AIMC Topic: RNA Splice Sites

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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...
Computational Biology RNA Splicing RNA Splice Sites Humans Machine Learning
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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...
Introns Sequence Alignment RNA Splicing Humans Neural Networks, Computer Deep Learning RNA Splice Sites
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Towards in silico CLIP-seq: predicting protein-RNA interaction via sequence-to-signal learning.

Genome biology Aug 4, 2023
We present RBPNet, a novel deep learning method, which predicts CLIP-seq crosslink count distribution from RNA sequence at single-nucleotide resolution. By training on up to a million regions, RBPNet achieves high generalization on eCLIP, iCLIP and m...
Humans RNA-Binding Proteins Bias Mutation Computer Simulation Deep Learning RNA, Messenger Datasets as Topic Alleles Base Sequence Nucleotides Internet Binding Sites RNA RNA, Viral Nucleotide Motifs RNA Splice Sites Consensus Sequence
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An automated framework for evaluation of deep learning models for splice site predictions.

Scientific reports Jun 23, 2023
A novel framework for the automated evaluation of various deep learning-based splice site detectors is presented. The framework eliminates time-consuming development and experimenting activities for different codebases, architectures, and configurati...
Caenorhabditis elegans RNA Splice Sites Genomics RNA, Messenger Humans Data Analysis Animals Deep Learning
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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...
RNA Splicing RNA Splice Sites Benchmarking ATP-Binding Cassette Transporters Introns Deep Learning Mutation Humans
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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...
Molecular Sequence Annotation Introns Sequence Alignment RNA Splicing RNA Splice Sites Reproducibility of Results Machine Learning RNA-Seq Software Computational Biology Algorithms
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EDeepSSP: Explainable deep neural networks for exact splice sites prediction.

Journal of bioinformatics and computational biology Jul 22, 2020
Splice site prediction is crucial for understanding underlying gene regulation, gene function for better genome annotation. Many computational methods exist for recognizing the splice sites. Although most of the methods achieve a competent performanc...
Computational Biology Databases, Genetic Drosophila melanogaster RNA Splice Sites Arabidopsis Data Visualization Animals Deep Learning ROC Curve Humans Neural Networks, Computer
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SpliceFinder: ab initio prediction of splice sites using convolutional neural network.

BMC bioinformatics Dec 27, 2019
BACKGROUND: Identifying splice sites is a necessary step to analyze the location and structure of genes. Two dinucleotides, GT and AG, are highly frequent on splice sites, and many other patterns are also on splice sites with important biological fun...
Software Algorithms Animals Humans Genome Computational Biology Neural Networks, Computer RNA Splicing Databases, Genetic RNA Splice Sites Base Sequence
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Using the Chou's 5-steps rule to predict splice junctions with interpretable bidirectional long short-term memory networks.

Computers in biology and medicine Nov 21, 2019
Neural models have been able to obtain state-of-the-art performances on several genome sequence-based prediction tasks. Such models take only nucleotide sequences as input and learn relevant features on their own. However, extracting the interpretabl...
Genomics Computational Biology Neural Networks, Computer RNA Splice Sites Software
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Splice sites detection using chaos game representation and neural network.

Genomics Nov 5, 2019
A novel method is proposed to detect the acceptor and donor splice sites using chaos game representation and artificial neural network. In order to achieve high accuracy, inputs to the neural network, or feature vector, shall reflect the true nature ...
Humans Sequence Analysis, DNA Neural Networks, Computer Software Nonlinear Dynamics RNA Splice Sites
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