Literature DB >> 24413519

MetDraw: automated visualization of genome-scale metabolic network reconstructions and high-throughput data.

Paul A Jensen1, Jason A Papin.   

Abstract

MOTIVATION: Metabolic reaction maps allow visualization of genome-scale models and high-throughput data in a format familiar to many biologists. However, creating a map of a large metabolic model is a difficult and time-consuming process. MetDraw fully automates the map-drawing process for metabolic models containing hundreds to thousands of reactions. MetDraw can also overlay high-throughput 'omics' data directly on the generated maps.

Mesh：

Year:  2014        PMID： 24413519      PMCID： PMC3998126          DOI： 10.1093/bioinformatics/btt758

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


  7 in total

1.  Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Authors:  Paul Shannon; Andrew Markiel; Owen Ozier; Nitin S Baliga; Jonathan T Wang; Daniel Ramage; Nada Amin; Benno Schwikowski; Trey Ideker
Journal:  Genome Res       Date:  2003-11       Impact factor: 9.043

2.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.

Authors:  Jan Schellenberger; Richard Que; Ronan M T Fleming; Ines Thiele; Jeffrey D Orth; Adam M Feist; Daniel C Zielinski; Aarash Bordbar; Nathan E Lewis; Sorena Rahmanian; Joseph Kang; Daniel R Hyduke; Bernhard Ø Palsson
Journal:  Nat Protoc       Date:  2011-08-04       Impact factor: 13.491

Review 3.  Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.

Authors:  Nathan E Lewis; Harish Nagarajan; Bernhard O Palsson
Journal:  Nat Rev Microbiol       Date:  2012-02-27       Impact factor: 60.633

4.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

Authors:  Jeffrey D Orth; Tom M Conrad; Jessica Na; Joshua A Lerman; Hojung Nam; Adam M Feist; Bernhard Ø Palsson
Journal:  Mol Syst Biol       Date:  2011-10-11       Impact factor: 11.429

5.  KEGG for integration and interpretation of large-scale molecular data sets.

Authors:  Minoru Kanehisa; Susumu Goto; Yoko Sato; Miho Furumichi; Mao Tanabe
Journal:  Nucleic Acids Res       Date:  2011-11-10       Impact factor: 16.971

6.  Structural and functional analysis of cellular networks with CellNetAnalyzer.

Authors:  Steffen Klamt; Julio Saez-Rodriguez; Ernst D Gilles
Journal:  BMC Syst Biol       Date:  2007-01-08

Review 7.  Applications of genome-scale metabolic reconstructions.

Authors:  Matthew A Oberhardt; Bernhard Ø Palsson; Jason A Papin
Journal:  Mol Syst Biol       Date:  2009-11-03       Impact factor: 11.429
  7 in total
  13 in total

1.  Metabolic network-guided binning of metagenomic sequence fragments.

Authors:  Matthew B Biggs; Jason A Papin
Journal:  Bioinformatics       Date:  2015-11-14       Impact factor: 6.937

2.  Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria.

Authors:  Paul A Jensen; Zeyu Zhu; Tim van Opijnen
Journal:  Cell Rep       Date:  2017-08-15       Impact factor: 9.423

3.  Mimoza: web-based semantic zooming and navigation in metabolic networks.

Authors:  Anna Zhukova; David J Sherman
Journal:  BMC Syst Biol       Date:  2015-02-26

4.  An integrated network visualization framework towards metabolic engineering applications.

Authors:  Alberto Noronha; Paulo Vilaça; Miguel Rocha
Journal:  BMC Bioinformatics       Date:  2014-12-30       Impact factor: 3.169

5.  Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0.

Authors:  Brian R Granger; Yi-Chien Chang; Yan Wang; Charles DeLisi; Daniel Segrè; Zhenjun Hu
Journal:  PLoS Comput Biol       Date:  2016-04-15       Impact factor: 4.475

6.  FindPrimaryPairs: An efficient algorithm for predicting element-transferring reactant/product pairs in metabolic networks.

Authors:  Jon Lund Steffensen; Keith Dufault-Thompson; Ying Zhang
Journal:  PLoS One       Date:  2018-02-15       Impact factor: 3.240

7.  ReconMap: an interactive visualization of human metabolism.

Authors:  Alberto Noronha; Anna Dröfn Daníelsdóttir; Piotr Gawron; Freyr Jóhannsson; Soffía Jónsdóttir; Sindri Jarlsson; Jón Pétur Gunnarsson; Sigurður Brynjólfsson; Reinhard Schneider; Ines Thiele; Ronan M T Fleming
Journal:  Bioinformatics       Date:  2017-02-15       Impact factor: 6.937

8.  Reconstruction of the metabolic network of Pseudomonas aeruginosa to interrogate virulence factor synthesis.

Authors:  Jennifer A Bartell; Anna S Blazier; Phillip Yen; Juliane C Thøgersen; Lars Jelsbak; Joanna B Goldberg; Jason A Papin
Journal:  Nat Commun       Date:  2017-03-07       Impact factor: 14.919

9.  Reconciled rat and human metabolic networks for comparative toxicogenomics and biomarker predictions.

Authors:  Edik M Blais; Kristopher D Rawls; Bonnie V Dougherty; Zhuo I Li; Glynis L Kolling; Ping Ye; Anders Wallqvist; Jason A Papin
Journal:  Nat Commun       Date:  2017-02-08       Impact factor: 14.919

Review 10.  Computational approaches for microalgal biofuel optimization: a review.

Authors:  Joseph Koussa; Amphun Chaiboonchoe; Kourosh Salehi-Ashtiani
Journal:  Biomed Res Int       Date:  2014-09-21       Impact factor: 3.411
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