Literature DB >> 18819078

Exploring biological networks with Cytoscape software.

Natalie Yeung1, Melissa S Cline, Allan Kuchinsky, Michael E Smoot, Gary D Bader.   

Abstract

Cytoscape is a free software package for visualizing, modeling, and analyzing molecular and genetic interaction networks. As a key feature, Cytoscape enables biologists to determine and analyze the interconnectivity of a list of genes or proteins. This unit explains how to use Cytoscape to load and navigate biological network information and view mRNA expression profiles and other functional genomics and proteomics data in the context of the network obtained for genes of interest. Additional analyses that can be performed with Cytoscape are also discussed. (c) 2008 by John Wiley & Sons, Inc.

Mesh：

Year:  2008        PMID： 18819078     DOI： 10.1002/0471250953.bi0813s23

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  28 in total

1.  Genome annotation and intraviral interactome for the Streptococcus pneumoniae virulent phage Dp-1.

Authors:  Mourad Sabri; Roman Häuser; Marc Ouellette; Jing Liu; Mohammed Dehbi; Greg Moeck; Ernesto García; Björn Titz; Peter Uetz; Sylvain Moineau
Journal:  J Bacteriol       Date:  2010-11-19       Impact factor: 3.490

2.  ChiBE: interactive visualization and manipulation of BioPAX pathway models.

Authors:  Ozgun Babur; Ugur Dogrusoz; Emek Demir; Chris Sander
Journal:  Bioinformatics       Date:  2009-12-09       Impact factor: 6.937

3.  iCAVE: an open source tool for visualizing biomolecular networks in 3D, stereoscopic 3D and immersive 3D.

Authors:  Vaja Liluashvili; Selim Kalayci; Eugene Fluder; Manda Wilson; Aaron Gabow; Zeynep H Gümüs
Journal:  Gigascience       Date:  2017-08-01       Impact factor: 6.524

4.  Molecular profiling of postnatal development of the hypothalamus in female and male rats.

Authors:  Deena M Walker; Dean Kirson; Lorenzo F Perez; Andrea C Gore
Journal:  Biol Reprod       Date:  2012-12-06       Impact factor: 4.285

5.  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

6.  VISIBIOweb: visualization and layout services for BioPAX pathway models.

Authors:  Alptug Dilek; Mehmet E Belviranli; Ugur Dogrusoz
Journal:  Nucleic Acids Res       Date:  2010-05-11       Impact factor: 16.971

7.  The mEPN scheme: an intuitive and flexible graphical system for rendering biological pathways.

Authors:  Tom C Freeman; Sobia Raza; Athanasios Theocharidis; Peter Ghazal
Journal:  BMC Syst Biol       Date:  2010-05-17

8.  A phenotypic screening platform to identify small molecule modulators of Chlamydomonas reinhardtii growth, motility and photosynthesis.

Authors:  Simon E Alfred; Anuradha Surendra; Chris Le; Ken Lin; Alexander Mok; Iain M Wallace; Michael Proctor; Malene L Urbanus; Guri Giaever; Corey Nislow
Journal:  Genome Biol       Date:  2012-11-18       Impact factor: 13.583

9.  Systems integration of biodefense omics data for analysis of pathogen-host interactions and identification of potential targets.

Authors:  Peter B McGarvey; Hongzhan Huang; Raja Mazumder; Jian Zhang; Yongxing Chen; Chengdong Zhang; Stephen Cammer; Rebecca Will; Margie Odle; Bruno Sobral; Margaret Moore; Cathy H Wu
Journal:  PLoS One       Date:  2009-09-25       Impact factor: 3.240

10.  Use of GenMAPP and MAPPFinder to analyse pathways involved in chickens infected with the protozoan parasite Eimeria.

Authors:  Dennis Prickett; Michael Watson
Journal:  BMC Proc       Date:  2009-07-16
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