[PDF][PDF] Efficient and accurate quantitative profiling of alternative splicing patterns of any complexity on a laptop

T Sterne-Weiler, RJ Weatheritt, AJ Best, KCH Ha… - Molecular cell, 2018 - cell.com
Alternative splicing (AS) is a widespread process underlying the generation of transcriptomic
and proteomic diversity and is frequently misregulated in human disease. Accordingly, an …

[HTML][HTML] Alternative splicing: Human disease and quantitative analysis from high-throughput sequencing

W Jiang, L Chen - Computational and structural biotechnology journal, 2021 - Elsevier
Alternative splicing contributes to the majority of protein diversity in higher eukaryotes by
allowing one gene to generate multiple distinct protein isoforms. It adds another regulation …

Leveraging transcript quantification for fast computation of alternative splicing profiles

GP Alamancos, A Pagès, JL Trincado, N Bellora… - Rna, 2015 - rnajournal.cshlp.org
Alternative splicing plays an essential role in many cellular processes and bears major
relevance in the understanding of multiple diseases, including cancer. High-throughput RNA …

SpliceTrap: a method to quantify alternative splicing under single cellular conditions

J Wu, M Akerman, S Sun, WR McCombie… - …, 2011 - academic.oup.com
Motivation: Alternative splicing (AS) is a pre-mRNA maturation process leading to the
expression of multiple mRNA variants from the same primary transcript. More than 90% of …

IsoformSwitchAnalyzeR: analysis of changes in genome-wide patterns of alternative splicing and its functional consequences

K Vitting-Seerup, A Sandelin - Bioinformatics, 2019 - academic.oup.com
Alternative splicing is an important mechanism involved in health and disease. Recent work
highlights the importance of investigating genome-wide changes in splicing patterns and the …

Improved methods for RNAseq-based alternative splicing analysis

RF Halperin, A Hegde, JD Lang, EA Raupach… - Scientific reports, 2021 - nature.com
The robust detection of disease-associated splice events from RNAseq data is challenging
due to the potential confounding effect of gene expression levels and the often limited …

The relationship between alternative splicing and proteomic complexity

BJ Blencowe - Trends in biochemical sciences, 2017 - cell.com
Tress and colleagues proposed that only a minor fraction of splice variants detected in
transcriptome profiling data are translated and, therefore, that most splice variants have little …

[HTML][HTML] Thousands of exon skipping events differentiate among splicing patterns in sixteen human tissues

L Florea, L Song, SL Salzberg - F1000Research, 2013 - ncbi.nlm.nih.gov
Alternative splicing is widely recognized for its roles in regulating genes and creating gene
diversity. However, despite many efforts, the repertoire of gene splicing variation is still …

BRIE2: computational identification of splicing phenotypes from single-cell transcriptomic experiments

Y Huang, G Sanguinetti - Genome biology, 2021 - Springer
RNA splicing is an important driver of heterogeneity in single cells through the expression of
alternative transcripts and as a determinant of transcriptional kinetics. However, the intrinsic …

SplAdder: identification, quantification and testing of alternative splicing events from RNA-Seq data

A Kahles, CS Ong, Y Zhong, G Rätsch - Bioinformatics, 2016 - academic.oup.com
Motivation: Understanding the occurrence and regulation of alternative splicing (AS) is a key
task towards explaining the regulatory processes that shape the complex transcriptomes of …