AIMC Topic: RNA Splicing

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An empirical study of ensemble-based semi-supervised learning approaches for imbalanced splice site datasets.

BMC systems biology Sep 1, 2015
BACKGROUND: Recent biochemical advances have led to inexpensive, time-efficient production of massive volumes of raw genomic data. Traditional machine learning approaches to genome annotation typically rely on large amounts of labeled data. The proce...
Supervised Machine Learning Algorithms Molecular Sequence Annotation Genomics RNA Splicing Databases, Genetic
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RNA splicing. The human splicing code reveals new insights into the genetic determinants of disease.

Science (New York, N.Y.) Dec 18, 2014
To facilitate precision medicine and whole-genome annotation, we developed a machine-learning technique that scores how strongly genetic variants affect RNA splicing, whose alteration contributes to many diseases. Analysis of more than 650,000 intron...
Genetic Variation RNA Splice Sites Molecular Sequence Annotation Artificial Intelligence Muscular Atrophy, Spinal Introns Computer Simulation Adaptor Proteins, Signal Transducing Exons Genome-Wide Association Study Mutation, Missense Genetic Code DNA Quantitative Trait Loci Polymorphism, Single Nucleotide MutL Protein Homolog 1 Humans RNA Splicing Genetic Markers RNA-Binding Proteins Models, Genetic Child Development Disorders, Pervasive Nuclear Proteins Colorectal Neoplasms, Hereditary Nonpolyposis
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Detection of pre-mRNA involved in abnormal splicing using Graph Neural Network and Nearest Correlation Method.

Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference Jul 1, 2024
BACKGROUND: DNA is the building block of genetic information, and is composed of alternating sequences of exons with genetic information and introns without no genetic information. DNA is damaged by normal metabolic activities and environmental facto...
Graph Neural Networks Polymorphism, Single Nucleotide RNA Precursors RNA Splicing Humans Neural Networks, Computer Algorithms ROC Curve
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Study of prognostic splicing factors in cancer using machine learning approaches.

Human molecular genetics Jun 21, 2024
Splicing factors (SFs) are the major RNA-binding proteins (RBPs) and key molecules that regulate the splicing of mRNA molecules through binding to mRNAs. The expression of splicing factors is frequently deregulated in different cancer types, causing ...
Humans Machine Learning Prognosis Gene Expression Regulation, Neoplastic RNA Splicing Alternative Splicing RNA Splicing Factors Carcinoma, Hepatocellular Computational Biology RNA, Messenger RNA-Binding Proteins Biomarkers, Tumor Neoplasms Liver Neoplasms
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An effective deep learning-based approach for splice site identification in gene expression.

Science progress Jan 1, 2024
A crucial stage in eukaryote gene expression involves mRNA splicing by a protein assembly known as the spliceosome. This step significantly contributes to generating and properly operating the ultimate gene product. Since non-coding introns disrupt e...
Humans Neural Networks, Computer Algorithms Introns RNA Splicing Exons RNA Splice Sites Deep Learning Computational Biology RNA, Messenger Gene Expression
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Decoding the effects of synonymous variants.

Nucleic acids research Dec 16, 2021
Synonymous single nucleotide variants (sSNVs) are common in the human genome but are often overlooked. However, sSNVs can have significant biological impact and may lead to disease. Existing computational methods for evaluating the effect of sSNVs su...
Humans Machine Learning RNA Splicing Proteins Genetic Variation Genome, Human Disease
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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 Jul 2, 2021
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...
Exons Oligonucleotides, Antisense Databases, Nucleic Acid Sequence Analysis RNA Splicing Machine Learning Software Internet Introns
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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 Feb 9, 2021
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...
RNA Splicing RNA Splice Sites Transcription Elongation, Genetic Histones Binding Sites RNA Polymerase II Nucleotide Motifs HEK293 Cells Base Sequence Genome, Human Humans Machine Learning Epigenesis, Genetic DNA Methylation Protein Processing, Post-Translational Models, Biological HeLa Cells
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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 Jan 19, 2021
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...
Humans Computer Simulation Animals Deep Learning Genome-Wide Association Study Mice Genetic Predisposition to Disease Polymorphism, Single Nucleotide Phospholipase C gamma High-Throughput Screening Assays RNA, Messenger Genome, Human Disease Models, Animal RNA Splicing Alzheimer Disease Exons
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Deep learning of the back-splicing code for circular RNA formation.

Bioinformatics (Oxford, England) Dec 15, 2019
MOTIVATION: Circular RNAs (circRNAs) are a new class of endogenous RNAs in animals and plants. During pre-RNA splicing, the 5' and 3' termini of exon(s) can be covalently ligated to form circRNAs through back-splicing (head-to-tail splicing). CircRNA...
Mice Sequence Analysis, RNA RNA Splicing RNA, Circular Animals Deep Learning
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