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RNA Processing, Post-Transcriptional

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Attention-based multi-label neural networks for integrated prediction and interpretation of twelve widely occurring RNA modifications.

Nature communications
Recent studies suggest that epi-transcriptome regulation via post-transcriptional RNA modifications is vital for all RNA types. Precise identification of RNA modification sites is essential for understanding the functions and regulatory mechanisms of...

Deep and accurate detection of m6A RNA modifications using miCLIP2 and m6Aboost machine learning.

Nucleic acids research
N6-methyladenosine (m6A) is the most abundant internal RNA modification in eukaryotic mRNAs and influences many aspects of RNA processing. miCLIP (m6A individual-nucleotide resolution UV crosslinking and immunoprecipitation) is an antibody-based appr...

Nm-Nano: a machine learning framework for transcriptome-wide single-molecule mapping of 2´-O-methylation (Nm) sites in nanopore direct RNA sequencing datasets.

RNA biology
2´-O-methylation (Nm) is one of the most abundant modifications found in both mRNAs and noncoding RNAs. It contributes to many biological processes, such as the normal functioning of tRNA, the protection of mRNA against degradation by the decapping a...

BiPSTP: Sequence feature encoding method for identifying different RNA modifications with bidirectional position-specific trinucleotides propensities.

The Journal of biological chemistry
RNA modification, a posttranscriptional regulatory mechanism, significantly influences RNA biogenesis and function. The accurate identification of modification sites is paramount for investigating their biological implications. Methods for encoding R...

Quantitative profiling N1-methyladenosine (m1A) RNA methylation from Oxford nanopore direct RNA sequencing data.

Methods (San Diego, Calif.)
With the recent advanced direct RNA sequencing technique that proposed by the Oxford Nanopore Technologies, RNA modifications can be detected and profiled in a simple and straightforward manner. Majority nanopore-based modification studies were devot...

MLm5C: A high-precision human RNA 5-methylcytosine sites predictor based on a combination of hybrid machine learning models.

Methods (San Diego, Calif.)
RNA modification serves as a pivotal component in numerous biological processes. Among the prevalent modifications, 5-methylcytosine (m5C) significantly influences mRNA export, translation efficiency and cell differentiation and are also associated w...

Nmix: a hybrid deep learning model for precise prediction of 2'-O-methylation sites based on multi-feature fusion and ensemble learning.

Briefings in bioinformatics
RNA 2'-O-methylation (Nm) is a crucial post-transcriptional modification with significant biological implications. However, experimental identification of Nm sites is challenging and resource-intensive. While multiple computational tools have been de...

Caps-ac4C: An effective computational framework for identifying N4-acetylcytidine sites in human mRNA based on deep learning.

Journal of molecular biology
N4-acetylcytidine (ac4C) is a crucial post-transcriptional modification in human mRNA, involving the acetylation of the nitrogen atom at the fourth position of cytidine. This modification, catalyzed by N-acetyltransferases such as NAT10, is primarily...

ERNIE-ac4C: A Novel Deep Learning Model for Effectively Predicting N4-acetylcytidine Sites.

Journal of molecular biology
RNA modifications are known to play a critical role in gene regulation and cellular processes. Specifically, N4-acetylcytidine (ac4C) modification has emerged as a significant marker involved in mRNA translation efficiency, stability, and various dis...

TransCNN: A novel architecture combining transformer and TextCNN for detecting N4-acetylcytidine sites in human mRNA.

Analytical biochemistry
N4-acetylcytidine (ac4C), a pivotal post-transcriptional RNA modification, is central to understanding transcriptional regulation and diverse biological processes. As a key determinant of RNA structural stability and functional regulation, ac4C has b...