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A model for predicting ncRNA-protein interactions based on graph neural networks and community detection.

Methods (San Diego, Calif.)
Non-coding RNA (ncRNA) s play an considerable role in the current biological sciences, such as gene transcription, gene expression, etc. Exploring the ncRNA-protein interactions(NPI) is of great significance, while some experimental techniques are ve...

Shared subspace-based radial basis function neural network for identifying ncRNAs subcellular localization.

Neural networks : the official journal of the International Neural Network Society
Non-coding RNAs (ncRNAs) play an important role in revealing the mechanism of human disease for anti-tumor and anti-virus substances. Detecting subcellular locations of ncRNAs is a necessary way to study ncRNA. Traditional biochemical methods are tim...

CTRR-ncRNA: A Knowledgebase for Cancer Therapy Resistance and Recurrence Associated Non-coding RNAs.

Genomics, proteomics & bioinformatics
Cancer therapy resistance and recurrence (CTRR) are the dominant causes of death in cancer patients. Recent studies have indicated that non-coding RNAs (ncRNAs) can not only reverse the resistance to cancer therapy but also are crucial biomarkers for...

PINC: A Tool for Non-Coding RNA Identification in Plants Based on an Automated Machine Learning Framework.

International journal of molecular sciences
There is evidence that non-coding RNAs play significant roles in the regulation of nutrient homeostasis, development, and stress responses in plants. Accurate identification of ncRNAs is the first step in determining their function. While a number of...

ncDENSE: a novel computational method based on a deep learning framework for non-coding RNAs family prediction.

BMC bioinformatics
BACKGROUND: Although research on non-coding RNAs (ncRNAs) is a hot topic in life sciences, the functions of numerous ncRNAs remain unclear. In recent years, researchers have found that ncRNAs of the same family have similar functions, therefore, it i...

HeadTailTransfer: An efficient sampling method to improve the performance of graph neural network method in predicting sparse ncRNA-protein interactions.

Computers in biology and medicine
Noncoding RNA (ncRNA) is a functional RNA derived from DNA transcription, and most transcribed genes are transcribed into ncRNA. ncRNA is not directly involved in the translation of proteins, but it can participate in gene expression in cells and aff...

RPI-EDLCN: An Ensemble Deep Learning Framework Based on Capsule Network for ncRNA-Protein Interaction Prediction.

Journal of chemical information and modeling
Noncoding RNAs (ncRNAs) play crucial roles in many cellular life activities by interacting with proteins. Identification of ncRNA-protein interactions (ncRPIs) is key to understanding the function of ncRNAs. Although a number of computational methods...

A comprehensive review and evaluation of graph neural networks for non-coding RNA and complex disease associations.

Briefings in bioinformatics
Non-coding RNAs (ncRNAs) play a critical role in the occurrence and development of numerous human diseases. Consequently, studying the associations between ncRNAs and diseases has garnered significant attention from researchers in recent years. Vario...

ConF: A Deep Learning Model Based on BiLSTM, CNN, and Cross Multi-Head Attention Mechanism for Noncoding RNA Family Prediction.

Biomolecules
This paper presents ConF, a novel deep learning model designed for accurate and efficient prediction of noncoding RNA families. NcRNAs are essential functional RNA molecules involved in various cellular processes, including replication, transcription...

Empowering Graph Neural Networks with Block-Based Dual Adaptive Deep Adjustment for Drug Resistance-Related NcRNA Discovery.

Journal of chemical information and modeling
Drug resistance to chemotherapeutic agents remains a formidable challenge in cancer treatment, significantly impacting treatment efficacy. Extensive research has exposed the intimate involvement of noncoding RNAs (ncRNAs) in conferring resistance to ...