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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: morris j. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. Nat Protoc. 2007. PMID: 17947979 Free PMC article.
GLay: community structure analysis of biological networks.
Su G, Kuchinsky A, Morris JH, States DJ, Meng F. Su G, et al. Among authors: morris jh. Bioinformatics. 2010 Dec 15;26(24):3135-7. doi: 10.1093/bioinformatics/btq596. Bioinformatics. 2010. PMID: 21123224 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. BMC Bioinformatics. 2011 Nov 9;12:436. doi: 10.1186/1471-2105-12-436. BMC Bioinformatics. 2011. PMID: 22070249 Free PMC article.
Biological network exploration with Cytoscape 3.
Su G, Morris JH, Demchak B, Bader GD. Su G, et al. Curr Protoc Bioinformatics. 2014 Sep 8;47:8.13.1-24. doi: 10.1002/0471250953.bi0813s47. Curr Protoc Bioinformatics. 2014. PMID: 25199793 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: morris jh. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. F1000Res. 2014. PMID: 25580224 Free PMC article.
CyAnimator: Simple Animations of Cytoscape Networks.
Morris JH, Vijay D, Federowicz S, Pico AR, Ferrin TE. Morris JH, et al. F1000Res. 2015 Aug 5;4:482. doi: 10.12688/f1000research.6852.2. eCollection 2015. F1000Res. 2015. PMID: 26937268 Free PMC article.
The Cytoscape Automation app article collection.
Demchak B, Otasek D, Pico AR, Bader GD, Ono K, Settle B, Sage E, Morris JH, Longabaugh W, Lopes C, Kucera M, Treister A, Schwikowski B, Molenaar P, Ideker T. Demchak B, et al. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. F1000Res. 2018. PMID: 29983926 Free PMC article.
9,393 results