AIMC Topic: Alternative Splicing

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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...
Carcinoma, Renal Cell Alternative Splicing Prognosis Survival Analysis Kidney Neoplasms Humans Machine Learning
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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...
Gene Expression Regulation Computational Biology Alternative Splicing Protein Isoforms Sequence Analysis, RNA Exons Humans High-Throughput Nucleotide Sequencing Neural Networks, Computer Software
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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...
Data Analysis Algorithms Sensitivity and Specificity Humans Machine Learning Alternative Splicing Sarcomeres Muscle Proteins Proteomics Protein Processing, Post-Translational Tandem Mass Spectrometry
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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...
Alternative Splicing Humans Deep Learning 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...
Alternative Splicing K562 Cells RNA Splicing Exons Humans Algorithms Models, Statistical Bayes Theorem Signal Processing, Computer-Assisted RNA Sequence Analysis, RNA Reproducibility of Results High-Throughput Nucleotide Sequencing Epigenomics Gene Expression Profiling Gene Expression Regulation Hep G2 Cells Deep Learning
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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 Variation Genetic Diseases, Inborn Alternative Splicing Neural Networks, Computer Models, Genetic
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DeepM6ASeq: prediction and characterization of m6A-containing sequences using deep learning.

BMC bioinformatics Dec 31, 2018
BACKGROUND: N6-methyladensine (m6A) is a common and abundant RNA methylation modification found in various species. As a type of post-transcriptional methylation, m6A plays an important role in diverse RNA activities such as alternative splicing, an ...
Methylation Adenosine Alternative Splicing Embryonic Stem Cells Animals Sequence Analysis, RNA Deep Learning Zebrafish Liver Neoplasms RNA Carcinoma, Hepatocellular Humans Mice Brain Computational Biology
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Biological classification with RNA-seq data: Can alternatively spliced transcript expression enhance machine learning classifiers?

RNA (New York, N.Y.) Jun 25, 2018
RNA sequencing (RNA-seq) is becoming a prevalent approach to quantify gene expression and is expected to gain better insights into a number of biological and biomedical questions compared to DNA microarrays. Most importantly, RNA-seq allows us to qua...
Data Mining RNA Organ Specificity Gene Expression Profiling Humans Sequence Analysis, RNA Animals Supervised Machine Learning Alternative Splicing
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Semi-supervised Learning Predicts Approximately One Third of the Alternative Splicing Isoforms as Functional Proteins.

Cell reports Jul 2, 2015
Alternative splicing acts on transcripts from almost all human multi-exon genes. Notwithstanding its ubiquity, fundamental ramifications of splicing on protein expression remain unresolved. The number and identity of spliced transcripts that form sta...
Proteins Protein Isoforms Alternative Splicing Humans Area Under Curve Protein Structure, Tertiary Supervised Machine Learning ROC Curve Exons
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Machine learning-optimized targeted detection of alternative splicing.

Nucleic acids research Jan 24, 2025
RNA sequencing (RNA-seq) is widely adopted for transcriptome analysis but has inherent biases that hinder the comprehensive detection and quantification of alternative splicing. To address this, we present an efficient targeted RNA-seq method that gr...
Humans Sequence Analysis, RNA High-Throughput Nucleotide Sequencing Alternative Splicing Machine Learning Algorithms RNA-Seq
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