Timothy Paul Stinear

This paper shows that phosphorylation by PknB at T101 promotes WalR dimer formation and strengthens DNA binding, revealing a direct functional link between PknB and WalR.

The paper identifies mutations in the mfd gene in S. aureus isolates from a CRS patient, linking them to a mucoid hyper-biofilm phenotype and increased enterotoxin production.

This study characterizes microbial communities in southeastern Australian montane fens, revealing high diversity and unique taxa not found in other environments.

This study integrates multi-omic data from Staphylococcus aureus exposed to human serum to identify genetic factors critical for survival, revealing interconnected metabolic, iron transport, and stress response mechanisms.

This study identifies a novel plasmid-borne ESX type VII secretion system in M. abscessus that enhances intracellular survival in macrophages.

This study uses genomic data to show that most multidrug-resistant tuberculosis in Bhutan comes from local transmission, forming a large, recent endemic cluster.

This paper introduces an R-based workflow for integrating microbial multi-omics data, enabling analysis of transcriptomic, proteomic, and metabolomic datasets and generating pathway-level insights.

This study evaluates the stability and viability of FMT products using metagenomic and culturomic analyses, showing high donor consistency and geographic specificity of gut microbiomes.

Autocycler improves bacterial genome assembly accuracy by combining multiple long-read assemblies without user input, outperforming existing tools in error reduction and structural accuracy.

This study develops a low-dose murine model of Mycobacterium ulcerans infection to analyze immune responses and identifies key cell types involved in disease progression.

This study shows that fumarate, regulated by host and pathogen, limits S. aureus growth by blocking metabolic pathways, while FumC enables adaptation through fumarate degradation and utilization.

The paper isolates soil bacteria using diffusion chambers, screens for antibiotic activity, and combines mass spectrometry and genomics to identify known and novel antibiotics from Australian soil samples.

This study identifies simple sequence repeats (SSRs) as key drivers of genetic heterogeneity and rapid adaptation in Staphylococcus aureus through loss-of-function mutations and phase-variable evolution.

The paper develops a TraDIS platform for Enterococcus faecium using nanopore sequencing and a WebAssembly tool to study vancomycin resistance and persistence.

This study evaluates variant calling from bacterial genome assemblies versus read-based methods, finding that assembly-based approaches require error-free assemblies to achieve high accuracy.

This study evaluates in vitro resistance development in MRSA to vancomycin, daptomycin, and linezolid, identifying mutations and mechanisms associated with resistance.

This paper reports the complete genome of Candidatus Paracoxiella cheracis, revealing insights into its pathogenesis and phylogeny within the Coxiellaceae family.

This study identifies quorum sensing and adenosine DNA methylation as two antagonistic systems controlling phase variation in Burkholderia ambifaria clinical isolates.

This paper compares strict and soft core SNP filtering strategies for bacterial phylogenetics, showing soft cores retain more informative sites and improve phylogenetic accuracy.

This study identifies cyclic lipodepsipeptides as the molecular basis of haemolytic activity in Chromobacterium haemolyticum and shows their role in biofilm formation and swarming.

This study investigates Buruli ulcer in possums in Victoria, Australia, finding M. ulcerans in 78% of clinically affected and 65% of non-lesioned possums, with lesions mapped and systemic bacterial dissemination observed.

This study benchmarks variant callers on bacterial nanopore data, finding deep learning tools outperform traditional methods and Illumina in accuracy and efficiency.

The paper develops a low-cost DNA extraction method using paramagnetic beads for environmental surveillance of Mycobacterium ulcerans in possum excreta and tissue swabs, showing cost savings and comparable DNA quality to commercial kits.

This paper describes the discovery of a marine sponge-associated mycobacterium closely related to M. tuberculosis, which shares virulence factors but lacks virulence in mice.

FANGORN provides a quality-checked database of full-length 16S-ITS-23S rRNA operons to improve microbial community classification and phylogenetic analysis.

Roughly 25× short-read depth polishes nearly all residual errors in Nanopore-only bacterial assemblies; new '--careful' modes in Pypolca and Polypolish largely avoid introducing low-depth errors.

This paper identifies M. ulcerans JKD8049 as a suitable human challenge strain for Buruli ulcer research due to its stability, antibiotic susceptibility, and ability to produce mycolactone.

This paper develops a benchmark dataset for SARS-CoV-2 amplicon sequencing to improve genomic surveillance in resource-constrained labs, finding that basecaller choice has minimal impact on consensus quality.

This paper develops a machine learning method to accurately attribute Legionella pneumophila outbreaks to environmental sources using genomic data, outperforming traditional phylogenetic approaches.