Major progress in disease genetics has been made through genome-wide association studies (GWASs). One of the key tasks for post-GWAS analyses is to identify causal noncoding variants with regulatory function. Here, on the basis of >2000 functional fe...
With advances in sequencing technology, a vast amount of genomic sequence information has become available. However, annotating biological functions particularly of non-protein-coding regions in genome sequences without experiments is still a challen...
Predicting effects of gene regulatory elements (GREs) is a longstanding challenge in biology. Machine learning may address this, but requires large datasets linking GREs to their quantitative function. However, experimental methods to generate such d...
BACKGROUND: Noncoding sequences have been demonstrated to possess regulatory functions. Its classification is challenging because they do not show well-defined nucleotide patterns that can correlate with their biological functions. Genomic signal pro...
Proceedings of the National Academy of Sciences of the United States of America
32978299
Although we know many sequence-specific transcription factors (TFs), how the DNA sequence of cis-regulatory elements is decoded and orchestrated on the genome scale to determine immune cell differentiation is beyond our grasp. Leveraging a granular a...
BACKGROUND: Enhancer-promoter interactions (EPIs) play key roles in transcriptional regulation and disease progression. Although several computational methods have been developed to predict such interactions, their performances are not satisfactory w...
Understanding the genetic regulatory code governing gene expression is an important challenge in molecular biology. However, how individual coding and non-coding regions of the gene regulatory structure interact and contribute to mRNA expression leve...
Enhancer-promoter interactions (EPIs) in the human genome are of great significance to transcriptional regulation, which tightly controls gene expression. Identification of EPIs can help us better decipher gene regulation and understand disease mecha...
ATAC-seq is a widely-applied assay used to measure genome-wide chromatin accessibility; however, its ability to detect active regulatory regions can depend on the depth of sequencing coverage and the signal-to-noise ratio. Here we introduce AtacWorks...
Quantifying DNA properties is a challenging task in the broad field of human genomics. Since the vast majority of non-coding DNA is still poorly understood in terms of function, this task is particularly important to have enormous benefit for biology...