In order to unravel the complete regulatory expression network, it is necessary to systematically identify protein-RNA interactions. In vitro techniques have been successful in identifying the motifs bound by regulators. However, these motifs are relatively short and bioinformatics searches produce a large number of false positives. Recent advances in sequencing technologies and systematic structural studies have provided new insight in how proteins interact with RNA. These technological advances provide an unprecedented opportunity to explore how RNA is regulated at a global level. These advances also pose new computational challenges. An extensive interaction between computational and experimental researchers is therfore required, aimed at building a community of shared resources and tools.