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Microarrays are at the center of a revolution in biotechnology, allowing researchers to simultaneously monitor the expression of tens of thousands of genes. The final aim of a typical microarray experiment is to find a molecular explanation for a given macroscopic observation (e.g., which pathways are affected by the loss of glucose in a cell, what biological processes differentiate a healthy control from a diseased case); this is called functional interpretation of gene expression data. The two developed methods presented in this book have proved to be of interest to medical experts. The extracted knowledge turns out to be consistent with the relevant literature, and proves to have the potential for guiding the biomedical research and generating new hypotheses that explain microarray measurements.