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Items: 1 to 20 of 184

1.

Cytoscape: a community-based framework for network modeling.

Killcoyne S, Carter GW, Smith J, Boyle J.

Methods Mol Biol. 2009;563:219-39. doi: 10.1007/978-1-60761-175-2_12.

PMID:
19597788
2.

CytoITMprobe: a network information flow plugin for Cytoscape.

Stojmirović A, Bliskovsky A, Yu YK.

BMC Res Notes. 2012 May 15;5:237. doi: 10.1186/1756-0500-5-237.

3.

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
4.

BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.

Maere S, Heymans K, Kuiper M.

Bioinformatics. 2005 Aug 15;21(16):3448-9. Epub 2005 Jun 21.

PMID:
15972284
5.

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.

6.

Cytoscape 2.8: new features for data integration and network visualization.

Smoot ME, Ono K, Ruscheinski J, Wang PL, Ideker T.

Bioinformatics. 2011 Feb 1;27(3):431-2. doi: 10.1093/bioinformatics/btq675. Epub 2010 Dec 12.

7.

NetMatch: a Cytoscape plugin for searching biological networks.

Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D.

Bioinformatics. 2007 Apr 1;23(7):910-2. Epub 2007 Feb 3.

PMID:
17277332
8.

Orthoscape: a cytoscape application for grouping and visualization KEGG based gene networks by taxonomy and homology principles.

Mustafin ZS, Lashin SA, Matushkin YG, Gunbin KV, Afonnikov DA.

BMC Bioinformatics. 2017 Jan 27;18(Suppl 1):1427. doi: 10.1186/s12859-016-1427-5.

9.

PetriScape - A plugin for discrete Petri net simulations in Cytoscape.

Almeida D, Azevedo V, Silva A, Baumbach J.

J Integr Bioinform. 2016 Jun 4;13(1):284. doi: 10.2390/biecoll-jib-2016-284.

PMID:
27402693
10.

Computing graphlet signatures of network nodes and motifs in Cytoscape with GraphletCounter.

Whelan C, Sönmez K.

Bioinformatics. 2012 Jan 15;28(2):290-1. doi: 10.1093/bioinformatics/btr637. Epub 2011 Dec 6.

PMID:
22155862
11.

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
12.

BioNetBuilder: automatic integration of biological networks.

Avila-Campillo I, Drew K, Lin J, Reiss DJ, Bonneau R.

Bioinformatics. 2007 Feb 1;23(3):392-3. Epub 2006 Nov 30.

PMID:
17138585
13.

Building Transcriptional Association Networks in Cytoscape with RegNetC.

Nepomuceno-Chamorro IA, Marquez-Chamorro A, Aguilar-Ruiz JS.

IEEE/ACM Trans Comput Biol Bioinform. 2015 Jul-Aug;12(4):823-4. doi: 10.1109/TCBB.2014.2385702.

PMID:
26357322
14.

Biological Network Inference and analysis using SEBINI and CABIN.

Taylor R, Singhal M.

Methods Mol Biol. 2009;541:551-76. doi: 10.1007/978-1-59745-243-4_24. Review.

PMID:
19381531
15.

An integrated network visualization framework towards metabolic engineering applications.

Noronha A, Vilaça P, Rocha M.

BMC Bioinformatics. 2014 Dec 30;15:420. doi: 10.1186/s12859-014-0420-0.

16.

BiNoM: a Cytoscape plugin for manipulating and analyzing biological networks.

Zinovyev A, Viara E, Calzone L, Barillot E.

Bioinformatics. 2008 Mar 15;24(6):876-7. Epub 2007 Nov 16.

PMID:
18024474
17.

Logical modelling of regulatory networks with GINsim 2.3.

Naldi A, Berenguier D, Fauré A, Lopez F, Thieffry D, Chaouiya C.

Biosystems. 2009 Aug;97(2):134-9. doi: 10.1016/j.biosystems.2009.04.008. Epub 2009 May 6.

PMID:
19426782
18.

CySBGN: a Cytoscape plug-in to integrate SBGN maps.

Gonçalves E, van Iersel M, Saez-Rodriguez J.

BMC Bioinformatics. 2013 Jan 16;14:17. doi: 10.1186/1471-2105-14-17.

19.

Fluxviz - Cytoscape plug-in for visualization of flux distributions in networks.

König M, Holzhütter HG.

Genome Inform. 2010;24:96-103.

PMID:
22081592
20.

structureViz: linking Cytoscape and UCSF Chimera.

Morris JH, Huang CC, Babbitt PC, Ferrin TE.

Bioinformatics. 2007 Sep 1;23(17):2345-7. Epub 2007 Jul 10.

PMID:
17623706

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