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Dr João A.N. Filipe
	Postdoctoral Research Associate Epidemiology and Modelling Group
Correspondence Address:	Dept Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, U.K.
Telephone:	+44 (0) 1223 330229
Fax:	+44 (0) 1223 333953
Email:	jf263 at cam.ac.uk
Research interests Brief c.v. Publications

Research interests

• Epidemiology and control of large-scale spread of plant diseases under changing policy and environmental conditions. With particular focus on the emerging spread and management of Sudden Oak Death in the California, Citrus Canker in Florida, and Phytophthora infestans (potato blight) and cereal rusts Puccinia triticina and Gaeumannomyces graminis in Europe.
• Mathematical models for the invasion of natural and crop populations by emerging and re-emerging pathogens, typically on geographically and ecologically heterogeneous landscapes. I apply a range of methods for predicting stochastic and spatial population dynamics and probabilities of successful disease control and management strategies.

Epidemiology and control of Sudden Oak Death

Phytophthora ramorum, the causative agent of Sudden Oak Death in temperate-wet forests of California and Oregon states (and to a lesser extent of Europe) is an important new pathogen. Sudden Oak Death was first detected in California in the mid 1990’s and has since been spreading in wild forests causing the dead of (estimated) millions of native oak and tanoak trees. The pathogen is unusual in that it can infect a very wide range of plant hosts, many of which exhibit foliar disease that sustains transmission to species with systemic disease and fast, high-rate disease-induced mortality.

This outbreak has the potential to cause substantial ecological, economical and cultural impact, but this is difficult to quantify. First, because this impact has happened over a short period of time (2-5 years) but will continue to unfold over a longer term (decades). Second, the impact of this outbreak on local communities and ecosystems is likely to take place through direct and indirect roots some of which are not well identified and understood. As P. ramorum is an emerging pathogen there is much not yet known about its biology and the epidemiology of Sudden Oak Death. Current and future research should help to better understand the epidemiology and implications of this non-specific disease and inform control and management policy.

We collaborate with several researchers in this area, including Dave Rizzo at the University of California, Davies and Ross Meentemeyer at the University of North Carolina at Charlotte.

We use stochastic and spatial mathematical models and data analyses to assess the potential of a range of intervention and management strategies for controlling the disease locally and for containing its spread to areas that are not yet infected. The illustrative figure shows the probability of invasion of a non-infected area 5 years after the start of two contrasting control interventions. This probability varies considerably with key, but not yet known, epidemiological parameters.

Brief Curriculum vitae

Previously I worked on the epidemiology and control of malaria and other human vector-borne diseases. I have also supervised several PhD and MSc students, co-lead research projects, co-organised the MSc module Modelling and dynamics of infectious diseases and Infectious-Disease Modelling seminar series, and taught in the latter MSc module and Short-Course Introduction to infectious disease modelling at LSHTM.

• Lecturer in infectious disease modelling, London School of Hygiene & Tropical Medicine
• Researcher, Imperial College London and Universities of Cambridge and Edinburgh
• PhD Theoretical Physics University of Manchester

Publications

• Ghani, A.C., Sutherland, C.J., Riley, E.M., Drakeley, C.J., Griffin, J., Gosling, R.D., and Filipe, J.A.N. (2008) Contribution of exposure-reducing interventions to the goal of malaria elimination endemic areas. (Submitted).
  
  
• Checchi F, Filipe, J.A.N., Barrett M.P., Chandramohan D. (2008) A Review of the Natural Progression of Gambiense Sleeping Sickness Infection. PLoS Neglected Tropical Diseases. (in press).
  
  
• Basanez, M.G., Pion, S.D.S., Boakes, E., Filipe, J.A.N., Churcher, T.S. Boussinesq, M. (2008) Effect of single-dose ivermectin on Onchocerca volvulus: a systematic review and meta-analysis. Lancet Infectious Diseases 8(5): 310-322.
  
  
• Checchi, F., Filipe, J.A.N., Haydon, D.T., Chandramohan, D., Chappuis, F. (2008). Estimates of the duration of the early and late stage of gambiense sleeping sickness. BMC Infectious Diseases 8(16).
  
  
• Filipe, J.A.N., Riley, E.M., Drakeley, C.J., Sutherland, C.J., Ghani, A.C. (2007) Determination of the processes driving the acquisition of immunity to malaria using a mathematical transmission model. PLOS Computational Biology 3(12): 2569-2579.
  
  
• Basanez, M.G., Pion, S.D.S., Boakes, E. Filipe, J.A.N., Churcher, T.S. Boussinesq, M. Effect of single dose ivermectin on Onchocerca volvulus: A systematic review. American Journal of Tropical Medicine and Hygiene 77(5): 222 Supplement: Suppl. S.
  
  
• Gibson, G.J., Otten, W.O., Filipe, J.A.N., Cook, A., Marion, G. and Gilligan C.A. (2006). Bayesian estimation for percolation models of disease spread in plant populations. Statistics and Computing 16(4): 391-402.
  
  
• Churcher, T.S., Filipe, J.A.N., and Basanez M.G. (2006). Density dependence and the control of helminth parasites. J Animal Ecology 75(6): 1313-1320.
  
  
• Pion, S.D.S., Filipe, J.A.N., Kamgno, J., Gardon, J., Basanez M.G. and Boussinesq, M. (2006). Microfilarial distribution of Loa loa in the human host: population dynamics and epidemiological implications. Parasitology 133: 101-109.
  
  
• Pion, S.D.S., Clarke, P., Filipe, J.A.N., Kamgno, J., Gardon, J., Basanez M.G. and Boussinesq, M. (2006). Co-infection with Onchocerca volvulus and Loa loa microfilariae in central Cameroon: are these two species interacting? Parasitology 132: 843-854.
  
  
• Filipe, J.A.N., Boussinesq, M., Renz, A., Collins, R.C., Vivas-Martinez, S., Grillet, M.E., Little, M.P., Basanez M.G. (2005). Human infection patterns and heterogeneous exposure in river blindness. Proc Natl Acad Sci USA 102: 15265-70.
  
  
• Otten, W.O., Filipe, J.A.N. and Gilligan C.A. (2005). Dynamics of contact structure and disease transmission in mixed species populations. Ecology 86: 1948-1957.
  
  
• Brewer, M.J., Filipe, J.A.N., Elston, D.A., Dawson, L.A. Mayes, R.W., Soulsby, C. and Dunn, S.M. (2005). A hierarchical model for compositional data analysis. J. Agric. Biol. Env. Stat. 10: 19-34.
  
  
• Little, M.P., Filipe, J.A.N., Prise, K.M., Folkard, M. and Belyakov, O.V. (2005). A model for radiation-induced bystander effects, with allowance for spatial position and the effects of cell turnover. Journal Theoretical Biology 232: 329-338.
  
  
• Filipe, J.A.N., Maule, M.M. and Gilligan C.A. (2004). On Analytic models for the patchy spread of plant disease. Bulletin of Mathematical Biology 66: 1027-1037.
  
  
• Filipe, J.A.N. and Maule, M.M. (2004). Effects of dispersal mechanisms on the spatio-temporal development of epidemics. Journal Theoretical Biology 226: 125-141.
  
  
• Filipe, J.A.N., Otten, W.O., Gibson, G.J. and Gilligan C.A. (2004). Inferring spatial dynamics of epidemics from time-series data. Bulletin of Mathematical Biology 66: 373-391.
  
  
• Otten, W.O., Filipe, J.A.N. and Gilligan C.A. (2004). An empirical method to estimate the effect of soil on the rate for transmission of damping-off disease. New Phytologist 162: 231-238.
  
  
• Filipe, J.A.N. and Maule, M.M. (2003).Analytical methods for predicting the behaviour of population models. Mathematical Biosciences 183: 15-35.
  
  
• Otten, W.O., Filipe, J.A.N., Bailey, D.J. and Gilligan C.A. (2003). Quantification and analysis of transmission rates for soil-borne epidemics. Ecology 226: 125-141.
  
  
• Filipe, J.A.N. and Gilligan C.A. (2003). Solution of epidemic models with quenched transients. Physical Review E 67: 021906-021914. Selected for Virtual J. Bio Phys.Res. 5.
  
  
• Filipe, J.A.N. and Rodgers, G.J. (2003). Solution of a generalized model for surface deposition. Physical Review E 68: 027102-027106.
  
  
• Filipe, J.A.N. and Gibson, G.J. (2001). Comparing approximations to spatio-temporal models for epidemics with local spread.Bulletin of Mathematical Biology 63: 603-624.
  
  
• Boag, B., Filipe, J.A.N. and Niesten, D. (2000). Spatial distribution of a Globodera rostochiensis foci in a potato field in Scotland. Asp Applied Biol. 59: 99-102.
  
  
• Filipe, J.A.N. (1999). Hybrid closure-approximation to epidemic models.Physica A 266: 238-241.
  
  
• Filipe, J.A.N. and Gibson, G.J. (1998). Studying and approximating spatio-temporal models for epidemic spread and control. Phil. Trans. R. Soc Lond. B 353: 2153-2162.
  
  
• Filipe, J.A.N., Rodgers, G.J. and Tavassoli, Z. (1998). Deposition on disordered substrates wih precursor layer diffusion. Journal of Physics A 31: 7417-7427.
  
  
• Rodgers G.J.and Filipe, J.A.N. (1997). Exact results for surface deposition with precursor layer diffusion. Journal of Physics A 30: 3449-3461.
  
  
• Filipe, J.A.N. and Rodgers G.J.(1996). Kinetics of fragmentation-annihilation processes. Physical Review E 54: 1290-1297
  
  
• Filipe, J.A.N. and Rodgers G.J.(1995). Theoretical and numerical studies of chemisorption on a line with precursor layer diffusion. Physical Review E 52: 6044-6054.
  
  
• Filipe, J.A.N., Bray, A.J. and Puri, S. (1995). Phase ordering kinetics with external fields and biased initial conditions. Physical Review E 51: 6082-6100.
  
  
• Filipe, J.A.N. and Bray, A.J. (1995). Gaussian approach for phase ordering in non-conserved scalar systems with long-range interactions. Physical Review E 50: 204-211.
  
  
• Filipe, J.A.N. and Bray, A.J. (1994). Phase ordering dynamics of cosmological models. Physical Review E 50: 2523-2538