AIMC Topic: RNA, Messenger

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Predicting functional consequences of SNPs on mRNA translation via machine learning.

Nucleic acids research Aug 25, 2023
The functional impact of single nucleotide polymorphisms (SNPs) on translation has yet to be considered when prioritizing disease-causing SNPs from genome-wide association studies (GWAS). Here we apply machine learning models to genome-wide ribosome ...
Machine Learning RNA, Messenger Protein Biosynthesis Codon, Terminator Genome-Wide Association Study Polymorphism, Single Nucleotide
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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...
RNA Precursors RNA Ligands Machine Learning RNA, Messenger Humans Artificial Intelligence
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Mechanism of liver X receptor α and ATP binding cassette transporter A1 involved in preeclampsia using an optimized deep learning model.

European review for medical and pharmacological sciences Jul 1, 2023
OBJECTIVE: Preeclampsia (PE) is a complex disease-causing multisystem damage. Many genes, environmental factors, and their interactions are involved in the development and progression of PE. The pathogenesis of PE is not fully understood, limiting th...
Humans RNA, Messenger Pre-Eclampsia Cholesterol, HDL Female Deep Learning Liver X Receptors Orphan Nuclear Receptors ATP-Binding Cassette Transporters ATP Binding Cassette Transporter 1
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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...
RNA Transcriptome RNA, Messenger Machine Learning
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Revealing determinants of translation efficiency via whole-gene codon randomization and machine learning.

Nucleic acids research Mar 21, 2023
It has been known for decades that codon usage contributes to translation efficiency and hence to protein production levels. However, its role in protein synthesis is still only partly understood. This lack of understanding hampers the design of synt...
Random Allocation Codon Protein Biosynthesis RNA, Messenger Escherichia coli Machine Learning
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An efficient deep learning based predictor for identifying miRNA-triggered phasiRNA loci in plant.

Mathematical biosciences and engineering : MBE Feb 7, 2023
Phasic small interfering RNAs are plant secondary small interference RNAs that typically generated by the convergence of miRNAs and polyadenylated mRNAs. A growing number of studies have shown that miRNA-initiated phasiRNA plays crucial roles in regu...
Plant Development Software RNA, Messenger MicroRNAs Deep Learning
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Integrated mRNA sequence optimization using deep learning.

Briefings in bioinformatics Jan 19, 2023
The coronavirus disease of 2019 pandemic has catalyzed the rapid development of mRNA vaccines, whereas, how to optimize the mRNA sequence of exogenous gene such as severe acute respiratory syndrome coronavirus 2 spike to fit human cells remains a cri...
RNA, Messenger Amino Acid Sequence COVID-19 Deep Learning Humans Base Sequence
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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...
RNA RNA Stability RNA, Messenger Nucleotides COVID-19 Deep Learning Humans COVID-19 Vaccines
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EVlncRNA-Dpred: improved prediction of experimentally validated lncRNAs by deep learning.

Briefings in bioinformatics Jan 19, 2023
Long non-coding RNAs (lncRNAs) played essential roles in nearly every biological process and disease. Many algorithms were developed to distinguish lncRNAs from mRNAs in transcriptomic data and facilitated discoveries of more than 600 000 of lncRNAs....
Humans Software Algorithms Animals RNA, Long Noncoding Computational Biology Deep Learning RNA, Messenger Mice
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Geographic encoding of transcripts enabled high-accuracy and isoform-aware deep learning of RNA methylation.

Nucleic acids research Oct 14, 2022
As the most pervasive epigenetic mark present on mRNA and lncRNA, N6-methyladenosine (m6A) RNA methylation regulates all stages of RNA life in various biological processes and disease mechanisms. Computational methods for deciphering RNA modification...
Methylation RNA, Long Noncoding 3' Untranslated Regions Protein Isoforms Deep Learning RNA RNA, Messenger
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