AI Medical Compendium Topic

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RNA, Plant

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Prediction of plant-derived xenomiRs from plant miRNA sequences using random forest and one-dimensional convolutional neural network models.

BMC genomics
BACKGROUND: An increasing number of studies reported that exogenous miRNAs (xenomiRs) can be detected in animal bodies, however, some others reported negative results. Some attributed this divergence to the selective absorption of plant-derived xenom...

Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants.

Mathematical biosciences
It has been found that each non-coding RNA (ncRNA) can act not only through its target gene, but also interact with each other to act on biological traits, and this interaction is more common. Many studies focus mainly on the analysis of microRNA(miR...

Multi-feature fusion for deep learning to predict plant lncRNA-protein interaction.

Genomics
Long non-coding RNAs (lncRNAs) play key roles in regulating cellular biological processes through diverse molecular mechanisms including binding to RNA binding proteins. The majority of plant lncRNAs are functionally uncharacterized, thus, accurate p...

A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.

BMC plant biology
BACKGROUND: Proteins are the workforce of the cell and their phosphorylation status tailors specific responses efficiently. One of the main challenges of phosphoproteomic approaches is to deconvolute biological processes that specifically respond to ...

Machine learning-aided microRNA discovery for olive oil quality.

PloS one
MicroRNAs (miRNAs) are key regulators of gene expression in plants, influencing various biological processes such as oil quality and seed development. Although, our knowledge about miRNAs in olive (Olea europaea L.) is progressing, with several miRNA...

Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network.

PeerJ
Deciphering the targets of microRNAs (miRNAs) in plants is crucial for comprehending their function and the variation in phenotype that they cause. As the highly cell-specific nature of miRNA regulation, recent computational approaches usually utiliz...

PlantC2U: deep learning of cross-species sequence landscapes predicts plastid C-to-U RNA editing in plants.

Journal of experimental botany
In plants, C-to-U RNA editing mainly occurs in plastid and mitochondrial transcripts, which contributes to a complex transcriptional regulatory network. More evidence reveals that RNA editing plays critical roles in plant growth and development. Howe...

An intelligent model for prediction of abiotic stress-responsive microRNAs in plants using statistical moments based features and ensemble approaches.

Methods (San Diego, Calif.)
This study proposed an intelligent model for predicting abiotic stress-responsive microRNAs in plants. MicroRNAs (miRNAs) are short RNA molecules regulates the stress in genes. Experimental methods are costly and time-consuming, as compare to in-sili...

PmiProPred: A novel method towards plant miRNA promoter prediction based on CNN-Transformer network and convolutional block attention mechanism.

International journal of biological macromolecules
It is crucial to understand the transcription mechanisms of miRNAs, especially considering the presence of peptides encoded by miRNAs. Since promoters function as the switch for gene transcription, precisely identifying these regions is essential for...

LMFE: A Novel Method for Predicting Plant LncRNA Based on Multi-Feature Fusion and Ensemble Learning.

Genes
: Long non-coding RNAs (lncRNAs) play a crucial regulatory role in plant trait expression and disease management, making their accurate prediction a key research focus for guiding biological experiments. While extensive studies have been conducted on...