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RNA Splicing

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SpliceFinder: ab initio prediction of splice sites using convolutional neural network.

BMC bioinformatics 31881982
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...
Algorithms Animals Base Sequence Computational Biology Databases, Genetic Genome Humans Neural Networks, Computer RNA Splice Sites RNA Splicing Software
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Epigenome-based splicing prediction using a recurrent neural network.

PLoS computational biology 32584815
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...
Epigenome Humans Neural Networks, Computer RNA Splicing
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Enhanced Integrated Gradients: improving interpretability of deep learning models using splicing codes as a case study.

Genome biology 32560708
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 Computational Biology Deep Learning Liver Mice, Knockout RNA Splicing
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Prediction of Alzheimer's disease-specific phospholipase c gamma-1 SNV by deep learning-based approach for high-throughput screening.

Proceedings of the National Academy of Sciences of the United States of America 33397809
Exon splicing triggered by unpredicted genetic mutation can cause translational variations in neurodegenerative disorders. In this study, we discover Alzheimer's disease (AD)-specific single-nucleotide variants (SNVs) and abnormal exon splicing of ph...
Alzheimer Disease Animals Computer Simulation Deep Learning Disease Models, Animal Exons Genetic Predisposition to Disease Genome-Wide Association Study Genome, Human High-Throughput Screening Assays Humans Mice Phospholipase C gamma Polymorphism, Single Nucleotide RNA Splicing RNA, Messenger
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CADD-Splice-improving genome-wide variant effect prediction using deep learning-derived splice scores.

Genome medicine 33618777
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...
Base Sequence Deep Learning Exons Genetic Variation Genome-Wide Association Study Humans Introns RNA Splicing
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A machine learning-based framework for modeling transcription elongation.

Proceedings of the National Academy of Sciences of the United States of America 33526657
RNA polymerase II (Pol II) generally pauses at certain positions along gene bodies, thereby interrupting the transcription elongation process, which is often coupled with various important biological functions, such as precursor mRNA splicing and gen...
Base Sequence Binding Sites DNA Methylation Epigenesis, Genetic Genome, Human HEK293 Cells HeLa Cells Histones Humans Machine Learning Models, Biological Nucleotide Motifs Protein Processing, Post-Translational RNA Polymerase II RNA Splice Sites RNA Splicing Transcription Elongation, Genetic
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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 33648554
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...
Algorithms Computational Biology Introns Machine Learning Molecular Sequence Annotation Reproducibility of Results RNA Splice Sites RNA Splicing RNA-Seq Sequence Alignment Software
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Benchmarking deep learning splice prediction tools using functional splice assays.

Human mutation 33942434
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...
ATP-Binding Cassette Transporters Benchmarking Deep Learning Humans Introns Mutation RNA Splice Sites RNA Splicing
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A deep learning approach to identify gene targets of a therapeutic for human splicing disorders.

Nature communications 34099697
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...
Animals Computational Biology Cystic Fibrosis Transmembrane Conductance Regulator Deep Learning Exons Gene Targeting HEK293 Cells Humans Mice Mice, Transgenic Mutation MutL Protein Homolog 1 Phenethylamines Pyridazines RNA Splicing Sterol Esterase tau Proteins Transcriptome
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eSkip-Finder: a machine learning-based web application and database to identify the optimal sequences of antisense oligonucleotides for exon skipping.

Nucleic acids research 34104972
Exon skipping using antisense oligonucleotides (ASOs) has recently proven to be a powerful tool for mRNA splicing modulation. Several exon-skipping ASOs have been approved to treat genetic diseases worldwide. However, a significant challenge is the d...
Databases, Nucleic Acid Exons Internet Introns Machine Learning Oligonucleotides, Antisense RNA Splicing Sequence Analysis Software
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