John T. McCrone

Nextstrain automates real-time phylogenetic analysis of open data for endemic and emerging pathogens

Standardized Snakemake pipelines on GitHub Actions fetch open sequence data, curate it, and publish daily or weekly updated phylogenies for 21 viruses and Mycobacterium tuberculosis.

Recovery of an 18th Century Rhinovirus Genome through Ancient RNA Isolation of Human Lungs

This study recovers an 18th-century rhinovirus genome from ancient RNA isolated from human lung specimens, revealing insights into viral evolution.

Evidence of latency reshapes our understanding of Ebola virus reservoir dynamics

This study models latency in Ebola virus using a novel phylogenetic approach, finding evidence of extended quiescence in the reservoir, which changes understanding of its evolutionary history and geographic spread.

HIPSTR: highest independent posterior subtree reconstruction in TreeAnnotator X

The paper introduces HIPSTR, a new consensus tree method that outperforms MCC in capturing high-support clades, and presents an updated TreeAnnotator X with faster computational routines.