AIMC Topic: RNA Splice Sites

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Human Splice-Site Prediction with Deep Neural Networks.

Journal of computational biology : a journal of computational molecular cell biology Apr 18, 2018
Accurate splice-site prediction is essential to delineate gene structures from sequence data. Several computational techniques have been applied to create a system to predict canonical splice sites. For classification tasks, deep neural networks (DNN...
Software Algorithms Deep Learning Computational Biology Computer Graphics RNA Splice Sites Position-Specific Scoring Matrices Humans Neural Networks, Computer
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Markovian encoding models in human splice site recognition using SVM.

Computational biology and chemistry Feb 14, 2018
Splice site recognition is among the most significant and challenging tasks in bioinformatics due to its key role in gene annotation. Effective prediction of splice site requires nucleotide encoding methods that reveal the characteristics of DNA sequ...
RNA Splice Sites Humans Support Vector Machine Markov Chains
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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...
Quantitative Trait Loci Models, Genetic RNA Splicing Nuclear Proteins Child Development Disorders, Pervasive Genetic Code Adaptor Proteins, Signal Transducing Genome-Wide Association Study MutL Protein Homolog 1 Colorectal Neoplasms, Hereditary Nonpolyposis DNA Polymorphism, Single Nucleotide RNA Splice Sites Molecular Sequence Annotation Muscular Atrophy, Spinal Humans Genetic Markers RNA-Binding Proteins Introns Exons Artificial Intelligence Genetic Variation Mutation, Missense Computer Simulation
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Probabilistic and machine-learning methods for predicting local rates of transcription elongation from nascent RNA sequencing data.

Nucleic acids research Feb 8, 2025
Rates of transcription elongation vary within and across eukaryotic gene bodies. Here, we introduce new methods for predicting elongation rates from nascent RNA sequencing data. First, we devise a probabilistic model that predicts nucleotide-specific...
Sequence Analysis, RNA Epigenomics RNA Splice Sites Models, Statistical CCCTC-Binding Factor Humans DNA Methylation Histones Transcription Elongation, Genetic Binding Sites Neural Networks, Computer Histone Code Machine Learning
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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...
RNA, Messenger Gene Expression Introns RNA Splicing Exons RNA Splice Sites Algorithms Deep Learning Computational Biology Humans Neural Networks, Computer
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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...
HEK293 Cells Base Sequence Genome, Human Protein Processing, Post-Translational Models, Biological HeLa Cells Nucleotide Motifs RNA Splicing RNA Splice Sites Histones Binding Sites RNA Polymerase II Humans Machine Learning Epigenesis, Genetic DNA Methylation Transcription Elongation, Genetic
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Biogenesis mechanisms of circular RNA can be categorized through feature extraction of a machine learning model.

Bioinformatics (Oxford, England) Dec 1, 2019
MOTIVATION: In recent years, multiple circular RNAs (circRNA) biogenesis mechanisms have been discovered. Although each reported mechanism has been experimentally verified in different circRNAs, no single biogenesis mechanism has been proposed that c...
RNA Splice Sites RNA, Circular Machine Learning RNA-Binding Proteins RNA Splicing Humans
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DeepDSSR: Deep Learning Structure for Human Donor Splice Sites Recognition.

Studies in health technology and informatics Jul 4, 2019
Human genes often, through alternative splicing of pre-messenger RNAs, produce multiple mRNAs and protein isoforms that may have similar or completely different functions. Identification of splice sites is, therefore, crucial to understand the gene s...
RNA, Messenger RNA Splice Sites Humans Deep Learning
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COSSMO: predicting competitive alternative splice site selection using deep learning.

Bioinformatics (Oxford, England) Jul 1, 2018
MOTIVATION: Alternative splice site selection is inherently competitive and the probability of a given splice site to be used also depends on the strength of neighboring sites. Here, we present a new model named the competitive splice site model (COS...
Models, Genetic Alternative Splicing Humans Deep Learning Probability RNA Splice Sites Software Computational Biology Sequence Analysis, RNA
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