Connor Chato

Human outbreak detection and best practice MPXV analysis and interpretation with squirrel

This paper introduces squirrel, a tool for analyzing MPXV genomes to detect outbreaks and classify APOBEC3 mutations, aiding public health responses.

Optimized phylogenetic clustering of HIV-1 sequence data for public health applications

This paper introduces a method to optimize phylogenetic clustering thresholds for HIV-1 sequence data, showing that optimal thresholds vary by population and improve cluster growth prediction.

From components to communities: bringing network science to clustering for genomic epidemiology

The paper introduces community detection methods to improve clustering of infectious disease sequences, demonstrating their application to HIV-1 data to better capture transmission dynamics.

Variance in Variants: Propagating Genome Sequence Uncertainty into Phylogenetic Lineage Assignment

This paper demonstrates how sequencing uncertainty affects phylogenetic lineage assignment and proposes a resampling method to propagate this uncertainty using SARS-CoV-2 data.

CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes

The paper introduces CoVizu, a tool for rapidly analyzing and visualizing large SARS-CoV-2 genome datasets, producing consensus trees and beadplot visualizations.