mRNA processing events introduce an intricate layer of complexity into gene expression processes, supporting a tremendous level of diversification of the genome’s coding and regulatory potential...
Read More »Predicting splicing from primary sequence with deep learning
The splicing of pre-mRNAs into mature transcripts is remarkable for its precision, but the mechanisms by which the cellular machinery achieves such specificity are incompletely understood. Illumina scientists...
Read More »RNA-seq has the potential to be used as a rapid diagnostic tool in genomic medicine
High-throughput next-generation sequencing technologies have led to a rapid increase in the number of sequence variants identified in clinical practice via diagnostic genetic tests. Current bioinformatic analysis pipelines fail to take adequate account...
Read More »HSRA – a Hadoop-based spliced read aligner for RNA sequencing data
The analysis of transcriptome sequencing (RNA-seq) data has become the standard method for quantifying the levels of gene expression. In RNA-seq experiments, the mapping of short reads to a reference genome or transcriptome is considered a crucial...
Read More »Finding branchpoint needles in a haystack of sequencing data
Proper expression of proteins in eukaryotic cells requires precise stitching of protein-coding fragments, or exons, from precursor mRNAs that also contain non-coding introns. This process, known as splicing, can be regulated to produce slightly different proteins from the same template...
Read More »SINC-seq: correlation of transient gene expressions between nucleus and cytoplasm reflects single-cell physiology
Kyoto University researchers report a microfluidic system that physically separates nuclear RNA (nucRNA) and cytoplasmic RNA (cytRNA) from a single cell and enables single-cell integrated nucRNA...
Read More »Recommendations for utilizing targeted RNA sequencing to evaluate potential spliceogenic variants
PCR-based RNA splicing assays are commonly used in diagnostic and research settings to assess the potential effects of variants of uncertain clinical significance in BRCA1 and BRCA2. The Evidence-based...
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 »Outlier detection for improved differential splicing quantification from RNA-Seq experiments with replicates
A key component in many RNA-Seq based studies is contrasting multiple replicates from different experimental conditions. In this setup, replicates play a key role as they allow to capture underlying biological variability inherent to the compared conditions, as well as ...
Read More »Improved transcript discovery from partially observed short reads caused by missing information
The automated transcript discovery and quantification of high-throughput RNA sequencing (RNA-seq) data are important tasks of next-generation sequencing (NGS) research. However, these tasks are challenging due to the uncertainties that arise in the inference of complete splicing isoform variants from ...
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