AIMC Topic: Cytosine
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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
Oct 28, 2024
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...
A hybrid residue based sequential encoding mechanism with XGBoost improved ensemble model for identifying 5-hydroxymethylcytosine modifications.
Scientific reports
Sep 6, 2024
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 ...
Using a hybrid neural network architecture for DNA sequence representation: A study on N-methylcytosine sites.
Computers in biology and medicine
May 27, 2024
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...
DeepSF-4mC: A deep learning model for predicting DNA cytosine 4mC methylation sites leveraging sequence features.
Computers in biology and medicine
Feb 16, 2024
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 base editor off-targets by deep learning.
Nature communications
Sep 2, 2023
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...
4mC-RF: Improving the prediction of 4mC sites using composition and position relative features and statistical moment.
Analytical biochemistry
Sep 25, 2021
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...
i4mC-Deep: An Intelligent Predictor of N4-Methylcytosine Sites Using a Deep Learning Approach with Chemical Properties.
Genes
Jul 23, 2021
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...
i4mC-EL: Identifying DNA N4-Methylcytosine Sites in the Mouse Genome Using Ensemble Learning.
BioMed research international
May 29, 2021
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
Feb 20, 2021
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...
Accurate prediction of DNA N-methylcytosine sites via boost-learning various types of sequence features.
BMC genomics
Sep 11, 2020
BACKGROUND: DNA N4-methylcytosine (4mC) is a critical epigenetic modification and has various roles in the restriction-modification system. Due to the high cost of experimental laboratory detection, computational methods using sequence characteristic...
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