Gerry Q. Tonkin‐Hill

StrainSpy fits zero-inflated beta mixed models to containment ANI, reaching >98% simulated sensitivity versus ~79% for logistic regression and detecting colorectal-cancer E. coli strain shifts.

This study traces the evolutionary path from ST131-B to ST131-C clades in E. coli by analyzing genomic data from ST131-B0 isolates, revealing genetic changes associated with antibiotic resistance and host adaptation.

MxSure estimates within-host substitution rates and transmission SNP thresholds from pairwise SNP distances, addressing challenges in microbial genome evolution analysis.

The paper develops a model to analyze pangenome dynamics and finds that differences in bacterial pangenomes are mainly due to variation in the number of rapidly exchanged genes.

The paper estimates the basic reproduction number (R0) for pandemic E. coli clones and finds that ST131-A has an R0 comparable to pandemic influenza viruses.

The paper uses long-read sequencing to analyze plasmids and chromosomes in E. coli over two decades, revealing long-term plasmid-lineage associations and success strategies.

This study quantifies how antibiotic resistance and within-host competition affect pneumococcal strain fitness using longitudinal carriage data.

TRACS improves transmission inference by accurately estimating SNP-level genetic distances, outperforming existing methods in multiple datasets and revealing species-specific transmission rates between mothers and infants.

PAN-GWES identifies co-selected and epistatic genomic variations in bacterial genomes using de Bruijn graphs to analyze drug resistance and adaptation traits.

The paper introduces LDWeaver, a method to detect co-selection in bacterial genomes by analyzing both short- and long-range linkage disequilibrium, and validates findings using functional annotation and phenotypic measurements.

A uniformly processed set of 2,440,377 bacterial and archaeal genomes with search tools and annotations, plus an AI-mined peptide set yielding ATB20, active in a mouse skin infection model.

ggCaller provides a fast and accurate method for pangenome annotation and clustering by integrating gene prediction, annotation, and clustering using de Bruijn Graphs, outperforming existing tools in speed and accuracy.

The paper introduces MutTui, a tool to calculate and compare mutational spectra of DNA and RNA pathogens using multiple sequence data types.

The paper introduces a computational pipeline for consistent plasmid typing using long-read sequencing data, enabling classification of novel and known plasmid types.

Mandrake reduces the dimensionality of large microbial genome datasets to visualize population structure, using both a pipeline and an interactive web application.

This study uses deep sequencing to analyze pneumococcal genetic diversity in infants and mothers, revealing transmission patterns and treatment impacts on resistant strains.

This paper applies genome-wide association, prediction, and heritability analyses to bacterial data, identifying genetic factors influencing antibiotic resistance and within-host survival in Streptococcus pneumoniae.

This study analyzes within-host genetic diversity in 1,181 SARS-CoV-2 samples, finding high mutation rates, strand asymmetries, and purifying selection, with implications for transmission chain reconstruction.

The paper identifies PfEMP1 variants associated with severe malaria in first-time infected adults and non-severe cases using RNA-seq and var gene analysis.

This paper curates a high-quality collection of over 10,000 E. coli and Shigella genomes to facilitate analysis of genetic diversity and lineage differences.

Panaroo's graph-based pangenome clustering uses gene adjacency across genomes to correct annotation errors, shrinking spurious accessory genomes and enlarging core genomes in simulated and real bacteria.

This paper introduces SpydrPick, a model-free method to detect co-selection and epistasis in bacterial genomes, revealing both known and novel targets in human pathogens.

fastbaps provides a fast Bayesian clustering method for genetic data, outperforming existing methods in speed while maintaining comparable accuracy on real and simulated datasets.

rPinecone defines sub-lineages in low-variant bacterial populations using phylogenetic trees to improve outbreak and endemic disease analysis.

PopPUNK provides fast, scalable clustering of bacterial genomes using k-mer analysis, enabling real-time outbreak detection and stable cluster naming across species and datasets.