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Items: 1 to 20 of 165

1.

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.

2.

The GeneMANIA prediction server: biological network integration for gene prioritization and predicting gene function.

Warde-Farley D, Donaldson SL, Comes O, Zuberi K, Badrawi R, Chao P, Franz M, Grouios C, Kazi F, Lopes CT, Maitland A, Mostafavi S, Montojo J, Shao Q, Wright G, Bader GD, Morris Q.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214-20. doi: 10.1093/nar/gkq537.

3.

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.

4.

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.

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.

6.

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.

7.

GeneMANIA prediction server 2013 update.

Zuberi K, Franz M, Rodriguez H, Montojo J, Lopes CT, Bader GD, Morris Q.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W115-22. doi: 10.1093/nar/gkt533.

8.

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.

9.

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.

10.

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.

11.

GeneMANIA: Fast gene network construction and function prediction for Cytoscape.

Montojo J, Zuberi K, Rodriguez H, Bader GD, Morris Q.

F1000Res. 2014 Jul 1;3:153. doi: 10.12688/f1000research.4572.1.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

NetAtlas: a Cytoscape plugin to examine signaling networks based on tissue gene expression.

Yang L, Walker JR, Hogenesch JB, Thomas RS.

In Silico Biol. 2008;8(1):47-52.

PMID:
18430989
18.

CABIN: collective analysis of biological interaction networks.

Singhal M, Domico K.

Comput Biol Chem. 2007 Jun;31(3):222-5.

PMID:
17500038
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.

20.

PerturbationAnalyzer: a tool for investigating the effects of concentration perturbation on protein interaction networks.

Li F, Li P, Xu W, Peng Y, Bo X, Wang S.

Bioinformatics. 2010 Jan 15;26(2):275-7. doi: 10.1093/bioinformatics/btp634.

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