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Items: 1 to 20 of 168

1.

PiNGO: a Cytoscape plugin to find candidate genes in biological networks.

Smoot M, Ono K, Ideker T, Maere S.

Bioinformatics. 2011 Apr 1;27(7):1030-1. doi: 10.1093/bioinformatics/btr045. Epub 2011 Jan 28.

2.

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.

3.

GeneMANIA Cytoscape plugin: fast gene function predictions on the desktop.

Montojo J, Zuberi K, Rodriguez H, Kazi F, Wright G, Donaldson SL, Morris Q, Bader GD.

Bioinformatics. 2010 Nov 15;26(22):2927-8. doi: 10.1093/bioinformatics/btq562. Epub 2010 Oct 5.

4.

Mosaic: making biological sense of complex networks.

Zhang C, Hanspers K, Kuchinsky A, Salomonis N, Xu D, Pico AR.

Bioinformatics. 2012 Jul 15;28(14):1943-4. doi: 10.1093/bioinformatics/bts278. Epub 2012 May 9.

5.

JEPETTO: a Cytoscape plugin for gene set enrichment and topological analysis based on interaction networks.

Winterhalter C, Widera P, Krasnogor N.

Bioinformatics. 2014 Apr 1;30(7):1029-30. doi: 10.1093/bioinformatics/btt732. Epub 2013 Dec 19.

6.

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
7.

CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data.

Bindea G, Galon J, Mlecnik B.

Bioinformatics. 2013 Mar 1;29(5):661-3. doi: 10.1093/bioinformatics/btt019. Epub 2013 Jan 16.

8.

DisGeNET: a Cytoscape plugin to visualize, integrate, search and analyze gene-disease networks.

Bauer-Mehren A, Rautschka M, Sanz F, Furlong LI.

Bioinformatics. 2010 Nov 15;26(22):2924-6. doi: 10.1093/bioinformatics/btq538. Epub 2010 Sep 21.

PMID:
20861032
9.

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.

10.

Integrating and annotating the interactome using the MiMI plugin for cytoscape.

Gao J, Ade AS, Tarcea VG, Weymouth TE, Mirel BR, Jagadish HV, States DJ.

Bioinformatics. 2009 Jan 1;25(1):137-8. doi: 10.1093/bioinformatics/btn501. Epub 2008 Sep 23.

11.

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
12.

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
13.

Integrative platform to translate gene sets to networks.

Laakso M, Hautaniemi S.

Bioinformatics. 2010 Jul 15;26(14):1802-3. doi: 10.1093/bioinformatics/btq277. Epub 2010 May 27.

PMID:
20507894
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.

SpotXplore: a Cytoscape plugin for visual exploration of hotspot expression in gene regulatory networks.

Westenberg MA, Roerdink JB, Kuipers OP, van Hijum SA.

Bioinformatics. 2010 Nov 15;26(22):2922-3. doi: 10.1093/bioinformatics/btq535. Epub 2010 Sep 21.

16.

The Cyni framework for network inference in Cytoscape.

Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B.

Bioinformatics. 2015 May 1;31(9):1499-501. doi: 10.1093/bioinformatics/btu812. Epub 2014 Dec 18.

17.

ReNE: a cytoscape plugin for regulatory network enhancement.

Politano G, Benso A, Savino A, Di Carlo S.

PLoS One. 2014 Dec 26;9(12):e115585. doi: 10.1371/journal.pone.0115585. eCollection 2014.

18.

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.

19.

GESTODIFFERENT: a Cytoscape plugin for the generation and the identification of gene regulatory networks describing a stochastic cell differentiation process.

Antoniotti M, Bader GD, Caravagna G, Crippa S, Graudenzi A, Mauri G.

Bioinformatics. 2013 Feb 15;29(4):513-4. doi: 10.1093/bioinformatics/bts726. Epub 2013 Jan 3.

20.

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.

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