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PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF

Ochs, Michael F.; Stein-O'Brien, Genevieve L.; Carey, Jacob L.; Lee, Wai Shing; Considine, Michael; Favorov, Alexander V.; Flam, Emily; Guo, Theresa; Li, Sijia; Marchionni, Luigi; Sherman, Thomas; Sivy, Shawn; Gaykalova, Daria A.; McKay, Ronald D.; Colantuoni, Carlo; Fertig, Elana J. (Oxford University Press, 2017)

Non-negative Matrix Factorization (NMF) algorithms associate gene expression with biological processes (e.g. time-course dynamics or disease subtypes). Compared with univariate associations, the relative weights of NMF ...

Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC

Ochs, Michael F.; Gaykalova, Daria A.; Zizkova, Veronika; Guo, Theresa; Tiscareno, Ilse; Wei, Yingying; Vatapalli, Rajita; Hennessey, Patrick T.; Ahn, Julie; Danilova, Ludmila V.; Khan, Zubair; Bishop, Justin A.; Gutkind, J. Silvio; Koch, Wayne M.; Westra, William H.; Fertig, Elana J.; Califano, Joseph A. (Impact Journals, 2017)

Over a half million new cases of Head and Neck Squamous Cell Carcinoma (HNSCC) are diagnosed annually worldwide, however, 5 year overall survival is only 50% for HNSCC patients. Recently, high throughput technologies have ...