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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: ideker t. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. Nat Protoc. 2007. PMID: 17947979 Free PMC article.
Differential network biology.
Ideker T, Krogan NJ. Ideker T, et al. Mol Syst Biol. 2012 Jan 17;8:565. doi: 10.1038/msb.2011.99. Mol Syst Biol. 2012. PMID: 22252388 Free PMC article. Review.
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: ideker t. 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.
NeXO Web: the NeXO ontology database and visualization platform.
Dutkowski J, Ono K, Kramer M, Yu M, Pratt D, Demchak B, Ideker T. Dutkowski J, et al. Among authors: ideker t. Nucleic Acids Res. 2014 Jan;42(Database issue):D1269-74. doi: 10.1093/nar/gkt1192. Epub 2013 Nov 23. Nucleic Acids Res. 2014. PMID: 24271398 Free PMC article.
Inferring gene ontologies from pairwise similarity data.
Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Kramer M, et al. Among authors: ideker t. Bioinformatics. 2014 Jun 15;30(12):i34-42. doi: 10.1093/bioinformatics/btu282. Bioinformatics. 2014. PMID: 24932003 Free PMC article.
293 results