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Dr David Cleary


Career Track Post-Doctoral Fellow

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Dr Cleary is a Career-track Post-Doctoral Fellow in the Faculty of Medicine and the Southampton NIHR Biomedical Research Centre. His research focuses on the application of computational biology approaches to understand the epidemiology and pathogenicity of infectious disease, primarily of those pathogens that can be carried in the human respiratory tract such as Streptococcus pneumoniae and Non-typeable Haemophilus influenzae. In addition, his research involves characterising respiratory tract microbiomes to determine the community-host interactions that underpin colonisation and progression to disease.

Landmark publications:

Cleary, D., Morris, D., Anderson, R., Jones, J., Alattraqchi , A. G.,   Rahman , N. I., Ismail, S., Razali, M., Amin, R. M., Amin, R. M., Aziz, A.   A., Esa, N. K., Amiruddin, S., Chew, C. H., Amat Simin, M. H., Abdullah, R.,   Yeo, C. C., & Clarke, S. (2021). The   upper respiratory tract microbiome of indigenous Orang Asli in north-eastern   Peninsular Malaysia. NPJ Biofilms and Microbiomes, 7(1),   [1].

Cleary, D., Devine, V., Morris, D., Osman, K., Gladstone, R.,   Bentley, S. D., Faust, S., & Clarke, S. (2018). Pneumococcal   vaccine impacts on the population genomics of non-typeable Haemophilus   influenzae. Microbial Genomics.

Osman, K., Jefferies, J. M. C., Woelk, C. H., Devos, N., Pascal, T.   G., Mortier, M-C., Devaster, J-M., Wilkinson, T. M. A., Cleary, D.*, Clarke,   S.*, & AERIS Study Group (2018). Patients   with Chronic Obstructive Pulmonary Disease harbour a variation of Haemophilus  species. Scientific Reports, 8(1), 1-11. [14734].

*Joint Senior Authors

Pandey, A., Cleary, D. W., Laver, J. R., Gorringe, A., Deasy, A. M.,   Dale, A. P., Morris, P. D., Didelot, X., Maiden, M. C. J., & Read, R. C.   (2018). Microevolution   of Neisseria lactamica during nasopharyngeal colonisation induced by   controlled human infection. Nature Communications, 9(1),   [4753].

Devine, V. T.*, Cleary, D. W.*, Jefferies, J. M. C., Anderson, R.,   Morris, D. E., Tuck, A. C., Gladstone, R. A., O'Doherty, G., Kuruparan, P.,   Bentley, S. D., Faust, S. N., & Clarke, S. C. (2017). The   rise and fall of pneumococcal serotypes carried in the PCV era. Vaccine,   35(9), 1293-1298.

*Joint 1st Authors

Major grants:

Impacts of Bordetella pertussis colonisation on the upper   respiratory tract microbiome (HIC-Vac)

Transcriptomics of host-microbiota interactions using direct dual   RNA-Seq (Wessex Medical Research)

From observations to mechanisms: linking analyses of upper   respiratory tract microbiomes with mechanistic microbial ecology (Rosetrees   Trust)

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