Gerry Tonkin-Hill

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

† = joint authorship



Mallawaarachchi, S., Tonkin-Hill, G., Croucher, NJ., Turner, P., Speed, D., & … (2022). Genome-wide association, prediction and heritability in bacteria with application to Streptococcus pneumoniae. NAR Genomics and Bioinformatics. 4 (1), lqac011

Feng, Q., Tiedje, KE., Ruybal-Pesántez, S., Tonkin-Hill, G., Duffy, MF., Day, KP., & … (2022). An accurate method for identifying recent recombinants from unaligned sequences. Bioinformatics.

Tonkin-Hill, G., Ling, C., Chaguza, C., Salter, SJ., Hinfonthong, P., Nikolaou, E., & … (2022). Pneumococcal within-host diversity during colonisation, transmission and treatment. bioRxiv.

Ruybal-Pesántez, S., Tiedje, KE., Pilosof, S., Tonkin-Hill, G., He, Q., Rask, TS., & … (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 …. International Journal for Parasitology.

Chaguza, C., Ebruke, C., Senghore, M., Lo, SW., Tientcheu, PE., Gladstone, RA., & … (2022). Comparative genomics of disease and carriage serotype 1 pneumococci. Genome Biology and Evolution. 14 (4), evac052

Ruis, C., Weimann, A., Tonkin-Hill, G., Pandurangan, AP., Matuszewska, M., & … (2022). Mutational spectra analysis reveals bacterial niche and transmission routes. bioRxiv.

Tonkin-Hill, G., Gladstone, RA., Pontinen, AK., Arredondo-Alonso, S., & … (2022). Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe. bioRxiv.


Tonkin-Hill†, G., Martincorena†, I., Amato, R., Lawson, ARJ., Gerstung, M., & … (2021). Patterns of within-host genetic diversity in SARS-CoV-2. Elife. 10, e66857

Pöntinen, AK., Top, J., Arredondo-Alonso, S., Tonkin-Hill, G., Freitas, AR., & … (2021). Apparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era. Nature Communications. 12 (1), 1-13

Horesh, G., Blackwell, GA., Tonkin-Hill, G., Corander, J., Heinz, E., & … (2021). A comprehensive and high-quality collection of Escherichia coli genomes and their genes. Microbial genomics. 7 (2)

Hamilton†, WL., Tonkin-Hill†, G., Smith, ER., Aggarwal, D., Houldcroft, CJ., & … (2021). Genomic epidemiology of COVID-19 in care homes in the east of England. Elife. 10, e64618

Gladstone, RA., McNally, A., Pöntinen, AK., Tonkin-Hill, G., Lees, JA., Skytén, K., & … (2021). Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002–17: a nationwide, longitudinal, microbial …. The Lancet Microbe. 2 (7), e331-e341

Tonkin-Hill, G., Ruybal-Pesántez, S., Tiedje, KE., Rougeron, V., Duffy, MF., & … (2021). Evolutionary analyses of the major variant surface antigen-encoding genes reveal population structure of Plasmodium falciparum within and between continents. PLoS genetics. 17 (2), e1009269

Wichers, JS., Tonkin-Hill, G., Thye, T., Krumkamp, R., Kreuels, B., Strauss, J., & … (2021). Common virulence gene expression in adult first-time infected malaria patients and severe cases. Elife. 10, e69040

Lees†, JA., Tonkin-Hill†, G., Yang, Z., & Corander, J. (2021). Mandrake: visualising microbial population structure by embedding millions of genomes into a low-dimensional representation. bioRxiv.

Rambhatla, JS., Tonkin-Hill, G.., Takashima, E., Tsuboi, T., Noviyanti, R., & … (2021). Identifying targets of protective antibodies against severe malaria in Papua, Indonesia using locally expressed domains of Plasmodium falciparum Erythrocyte …. Infection and Immunity, IAI.. 00435-21

Chaguza, C., Tonkin-Hill, G., Lo, SW., Hadfield, J., Croucher, NJ., Harris, SR., & … (2021). RCandy: an R package for visualising homologous recombinations in bacterial genomes. Bioinformatics.


Tonkin-Hill, G., MacAlasdair, N., Ruis, C., Weimann, A., Horesh, G., Lees, JA., & … (2020). Producing polished prokaryotic pangenomes with the Panaroo pipeline. Genome biology. 21 (1), 1-21

COVID, T. (2020). An integrated national scale SARS-CoV-2 genomic surveillance network. The Lancet. Microbe. 1 (3), e99

Mitchell, ML., Tonkin-Hill, G.., Morales, RAV., Purcell, AW., Papenfuss, AT., & … (2020). Tentacle transcriptomes of the speckled anemone (Actiniaria: Actiniidae: Oulactis Sp.): Venom-related components and their domain structure. Marine Biotechnology. 22 (2), 207-219

Chaguza, C., Yang, M., Cornick, JE., Plessis, M du., Gladstone, RA., & … (2020). Bacterial genome-wide association study of hyper-virulent pneumococcal serotype 1 identifies genetic variation associated with neurotropism. Communications Biology. 3 (1), 1-12

Tonkin-Hill, G. (2020). Pathogen evolution within and between hosts with applications to the pneumococcus and SARS-CoV-2. University of Cambridge.


Lees, JA., Harris, SR., Tonkin-Hill, G., Gladstone, RA., Lo, SW., Weiser, JN., & … (2019). Fast and flexible bacterial genomic epidemiology with PopPUNK. Genome research. 29 (2), 304-316

Tonkin-Hill, G., Lees, JA., Bentley, SD., Frost, SDW., & Corander, J. (2019). Fast hierarchical Bayesian analysis of population structure. Nucleic acids research. 47 (11), 5539-5549

Thomas, ORB., Swearer, SE., Kapp, EA., Peng, P., Tonkin‐Hill, GQ., & … (2019). The inner ear proteome of fish. The FEBS journal. 286 (1), 66-81

Pensar, J., Puranen, S., Arnold, B., MacAlasdair, N., Kuronen, J., Tonkin-Hill, G., & … (2019). Genome-wide epistasis and co-selection study using mutual information. Nucleic acids research. 47 (18), e112-e112

Wailan, AM., Coll, F., Heinz, E., Tonkin-Hill, G., Corander, J., Feasey, NA., & … (2019). rPinecone: Define sub-lineages of a clonal expansion via a phylogenetic tree. Microbial genomics. 5 (4)

Corander, J., Croucher, NJ., Harris, SR., Lees, JA., & Tonkin‐Hill, G. (2019). Bacterial population genomics. Handbook of Statistical Genomics: Two Volume Set. 997-1020


Tonkin-Hill, G., Lees, JA., Bentley, SD., Frost, SDW., & Corander, J. (2018). RhierBAPS: An R implementation of the population clustering algorithm hierBAPS. Wellcome Open Research. 3

Tonkin-Hill, G.., Trianty, L., Noviyanti, R., Nguyen, HHT., Sebayang, BF., & … (2018). The Plasmodium falciparum transcriptome in severe malaria reveals altered expression of genes involved in important processes including surface antigen–encoding var genes. PLoS biology. 16 (3), e2004328

Chou, ES., Abidi, SZ., Teye, M., Leliwa‐Sytek, A., Rask, TS., Cobbold, SA., & … (2018). A high parasite density environment induces transcriptional changes and cell death in Plasmodium falciparum blood stages. The FEBS journal. 285 (5), 848-870

Ruybal-Pesántez, S., Tiedje, KE., Tonkin-Hill, G., Rask, TS., Kamya, MR., & … (2017). Population genomics of virulence genes of Plasmodium falciparum in clinical isolates from Uganda. Scientific reports. 7 (1), 1-12

Mitchell, ML., Hamilton, BR., Madio, B., Morales, RAV., Tonkin-Hill, G.., & … (2017). The use of imaging mass spectrometry to study peptide toxin distribution in Australian sea anemones. Australian Journal of Chemistry. 70 (11), 1235-1237

Lees, JA., Tonkin-Hill, G., & Bentley, SD. (2017). Stronger together. Nature Reviews Microbiology. 15 (9), 516-516