Publications -

This list is updated occasionally. A full list can be found on Google Scholar or Orcid.

2026

Rapid gene exchange explains differences in bacterial pangenome structure. Horsfield, S., Peng, A., Russell, M., Wachsmann, J., Toussaint, J. et al., Preprint (2026)

2025

Basic reproduction number varies markedly between closely related pandemic Escherichia coli clones. Ojala, F., Pesonen, H., Gladstone, R., Mäklin, T., Tonkin-Hill, G et al., Nature Communications (2025)
Within-host bacterial evolution and the emergence of pathogenicity. Tonkin-Hill, G, Ruis, C., Bentley, S., Lythgoe, K., Bryant, J. Nature Microbiology (2025)
Plasmid-driven strategies for clone success in Escherichia coli. Arredondo-Alonso, S., Pöntinen, A., Gama, J., Gladstone, R., Harms, K. et al., Nature Communications (2025)
Quantifying the effects of antibiotic resistance and within-host competition on strain fitness in Streptococcus pneumoniae. Krishna, A., Tonkin-Hill, G, Morel-Journel, T., Bentley, S., Turner, P. et al., Preprint (2025)
Invasive Streptococcus dysgalactiae subspecies equisimilis compared with Streptococcus pyogenes in Australia, 2011–23, and the emergence of a multi-continent stG62647 lineage: a retrospective clinical and genomic epidemiology study. O., X., L., F., A.N.T., N., A.J., H., M.E., P. et al., Lancet Microbe (2025)
Mapping the evolutionary path towards multi-drug resistance in the pandemic Escherichia coli ST131 lineage. A.K., P., N.V., T., S., M., R.A., G., J., K. et al., Biorxiv (2025)
Multiple mechanisms of strain competition are needed to explain pneumococcal serotype-specific antibiotic resistance. H.C., L., E., P., J., H., K., v., K., M. et al., Medrxiv (2025)
Temporal and geographical lineage dynamics of invasive Streptococcus pyogenes in Australia from 2011 to 2023: a retrospective, multicentre, clinical and genomic epidemiology study. O., X., R.H., C., L., F., A.N.T., N., A.J., H. et al., Lancet Microbe (2025)

2024

Enhanced metagenomics-enabled transmission inference with TRACS. Tonkin-Hill, G, Shao, Y., Zarebski, A., Mallawaarachchi, S, Xie, O. et al., Preprint (2024)
Basic reproduction number for pandemic Escherichia coli clones varies markedly and can be comparable to pandemic influenza viruses. Ojala, F., Pesonen, H., Gladstone, R., Mäklin, T., Tonkin-Hill, G et al., Preprint (2024)
Overlapping Streptococcus pyogenes and Streptococcus dysgalactiae subspecies equisimilis household transmission and mobile genetic element exchange. Xie, O., Zachreson, C., Tonkin-Hill, G, Price, D., Lacey, J. et al., Nature Communications (2024)
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis. Xie, O., Morris, J., Hayes, A., Towers, R., Jespersen, M. et al., Nature Communications (2024)
Correction to: Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda (Scientific Reports, (2017), 7, 1, (11810), 10.1038/s41598-017-11814-9). S., R., K.E., T., G., T., T.S., R., M.R., K. et al., Scientific Reports (2024)
Detecting co-selection through excess linkage disequilibrium in bacterial genomes. S., M., G., T., A.K., P., J.K., C., R.A., G. et al., Nar Genomics and Bioinformatics (2024)
Evaluating methods for identifying and quantifying Streptococcus pneumoniae co-colonization using next-generation sequencing data. J., H., M.L., H., T.D., S., J., H., J., A. et al., Microbiology Spectrum (2024)
Group 2 and 3 ABC-transporter-dependent capsular K-loci contribute significantly to variation in the estimated invasive potential of Escherichia coli. R.A., G., M., P., A.K., P., T., M., N., M. et al., Medrxiv (2024)
Pan-pathogen deep sequencing of nosocomial bacterial pathogens in Italy in spring 2020: a prospective cohort study. H.A., T., M., P., M., C., H., P., S., G. et al., Lancet Microbe (2024)
Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. J., K., S.T., H., A.K., P., S., M., S., A. et al., Genome Research (2024)
Temporal and Geographic Strain Dynamics of Invasive Streptococcus Pyogenes In Australia: A Multi-Centre Clinical and Genomic Epidemiology Study 2011-2023. O., X., R.H., C., L., F., A.N.T., N., A.J., H. et al., Ssrn (2024)

2023

Measuring changes in Plasmodium falciparum census population size in response to sequential malaria control interventions. Tiedje, K., Zhan, Q., Ruybal-Pésantez, S., Tonkin-Hill, G, He, Q. et al., eLife (2023)
Mutational spectra are associated with bacterial niche. Ruis, C., Weimann, A., Tonkin-Hill, G, Pandurangan, A., Matuszewska, M. et al., Nature Communications (2023)
Mge-cluster: a reference-free approach for typing bacterial plasmids. Arredondo-Alonso, S., Gladstone, R., Pöntinen, A., Gama, J., Schürch, A. et al., NAR Genomics and Bioinformatics (2023)
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. Tonkin-Hill, G, Gladstone, R., Pöntinen, A., Arredondo-Alonso, S., Bentley, S. et al., Genome Research (2023)
Accurate and fast graph-based pangenome annotation and clustering with ggCaller. S.T., H., G., T., N.J., C., J.A., L. Genome Research (2023)
Calculating and applying pathogen mutational spectra using MutTui. C., R., G., T., R.A., F., J., P. Biorxiv (2023)
Challenges in prokaryote pangenomics. G., T., J., C., J., P. Microbial Genomics (2023)
Overlapping transmission of group A and C/G Streptococcus facilitates inter-species mobile genetic element exchange. O., X., C., Z., G., T., D.J., P., J.A., L. et al., Medrxiv (2023)
PAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs. J., K., S., H., A.K., P., S., A., H., T. et al., Biorxiv (2023)
Quantifying the common genetic variability of bacterial traits. T.T., M., G., T., J.A., L., J., C. Arxiv (2023)

2022

Mandrake: visualizing microbial population structure by embedding millions of genomes into a low-dimensional representation. Lees, J., Tonkin-Hill, G, Yang, Z., Corander, J. Philosophical Transactions of the Royal Society B: Biological Sciences (2022)
Pneumococcal within-host diversity during colonization, transmission and treatment. Tonkin-Hill, G, Ling, C., Chaguza, C., Salter, S., Hinfonthong, P. et al., Nature Microbiology (2022)
Age-specific patterns of DBLα var diversity can explain why residents of high malaria transmission areas remain susceptible to Plasmodium falciparum blood stage infection throughout life. Ruybal-Pesántez, S., Tiedje, K., Pilosof, S., Tonkin-Hill, G, He, Q. et al., International Journal for Parasitology (2022)
Relationship of circulating Plasmodium falciparum lifecycle stage to circulating parasitemia and total parasite biomass. Duffy, M., Tonkin-Hill, G, Trianty, L., Noviyanti, R., Nguyen, H. et al., Nature Communications (2022)
Comparative Genomics of Disease and Carriage Serotype 1 Pneumococci. Chaguza, C., Ebruke, C., Senghore, M., Lo, S., Tientcheu, P. et al., Genome Biology and Evolution (2022)
An accurate method for identifying recent recombinants from unaligned sequences. Feng, Q., Tiedje, K., Ruybal-Pesántez, S., Tonkin-Hill, G, Duffy, M. et al., Bioinformatics (2022)
Identifying Targets of Protective Antibodies against Severe Malaria in Papua, Indonesia, Using Locally Expressed Domains of Plasmodium falciparum Erythrocyte Membrane Protein 1. Rambhatla, J., Tonkin-Hill, G, Takashima, E., Tsuboi, T., Noviyanti, R. et al., Infection and Immunity (2022)
RCandy: an R package for visualizing homologous recombinations in bacterial genomes. Chaguza, C., Tonkin-Hill, G, Lo, S., Hadfield, J., Croucher, N. et al., Bioinformatics (2022)
Consistent typing of plasmids with the mge-cluster pipeline. S., A., R.A., G., A.K., P., J.A., G., A.C., S. et al., Biorxiv (2022)
Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. S., M., G., T., N.J., C., P., T., D., S. et al., Nar Genomics and Bioinformatics (2022)
Mutational spectra analysis reveals bacterial niche and transmission routes. C., R., A., W., G., T., A.P., P., M., M. et al., Biorxiv (2022)

2021

Patterns of within-host genetic diversity in SARS-CoV-2. Tonkin-Hill, G, Martincorena, I., Amato, R., Lawson, A., Gerstung, M. et al., eLife (2021)
Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial population genomic study. Gladstone, R., McNally, A., Pöntinen, A., Tonkin-Hill, G, Lees, J. et al., The Lancet Microbe (2021)
Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Pöntinen, A., Top, J., Arredondo-Alonso, S., Tonkin-Hill, G, Freitas, A. et al., Nature Communications (2021)
A comprehensive and high-quality collection of escherichia coli genomes and their genes. G., H., G.A., B., G., T., J., C., E., H. et al., Microbial Genomics (2021)
Common virulence gene expression in adult first-time infected malaria patients and severe cases. J.S., W., G., T., T., T., R., K., B., K. et al., Elife (2021)
Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents. G., T., S., R., K.E., T., V., R., M.F., D. et al., Plos Genetics (2021)
Genome-wide association, prediction and heritability in bacteria. S., M., G., T., N.J., C., P., T., D., S. et al., Biorxiv (2021)
Genomic epidemiology of covid-19 in care homes in the east of England. W.L., H., G., T., E.R., S., D., A., C.J., H. et al., Elife (2021)
Genomic epidemiology of the SARS-CoV-2 epidemic in Zimbabwe: Role of international travel and regional migration in spread. T., M., F.T., T., L., d., M., G., J., C. et al., Medrxiv (2021)
Genomic reconstruction of the SARS-CoV-2 epidemic in England. H.S., V., T., S., M., S., N., D., T., N. et al., Nature (2021)
Genomics-informed outbreak investigations of SARS-CoV-2 using civet. S.C., R., T.R., C., N.J., L., T., G., R.T.M., N. et al., Medrxiv (2021)
Mandrake: Visualising microbial population structure by embedding millions of genomes into a low-dimensional representation. J.A., L., G., T., Z., Y., J., C. Biorxiv (2021)
Recurrent emergence of SARS-CoV-2 spike deletion H69/V70 and its role in the Alpha variant B.1.1.7. B., M., S.A., K., G., P., R., D., I.A.T.M., F. et al., Cell Reports (2021)
SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. D.A., C., A., d., I.A.T.M., F., B., M., R., D. et al., Medrxiv (2021)
SARS-CoV-2 evolution during treatment of chronic infection. S.A., K., D.A., C., R.P., D., I.A.T.M., F., S., G. et al., Nature (2021)
Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. D.A., C., A., D., I.A.T.M., F., B., M., R.P., D. et al., Nature (2021)
The impact of viral mutations on recognition by SARS-CoV-2 specific T cells. T.I., d., G., L., B.B., L., D., D., S.C., M. et al., Iscience (2021)
Transmission of SARS-CoV-2 Lineage B.1.1.7 in England: Insights from linking epidemiological and genetic data. E., V., S., M., M., C., J.C., B., R., J. et al., Medrxiv (2021)

2020

Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. Tonkin-Hill, G, MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G. et al., Preprint (2020)
A comprehensive and high-quality collection of E. coli genomes and their genes. G., H., G., B., G., T., J., C., E., H. et al., Biorxiv (2020)
A scalable method for identifying recombinants from unaligned sequences. Q., F., K., T., S., R., G., T., M., D. et al., Biorxiv (2020)
Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. C., C., M., Y., J.E., C., M., d., R.A., G. et al., Communications Biology (2020)
Common virulence gene expression in naïve and severe malaria cases. J.S., W., G., T., T., T., R., K., J., S. et al., Biorxiv (2020)
Emergence and Dissemination of Antimicrobial Resistance in Escherichia Coli Causing Bloodstream Infections: A Nationwide Longitudinal Microbial Population Genomic Cohort Study in Norway between 2002-2017. R.A., G., A., M., A.K., P., G., T., J.A., L. et al., Ssrn (2020)
Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure. M.L., M., G.Q., T., R.A.V., M., A.W., P., A.T., P. et al., Marine Biotechnology (2020)
The circulating SARS-CoV-2 spike variant N439K maintains fitness while evading antibody-mediated immunity. E.C., T., L.E., R., J.G., S., R., S., A., d. et al., Biorxiv (2020)

2019

Bacterial Population Genomics. Corander, J., Croucher, N., Harris, S., Lees, J., Tonkin‐Hill, G. Handbook of Statistical Genomics (2019)
rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Wailan, A., Coll, F., Heinz, E., Tonkin-Hill, G, Corander, J. et al., Microbial Genomics (2019)
Fast and flexible bacterial genomic epidemiology with PopPUNK. Lees, J., Harris, S., Tonkin-Hill, G, Gladstone, R., Lo, S. et al., Genome Research (2019)
The inner ear proteome of fish. Thomas, O., Swearer, S., Kapp, E., Peng, P., Tonkin‐Hill, G. et al., The FEBS Journal (2019)
Genome-wide epistasis and co-selection study using mutual information. J., P., S., P., B., A., N., M., J., K. et al., Nucleic Acids Research (2019)

2018

The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes. Tonkin-Hill, G, Trianty, L., Noviyanti, R., Nguyen, H., Sebayang, B. et al., PLOS Biology (2018)
A high parasite density environment induces transcriptional changes and cell death in Plasmodium falciparum blood stages. Chou, E., Abidi, S., Teye, M., Leliwa‐Sytek, A., Rask, T. et al., The FEBS Journal (2018)
Fast Hierarchical Bayesian Analysis of Population Structure. G., T., J.A., L., S.D., B., S.D.W., F., J., C. Biorxiv (2018)
RhierBAPs: An R implementation of the population clustering algorithm hierbaps.. G., T., J.A., L., S.D., B., S.D.W., F., J., C. Wellcome Open Research (2018)

2017

Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda. Ruybal-Pesántez, S., Tiedje, K., Tonkin-Hill, G, Rask, T., Kamya, M. et al., Scientific Reports (2017)
Stronger together. Lees, J., Tonkin-Hill, G, Bentley, S. Nature Reviews Microbiology (2017)
The use of imaging mass spectrometry to study peptide toxin distribution in Australian sea anemones. M.L., M., B.R., H., B., M., R.A.V., M., G.Q., T. et al., Australian Journal of Chemistry (2017)