![Thomas Whalley](https://profiles-cardiff.imgix.net/attachments/1252?w=200&h=200&auto=format&crop=faces&fit=crop&q=90")
Mr Thomas Whalley
Senior Professional Specialist
School of Biosciences
- WhalleyT@cardiff.ac.uk
- Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX
Overview
My research interests broadly center around the application of computational methods in microbial bioinformatics and immunoinformatics.
More specifically, these include:
- User acceptance testing (UAT) and module testing on the Scalable Pathogen Pipeline (SP3)
- Development of genomics pipelines
- Immunoinformatics, including TCR sequencing and analysis of T-cell peptide MHC (TCR-pMHC) protein complexes
- High performance computing (HPC), including the application of CUDA
Publication
2023
- Cotton, S. et al. 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135, pp. 28-36. (10.1016/j.jhin.2023.02.010)
2022
- Guest, K., Whalley, T., Maillard, J., Artemiou, A., Szomolay, B. and Webber, M. A. 2022. Responses of Salmonella biofilms to oxidizing biocides: evidence of spatial clustering. Environmental Microbiology 24(12), pp. 6426-6438. (10.1111/1462-2920.16263)
- Willett, B. J. et al. 2022. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology 7, pp. 1161-1179. (10.1038/s41564-022-01143-7)
- Dolton, G. et al. 2022. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 185(16), pp. 2936-2951. (10.1016/j.cell.2022.07.002)
- Eales, O. et al. 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22(1), article number: 647. (10.1186/s12879-022-07628-4)
- Nickbakhsh, S. et al. 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports 12(1), article number: 11735. (10.1038/s41598-022-15661-1)
- Kläser, K. et al. 2022. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports 12(1), article number: 10904. (10.1038/s41598-022-14016-0)
- Whalley, T. 2022. Novel bioinformatics tools for epitope-based peptide vaccine design. PhD Thesis, Cardiff University.
2021
- Pratt, H. G. et al. 2021. Macrophage and neutrophil interactions in the pancreatic tumor microenvironment drive the pathogenesis of pancreatic cancer. Cancers 14(1), article number: 194. (10.3390/cancers14010194)
- Chiaro, J. et al. 2021. Viral molecular mimicry influences the antitumor immune response in murine and human melanoma. Cancer Immunology Research 9(8), pp. 981-983. (10.1158/2326-6066.CIR-20-0814)
2020
- Greenshields-Watson, A. et al. 2020. CD4 + T cells recognize conserved influenza A epitopes through shared patterns of V-Gene usage and complementary biochemical features. Cell Reports 32(2), article number: 107885. (10.1016/j.celrep.2020.107885)
- Whalley, T. et al. 2020. GPU-accelerated discovery of pathogen-derived molecular mimics of a T-cell insulin epitope. Frontiers in Immunology 11, article number: 296. (10.3389/fimmu.2020.00296)
2018
- Tungatt, K. et al. 2018. Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig. PLoS Pathogens 14(5), article number: e1007017. (10.1371/journal.ppat.1007017)
Articles
- Cotton, S. et al. 2023. Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes. Journal of Hospital Infection 135, pp. 28-36. (10.1016/j.jhin.2023.02.010)
- Guest, K., Whalley, T., Maillard, J., Artemiou, A., Szomolay, B. and Webber, M. A. 2022. Responses of Salmonella biofilms to oxidizing biocides: evidence of spatial clustering. Environmental Microbiology 24(12), pp. 6426-6438. (10.1111/1462-2920.16263)
- Willett, B. J. et al. 2022. SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway. Nature Microbiology 7, pp. 1161-1179. (10.1038/s41564-022-01143-7)
- Dolton, G. et al. 2022. Emergence of immune escape at dominant SARS-CoV-2 killer T cell epitope. Cell 185(16), pp. 2936-2951. (10.1016/j.cell.2022.07.002)
- Eales, O. et al. 2022. SARS-CoV-2 lineage dynamics in England from September to November 2021: high diversity of Delta sub-lineages and increased transmissibility of AY.4.2. BMC Infectious Diseases 22(1), article number: 647. (10.1186/s12879-022-07628-4)
- Nickbakhsh, S. et al. 2022. Genomic epidemiology of SARS-CoV-2 in a university outbreak setting and implications for public health planning. Scientific Reports 12(1), article number: 11735. (10.1038/s41598-022-15661-1)
- Kläser, K. et al. 2022. COVID-19 due to the B.1.617.2 (Delta) variant compared to B.1.1.7 (Alpha) variant of SARS-CoV-2: a prospective observational cohort study. Scientific Reports 12(1), article number: 10904. (10.1038/s41598-022-14016-0)
- Pratt, H. G. et al. 2021. Macrophage and neutrophil interactions in the pancreatic tumor microenvironment drive the pathogenesis of pancreatic cancer. Cancers 14(1), article number: 194. (10.3390/cancers14010194)
- Chiaro, J. et al. 2021. Viral molecular mimicry influences the antitumor immune response in murine and human melanoma. Cancer Immunology Research 9(8), pp. 981-983. (10.1158/2326-6066.CIR-20-0814)
- Greenshields-Watson, A. et al. 2020. CD4 + T cells recognize conserved influenza A epitopes through shared patterns of V-Gene usage and complementary biochemical features. Cell Reports 32(2), article number: 107885. (10.1016/j.celrep.2020.107885)
- Whalley, T. et al. 2020. GPU-accelerated discovery of pathogen-derived molecular mimics of a T-cell insulin epitope. Frontiers in Immunology 11, article number: 296. (10.3389/fimmu.2020.00296)
- Tungatt, K. et al. 2018. Induction of influenza-specific local CD8 T-cells in the respiratory tract after aerosol delivery of vaccine antigen or virus in the Babraham inbred pig. PLoS Pathogens 14(5), article number: e1007017. (10.1371/journal.ppat.1007017)
Thesis
- Whalley, T. 2022. Novel bioinformatics tools for epitope-based peptide vaccine design. PhD Thesis, Cardiff University.
Biography
- BSc physiological sciences, Newcastle University, 2012-2015
- MRes in systems biology, Newcastle University, 2015-2016
- PhD in bioinformatics, Cardiff University, 2016-2022