To understand the biological impact of alternative pre-mRNA splicing, it is vital to know which exons are involved, what protein domains they encode...
Read More »MkcDBGAS – a reference-free approach to identify comprehensive alternative splicing events in a transcriptome
Alternative splicing (AS) is an essential post-transcriptional mechanism that regulates many biological processes. However, identifying comprehensive types of AS events without guidance from a...
Read More »Deciphering RNA splicing logic with interpretable machine learning
Machine learning methods, particularly neural networks trained on large datasets, are transforming how scientists approach scientific discovery and experimental design. However, current state-of-the...
Read More »New algorithm six times more reliable at predicting defective RNA
So far, it has not been possible to explain the causes of around half of all rare hereditary diseases. A Munich research team has developed an algorithm that predicts the effects of genetic mutations...
Read More »Alternative splicing analysis benchmark with DICAST
Alternative splicing is a major contributor to transcriptome and proteome diversity in health and disease. A plethora of tools have been developed for studying alternative splicing in RNA-seq data...
Read More »SpliceTools – a suite of downstream RNA splicing analysis tools to investigate mechanisms and impact of alternative splicing
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...
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