Methods

Next generation sequencing (NGS) technologies enable rapid and cheap genome-wide transcriptome analysis, providing vital information about gene structure, transcript expression and alternative splicing. Key to this is the the accurate identification of...

Tumor ecosystems are composed of multiple cell types that communicate by ligand-receptor interactions. Targeting ligand-receptor interactions (for instance, with immune checkpoint inhibitors) can...

DASHR (Database of small human non-coding RNAs) v2.0 provides a complete catalog of annotation, expression, processing, conservation, tissue-specificity and other biological features for all human small non-coding (sncRNA) genes, full sncRNA transcripts and mature products derived from all major small ...

The emergence of single-cell RNA sequencing (scRNA-seq) technologies has enabled us to measure the expression levels of thousands of genes at single-cell resolution. However, insufficient quantities of starting RNA in the individual cells cause...

Advaita Bioinformatics has announced a new release of iPathwayGuide, the world’s most advanced RNA-seq and gene expression analysis software. This release includes unprecedented gene network analysis and literature mining capabilities. The newly added...

In RNA-seq differential expression analysis, investigators aim to detect those genes with changes in expression level across conditions, despite technical and biological variability in the observations. A common task is to accurately estimate the effect...

Karolinska Institutet researchers have developed FuSeq, a fast and accurate method to discover fusion genes based on quasi-mapping to quickly map the reads, extract initial candidates from split reads and fusion equivalence classes of mapped reads, and...

All RNA molecules are subject to post-transcriptional gene regulation, including mechanisms such as splicing, cleavage and polyadenylation, editing, transport, stability, and translation. These mechanisms rely on the specific recognition of functional RNA elements by RNA-binding proteins (RBPs) and a range ...

Single cell transcriptomics is critical for understanding cellular heterogeneity and identification of novel cell types. Leveraging the recent advances in single cell RNA sequencing (scRNA-Seq) technology requires novel unsupervised...

Detection of differential transcript usage (DTU) from RNA-seq data is an important bioinformatic analysis that complements differential gene expression analysis. Researchers at the University of North Carolina at Chapel Hill have developed a simple workflow...