AIMC Topic: RNA, Small Interfering

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Mitigating off-target effects of small RNAs: conventional approaches, network theory and artificial intelligence.

British journal of pharmacology
Three types of highly promising small RNA therapeutics, namely, small interfering RNAs (siRNAs), microRNAs (miRNAs) and the RNA subtype of antisense oligonucleotides (ASOs), offer advantages over small-molecule drugs. These small RNAs can target any ...

piRNA in Machine-Learning-Based Diagnostics of Colorectal Cancer.

Molecules (Basel, Switzerland)
Objective biomarkers are crucial for early diagnosis to promote treatment and raise survival rates for diseases. With the smallest non-coding RNAs-piwi-RNAs (piRNAs)-and their transcripts, we sought to identify if these piRNAs could be used as biomar...

Cm-siRPred: Predicting chemically modified siRNA efficiency based on multi-view learning strategy.

International journal of biological macromolecules
The rational modification of siRNA molecules is crucial for ensuring their drug-like properties. Machine learning-based prediction of chemically modified siRNA (cm-siRNA) efficiency can significantly optimize the design process of siRNA chemical modi...

LSTM4piRNA: Efficient piRNA Detection in Large-Scale Genome Databases Using a Deep Learning-Based LSTM Network.

International journal of molecular sciences
Piwi-interacting RNAs (piRNAs) are a new class of small, non-coding RNAs, crucial in the regulation of gene expression. Recent research has revealed links between piRNAs, viral defense mechanisms, and certain human cancers. Due to their clinical pote...

A bi-layer model for identification of piwiRNA using deep neural learning.

Journal of biomolecular structure & dynamics
piwiRNA is a kind of non-coding RNA (ncRNA) that cannot be translated into proteins. It helps in understanding the study of gametes generation and regulation of gene expression over both transcriptional and post-transcriptional levels. piwiRNA has th...

A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks.

International journal of molecular sciences
Many biological systems are characterised by biological entities, as well as their relationships. These interaction networks can be modelled as graphs, with nodes representing bio-entities, such as molecules, and edges representing relations among th...

iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network.

PLoS computational biology
MOTIVATION: Piwi-interacting RNAs (piRNAs) play a critical role in the progression of various diseases. Accurately identifying the associations between piRNAs and diseases is important for diagnosing and prognosticating diseases. Although some comput...

Identification of Functional piRNAs Using a Convolutional Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics
Piwi-interacting RNAs (piRNAs) are a distinct sub-class of small non-coding RNAs that are mainly responsible for germline stem cell maintenance, gene stability, and maintaining genome integrity by repression of transposable elements. piRNAs are also ...

Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.

PLoS computational biology
Advancements in sequencing have led to the proliferation of multi-omic profiles of human cells under different conditions and perturbations. In addition, many databases have amassed information about pathways and gene "signatures"-patterns of gene ex...

iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples.

Computational biology and chemistry
As a large group of small non-coding RNAs (ncRNAs), Piwi-interacting RNAs (piRNAs) have been detected to be associated with various diseases. Identifying disease associated piRNAs can provide promising candidate molecular targets to promote the drug ...