Lewis Quayle

Bioinformatics Core Associate


2023 - Present: Senior Lecturer in Data Science and Analytics, Sheffield Hallam University
2023 - Present: Honorary Senior Lecturer in Bioinformatics, University of Sheffield
2022 - 2023: Cancer Bioinformatician - Bioinformatics Core Facility, University of Sheffield
2019 – 2022: Postdoctoral Bioinformatician - Medical School, University of Sheffield
2017 – 2019: Postdoctoral Research Associate - Medical School, University of Sheffield
2014 – 2017: PhD Medicine - Medical School, University of Sheffield
2013 – 2014: MRes Medical & Biomedical Science - University of Lincoln
2010 – 2013: BSc (Hons) Biomedical Science - University of Lincoln


  • Programming: R, Python, SQL, Unix (BASh), Markdown, Git, Nextflow, Docker, Singularity (Apptainer)
  • Pipeline development and deployment on high-performance computing (HPC) or cloud-based infrastructure
  • Microarray, RNA-Seq (bulk and single-cell), Whole Genome (WGS) and Whole Exome (WES) sequencing data analysis
  • Relational database access and analysis
  • Large-scale public and clinical data cleaning and integration
  • Time-to-event (survival) analysis
  • Interaction network construction, validation and analysis
  • Geospatial data analysis
  • Unsupervised and supervised machine learning model development and deployment
  • Advanced data visualisation
  • Dashboard and web app development


I obtained my PhD in the Bone Oncology group of Prof. Ingunn Holen and Dr Penelope Ottewell in the Department of Oncology & Metabolism at The University of Sheffield Medical School. My PhD project focussed on developing novel models of mitotic quiescence in human breast cancer cells in vitro and metastatic dormancy in vivo. My early postdoctoral work was focussed on characterising the cellular sub-populations isolated from these models using a multitude of approaches, including next-generation sequencing. During 2019, I undertook a three-month training placement in high-performance computing (HPC) and bioinformatic analysis of RNA-Seq data at the Kinghorn Centre for Clinical Genomics at the Garvan Institute of Medical Research in Sydney, Australia working under Dr Nenad Bartonicek. Upon my return to The University of Sheffield, I transitioned to a two-year position as a postdoctoral cancer bioinformatician and in June 2022 moved to the role of cancer bioinformatician embedded within the Sheffield Bioinformatics Core Facility and working in the groups of Prof. James Catto and Dr Dennis Wang. I was appointed as Senior Lecturer in Data Science and Analytics in the Department of Computing, Sheffield Hallam University in May 2023 and awarded a 3 year Honorary Senior Lectureship in the University of Sheffield Medical School at the same time.

My current research activity includes two Genomics England 100,000 project studies aiming to create a mutational map in bladder and low-grade serous ovarian cancers, provision of bioinformatics support to the Genotype of Urothelial Cancer - Stratified Treatment and Oncological outcomes (GUSTO) phase II clinical trial, a project aiming to develop a test for prediction of response to chemotherapy in gestational trophoblastic disease, and a project continuing my early post-doctoral work which aim to identify molecular drivers and biomarkers of metastatic dormancy in breast cancer. I am also involved in several smaller clinical and pure research projects in a range of areas including high-throughput screening, public healthcare data analytics, and predictive modelling of prognostic risk factors in a range of settings.


Original Manuscripts

Catto, J.W.F., Mandrik, O., Quayle, L.A., Hussain, S.A., McGrath, J., Cresswell, J., Birtle, A.J., Jones, R.J., Mariappan, P., Makaroff, L.E., Knight, A., Mostafid, H., Chilcott, J., Sasieni, P., Cumberbatch M. (2023). Diagnosis, treatment and survival from bladder, upper urinary tract and urethral cancers: Real world findings from NHS England between 2013 and 2019. BJU Int, 131(6): 734-744.

Quayle, L.A., Spicer, A., Ottewell, P.D., Holen, I. (2021). Transcriptomic Profiling Reveals Novel Candidate Genes and Signaling Programs in Breast Cancer Quiescence and Dormancy. Cancers, 13(16): 3922.

Tulotta, C., Lefley, D., Moore,. C., Amariutei, A., Spicer, A., Quayle, L., Hughes, R., Ahmed, K., Cookson, V., Evans, C., Vadakekolathu, J., Heath, P., Francis, F., Pinteaux, E., Pockley, A., Ottewell, P.D. (2021). IL-1B drives opposing responses in primary tumours and bone metastases; harnessing combination therapies to improve outcome in breast cancer. NPJ Breast Cancer, 7(1): 95.

Quayle, L.A., Ottewell, P.D., Holen, I. (2018). Chemotherapy Resistance and Stemness in Mitotically Quiescent Human Breast Cancer Cells Identified by Fluorescent Dye Retention. Clin Exp Metastasis, 35(8): 831-846.

Quayle, L.A., Pereira, M.G., Scheper, G., Wiltshire, T., Peake, R.E., Hussain, I., Rea, C.A. & Bates, T.E. (2017). Anti-angiogenic drugs: direct anti-cancer agents with mitochondrial mechanisms of action. Oncotarget, 8 (51): 88670-88688.

Quayle, L., Ottewell, P.D., Holen, I. (2015). Bone Metastasis: Molecular Mechanisms Implicated in Tumour Cell Dormancy in Breast and Prostate Cancer. Curr Cancer Drug Targets. 15: 469-480.

Book Chapters

Holen, I. and Quayle, L.A. (2020). Stem cell niches in bone and their roles in cancer metastasis. Advances in Stem Cells and their Niches. Elsevier. 5: 35-62.

Ottewell, P.D. and Quayle, L.A. (2019) Tumor Dormancy in the Bone. Encyclopaedia of Bone Biology. Elsevier. 166 - 179.

Conference Proceedings

Quayle, L., Ottewell, P.D., Holen, I. (2018), Therapeutic Resistance and Stemness in Mitotically Quiescent Human Breast Cancer Cells. 1st UK Interdisciplinary Breast Cancer Symposium 15th – 16th January 2018; Manchester, U.K. Breast Cancer Res Treat. 167:309–405: Abstract P10.12.

Quayle, L., Park, S., McDonnell, D.P., Ottewell, P.D., Holen, I. (2017) Targeting ERR-α Regulated Lactate Metabolism Eliminates Drug-Resistant Breast Cancer Cells. Proceedings of the 2016 San Antonio Breast Cancer Symposium 6th – 10th December 2016; San Antonio, TX, U.S.A. Cancer Res. 77(4 Suppl): Abstract P3-07-14.