John Connelly

Biography

Dr John Connelly is a Clinical Lecturer and Wellcome Trust Clinical PhD student currently visiting the lab of Dr Sarah Aitken. John's PhD is supervised by Professor Martin Taylor (MRC HGU, Edinburgh), Professor Ian Tomlinson (Cancer Centre, Edinburgh) and Dr Sarah Aitken (MRC Toxicology Unit). Prior to this, John completed BMedSci Hons (Glasgow), MBChB Hons (Glasgow), PGCert Distinction - Molecular Pathology and Genomic Medicine (Edinburgh) and obtained MRCP(UK) by examination. John undertook a range of posts in hospital medicine before commencing specialty training in histopathology in Edinburgh on the Edinburgh Clinical Academic Track.

Research Interests

John's focus is on the application of data science, machine learning and computer vision to computational pathology and precision medicine. His current project aims to relate histological morphology to genomic data in a model of somatic mutagenesis and tumour evolution, using explainable machine learning and deep learning techniques.

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Publications

Key publications:

Anderson CJ, Talmane L, Luft J, Nicholson MD, Connelly J, Pich O, Campbell S, Sundaram V, Connor F, Ginno PA, Liver Cancer Evolution Consortium, López-Bigas N, Flicek P, Semple CA, Odom DT, Aitken SJ and Taylor MS. Strand-resolved mutagenicity of DNA damage and repair. bioRxiv, doi.org/10.1101/2022.06.10.495644. (2022).

Millar FR, Pennycuick A, Muir M, Quintanella A, Hari P, Freyer E, Gautier P, Meynert A, Teixeira VH, Connelly J, Wallace WAH, Sims AH, Frame MC, Boulter L, Janes SM, Wilkinson S and Acosta JC. Toll-like receptor 2 orchestrates a potent anti-tumor response in non-small cell lung cancer. bioRxiv, doi.org/10.1101/2021.06.04.446876. (2021).

Steele CW, Karim SA, Leach JDG, Bailey P, Upstill-Goddard R, Rishi L, Foth M, Bryson S, McDaid K, Wilson Z, Eberlein C, Candido JB, Clarke M, Nixon C, Connelly J, Jamieson N, Carter CR, Balkwill F, Chang DK, Evans TRJ, Strathdee D, Biankin AV, Nibbs RJB, Barry ST, Sansom OJ and Morton JP. CXCR2 inhibition profoundly suppresses metastases and augments immunotherapy in pancreatic ductal adenocarcinoma. Cancer Cell; 29(6):832-845. (2016).