N. Vakirlis

Ancestral Sequence Reconstruction as a tool to detect and study de novo gene emergence

This study evaluates Ancestral Sequence Reconstruction (ASR) as a tool to detect de novo genes by analyzing ~2,600 yeast genes and identifying 33 de novo emerged genes.

Large-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins

The paper investigates species-specific orphan genes in the human gut microbiome, finding most originate internally rather than from external sources like viruses.

De novo birth of functional, human-specific microproteins

The paper demonstrates that de novo gene birth can produce functional microproteins with significant phenotypic effects in humans and other animals.

Synteny-based analyses indicate that sequence divergence is not the main source of orphan genes

The paper estimates that sequence divergence accounts for at most a third of eukaryotic orphan genes using conserved synteny analysis across yeast, fly, and human.

De novo emergence of adaptive membrane proteins from thymine-rich intergenic sequences

This study shows that de novo emerging coding sequences in yeast often encode beneficial transmembrane proteins, suggesting that intergenic regions may contain pre-existing blueprints for such functions.

Yeast de novo genes preferentially emerge from divergently transcribed, GC-rich intergenic regions

The paper identifies 703 de novo genes in 15 yeast species and finds they preferentially arise from GC-rich intergenic regions near divergent promoters and recombination hotspots.