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Items: 1 to 20 of 111

1.

Clust&See: a Cytoscape plugin for the identification, visualization and manipulation of network clusters.

Spinelli L, Gambette P, Chapple CE, Robisson B, Baudot A, Garreta H, Tichit L, Guénoche A, Brun C.

Biosystems. 2013 Aug;113(2):91-5. doi: 10.1016/j.biosystems.2013.05.010. Epub 2013 Jun 3.

2.

CyClus3D: a Cytoscape plugin for clustering network motifs in integrated networks.

Audenaert P, Van Parys T, Brondel F, Pickavet M, Demeester P, Van de Peer Y, Michoel T.

Bioinformatics. 2011 Jun 1;27(11):1587-8. doi: 10.1093/bioinformatics/btr182. Epub 2011 Apr 8.

PMID:
21478195
3.

clusterMaker: a multi-algorithm clustering plugin for Cytoscape.

Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE.

BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436.

4.

CytoNCA: a cytoscape plugin for centrality analysis and evaluation of protein interaction networks.

Tang Y, Li M, Wang J, Pan Y, Wu FX.

Biosystems. 2015 Jan;127:67-72. doi: 10.1016/j.biosystems.2014.11.005. Epub 2014 Nov 15.

PMID:
25451770
5.

Visualization of protein interaction networks: problems and solutions.

Agapito G, Guzzi PH, Cannataro M.

BMC Bioinformatics. 2013;14 Suppl 1:S1. doi: 10.1186/1471-2105-14-S1-S1. Epub 2013 Jan 14.

6.

SLiMScape: a protein short linear motif analysis plugin for Cytoscape.

O'Brien KT, Haslam NJ, Shields DC.

BMC Bioinformatics. 2013 Jul 15;14:224. doi: 10.1186/1471-2105-14-224.

7.

Visualization and analysis of biological networks.

Millán PP.

Methods Mol Biol. 2013;1021:63-88. doi: 10.1007/978-1-62703-450-0_4.

PMID:
23715980
8.

GenePro: a Cytoscape plug-in for advanced visualization and analysis of interaction networks.

Vlasblom J, Wu S, Pu S, Superina M, Liu G, Orsi C, Wodak SJ.

Bioinformatics. 2006 Sep 1;22(17):2178-9.

PMID:
16921162
9.

CytoCluster: A Cytoscape Plugin for Cluster Analysis and Visualization of Biological Networks.

Li M, Li D, Tang Y, Wu F, Wang J.

Int J Mol Sci. 2017 Aug 31;18(9). pii: E1880. doi: 10.3390/ijms18091880.

10.

DrugViz: a Cytoscape plugin for visualizing and analyzing small molecule drugs in biological networks.

Xiong B, Liu K, Wu J, Burk DL, Jiang H, Shen J.

Bioinformatics. 2008 Sep 15;24(18):2117-8. doi: 10.1093/bioinformatics/btn389. Epub 2008 Jul 25.

PMID:
18658180
11.

BioQuali Cytoscape plugin: analysing the global consistency of regulatory networks.

Guziolowski C, Bourdé A, Moreews F, Siegel A.

BMC Genomics. 2009 May 26;10:244. doi: 10.1186/1471-2164-10-244.

12.

iCTNet: a Cytoscape plugin to produce and analyze integrative complex traits networks.

Wang L, Khankhanian P, Baranzini SE, Mousavi P.

BMC Bioinformatics. 2011 Sep 26;12:380. doi: 10.1186/1471-2105-12-380.

13.

Cytoscape ESP: simple search of complex biological networks.

Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ.

Bioinformatics. 2008 Jun 15;24(12):1465-6. doi: 10.1093/bioinformatics/btn208. Epub 2008 Apr 28.

14.

GALANT: a Cytoscape plugin for visualizing data as functional landscapes projected onto biological networks.

Camilo E, Bovolenta LA, Acencio ML, Rybarczyk-Filho JL, Castro MA, Moreira JC, Lemke N.

Bioinformatics. 2013 Oct 1;29(19):2505-6. doi: 10.1093/bioinformatics/btt377. Epub 2013 Jul 26.

PMID:
23894138
15.

MODEVO: exploring modularity and evolution of protein interaction networks.

Woźniak M, Tiuryn J, Dutkowski J.

Bioinformatics. 2010 Jul 15;26(14):1790-1. doi: 10.1093/bioinformatics/btq274. Epub 2010 May 27.

PMID:
20507893
16.

BiNoM 2.0, a Cytoscape plugin for accessing and analyzing pathways using standard systems biology formats.

Bonnet E, Calzone L, Rovera D, Stoll G, Barillot E, Zinovyev A.

BMC Syst Biol. 2013 Mar 1;7:18. doi: 10.1186/1752-0509-7-18.

17.

Network Analysis Tools: from biological networks to clusters and pathways.

Brohée S, Faust K, Lima-Mendez G, Vanderstocken G, van Helden J.

Nat Protoc. 2008;3(10):1616-29. doi: 10.1038/nprot.2008.100.

PMID:
18802442
18.

Flexible network reconstruction from relational databases with Cytoscape and CytoSQL.

Laukens K, Hollunder J, Dang TH, De Jaeger G, Kuiper M, Witters E, Verschoren A, Van Leemput K.

BMC Bioinformatics. 2010 Jul 1;11:360. doi: 10.1186/1471-2105-11-360.

19.

NOA: a cytoscape plugin for network ontology analysis.

Zhang C, Wang J, Hanspers K, Xu D, Chen L, Pico AR.

Bioinformatics. 2013 Aug 15;29(16):2066-7. doi: 10.1093/bioinformatics/btt334. Epub 2013 Jun 7.

20.

Decomposing protein networks into domain-domain interactions.

Albrecht M, Huthmacher C, Tosatto SC, Lengauer T.

Bioinformatics. 2005 Sep 1;21 Suppl 2:ii220-1.

PMID:
16204107

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