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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.
Network propagation in the cytoscape cyberinfrastructure.
Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Carlin DE, et al. Among authors: demchak b. PLoS Comput Biol. 2017 Oct 12;13(10):e1005598. doi: 10.1371/journal.pcbi.1005598. eCollection 2017 Oct. PLoS Comput Biol. 2017. PMID: 29023449 Free PMC article.
cyNeo4j: connecting Neo4j and Cytoscape.
Summer G, Kelder T, Ono K, Radonjic M, Heymans S, Demchak B. Summer G, et al. Among authors: demchak b. Bioinformatics. 2015 Dec 1;31(23):3868-9. doi: 10.1093/bioinformatics/btv460. Epub 2015 Aug 12. Bioinformatics. 2015. PMID: 26272981 Free PMC article.
dot-app: a Graphviz-Cytoscape conversion plug-in.
Fitts B, Zhang Z, Maher M, Demchak B. Fitts B, et al. Among authors: demchak b. F1000Res. 2016 Oct 20;5:2543. doi: 10.12688/f1000research.9751.2. eCollection 2016. F1000Res. 2016. PMID: 27853520 Free PMC article.
RCy3: Network biology using Cytoscape from within R.
Gustavsen JA, Pai S, Isserlin R, Demchak B, Pico AR. Gustavsen JA, et al. Among authors: demchak b. F1000Res. 2019 Oct 18;8:1774. doi: 10.12688/f1000research.20887.3. eCollection 2019. F1000Res. 2019. PMID: 31819800 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: demchak b. 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.
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: demchak b. F1000Res. 2014 Jul 1;3:138. doi: 10.12688/f1000research.4642.1. eCollection 2014. F1000Res. 2014. PMID: 25580224 Free PMC article.
Copycat Layout: Network layout alignment via Cytoscape Automation.
Settle B, Otasek D, Morris JH, Demchak B. Settle B, et al. Among authors: demchak b. F1000Res. 2018 Jun 21;7:ISCB Comm J-822. doi: 10.12688/f1000research.15144.2. eCollection 2018. F1000Res. 2018. PMID: 30026936 Free PMC article.
28 results