AIMC Topic: Methylation

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GR-m6A: Prediction of N6-methyladenosine sites in mammals with molecular graph and residual network.

Computers in biology and medicine Jun 30, 2023
RNA N6-methyladenine (m6A), which is produced by the methylation of the N6 position of eukaryotic adenine, is a relatively common post-transcriptional modification on the surface of the molecule, which frequently plays a crucial role in biological pr...
Neural Networks, Computer RNA Methylation Animals Mammals
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m5U-SVM: identification of RNA 5-methyluridine modification sites based on multi-view features of physicochemical features and distributed representation.

BMC biology Apr 24, 2023
BACKGROUND: RNA 5-methyluridine (m5U) modifications are obtained by methylation at the C position of uridine catalyzed by pyrimidine methylation transferase, which is related to the development of human diseases. Accurate identification of m5U modifi...
Methylation Support Vector Machine RNA Humans Algorithms Computational Biology
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Predicting genes associated with RNA methylation pathways using machine learning.

Communications biology Aug 25, 2022
RNA methylation plays an important role in functional regulation of RNAs, and has thus attracted an increasing interest in biology and drug discovery. Here, we collected and collated transcriptomic, proteomic, structural and physical interaction data...
Humans Methylation Supervised Machine Learning RNA Machine Learning Proteomics
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EMDLP: Ensemble multiscale deep learning model for RNA methylation site prediction.

BMC bioinformatics Jun 8, 2022
BACKGROUND: Recent research recommends that epi-transcriptome regulation through post-transcriptional RNA modifications is essential for all sorts of RNA. Exact identification of RNA modification is vital for understanding their purposes and regulato...
Deep Learning Natural Language Processing Base Sequence RNA Methylation
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A three-methylation-driven gene-based deep learning model for tuberculosis diagnosis in patients with and without human immunodeficiency virus co-infection.

Microbiology and immunology May 27, 2022
Improved diagnostic tests for tuberculosis (TB) among people with human immunodeficiency virus (HIV) are urgently required. We hypothesized that methylation-driven genes (MDGs) of host blood could be used to diagnose patients co-infected with HIV/TB....
HIV Methylation Deep Learning HIV Infections Coinfection Tuberculosis Humans
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Deep learning modeling mA deposition reveals the importance of downstream cis-element sequences.

Nature communications May 17, 2022
The N-methyladenosine (mA) modification is deposited to nascent transcripts on chromatin, but its site-specificity mechanism is mostly unknown. Here we model the mA deposition to pre-mRNA by iM6A (intelligent mA), a deep learning method, demonstratin...
Codon, Terminator Regulatory Sequences, Nucleic Acid Deep Learning Methylation Base Sequence
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Machine learning algorithm for precise prediction of 2'-O-methylation (Nm) sites from experimental RiboMethSeq datasets.

Methods (San Diego, Calif.) Mar 18, 2022
Analysis of epitranscriptomic RNA modifications by deep sequencing-based approaches brings an essential contribution to the general knowledge on their precise locations and relative stoichiometry in cellular RNAs. To reveal RNA modifications, several...
Algorithms RNA Methylation Saccharomyces cerevisiae Humans Machine Learning RNA, Transfer
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A brief review of machine learning methods for RNA methylation sites prediction.

Methods (San Diego, Calif.) Mar 3, 2022
Thanks to the tremendous advancement of deep sequencing and large-scale profiling, epitranscriptomics has become a rapidly growing field. As one of the most important parts of epitranscriptomics, ribonucleic acid (RNA) methylation has been focused on...
Base Sequence RNA Methylation Machine Learning
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EDLmAPred: ensemble deep learning approach for mRNA mA site prediction.

BMC bioinformatics May 29, 2021
BACKGROUND: As a common and abundant RNA methylation modification, N6-methyladenosine (mA) is widely spread in various species' transcriptomes, and it is closely related to the occurrence and development of various life processes and diseases. Thus, ...
Methylation Animals Adenosine RNA, Messenger RNA Deep Learning Mice
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HSM6AP: a high-precision predictor for the Homo N6-methyladenosine (m^6 A) based on multiple weights and feature stitching.

RNA biology Feb 12, 2021
Recent studies have shown that RNA methylation modification can affect RNA transcription, metabolism, splicing and stability. In addition, RNA methylation modification has been associated with cancer, obesity and other diseases. Based on information ...
Adenosine HEK293 Cells Gene Expression Regulation Computational Biology A549 Cells HeLa Cells Methylation Humans Machine Learning Algorithms
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