Mark Achtman

This study traces the evolutionary changes in the human oral microbiome over 102,400 years, revealing co-evolution with cultural and medical transitions and highlighting shifts in microbial ecology and antimicrobial resistance.

HierCC assigns genomes to hierarchical population structures using core genome MLST, enabling scalable and incremental clustering.

BlastFrost efficiently queries bacterial genomes using Bifrost graphs to identify gene presence and SNVs in large collections.

PEPPAN reconstructs bacterial pan- and core-genomes with high accuracy and speed, outperforming existing methods in a case study of Streptococcus genomes.

The paper analyzes the oral microbiome of historical and modern humans using metagenomics, revealing microbial diversity and changes in caries-associated species over time.

GrapeTree visualizes genomic relationships among 100,000 bacterial pathogens using a minimum spanning tree algorithm and interactive layouts.

SPARSE improves taxonomic classification of metagenomic reads by reducing false positives and enhancing sensitivity for low-abundance species detection.