AIMC Topic: RNA, Messenger
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DRpred: A Novel Deep Learning-Based Predictor for Multi-Label mRNA Subcellular Localization Prediction by Incorporating Bayesian Inferred Prior Label Relationships.
Biomolecules
Aug 26, 2024
The subcellular localization of messenger RNA (mRNA) not only helps us to understand the localization regulation of gene expression but also helps to understand the relationship between RNA localization pattern and human disease mechanism, which has ...
Benchmarking the negatives: Effect of negative data generation on the classification of miRNA-mRNA interactions.
PLoS computational biology
Aug 26, 2024
MicroRNAs (miRNAs) are small non-coding RNAs that regulate gene expression post-transcriptionally. In animals, this regulation is achieved via base-pairing with partially complementary sequences on mainly 3' UTR region of messenger RNAs (mRNAs). Comp...
Adapting nanopore sequencing basecalling models for modification detection via incremental learning and anomaly detection.
Nature communications
Aug 21, 2024
We leverage machine learning approaches to adapt nanopore sequencing basecallers for nucleotide modification detection. We first apply the incremental learning (IL) technique to improve the basecalling of modification-rich sequences, which are usuall...
Current limitations in predicting mRNA translation with deep learning models.
Genome biology
Aug 20, 2024
BACKGROUND: The design of nucleotide sequences with defined properties is a long-standing problem in bioengineering. An important application is protein expression, be it in the context of research or the production of mRNA vaccines. The rate of prot...
Delineating yeast cleavage and polyadenylation signals using deep learning.
Genome research
Aug 20, 2024
3'-end cleavage and polyadenylation is an essential process for eukaryotic mRNA maturation. In yeast species, the polyadenylation signals that recruit the processing machinery are degenerate and remain poorly characterized compared with the well-defi...
Deciphering 3'UTR Mediated Gene Regulation Using Interpretable Deep Representation Learning.
Advanced science (Weinheim, Baden-Wurttemberg, Germany)
Aug 19, 2024
The 3' untranslated regions (3'UTRs) of messenger RNAs contain many important cis-regulatory elements that are under functional and evolutionary constraints. It is hypothesized that these constraints are similar to grammars and syntaxes in human lang...
AGILE platform: a deep learning powered approach to accelerate LNP development for mRNA delivery.
Nature communications
Jul 26, 2024
Ionizable lipid nanoparticles (LNPs) are seeing widespread use in mRNA delivery, notably in SARS-CoV-2 mRNA vaccines. However, the expansion of mRNA therapies beyond COVID-19 is impeded by the absence of LNPs tailored for diverse cell types. In this ...
A personalized mRNA signature for predicting hypertrophic cardiomyopathy applying machine learning methods.
Scientific reports
Jul 24, 2024
Hypertrophic cardiomyopathy (HCM) may lead to cardiac dysfunction and sudden death. This study was designed to develop a HCM signature applying bioinformatics and machine learning methods. Data of HCM and normal tissues were obtained from public data...
Optimizing 5'UTRs for mRNA-delivered gene editing using deep learning.
Nature communications
Jun 20, 2024
mRNA therapeutics are revolutionizing the pharmaceutical industry, but methods to optimize the primary sequence for increased expression are still lacking. Here, we design 5'UTRs for efficient mRNA translation using deep learning. We perform polysome...
Context-Aware Poly(A) Signal Prediction Model via Deep Spatial-Temporal Neural Networks.
IEEE transactions on neural networks and learning systems
Jun 3, 2024
Polyadenylation [Poly(A)] is an essential process during messenger RNA (mRNA) maturation in biological eukaryote systems. Identifying Poly(A) signals (PASs) from the genome level is the key to understanding the mechanism of translation regulation and...
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