Proteogenomics, i.e. comprehensive integration of genomics and proteomics data, is a powerful approach identifying novel protein biomarkers. This is especially the case for proteins that differ structurally between disease and control conditions. As tumor development is associated with aberrant splicing, ...
Read More »SQUID – Transcriptomic Structural Variation Detection from RNA-seq
Transcripts are frequently modified by structural variations, which leads to either a fused transcript of two genes (known as a fusion gene) or an insertion of intergenic sequence into a transcript. These modifications, called transcriptomic structural variants (TSV), can lead ...
Read More »BRIE – transcriptome-wide splicing quantification in single cells
Single-cell RNA-seq (scRNA-seq) provides a comprehensive measurement of stochasticity in transcription, but the limitations of the technology have prevented its application to dissect variability in RNA processing events such as splicing. Here, University of Edinburgh researchers present BRIE (Bayesian regression ...
Read More »ChimeRScope – a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data
The RNA-Seq technology has revolutionized transcriptome characterization not only by accurately quantifying gene expression, but also by the identification of novel transcripts like chimeric fusion transcripts. The ‘fusion’ or ‘chimeric’ transcripts have improved the diagnosis and prognosis of several tumors, ...
Read More »Evaluation of tools for long read RNA-seq splice-aware alignment
High-throughput sequencing has transformed the study of gene expression levels through RNA-seq, a technique that is now routinely used by various fields, such as genetic research or diagnostics. The advent of third generation sequencing technologies providing significantly longer reads opens ...
Read More »CASH – a constructing comprehensive splice site method for detecting alternative splicing events
RNA-sequencing (RNA-seq) can generate millions of reads to provide clues for analyzing novel or abnormal alternative splicing (AS) events in cells. However, current methods for exploring AS events are still far from being satisfactory. Here, researchers from Zhejiang A & ...
Read More »Researchers identify first familially-inherited fusion gene based on RNA-seq data
SplicingCodes.com’s scientists, in collaboration with colleagues from USA and China, have identified the KANSARL fusion gene as the first familially-inherited cancer susceptible fusion gene specific to the population of European ancestry origin. The KANSARL fusion gene is also the cancer ...
Read More »Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
A key component in many RNA-Seq based studies is the production of multiple replicates for varying experimental conditions. Such replicates allow to capture underlying biological variability and control for experimental ones. However, during data production researchers often lack clear definitions ...
Read More »Workflow for Genome-Wide Determination of Pre-mRNA Splicing Efficiency from Yeast RNA-seq Data
Pre-mRNA splicing represents an important regulatory layer of eukaryotic gene expression. In the simple budding yeast Saccharomyces cerevisiae, about one-third of all mRNA molecules undergo splicing, and splicing efficiency is tightly regulated, for example, during meiotic differentiation. S. cerevisiae features ...
Read More »Comprehensive benchmarking of RNA-Seq aligners
Alignment is the first step in most RNA-seq analysis pipelines, and the accuracy of downstream analyses depends heavily on it. Unlike most steps in the pipeline, alignment is particularly amenable to benchmarking with simulated data. Researchers from the University of ...
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