Bioinformatic approaches to the identification of regulatory elements in genomic sequences

The regulation of gene expression in eukaryotes is a very complex process, occurring at various hierarchical levels: from chromatin structure and organization to protein post-translational modifications. In this thesis we present novel bioinformatics approaches, developed during the PhD, suitable for the identification and characterization in genomic sequences of regulatory elements involved in the modulation of gene transcription and mRNA translation. The methods we introduced tackle the problem from different sides: from traditional in silico approaches like motif find- ing and phylogenetic footprinting, to the analysis of data produced with the latest experimental techniques like Chromatin ImmunoPrecipitation and next-generation sequencing.