Overview
My research is focused on how the explosion of data that is collected and generated by researchers, clinical trials and the NHS can be combined and analysed to drive advances in treatment options for patients as well as advance our scientific understanding of disease.
To do this requires a number of underpinning technologies and techniques, so I have expertise in the design, deployment and management of high-performance computing infrastructure (including GPU analysis) and petabyte scale data storage as well as the bioinformatic and AI techniques needed to analyse and extract information from genomic, transcriptomic, radiomic and digital pathology datasets.
My current work is centred around exploiting the opportunities that Trusted Research Environments can unlock to bring together data collected for a single patient during their treatment journey and how we can then apply machine learning techniques to unlock information from these interlinked datasets.
Publication
2025
- Jones, R. et al. 2025. Characterizing the tumor suppressor activity of FLCN in Birt-Hogg-Dubé syndrome through transcriptiomic and proteomic analysis. Oncogene (10.1038/s41388-025-03325-z)
2024
- Meuser, E. et al. 2024. PIGA mutations and glycosylphosphatidylinositol anchor dysregulation in polyposis-associated duodenal tumorigenesis. Molecular Cancer Research 22(6), pp. 515–523. (10.1158/1541-7786.MCR-23-0810)
2023
- West, H. D. et al. 2023. Targeted genomic sequencing of TSC1 and TSC2 reveals causal variants in individuals for whom previous genetic testing for tuberous sclerosis complex was normal. Human Mutation: Variation, Informatics and Disease 2023, article number: 4899372. (10.1155/2023/4899372)
- Lohana, P. et al. 2023. Role of enzymic antioxidants in mediating oxidative stress and contrasting wound healing capabilities in oral mucosal/skin fibroblasts and tissues. Antioxidants 12(7), article number: 1374. (10.3390/antiox12071374)
2021
- Shephard, A. P. et al. 2021. Stroma-derived extracellular vesicle mRNA signatures inform histological nature of prostate cancer. Journal of Extracellular Vesicles 10(12), article number: e12150. (10.1002/jev2.12150)
- Ordonez, L. D. et al. 2021. Reproductive history determines ErbB2 locus amplification, WNT signalling and tumour phenotype in a murine breast cancer model. Disease Models and Mechanisms 14(5), article number: dmm048736. (10.1242/dmm.048736)
- Lewis, T. et al. 2021. Novel pyrrolobenzodiazepine benzofused hybrid molecules inhibit NF-κB activity and synergise with bortezomib and ibrutinib in hematological cancers. Haematologica 106(4), pp. 958-967. (10.3324/haematol.2019.238584)
- Lawson, H. et al. 2021. JMJD6 promotes self-renewal and regenerative capacity of hematopoietic stem cells. Blood Advances 5(3), pp. 889-899. (10.1182/bloodadvances.2020002702)
- Almotiri, A. et al. 2021. Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia. Journal of Clinical Investigation 131(1), article number: e129115. (10.1172/JCI129115)
2020
- Holzhauser, S. et al. 2020. Sensitivity of human papillomavirus-positive and -negative oropharyngeal cancer cell lines to ionizing irradiation. Oncology Reports (10.3892/or.2020.7709)
- Short, E. et al. 2020. APC transcription studies and molecular diagnosis of familial adenomatous polyposis. European Journal of Human Genetics 28(1), pp. 118-121. (10.1038/s41431-019-0486-2)
2019
- Menendez Gonzalez, J. B. et al. 2019. Gata2 as a crucial regulator of stem cells in adult hematopoiesis and acute myeloid leukemia. Stem Cell Reports 13(2), pp. 291-306. (10.1016/j.stemcr.2019.07.005)
2018
- Pirotte, E. F. et al. 2018. Sensitivity to inhibition of DNA repair by Olaparib in novel oropharyngeal cancer cell lines infected with Human Papillomavirus. PLoS ONE 13(12), pp. -., article number: e0207934. (10.1371/journal.pone.0207934)
- Johnson, C. E. et al. 2018. Loss of tuberous sclerosis complex 2 sensitizes tumors to nelfinavir−bortezomib therapy to intensify endoplasmic reticulum stress-induced cell death. Oncogene 37, pp. 5913-5925. (10.1038/s41388-018-0381-2)
- Caley, M., Wall, I., Peake, M., Kipling, D., Giles, P., Thomas, D. and Stephens, P. 2018. Development and characterisation of a human chronic skin wound cell line - towards an alternative for animal experimentation. International Journal of Molecular Sciences 19(4), article number: 1001. (10.3390/ijms19041001)
2016
- Liao, C. et al. 2016. IL-10 differentially controls the infiltration of inflammatory macrophages and antigen-presenting cells during inflammation. European Journal of Immunology 46(9), pp. 2222-2232. (10.1002/eji.201646528)
2015
- Bayram-Weston, Z. et al. 2015. Similar striatal gene expression profiles in the striatum of the YAC128 and HdhQ150 mouse models of Huntington's disease are not reflected in mutant Huntingtin inclusion prevalence. BMC Genomics 16, pp. -., article number: 1079. (10.1186/s12864-015-2251-4)
2014
- Giles, J. L., Choy, E., van den Berg, C., Morgan, B. P. and Harris, C. L. 2014. Functional analysis of a complement polymorphism (rs17611) associated with Rheumatoid Arthritis. Immunology 143(s2), pp. 181-182. (10.1111/imm.12407)
- Bryant, D. et al. 2014. mRNA sequencing of novel cell lines from human papillomavirus type-16 related vulval intraepithelial neoplasia: Consequences of expression of HPV16 E4 and E5. Journal of Medical Virology 86(9), pp. 1534-1541. (10.1002/jmv.23994)
- Peake, M. A. et al. 2014. Identification of a transcriptional signature for the wound healing continuum. Wound Repair and Regeneration 22(3), pp. 399-405. (10.1111/wrr.12170)
- Rosas, M. et al. 2014. The transcription factor Gata6 links tissue macrophage phenotype and proliferative renewal. Science 344(6184), pp. 645-648. (10.1126/science.1251414)
2012
- Giles, P. J., Elliston, L. A., Higgs, G., Brooks, S. P., Dunnett, S. B. and Jones, L. 2012. Longitudinal analysis of gene expression and behaviour in the HdhQ150 mouse model of Huntington's disease. Brain Research Bulletin 88(2-3), pp. 199-209. (10.1016/j.brainresbull.2011.10.001)
- Bennett, M. R. et al. 2012. Bioinformatic analyses of genome wide nucleotide excision repair datasets in Saccharomyces cerevisiae [Abstract]. Mutagenesis 27(1), pp. 121. (10.1093/mutage/ger068)
- Feyeux, M. et al. 2012. Early transcriptional changes linked to naturally occurring Huntington's disease mutations in neural derivatives of human embryonic stem cells. Human Molecular Genetics 21(17), pp. 3883-3895. (10.1093/hmg/dds216)
2010
- Enoch, S. et al. 2010. 'Young' oral fibroblasts are geno/phenotypically distinct. Journal of Dental Research 89(12), pp. 1407-1413. (10.1177/0022034510377796)
- Welton, J. L. et al. 2010. Proteomics analysis of bladder cancer exosomes. Molecular & Cellular Proteomics 9(6), pp. 1324-1338. (10.1074/mcp.M000063-MCP201)
2009
- Enoch, S. et al. 2009. Increased oral fibroblast lifespan is telomerase-independent. Journal of Dental Research 88(10), pp. 916-921. (10.1177/0022034509342979)
- Zhang, L. et al. 2009. Thyrotropin receptor activation increases hyaluronan production in preadipocyte fibroblasts: Contributory role in hyaluronan accumulation in thyroid dysfunction. Journal of Biological Chemistry 284(39), pp. 26447-26455. (10.1074/jbc.M109.003616)
- Brennan, P. et al. 2009. Quantitative nuclear proteomics reveals new phenotypes altered in lymphoblastoid cells. Proteomics - Clinical Applications 3(3), pp. 359-369. (10.1002/prca.200800137)
- Burton, D. G. A. et al. 2009. Microarray analysis of senescent vascular smooth muscle cells: a link to atherosclerosis and vascular calcification. Experimental Gerontology 44(10), pp. 659-665. (10.1016/j.exger.2009.07.004)
- Kipling, D. G. et al. 2009. A transcriptomic analysis of the EK1.Br strain of human fibroblastoid keratocytes: the effects of growth, quiescence and senescence. Experimental Eye Research 88(2), pp. 277-285. (10.1016/j.exer.2008.11.030)
- Rees, D. A., Giles, P. J., Lewis, M. D. and Ham, J. 2009. Adenosine regulates thrombomodulin and endothelial protein C receptor expression in folliculostellate cells of the pituitary gland. Purinergic Signalling 6(1), pp. 19-29. (10.1007/s11302-009-9172-0)
2008
- Wall, I. B. et al. 2008. Fibroblast dysfunction is a key factor in the non-healing of chronic venous leg ulcers. Journal of Investigative Dermatology 128(10), pp. 2526-2540. (10.1038/jid.2008.114)
- Peake, M. A., Giles, P. J., Wall, I. B., Enoch, S., Kipling, D. G., Thomas, D. W. and Stephens, P. 2008. Identifying a Gene signature for the wound healing continuum [Abstract]. Wound Repair and Regeneration 16(6), pp. A71. (10.1111/j.1524-475X.2008.00424.x)
2005
- Giles, P. J. 2005. Microarray-based expression profiling: improving data mining and the links to biological knowledge pools. PhD Thesis, Cardiff University.
2002
- Myers, A. et al. 2002. Full genome screen for Alzheimer disease: Stage II analysis. American Journal Of Medical Genetics Part A 114(2), pp. 235-244. (10.1002/ajmg.10183)
2001
- Hamshere, M. L., Giles, P., Krawczak, M. and Owen, M. J. 2001. Statistical analysis of genotypic association data with HAPMAXII. AMERICAN JOURNAL OF HUMAN GENETICS 69(4), pp. 390-390.
Articles
- Jones, R. et al. 2025. Characterizing the tumor suppressor activity of FLCN in Birt-Hogg-Dubé syndrome through transcriptiomic and proteomic analysis. Oncogene (10.1038/s41388-025-03325-z)
- Meuser, E. et al. 2024. PIGA mutations and glycosylphosphatidylinositol anchor dysregulation in polyposis-associated duodenal tumorigenesis. Molecular Cancer Research 22(6), pp. 515–523. (10.1158/1541-7786.MCR-23-0810)
- West, H. D. et al. 2023. Targeted genomic sequencing of TSC1 and TSC2 reveals causal variants in individuals for whom previous genetic testing for tuberous sclerosis complex was normal. Human Mutation: Variation, Informatics and Disease 2023, article number: 4899372. (10.1155/2023/4899372)
- Lohana, P. et al. 2023. Role of enzymic antioxidants in mediating oxidative stress and contrasting wound healing capabilities in oral mucosal/skin fibroblasts and tissues. Antioxidants 12(7), article number: 1374. (10.3390/antiox12071374)
- Shephard, A. P. et al. 2021. Stroma-derived extracellular vesicle mRNA signatures inform histological nature of prostate cancer. Journal of Extracellular Vesicles 10(12), article number: e12150. (10.1002/jev2.12150)
- Ordonez, L. D. et al. 2021. Reproductive history determines ErbB2 locus amplification, WNT signalling and tumour phenotype in a murine breast cancer model. Disease Models and Mechanisms 14(5), article number: dmm048736. (10.1242/dmm.048736)
- Lewis, T. et al. 2021. Novel pyrrolobenzodiazepine benzofused hybrid molecules inhibit NF-κB activity and synergise with bortezomib and ibrutinib in hematological cancers. Haematologica 106(4), pp. 958-967. (10.3324/haematol.2019.238584)
- Lawson, H. et al. 2021. JMJD6 promotes self-renewal and regenerative capacity of hematopoietic stem cells. Blood Advances 5(3), pp. 889-899. (10.1182/bloodadvances.2020002702)
- Almotiri, A. et al. 2021. Zeb1 modulates hematopoietic stem cell fates required for suppressing acute myeloid leukemia. Journal of Clinical Investigation 131(1), article number: e129115. (10.1172/JCI129115)
- Holzhauser, S. et al. 2020. Sensitivity of human papillomavirus-positive and -negative oropharyngeal cancer cell lines to ionizing irradiation. Oncology Reports (10.3892/or.2020.7709)
- Short, E. et al. 2020. APC transcription studies and molecular diagnosis of familial adenomatous polyposis. European Journal of Human Genetics 28(1), pp. 118-121. (10.1038/s41431-019-0486-2)
- Menendez Gonzalez, J. B. et al. 2019. Gata2 as a crucial regulator of stem cells in adult hematopoiesis and acute myeloid leukemia. Stem Cell Reports 13(2), pp. 291-306. (10.1016/j.stemcr.2019.07.005)
- Pirotte, E. F. et al. 2018. Sensitivity to inhibition of DNA repair by Olaparib in novel oropharyngeal cancer cell lines infected with Human Papillomavirus. PLoS ONE 13(12), pp. -., article number: e0207934. (10.1371/journal.pone.0207934)
- Johnson, C. E. et al. 2018. Loss of tuberous sclerosis complex 2 sensitizes tumors to nelfinavir−bortezomib therapy to intensify endoplasmic reticulum stress-induced cell death. Oncogene 37, pp. 5913-5925. (10.1038/s41388-018-0381-2)
- Caley, M., Wall, I., Peake, M., Kipling, D., Giles, P., Thomas, D. and Stephens, P. 2018. Development and characterisation of a human chronic skin wound cell line - towards an alternative for animal experimentation. International Journal of Molecular Sciences 19(4), article number: 1001. (10.3390/ijms19041001)
- Liao, C. et al. 2016. IL-10 differentially controls the infiltration of inflammatory macrophages and antigen-presenting cells during inflammation. European Journal of Immunology 46(9), pp. 2222-2232. (10.1002/eji.201646528)
- Bayram-Weston, Z. et al. 2015. Similar striatal gene expression profiles in the striatum of the YAC128 and HdhQ150 mouse models of Huntington's disease are not reflected in mutant Huntingtin inclusion prevalence. BMC Genomics 16, pp. -., article number: 1079. (10.1186/s12864-015-2251-4)
- Giles, J. L., Choy, E., van den Berg, C., Morgan, B. P. and Harris, C. L. 2014. Functional analysis of a complement polymorphism (rs17611) associated with Rheumatoid Arthritis. Immunology 143(s2), pp. 181-182. (10.1111/imm.12407)
- Bryant, D. et al. 2014. mRNA sequencing of novel cell lines from human papillomavirus type-16 related vulval intraepithelial neoplasia: Consequences of expression of HPV16 E4 and E5. Journal of Medical Virology 86(9), pp. 1534-1541. (10.1002/jmv.23994)
- Peake, M. A. et al. 2014. Identification of a transcriptional signature for the wound healing continuum. Wound Repair and Regeneration 22(3), pp. 399-405. (10.1111/wrr.12170)
- Rosas, M. et al. 2014. The transcription factor Gata6 links tissue macrophage phenotype and proliferative renewal. Science 344(6184), pp. 645-648. (10.1126/science.1251414)
- Giles, P. J., Elliston, L. A., Higgs, G., Brooks, S. P., Dunnett, S. B. and Jones, L. 2012. Longitudinal analysis of gene expression and behaviour in the HdhQ150 mouse model of Huntington's disease. Brain Research Bulletin 88(2-3), pp. 199-209. (10.1016/j.brainresbull.2011.10.001)
- Bennett, M. R. et al. 2012. Bioinformatic analyses of genome wide nucleotide excision repair datasets in Saccharomyces cerevisiae [Abstract]. Mutagenesis 27(1), pp. 121. (10.1093/mutage/ger068)
- Feyeux, M. et al. 2012. Early transcriptional changes linked to naturally occurring Huntington's disease mutations in neural derivatives of human embryonic stem cells. Human Molecular Genetics 21(17), pp. 3883-3895. (10.1093/hmg/dds216)
- Enoch, S. et al. 2010. 'Young' oral fibroblasts are geno/phenotypically distinct. Journal of Dental Research 89(12), pp. 1407-1413. (10.1177/0022034510377796)
- Welton, J. L. et al. 2010. Proteomics analysis of bladder cancer exosomes. Molecular & Cellular Proteomics 9(6), pp. 1324-1338. (10.1074/mcp.M000063-MCP201)
- Enoch, S. et al. 2009. Increased oral fibroblast lifespan is telomerase-independent. Journal of Dental Research 88(10), pp. 916-921. (10.1177/0022034509342979)
- Zhang, L. et al. 2009. Thyrotropin receptor activation increases hyaluronan production in preadipocyte fibroblasts: Contributory role in hyaluronan accumulation in thyroid dysfunction. Journal of Biological Chemistry 284(39), pp. 26447-26455. (10.1074/jbc.M109.003616)
- Brennan, P. et al. 2009. Quantitative nuclear proteomics reveals new phenotypes altered in lymphoblastoid cells. Proteomics - Clinical Applications 3(3), pp. 359-369. (10.1002/prca.200800137)
- Burton, D. G. A. et al. 2009. Microarray analysis of senescent vascular smooth muscle cells: a link to atherosclerosis and vascular calcification. Experimental Gerontology 44(10), pp. 659-665. (10.1016/j.exger.2009.07.004)
- Kipling, D. G. et al. 2009. A transcriptomic analysis of the EK1.Br strain of human fibroblastoid keratocytes: the effects of growth, quiescence and senescence. Experimental Eye Research 88(2), pp. 277-285. (10.1016/j.exer.2008.11.030)
- Rees, D. A., Giles, P. J., Lewis, M. D. and Ham, J. 2009. Adenosine regulates thrombomodulin and endothelial protein C receptor expression in folliculostellate cells of the pituitary gland. Purinergic Signalling 6(1), pp. 19-29. (10.1007/s11302-009-9172-0)
- Wall, I. B. et al. 2008. Fibroblast dysfunction is a key factor in the non-healing of chronic venous leg ulcers. Journal of Investigative Dermatology 128(10), pp. 2526-2540. (10.1038/jid.2008.114)
- Peake, M. A., Giles, P. J., Wall, I. B., Enoch, S., Kipling, D. G., Thomas, D. W. and Stephens, P. 2008. Identifying a Gene signature for the wound healing continuum [Abstract]. Wound Repair and Regeneration 16(6), pp. A71. (10.1111/j.1524-475X.2008.00424.x)
- Myers, A. et al. 2002. Full genome screen for Alzheimer disease: Stage II analysis. American Journal Of Medical Genetics Part A 114(2), pp. 235-244. (10.1002/ajmg.10183)
- Hamshere, M. L., Giles, P., Krawczak, M. and Owen, M. J. 2001. Statistical analysis of genotypic association data with HAPMAXII. AMERICAN JOURNAL OF HUMAN GENETICS 69(4), pp. 390-390.
Thesis
- Giles, P. J. 2005. Microarray-based expression profiling: improving data mining and the links to biological knowledge pools. PhD Thesis, Cardiff University.
Biography
Career overview
2022-present Professional Advisor for Data Science - Division of Cancer and Genetics, Cardiff University
2019-2022 Lead Bioinformatician and Bioinformatics Manager - Wales Gene Park, Cardiff University
2011-2019 Research Associate in NGS Bioinformatics - Wales Cancer Research Centre, Cardiff University
2005-2011 Research Fellow in Microarray Bioinformatics - Central Biotechnology Services, Cardiff University
2000-2001 Research Assistant in Bioinformatics and Computing - University of Wales College of Medicine
Education and qualifications
2005 - PhD Medicine, Cardiff University - Microarray-based expression profiling: improving data mining and the links to biological knowledge pools [supervisor Prof David Kipling]
2002 - Diploma in Biomedical Methods, University of Wales College of Medicine
1999 - BSc (Hons) Pharmacology, Cardiff University
Contact Details
Specialisms
- Data science
- Bioinformatics and computational biology
- High performance computing
- Trusted research environments (TREs)
- Machine learning