Gavin M. Douglas

This paper evaluates 30 amino acid distance measures, including a new one based on deep mutational scanning, to identify the best for modeling codon substitutions and inferring natural selection across diverse lineages.

The paper investigates the relationship between co-occurrence and horizontal gene transfer (HGT) in marine bacteria, finding a significant association independent of phylogeny.

The paper quantifies introgression across bacterial lineages, finding varying levels of gene flow and its association with ecological proximity, but not substantial blurring of species borders.

The paper introduces POMS, a phylogeny-aware framework for identifying enriched functions in microbiome data, showing improved accuracy over existing methods in simulated and real datasets.

In 38 two-group 16S rRNA datasets, 14 differential abundance tools disagreed sharply; ALDEx2 and ANCOM-II were conservative and consistent, while edgeR and LEfSe inflated false positives.

PICRUSt2 places 16S rRNA variants into a 20,000-gene reference tree, predicting gene families, pathways and phenotypes; gene-family predictions matched or beat four tools against shotgun metagenomes.