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...
Identifying the function of DNA sequences accurately is an essential and challenging task in the genomic field. Until now, deep learning has been widely used in the functional analysis of DNA sequences, including DeepSEA, DanQ, DeepATT and TBiNet. Ho...
N6-methyladinosine (m6A) modification is the most abundant co-transcriptional modification in eukaryotic RNA and plays important roles in cellular regulation. Traditional high-throughput sequencing experiments used to explore functional mechanisms ar...
The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a cri...
MOTIVATION: Genome sequencing experiments have revolutionized molecular biology by allowing researchers to identify important DNA-encoded elements genome wide. Regions where these elements are found appear as peaks in the analog signal of an assay's ...
MOTIVATION: Histone modifications are epigenetic markers that impact gene expression by altering the chromatin structure or recruiting histone modifiers. Their accurate identification is key to unraveling the mechanisms by which they regulate gene ex...
2'-O-methylation (Nm) is a post-transcriptional modification of RNA that is catalyzed by 2'-O-methyltransferase and involves replacing the H on the 2'-hydroxyl group with a methyl group. The 2'-O-methylation modification site is detected in a variety...
Identifying cis-regulatory motifs from genomic sequencing data (e.g. ChIP-seq and CLIP-seq) is crucial in identifying transcription factor (TF) binding sites and inferring gene regulatory mechanisms for any organism. Since 2015, deep learning (DL) me...
Combinatorial chemistry & high throughput screening
Jan 1, 2022
BACKGROUND: The process of nucleotides modification or methyl groups addition to nucleotides is known as post-transcriptional modification (PTM). 1-methyladenosine (m1A) is a type of PTM formed by adding a methyl group to the nitrogen at the 1st posi...
Circular RNAs (circRNAs) are widely expressed in highly diverged eukaryotes. Although circRNAs have been known for many years, their function remains unclear. Interaction with RNA-binding protein (RBP) to influence post-transcriptional regulation is ...