AIMC Topic: RNA, Plant

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

Genes Mar 31, 2025
: 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...
RNA, Plant Plants Ensemble Learning Machine Learning Computational Biology RNA, Long Noncoding Algorithms
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PmiProPred: A novel method towards plant miRNA promoter prediction based on CNN-Transformer network and convolutional block attention mechanism.

International journal of biological macromolecules Feb 3, 2025
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...
Neural Networks, Computer RNA, Plant Plants Software Computational Biology Promoter Regions, Genetic MicroRNAs
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Machine learning-aided microRNA discovery for olive oil quality.

PloS one Oct 11, 2024
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...
RNA, Plant Olive Oil Machine Learning Gene Expression Regulation, Plant Support Vector Machine MicroRNAs Olea
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Plant lncRNA-miRNA Interaction Prediction Based on Counterfactual Heterogeneous Graph Attention Network.

Interdisciplinary sciences, computational life sciences Oct 9, 2024
Identifying interactions between long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) provides a new perspective for understanding regulatory relationships in plant life processes. Recently, computational methods based on graph neural networks (GNNs...
Neural Networks, Computer Algorithms RNA, Long Noncoding Plants RNA, Plant Computational Biology MicroRNAs
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Improving plant miRNA-target prediction with self-supervised k-mer embedding and spectral graph convolutional neural network.

PeerJ May 21, 2024
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...
RNA, Plant Neural Networks, Computer MicroRNAs Gene Expression Regulation, Plant Computational Biology
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An intelligent model for prediction of abiotic stress-responsive microRNAs in plants using statistical moments based features and ensemble approaches.

Methods (San Diego, Calif.) May 18, 2024
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...
Computational Biology Support Vector Machine MicroRNAs Algorithms Gene Expression Regulation, Plant RNA, Plant Plants Stress, Physiological
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A novel strategy to uncover specific GO terms/phosphorylation pathways in phosphoproteomic data in Arabidopsis thaliana.

BMC plant biology Dec 14, 2021
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 ...
RNA, Messenger Arabidopsis Proteins Proteome Gene Ontology Phosphorylation RNA, Plant Databases, Protein Arabidopsis Genes, Plant Phosphoproteins Seedlings RNA Splicing Microtubules
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Multi-feature fusion for deep learning to predict plant lncRNA-protein interaction.

Genomics May 11, 2020
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...
Plant Proteins Arabidopsis RNA, Plant Deep Learning RNA, Long Noncoding RNA-Binding Proteins Zea mays
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Predicting miRNA-lncRNA interactions and recognizing their regulatory roles in stress response of plants.

Mathematical biosciences Apr 26, 2019
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...
Support Vector Machine MicroRNAs RNA, Long Noncoding RNA, Messenger RNA, Plant Gene Regulatory Networks Stress, Physiological Models, Genetic Arabidopsis
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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 Nov 26, 2018
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...
Plants Biomarkers RNA, Plant Databases, Nucleic Acid Humans High-Throughput Nucleotide Sequencing MicroRNAs Neural Networks, Computer
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