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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: schwikowski b. Nat Protoc. 2007;2(10):2366-82. doi: 10.1038/nprot.2007.324. Nat Protoc. 2007. PMID: 17947979 Free PMC article.
The Cyni framework for network inference in Cytoscape.
Guitart-Pla O, Kustagi M, Rügheimer F, Califano A, Schwikowski B. Guitart-Pla O, et al. Among authors: schwikowski b. Bioinformatics. 2015 May 1;31(9):1499-501. doi: 10.1093/bioinformatics/btu812. Epub 2014 Dec 18. Bioinformatics. 2015. PMID: 25527096 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: schwikowski b. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. F1000Res. 2014. PMID: 25580224 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. Among authors: schwikowski b. F1000Res. 2018 Jun 20;7:800. doi: 10.12688/f1000research.15355.1. eCollection 2018. F1000Res. 2018. PMID: 29983926 Free PMC article.
Graph-based methods for analysing networks in cell biology.
Aittokallio T, Schwikowski B. Aittokallio T, et al. Among authors: schwikowski b. Brief Bioinform. 2006 Sep;7(3):243-55. doi: 10.1093/bib/bbl022. Epub 2006 Jul 30. Brief Bioinform. 2006. PMID: 16880171 Review.
78 results