Literature DB >> 16287939

PATIKAweb: a Web interface for analyzing biological pathways through advanced querying and visualization.

U Dogrusoz1, E Z Erson, E Giral, E Demir, O Babur, A Cetintas, R Colak.   

Abstract

Patikaweb provides a Web interface for retrieving and analyzing biological pathways in the Patika database, which contains data integrated from various prominent public pathway databases. It features a user-friendly interface, dynamic visualization and automated layout, advanced graph-theoretic queries for extracting biologically important phenomena, local persistence capability and exporting facilities to various pathway exchange formats.

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Year:  2005        PMID： 16287939     DOI： 10.1093/bioinformatics/bti776

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


  20 in total

1.  AVIS: AJAX viewer of interactive signaling networks.

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Journal:  Bioinformatics       Date:  2007-09-12       Impact factor: 6.937

Review 2.  Network integration and graph analysis in mammalian molecular systems biology.

Authors:  A Ma'ayan
Journal:  IET Syst Biol       Date:  2008-09       Impact factor: 1.615

3.  Network2Canvas: network visualization on a canvas with enrichment analysis.

Authors:  Christopher M Tan; Edward Y Chen; Ruth Dannenfelser; Neil R Clark; Avi Ma'ayan
Journal:  Bioinformatics       Date:  2013-06-07       Impact factor: 6.937

4.  FNV: light-weight flash-based network and pathway viewer.

Authors:  Ruth Dannenfelser; Alexander Lachmann; Mariola Szenk; Avi Ma'ayan
Journal:  Bioinformatics       Date:  2011-02-23       Impact factor: 6.937

Review 5.  Visualization of omics data for systems biology.

Authors:  Nils Gehlenborg; Seán I O'Donoghue; Nitin S Baliga; Alexander Goesmann; Matthew A Hibbs; Hiroaki Kitano; Oliver Kohlbacher; Heiko Neuweger; Reinhard Schneider; Dan Tenenbaum; Anne-Claude Gavin
Journal:  Nat Methods       Date:  2010-03       Impact factor: 28.547

Review 6.  Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review.

Authors:  Peter Csermely; Tamás Korcsmáros; Huba J M Kiss; Gábor London; Ruth Nussinov
Journal:  Pharmacol Ther       Date:  2013-02-04       Impact factor: 12.310

7.  An efficient biological pathway layout algorithm combining grid-layout and spring embedder for complicated cellular location information.

Authors:  Kaname Kojima; Masao Nagasaki; Satoru Miyano
Journal:  BMC Bioinformatics       Date:  2010-06-18       Impact factor: 3.169

8.  Algorithms for effective querying of compound graph-based pathway databases.

Authors:  Ugur Dogrusoz; Ahmet Cetintas; Emek Demir; Ozgun Babur
Journal:  BMC Bioinformatics       Date:  2009-11-16       Impact factor: 3.169

9.  FORG3D: force-directed 3D graph editor for visualization of integrated genome scale data.

Authors:  Jussi Paananen; Garry Wong
Journal:  BMC Syst Biol       Date:  2009-02-24

10.  SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks.

Authors:  Pablo Minguez; Stefan Götz; David Montaner; Fatima Al-Shahrour; Joaquin Dopazo
Journal:  Nucleic Acids Res       Date:  2009-05-19       Impact factor: 16.971
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