As a fundamental aspect of normal cell signaling and disease states, there is great interest in determining alternative splicing (AS) changes in physiologic, pathologic, and pharmacologic settings. High throughput...
Read More »SpliceVault – predicting the precise nature of variant-associated mis-splicing
Even for essential splice-site variants that are almost guaranteed to alter mRNA splicing, no current method can reliably predict whether exon-skipping, cryptic activation or multiple events will result, greatly complicating clinical interpretation of pathogenicity...
Read More »ESPRESSO – robust discovery and quantification of transcript isoforms from error-prone long-read RNA-seq data
Long-read RNA sequencing (RNA-seq) holds great potential for characterizing transcriptome variation and full-length transcript isoforms, but the relatively high error rate of current long-read sequencing...
Read More »MARVEL – an integrated alternative splicing analysis platform for single-cell RNA sequencing data
Alternative splicing is an important source of heterogeneity underlying gene expression between individual cells but remains an understudied area due to the paucity of computational tools to analyze...
Read More »FusionSeeker – gene fusion detection and characterization in long-read cancer transcriptome sequencing data
Gene fusions are prevalent in a wide array of cancer types with different frequencies. Long-read transcriptome sequencing technologies, such as PacBio, Iso-Seq, and Nanopore direct RNA sequencing...
Read More »Micro-dissection and integration of long and short reads for identifying isoforms at microscopic structure-level
Studying isoform expression at the microscopic level has always been a challenging task. A classical example is kidney, where glomerular and tubulo-interstitial compartments carry out drastically different...
Read More »Slinker – visualising novel splicing events in RNA-Seq data
Visualisation of the transcriptome relative to a reference genome is fraught with sparsity. This is due to RNA sequencing (RNA-Seq) reads being predominantly mapped to exons that account for...
Read More »New RNA-Seq mapping pipeline reveals the landscape of coding RNA editing events in pediatric cancer
RNA editing leads to post-transcriptional variation in protein sequences and has important biological implications. Researchers from the St. Jude Children’s Research Hospital sought to elucidate the...
Read More »LR-Split-seq – mapping and modeling the genomic basis of differential RNA isoform expression at single-cell resolution
Alternative RNA isoforms are defined by promoter choice, alternative splicing, and polyA site selection. Although differential isoform expression is known to play a large regulatory role in eukaryotes, it has proved challenging to study with standard short-read RNA-seq because of ...
Read More »AS-Quant – Detection and Visualization of Alternative Splicing Events with RNA-seq Data
A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome.
Read More »