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Items: 1 to 20 of 89

1.

Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks.

Clément-Ziza M, Malabat C, Weber C, Moszer I, Aittokallio T, Letondal C, Rousseau S.

Bioinformatics. 2009 Oct 1;25(19):2617-8. doi: 10.1093/bioinformatics/btp464. Epub 2009 Aug 3.

2.

OmicsViz: Cytoscape plug-in for visualizing omics data across species.

Xia T, Dickerson JA.

Bioinformatics. 2008 Nov 1;24(21):2557-8. doi: 10.1093/bioinformatics/btn473. Epub 2008 Sep 8.

3.

BioNetBuilder2.0: bringing systems biology to chicken and other model organisms.

Konieczka JH, Drew K, Pine A, Belasco K, Davey S, Yatskievych TA, Bonneau R, Antin PB.

BMC Genomics. 2009 Jul 14;10 Suppl 2:S6. doi: 10.1186/1471-2164-10-S2-S6.

4.

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

König M, Holzhütter HG.

Genome Inform. 2010;24:96-103.

PMID:
22081592
5.

The Gaggle: an open-source software system for integrating bioinformatics software and data sources.

Shannon PT, Reiss DJ, Bonneau R, Baliga NS.

BMC Bioinformatics. 2006 Mar 28;7:176.

6.

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.

Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, Fridman WH, Pagès F, Trajanoski Z, Galon J.

Bioinformatics. 2009 Apr 15;25(8):1091-3. doi: 10.1093/bioinformatics/btp101. Epub 2009 Feb 23.

7.

Integration of genomic information with biological networks using Cytoscape.

Bauer-Mehren A.

Methods Mol Biol. 2013;1021:37-61. doi: 10.1007/978-1-62703-450-0_3.

PMID:
23715979
8.

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.

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. Epub 2010 Sep 21.

PMID:
20861032
10.

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.

11.

Integration of biological networks and gene expression data using Cytoscape.

Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, Workman C, Christmas R, Avila-Campilo I, Creech M, Gross B, Hanspers K, Isserlin R, Kelley R, Killcoyne S, Lotia S, Maere S, Morris J, Ono K, Pavlovic V, Pico AR, Vailaya A, Wang PL, Adler A, Conklin BR, Hood L, Kuiper M, Sander C, Schmulevich I, Schwikowski B, Warner GJ, Ideker T, Bader GD.

Nat Protoc. 2007;2(10):2366-82.

12.

OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data.

Xia T, Hemert JV, Dickerson JA.

Bioinformatics. 2010 Dec 1;26(23):2995-6. doi: 10.1093/bioinformatics/btq583. Epub 2010 Oct 14.

13.

Atlas - a data warehouse for integrative bioinformatics.

Shah SP, Huang Y, Xu T, Yuen MM, Ling J, Ouellette BF.

BMC Bioinformatics. 2005 Feb 21;6:34.

14.

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
15.

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.

16.

Microarray data analysis.

Mohapatra SK, Krishnan A.

Methods Mol Biol. 2011;678:27-43. doi: 10.1007/978-1-60761-682-5_3.

PMID:
20931370
17.

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.

18.

ModuLand plug-in for Cytoscape: determination of hierarchical layers of overlapping network modules and community centrality.

Szalay-Beko M, Palotai R, Szappanos B, Kovács IA, Papp B, Csermely P.

Bioinformatics. 2012 Aug 15;28(16):2202-4. doi: 10.1093/bioinformatics/bts352. Epub 2012 Jun 19.

PMID:
22718784
19.

Integration of bioinformatics resources for functional analysis of gene expression and proteomic data.

Huang H, Hu ZZ, Arighi CN, Wu CH.

Front Biosci. 2007 Sep 1;12:5071-88. Review.

PMID:
17569631
20.

PathGen: a transitive gene pathway generator.

Clement K, Gustafson N, Berbert A, Carroll H, Merris C, Olsen A, Clement M, Snell Q, Allen J, Roper RJ.

Bioinformatics. 2010 Feb 1;26(3):423-5. doi: 10.1093/bioinformatics/btp661. Epub 2009 Dec 4.

PMID:
19965882

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