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Site identification in high-throughput RNA-protein interaction data.


Uren PJPhilip J , Bahrami-Samani E Emad , Burns SC Suzanne C , Qiao M Mei , Karginov FV Fedor V , Hodges E Emily , Hannon GJ Gregory J , Sanford JR Jeremy R , Penalva LO Luiz O F , Smith AD Andrew D . Bioinformatics (Oxford, England). 2012 12 1; 28(23). 3013-20


Post-transcriptional and co-transcriptional regulation is a crucial link between genotype and phenotype. The central players are the RNA-binding proteins, and experimental technologies [such as cross-linking with immunoprecipitation- (CLIP-) and RIP-seq] for probing their activities have advanced rapidly over the course of the past decade. Statistically robust, flexible computational methods for binding site identification from high-throughput immunoprecipitation assays are largely lacking however.