AIMC Topic: RNA Splicing

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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 Introns RNA Splicing Exons Genome-Wide Association Study Genetic Variation Base Sequence
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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...
Humans Neural Networks, Computer Epigenome RNA Splicing
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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 ...
RNA Splicing Computational Biology Liver Mice, Knockout Animals Deep Learning
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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...
Algorithms Animals Computational Biology Humans Neural Networks, Computer Software Genome RNA Splicing RNA Splice Sites Databases, Genetic Base Sequence
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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...
Molecular Sequence Annotation RNA Precursors RNA Splicing Computational Biology Models, Biological Genetic Variation Humans Machine Learning 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...
Gene Expression Profiling Deep Learning Sequence Analysis, RNA Epigenomics Hep G2 Cells Models, Statistical Humans Algorithms Reproducibility of Results RNA Splicing Exons Alternative Splicing High-Throughput Nucleotide Sequencing Bayes Theorem Gene Expression Regulation Signal Processing, Computer-Assisted K562 Cells RNA
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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...
DNA, Complementary RNA Splicing Support Vector Machine High-Throughput Nucleotide Sequencing RNA, Messenger Humans Blood Platelets Sequence Analysis, RNA Biomarkers Computational Biology
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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...
Humans RNA Splicing Exons Sequence Analysis, RNA Genome, Human Sequence Alignment Software Gene Expression Profiling Deep Learning
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Modeling and Predicting the Activities of Trans-Acting Splicing Factors with Machine Learning.

Cell systems Nov 7, 2018
Alternative splicing (AS) is generally regulated by trans-splicing factors that specifically bind to cis-elements in pre-mRNAs. The human genome encodes ∼1,500 RNA binding proteins (RBPs) that potentially regulate AS, yet their functions remain large...
RNA Splicing RNA Splicing Factors Machine Learning Humans Computational Biology Models, Genetic
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Predicting human splicing branchpoints by combining sequence-derived features and multi-label learning methods.

BMC bioinformatics Dec 1, 2017
BACKGROUND: Alternative splicing is the critical process in a single gene coding, which removes introns and joins exons, and splicing branchpoints are indicators for the alternative splicing. Wet experiments have identified a great number of human sp...
Introns Computational Biology Exons Humans Nucleotide Motifs Base Sequence Position-Specific Scoring Matrices Machine Learning RNA Splicing Genome, Human
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