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A travel guide to Cytoscape plugins.
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Exploring biological networks with Cytoscape software.
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3
Linking Cytoscape and the corynebacterial reference database CoryneRegNet.
BMC Genomics. 2008 Apr 21;9:184. doi: 10.1186/1471-2164-9-184.
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Integration of biological networks and gene expression data using Cytoscape.
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Cytoscape: a community-based framework for network modeling.
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FERN - a Java framework for stochastic simulation and evaluation of reaction networks.
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Efficient key pathway mining: combining networks and OMICS data.
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GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.
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Building Transcriptional Association Networks in Cytoscape with RegNetC.
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2
Biodegradation of plastics and pesticides by soil bacteria in Bangladesh: Insights into antibiotic resistance and potential therapeutic targets.
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1
Which clustering algorithm is better for predicting protein complexes?
BMC Res Notes. 2011 Dec 20;4:549. doi: 10.1186/1756-0500-4-549.
2
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.
3
iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.
BMC Bioinformatics. 2011 Sep 26;12:380. doi: 10.1186/1471-2105-12-380.
5
PSICQUIC and PSISCORE: accessing and scoring molecular interactions.
Nat Methods. 2011 Jun 29;8(7):528-9. doi: 10.1038/nmeth.1637.
6
MINE: Module Identification in Networks.
BMC Bioinformatics. 2011 May 23;12:192. doi: 10.1186/1471-2105-12-192.
7
WordCloud: a Cytoscape plugin to create a visual semantic summary of networks.
Source Code Biol Med. 2011 Apr 7;6:7. doi: 10.1186/1751-0473-6-7.
8
Comprehensive cluster analysis with Transitivity Clustering.
Nat Protoc. 2011 Mar;6(3):285-95. doi: 10.1038/nprot.2010.197. Epub 2011 Feb 10.
9
Analyzing and visualizing residue networks of protein structures.
Trends Biochem Sci. 2011 Apr;36(4):179-82. doi: 10.1016/j.tibs.2011.01.002. Epub 2011 Feb 21.
10
PiNGO: a Cytoscape plugin to find candidate genes in biological networks.
Bioinformatics. 2011 Apr 1;27(7):1030-1. doi: 10.1093/bioinformatics/btr045. Epub 2011 Jan 28.

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