Z. Ardern

Why is the average collateral effect of synonymous mutations so similar across alternative reading frames?

The paper shows that the standard genetic code's ability to produce similar average collateral mutation effects across alternative reading frames is rare and suggests it may be adaptive for evolvability.

Shadow ORFs illuminated: long overlapping genes in Pseudomonas aeruginosa are translated and under purifying selection

The paper identifies two long overlapping genes in Pseudomonas aeruginosa that are translated and under purifying selection, expanding understanding of prokaryotic genomic complexity.

Evidence for Numerous Embedded Antisense Overlapping Genes in Diverse E. coli Strains

The paper identifies numerous embedded antisense overlapping genes in E. coli strains using RNAseq and ribosome profiling, suggesting they may be functionally significant and underappreciated in genome annotation.

Dynamically evolving novel overlapping gene as a factor in the SARS-CoV-2 pandemic

The paper identifies and characterizes ORF3d, a novel overlapping gene in SARS-CoV-2, showing its presence in pangolin-CoVs and its evolutionary significance.

Are Antisense Proteins in Prokaryotes Functional?

The paper investigates whether antisense proteins in prokaryotes are functional, finding evidence supporting their utility and suggesting they should be included in genome annotations.

OLGenie: Estimating Natural Selection to Predict Functional Overlapping Genes

OLGenie estimates natural selection in overlapping genes to identify functionally constrained gene pairs with high accuracy.

A novel pH-regulated, unusual 603 bp overlapping protein coding gene pop is encoded antisense to ompA in Escherichia coli O157:H7 (EHEC)

The paper identifies a novel pH-regulated, antisense protein-coding gene overlapping ompA in E. coli O157:H7, showing translation and a pH-dependent phenotype.