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

2024

  • Enhanced metagenomics-enabled transmission inference with TRACS. Tonkin-Hill, G, Shao, Y., Zarebski, A., Mallawaarachchi, S, Xie, O. et al., Preprint (2024)
  • Pangenome-spanning epistasis and coselection analysis via de Bruijn graphs. Kuronen, J., Horsfield, S., Pöntinen, A., Mallawaarachchi, S, Arredondo-Alonso, S. et al., Genome Research (2024)
  • Basic reproduction number for pandemic Escherichia coli clones is comparable to typical pandemic 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)
  • Detecting co-selection through excess linkage disequilibrium in bacterial genomes. Mallawaarachchi, S, Tonkin-Hill, G, Pöntinen, A., Calland, J., Gladstone, R. et al., NAR Genomics and Bioinformatics (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)

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)
  • Plasmid-driven strategies for clone success inEscherichia coli. Arredondo-Alonso, S., Pöntinen, A., Gama, J., Gladstone, R., Harms, K. et al., Preprint (2023)
  • Accurate and fast graph-based pangenome annotation and clustering with ggCaller. Horsfield, S., Tonkin-Hill, G, Croucher, N., Lees, J. Genome Research (2023)
  • Detecting co-selection through excess linkage disequilibrium in bacterial genomes. Mallawaarachchi, S, Tonkin-Hill, G, Pöntinen, A., Calland, J., Gladstone, R. et al., Preprint (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)
  • Calculating and applying pathogen mutational spectra using MutTui. Ruis, C., Tonkin-Hill, G, Floto, R., Parkhill, J. Preprint (2023)
  • Challenges in prokaryote pangenomics. Tonkin-Hill, G, Corander, J., Parkhill, J. Microbial Genomics (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)

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)
  • Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. Mallawaarachchi, S, Tonkin-Hill, G, Croucher, N., Turner, P., Speed, D. et al., NAR Genomics and Bioinformatics (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)
  • Common virulence gene expression in adult first-time infected malaria patients and severe cases. Wichers, J., Tonkin-Hill, G, Thye, T., Krumkamp, R., Kreuels, B. et al., eLife (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)
  • Genomic epidemiology of COVID-19 in care homes in the east of England. Hamilton, W., Tonkin-Hill, G, Smith, E., Aggarwal, D., Houldcroft, C. et al., eLife (2021)
  • Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents. Tonkin-Hill, G, Buchrieser, C., Ruybal-Pesántez, S., Tiedje, K., Rougeron, V. et al., PLOS Genetics (2021)
  • A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Horesh, G., Blackwell, G., Tonkin-Hill, G, Corander, J., Heinz, E. et al., Microbial Genomics (2021)

2020

  • Patterns of within-host genetic diversity in SARS-CoV-2. Tonkin-Hill, G, Martincorena, I., Amato, R., Lawson, A., Gerstung, M. et al., Preprint (2020)
  • Producing polished prokaryotic pangenomes with the Panaroo pipeline. Tonkin-Hill, G, MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G. et al., Genome Biology (2020)
  • Gene expression profiling of malaria parasites reveals common virulence gene expression in adult first-time infected patients and severe cases. Wichers, J., Tonkin-Hill, G, Thye, T., Krumkamp, R., Kreuels, B. et al., Preprint (2020)
  • Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. Chaguza, C., Yang, M., Cornick, J., Plessis, M., Gladstone, R. et al., Communications Biology (2020)
  • Tentacle Transcriptomes of the Speckled Anemone (Actiniaria: Actiniidae: Oulactis sp.): Venom-Related Components and Their Domain Structure. Mitchell, M., Tonkin-Hill, G, Morales, R., Purcell, A., Papenfuss, A. et al., Marine Biotechnology (2020)
  • Producing Polished Prokaryotic Pangenomes with the Panaroo Pipeline. Tonkin-Hill, G, MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G. et al., Preprint (2020)

2019

  • Genome-wide epistasis and co-selection study using mutual information. Pensar, J., Puranen, S., Arnold, B., MacAlasdair, N., Kuronen, J. et al., Nucleic Acids Research (2019)
  • Bacterial Population Genomics. Corander, J., Croucher, N., Harris, S., Lees, J., Tonkin‐Hill, G. Handbook of Statistical Genomics (2019)
  • Fast hierarchical Bayesian analysis of population structure. Tonkin-Hill, G, Lees, J., Bentley, S., Frost, S., Corander, J. Nucleic Acids Research (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)

2018

  • RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Tonkin-Hill, G, Lees, J., Bentley, S., Frost, S., Corander, J. Wellcome Open Research (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)

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. Mitchell, M., Hamilton, B., Madio, B., Morales, R., Tonkin-Hill, G et al., Australian Journal of Chemistry (2017)