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Cytoscape app store.
Lotia S, Montojo J, Dong Y, Bader GD, Pico AR. Lotia S, et al. Among authors: bader gd. Bioinformatics. 2013 May 15;29(10):1350-1. doi: 10.1093/bioinformatics/btt138. Epub 2013 Apr 16. Bioinformatics. 2013. PMID: 23595664 Free PMC article.
NetMatch: a Cytoscape plugin for searching biological networks.
Ferro A, Giugno R, Pigola G, Pulvirenti A, Skripin D, Bader GD, Shasha D. Ferro A, et al. Among authors: bader gd. Bioinformatics. 2007 Apr 1;23(7):910-2. doi: 10.1093/bioinformatics/btm032. Epub 2007 Feb 3. Bioinformatics. 2007. PMID: 17277332
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. Cline MS, et al. Among authors: bader gd. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. Nat Protoc. 2007. PMID: 17947979 Free PMC article.
Cytoscape ESP: simple search of complex biological networks.
Ashkenazi M, Bader GD, Kuchinsky A, Moshelion M, States DJ. Ashkenazi M, et al. Among authors: bader gd. Bioinformatics. 2008 Jun 15;24(12):1465-6. doi: 10.1093/bioinformatics/btn208. Epub 2008 Apr 28. Bioinformatics. 2008. PMID: 18445605 Free PMC article.
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. Warde-Farley D, et al. Among authors: bader gd. Nucleic Acids Res. 2010 Jul;38(Web Server issue):W214-20. doi: 10.1093/nar/gkq537. Nucleic Acids Res. 2010. PMID: 20576703 Free PMC article.
Cytoscape Web: an interactive web-based network browser.
Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, Bader GD. Lopes CT, et al. Among authors: bader gd. Bioinformatics. 2010 Sep 15;26(18):2347-8. doi: 10.1093/bioinformatics/btq430. Epub 2010 Jul 23. Bioinformatics. 2010. PMID: 20656902 Free PMC article.
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. Montojo J, et al. Among authors: bader gd. Bioinformatics. 2010 Nov 15;26(22):2927-8. doi: 10.1093/bioinformatics/btq562. Epub 2010 Oct 5. Bioinformatics. 2010. PMID: 20926419 Free PMC article.
clusterMaker: a multi-algorithm clustering plugin for Cytoscape.
Morris JH, Apeltsin L, Newman AM, Baumbach J, Wittkop T, Su G, Bader GD, Ferrin TE. Morris JH, et al. Among authors: bader gd. BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436. BMC Bioinformatics. 2011. PMID: 22070249 Free PMC article.
A travel guide to Cytoscape plugins.
Saito R, Smoot ME, Ono K, Ruscheinski J, Wang PL, Lotia S, Pico AR, Bader GD, Ideker T. Saito R, et al. Among authors: bader gd. Nat Methods. 2012 Nov;9(11):1069-76. doi: 10.1038/nmeth.2212. Epub 2012 Nov 6. Nat Methods. 2012. PMID: 23132118 Free PMC article.
352 results