AIMC Topic: Deoxyribonuclease I
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LangMoDHS: A deep learning language model for predicting DNase I hypersensitive sites in mouse genome.
Mathematical biosciences and engineering : MBE
Oct 24, 2022
DNase I hypersensitive sites (DHSs) are a specific genomic region, which is critical to detect or understand cis-regulatory elements. Although there are many methods developed to detect DHSs, there is a big gap in practice. We presented a deep learni...
iDHS-DT: Identifying DNase I hypersensitive sites by integrating DNA dinucleotide and trinucleotide information.
Biophysical chemistry
Nov 14, 2021
DNase I hypersensitive sites (DHSs) is important for identifying the location of gene regulatory elements, such as promoters, enhancers, silencers, and so on. Thus, it is crucial for discriminating DHSs from non-DHSs. Although some traditional method...
Deep learning for DNase I hypersensitive sites identification.
BMC genomics
Dec 31, 2018
BACKGROUND: The DNase I hypersensitive sites (DHSs) are associated with the cis-regulatory DNA elements. An efficient method of identifying DHSs can enhance the understanding on the accessibility of chromatin. Despite a multitude of resources availab...
Automation of the Differential Digestion Process of Sexual Assault Evidence.
Journal of forensic sciences
Jul 25, 2018
Sexual assault evidence samples require the use of a specific process known as a differential digestion to separate sperm from nonsperm cells prior to DNA extraction. An automated differential digestion process was developed using a selective degrada...
Prediction of DNase I hypersensitive sites in plant genome using multiple modes of pseudo components.
Analytical biochemistry
Mar 28, 2018
DNase I hypersensitive sites (DHSs) are accessible chromatin zones hypersensitive to DNase I endonucleases in plant genome. DHSs have been used as markers for the presence of transcriptional regulatory elements. It is an important complement to devel...
McEnhancer: predicting gene expression via semi-supervised assignment of enhancers to target genes.
Genome biology
Oct 26, 2017
Transcriptional enhancers regulate spatio-temporal gene expression. While genomic assays can identify putative enhancers en masse, assigning target genes is a complex challenge. We devised a machine learning approach, McEnhancer, which links target g...
pDHS-SVM: A prediction method for plant DNase I hypersensitive sites based on support vector machine.
Journal of theoretical biology
May 26, 2017
DNase I hypersensitive sites (DHSs) are accessible chromatin regions hypersensitive to cleavages by DNase I endonucleases. DHSs are indicative of cis-regulatory DNA elements (CREs), all of which play important roles in global gene expression regulati...
iDHS-Deep: an integrated tool for predicting DNase I hypersensitive sites by deep neural network.
Briefings in bioinformatics
Sep 2, 2021
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...
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