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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. Among authors: ochs mf. 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.
CoGAPS matrix factorization algorithm identifies transcriptional changes in AP-2alpha target genes in feedback from therapeutic inhibition of the EGFR network.
Fertig EJ, Ozawa H, Thakar M, Howard JD, Kagohara LT, Krigsfeld G, Ranaweera RS, Hughes RM, Perez J, Jones S, Favorov AV, Carey J, Stein-O'Brien G, Gaykalova DA, Ochs MF, Chung CH. Fertig EJ, et al. Among authors: ochs mf. Oncotarget. 2016 Nov 8;7(45):73845-73864. doi: 10.18632/oncotarget.12075. Oncotarget. 2016. PMID: 27650546 Free PMC article.
PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF.
Stein-O'Brien GL, Carey JL, Lee WS, Considine M, Favorov AV, Flam E, Guo T, Li S, Marchionni L, Sherman T, Sivy S, Gaykalova DA, McKay RD, Ochs MF, Colantuoni C, Fertig EJ. Stein-O'Brien GL, et al. Among authors: ochs mf. Bioinformatics. 2017 Jun 15;33(12):1892-1894. doi: 10.1093/bioinformatics/btx058. Bioinformatics. 2017. PMID: 28174896 Free PMC article.
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer.
Afsari B, Guo T, Considine M, Florea L, Kagohara LT, Stein-O'Brien GL, Kelley D, Flam E, Zambo KD, Ha PK, Geman D, Ochs MF, Califano JA, Gaykalova DA, Favorov AV, Fertig EJ. Afsari B, et al. Among authors: ochs mf. Bioinformatics. 2018 Jun 1;34(11):1859-1867. doi: 10.1093/bioinformatics/bty004. Bioinformatics. 2018. PMID: 29342249 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.
79 results