AIMC Topic: RNA

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m5c-iDeep: 5-Methylcytosine sites identification through deep learning.

Methods (San Diego, Calif.) Jul 31, 2024
5-Methylcytosine (m5c) is a modified cytosine base which is formed as the result of addition of methyl group added at position 5 of carbon. This modification is one of the most common PTM that used to occur in almost all types of RNA. The conventiona...
RNA 5-Methylcytosine Deep Learning Computational Biology Humans Computer Simulation
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pyRBDome: a comprehensive computational platform for enhancing RNA-binding proteome data.

Life science alliance Jul 30, 2024
High-throughput proteomics approaches have revolutionised the identification of RNA-binding proteins (RBPome) and RNA-binding sequences (RBDome) across organisms. Yet, the extent of noise, including false positives, associated with these methodologie...
Computational Biology RNA-Binding Proteins Software Protein Binding Databases, Protein RNA Binding Sites Proteomics Proteome Humans Machine Learning
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Exploring the roles of RNAs in chromatin architecture using deep learning.

Nature communications Jul 29, 2024
Recent studies have highlighted the impact of both transcription and transcripts on 3D genome organization, particularly its dynamics. Here, we propose a deep learning framework, called AkitaR, that leverages both genome sequences and genome-wide RNA...
DNA RNA Chromatin Cell Line RNA, Long Noncoding Humans Deep Learning
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Moss-m7G: A Motif-Based Interpretable Deep Learning Method for RNA N7-Methlguanosine Site Prediction.

Journal of chemical information and modeling Jul 16, 2024
N-7methylguanosine (m7G) modification plays a crucial role in various biological processes and is closely associated with the development and progression of many cancers. Accurate identification of m7G modification sites is essential for understandin...
Deep Learning Guanosine RNA Nucleotide Motifs
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Self-supervised learning for characterising histomorphological diversity and spatial RNA expression prediction across 23 human tissue types.

Nature communications Jul 13, 2024
As vast histological archives are digitised, there is a pressing need to be able to associate specific tissue substructures and incident pathology to disease outcomes without arduous annotation. Here, we learn self-supervised representations using a ...
Humans Supervised Machine Learning RNA Organ Specificity Gene Expression Profiling Image Processing, Computer-Assisted
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Improving platelet-RNA-based diagnostics: a comparative analysis of machine learning models for cancer detection and multiclass classification.

Molecular oncology Jun 17, 2024
Liquid biopsy demonstrates excellent potential in patient management by providing a minimally invasive and cost-effective approach to detecting and monitoring cancer, even at its early stages. Due to the complexity of liquid biopsy data, machine-lear...
Blood Platelets Liquid Biopsy Neoplasms RNA Humans RNA, Neoplasm Machine Learning
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Machine Learning-Assisted Direct RNA Sequencing with Epigenetic RNA Modification Detection via Quantum Tunneling.

Analytical chemistry Jun 14, 2024
RNA sequence information holds immense potential as a drug target for diagnosing various RNA-mediated diseases and viral/bacterial infections. Massively parallel complementary DNA (c-DNA) sequencing helps but results in a loss of valuable information...
High-Throughput Nucleotide Sequencing Machine Learning Quantum Theory Sequence Analysis, RNA RNA Epigenesis, Genetic Humans
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Big data and deep learning for RNA biology.

Experimental & molecular medicine Jun 14, 2024
The exponential growth of big data in RNA biology (RB) has led to the development of deep learning (DL) models that have driven crucial discoveries. As constantly evidenced by DL studies in other fields, the successful implementation of DL in RB depe...
Algorithms Animals Deep Learning Computational Biology Big Data Humans RNA
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MAHyNet: Parallel Hybrid Network for RNA-Protein Binding Sites Prediction Based on Multi-Head Attention and Expectation Pooling.

IEEE/ACM transactions on computational biology and bioinformatics Jun 5, 2024
RNA-binding proteins (RBPs) can regulate biological functions by interacting with specific RNAs, and play an important role in many life activities. Therefore, the rapid identification of RNA-protein binding sites is crucial for functional annotation...
RNA Computational Biology Binding Sites Neural Networks, Computer RNA-Binding Proteins Algorithms
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[Not Available].

Proteomics Jun 2, 2024
RNA-dependent liquid-liquid phase separation (LLPS) proteins play critical roles in cellular processes such as stress granule formation, DNA repair, RNA metabolism, germ cell development, and protein translation regulation. The abnormal behavior of t...
Computational Biology Proteins RNA Phase Separation Databases, Protein Humans Artificial Intelligence
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