Jacob S. Baker

High-accuracy SNV calling for bacterial isolates using deep learning with AccuSNV

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

Phage-mediated lysis does not determine Cutibacterium acnes colonization on human skin

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.

Intraspecies associations from strain-rich metagenome samples

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

Intraspecies warfare restricts strain coexistence in human skin microbiomes

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

The microbiome of the human facial skin is unique compared to that of other hominids

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.