Literature DB >> 20976032

Information Visualization Techniques in Bioinformatics during the Postgenomic Era.

Ying Tao1, Yang Liu, Carol Friedman, Yves A Lussier.   

Abstract

Information visualization techniques, which take advantage of the bandwidth of human vision, are powerful tools for organizing and analyzing a large amount of data. In the postgenomic era, information visualization tools are indispensable for biomedical research. This paper aims to present an overview of current applications of information visualization techniques in bioinformatics for visualizing different types of biological data, such as from genomics, proteomics, expression profiling and structural studies. Finally, we discuss the challenges of information visualization in bioinformatics related to dealing with more complex biological information in the emerging fields of systems biology and systems medicine.

Entities:  

Year:  2004        PMID: 20976032      PMCID: PMC2957900          DOI: 10.1016/S1741-8364(04)02423-0

Source DB:  PubMed          Journal:  Drug Discov Today Biosilico        ISSN: 1741-8364


  59 in total

1.  The TRANSPATH signal transduction database: a knowledge base on signal transduction networks.

Authors:  F Schacherer; C Choi; U Götze; M Krull; S Pistor; E Wingender
Journal:  Bioinformatics       Date:  2001-11       Impact factor: 6.937

2.  Visualizing plant metabolomic correlation networks using clique-metabolite matrices.

Authors:  F Kose; W Weckwerth; T Linke; O Fiehn
Journal:  Bioinformatics       Date:  2001-12       Impact factor: 6.937

3.  MolMovDB: analysis and visualization of conformational change and structural flexibility.

Authors:  Nathaniel Echols; Duncan Milburn; Mark Gerstein
Journal:  Nucleic Acids Res       Date:  2003-01-01       Impact factor: 16.971

4.  Phylo-VISTA: interactive visualization of multiple DNA sequence alignments.

Authors:  Nameeta Shah; Olivier Couronne; Len A Pennacchio; Michael Brudno; Serafim Batzoglou; E Wes Bethel; Edward M Rubin; Bernd Hamann; Inna Dubchak
Journal:  Bioinformatics       Date:  2004-01-22       Impact factor: 6.937

5.  CNplot: visualizing pre-clustered networks.

Authors:  Nizar N Batada
Journal:  Bioinformatics       Date:  2004-02-10       Impact factor: 6.937

6.  Cluster analysis and display of genome-wide expression patterns.

Authors:  M B Eisen; P T Spellman; P O Brown; D Botstein
Journal:  Proc Natl Acad Sci U S A       Date:  1998-12-08       Impact factor: 11.205

7.  A cophylogenetic perspective of RNA-virus evolution.

Authors:  Andrew P Jackson; Michael A Charleston
Journal:  Mol Biol Evol       Date:  2003-08-29       Impact factor: 16.240

8.  Omic space: coordinate-based integration and analysis of genomic phenomic interactions.

Authors:  Tetsuro Toyoda; Akiyoshi Wada
Journal:  Bioinformatics       Date:  2004-03-22       Impact factor: 6.937

9.  GeneViTo: visualizing gene-product functional and structural features in genomic datasets.

Authors:  Georgios S Vernikos; Christos G Gkogkas; Vasilis J Promponas; Stavros J Hamodrakas
Journal:  BMC Bioinformatics       Date:  2003-10-31       Impact factor: 3.169

10.  Visualization and analysis of microarray and gene ontology data with treemaps.

Authors:  Eric H Baehrecke; Niem Dang; Ketan Babaria; Ben Shneiderman
Journal:  BMC Bioinformatics       Date:  2004-06-28       Impact factor: 3.169

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  15 in total

1.  Visualizing information across multidimensional post-genomic structured and textual databases.

Authors:  Ying Tao; Carol Friedman; Yves A Lussier
Journal:  Bioinformatics       Date:  2004-12-14       Impact factor: 6.937

2.  Interpretation of differential gene expression results of RNA-seq data: review and integration.

Authors:  Adam McDermaid; Brandon Monier; Jing Zhao; Bingqiang Liu; Qin Ma
Journal:  Brief Bioinform       Date:  2019-11-27       Impact factor: 11.622

3.  Consistent visualizations of changing knowledge.

Authors:  Hannah J Tipney; Ronald P Schuyler; Lawrence Hunter
Journal:  Summit Transl Bioinform       Date:  2009-03-01

4.  Visualizing meta-features in proteomic maps.

Authors:  Eugenia G Giannopoulou; George Lepouras; Elias S Manolakos
Journal:  BMC Bioinformatics       Date:  2011-07-28       Impact factor: 3.169

5.  WebGestalt: an integrated system for exploring gene sets in various biological contexts.

Authors:  Bing Zhang; Stefan Kirov; Jay Snoddy
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

6.  TreeDyn: towards dynamic graphics and annotations for analyses of trees.

Authors:  François Chevenet; Christine Brun; Anne-Laure Bañuls; Bernard Jacq; Richard Christen
Journal:  BMC Bioinformatics       Date:  2006-10-10       Impact factor: 3.169

7.  Pathway projector: web-based zoomable pathway browser using KEGG atlas and Google Maps API.

Authors:  Nobuaki Kono; Kazuharu Arakawa; Ryu Ogawa; Nobuhiro Kido; Kazuki Oshita; Keita Ikegami; Satoshi Tamaki; Masaru Tomita
Journal:  PLoS One       Date:  2009-11-11       Impact factor: 3.240

8.  OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology.

Authors:  Kieran O'Neill; Alexander Garcia; Anita Schwegmann; Rafael C Jimenez; Dan Jacobson; Henning Hermjakob
Journal:  BMC Bioinformatics       Date:  2008-10-16       Impact factor: 3.169

9.  JNets: exploring networks by integrating annotation.

Authors:  Jamie I Macpherson; John W Pinney; David L Robertson
Journal:  BMC Bioinformatics       Date:  2009-03-26       Impact factor: 3.169

10.  An exploration of alternative visualisations of the basic helix-loop-helix protein interaction network.

Authors:  Brian J Holden; John W Pinney; Simon C Lovell; Grigoris D Amoutzias; David L Robertson
Journal:  BMC Bioinformatics       Date:  2007-08-06       Impact factor: 3.169

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