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Mapping the common gene networks that underlie related diseases.
Rosenthal SB, Wright SN, Liu S, Churas C, Chilin-Fuentes D, Chen CH, Fisch KM, Pratt D, Kreisberg JF, Ideker T. Rosenthal SB, et al. Among authors: pratt d. Nat Protoc. 2023 Jun;18(6):1745-1759. doi: 10.1038/s41596-022-00797-1. Epub 2023 Jan 18. Nat Protoc. 2023. PMID: 36653526 Free PMC article. Review.
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.
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.
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.
Identifying persistent structures in multiscale 'omics data.
Zheng F, Zhang S, Churas C, Pratt D, Bahar I, Ideker T. Zheng F, et al. Among authors: pratt d. bioRxiv [Preprint]. 2020 Oct 3:2020.06.16.151555. doi: 10.1101/2020.06.16.151555. bioRxiv. 2020. PMID: 32587977 Free PMC article. Updated. Preprint.
Functional Landscape of SARS-CoV-2 Cellular Restriction.
Martin-Sancho L, Lewinski MK, Pache L, Stoneham CA, Yin X, Pratt D, Churas C, Rosenthal SB, Liu S, De Jesus PD, O'Neill AM, Gounder AP, Nguyen C, Pu Y, Oom AL, Miorin L, Rodriguez-Frandsen A, Urbanowski M, Shaw ML, Chang MW, Benner C, Frieman MB, García-Sastre A, Ideker T, Hultquist JF, Guatelli J, Chanda SK. Martin-Sancho L, et al. Among authors: pratt d. bioRxiv [Preprint]. 2020 Sep 30:2020.09.29.319566. doi: 10.1101/2020.09.29.319566. bioRxiv. 2020. PMID: 33024967 Free PMC article. Updated. Preprint.
908 results