AIMC Topic: RNA, Small Interfering

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

Journal of biomolecular structure & dynamics Aug 22, 2023
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...
Humans Neural Networks, Computer Computational Biology Support Vector Machine RNA, Small Interfering Animals Deep Learning Algorithms
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A Graph Neural Network Approach for the Analysis of siRNA-Target Biological Networks.

International journal of molecular sciences Nov 17, 2022
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...
Base Sequence Algorithms RNA, Small Interfering Neural Networks, Computer Machine Learning
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iPiDA-GCN: Identification of piRNA-disease associations based on Graph Convolutional Network.

PLoS computational biology Oct 27, 2022
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...
Software Support Vector Machine RNA, Small Interfering
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Identification of Functional piRNAs Using a Convolutional Neural Network.

IEEE/ACM transactions on computational biology and bioinformatics Jun 3, 2022
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 ...
Humans RNA, Messenger Neural Networks, Computer RNA, Small Interfering Neoplasms DNA Transposable Elements
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Accurate cancer phenotype prediction with AKLIMATE, a stacked kernel learner integrating multimodal genomic data and pathway knowledge.

PLoS computational biology Apr 16, 2021
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...
Machine Learning Phenotype Neoplasms Humans Survival Analysis Gene Knockdown Techniques Genomics RNA, Small Interfering Cell Line, Tumor
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iPiDA-sHN: Identification of Piwi-interacting RNA-disease associations by selecting high quality negative samples.

Computational biology and chemistry Aug 29, 2020
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 ...
Disease Neural Networks, Computer RNA, Small Interfering Humans
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Combining Supervised and Unsupervised Machine Learning Methods for Phenotypic Functional Genomics Screening.

SLAS discovery : advancing life sciences R & D May 13, 2020
There has been an increase in the use of machine learning and artificial intelligence (AI) for the analysis of image-based cellular screens. The accuracy of these analyses, however, is greatly dependent on the quality of the training sets used for bu...
High-Throughput Screening Assays Genome, Human Unsupervised Machine Learning RNA, Small Interfering Supervised Machine Learning Humans Phenotype Genomics
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A deep learning framework to predict binding preference of RNA constituents on protein surface.

Nature communications Oct 30, 2019
Protein-RNA interaction plays important roles in post-transcriptional regulation. However, the task of predicting these interactions given a protein structure is difficult. Here we show that, by leveraging a deep learning model NucleicNet, attributes...
Protein Binding Mice Area Under Curve RNA, Small Interfering RNA-Binding Proteins Animals Deep Learning ROC Curve Humans Ribonuclease III Argonaute Proteins Adenine Ribose Uracil Cytosine RNA Guanine Gene Knockdown Techniques Phosphates
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SiRNA silencing efficacy prediction based on a deep architecture.

BMC genomics Sep 24, 2018
BACKGROUND: Small interfering RNA (siRNA) can be used to post-transcriptional gene regulation by knocking down targeted genes. In functional genomics, biomedical research and cancer therapeutics, siRNA design is a critical research topic. Various com...
Humans Neural Networks, Computer Machine Learning RNA, Messenger RNA, Small Interfering Gene Silencing Gene Targeting Algorithms Computational Biology
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Identification of lead anti-human cytomegalovirus compounds targeting MAP4K4 via machine learning analysis of kinase inhibitor screening data.

PloS one Jul 26, 2018
Chemogenomic approaches involving highly annotated compound sets and cell based high throughput screening are emerging as a means to identify novel drug targets. We have previously screened a collection of highly characterized kinase inhibitors (Khan...
Protein Kinase Inhibitors Protein Serine-Threonine Kinases Intracellular Signaling Peptides and Proteins Cytomegalovirus Drug Discovery Humans RNA, Small Interfering Antiviral Agents Cytomegalovirus Infections Machine Learning Virus Replication Cell Line
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