University of Exeter Medical School

TJ (Trevelyan) McKinley

TJ (Trevelyan) McKinley

Senior Lecturer in Bayesian Statistics

 T.McKinley@exeter.ac.uk

 01326 259331

 RILD Building 

 

University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK

Overview

Trevelyan McKinley graduated with a BSc in Mathematics and a PhD in Statistics from the University of Exeter before joining the Department of Veterinary Medicine at the University of Cambridge. He then became a Lecturer in Mathematical Biology in the University of Exeter's Penryn Campus, before joining the Medical School as a Senior Lecturer in Bayesian Statistics.

Qualifications

  • PhD in Statistics, University of Exeter, UK.
  • BSc Mathematics (Hons. First Class), University of Exeter, UK.

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Research

Research interests

His research interests lie in the application and development of statistical methodology for the study of infectious diseases, in particular spatial epidemiology using Bayesian techniques. He has worked on disease dynamics at many levels, from within-host infections through to large-scale spatial spread of infection. He has contributed to methodological advances / applications of a range of statistical inference techniques for calibrating complex, computationally demanding models, such as: Approximate Bayesian Computation, pseudo-marginal Markov chain Monte Carlo, and History Matching with emulation.

Research projects

  • Wellcome Trust funded grant to develop an R package to perform history matching and emulation for large-scale complex models.
  • Innovate UK funded project with Chelonia Ltd. to develop better statistical tools for analysing passive acoustic monitoring data for cetacean conservation

Grants/Funding

  • 2019-2021: Lead Academic on Innovate UK Knowledge Transfer Partnership with Chelonia Ltd., with Dr Saptarshi Das and Professor Tom Tregenza.
  • 2019–2021: Co-investigator on a Wellcome Trust Technology Transfer Grant with the London School of Hygiene and Tropical Medicine (Richard White and Nicky McCreesh) and Durham University (Ian Vernon and Michael Goldstein).
  • 2015–2019: Co-investigator on NERC funded Industrial CASE studentship, with Dave Hodgson (PI) and Dez Delahay (Co-I).
  • 2015–2019: Co-investigator on BBSRC funded Industrial CASE studentship, “Targeting superspreader farms for bovine tuberculosis control”, with Robbie McDonald (PI) and Dez Delahay (Co-I).
  • 2014–2019: Named investigator on BBSRC funded LoLa project, “Understanding influenza A virus: linking transmission, evolutionary dynamics, pathogenesis and immunity in pigs”, with Bryan Charleston (PI) et al., grant number BB/L001330/1.
  • 2013–2015: Named investigator on Defra funded project, “A study to identify factors associated with the detection of new TB breakdowns via abattoir surveillance in GB”, with James Wood (PI), grant number SE3133.
  • 2012–2015: Collaborator on MRC funded project, “Calibration and analysis of complex individual-based stochastic models: methodological development and application to explore the impact of HAART on HIV/AIDS in Africa”, with Richard White (PI) et al., grant number MR/J005088/1.
  • 2011–2014: Research co-investigator on BBSRC/Defra funded project, “A longitudinal model for the spread of bovine tuberculosis”, with James Wood (PI), Gareth Roberts (Co-I) et al., grant number BB/I012192/1.
  • 2010: Co-investigator on TGAC funded project, “Intra- and inter-host evolutionary dynamics of mammalian influenza viruses”, with Pablo Murcia (PI) and James Wood (Co-I).

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Publications

Journal articles

McKinley T (In Press). Dirichlet process mixture models to impute missing predictor data in counterfactual prediction models: an application to predict optimal type 2 diabetes therapy. BMC Medical Informatics and Decision Making
McKinley TJ, Neal P, Spencer SEF, Conlan AJK, Tiley L (In Press). Efficient Bayesian model choice for partially observed processes: with application to an experimental transmission study of an infectious disease. Bayesian Analysis
Andrianakis I, McCreesh N, Vernon I, McKinley TJ, Oakley JE, Nsubuga RN, Goldstein M, White RJ (In Press). Efficient history matching of a high dimensional individual based HIV transmission model. Journal of Uncertainty Quantification
McKinley T (In Press). Emulation and History Matching using the hmer Package. Journal of Statistical Software
Andrianakis I, Vernon I, McCreesh N, McKinley TJ, Oakley J, Nsubuga R, Goldstein M, White R (In Press). History matching of a complex epidemiological model of HIV transmission using variance emulation. Journal of the Royal Statistical Society Series C: Applied Statistics
Omeyer L, McKinley TJ, Bréheret N, Bal G, Petchell Balchin G, Bitsindou A, Chauvet E, Collins T, Curran BK, Formia A, et al (In Press). Missing Data in Sea Turtle Population Monitoring: a Bayesian Statistical Framework Accounting for Incomplete Sampling. Frontiers in Marine Science, 9
Neal P, Alzahrani N, Spencer S, McKinley TJ, Touloupou P (In Press). Model selection for time series of count data. Computational Statistics and Data Analysis
McCreesh N, Andrianakis I, Nsubuga RN, Strong M, Vernon I, McKinley TJ, Oakley J, Goldstein M, Hayes R, White RG, et al (In Press). Universal Test, Treat, and Keep: Improving ART Retention is Key in Cost-effective HIV Control in Uganda. BMC Infectious Diseases
Karageorgiou V, Casanova F, O'Loughlin J, Green H, McKinley TJ, Bowden J, Tyrrell J (2023). Body mass index and inflammation in depression and treatment-resistant depression: a Mendelian randomisation study. BMC Med, 21(1). Abstract.  Author URL.
Scarponi D, Iskauskas A, Clark RA, Vernon I, McKinley TJ, Goldstein M, Mukandavire C, Deol A, Weerasuriya C, Bakker R, et al (2023). Demonstrating multi-country calibration of a tuberculosis model using new history matching and emulation package - hmer. Epidemics, 43 Abstract.  Author URL.
Hudson DW, Hodgson DJ, Cant MA, Thompson FJ, Delahay R, McDonald RA, McKinley TJ (2023). Importance sampling and Bayesian model comparison in ecology and evolution. Methods in Ecology and Evolution, 14(12), 2994-3006. Abstract.
Hudson DW, McKinley TJ, Benton CH, Delahay R, McDonald RA, Hodgson DJ (2023). Multi‐locus homozygosity promotes actuarial senescence in a wild mammal. Journal of Animal Ecology, 92(9), 1881-1892. Abstract.
Cardoso P, Young KG, Nair ATN, Hopkins R, McGovern AP, Haider E, Karunaratne P, Donnelly L, Mateen BA, Sattar N, et al (2023). Phenotype-based targeted treatment of SGLT2 inhibitors and GLP-1 receptor agonists in type 2 diabetes. Abstract.
Swallow B, Birrell P, Blake J, Burgman M, Challenor P, Coffeng LE, Dawid P, De Angelis D, Goldstein M, Hemming V, et al (2022). Challenges in estimation, uncertainty quantification and elicitation for pandemic modelling. Epidemics, 38, 100547-100547.
Grist E, McKinley T, Das S, Tregenza T (2022). Estimating cetacean population trends from static acoustic monitoring data using Paired Year Ratio Assessment (PYRA). PLoS ONE
Grace SL, Bowden J, Walkey HC, Kaur A, Misra S, Shields BM, McKinley TJ, Oliver NS, McDonald TJ, Johnston DG, et al (2022). Islet Autoantibody Level Distribution in Type 1 Diabetes and Their Association with Genetic and Clinical Characteristics. J Clin Endocrinol Metab, 107(12), e4341-e4349. Abstract.  Author URL.
Woods C, Hedges L, Edsall C, Brooks-Pollock E, Parton-Fenton C, McKinley T, Keeling M, Danon L (2022). MetaWards: a flexible metapopulation framework for modelling disease spread. Journal of Open Source Software, 7(70), 3914-3914.
Karageorgiou V, Tyrrell J, McKinley TJ, Bowden J (2022). Weak and pleiotropy robust Sex-stratified Mendelian Randomization in the one sample and two sample settings. HUMAN HEREDITY, VOL.(SUPPL 1), 24-25.  Author URL.
Fielding HR, McKinley TJ, Delahay RJ, Silk MJ, McDonald RA (2021). Characterization of potential superspreader farms for bovine tuberculosis: a review. Vet Med Sci, 7(2), 310-321. Abstract.  Author URL.
Fielding HR, Silk MJ, McKinley TJ, Delahay RJ, Wilson-Aggarwal JK, Gauvin L, Ozella L, Cattuto C, McDonald RA (2021). Spatial and temporal variation in proximity networks of commercial dairy cattle in Great Britain. Preventive Veterinary Medicine, 194, 105443-105443.
Fielding HR, McKinley TJ, Delahay RJ, Silk MJ, McDonald RA (2020). Effects of trading networks on the risk of bovine tuberculosis incidents on cattle farms in Great Britain. Royal Society Open Science, 7(4), 191806-191806. Abstract.
Thompson RN, Hollingsworth TD, Isham V, Arribas-Bel D, Ashby B, Britton T, Challoner P, Chappell LHK, Clapham H, Cunniffe NJ, et al (2020). Key Questions for Modelling COVID-19 Exit Strategies. Proc. Roy. Soc. B, 2020 Abstract.  Author URL.
Bulson L, Becher MA, McKinley TJ, Wilfert L (2020). Long-term effects of antibiotic treatments on honeybee colony fitness: a modelling approach. Journal of Applied Ecology
Hudson DW, Delahay R, McDonald RA, McKinley TJ, Hodgson DJ (2019). Analysis of Lifetime Mortality Trajectories in Wildlife Disease Research: BaSTA and Beyond. DIVERSITY-BASEL, 11(10).  Author URL.
Cunningham AA, Smith F, McKinley TJ, Perkins MW, Fitzpatrick LD, Wright ON, Lawson B (2019). Apparent absence of Batrachochytrium salamandrivorans in wild urodeles in the United Kingdom. Scientific Reports
Fielding HR, McKinley TJ, Silk MJ, Delahay RJ, McDonald RA (2019). Contact chains of cattle farms in Great Britain. Royal Society Open Science, 6
Tennant W, McKinley T, Recker M (2019). Inferring the ecological drivers of arboviral outbreaks. Abstract.
McKinley TJ, Vernon I, Andrianakis I, McCreesh N, Oakley JE, Nsubuga RN, Goldstein M, White RG (2018). Approximate Bayesian Computation and simulation-based inference for complex stochastic epidemic models. Statistical Science, 33, 4-18.
McCreesh N, Andrianakis I, Nsubuga RN, Strong M, Vernon I, McKinley TJ, Oakley JE, Goldstein M, Hayes R, White RG, et al (2018). Choice of time horizon critical in estimating costs and effects of changes to HIV programmes. PLoS One, 13(5). Abstract.  Author URL.
Touloupou P, Alzahrani N, Neal P, Spencer SEF, McKinley TJ (2018). Efficient Model Comparison Techniques for Models Requiring Large Scale Data Augmentation. Bayesian Analysis, 13(2).
McKinley TJ, Lipschutz-Powell D, Mitchell AP, Wood JLN, Conlan AJK (2018). Risk factors and variations in detection of new bovine tuberculosis breakdowns via slaughterhouse surveillance in Great Britain. PLoS ONE, 13, e0198760-e0198760.
McCreesh N, Andrianakis I, Nsubuga RN, Strong M, Vernon I, McKinley TJ, Oakley JE, Goldstein M, Hayes R, White RG, et al (2017). Improving ART programme retention and viral suppression are key to maximising impact of treatment as prevention - a modelling study. BMC Infect Dis, 17(1). Abstract.  Author URL.
Esson D, Mather AE, Scanlan E, Gupta S, de Vries SPW, Bailey D, Harris SR, McKinley TJ, Méric G, Berry SK, et al (2016). Genomic variations leading to alterations in cell morphology of Campylobacter spp. Sci Rep, 6 Abstract.  Author URL.
McKinley TJ, Morters M, Wood JLN (2015). Bayesian Model Choice in Cumulative Link Ordinal Regression Models. BAYESIAN ANALYSIS, 10(1), 1-30.  Author URL.
Andrianakis I, Vernon IR, McCreesh N, McKinley TJ, Oakley JE, Nsubuga RN, Goldstein M, White RG (2015). Bayesian history matching of complex infectious disease models using emulation: a tutorial and a case study on HIV in Uganda. PLoS Comput Biol, 11(1). Abstract.  Author URL.
Conlan AJK, Brooks Pollock E, McKinley TJ, Mitchell AP, Jones GJ, Vordermeier M, Wood JLN (2015). Potential benefits of cattle vaccination as a supplementary control for bovine tuberculosis. PLoS Comput Biol, 11(2). Abstract.  Author URL.
Morters MK, McKinley TJ, Horton DL, Cleaveland S, Schoeman JP, Restif O, Whay HR, Goddard A, Fooks AR, Damriyasa IM, et al (2014). Achieving population-level immunity to rabies in free-roaming dogs in Africa and Asia. PLoS Negl Trop Dis, 8(11). Abstract.  Author URL.
McKinley TJ, Ross JV, Deardon R, Cook AR (2014). Simulation-based Bayesian inference for epidemic models. Computational Statistics and Data Analysis, 71, 434-447. Abstract.
Morters MK, Mckinley TJ, Restif O, Conlan AJK, Cleaveland S, Hampson K, Whay HR, Damriyasa IM, Wood JLN (2014). The demography of free-roaming dog populations and applications to disease and population control. Journal of Applied Ecology, 51(4), 1096-1106. Abstract.
Brooks-Pollock E, Conlan AJK, Mitchell AP, Blackwell R, McKinley TJ, Wood JLN (2013). Age-dependent patterns of bovine tuberculosis in cattle. Vet Res, 44(1). Abstract.  Author URL.
Varela M, Verschoor E, Lai RPJ, Hughes J, Mooj P, McKinley TJ, Fitzmaurice TJ, Landskron L, Willett BJ, Frost SDW, et al (2013). Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques. PLoS One, 8(8). Abstract.  Author URL.
Dybowski R, McKinley TJ, Mastroeni P, Restif O (2013). Nested sampling for Bayesian model comparison in the context of Salmonella disease dynamics. PLoS One, 8(12). Abstract.  Author URL.
Restif O, Goh YS, Palayret M, Grant AJ, McKinley TJ, Clark MR, Mastroeni P (2013). Quantification of the effects of antibodies on the extra- and intracellular dynamics of Salmonella enterica. J R Soc Interface, 10(79). Abstract.  Author URL.
Peel AJ, McKinley TJ, Baker KS, Barr JA, Crameri G, Hayman DTS, Feng Y-R, Broder CC, Wang L-F, Cunningham AA, et al (2013). Use of cross-reactive serological assays for detecting novel pathogens in wildlife: assessing an appropriate cutoff for henipavirus assays in African bats. J Virol Methods, 193(2), 295-303. Abstract.  Author URL.
Grant AJ, Morgan FJE, McKinley TJ, Foster GL, Maskell DJ, Mastroeni P (2012). Attenuated Salmonella Typhimurium lacking the pathogenicity island-2 type 3 secretion system grow to high bacterial numbers inside phagocytes in mice. PLoS Pathog, 8(12). Abstract.  Author URL.
Gog JR, Murcia A, Osterman N, Restif O, McKinley TJ, Sheppard M, Achouri S, Wei B, Mastroeni P, Wood JLN, et al (2012). Dynamics of Salmonella infection of macrophages at the single cell level. J R Soc Interface, 9(75), 2696-2707. Abstract.  Author URL.
Conlan AJK, McKinley TJ, Karolemeas K, Pollock EB, Goodchild AV, Mitchell AP, Birch CPD, Clifton-Hadley RS, Wood JLN (2012). Estimating the hidden burden of bovine tuberculosis in Great Britain. PLoS Comput Biol, 8(10). Abstract.  Author URL.
Karolemeas K, de la Rua-Domenech R, Cooper R, Goodchild AV, Clifton-Hadley RS, Conlan AJK, Mitchell AP, Hewinson RG, Donnelly CA, Wood JLN, et al (2012). Estimation of the relative sensitivity of the comparative tuberculin skin test in tuberculous cattle herds subjected to depopulation. PLoS One, 7(8). Abstract.  Author URL.
Jäger HC, McKinley TJ, Wood JLN, Pearce GP, Williamson S, Strugnell B, Done S, Habernoll H, Palzer A, Tucker AW, et al (2012). Factors associated with pleurisy in pigs: a case-control analysis of slaughter pig data for England and Wales. PLoS One, 7(2). Abstract.  Author URL.
Conlan AJK, McKinley TJ, Wood JLN (2012). Letters. Veterinary Record, 171(21).
Conlan AJK, McKinley TJ, Wood JLN (2012). Modelling the burden of bovine TB infection Comment. VETERINARY RECORD, 171(21), 540-540.  Author URL.
Karolemeas K, Donnelly CA, Conlan AJK, Mitchell AP, Clifton-Hadley RS, Upton P, Wood JLN, McKinley TJ (2012). The effect of badger culling on breakdown prolongation and recurrence of bovine tuberculosis in cattle herds in Great Britain. PLoS One, 7(12). Abstract.  Author URL.
McKinley TJ, Murcia PR, Gog JR, Varela M, Wood JLN (2011). A Bayesian approach to analyse genetic variation within RNA viral populations. PLoS Comput Biol, 7(3). Abstract.  Author URL.
Mastroeni P, Morgan FJE, McKinley TJ, Shawcroft E, Clare S, Maskell DJ, Grant AJ (2011). Enhanced virulence of Salmonella enterica serovar typhimurium after passage through mice. Infect Immun, 79(2), 636-643. Abstract.  Author URL.
Goh YS, Grant AJ, Restif O, McKinley TJ, Armour KL, Clark MR, Mastroeni P (2011). Human IgG isotypes and activating Fcγ receptors in the interaction of Salmonella enterica serovar Typhimurium with phagocytic cells. Immunology, 133(1), 74-83. Abstract.  Author URL.
Janis C, Grant AJ, McKinley TJ, Morgan FJE, John VF, Houghton J, Kingsley RA, Dougan G, Mastroeni P (2011). In vivo regulation of the Vi antigen in Salmonella and induction of immune responses with an in vivo-inducible promoter. Infect Immun, 79(6), 2481-2488. Abstract.  Author URL.
Varela M, Landskron L, Lai RPJ, McKinley TJ, Bogers WM, Verschoor EJ, Dubbes R, Barnett SW, Frost SDW, Heeney JL, et al (2011). Molecular evolution analysis of the human immunodeficiency virus type 1 envelope in simian/human immunodeficiency virus-infected macaques: implications for challenge dose selection. J Virol, 85(19), 10332-10345. Abstract.  Author URL.
Karolemeas K, McKinley TJ, Clifton-Hadley RS, Goodchild AV, Mitchell A, Johnston WT, Conlan AJK, Donnelly CA, Wood JLN (2011). Recurrence of bovine tuberculosis breakdowns in Great Britain: risk factors and prediction. Prev Vet Med, 102(1), 22-29. Abstract.  Author URL.
Lyall J, Irvine RM, Sherman A, McKinley TJ, Núñez A, Purdie A, Outtrim L, Brown IH, Rolleston-Smith G, Sang H, et al (2011). Suppression of avian influenza transmission in genetically modified chickens. Science, 331(6014), 223-226. Abstract.  Author URL.
Sanchez-Bustinduy M, de Medeiros MA, Radke H, Langley-Hobbs S, McKinley T, Jeffery N (2010). Comparison of kinematic variables in defining lameness caused by naturally occurring rupture of the cranial cruciate ligament in dogs. Vet Surg, 39(4), 523-530. Abstract.  Author URL.
Greenhalgh SN, Dunning MD, McKinley TJ, Goodfellow MR, Kelman KR, Freitag T, O'Neill EJ, Hall EJ, Watson PJ, Jeffery ND, et al (2010). Comparison of survival after surgical or medical treatment in dogs with a congenital portosystemic shunt. Journal of the American Veterinary Medical Association, 236(11), 1215-1220. Abstract.
Murcia PR, Baillie GJ, Daly J, Elton D, Jervis C, Mumford JA, Newton R, Parrish CR, Hoelzer K, Dougan G, et al (2010). Intra- and interhost evolutionary dynamics of equine influenza virus. J Virol, 84(14), 6943-6954. Abstract.  Author URL.
Karolemeas K, McKinley TJ, Clifton-Hadley RS, Goodchild AV, Mitchell A, Johnston WT, Conlan AJK, Donnelly CA, Wood JLN (2010). Predicting prolonged bovine tuberculosis breakdowns in Great Britain as an aid to control. Prev Vet Med, 97(3-4), 183-190. Abstract.  Author URL.
McKinley TJ, Chase-Topping M (2010). Quantitative epidemiology in the 21st century. VETERINARY RECORD, 166(8), 224-225.  Author URL.
Grant AJ, Foster GL, McKinley TJ, Brown SP, Clare S, Maskell DJ, Mastroeni P (2009). Bacterial growth rate and host factors as determinants of intracellular bacterial distributions in systemic Salmonella enterica infections. Infect Immun, 77(12), 5608-5611. Abstract.  Author URL.
McKinley TJ, Cook AR, Deardon R (2009). Inference in epidemic models without likelihoods. The INternational Journal of Biostatistics, 5(1).
Dobson J, Hoather T, McKinley TJ, Wood JLN (2009). Mortality in a cohort of flat-coated retrievers in the UK. Vet Comp Oncol, 7(2), 115-121. Abstract.  Author URL.
Walsh C, Gangloff M, Monie T, Smyth T, Wei B, McKinley TJ, Maskell D, Gay N, Bryant C (2008). Elucidation of the MD-2/TLR4 interface required for signaling by lipid IVa. J Immunol, 181(2), 1245-1254. Abstract.  Author URL.
Grant AJ, Restif O, McKinley TJ, Sheppard M, Maskell DJ, Mastroeni P (2008). Modelling within-host spatiotemporal dynamics of invasive bacterial disease. PLoS Biology, 6(4), 757-770. Abstract.
Grant AJ, Restif O, McKinley TJ, Sheppard M, Maskell DJ, Mastroeni P (2008). Modelling within-host spatiotemporal dynamics of invasive bacterial disease. PLoS Biol, 6(4). Abstract.  Author URL.
Foster GL, Barr TA, Grant AJ, McKinley TJ, Bryant CE, MacDonald A, Gray D, Yamamoto M, Akira S, Maskell DJ, et al (2008). Virulent Salmonella enterica infections can be exacerbated by concomitant infection of the host with a live attenuated S. enterica vaccine via Toll-like receptor 4-dependent interleukin-10 production with the involvement of both TRIF and MyD88. Immunology, 124(4), 469-479. Abstract.  Author URL.
McKinley TJ, Wood J (2007). Infection dynamics: from organ to host population. J R Soc Interface, 4(14), 583-586. Abstract.  Author URL.

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Teaching

2019/20

  • 2020 ECMM904 Ecological Dynamics(with M. Recker and S. Townley)
  • 2017-2020 ECM2907 Statistical Modelling
  • 2019 Mathematical Biology (with B. Kuijper and M. Recker)
  • 2016-2019 ECM1909 Probability and Statistics
  • 2016 ECM1904 Scientific Computing II (with M. Recker and M. Mueller)
  • 2015-2016 BIOM4025 Statistical Modelling

Modules

2023/24


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