Christopher B. Burge

The paper shows that neural RNA splicing models rely on reading frame information that the splicing machinery cannot access, leading to errors in predicting poison exons.

The paper shows that the strength of a gene's first 5' splice site determines its expression level through intron-mediated enhancement, independent of 3' splice site strength.

The paper identifies naturally variable exons in human transcripts, showing their prevalence and impact on gene expression and genetic interpretation.

This study identifies splice-switching antisense oligonucleotides that correct splicing defects in SCN8A, reducing seizures and improving survival in a mouse model of genetic epilepsy.

The paper identifies two major classes of 5' splice sites regulated by LUC7 proteins in animals and plants, showing conserved function across species.

This study identifies sequence features that determine intron-mediated enhancement by analyzing thousands of synthetic introns in human cells.

The paper examines interspecies differences in RNA-protein interactions using the neuronal RNA binding protein UNK, finding conserved binding patterns and species-specific sequence determinants.

KATMAP infers splicing factor activity and regulatory targets from knockdown data by modeling splicing changes and predicting SF regulation at individual exons.

This study examines how alternative splicing and cellular context affect the functional properties of SCN8A variants associated with neurodevelopmental disorders.

The paper introduces SMsplice, an interpretable model for pre-mRNA splicing that predicts splice site locations and identifies SRE motifs across species.

The paper identifies regulatory features in 3'UTR variants that are more likely to affect gene expression and phenotype, and introduces a tool to interpret these variants.

The paper introduces an interpretable neural model for RNA splicing that improves RBP binding and activity predictions using an Adjusted Motif architecture.

This study identifies DHX15 as a splicing quality control factor in human cells, activated by SUGP1, which represses suboptimal introns and promotes splicing fidelity.

This study identifies disease-causing promoter and untranslated region variants in 8,040 undiagnosed rare disease patients using a new framework and finds 12 variants with potential pathogenicity.

RBPamp models protein-RNA interactions using RBNS data to predict in vivo binding affinities and eCLIP densities for 79 human RBPs.

The paper identifies hybrid internal-terminal exons in human transcriptomes using a new pipeline and shows their tissue-specific usage and association with RNA splicing genes.

The paper maps and characterizes RNA elements recognized by human RNA binding proteins in K562 and HepG2 cells, expanding the catalog of functional elements in the human genome.

The paper identifies exon-mediated activation of transcription starts (EMATS) as a mechanism where splicing of internal exons influences promoter usage and gene expression in mammals.

The paper introduces BEAPR, a computational method to detect allele-specific binding of RNA-binding proteins, showing it outperforms existing methods and identifies disease-relevant variants.

The paper investigates PERK's role in ER stress response by analyzing gene expression in PERK -/- MEFs, finding widespread PERK-dependent repression of ER-targeted genes.

The paper identifies hundreds of novel recursive splicing sites in Drosophila introns, showing they are more accurately spliced and often located in long introns involved in development.

The paper measures splicing rates genome-wide in Drosophila to understand how gene architecture affects splicing efficiency and accuracy.