DNase I hypersensitive site (DHS) refers to the hypersensitive region of chromatin for the DNase I enzyme. It is an important part of the noncoding region and contains a variety of regulatory elements, such as promoter, enhancer, and transcription fa...
Haploinsufficiency, wherein a single allele is not enough to maintain normal functions, can lead to many diseases including cancers and neurodevelopmental disorders. Recently, computational methods for identifying haploinsufficiency have been develop...
Deep learning has demonstrated its predictive power in modeling complex biological phenomena such as gene expression. The value of these models hinges not only on their accuracy, but also on the ability to extract biologically relevant information fr...
A promoter is a region in the DNA sequence that defines where the transcription of a gene by RNA polymerase initiates, which is typically located proximal to the transcription start site (TSS). How to correctly identify the gene TSS and the core prom...
Enhancer-promoter interactions (EPIs) play an important role in transcriptional regulation. Recently, machine learning-based methods have been widely used in the genome-scale identification of EPIs due to their promising predictive performance. In th...
Promoters are short consensus sequences of DNA, which are responsible for transcription activation or the repression of all genes. There are many types of promoters in bacteria with important roles in initiating gene transcription. Therefore, solving...
Methods in molecular biology (Clifton, N.J.)
Jan 1, 2021
As the interest in genetic resequencing increases, so does the need for effective mathematical, computational, and statistical approaches. One of the difficult problems in genome annotation is determination of precise positions of transcription start...
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...
Recent advances in genomic technologies have generated data on large-scale protein-DNA interactions and open chromatin regions for many eukaryotic species. How to identify condition-specific functions of transcription factors using these data has bec...
MOTIVATION: Identification of enhancer-promoter interactions (EPIs) is of great significance to human development. However, experimental methods to identify EPIs cost too much in terms of time, manpower and money. Therefore, more and more research ef...