Tag Archives: Salmon

Gene expression quantification is a fundamental computational inference problem at the intersection of genomics, machine learning, and biology. The expression levels (abundances) of genes and transcripts...

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...

Alternatively spliced transcript isoforms are commonly observed in higher eukaryotes. The expression levels of these isoforms are key for understanding normal functions in healthy tissues and the progression of disease states. However, accurate quantification of expression at the transcript level ...

By Lior Pachter –  One of the maxims of computational biology is that “no two programs ever give the same result.” This is perhaps not so surprising; after all, most journals seek papers that report a significant improvement to an existing method. ...

RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. Multiple algorithms have been developed to derive gene counts from sequencing reads. While a number of benchmarking studies have been conducted, the question remains how individual methods perform at ...

Rob Patro, an assistant professor in the Department of Computer Science in Stony Brook’s College of Engineering and Applied Sciences, leads a group of computational biological researchers that developed a new software tool, Salmon — a lightweight method to provide ...

Technique detects technical biases that otherwise confound test results A new computational method can improve the accuracy of gene expression analyses, which are increasingly used to diagnose and monitor cancers and are a major tool for basic biological research. Researchers ...

Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance ...

Transcript quantification is a central task in the analysis of RNA-seq data. Accurate computational methods for the quantification of transcript abundances are essential for downstream analysis. However, most existing approaches are much slower than is necessary for their degree of ...