Irwin Jungreis

Regulatory landscape of widespread stop codon readthrough in Drosophila

The paper identifies 1,400 stop codon readthrough genes in Drosophila, reveals sequence features associated with programmed readthrough, and shows conserved cis-elements functional in mammalian cells.

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

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 GENCODE CLS project: massively expanding the lncRNA catalog through capture long-read RNA sequencing

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

Programmed ribosomal frameshifting during PLEKHM2 mRNA decoding generates a constitutively active mediator of kinesin-1-dependent lysosome transport

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.

Biophysical characterization of high-confidence, small human proteins

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.

Global landscape of the host response to SARS-CoV-2 variants reveals viral evolutionary trajectories

The paper systematically analyzes proteomic and genomic data of SARS-CoV-2 variants to identify how mutations affect viral gene expression, host interactions, and immune evasion.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

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.

SARS-CoV-2 gene content and COVID-19 mutation impact by comparing 44 Sarbecovirus genomes

The paper identifies a high-confidence SARS-CoV-2 gene set and analyzes evolutionary constraints and mutation impacts across 44 Sarbecovirus genomes.

Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy

The paper analyzes secondary-variant burden in BBS cohorts and finds enrichment of trans-acting rare nonsynonymous variants in chaperonin-encoding genes.

Genus-wide characterization of bumblebee genomes reveals variation associated with key ecological and behavioral traits of pollinators

The paper characterizes bumblebee genomes across 17 species to identify genetic variation linked to ecological and behavioral traits, revealing insights into genome structure, evolution, and adaptation.

A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs.

The paper creates a spatiotemporal gene expression atlas of Drosophila embryonic neurogenesis, revealing dynamic lncRNA expression patterns and cell type-specific gene regulation.

Nearly all new protein-coding predictions in the CHESS database are not protein-coding

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.