Staff Profile

Lecturer in Biological Systems Modelling

Google Scholar page: http://scholar.google.co.uk/citations?user=2Kcd0zoAAAAJ&hl=en

Research Interests

I am interested in ecological modelling in general, specifically simulation modelling of spatial systems and epidemiology

Current Work

I am currently researching the transmission of diseases in a small-world context. This type of model concentrates primarily on the heterogeneous nature of routes of transmission between individuals in a population, including in models real-world social features such as clustering (where some individuals are more tightly linked with each other than on average), long-distance linkage (where some clusters are connected to others by a low incidence of widely connected individuals) and highly-connected individuals (where members of the network are members of multiple clusters).

My current work also includes modelling aspects of wildlife biology such as competition between red and arctic foxes in Fenno-Scandia and the epidemiology of TB in badger populations in the UK.

Research Group: Centre for Life Sciences Modelling

Degree Programme Director for Zoology (BSc and MBiol)

Diversity of Life (Stage 1)

UK Wildlife (Stage 1)

Vertebrate Biology (Stage2)

Current Zoology (Stage 3)

Invasive Species (Stage 4)

• Articles

  • Rowland BW, Rushton SP, Shirley MDF, Brown MA, Budge GE. Identifying the climatic drivers of honey bee disease in England and Wales. Scientific Reports 2021, 11(1), 21953.
  • Rice S, Albani V, Minos D, Fattakhova G, Mells GF, Carbone M, Flack S, Varvaropoulou N, Badrock J, Spicer A, Sandford RN, Shirley MDF, Coughlan D, Hirschfield G, Taylor-Robinson SD, Vale L, Jones DEJ. Effects of Primary Biliary Cholangitis on Quality of Life and Health Care Costs in the United Kingdom. Clinical Gastroenterology and Hepatology 2021, 19(4), 768-776.e10.
  • Shirley M, Howlett S, Port G. Not All Slugs Are the Same: Variation in Growth and Development of the Slug Deroceras reticulatum. Insects 2020, 11.
  • Budge GE, Simcock NK, Holder PJ, Shirley MDF, Brown MA, Van Weymers PSM, Evans DJ, Rushton SP. Chronic bee paralysis as a serious emerging threat to honey bees. Nature Communications 2020, 11, 2164.
  • Robertson PA, Mill A, Novoa A, Jeschke JM, Essl F, Gallardo B, Geist J, Jaric I, Lambin X, Musseau C, Pergle J, Pysek P, Rabitsch W, von Schmalensee M, Shirley M, Strayer DL, Stefansson RA, Smith K, Booy O. A proposed unified framework to describe the management of biological invasions. Biological Invasions 2020, 22, 2633-2645.
  • Rushton SP, Sanderson RA, Reid WDK, Shirley MDF, Harris JP, Hunter PR, O'Brien SJ. Transmission routes of rare seasonal diseases: the case of norovirus infections. Philosophical Transactions of the Royal Society B: Biological Sciences 2019, 374(1776), 20180267.
  • Holleyman RJ, Deehan DJ, Walker L, Charlett A, Samuel J, Shirley MDF, Baker PN. Staphylococcal resistance profiles in deep infection following primary hip and knee arthroplasty: a study using the NJR dataset. Archives of Orthopaedic and Trauma Surgery 2019, 139, 1209–1215.
  • Rushton SP, Sanderson RA, Diggle PJ, Shirley MDF, Blain AP, Lake I, Maas JA, Reid WDK, Hardstaff J, Williams N, Jones NR, Rigby D, Stachan NJC, Forbes KJ, Hunter PR, Humphrey TJ, O'Brien SJ. Climate, human behaviour or environment: individual-based modelling of Campylobacter seasonality and strategies to reduce disease burden. Journal of Translational Medicine 2019, 17, 34.
  • Mair L, Mill AC, Robertson PA, Rushton SP, Shirley MDF, Rodriguez JP, McGowan PJK. The contribution of scientific research to conservation planning. Biological Conservation 2018, 223, 82-96.
  • Ewan VC, Reid WDK, Shirley M, Simpson AJ, Rushton SP, Wade W. Oropharyngeal microbiota in frail older patients unaffected by time in hospital. Frontiers in Cellular and Infection Microbiology 2018, 8, 42.
  • Embleton ND, Berrington JE, Dorling J, Ewer AK, Juszczak E, Kirby JA, Lamb CA, Lanyon CV, McGuire W, Probert CS, Rushton SP, Shirley MD, Stewart CJ, Cummings SP. Mechanisms Affecting the Gut of Preterm Infants in Enteral Feeding Trials. Frontiers in Microbiology 2017, 4, 14.
  • Brock TM, Shirley M, Bardgett M, Walker M, Deehan DJ. Inadequate pre-operative glycaemic control in patients with diabetes mellitus adversely influences functional recovery after total knee arthroplasty: Patients with impaired glycaemic control exhibit poorer functional outcomes at 1-year post-arthroplasty. Knee Surgery, Sports Traumatology, Arthroscopy 2017, 25(6), 1801-1806.
  • Thomas M, Khan SK, Phipps N, Shirley MDF, Aldridge S, Fearon PV, Deehan DJ. GP contact with patients after treatment for hip fracture: frequency and determinants. Postgraduate Medical Journal 2016, 92(1092), 587-591.
  • Mackie A, Muthumayandi K, Shirley M, Deehan D, Gerrand C. Association Between Body Mass Index Change and Outcome in the First Year After Total Knee Arthroplasty. Journal of Arthroplasty 2015, 30(2), 206-209.
  • Blain AP, Thomas MF, Shirley MDF, Simmister C, Elemraid MA, Gorton R, Pearce MS, Clark JE, Rushton SP, Spencer DA. Spatial variation in the risk of hospitalization with childhood pneumonia and empyema in the North of England. Epidemiology and Infection 2014, 142(2), 388-398.
  • Budge GE, Shirley MDF, Jones B, Quill E, Tomkies V, Feil EJ, Brown MA, Haynes EG. Molecular epidemiology and population structure of the honey bee brood pathogen Melissococcus plutonius. ISME Journal 2014, 8(8), 1588-1597.
  • Shah T, Cloke DJ, Rushton S, Shirley MDF, Deehan DJ. Lower back symptoms in adolescent soccer players predictors of functional recovery. Orthopaedic Journal of Sports Medicine 2014, 2(4).
  • Mill AC, Rushton SP, Shirley MDF, Smith GC, Mason P, Brown MA, Budge GE. Clustering, persistence and control of a pollinator brood disease: epidemiology of American foulbrood. Environmental Microbiology 2014, 16(12), 3753-3763.
  • Khan SK, Shirley MDF, Glennie C, Fearon PV, Deehan DJ. Achieving best practice tariff may not reflect improved survival after hip fracture treatment. Clinical Interventions in Aging 2014, 9, 2097-2102.
  • Elemraid MA, Rushton SP, Shirley MDF, Thomas MF, Spencer DA, Eastham KM, Hampton F, Gorton R, Pollard K, Gennery AR, Clark JE, North East of England Paediatric Respiratory Infection Study Group. Impact of the 7-valent pneumococcal conjugate vaccine on the incidence of childhood pneumonia. Epidemiology and Infection 2013, 141(8), 1697-1704.
  • Close A, Robertson C, Rushton S, Shirley M, Vale L, Ramsay C, Pickard R. Comparative Cost-effectiveness of Robot-assisted and Standard Laparoscopic Prostatectomy as Alternatives to Open Radical Prostatectomy for Treatment of Men with Localised Prostate Cancer: A Health Technology Assessment from the Perspective of the UK National Health Service. European Urology 2013, 64(3), 361-369.
  • Cloke D, Moore O, Shab T, Rushton S, Shirley MDF, Deehan DJ. Thigh Muscle Injuries in Youth Soccer Predictors of Recovery. American Journal of Sports Medicine 2012, 40(2), 433-439.
  • Mill AC, Rushton SP, Shirley MDF, Murray AWA, Smith GC, Delahay RJ, McDonald RA. Farm-scale risk factors for bovine tuberculosis incidence in cattle herds during the Randomised Badger Culling Trial. Epidemiology and Infection 2012, 140(2), 219-230.
  • Carter SP, Chambers MA, Rushton SP, Shirley MDF, Schuchert P, Pietravalle S, Murray A, Rogers F, Gettinby G, Smith GC, Delahay RJ, Hewinson RG, McDonald RA. BCG Vaccination Reduces Risk of Tuberculosis Infection in Vaccinated Badgers and Unvaccinated Badger Cubs. PLoS One 2012, 7(12), e49833.
  • Chambers MA, Rogers F, Delahay RJ, Lesellier S, Ashford R, Dalley D, Gowtage S, Davé D, Palmer S, Brewer J, Crawshaw T, Clifton-Hadley R, Carter S, Cheeseman C, Hanks C, Murray A, Palphramand K, Pietravalle S, Smith GC, Tomlinson A, Walker NJ, Wilson GJ, Corner LAL, Rushton SP, Shirley MDF, Gettinby G, McDonald RA, Hewinson RG. Bacillus Calmette-Guérin vaccination reduces the severity and progression of tuberculosis in badgers. Proceedings of the Royal Society B: Biological Sciences 2011, 278(1713), 1913-1920.
  • Rushton SP, Shirley MDF, Sheridan EA, Lanyon CV, O'Donnell AG. The transmission of nosocomial pathogens in an intensive care unit: a space-time clustering and structural equation modelling approach. Epidemiology and Infection 2010, 138(6), 915-926.
  • Hodgson S, Shirley M, Bythell M, Rankin J. Residential mobility during pregnancy in the north of England. BMC Pregnancy and Childbirth 2009, 9(1), 52.
  • Shirley MDF, Elmhagen B, Lurz PWW, Rushton SP, Angerbjorn A. Modelling the spatial population dynamics of arctic foxes: the effects of red foxes and microtine cycles. Canadian Journal of Zoology 2009, 87(12), 1170-1183.
  • Dadvand P, Rankin J, Shirley MDF, Rushton SP, Pless-Mulloli T. Descriptive epidemiology of congenital heart disease in Northern England. Paediatric and Perinatal Epidemiology 2009, 23(1), 58-65.
  • Wilkinson D, Bennett R, McFarlane I, Rushton S, Shirley M, Smith G. Cost-benefit analysis model of badger (Meles meles) culling to reduce herd tuberculosis breakdowns in Britain, with particular reference to badger perturbation. Journal of Wildlife Diseases 2009, 45(4), 1062–1088.
  • Rushton SP, Humphrey TJ, Shirley MDF, Bull S, Jorgensen F. Campylobacter in housed broiler chickens: a longitudinal study of risk factors. Epidemiology and Infection 2009, 137(8), 1099-1110.
  • McNally RJQ, Rankin J, Shirley MDF, Rushton SP, Pless-Mulloli T. Space-time analysis of Down syndrome: Results consistent with transient pre-disposing contagious agent. International Journal of Epidemiology 2008, 37(5), 1169-1179.
  • Lurz PWW, Shirley MDF, Geddes N. Monitoring low density populations: A perspective on what level of population decline we can truly detect. Animal Biodiversity and Conservation 2008, 31(1), 29-39.
  • Pless-Mulloli T, Glinianaia SV, Rankin J, Pearce MS, Rushton S, Ghosh R, Lurz P, Sanderson R, Shirley M, Diggle P, Fanshawe T, Charlton M, Parker L. Maternal exposure to air pollution and perinatal outcomes: methodological approaches to exposure assessment and preliminary findings of the UK particulate matter and perinatal events research (PAMPER) study. European Epimarker 2008, 12(2), 1-12.
  • Gurnell J, Rushton SP, Lurz PWW, Sainsbury A, Nettleton P, Shirley MDF, Bruemmer CM, Geddes N. Squirrel poxvirus: Landscape scale strategies for managing disease threat. Biological Conservation 2006, 131(2), 287-295.
  • Rushton SP, Shirley MDF, Macdonald DW, Reynolds JC. Effects of culling fox populations at the landscape scale: A spatially explicit population modeling approach. Journal of Wildlife Management 2006, 70(4), 1102-1110.
  • Rushton SP, Lurz PWW, Gurnell J, Nettleton P, Bruemmer CM, Shirley MDF, Sainsbury A. Disease threats posed by alien species: The role of a poxvirus in the decline of the native red squirrel in Britain. Epidemiology and Infection 2006, 134(3), 521-533.
  • Shirley MDF, Rushton SP. Where diseases and networks collide: Lessons to be learnt from a study of the 2001 foot-and-mouth disease epidemic. Epidemiology and Infection 2005, 133(6), 1023-1032.
  • Shirley MDF, Rushton SP. Where diseases and networks collide, Lessons form the Foot and Mouth Disease in UK 2001. Epidemiology and Infection 2005, 133(6), 1023-1032.
  • Shirley MDF, Rushton SP. The impacts of network topology on disease spread. Ecological Complexity 2005, 2(3), 287-299. In Press.
  • Shirley MDF, Rushton SP. The impacts of network topology on disease spread. Ecological Complexity 2005, 2(3), 287-299.
  • Lurz PWW, Hewitt SM, Shirley MDF, Bruce J. Mammals in Cumbria: examples of what publicly collected records can tell us about the distribution and ecology of our local species. Carlisle Naturalist 2005, 13, 1-15.
  • Gurnell J, Lurz PWW, Shirley MDF, Cartmel S, Garson PJ, Magris L, Steele JW. Monitoring red squirrels Sciurus vulgaris and grey squirrels Sciurus carolinensis in Britain. Mammal Review 2004, 34(1-2), 51-74.
  • Lurz PWW, Geddes N, Lloyd AJ, Shirley MDF, Rushton SP, Burlton B. Planning a red squirrel conservation area: Using a spatially explicit population dynamics model to predict the impact of felling and forest design plans. Forestry 2003, 76(1), 95-108.
  • Shirley MDF, Rushton SP, Smith G, South AB, Lurz PWW. Investigating the spatial dynamics of bovine tuberculosis in badger populations: Evaluating an individual-based simulation model. Ecological Modelling 2003, 167(1-2), 139-157.
  • Lurz PWW, Shirley MDF, Rushton SP, Sanderson RA. Modelling the consequences of duck migration patterns on the genetic diversity of aquatic organisms: A first step towards a predictive tool for wetland management. Acta Oecologica 2002, 23(3), 205-212.
  • Barr JJF, Lurz PWW, Shirley MDF, Rushton SP. Evaluation of immunocontraception as a publicly acceptable form of vertebrate pest species control: The introduced grey squirrel in Britain as an example. Environmental Management 2002, 30(3), 342-351.
  • Gurnell J, Clark M, Lurz PWW, Shirley MDF, Rushton SP. Conserving red squirrels (Sciurus vulgaris): Mapping and forecasting habitat suitability using a Geographic Information Systems Approach. Biological Conservation 2002, 105(1), 53-64.
  • Mair J, Shirley MDF, Rushton SP, Port GR. Spatial dynamics of predation by carabid beetles on slugs. Journal of Animal Ecology 2001, 70(5), 875-876.
  • Shirley MDF, Rushton SP, Young AG, Port GR. Simulating the long-term dynamics of slug populations: A process-based modelling approach for pest control. Journal of Applied Ecology 2001, 38(2), 401-411.
  • Lurz PWW, Rushton SP, Wauters L, Bertolino S, Currado I, Mazzoglio P, Shirley MDF. Predicting grey squirrel expansion in North Italy: A spatially explicit modelling approach. Landscape Ecology 2001, 16(5), 407-420.
  • Shirley MDF, Sibly RM. Metapopulation dynamics of fruit flies undergoing evolutionary change in patchy environments. Ecology 2001, 82(11), 3257-3262.
  • Hale ML, Lurz PWW, Shirley MDF, Rushton S, Fuller RM, Wolff K. Impact of Landscape Management on the Genetic Structure of Red Squirrel Populations. Science 2001, 293(5538), 2246-2248.
  • Shirley MDF, Armitage VL, Barden TL, Gough MC, Lurz PWW, Oatway DE, South AB, Rushton SP. Assessing the impact of a music festival on the emergence behaviour of a breeding colony of Daubenton's bats (Myotis daubentonii). Journal of Zoology 2001, 254(3), 367-373.
  • Shirley MDF, Sibly RM. Genetic basis of a between-environment trade-off involving resistance to cadmium in Drosophila melanogaster. Evolution 1999, 53(3), 826-836.
  • D.A. Bohan,P. Brain,D.M. Glen,C.W. Wiltshire,L. Hughes,M. Shirley,G. Port. Decision making in slug pest control: Slug population dynamics in space and time. Aspects of Applied Biology 1997, 50, 323-332.
  • M.D.F. Shirley,S.P. Rushton,G.R. Port,A.G. Young. Decision making in slug pest control: Simulation models of slug populations. Aspects of Applied Biology 1997, 50, 333-340.

• Conference Proceedings (inc. Abstracts)

  • Robertson PA, Roy S, Mill AC, Shirley M, Adriaens T, Ward AI, Tatayah V, Booy O. Invasive species removals and scale–contrasting island and mainland experience. In: Island Invasives 2017 Conference. 2019, Dundee, Scotland: IUCN Species Survival Commission (SSC).
  • Robertson PA, Roy S, Mill AC, Shirley M, Adriaens T, Ward AI, Tatayah V, Booy O. Invasive species removals and scale – contrasting island and mainland experience. In: Island Invasives: Scaling up to Meet the Challenge. 2017, Dundee, UK: IUCN.
  • Mill AC, Rushton SP, Shirley MDF, Smith GC, Mason P, Brown MA, Budge GE, Sandhutton UK. Spatial point process models to determine clustering of American Foulbrook in UK Honeybees. In: International Statistical Ecology Conference. 2014, Montpellier, France: ISEC.
  • Mercer CH, Macdonald N, Shirley MDF, Aicken CRH, Estcourt CS, Keane F, Brook MG, White PJ, Cassell JA. The Maximising STI Control (MSTIC) webtool: a new approach to facilitate the planning of services for sexually transmitted infections to maximise public health benefit. In: Lancet. 2013, The Lancet Publishing Group.
  • Elemraid MA, Eastham KM, Rushton SP, Shirley MDF, Spencer DA, Thomas MF, Hampton F, Gorton R, Pollard K, Gennery AR, Clark JE. Impact of heptavalent pneumococcal conjugate vaccine on the incidence of childhood pneumonia seen in hospital in the North East of England. In: Thorax: Winter Meeting of the British Thoracic Society. 2011, Westminster: BMJ Group.
  • Thomas MF, Blain AP, Shirley MDF, Simmister C, Elemraid MA, Gorton R, Pearce MS, Clark JE, Rushton SP, Spencer DA. Geographical variation in the risk of childhood pneumonia and relationships to socio-economic and health deprivation. In: European Respiratory Society Annual Congress. 2011, Amsterdam, The Netherlands.
  • Hodgson S, Karunapema P, Dadvand P, Shirley M, Bythell M, Rankin J. Residential Mobility During Pregnancy in the North of England. In: 21st Annual Conference of the International Society for Environmental Epidemiology. 2009, Dublin, Ireland: Epidemiology: Lippincott Williams & Wilkins.
  • Hodgson S, Shirley M, Rankin J. Residential Mobility During Pregnancy in the North of England. In: Epidemiology. 2008, Lippincott Williams & Wilkins.
  • Rushton SP, Cliff D, Shirley MDF, Pearce M, Gorton R, Clark J, Spencer DA. Modelling of increasing paediatric empyema and pneumonia admissions in England 1996-2006 using hospital episode statistics. In: Thorax: Winter Meeting of the British Thoracic Society. 2008, London, UK: BMJ Group.
  • Mcnally R, Rankin J, Shirley M, Rushton S, Pless-Mulloli T. Space-time clustering analyses of trisomies 13, 18, and 21. In: 19th Annual Conference of the International Society for Environmental Epidemiology. 2007, Mexico City: Epidemiology, Lippincott Williams & Wilkins.
  • Glinianaia SV, Pless-Mulloli T, Rankin J, Pearce MS, Charlton M, Parker L. Family, mother and child characteristics in singleton births in an industrial city over 32 years: The UK PAMPER study. In: Vulnerability of the Fetus and Infant to ambient pollutants and reduced food intake in pregnancy. 2007, Krakow, Poland.
  • Lurz PWW, Pless-Mulloli T, Rushton SP, Shirley MDF, Glinianaia SV, Rankin J, Pearce MS, Parker L. Air pollution exposure during pregnancy and infancy in an industrial city over 32 years: the UK PAMPER study. In: Vulnerability of the Fetus and Infant to ambient pollutants and reduced food intake in pregnancy. 2007, Krakow, Poland: Uniwersytetu Jagiellońskiego.
  • McNally RJQ, Rankin JM, Shirley MDF, Rushton SP, Pless-Mulloli T. [Abstract] Space-time clustering analyses of trisomies 13, 18 and 21. In: 19th Annual Conference of the International Society for Environmental Epidemiology. 2007, Mexico City, Mexico: Salud Publica de Mexico: Instituto Nacional de Salud Publica.
  • Lurz P, Rushton S, Pless-Mulloli T, Edwards R, Shirley M. Spatiotemporal modelling of exposure to airborne pollutants. In: Epidemiology: ISEE/ISEA 2006 Conference. 2006, Paris, France: Lippincott Williams & Wilkins.
  • Port GR, Shirley MDF, Collier RH, Bohan DA, Symondson WOC, Glen DM. An IPM strategy for slugs in vegetable and salad crops. In: The BCPC international congress : crop science & technology 2003. 2003, British Crop Protection Council.
  • Shirley MDF, Port GR, Young AG. Weather in relation to long and short term modelling of slug damage. In: Crop Protection in Northern Britain. 1999, Dundee.
  • M.D.F. Shirley,S.P. Rushton,G.R. Port,A.G. Young. Spatial modelling of slug populations in arable crops. In: British Crop Protection Council Brighton Conference - Pests & Diseases. 1998, Brighton.

• Reports

  • Ramsay CR, Adewuyi TE, Gray J, Hislop J, Shirley MDF, Jayakody S, MacLennan G, Fraser C, MacLennan S, Brazzelli M, N'Dow J, Pickard R, Robertson C, Rothnie K, Rushton SP, Vale L, Lam TB. Ablative therapy for people with localised prostate cancer: a systematic review and economic evaluation. NIHR Journals Library, 2015. Health Technology Assessment (HTA) 19(49).
  • Vale L, Adamson A, Critchley J, Rushton S, Kelly S, Shen J, Shirley M, Mason H, Donaldson C, Armstrong N. Economic evaluation: evaluating the short-term impacts of the school food policy and experimental modelling of longer term impacts. London: Newcastle University and the University of Stirling as part of the Public Health Research Consortium, 2011. B5-07A.
  • Macdonald DW, Tattersall FH, Johnson PJ, Carbone C, Reynolds JC, Langbein J, Rushton SP, Shirley MDF. Management and control of populations of foxes, deer, hares and mink in England and Wales, and the impact of hunting with dogs. London: Committee of Inquiry into Hunting with Dogs, Her Majesty's Government, 2000.

• Reviews

  • Gan JL, Grainger MJ, Shirley MDF, Pfeifer M. How effective are perches in promoting bird-mediated seed dispersal for natural forest regeneration? A systematic review protocol. Environmental Evidence 2023, 12, 15.
  • Ramsay C, Pickard R, Robertson C, Close A, Vale L, Armstrong N, Barocas DA, Eden CG, Fraser C, Gurung T, Jenkinson D, Jia X, Lam TB, Mowatt G, Nea DE, Robinson MC, Royle J, Rushton SP, Sharma P, Shirley MDF, Soomro N. Systematic review and economic modelling of the relative clinical benefit and cost-effectiveness of laparoscopic surgery and robotic surgery for removal of the prostate in men with localised prostate cancer. Health Technology Assessment 2012, 16(41), xiv, 313.
  • O'Donnell AG, Young IM, Rushton SP, Shirley MD, Crawford JW. Visualization, modelling and prediction in soil microbiology. Nature Reviews Microbiology 2007, 5(9), 689-699.