Enformer
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Related Articles from SNS
CREP: Cis-Regulatory Element Predictor Based on Fine-Tuned Enformer
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...
The Dark Regulome: Disentangling Predictability from Regulation in Genomic Foundation Models
Announce Type: new Abstract: High-grade gliomas integrate into neural circuits through functional synapses with neurons, raising the question of which noncoding elements shape synaptogenic gene expression in tumor cells. The regulatory program written across the dark genome, what we call the $\textit{dark regulome}$, is the natural substrate to probe, and sequence foundation models offer a zero-shot route through in-silico mutagenesis (ISM); yet likelihood-based scoring is tautologically...