Sequencing studies on non-model organisms often interrogate both genomes and transcriptomes with massive amounts of short sequences. Such studies require de novo analysis tools and techniques...
Read More »RNA-Seq reveals the landscape of human mutually exclusive splicing
Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and...
Read More »Researchers use a combination of third generation long-read RNA sequencing technology and short-read RNAseq to characterize the splicing landscape of prostate cancer
Researchers from the Icahn School of Medicine characterize the transcriptional splicing landscape of a prostate cancer cell line treated with a previously identified synergistic drug combination. They use...
Read More »Analysis and prediction of exon skipping events from RNA-Seq with sequence information using rotation forest
In bioinformatics, exon skipping (ES) event prediction is an essential part of alternative splicing (AS) event analysis. Although many methods have been developed to predict ES events, a solution has yet to be found. In this study, given the limitations ...
Read More »Featured RNA-Seq Job – Bioinformatics Analyst
RNA is unique among all biomolecules as it can be both information-storing and enzymatic. These features are tightly linked to its structure, in which base-pairing interactions give rise to a highly...
Read More »FreePSI – an alignment-free approach to estimating exon-inclusion ratios without a reference transcriptome
Alternative splicing plays an important role in many cellular processes of eukaryotic organisms. The exon-inclusion ratio, also known as percent spliced in, is often regarded as one of the most effective measures of alternative splicing events. The existing methods for ...
Read More »Bayesian estimation of differential transcript usage from RNA-seq data
Next generation sequencing allows the identification of genes consisting of differentially expressed transcripts, a term which usually refers to changes in the overall expression level. A specific type of differential expression is differential transcript usage (DTU) and targets changes in ...
Read More »Best practices and appropriate workflows to analyse alternative and differential splicing
Over the last few years, RNA-seq has been used to study alterations in alternative splicing related to several diseases. Bioinformatics workflows used to perform these studies can be divided into two groups, those finding changes in the absolute isoform expression ...
Read More »Identification of genome-wide non-canonical spliced regions and analysis of biological functions for spliced sequences using Read-Split-Fly
It is generally thought that most canonical or non-canonical splicing events involving U2- and U12 spliceosomes occur within nuclear pre-mRNAs. However, the question of whether at least some U12-type splicing occurs in the cytoplasm is still unclear. In recent years ...
Read More »Exon-junction arrays – a viable alternative to RNA-seq for detection of alternative splicing events?
RNA-seq is a reference technology for determining alternative splicing at genome-wide level. Exon arrays remain widely used for the analysis of gene expression, but show poor validation rate with regard to splicing events. Commercial arrays that include probes within exon ...
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