Jennifer L. Gardy

This study quantifies antibiotic resistance in tuberculosis using genomic data and MIC measurements to identify genetic determinants of resistance and hypersensitivity across multiple drugs.

This study compares seven transmission reconstruction tools for Mycobacterium tuberculosis using simulated and real-world data, finding that some tools better identify true transmission events than others.

GenomegaMap estimates genome-wide dN/dS ratios across 10,209 tuberculosis genomes to identify selection pressures shaping the pathogen's evolution.

The paper introduces a transmission-based clustering method for identifying outbreak clusters using whole genome sequencing data, showing it outperforms SNP threshold methods in some scenarios.

The paper introduces a method to systematically survey data visualizations and creates a genomic epidemiology visualization typology (GEViT) with an online gallery.

Adjutant is an R-based tool that helps users mine PubMed for systematic reviews by clustering articles into topics and sampling documents efficiently.

A decentralized open-source web platform lets public health labs run outbreak sequencing pipelines on local compute, keeping data under their own governance while still exchanging results between instances.

The paper designs and evaluates a whole genome sequencing clinical report for tuberculosis using a human-centered approach with expert feedback and surveys.

MentaLiST is a fast and accurate MLST caller designed for large MLST schemes, outperforming existing tools in speed while maintaining or improving accuracy.