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Visible Machine Learning for Biomedicine.
Yu MK, Ma J, Fisher J, Kreisberg JF, Raphael BJ, Ideker T. Yu MK, et al. Cell. 2018 Jun 14;173(7):1562-1565. doi: 10.1016/j.cell.2018.05.056. Cell. 2018. PMID: 29906441 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. 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.
Inferring gene ontologies from pairwise similarity data.
Kramer M, Dutkowski J, Yu M, Bafna V, Ideker T. Kramer M, et al. Bioinformatics. 2014 Jun 15;30(12):i34-42. doi: 10.1093/bioinformatics/btu282. Bioinformatics. 2014. PMID: 24932003 Free PMC article.
Active Interaction Mapping Reveals the Hierarchical Organization of Autophagy.
Kramer MH, Farré JC, Mitra K, Yu MK, Ono K, Demchak B, Licon K, Flagg M, Balakrishnan R, Cherry JM, Subramani S, Ideker T. Kramer MH, et al. Among authors: yu mk. Mol Cell. 2017 Feb 16;65(4):761-774.e5. doi: 10.1016/j.molcel.2016.12.024. Epub 2017 Jan 26. Mol Cell. 2017. PMID: 28132844 Free PMC article.
A global transcriptional network connecting noncoding mutations to changes in tumor gene expression.
Zhang W, Bojorquez-Gomez A, Velez DO, Xu G, Sanchez KS, Shen JP, Chen K, Licon K, Melton C, Olson KM, Yu MK, Huang JK, Carter H, Farley EK, Snyder M, Fraley SI, Kreisberg JF, Ideker T. Zhang W, et al. Among authors: yu mk. Nat Genet. 2018 Apr;50(4):613-620. doi: 10.1038/s41588-018-0091-2. Epub 2018 Apr 2. Nat Genet. 2018. PMID: 29610481 Free PMC article.
226 results