Daniel McDonald

Homology-aware average nucleotide identity estimation at scale with TurboANI

TurboANI is a fast, homology-aware ANI estimator with up to ~40,000x speedup over alignment-based methods and better accuracy than FastANI and skani.

Genome-resolved ecology and evolution of the microbiome enabled by quantitative long-read metagenomics

This paper introduces LRQ, a long-read metagenomics method that enables absolute strain abundance measurement and resolves microbial evolution in a Crohn's disease patient over eight years.

Community assembly modeling of microbial evolution within Barrett's esophagus and esophageal adenocarcinoma

The paper models microbial community assembly dynamics in Barrett's esophagus and esophageal adenocarcinoma, finding neutral dynamics in normal tissue and BE but not EAC, with H. pylori showing non-neutral behavior in BE non-cancer outcomes.

Industrialization drives convergent microbial and physiological shifts in the human metaorganism

The paper investigates how industrialization affects microbial and physiological traits in the human gut across diverse populations, finding homogenized microbiomes, reduced diversity, and impaired disease prediction accuracy in less industrialized groups.