis Toolbox: a MATLAB-based environment for systems glycobiology.

Gang Liu1, Apurv Puri, Sriram Neelamegham.   

Abstract

UNLABELLED: Systems glycobiology studies the interaction of various pathways that regulate glycan biosynthesis and function. Software tools for the construction and analysis of such pathways are not yet available. We present GNAT, a platform-independent, user-extensible MATLAB-based toolbox that provides an integrated computational environment to construct, manipulate and simulate glycans and their networks. It enables integration of XML-based glycan structure data into SBML (Systems Biology Markup Language) files that describe glycosylation reaction networks. Curation and manipulation of networks is facilitated using class definitions and glycomics database query tools. High quality visualization of networks and their steady-state and dynamic simulation are also supported. AVAILABILITY: The software package including source code, help documentation and demonstrations are available at http://sourceforge.net/projects/gnatmatlab/files/.

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Year:  2012        PMID： 23230149      PMCID： PMC3562062          DOI： 10.1093/bioinformatics/bts703

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  10 in total

1.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models.

Authors:  M Hucka; A Finney; H M Sauro; H Bolouri; J C Doyle; H Kitano; A P Arkin; B J Bornstein; D Bray; A Cornish-Bowden; A A Cuellar; S Dronov; E D Gilles; M Ginkel; V Gor; I I Goryanin; W J Hedley; T C Hodgman; J-H Hofmeyr; P J Hunter; N S Juty; J L Kasberger; A Kremling; U Kummer; N Le Novère; L M Loew; D Lucio; P Mendes; E Minch; E D Mjolsness; Y Nakayama; M R Nelson; P F Nielsen; T Sakurada; J C Schaff; B E Shapiro; T S Shimizu; H D Spence; J Stelling; K Takahashi; M Tomita; J Wagner; J Wang
Journal:  Bioinformatics       Date:  2003-03-01       Impact factor: 6.937

2.  SBMLToolbox: an SBML toolbox for MATLAB users.

Authors:  Sarah M Keating; Benjamin J Bornstein; Andrew Finney; Michael Hucka
Journal:  Bioinformatics       Date:  2006-03-30       Impact factor: 6.937

Review 3.  Advancing glycomics: implementation strategies at the consortium for functional glycomics.

Authors:  Rahul Raman; Maha Venkataraman; Subu Ramakrishnan; Wei Lang; S Raguram; Ram Sasisekharan
Journal:  Glycobiology       Date:  2006-02-14       Impact factor: 4.313

Review 4.  Systems glycobiology: biochemical reaction networks regulating glycan structure and function.

Authors:  Sriram Neelamegham; Gang Liu
Journal:  Glycobiology       Date:  2011-03-24       Impact factor: 4.313

5.  Systems-level modeling of cellular glycosylation reaction networks: O-linked glycan formation on natural selectin ligands.

Authors:  Gang Liu; Dhananjay D Marathe; Khushi L Matta; Sriram Neelamegham
Journal:  Bioinformatics       Date:  2008-10-07       Impact factor: 6.937

6.  The GlycomeAtlas tool for visualizing and querying glycome data.

Authors:  Yoshitsugu Konishi; Kiyoko F Aoki-Kinoshita
Journal:  Bioinformatics       Date:  2012-08-24       Impact factor: 6.937

7.  A mathematical model to derive N-glycan structures and cellular enzyme activities from mass spectrometric data.

Authors:  Frederick J Krambeck; Sandra V Bennun; Someet Narang; Sean Choi; Kevin J Yarema; Michael J Betenbaugh
Journal:  Glycobiology       Date:  2009-06-08       Impact factor: 4.313

8.  A mathematical model of N-linked glycoform biosynthesis.

Authors:  P Umaña; J E Bailey
Journal:  Biotechnol Bioeng       Date:  1997-09-20       Impact factor: 4.530

9.  GlycomeDB--a unified database for carbohydrate structures.

Authors:  René Ranzinger; Stephan Herget; Claus-Wilhelm von der Lieth; Martin Frank
Journal:  Nucleic Acids Res       Date:  2010-11-02       Impact factor: 16.971

10.  The GlycanBuilder: a fast, intuitive and flexible software tool for building and displaying glycan structures.

Authors:  Alessio Ceroni; Anne Dell; Stuart M Haslam
Journal:  Source Code Biol Med       Date:  2007-08-07
  10 in total
  12 in total

Review 1.  Integration of systems glycobiology with bioinformatics toolboxes, glycoinformatics resources, and glycoproteomics data.

Authors:  Gang Liu; Sriram Neelamegham
Journal:  Wiley Interdiscip Rev Syst Biol Med       Date:  2015-04-13

Review 2.  Multi-level regulation of cellular glycosylation: from genes to transcript to enzyme to structure.

Authors:  Sriram Neelamegham; Lara K Mahal
Journal:  Curr Opin Struct Biol       Date:  2016-10-13       Impact factor: 6.809

3.  DrawGlycan-SNFG: a robust tool to render glycans and glycopeptides with fragmentation information.

Authors:  Kai Cheng; Yusen Zhou; Sriram Neelamegham
Journal:  Glycobiology       Date:  2017-03-15       Impact factor: 4.313

4.  A Comprehensive, Open-source Platform for Mass Spectrometry-based Glycoproteomics Data Analysis.

Authors:  Gang Liu; Kai Cheng; Chi Y Lo; Jun Li; Jun Qu; Sriram Neelamegham
Journal:  Mol Cell Proteomics       Date:  2017-09-08       Impact factor: 5.911

5.  Global mapping of glycosylation pathways in human-derived cells.

Authors:  Yi-Fan Huang; Kazuhiro Aoki; Sachiko Akase; Mayumi Ishihara; Yi-Shi Liu; Ganglong Yang; Yasuhiko Kizuka; Shuji Mizumoto; Michael Tiemeyer; Xiao-Dong Gao; Kiyoko F Aoki-Kinoshita; Morihisa Fujita
Journal:  Dev Cell       Date:  2021-03-16       Impact factor: 12.270

6.  A Knowledge-Based System for Display and Prediction of O-Glycosylation Network Behaviour in Response to Enzyme Knockouts.

Authors:  Andrew G McDonald; Keith F Tipton; Gavin P Davey
Journal:  PLoS Comput Biol       Date:  2016-04-07       Impact factor: 4.475

7.  Development and application of an algorithm to compute weighted multiple glycan alignments.

Authors:  Masae Hosoda; Yukie Akune; Kiyoko F Aoki-Kinoshita
Journal:  Bioinformatics       Date:  2017-05-01       Impact factor: 6.937

Review 8.  What can mathematical modelling say about CHO metabolism and protein glycosylation?

Authors:  Sarah N Galleguillos; David Ruckerbauer; Matthias P Gerstl; Nicole Borth; Michael Hanscho; Jürgen Zanghellini
Journal:  Comput Struct Biotechnol J       Date:  2017-01-28       Impact factor: 7.271

9.  A computational framework for the automated construction of glycosylation reaction networks.

Authors:  Gang Liu; Sriram Neelamegham
Journal:  PLoS One       Date:  2014-06-30       Impact factor: 3.240

10.  A consensus-based and readable extension of Linear Code for Reaction Rules (LiCoRR).

Authors:  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; Nathan E Lewis
Journal:  Beilstein J Org Chem       Date:  2020-10-27       Impact factor: 2.883
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