CREP: Cis-Regulatory Element Predictor Based on Fine-Tuned Enformer (opens in new tab)

A substantial fraction of disease-associated genetic variants reside in non-coding regions of the genome, where they act by perturbing cis-regulatory elements (CREs) such as enhancers, promoters, and insulators. While recent sequence-based deep learning models, such as Enformer, accurately predict continuous epigenomic signals from DNA sequence, they do not directly provide discrete and interpretable CRE annotations. Here, we present CREP (Cis-Regulatory Element Predictor), a fine-tuned versi...