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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. 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.
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: pratt d. 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.
Network propagation in the cytoscape cyberinfrastructure.
Carlin DE, Demchak B, Pratt D, Sage E, Ideker T. Carlin DE, et al. Among authors: pratt d. 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.
ndexr-an R package to interface with the network data exchange.
Auer F, Hammoud Z, Ishkin A, Pratt D, Ideker T, Kramer F. Auer F, et al. Among authors: pratt d. Bioinformatics. 2018 Feb 15;34(4):716-717. doi: 10.1093/bioinformatics/btx683. Bioinformatics. 2018. PMID: 29087446 Free PMC article.
NDEx 2.0: A Clearinghouse for Research on Cancer Pathways.
Pratt D, Chen J, Pillich R, Rynkov V, Gary A, Demchak B, Ideker T. Pratt D, et al. Cancer Res. 2017 Nov 1;77(21):e58-e61. doi: 10.1158/0008-5472.CAN-17-0606. Cancer Res. 2017. PMID: 29092941 Free PMC article.
Multiscale community detection in Cytoscape.
Singhal A, Cao S, Churas C, Pratt D, Fortunato S, Zheng F, Ideker T. Singhal A, et al. Among authors: pratt d. PLoS Comput Biol. 2020 Oct 23;16(10):e1008239. doi: 10.1371/journal.pcbi.1008239. eCollection 2020 Oct. PLoS Comput Biol. 2020. PMID: 33095781 Free PMC article.
937 results