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Chapter and Conference Paper
Outlier Gene Set Analysis Combined with Top Scoring Pair Provides Robust Biomarkers of Pathway Activity
Cancer is a disease driven by pathway activity, while useful biomarkers to predict outcome (prognostic markers) or determine treatment (treatment markers) rely on individual genes, proteins, or metabolites. We...
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Article
Open AccessGene expression signatures modulated by epidermal growth factor receptor activation and their relationship to cetuximab resistance in head and neck squamous cell carcinoma
Aberrant activation of signaling pathways downstream of epidermal growth factor receptor (EGFR) has been hypothesized to be one of the mechanisms of cetuximab (a monoclonal antibody against EGFR) resistance in...
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Article
Open AccessThree allele combinations associated with Multiple Sclerosis
Multiple sclerosis (MS) is an immune-mediated disease of polygenic etiology. Dissection of its genetic background is a complex problem, because of the combinatorial possibilities of gene-gene interactions. As ...
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Article
Open AccessLS-NMF: A modified non-negative matrix factorization algorithm utilizing uncertainty estimates
Non-negative matrix factorisation (NMF), a machine learning algorithm, has been applied to the analysis of microarray data. A key feature of NMF is the ability to identify patterns that together explain the da...
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Article
Open AccessDetermination of strongly overlap** signaling activity from microarray data
As numerous diseases involve errors in signal transduction, modern therapeutics often target proteins involved in cellular signaling. Interpretation of the activity of signaling pathways during disease develop...