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PatternMarkers & GWCoGAPS for novel data-driven biomarkers via whole transcriptome NMF
(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 ...
Splice Expression Variation Analysis (SEVA) for inter-tumor heterogeneity of gene isoform usage in cancer
(Oxford University Press, 2018)
Motivation Current bioinformatics methods to detect changes in gene isoform usage in distinct phenotypes compare the relative expected isoform usage in phenotypes. These statistics model differences in isoform usage in ...
NF‐κB and stat3 transcription factor signatures differentiate HPV‐positive and HPV‐negative head and neck squamous cell carcinoma
Using high-throughput analyses and the TRANSFAC database, we characterized TF signatures of head and neck squamous cell carcinoma (HNSCC) subgroups by inferential analysis of target gene expression, correcting for the ...