DNA synthesis is widely used in synthetic biology to construct and assemble sequences ranging from short RBS to ultra-long synthetic genomes. Many sequence features, such as the GC content and repeat sequences, are known to affect the synthesis diffi...
BACKGROUND: Promoters are DNA regions that initiate the transcription of specific genes near the transcription start sites. In bacteria, promoters are recognized by RNA polymerases and associated sigma factors. Effective promoter recognition is essen...
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, iCLIP and m...
Enhancers are crucial cis-regulatory elements that control gene expression in a cell-type-specific manner. Despite extensive genetic and computational studies, accurately predicting enhancer activity in different cell types remains a challenge, and t...
Fast and accurate 3D RNA structure prediction remains a major challenge in structural biology, mostly due to the size and flexibility of RNA molecules, as well as the lack of diverse experimentally determined structures of RNA molecules. Unlike DNA s...
Deep learning methods have recently become the state of the art in a variety of regulatory genomic tasks, including the prediction of gene expression from genomic DNA. As such, these methods promise to serve as important tools in interpreting the ful...
SUMMARY: We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to cluster DNA sequences, without the need for sequence alignment or taxonomic ...
This paper presents ConF, a novel deep learning model designed for accurate and efficient prediction of noncoding RNA families. NcRNAs are essential functional RNA molecules involved in various cellular processes, including replication, transcription...
MOTIVATION: The origins of replication sites (ORIs) are precise regions inside the DNA sequence where the replication process begins. These locations are critical for preserving the genome's integrity during cell division and guaranteeing the faithfu...
IEEE/ACM transactions on computational biology and bioinformatics
38051616
Accurate identification of DNA promoter sequences is of crucial importance in unraveling the underlying mechanisms that regulate gene transcription. Initiation of transcription is controlled through regulatory transcription factors binding to promote...