AIMC Topic: RNA Splicing

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Exon-intron boundary detection made easy by physicochemical properties of DNA.

Molecular omics May 15, 2025
Genome architecture in eukaryotes exhibits a high degree of complexity. Amidst the numerous intricacies, the existence of genes as non-continuous stretches composed of exons and introns has garnered significant attention and curiosity among researche...
Humans Animals Introns RNA Splicing Exons Deep Learning Computational Biology DNA
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Transformers significantly improve splice site prediction.

Communications biology Dec 4, 2024
Mutations that affect RNA splicing significantly impact human diversity and disease. Here we present a method using transformers, a type of machine learning model, to detect splicing from raw 45,000-nucleotide sequences. We generate embeddings with r...
RNA Splice Sites Machine Learning Computational Biology RNA Splicing Humans
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Splam: a deep-learning-based splice site predictor that improves spliced alignments.

Genome biology Sep 16, 2024
The process of splicing messenger RNA to remove introns plays a central role in creating genes and gene variants. We describe Splam, a novel method for predicting splice junctions in DNA using deep residual convolutional neural networks. Unlike previ...
Deep Learning Introns Sequence Alignment RNA Splicing RNA Splice Sites Humans Neural Networks, Computer
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CircCNNs, a convolutional neural network framework to better understand the biogenesis of exonic circRNAs.

Scientific reports Aug 16, 2024
Circular RNAs (circRNAs) as biomarkers for cancer detection have been extensively explored, however, the biogenesis mechanism is still elusive. In contrast to linear splicing (LS) involved in linear transcript formation, the so-called back splicing (...
Neural Networks, Computer Machine Learning Computational Biology Humans RNA, Circular RNA Splicing Exons
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Deciphering RNA splicing logic with interpretable machine learning.

Proceedings of the National Academy of Sciences of the United States of America Oct 5, 2023
Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the-art neural networks are limited by their uninterpre...
Neural Networks, Computer Machine Learning Genomics Logic RNA Splicing
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CRBPDL: Identification of circRNA-RBP interaction sites using an ensemble neural network approach.

PLoS computational biology Jan 20, 2022
Circular RNAs (circRNAs) are non-coding RNAs with a special circular structure produced formed by the reverse splicing mechanism. Increasing evidence shows that circular RNAs can directly bind to RNA-binding proteins (RBP) and play an important role ...
Binding Sites RNA Splicing RNA, Circular Machine Learning Algorithms Neural Networks, Computer Animals Computational Biology RNA-Binding Proteins Models, Biological
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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 ...
Arabidopsis RNA, Plant Phosphorylation RNA Splicing Seedlings Arabidopsis Proteins Phosphoproteins Microtubules Gene Ontology RNA, Messenger Genes, Plant Proteome Databases, Protein
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A deep learning approach to identify gene targets of a therapeutic for human splicing disorders.

Nature communications Jun 7, 2021
Pre-mRNA splicing is a key controller of human gene expression. Disturbances in splicing due to mutation lead to dysregulated protein expression and contribute to a substantial fraction of human disease. Several classes of splicing modulator compound...
tau Proteins Sterol Esterase Pyridazines Animals Mice, Transgenic Transcriptome Humans Cystic Fibrosis Transmembrane Conductance Regulator Deep Learning RNA Splicing Mutation Exons Mice Phenethylamines MutL Protein Homolog 1 Computational Biology HEK293 Cells Gene Targeting
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Benchmarking deep learning splice prediction tools using functional splice assays.

Human mutation May 20, 2021
Hereditary disorders are frequently caused by genetic variants that affect pre-messenger RNA splicing. Though genetic variants in the canonical splice motifs are almost always disrupting splicing, the pathogenicity of variants in the noncanonical spl...
Benchmarking ATP-Binding Cassette Transporters Introns Humans Deep Learning Mutation RNA Splicing RNA Splice Sites
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2passtools: two-pass alignment using machine-learning-filtered splice junctions increases the accuracy of intron detection in long-read RNA sequencing.

Genome biology Mar 1, 2021
Transcription of eukaryotic genomes involves complex alternative processing of RNAs. Sequencing of full-length RNAs using long reads reveals the true complexity of processing. However, the relatively high error rates of long-read sequencing technolog...
Computational Biology Algorithms Machine Learning Molecular Sequence Annotation Sequence Alignment Reproducibility of Results Introns RNA Splicing Software RNA-Seq RNA Splice Sites
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