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Enter the Matrix: Factorization Uncovers Knowledge from Omics.
Stein-O'Brien GL, Arora R, Culhane AC, Favorov AV, Garmire LX, Greene CS, Goff LA, Li Y, Ngom A, Ochs MF, Xu Y, Fertig EJ. Stein-O'Brien GL, et al. Trends Genet. 2018 Oct;34(10):790-805. doi: 10.1016/j.tig.2018.07.003. Epub 2018 Aug 22. Trends Genet. 2018. PMID: 30143323 Free PMC article. Review.
NF-κB and stat3 transcription factor signatures differentiate HPV-positive and HPV-negative head and neck squamous cell carcinoma.
Gaykalova DA, Manola JB, Ozawa H, Zizkova V, Morton K, Bishop JA, Sharma R, Zhang C, Michailidi C, Considine M, Tan M, Fertig EJ, Hennessey PT, Ahn J, Koch WM, Westra WH, Khan Z, Chung CH, Ochs MF, Califano JA. Gaykalova DA, et al. Int J Cancer. 2015 Oct 15;137(8):1879-89. doi: 10.1002/ijc.29558. Epub 2015 Jun 23. Int J Cancer. 2015. PMID: 25857630 Free PMC article.
Integrative computational analysis of transcriptional and epigenetic alterations implicates DTX1 as a putative tumor suppressor gene in HNSCC.
Gaykalova DA, Zizkova V, Guo T, Tiscareno I, Wei Y, Vatapalli R, Hennessey PT, Ahn J, Danilova L, Khan Z, Bishop JA, Gutkind JS, Koch WM, Westra WH, Fertig EJ, Ochs MF, Califano JA. Gaykalova DA, et al. Oncotarget. 2017 Feb 28;8(9):15349-15363. doi: 10.18632/oncotarget.14856. Oncotarget. 2017. PMID: 28146432 Free PMC article.
Outlier Analysis Defines Zinc Finger Gene Family DNA Methylation in Tumors and Saliva of Head and Neck Cancer Patients.
Gaykalova DA, Vatapalli R, Wei Y, Tsai HL, Wang H, Zhang C, Hennessey PT, Guo T, Tan M, Li R, Ahn J, Khan Z, Westra WH, Bishop JA, Zaboli D, Koch WM, Khan T, Ochs MF, Califano JA. Gaykalova DA, et al. PLoS One. 2015 Nov 6;10(11):e0142148. doi: 10.1371/journal.pone.0142148. eCollection 2015. PLoS One. 2015. PMID: 26544568 Free PMC article.
AGA: Interactive pipeline for reproducible genomics analyses.
Considine M, Parker H, Wei Y, Xia X, Cope L, Ochs M, Fertig E. Considine M, et al. F1000Res. 2015 Jan 28;4:28. doi: 10.12688/f1000research.6030.1. eCollection 2015. F1000Res. 2015. PMID: 26535111 Free PMC article.
14 results