- Jacquez, J. A. and O'Neill, P. D. (1991) Reproduction
numbers and thresholds in stochastic epidemic models I. Homogeneous
populations.
*Mathematical Biosciences*107, 161-186. - Ball, F. G. and O'Neill, P. D. (1993) A modification of
the general stochastic epidemic motivated by AIDS modelling.
*Advances in Applied Probability*25, 39-62. - Ball, F. G. and O' Neill, P. D. (1994) Strong convergence
of stochastic epidemics.
*Advances in Applied Probability*26, 629-655. - O'Neill, P. D. (1995) Epidemic models featuring behaviour
change.
*Advances in Applied Probability*27, 960-979. - O'Neill, P. D. (1996) Strong approximations for some open
population epidemic models.
*Journal of Applied Probability*33, 448-457. - O'Neill, P. D. and Bunday, B. D. (1997) The transient
state probabilities of the M/M/1/ queue via a random walk
approach.
*The Mathematical Scientist*22, 32-36. - O'Neill, P. D. (1997) An epidemic model with
removal-dependent infection rate.
*Annals of Applied Probability*7, 90-109. - Clancy, D. and O'Neill, P. D. (1998) Approximation of
epidemics by time-inhomogeneous birth-and-death processes.
*Stochastic Processes and Their Applications*73, 233-245. - Ball, F. G. and O'Neill, P. D. (1999)
The distribution of general final state random variables for
stochastic epidemic models.
*Journal of Applied Probability*36, 473-491. - O'Neill, P. D. and Roberts, G. O. (1999) Bayesian
inference for partially observed stochastic epidemics.
*Journal of the Royal Statistical Society Series A*162, 121-129. - O'Neill, P. D. (1999) On a branching model of
division-within-division.
*I.M.A. Journal of Mathematics Applied in Medicine and Biology*16, 395-405. - O'Neill, P. D., Balding, D. J., Becker, N. G., Eerola, M.
and Mollison, D. (2000) Analyses of infectious disease data from household
outbreaks by Markov Chain Monte Carlo methods.
*Applied Statistics*49, 517-542. - O'Neill, P. D. and Becker, N. G. (2001) Inference for an
epidemic when susceptibility varies.
*Biostatistics*2, 99-108. - Clancy, D. and O'Neill, P. D. and Pollett, P. K. (2001)
Approximations for the long- term behaviour of an open-population
epidemic model.
*Methodology and Computing in Applied Probability*3, 75-95. - Ball, F. G., Britton, T. and O'Neill, P. D. (2001) Empty
confidence sets for epidemics, branching processes and Brownian motion.
*Biometrika*89, 211-224. - Britton, T. and O'Neill, P. D. (2002) Bayesian inference
for stochastic epidemics in populations with random social structure.
*Scandinavian Journal of Statistics*29, 375-390. - O'Neill, P. D. (2002) A tutorial introduction to Bayesian
inference for stochastic epidemic models using Markov chain Monte Carlo
methods.
*Mathematical Biosciences*180, 103-114. - O'Neill, P. D. (2002) MCMC methods for stochastic
epidemic models. In
*Models and Inference in HSSS: Recent Developments and Perspectives*, eds. Green, P. J., Lauritzen, S., and Richardson, S. Oxford University Press. - O'Neill, P. D. (2003) Perfect simulation for Reed-Frost epidemic models.
*Statistics and Computing*13, 37-44. - Hayakawa, Y., O'Neill, P. D., Upton, D., and Yip, P. S. F. (2003)
Bayesian inference for a stochastic epidemic model with uncertain
numbers of susceptibles of several types.
*Australian and New Zealand Journal of Statistics*45, 491-502. - Clough, H., Clancy, D., O'Neill, P. D. and French, N. P. (2003)
Bayesian methods for estimating pathogen prevalence within groups
of animals from faecal pat sampling.
*Preventive Veterinary Medicine*58, 145-169. - Becker, N. G., Britton, T. and O'Neill, P. D. (2003)
Estimating vaccine effects on transmission of infection from household
outbreak data.
*Biometrics*59, 467-475. - O'Neill, P. D. (2005) Epidemic models, structured population. In
*The Encyclopedia of Biostatistics*, 2nd edition. - Höhle, M., Jørgensen, E. and O'Neill, P. D. (2005)
Inference in disease transmission experiments by using stochastic epidemic
models.
*Applied Statistics*54, 349-366. - Demiris, N. and O'Neill, P. D. (2005)
Bayesian inference for stochastic epidemic models
with two levels of mixing.
*Scandinavian Journal of Statistics*32, 265-280. - Clough, H. E., Clancy, D., French, N. P., O'Neill, P. D.
and Robinson, S. E. (2005) A Bayesian method for quantifying uncertainty
associated with numbers of
*E. Coli*0157 present in faecal samples.*Biometrics*61, 610-616. - O'Neill, P. D. and Marks, P. J. (2005)
Bayesian model choice and
infection route modelling in an outbreak of Norovirus.
*Statistics in Medicine*24, 2011-2024. - Demiris, N. and O'Neill, P. D. (2005)
Bayesian inference for stochastic multitype
epidemics in structured populations via random graphs.
*Journal of the Royal Statistical Society, Series B*67, 731-746. - Demiris, N. and O'Neill, P. D. (2006)
Computation of final outcome probabilities
for the generalised stochastic epidemic.
*Statistics and Computing*16, 309-317. - Becker, N. G., Britton, T. and O'Neill, P. D. (2006)
Estimating vaccine effects from studies of outbreaks in household pairs.
*Statistics in Medicine*25, 1079-1093. - Clancy, D. and O'Neill, P. D. (2007)
Exact Bayesian inference and model
selection for stochastic models of epidemics among a community of households.
*Scandinavian Journal of Statistics*34, 259-274. - O'Neill, P. D. (2007)
Constructing population processes with specified quasi-stationary distributions.
*Stochastic Models*23, 439-449. - Ball, F. G., O'Neill, P. D. and Pike, J. (2007)
Stochastic epidemic models in structured populations
featuring dynamic vaccination and isolation.
*Journal of Applied Probability*44, 571-585. - Clancy, D. and O'Neill, P.D. (2008)
Bayesian estimation of the basic reproduction number in stochastic epidemic models.
*Bayesian Analysis*3, No. 4, 737-758. - Ball, F. G., Knock, E. S. and O'Neill, P. D. (2008)
Control of emerging infectious diseases using responsive imperfect vaccination
and isolation.
*Mathematical Biosciences*216, 100-113. - O'Neill, P.D. (2009)
Bayesian inference for stochastic multitype epidemics in structured populations using sample data.
*Biostatistics*10(4), 779-791. - Kypraios, T., O'Neill, P. D., Huang, S. S., Rifas-Shiman, S. L. and Cooper, B. S. (2010)
Assessing the role of undetected colonization and isolation precautions in reducing Methicillin-Resistant
Staphylococcus aureus transmission in intensive care units.
*BMC Infectious Diseases*10(29). - van Boven, M., Kretzschmar, M., Wallinga, J., O'Neill, P. D., Wichmann, O. and Hahne, S. (2010)
Estimation of measles vaccine efficacy and cricital vaccination coverage in a highly vaccinated population.
*Journal of the Royal Society Interface*7, 1537-1544. - O'Neill, P.D. (2010)
Introduction and snapshot review: Relating infectious disease transmission models to data.
*Statistics in Medicine*29, 2069-2077. - Britton, T., Kypraios, T. and O'Neill, P.D. (2011)
Inference for epidemics with three levels of mixing: methodology and application to a measles outbreak.
*Scandinavian Journal of Statistics*38, 578-599. - Spencer, S. E. F. and O'Neill, P. D. (2011)
The probability of containment for multitype branching process models for emerging epidemics.
*Journal of Applied Probability*48, 173-188. - Kypraios, T., O'Neill, P. D., Jones, D. E., Ware, J., Batra, R., Edgeworth, D. E. and Cooper, B. S. (2011)
Effect of systemic antibiotics and topical chlorhexidine on methicillin-resistant Staphylococcus aureus (MRSA) carriage in intensive care unit patients.
*Journal of Hospital Infection*7, 222-226. - Ball, F. G., Knock, E. S. and O'Neill, P. D. (2011) Threshold behaviour of emerging epidemics featuring contact tracing.
*Advances in Applied Probability*43, 1048-1065. - O'Neill, P. D. and Wen, C. H. (2012)
Modelling and inference for epidemic models featuring non-linear infection pressure.
*Mathematical Biosciences*238, 36-48. - Spencer, S. E. F. and O'Neill, P. D. (2012)
Assessing the impact of intervention delays on stochastic epidemics.
*Methodology and Computing in Applied Probability*, 15, 803-820. - van Boven, M., Ruijs, W.L., Wallinga, J., O'Neill, P. D. and Hahne, S. (2013)
Estimation of mumps vaccine efficacy and critical vaccination coverage.
*Public Library of Science Computational Biology*9(5): e1003061. - Worby, C., Jeyaratnam, D., Robotham, J. V., Kypraios, T., O.Neill, P. D., De Angelis, D., French, G. and Cooper, B. S. (2013)
Estimating the effectiveness of isolation and decolonization measures in reducing transmission of methicillin-resistant Staphylococcus aureus in hospital general wards.
*American Journal of Epidemiology*177 (11), 1306-1313. - Knock, E.S. and O'Neill, P.D. (2014)
Bayesian model choice for epidemic models with two levels of mixing.
*Biostatistics*, 15, 46-59. - Ball, F. G., Knock, E. S. and O'Neill, P. D. (2015)
Stochastic epidemic models featuring contact tracing with delays.
*Mathematical Biosciences*266, 23-35. - Verykouki, E., Kypraios, T. and O'Neill, P. D. (2016)
Modelling the effect of antimicrobial treatment on carriage of hospital pathogens with application to MRSA.
*Biostatistics.*17, 65-78. - Worby, C. J., O'Neill, P. D., Kypraios, T., Robotham, J. V., De Angelis, D., Cartwright, E. J. P., Peacock, S. J. and Cooper, B. S. (2016)
Reconstructing transmission trees for communicable diseases using densely sampled genetic data.
*Annals of Applied Statistics.*10(1), 395-417. arXiv paper - Wei, Y., Kypraios, T., O'Neill, P. D., Huang, S. S., Rifas-Shiman, S. L. and Cooper, B. S. (2016)
Evaluating hospital infection control measures for antimicrobial-resistant pathogens using stochastic transmission models: application to Vancomycin Resistant Enterococci in Intensive Care Units.
To appear,
*Statistical Methods in Medical Research.*arXiv paper - Xu, X. Kypraios, T. and O'Neill, P. D. (2016)
Bayesian nonparametric inference for stochastic epidemic models using Gaussian processes.
To appear,
*Biostatistics.*