Aaron C. Wacholder

The paper shows that environmental stress influences the phenotypic impact of de novo ORFs, with tradeoffs and stress-dependent growth effects observed in yeast.

This study resolves the debate on the origin of taxonomically restricted genes in yeast by showing most are de novo genes while others derive from diverged ancestors.

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.

This study investigates how de novo proteins in yeast integrate into cellular systems using ancient targeting and degradation pathways, revealing a conserved molecular signature that enables their ER localization and regulation.

The paper investigates why noncanonical proteins are rarely detected by mass spectrometry in yeast, finding that their low abundance and small size, rather than instability, are the main factors.

The paper identifies a large noncanonical translatome in yeast, showing most translated elements are not conserved genes and contribute to phenotype through fast-evolving mechanisms.

The paper shows that yeast cells lacking Met15 can assimilate inorganic sulfur via Yll058w, but require exogenous methionine or hydrogen sulfide chelators to grow, challenging the traditional view of MET15 as essential for sulfur assimilation.

The paper identifies and extends ancient simple sequence repeat-derived regions in the human genome using a kmer-based approach, finding 6.77% of the genome likely derived from SSRs.

The paper identifies an excess of gene conversion and recombination events in gorillas linked to PRDM9 and Alu elements, showing lineage-specific motif targeting and depletion.

The paper improves a Bayesian method to analyze Alu element evolution, revealing fluctuating sequence constraints and over 4,000 replicative loci, challenging previous classifications.