Lab members

Current Members

Professor Chris Gilligan

Head of group

Current research is focused on establishing and testing a theoretical framework that identifies the mechanisms that control invasion, persistence, scaling and variability of epidemics within changing agricultural and natural landscapes. Applications range from large-scale pandemics (sudden oak death, citrus canker, African cassava mosaic virus), through pesticide resistance and genetical control to biocontrol in sustainable agricultural systems, and to the design of intervention strategies for exotic pathogen threats to the UK.

The research involves a synthesis of epidemiological theory, population and evolutionary genetics, landscape ecology and economic modelling, drawing upon methods from statistical physics and Bayesian statistical inference, supported by a complementary experimental programme involving laboratory microcosms and collation of extensive field and regional data-sets to test the models.

For more details, please visit the departmental website.

Lawrence Bower

Scientific IT Developer

Providing scientific programming support for large-scale epidemiological forecasting programmes. Currently contributing to an on-going wheat rust collaborative project which provides current predictions for long-distance dispersal pathways of wheat rust spores across Africa, the Middle East and Asia. Areas of expertise include Pipelines, HPC, plotting and user interfaces.

Dr Ruairi Donnelly

Postdoc

My research interests lie in ecology, epidemiology and evolution. At present I study the dynamics of a number of plant arboviruses. These include those that are "non-persistently" transmitted by aphids, as well as several important viruses of cassava that are transmitted by whitefly (cassava mosaic virus, cassava brown streak virus). I collaborate on empirical and modelling research with colleagues in the molecular plant pathology group of Prof. John Carr (Plant Sciences, Cambridge), and on field experiments in East Africa with colleagues at BecA ILRI (Nairobi).

Sally Hames

Group Administrator and PA

Dr Tamas Mona

Postdoc

Working as a weather modeller in the wheat rust forecasting project which is a collaboration between the Epidemiology and Modelling Group at the University of Cambridge, the UK Met Office, CIMMYT (International Maize and Wheat Improvement Centre) and the Ethiopian Institute of Agricultural Research. The project uses NAME to forecast the spread of these epidemics of wheat rust in near real-time to enable growers to take preventative action. The project grew from an initial analysis of pathways for long-distance dispersal of wheat rust spores extending from Southern and East Africa through the Middle East, West and South Asia.

Dr Renata Retkute

Postdoc

My research has focused on modelling and parametrisation of biological systems at different spatial and temporal scales, based on the experimental and observed data.

Dr Alison Scott-Brown

A current member of the Epidemiology and Modelling Group, promoting research impact with relevance to food security, plant biosecurity and biodiversity across regions in Sub-Saharan Africa, South Asia, Europe and UK. Additionally, collating science impact for an international food security programme, TIGR2ESS, across the six interdisciplinary flagship projects (India and UK).Research Interests Plant-insect interactions, using thrips as a model to unravel questions on host-plant selection, tolerance and resistance to invasive species. More recently focusing on mechanisms underpinning beneficial interactions (pollinating and predatory thrips), accumulating knowledge on benefits these bring in natural and agricultural settings.

Dr Jacob Smith

Postdoc

With a background in climate science, I want to improve understanding of plant diseases dispersed by the wind. Wheat crops often suffer from wheat rust, a family of aerially dispersed fungal pathogens. Similarly, wheat blast is an emerging threat. Key to mitigating their impacts is the research and development of models equipped with appropriate processes, including Lagrangian dispersal models and full-landscape epidemiological models. In collaboration with others, my research brings these aspects together.

Dr Yevhen Suprunenko

Postdoc

Using methods of mathematics and physics I study complex dynamics of living organisms. I am fascinated with how living systems and groups of living organisms maintain their function and their existence, despite being open systems and being subject to continuous perturbations and fluctuations. In my research, I develop models and theoretical descriptions of such dynamics, focusing on underlying mechanisms, and on the role of spatially explicit dynamics, stochasticity, and time-variability.

I received my PhD in Theoretical Physics (2011, Lancaster University, UK). Before joining Epidemiology and Modelling group of Prof Chris Gilligan, I worked as a postdoc in Nonlinear and Biomedical Physics (2011-2014, and 2017-2018, Lancaster University, UK), and in Theoretical Ecology (2014 – 2017, University of Liverpool).

Dr Rich Stutt

Postdoc

My research is focused on large scale predictions for disease spread and management.

Current Projects

My current projects involve modelling the spread of the Ramorum disease epidemic (also known as Sudden Oak Death, caused by P. ramorum) in the UK, working with regulators to provide outputs including predictions of disease spread and the effect of management strategies. I am also involved in predicting the potential for future spread of Sudden Oak Death on the east coast of the USA, and looking at the effects of spread of citrus diseases at the state scale in Florida.

I am part of the production and deployment of a web based interactive utility to demonstrate the effect of control in realistic landscapes and additionally the development of a generic computational framework for stochastic simulation of spatial models of epidemics and developing a flexible, computationally-efficient suite of models for the analysis of disease spread and control in heterogeneous environments.

Dr Cerian Webb

Postdoc

I am a Mathematical Epidemiologist with a background in both plant and animal systems. I received a degree in Pure Mathematics from the University of York (1992) an MSc in Mathematical Biology from the University of Dundee (1993) and a PhD modelling crop growth and disease dynamics from the Department of Plant Sciences, University of Cambridge under the supervision of Professor Chris Gilligan and Dr Rik Werker. After completing my PhD I joined the veterinary epidemiology group at VLA-Weybridge where I developed models to investigate the dynamics of scrapie and likely efficacy of control policies. I have contributed to disease modelling internationally through involvement in an EU transmissible spongiform encephalopathies (TSEs) project and collaborations with Massey University, New Zealand. In 2000 I moved back to the University of Cambridge, although this time to the Vet School, as the Kirsten Rausing Research Fellow which enabled me to pursue more theoretical work investigating the role of animal movement networks in determining the dynamics of farm animal disease.

Having taken a break from research (but not from lecturing and teaching) while my daughter went through primary school, I have found myself back in Plant Sciences where I work on mathematical models for a range of tree pests and pathogens.

In addition to my research role, I lecture for the Part 1A Mathematical Biology course and am a lecturer on the Wellcome Trust 'Mathematical Models for Infectious Disease Dynamics' course. I regularly deliver courses on MATLAB for Biologists and have recently co-authored the textbook “Introduction to MATLAB for Biologists”.

As well as my research position in this group I am the Associate Lecturer in Mathematical Biology for Newnham College, Cambridge.

Collaborators

Dr Marcel Meyer

Postdoc

Visiting Researchers

Alex Ferris

Gates Intern and PhD student, Stanford University.

Former Members

  • Dr Israël Tankam Chedjou, MSCA Bienvenüe Postdoctoral researcher, Institut Agro Rennes-Angers, France

  • Dr David Godding, Information and Data Officer at Enferm.

  • Dr Daniel Bonnery, Analyst (Chargé d'études), Direction Régionale de l'Insee de l'Île de France in Saint Quentin en Yvelines.

  • Dr Anna Szyniszewska, Technical Lead on the Global Burden of Crop Loss initiative, CABI. Formerly Postdoctoral Research Associate working on cassava pathogens in sub-Saharan Africa.

  • Francisco F. Laranjeira, Embrapa Cassava & Fruits, Brazilian Agricultural Research Corporation (Embrapa).

  • Dr Hola Adrakay, Senior Statistician and Modeller, INRA French National Institute for Agricultural Research.

  • Dan Safka. Former programming support for epidemic mapping and handling of host and meteorological data.

  • Dr Clare Allen, British Antarctic Survey. Former postdoctoral research associate in atmospheric physics working on the Ethiopian wheat rust early warning system.

  • Dr Ciara Dangerfield, Isaac Newton Institute, working to improve the use of maths in industry. Former postdoctoral research associate working on tree health and plant biosecurity.

  • Dr Martin Vyska, research in connection with banking and hedge fund management. Former postgraduate student working on options theory for disease control.

  • Dr Matthew Castle, Human Resources Division, University of Cambridge. Former postdoctoral research associate.

  • Dr Matthew Patrick, postdoctoral research fellow, Department of Dermatology, University of Michigan. Former postdoctoral research associate working on computational methods for epidemic models.

  • Dr Joao Filipe, postdoctoral research fellow, School of Agriculture, Food and Rural Development, University of Newcastle. Former postdoctoral research associate working on oak diseases.

  • Dr Franco Neri, European Food Safety Authority. Former postdoctoral research associate working on Bayesian estimation for epidemic models.

  • Dr Irina Tikhonova, Senior Research Fellow in Health Economic Modelling, University of Exeter Medical School. Former postdoctoral research associate working on individual based models.

  • Anne Bates, former Senior Research Technician.

  • Dr Alex Cook, Assistant Professor, Department of Statistics and Applied Probability, National University of Singapore. Former postdoctoral research associate working on the optimal design of experiments relating to epidemics.

  • Dr Wilfred Otten, Senior Lecturer, Biophysics of Soil Ecosystems, University of Abertay. Former senior research associate in soil physics working on testing an epidemiological framework to quantify the spatio-temporal dynamics of saprotrophic activity of soil-borne fungi.

  • Dr Adam Kleczkowski, Senior Lecturer, Department of Computing Science and Mathematics, University of Stirling. Former senior research associate modelling the influence of spatial and temporal heterogenities on dynamics of ecological and epidemiological systems.

  • Dr Stephen Parnell, PDRA USDA Horticulture Laboratory, Fort Pierce, Florida. Former postgraduate student working on modelling invasion of fungicide resistant strains in disease complexes.

  • Dr David Claessen, Veni Vidi Vici Fellowship, Netherlands. Former postdoctoral research assistant in modelling. Transgene-induced life history changes and the ecology of transgenic crops based at Rothamsted Research in joint project with Dr van den Bosch.

  • Dr Graeme Forster, Research Associate, Orbis Investment. Former postgraduate student working on dynamics and control of disease in populations: linking epidemiology and economic modelling.

  • Isabelle Moltini, former technical research assistant (DEFRA).

  • Dr Chad Pillinger, Research Services Division, University of Cambridge. Former postdoctoral research associate in plant pathology working on an integrated epidemiological approach to evaluate control strategies and disease risk of Rhizoctonia in field vegetables.

  • Dr Lara Jamieson, MRC Statistics, University of Cambridge. Former research associate working on Markov chain Monte Carlo analysis of spatio-temporal disease maps.

  • Dr Jonathan Ludlam, Postdoctoral Research Associate, Department of Chemistry, University of Cambridge. Former postdoctoral research associate testing an epidemiological framework to quantify the spatio-temporal dynamics of saprotrophic activity of soil-borne fungi.

  • Dr Dawn Muddyman, Plant Pathologist, UK Cereal Pathogen Virulence Survey, NIAB. Former postgraduate student working on chemical and biological control of the invasion of soil-borne fungal disease.

  • Dr James Truscott, Postdoctoral Research Associate, Imperial College. Former postdoctoral research associate working on application of perturbation theory to temporal and spatio-temporal models for disease dynamics and spread of Rhizomania disease.

  • Dr Adrian Stacey, computing consultant on robotics, Royston. Former postgraduate student and postdoctoral research associate working on development of computer models for epidemiological analyses and modelling of fungal growth.

  • Dr Paula Kantola, Postdoctoral Research Assistant, University of Helsinki. Former postgraduate student working on microcosms experiments of epidemics of Rhizoctonia solani.

  • Dr Déirdre Hollingsworth, Postdoctoral Research Assistant, Imperial College. Former postgraduate student working on invasion and persistence of disease and other micro-organisms in crop environments.

  • Dr Richard Hall, Postdoctoral Research Assistant, Environmental Science and Policy, UC Davis. Former postgraduate student working on modelling invasion of fungicide resistant strains in heterogeneous crop environments.

  • Dr Andrew Park, Postdoctoral Research Associate, Parasite Ecology Group, Department of Zoology, University of Cambridge. Former postgraduate student funded by NERC working on temporal and spatial models for metapopulation dynamics involving fungal infection of plants.

  • Dr Simon Gubbins, Mathematical Modeller, Veterinary Laboratory Agency. Former junior research fellow working on epidemiology and modelling of plant disease with particular reference to biological control and pesticide resistance.

  • Dr Jane White, Lecturer in Mathematical Biology, University of Bath. Former Wellcome Research Fellow, Department of Zoology, working on development of reaction-diffusion-advection models for temporal and spatial dynamics of three species interactions involved in biocontrol of plant pathogens.

  • Dr Chris Thornton, Research Fellow in Plant Pathology, University of Exeter. Former BBSRC postdoctoral research assistant working on use of monoclonal antibodies to detect and quantify populations of Rhizoctonia solani and Trichoderma viride. Joint project with Dr Dewey, Department of Plant Sciences, University of Oxford.

  • Barrie Goddard, Computer Officer, Department of Chemical Engineering, University of Cambridge. Responsible for computer maintenance, graphics and data preparation as well as mycological experimentation assists with spatial and temporal modelling project.

  • Dr David Jaccoud, Lecturer in Plant Pathology, Universidade Estadual de Ponta Grossa, Brazil. Former affiliated postgraduate student working at NIAB on RAPD methods for detection of seed-borne pathogens of soyabean.

  • Dr Kai Schmidt, Affiliated Researcher, University of Bonn. Formerly postdoctoral research associate funded by MAFF working on models for crop growth in relation to soil water and nitrogen response. Joint project with Dr Sylvester-Bradley ADAS, Soil Science Group.

  • Dr Mette Creaser, Postdoctoral Research Associate, Department of Applied and Molecular Ecology, University of Adelaide. Former postgraduate student working on use of molecular and other methods to quantify the behaviour of pathogens and microbial antagonists in the rhizosphere and bulk soil.

  • Dr Keith Briggs, Senior Research Associate, BT Research Laboratories, Martlesham Heath. Formerly postdoctoral research associate funded by BBSRC working on estimation of parameters of ecological models. Joint project with GJS Ross, Statistics Department, IACR, Rothamsted Experimental Station.

  • Dr Jonathan Swinton, NERC Advanced Research Fellow, Department of Zoology, University of Cambridge. Former postdoctoral research associate on Dutch elm disease and seal distemper virus. Epidemics in spatially structured populations.

  • Dr Deborah Long, Mathematical Analyst, Merchant Bank. Former postgraduate student working on analysis and prediction of nonlinear dynamics in biological control of plant pathogens.

  • Kirsty Harris, Research scientist in soil science, Scottish Crops Research Institute. Former technical research assistant working on thin section analysis thin section analysis of fungal growth in soil, working at Scottish Crops Research Institute in connection with the joint project with Dr Otten, Cambridge, and Dr Young and Dr Ritz at SCRI.

  • Dr Gemma Biran, Patent Lawyer. Former postgraduate student working on biological control of soil-borne nematodes. Joint project with Professor Kerry, IACR Rothamsted.

  • Dr Israel Tankam, MSCA-Bienvenue Postdoctoral Fellow at Institut Agro Rennes-Angers.

  • Dr Jeff Reid, Independent Consultant. Modelling in relation to African plant health.

  • Dr Matthew Parry, Department of Mathematics and Statistics, University of Otago, New Zealand. Bayesian methods for parameter estimation of emerging epidemics.

  • Dr Alex Ferris, Bill and Melinda Gates Foundation. Former Bioengineering PhD student, Stanford University and Bill and Melinda Gates Foundation. Modelling within-field dynamics and surveillance for cassava disease.