deep learning

DNA-DETR: Sequence representation matters in object detection for functional genomic elements

Object detection has revolutionized multiple domains by enabling models to jointly classify and localize targets within data. Yet, its potential in genomic sequence analysis remains largely unexplored. Here, we introduce DNA-DETR, an adaptation of …

A feature extraction free approach for protein interactome inference from co-elution data

Protein complexes are key functional units in cellular processes. High-throughput techniques, such as co-fractionation coupled with mass spectrometry (CF-MS), have advanced protein complex studies by enabling global interactome inference. However, …

Short human eccDNAs are predictable from sequences

Ubiquitous presence of short extrachromosomal circular DNAs (eccDNAs) in eukaryotic cells has perplexed generations of biologists. Their widespread origins in the genome lacking apparent specificity led some studies to conclude their formation as …