AIMC Topic: Nucleotides

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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 Stability Nucleotides RNA COVID-19 Deep Learning Humans COVID-19 Vaccines RNA, Messenger
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DNA-MP: a generalized DNA modifications predictor for multiple species based on powerful sequence encoding method.

Briefings in bioinformatics Jan 19, 2023
Accurate prediction of deoxyribonucleic acid (DNA) modifications is essential to explore and discern the process of cell differentiation, gene expression and epigenetic regulation. Several computational approaches have been proposed for particular ty...
Machine Learning DNA Nucleotides Software Epigenesis, Genetic
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R5hmCFDV: computational identification of RNA 5-hydroxymethylcytosine based on deep feature fusion and deep voting.

Briefings in bioinformatics Sep 20, 2022
RNA 5-hydroxymethylcytosine (5hmC) is a kind of RNA modification, which is related to the life activities of many organisms. Studying its distribution is very important to reveal its biological function. Previously, high-throughput sequencing was use...
Machine Learning Nucleotides Neural Networks, Computer 5-Methylcytosine RNA
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PIPENN: protein interface prediction from sequence with an ensemble of neural nets.

Bioinformatics (Oxford, England) Apr 12, 2022
MOTIVATION: The interactions between proteins and other molecules are essential to many biological and cellular processes. Experimental identification of interface residues is a time-consuming, costly and challenging task, while protein sequence data...
Proteins Amino Acid Sequence Software Computational Biology Nucleotides Machine Learning
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Machine Learning Prediction of Non-Coding Variant Impact in Human Retinal cis-Regulatory Elements.

Translational vision science & technology Apr 1, 2022
PURPOSE: Prior studies have demonstrated the significance of specific cis-regulatory variants in retinal disease; however, determining the functional impact of regulatory variants remains a major challenge. In this study, we utilized a machine learni...
Retina Nucleotides Retinal Diseases Phylogeny Transcription Factors Machine Learning Humans
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DeepSVP: integration of genotype and phenotype for structural variant prioritization using deep learning.

Bioinformatics (Oxford, England) Mar 4, 2022
MOTIVATION: Structural genomic variants account for much of human variability and are involved in several diseases. Structural variants are complex and may affect coding regions of multiple genes, or affect the functions of genomic regions in differe...
Genomics Genotype Nucleotides Phenotype Deep Learning Humans
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m1A-pred: Prediction of Modified 1-methyladenosine Sites in RNA Sequences through Artificial Intelligence.

Combinatorial chemistry & high throughput screening Jan 1, 2022
BACKGROUND: The process of nucleotides modification or methyl groups addition to nucleotides is known as post-transcriptional modification (PTM). 1-methyladenosine (m1A) is a type of PTM formed by adding a methyl group to the nitrogen at the 1st posi...
Humans Artificial Intelligence Nucleotides RNA Base Sequence
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IDRMutPred: predicting disease-associated germline nonsynonymous single nucleotide variants (nsSNVs) in intrinsically disordered regions.

Bioinformatics (Oxford, England) Dec 22, 2020
MOTIVATION: Despite of the lack of folded structure, intrinsically disordered regions (IDRs) of proteins play versatile roles in various biological processes, and many nonsynonymous single nucleotide variants (nsSNVs) in IDRs are associated with huma...
Sequence Alignment Germ Cells Intrinsically Disordered Proteins Algorithms Humans Nucleotides Machine Learning
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iRNAD: a computational tool for identifying D modification sites in RNA sequence.

Bioinformatics (Oxford, England) Dec 1, 2019
MOTIVATION: Dihydrouridine (D) is a common RNA post-transcriptional modification found in eukaryotes, bacteria and a few archaea. The modification can promote the conformational flexibility of individual nucleotide bases. And its levels are increased...
RNA Base Sequence Support Vector Machine Reproducibility of Results Nucleotides Computational Biology
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Boosting Granular Support Vector Machines for the Accurate Prediction of Protein-Nucleotide Binding Sites.

Combinatorial chemistry & high throughput screening Jan 1, 2019
AIM AND OBJECTIVE: The accurate identification of protein-ligand binding sites helps elucidate protein function and facilitate the design of new drugs. Machine-learning-based methods have been widely used for the prediction of protein-ligand binding ...
High-Throughput Screening Assays Proteins Support Vector Machine Binding Sites Nucleotides
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