AIMC Topic: RNA

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The Deep Generative Decoder: MAP estimation of representations improves modelling of single-cell RNA data.

Bioinformatics (Oxford, England) Sep 2, 2023
MOTIVATION: Learning low-dimensional representations of single-cell transcriptomics has become instrumental to its downstream analysis. The state of the art is currently represented by neural network models, such as variational autoencoders, which us...
Neural Networks, Computer Gene Expression Profiling Probability Normal Distribution Single-Cell Analysis RNA
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Platelet RNA signature independently predicts ovarian cancer prognosis by deep learning neural network model.

Protein & cell Aug 1, 2023
RNA Carcinoma, Ovarian Epithelial Neural Networks, Computer Female Humans Deep Learning Ovarian Neoplasms
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Recent trends in RNA informatics: a review of machine learning and deep learning for RNA secondary structure prediction and RNA drug discovery.

Briefings in bioinformatics Jul 20, 2023
Computational analysis of RNA sequences constitutes a crucial step in the field of RNA biology. As in other domains of the life sciences, the incorporation of artificial intelligence and machine learning techniques into RNA sequence analysis has gain...
RNA Informatics Deep Learning Aptamers, Nucleotide Artificial Intelligence Machine Learning Drug Discovery
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Structural interaction fingerprints and machine learning for predicting and explaining binding of small molecule ligands to RNA.

Briefings in bioinformatics Jul 20, 2023
Ribonucleic acids (RNAs) play crucial roles in living organisms and some of them, such as bacterial ribosomes and precursor messenger RNA, are targets of small molecule drugs, whereas others, e.g. bacterial riboswitches or viral RNA motifs are consid...
Machine Learning RNA, Messenger Humans Artificial Intelligence RNA RNA Precursors Ligands
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Concepts and methods for transcriptome-wide prediction of chemical messenger RNA modifications with machine learning.

Briefings in bioinformatics May 19, 2023
The expanding field of epitranscriptomics might rival the epigenome in the diversity of biological processes impacted. In recent years, the development of new high-throughput experimental and computational techniques has been a key driving force in d...
Transcriptome RNA, Messenger RNA Machine Learning
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Machine learning for RNA 2D structure prediction benchmarked on experimental data.

Briefings in bioinformatics May 19, 2023
Since the 1980s, dozens of computational methods have addressed the problem of predicting RNA secondary structure. Among them are those that follow standard optimization approaches and, more recently, machine learning (ML) algorithms. The former were...
RNA Algorithms Benchmarking Machine Learning Humans
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Identification of metal ion-binding sites in RNA structures using deep learning method.

Briefings in bioinformatics Mar 19, 2023
Metal ion is an indispensable factor for the proper folding, structural stability and functioning of RNA molecules. However, it is very difficult for experimental methods to detect them in RNAs. With the increase of experimentally resolved RNA struct...
RNA Ions Binding Sites Deep Learning Neural Networks, Computer Metals
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Identification of species-specific RNA N6-methyladinosine modification sites from RNA sequences.

Briefings in bioinformatics Mar 19, 2023
N6-methyladinosine (m6A) modification is the most abundant co-transcriptional modification in eukaryotic RNA and plays important roles in cellular regulation. Traditional high-throughput sequencing experiments used to explore functional mechanisms ar...
Neural Networks, Computer Base Sequence Machine Learning RNA
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RNAdegformer: accurate prediction of mRNA degradation at nucleotide resolution with deep learning.

Briefings in bioinformatics Jan 19, 2023
Messenger RNA-based therapeutics have shown tremendous potential, as demonstrated by the rapid development of messenger RNA based vaccines for COVID-19. Nevertheless, distribution of mRNA vaccines worldwide has been hampered by mRNA's inherent therma...
COVID-19 Vaccines RNA Stability RNA, Messenger Nucleotides COVID-19 Humans Deep Learning RNA
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The hitchhikers' guide to RNA sequencing and functional analysis.

Briefings in bioinformatics Jan 19, 2023
DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantific...
High-Throughput Nucleotide Sequencing Sequence Analysis, RNA Artificial Intelligence Genome RNA Gene Expression Profiling Transcriptome
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