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Gene Function Analysis

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  1. 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...

    Michael F. Ochs, Jason E. Farrar in Pattern Recognition in Bioinformatics (2013)

  2. Article

    Open Access

    Gene 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...

    Elana J Fertig, Qing Ren, Haixia Cheng, Hiromitsu Hatakeyama, Adam P Dicker in BMC Genomics (2012)

  3. Article

    Open Access

    Three 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 ...

    Olga O Favorova, Alexander V Favorov, Alexey N Boiko in BMC Medical Genetics (2006)

  4. Article

    Open Access

    LS-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...

    Guoli Wang, Andrew V Kossenkov, Michael F Ochs in BMC Bioinformatics (2006)

  5. Article

    Open Access

    Determination 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...

    Ghislain Bidaut, Karsten Suhre, Jean-Michel Claverie, Michael F Ochs in BMC Bioinformatics (2006)