AIMC Topic: RNA, Messenger

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miCGR: interpretable deep neural network for predicting both site-level and gene-level functional targets of microRNA.

Briefings in bioinformatics
MicroRNAs (miRNAs) are critical regulators in various biological processes to cleave or repress translation of messenger RNAs (mRNAs). Accurately predicting miRNA targets is essential for developing miRNA-based therapies for diseases such as cancer a...

A deep learning method to integrate extracelluar miRNA with mRNA for cancer studies.

Bioinformatics (Oxford, England)
MOTIVATION: Extracellular miRNAs (exmiRs) and intracellular mRNAs both can serve as promising biomarkers and therapeutic targets for various diseases. However, exmiR expression data is often noisy, and obtaining intracellular mRNA expression data usu...

DPNN-ac4C: a dual-path neural network with self-attention mechanism for identification of N4-acetylcytidine (ac4C) in mRNA.

Bioinformatics (Oxford, England)
MOTIVATION: The modification of N4-acetylcytidine (ac4C) in RNA is a conserved epigenetic mark that plays a crucial role in post-transcriptional regulation, mRNA stability, and translation efficiency. Traditional methods for detecting ac4C modificati...

siRNADiscovery: a graph neural network for siRNA efficacy prediction via deep RNA sequence analysis.

Briefings in bioinformatics
The clinical adoption of small interfering RNAs (siRNAs) has prompted the development of various computational strategies for siRNA design, from traditional data analysis to advanced machine learning techniques. However, previous studies have inadequ...

m6ATM: a deep learning framework for demystifying the m6A epitranscriptome with Nanopore long-read RNA-seq data.

Briefings in bioinformatics
N6-methyladenosine (m6A) is one of the most abundant and well-known modifications in messenger RNAs since its discovery in the 1970s. Recent studies have demonstrated that m6A is involved in various biological processes, such as alternative splicing ...

MSlocPRED: deep transfer learning-based identification of multi-label mRNA subcellular localization.

Briefings in bioinformatics
Subcellular localization of messenger ribonucleic acid (mRNA) is a universal mechanism for precise and efficient control of the translation process. Although many computational methods have been constructed by researchers for predicting mRNA subcellu...

Advancing mRNA subcellular localization prediction with graph neural network and RNA structure.

Bioinformatics (Oxford, England)
MOTIVATION: The asymmetrical distribution of expressed mRNAs tightly controls the precise synthesis of proteins within human cells. This non-uniform distribution, a cornerstone of developmental biology, plays a pivotal role in numerous cellular proce...

DeepIRES: a hybrid deep learning model for accurate identification of internal ribosome entry sites in cellular and viral mRNAs.

Briefings in bioinformatics
The internal ribosome entry site (IRES) is a cis-regulatory element that can initiate translation in a cap-independent manner. It is often related to cellular processes and many diseases. Thus, identifying the IRES is important for understanding its ...