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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: ono k. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. Nat Protoc. 2007. PMID: 17947979 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: ono k. 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: ono k. 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.
The Cytoscape app article collection.
Pico AR, Bader GD, Demchak B, Guitart Pla O, Hull T, Longabaugh W, Lopes C, Lotia S, Molenaar P, Montojo J, Morris JH, Ono K, Schwikowski B, Welker D, Ideker T. Pico AR, et al. Among authors: ono k. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. F1000Res. 2014. PMID: 25580224 Free PMC article.
NDEx, the Network Data Exchange.
Pratt D, Chen J, Welker D, Rivas R, Pillich R, Rynkov V, Ono K, Miello C, Hicks L, Szalma S, Stojmirovic A, Dobrin R, Braxenthaler M, Kuentzer J, Demchak B, Ideker T. Pratt D, et al. Among authors: ono k. Cell Syst. 2015 Oct 28;1(4):302-305. doi: 10.1016/j.cels.2015.10.001. Cell Syst. 2015. PMID: 26594663 Free PMC article.
Systems biology analysis reveals role of MDM2 in diabetic nephropathy.
Saito R, Rocanin-Arjo A, You YH, Darshi M, Van Espen B, Miyamoto S, Pham J, Pu M, Romoli S, Natarajan L, Ju W, Kretzler M, Nelson R, Ono K, Thomasova D, Mulay SR, Ideker T, D'Agati V, Beyret E, Belmonte JCI, Anders HJ, Sharma K. Saito R, et al. Among authors: ono k. JCI Insight. 2016 Oct 20;1(17):e87877. doi: 10.1172/jci.insight.87877. JCI Insight. 2016. PMID: 27777973 Free PMC article.
4,782 results