Jonathan M. Mudge

The paper shows EWSR1::FLI1 fusion drives the production of cancer-specific neoproteins in Ewing sarcoma, revealing a reversible dark proteome with therapeutic potential.

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

The paper expands and refines a reference catalog of human non-canonical open reading frames (ncORFs) by incorporating more datasets and introducing a translation signature score framework to prioritize high-quality ncORFs.

The paper assesses MS-based identifications of unannotated human microproteins, finding large variation in reported proteins and PSM quality across studies.

The paper expands the lncRNA catalog using capture long-read RNA sequencing, significantly increasing the number of annotated transcripts in human and mouse genomes.

The paper identifies a programmed ribosomal frameshifting event in PLEKHM2 mRNA that generates a constitutively active protein domain essential for lysosome transport and cardiac function.

The paper characterizes biophysical properties of small human proteins, finding significant differences compared to larger proteins and providing insights for distinguishing functional from non-coding small open reading frames.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

This paper introduces Ribosome Decision Graphs (RDGs) to represent eukaryotic RNA translation complexity, enabling analysis of translation patterns and genetic variation effects.

This paper discusses the current state of research on non-canonical open reading frames (ORFs) and proposes standards for their investigation and reporting using Ribo-seq and proteomics.

The paper introduces the EN-TEx resource, which provides personal epigenomes and variant-impact models across multiple tissues, revealing allele-specific loci and their associations with GWAS loci.

The paper identifies thousands of non-AUG initiated proteoforms in humans and mice, many lacking evolutionary selection evidence, using ribo-seq and phylogenetic analysis.

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

The paper investigates evolutionarily young CTCF binding sites in two Mus subspecies, finding some functional signatures and a novel immune locus formed by tandem duplication.

The paper develops an expression-based annotation metric to improve rare variant interpretation by filtering false-positive loss-of-function variants and identifying pathogenic variants in highly expressed exons.

The paper identifies novel long non-coding RNAs and circular RNAs in hematopoietic cells using BLUEPRINT consortium data, highlighting their cell type specificity.

The paper updates gene annotations for 191 epilepsy genes, reclassifying variants and identifying new de novo SCN1A variants in Dravet syndrome patients.

The paper reanalyzes the CHESS database's new protein-coding predictions and finds most are false positives due to homology errors and lack of experimental evidence.