AIMC Topic: RNA, Messenger

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Interpreting deep neural networks for the prediction of translation rates.

BMC genomics Nov 9, 2024
BACKGROUND: The 5' untranslated region of mRNA strongly impacts the rate of translation initiation. A recent convolutional neural network (CNN) model accurately quantifies the relationship between massively parallel synthetic 5' untranslated regions ...
Humans Neural Networks, Computer 5' Untranslated Regions RNA, Messenger Protein Biosynthesis Open Reading Frames
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Predicting synthetic mRNA stability using massively parallel kinetic measurements, biophysical modeling, and machine learning.

Nature communications Nov 6, 2024
mRNA degradation is a central process that affects all gene expression levels, though it remains challenging to predict the stability of a mRNA from its sequence, due to the many coupled interactions that control degradation rate. Here, we carried ou...
Machine Learning RNA, Messenger Ribosomes RNA Stability Nucleic Acid Conformation Protein Biosynthesis RNA, Bacterial Escherichia coli Kinetics
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Development of a web-based tool for estimating individualized survival curves in glioblastoma using clinical, mRNA, and tumor microenvironment features with fusion techniques.

Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico Oct 30, 2024
OBJECTIVE: Glioblastoma (GBM), one of the most common brain tumors, is known for its low survival rates and poor treatment responses. This study aims to create a robust predictive model that integrates multiple feature types, including clinical data,...
Survival Rate Tumor Microenvironment Brain Neoplasms Aged Adult Glioblastoma Internet SEER Program Male Humans Machine Learning Middle Aged Prognosis RNA, Messenger Female
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TransC-ac4C: Identification of N4-Acetylcytidine (ac4C) Sites in mRNA Using Deep Learning.

IEEE/ACM transactions on computational biology and bioinformatics Oct 9, 2024
N4-acetylcytidine (ac4C) is a post-transcriptional modification in mRNA that is critical in mRNA translation in terms of stability and regulation. In the past few years, numerous approaches employing convolutional neural networks (CNN) and Transforme...
Cytidine RNA, Messenger Sequence Analysis, RNA Algorithms Deep Learning Computational Biology
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Rational Design of Lipid Nanoparticles for Enhanced mRNA Vaccine Delivery via Machine Learning.

Small (Weinheim an der Bergstrasse, Germany) Sep 12, 2024
Since the coronavirus pandemic, mRNA vaccines have revolutionized the field of vaccinology. Lipid nanoparticles (LNPs) are proposed to enhance mRNA delivery efficiency; however, their design is suboptimal. Here, a rational method for designing LNPs i...
Nanoparticles Lipids Liposomes Mice mRNA Vaccines RNA, Messenger Machine Learning Animals
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Identification of immune-related biomarkers for intracerebral hemorrhage diagnosis based on RNA sequencing and machine learning.

Frontiers in immunology Aug 30, 2024
BACKGROUND: Intracerebral hemorrhage (ICH) is a severe stroke subtype with high morbidity, disability, and mortality rates. Currently, no biomarkers for ICH are available for use in clinical practice. We aimed to explore the roles of RNAs in ICH path...
Sequence Analysis, RNA RNA, Long Noncoding Cerebral Hemorrhage Aged Case-Control Studies Macrophages Middle Aged Animals RNA, Messenger Biomarkers Gene Expression Profiling Humans Male Female Machine Learning Transcriptome
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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 ...
Computational Biology RNA, Messenger Bayes Theorem Humans Neural Networks, Computer Deep Learning
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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...
RNA, Messenger MicroRNAs Benchmarking Algorithms Humans Animals Machine Learning Computational Biology
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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...
Nanopore Sequencing Humans Machine Learning Animals Saccharomyces cerevisiae RNA, Messenger RNA, Transfer Escherichia coli Adenosine
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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...
Humans Deep Learning RNA, Messenger Protein Biosynthesis 5' Untranslated Regions
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