An article published in GenomeBiology presents RBPNet: a sequence-to-signal model that predicts the distribution of crosslinking events across an input RNA sequence at single-nucleotide resolution.
, enabling prediction of signal profiles and sequence attribution maps with pre-trained models used in this study on user-provided RNA sequences.While high-throughput single-nucleotide CLIP-seq methods offer unprecedented insights into the protein-RNA interaction landscape of RNA-binding proteins, they are limited to transcripts expressed in the experimental cell type at the time of the experiment.
Unspecific background signal, as well as experimental biases, is an inherent issue of CLIP-based protocols and thus downstream analysis, as bias towards certain sequence elements confounds the learning of genuine, protein-specific sequence features by modeling approaches. For classification-based models, few strategies have been developed to prevent models from learning bias instead of true signal.
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