AIMC Topic: Alternative Splicing

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DeepIII: Predicting Isoform-Isoform Interactions by Deep Neural Networks and Data Fusion.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
Alternative splicing enables a gene translating into different isoforms and into the corresponding proteoforms, which actually accomplish various biological functions of a living body. Isoform-isoform interactions (IIIs) provide a higher resolution i...
Protein Isoforms Alternative Splicing Humans Neural Networks, Computer
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DeepIDA: Predicting Isoform-Disease Associations by Data Fusion and Deep Neural Networks.

IEEE/ACM transactions on computational biology and bioinformatics Aug 8, 2022
Alternative splicing produces different isoforms from the same gene locus, it is an important mechanism for regulating gene expression and proteome diversity. Although the prediction of gene(ncRNA)-disease associations has been extensively studied, f...
Neural Networks, Computer Computational Biology Gene Ontology Proteome Alternative Splicing Protein Isoforms
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Using machine learning to detect the differential usage of novel gene isoforms.

BMC bioinformatics Jan 18, 2022
BACKGROUND: Differential isoform usage is an important driver of inter-individual phenotypic diversity and is linked to various diseases and traits. However, accurately detecting the differential usage of different gene transcripts between groups can...
Gene Expression Profiling Exons Machine Learning Protein Isoforms Alternative Splicing Sequence Analysis, RNA
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PIC-Me: paralogs and isoforms classifier based on machine-learning approaches.

BMC bioinformatics Oct 21, 2021
BACKGROUND: Paralogs formed through gene duplication and isoforms formed through alternative splicing have been important processes for increasing protein diversity and maintaining cellular homeostasis. Despite their recognized importance and the adv...
Machine Learning Molecular Sequence Annotation Alternative Splicing Protein Isoforms Sequence Alignment
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Alternative splicing associated with cancer stemness in kidney renal clear cell carcinoma.

BMC cancer Jun 15, 2021
BACKGROUD: Cancer stemness is associated with metastases in kidney renal clear cell carcinoma (KIRC) and negatively correlates with immune infiltrates. Recent stemness evaluation methods based on the absolute expression have been proposed to reveal t...
Machine Learning Prognosis Survival Analysis Humans Alternative Splicing Kidney Neoplasms Carcinoma, Renal Cell
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A network-based computational framework to predict and differentiate functions for gene isoforms using exon-level expression data.

Methods (San Diego, Calif.) Jun 10, 2020
MOTIVATION: Alternative splicing makes significant contributions to functional diversity of transcripts and proteins. Many alternatively spliced gene isoforms have been shown to perform specific biological functions under different contexts. In addit...
Alternative Splicing Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Protein Isoforms Exons Gene Expression Regulation Software Computational Biology Humans Neural Networks, Computer
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Enhancing Top-Down Proteomics Data Analysis by Combining Deconvolution Results through a Machine Learning Strategy.

Journal of the American Society for Mass Spectrometry Apr 8, 2020
Top-down mass spectrometry (MS) is a powerful tool for the identification and comprehensive characterization of proteoforms arising from alternative splicing, sequence variation, and post-translational modifications. However, the complex data set gen...
Humans Protein Processing, Post-Translational Tandem Mass Spectrometry Sarcomeres Muscle Proteins Alternative Splicing Machine Learning Sensitivity and Specificity Algorithms Proteomics Data Analysis
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Deep Splicing Code: Classifying Alternative Splicing Events Using Deep Learning.

Genes Aug 1, 2019
Alternative splicing (AS) is the process of combining different parts of the pre-mRNA to produce diverse transcripts and eventually different protein products from a single gene. In computational biology field, researchers try to understand AS behavi...
Humans Deep Learning Alternative Splicing Sequence Analysis, DNA
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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...
RNA High-Throughput Nucleotide Sequencing Gene Expression Regulation Deep Learning Bayes Theorem Hep G2 Cells Reproducibility of Results Exons Sequence Analysis, RNA Signal Processing, Computer-Assisted Models, Statistical Gene Expression Profiling K562 Cells Humans Alternative Splicing Epigenomics RNA Splicing Algorithms
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MMSplice: modular modeling improves the predictions of genetic variant effects on splicing.

Genome biology Mar 1, 2019
Predicting the effects of genetic variants on splicing is highly relevant for human genetics. We describe the framework MMSplice (modular modeling of splicing) with which we built the winning model of the CAGI5 exon skipping prediction challenge. The...
Genetic Diseases, Inborn Alternative Splicing Models, Genetic Genetic Variation Neural Networks, Computer
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