Jacob S. Baker

AccuSNV is a deep learning tool for high-accuracy bacterial SNV calling that outperforms existing methods in simulated and real datasets.

The paper investigates the role of phage-mediated selection in shaping Cutibacterium acnes populations on human skin and finds weak phage pressure due to physical barriers limiting phage exposure.

PHLAME improves strain-resolved metagenomic analysis by combining reference-based methods with novelty detection, revealing new intraspecies associations in human microbiomes.

The paper shows that intraspecies warfare limits strain coexistence in human skin microbiomes by analyzing interactions between Staphylococcus epidermidis isolates.

This study compares the facial skin microbiome of humans, chimpanzees, and gorillas, finding humans have a unique, low-diversity microbiome dominated by Cutibacterium, absent in other primates.

The paper reveals hidden strain dynamics in skin microbiome species, showing that while strains are transient, some are more stable and may be targets for therapeutic interventions.