Transposable elements (TEs), one of the major components of the so-called dark (non-coding) genome, and their functional roles in human cancers are of central interest to our research group. We develop and apply integrative methods to study the magnitude of TE-mediated aberrant gene expression in human cancers and delineate the perturbed regulatory mechanisms or epigenetic pathways responsible for this phenomenon. Moreover, the ‘exonized’ parts of aberrantly expressed TEs can serve as a source of novel immunogenic peptides that can be exploited for T cell-based immunotherapy or as peptidic sequences that confer novel structural or functional properties to the involved proteins. TE-derived structural components introduced into cell surface proteins could be targeted by antibody-based approaches, raising the prospect of highly selective therapeutic strategies.