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Cytosine

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i4mC-EL: Identifying DNA N4-Methylcytosine Sites in the Mouse Genome Using Ensemble Learning.

BioMed research international
As one of important epigenetic modifications, DNA N4-methylcytosine (4mC) plays a crucial role in controlling gene replication, expression, cell cycle, DNA replication, and differentiation. The accurate identification of 4mC sites is necessary to und...

4mCPred-CNN-Prediction of DNA N4-Methylcytosine in the Mouse Genome Using a Convolutional Neural Network.

Genes
Among DNA modifications, N4-methylcytosine (4mC) is one of the most significant ones, and it is linked to the development of cell proliferation and gene expression. To know different its biological functions, the accurate detection of 4mC sites is re...

i4mC-Deep: An Intelligent Predictor of N4-Methylcytosine Sites Using a Deep Learning Approach with Chemical Properties.

Genes
DNA is subject to epigenetic modification by the molecule N4-methylcytosine (4mC). N4-methylcytosine plays a crucial role in DNA repair and replication, protects host DNA from degradation, and regulates DNA expression. However, though current experim...

4mC-RF: Improving the prediction of 4mC sites using composition and position relative features and statistical moment.

Analytical biochemistry
N4-methylcytosine (4 mC) is an important epigenetic modification that occurs enzymatically by the action of DNA methyltransferases. 4 mC sites exist in prokaryotes and eukaryotes while playing a vital role in regulating gene expression, DNA replicati...

Prediction of base editor off-targets by deep learning.

Nature communications
Due to the tolerance of mismatches between gRNA and targeting sequence, base editors frequently induce unwanted Cas9-dependent off-target mutations. Here, to develop models to predict such off-targets, we design gRNA-off- target pairs for adenine bas...

DeepSF-4mC: A deep learning model for predicting DNA cytosine 4mC methylation sites leveraging sequence features.

Computers in biology and medicine
N-methylcytosine (4mC) is a DNA modification involving the addition of a methyl group to the fourth nitrogen atom of the cytosine base. This modification may influence gene regulation, providing potential insights into gene control mechanisms. Tradit...

Prediction of DNA i-motifs via machine learning.

Nucleic acids research
i-Motifs (iMs), are secondary structures formed in cytosine-rich DNA sequences and are involved in multiple functions in the genome. Although putative iM forming sequences are widely distributed in the human genome, the folding status and strength of...

Using a hybrid neural network architecture for DNA sequence representation: A study on N-methylcytosine sites.

Computers in biology and medicine
N-methylcytosine (4mC) is a modified form of cytosine found in DNA, contributing to epigenetic regulation. It exists in various genomes, including the Rosaceae family encompassing significant fruit crops like apples, cherries, and roses. Previous inv...

A hybrid residue based sequential encoding mechanism with XGBoost improved ensemble model for identifying 5-hydroxymethylcytosine modifications.

Scientific reports
RNA modifications play an important role in actively controlling recently created formation in cellular regulation mechanisms, which link them to gene expression and protein. The RNA modifications have numerous alterations, presenting broad glimpses ...

An Integrated Multi-Model Framework Utilizing Convolutional Neural Networks Coupled with Feature Extraction for Identification of 4mC Sites in DNA Sequences.

Computers in biology and medicine
N4-methylcytosine (4mC) is a chemical modification that occurs on one of the four nucleotide bases in DNA and plays a vital role in DNA expression, repair, and replication. It also actively participates in the regulation of cell differentiation and g...