Pre-prints, not yet peer reviewed:

• ​Smith, E., et al. Variable rates of SARS-CoV-2 evolution in chronic infections. bioRxiv 2024. doi: https://doi.org/10.1101/2024.05.31.596818.

• Hamilton, W.L., et al. A fourth locus in the Plasmodium falciparum genome associated with sickle haemoglobin. bioRxiv 2023. doi: https://doi.org/10.1101/2023.09.14.557461.

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Peer reviewed:

• Miotto, O., et al. Identification of complex Plasmodium falciparum genetic backgrounds circulating in Africa: a multicountry genomic epidemiology analysis. Lancet Microbe. 2024 Nov 7:100941. URL: https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(24)00194-0/fulltext

• ** Girgis, S.T., Adika, E., … Amenga-Etego, L.N., Hamilton, W.L. 2023. Drug resistance and vaccine target surveillance of Plasmodium falciparum using nanopore sequencing in Ghana. Nat Microbiol (2023). https://doi.org/10.1038/s41564-023-01516-6. URL: https://www.nature.com/articles/s41564-023-01516-6

• * Hamilton, W.L., et al. 2023. Nanopore sequencing for malaria molecular surveillance: opportunities and challenges. Trends in Parasitology. 2023 Dec;39(12):996-1000. doi: 10.1016/j.pt.2023.09.014. Epub 2023 Oct 19. URL: https://www.cell.com/trends/parasitology/fulltext/S1471-4922(23)00235-0

• * Hamilton, W.L., et al. 2023. The clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom. Microbial Genomics. 2023 Oct;9(10). doi: 10.1099/mgen.0.001122. URL: https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001122

• Kemp, S.A., Cheng, M.T.K., et al. 2022. Transmission of B.1.617.2 Delta variant between vaccinated healthcare workers. Sci Rep 12, 10492 (2022). URL: https://doi.org/10.1038/s41598-022-14411-7

• Aggarwal, D., Warne, B., et al. 2022. Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission. Nat Commun 13, 751 (2022). URL: https://doi.org/10.1038/s41467-021-27942-w

• * Illingworth, C.J.R., Hamilton, W.L., Jackson, C., et al. 2022. A2B-COVID: A Tool for Rapidly Evaluating Potential SARS-CoV-2 Transmission Events. Mol Biol Evol. 2022 Mar 2;39(3):msac025. URL: https://academic.oup.com/mbe/article/39/3/msac025/6519868

• Mlcochova, P., Kemp, S., Dhar, M.S., et al. SARS-CoV-2 B.1.617.2 Delta variant replication and immune evasion. Nature. 2021 Sep 6. doi: 10.1038/s41586-021-03944-y. URL: https://www.nature.com/articles/s41586-021-03944-y

• Aggarwal, D., et al. 2021. The role of viral genomics in understanding COVID-19 outbreaks in long-term care facilities. Lancet Microbe. 2021 Sep 29. doi: 10.1016/S2666-5247(21)00208-1. URL: https://www.thelancet.com/journals/lanmic/article/PIIS2666-5247(21)00208-1/fulltext

• * Illingworth, C.J.R, Hamilton, W.L., et al. 2021. Superspreaders drive the largest outbreaks of hospital onset COVID-19 infections. eLife 2021;10:e67308 DOI: 10.7554/eLife.67308. URL: https://elifesciences.org/articles/67308

• Tonkin-Hill, G., Martincorena, I., et al. 2021. Patterns of within-host genetic diversity in SARS-CoV-2. eLife 2021;10:e66857 doi: 10.7554/eLife.66857. URL: https://elifesciences.org/articles/66857

• * Hamilton, W.L., Fieldman, T., Jahun, A., et al. 2021. Applying prospective genomic surveillance to support investigation of hospital-onset COVID-19. Lancet Infect Dis. 2021 Jul;21(7):916-917. DOI: https://doi.org/10.1016/S1473-3099(21)00251-6. URL: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(21)00251-6/fulltext

• * Hamilton, W. L., Tonkin-Hill, G., et al. 2021. Genomic epidemiology of COVID-19 in care homes in the East of England. eLife 2021;10:e64618. DOI: 10.7554/eLife.64618. URL: https://elifesciences.org/articles/64618

• MalariaGEN Plasmodium falciparum Community Project. 2021. An open dataset of Plasmodium falciparum genome variation in 7,000 worldwide samples. Wellcome Open Res 2021, 6:42. PMID: 33824913. DOI: 10.12688/wellcomeopenres.16168.1. URL: https://wellcomeopenresearch.org/articles/6-42

• Buckland, M.S., et al. Treatment of COVID-19 with remdesivir in the absence of humoral immunity: a case report. Nat Commun. 2020 Dec 14;11(1):6385. URL: https://www.nature.com/articles/s41467-020-19761-2

• * Meredith, L.W., Hamilton, W.L., et al. 2020. Rapid implementation of SARS-CoV-2 sequencing to investigate cases of health-care associated COVID-19: a prospective genomic surveillance study. Lancet Infect Dis. 2020 Nov;20(11):1263-1271. doi: 10.1016/S1473-3099(20)30562-4. URL: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(20)30562-4/fulltext

• Rivett, L., Sridhar, S., Sparkes, D., Routledge, M., Jones, N.K., et al. 2020. Screening of healthcare workers for SARS-CoV-2 highlights the role of asymptomatic carriage in COVID-19 transmission. eLife 9, e58728. URL: https://elifesciences.org/articles/58728

• * Hamilton, W.L., et al. 2020. The impact of diagnostic microbiology on de-escalation of antimicrobial therapy in hospitalised adults. BMC infectious diseases 20 (1), 102. URL: https://bmcinfectdis.biomedcentral.com/articles/10.1186/s12879-020-4823-4

• * Hamilton, W.L., Amato, R., et al. 2019. Evolution and expansion of multidrug-resistant malaria in southeast Asia: a genomic epidemiology study. Lancet Infect Dis. 19 (9), 943-951. URL: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30392-5/fulltext

• van der Pluijm, R.W., et al. 2019. Determinants of dihydroartemisinin-piperaquine treatment failure in Plasmodium falciparum malaria in Cambodia, Thailand, and Vietnam: a prospective clinical, pharmacological, and genetic study. Lancet Infect Dis. 19 (9), 952-961. URL: https://www.thelancet.com/journals/laninf/article/PIIS1473-3099(19)30391-3/fulltext

• * Hamilton, W.L., Agranoff, D. 2018. Imported gnathostomiasis manifesting as cutaneous larva migrans and Löffler’s syndrome. BMJ case reports, bcr-2017-223132. URL: https://casereports.bmj.com/content/2018/bcr-2017-223132.long

• Otto, T.D., et al. 2018. Long read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres. Wellcome Open Research. URL: https://wellcomeopenresearch.org/articles/3-52/v1

• Oyola, S.O., Ariani, C.V., et al. 2016. Whole genome sequencing of Plasmodium falciparum from dried blood spots using selective whole genome amplification. Malaria journal 15 (1), 597. URL: https://malariajournal.biomedcentral.com/articles/10.1186/s12936-016-1641-7

• * Hamilton, W.L., Claessens, A., et al. 2016. Extreme mutation bias and high AT content in Plasmodium falciparum. Nucleic Acids Res. 28;45(4):1889-1901. URL: https://academic.oup.com/nar/article/45/4/1889/2716522

• * Hamilton, W.L., et al. 2016. Public health interventions to protect against falsified medicines: a systematic review of international, national and local policies. Health Policy Plan. 31(10):1448-1466. URL: https://academic.oup.com/heapol/article/31/10/1448/2567085

• Freedman S.B., et al. 2016. Shiga Toxin-Producing Escherichia coli Infection, Antibiotics, and Risk of Developing Hemolytic Uremic Syndrome: A Meta-analysis. Clin Infect Dis. 62(10):1251-8. URL: https://academic.oup.com/cid/article/62/10/1251/2462717

• * Claessens, A., Hamilton, W.L., et al. 2014. Generation of antigenic diversity in Plasmodium falciparum by structured rearrangement of var genes during mitosis. PLoS Genet 10(12): e1004812. URL: https://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004812

• Oyola, S.O., et al. 2014. Optimized whole-genome amplification strategy for extremely AT-biased template. DNA research 21 (6), 661-671. URL: https://academic.oup.com/dnaresearch/article/21/6/661/2754550

• Uchil, P.D., et al. 2014. TRIM15 is a focal adhesion protein that regulates focal adhesion disassembly. J Cell Sci 127 (18), 3928-3942. URL: https://jcs.biologists.org/content/127/18/3928