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Items: 1 to 20 of 142

1.

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.

2.

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
3.

KeyPathwayMiner 4.0: condition-specific pathway analysis by combining multiple omics studies and networks with Cytoscape.

Alcaraz N, Pauling J, Batra R, Barbosa E, Junge A, Christensen AG, Azevedo V, Ditzel HJ, Baumbach J.

BMC Syst Biol. 2014 Aug 19;8:99. doi: 10.1186/s12918-014-0099-x.

4.

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
5.

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.

6.

OpenStructure: a flexible software framework for computational structural biology.

Biasini M, Mariani V, Haas J, Scheuber S, Schenk AD, Schwede T, Philippsen A.

Bioinformatics. 2010 Oct 15;26(20):2626-8. doi: 10.1093/bioinformatics/btq481. Epub 2010 Aug 23.

7.

Cytoscape.js: a graph theory library for visualisation and analysis.

Franz M, Lopes CT, Huck G, Dong Y, Sumer O, Bader GD.

Bioinformatics. 2016 Jan 15;32(2):309-11. doi: 10.1093/bioinformatics/btv557. Epub 2015 Sep 28.

8.

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.

9.

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.

10.

Cytoscape app store.

Lotia S, Montojo J, Dong Y, Bader GD, Pico AR.

Bioinformatics. 2013 May 15;29(10):1350-1. doi: 10.1093/bioinformatics/btt138. Epub 2013 Apr 16.

11.

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

König M, Holzhütter HG.

Genome Inform. 2010;24:96-103.

PMID:
22081592
12.

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.

13.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.

Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.

Genome Res. 2003 Nov;13(11):2498-504.

14.

EGAN: exploratory gene association networks.

Paquette J, Tokuyasu T.

Bioinformatics. 2010 Jan 15;26(2):285-6. doi: 10.1093/bioinformatics/btp656. Epub 2009 Nov 23.

15.

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.

16.

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.

17.

DeDaL: Cytoscape 3 app for producing and morphing data-driven and structure-driven network layouts.

Czerwinska U, Calzone L, Barillot E, Zinovyev A.

BMC Syst Biol. 2015 Aug 14;9:46. doi: 10.1186/s12918-015-0189-4.

18.

BALL--biochemical algorithms library 1.3.

Hildebrandt A, Dehof AK, Rurainski A, Bertsch A, Schumann M, Toussaint NC, Moll A, Stöckel D, Nickels S, Mueller SC, Lenhof HP, Kohlbacher O.

BMC Bioinformatics. 2010 Oct 25;11:531. doi: 10.1186/1471-2105-11-531.

19.

VistaClara: an expression browser plug-in for Cytoscape.

Kincaid R, Kuchinsky A, Creech M.

Bioinformatics. 2008 Sep 15;24(18):2112-4. doi: 10.1093/bioinformatics/btn368. Epub 2008 Aug 4.

20.

cddApp: a Cytoscape app for accessing the NCBI conserved domain database.

Morris JH, Wu A, Yamashita RA, Marchler-Bauer A, Ferrin TE.

Bioinformatics. 2015 Jan 1;31(1):134-6. doi: 10.1093/bioinformatics/btu605. Epub 2014 Sep 10.

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