AIMC Topic: RNA Splicing

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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...
Humans Deep Learning Introns RNA Splicing RNA Splice Sites Mutation Benchmarking ATP-Binding Cassette Transporters
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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...
RNA Splice Sites RNA-Seq Introns Software Computational Biology Sequence Alignment Machine Learning RNA Splicing Algorithms Molecular Sequence Annotation Reproducibility of Results
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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.

Genome medicine Feb 22, 2021
BACKGROUND: Splicing of genomic exons into mRNAs is a critical prerequisite for the accurate synthesis of human proteins. Genetic variants impacting splicing underlie a substantial proportion of genetic disease, but are challenging to identify beyond...
Humans Deep Learning Genome-Wide Association Study RNA Splicing Exons Genetic Variation Base Sequence Introns
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Epigenome-based splicing prediction using a recurrent neural network.

PLoS computational biology Jun 25, 2020
Alternative RNA splicing provides an important means to expand metazoan transcriptome diversity. Contrary to what was accepted previously, splicing is now thought to predominantly take place during transcription. Motivated by emerging data showing th...
Neural Networks, Computer Epigenome RNA Splicing Humans
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Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study.

Genome biology Jun 19, 2020
Despite the success and fast adaptation of deep learning models in biomedical domains, their lack of interpretability remains an issue. Here, we introduce Enhanced Integrated Gradients (EIG), a method to identify significant features associated with ...
Animals Deep Learning Computational Biology Liver Mice, Knockout RNA Splicing
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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...
Databases, Genetic Base Sequence Genome RNA Splicing RNA Splice Sites Algorithms Animals Computational Biology Humans Neural Networks, Computer Software
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Machine Learning Approaches for the Prioritization of Genomic Variants Impacting Pre-mRNA Splicing.

Cells Nov 26, 2019
Defects in pre-mRNA splicing are frequently a cause of Mendelian disease. Despite the advent of next-generation sequencing, allowing a deeper insight into a patient's variant landscape, the ability to characterize variants causing splicing defects ha...
Computational Biology Models, Biological Genetic Variation Molecular Sequence Annotation RNA Precursors RNA Splicing Machine Learning Humans Genomics Genetic Predisposition to Disease
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Deep-learning augmented RNA-seq analysis of transcript splicing.

Nature methods Mar 25, 2019
A major limitation of RNA sequencing (RNA-seq) analysis of alternative splicing is its reliance on high sequencing coverage. We report DARTS (https://github.com/Xinglab/DARTS), a computational framework that integrates deep-learning-based predictions...
Alternative Splicing Sequence Analysis, RNA Epigenomics K562 Cells Hep G2 Cells RNA Splicing Exons Reproducibility of Results Humans Gene Expression Profiling Models, Statistical Algorithms RNA Deep Learning Bayes Theorem High-Throughput Nucleotide Sequencing Signal Processing, Computer-Assisted Gene Expression Regulation
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RNA sequencing and swarm intelligence-enhanced classification algorithm development for blood-based disease diagnostics using spliced blood platelet RNA.

Nature protocols Mar 20, 2019
Blood-based diagnostics tests, using individual or panels of biomarkers, may revolutionize disease diagnostics and enable minimally invasive therapy monitoring. However, selection of the most relevant biomarkers from liquid biosources remains an imme...
Computational Biology DNA, Complementary Humans RNA, Messenger Biomarkers RNA Splicing Support Vector Machine Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Blood Platelets
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Discerning novel splice junctions derived from RNA-seq alignment: a deep learning approach.

BMC genomics Dec 27, 2018
BACKGROUND: Exon splicing is a regulated cellular process in the transcription of protein-coding genes. Technological advancements and cost reductions in RNA sequencing have made quantitative and qualitative assessments of the transcriptome both poss...
Genome, Human Humans Exons Gene Expression Profiling Software Sequence Alignment Deep Learning RNA Splicing Sequence Analysis, RNA
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