Publications and Preprints

Below are details of my publications and preprints. Some include links to online versions of the papers. Alternatively you can search for my publications on the Lancaster e-prints site

Preprints

• Markov chain Monte Carlo for exact inference for diffusions Giorgos Sermaidis, Omiros Papaspiliopoulos, Gareth O. Roberts, Alex Beskos and Paul Fearnhead.
• Optimal detection of changepoints with a linear computational cost. Rebecca Killick, Paul Fearnhead and Idris Eckley.
• An adaptive sequential Monte Carlo sampler. Paul Fearnhead and Benjamin M Taylor.
• Semi-automatic Approximate Bayesian Computation. Paul Fearnhead and Dennis Prangle.

2011

• Whole-Genome Comparison of Two Campylobacter jejuni Isolates of the Same Sequence Type Reveals Multiple Loci of Different Ancestral Lineage. Patrick J. Biggs, Paul Fearnhead, Grant Hotter, Vathsala Mohan, Julie Collins-Emerson, Errol Kwan, Thomas E. Besser, Adrian Cookson, Philip E. Carter, Nigel P. French. PLoS ONE 6(11): e27121. doi:10.1371/journal.pone.0027121
• On Estimating the Ability of NBA Players. Paul Fearnhead and Benjamin M Taylor. Journal of Quantitative Analysis of Sports, 7, Issue 3, Article 11.
• Efficient Bayesian analysis of multiple changepoint models with dependence across segments. Paul Fearnhead and Zhen Liu. Statistics and Computing, 21 , 217-229.
• Composite likelihood methods in statistical genetics. Fabrice Larribe and Paul Fearnhead. Statistica Sinica, 21 , 43-69
• MCMC for state-space models. Paul Fearnhead. In Handbook of Markov Chain Monte Carlo (Chapman & Hall/CRC Handbook of Modern Statistical Methods), Brooks, Gelman, Jones and Meng (Eds), 513-529.
• Analysis of Changepoint Problems Idris Eckley, Paul Fearnhead and Rebecca Killick. In Bayesian Time Series Models (CUP) Barber, Cemgil and Chiappa (Eds), 203-224.

2010

• The random walk Metropolis : linking theory and practice through a case study Chris Sherlock, Paul Fearnhead and Gareth Roberts. Statistical Science, 25 , 172-190.
• Spatio-temporal epidemiology of Campylobacter jejuni enteritis, in an area of Northwest England, 2000-2002. Edith Gabriel, Daniel J. Wilson, Andrew J.H. Leatherbarrow, John Cheesbrough, Steve Gee, Eric Bolton, Andrew Fox, Paul Fearnhead, C. Anthony Hart and Peter J. Diggle. Epidemiology and Infection, 138, 1384-1390.
• Random weight particle filtering of continuous-time processes. Paul Fearnhead, Omiros Papaspilipoulos, Gareth Roberts and Andrew Stuart. Journal of the Royal Statistical Society, Series B, 72, 497-512.
• A sequential smoothing algorithm with linear computational cost. Paul Fearnhead, David Wyncoll and Jon Tawn. Biometrika, 97, 447-464.
• Calculating Strength of Schedule, and Choosing Teams for March Madness Paul Fearnhead and Benjamin M Taylor. (2010) The American Statistician , 64, 108-115.

2009

• Bayesian Analysis of Isochores. Paul Fearnhead and Despina Vasilieou. (2009) Journal of the American Statistical Association, 485, 132-141.
• Rapid Evolution and the Importance of Recombination to the Gastroenteric Pathogen Campylobacter jejuni. Daniel J. Wilson, Edith Gabriel, Andrew J.H. Leatherbarrow, John Cheesbrough, Steven Gee, Eric Bolton, Andrew Fox, C. Anthony Hart, Peter J. Diggle, and Paul Fearnhead. (2009) Molecular Biology and Evolution, 26, 385-397.

2008

• Tracing the Source of Campylobacteriosis. D. J. Wilson, E. Gabriel, A. J. H. Leatherbarrow, J. Cheesbrough, S. Gee, E. Bolton, A. Fox, P. Fearnhead, C. A. Hart, P.. J. Diggle. (2008) Plos Genetics, 4(9):e1000203 doi:10.1371/journal.pgen.1000203.
• Particle filters for partially-observed diffusions.P. Fearnhead, O. Papaspiliopoulos and G. O. Roberts. (2008) Journal of the Royal Statistical Society, Series B, 70, 755-777.
• Computational Methods for Complex Stochastic Systems: A Review of Some Alternatives to MCMC. Paul Fearnhead. (2008) Statistics and Computing, 18, 151-171.
  [abstract and code]

2007

• Filtering methods for Mixture Models. P. Fearnhead and L. Meligkotsidou. (2007) Journal of Computational and Graphical Statistics, 16 586-607.
• On the Choice of Genetic Distance in Spatial-Genetic Studies.Paul Fearnhead. (2007) Genetics, 177, 427--434.
• Postprocessing of Genealogical Trees. Loukia Meligkotsidou and Paul Fearnhead. (2007) Genetics, 177, 347-358.
• Online Inference for Multiple Changepoint Problems. P. Fearnhead and Z. Liu. (2007) Journal of the Royal Statistical Society, Series B 69, 589-605.
• Genome-wide association study of prostate cancer identifies a second risk locus at 8q24. M Yeager, N. Orr, R.B. Hayes, P. Kraft, S. Wacholder, M.J. Minichielo, P. Fearnhead, K. Yu et al. (2007) Nature Genetics 39, 645-649.

2006

• SequenceLDhot: Detecting Recombination Hotspots. Paul Fearnhead (2006) Bioinformatics, 22, 3061-3066.
  [Code and Data]
• Perfect Simulation from Non-neutral Population Genetic Models: Variable Population Size and Population sub-division. Paul Fearnhead (2006) Genetics, 174 1397-1406.
  [Software]
• An exact Gibbs Sampler for the Markov Modulated Poisson Processes. P. Fearnhead and C Sherlock. (2006) Journal of the Royal Statistical Society Series B, 68 , 767-784.
  [Software]
• The Stationary Distribution of Allele Frequencies when Selection acts at Unlinked Loci. P. Fearnhead. (2006) Theoretical Population Biology, 70 , 376-386.
• Exact and Efficient Likelihood-based inference for Discretely Observed Diffusion Processes (with discussion). A. Beskos, O. Papaspiliopoulos, G.O. Roberts and P. Fearnhead (2006). Journal of the Royal Statistical Society Series B 68, 333-382.
• Exact and Efficient Bayesian inference for Multiple Changepoint Problems. P. Fearnhead (2006). Statistics and Computing, 16 203-213.

2005

• Maximum Likelihood Estimation of Coalescent Times in Genealogical Trees. L. Meligkotsidou and P. Fearnhead (2005). Genetics, 171, 2073-2084.
• A Comparison of Three Estimators of the Population-scaled Recombination Rate: Accuracy and Robustness. N G C Smith and P Fearnhead (2005). Genetics, 171, 2051-2062.
• Using Random Quasi-Monte-Carlo within Particle Filters, with Application to Financial Time Series. P. Fearnhead (2005). Journal of Computational and Graphical Statistics, 14 751-769.
  [Software]
• A novel method with improved power to detect recombination hotspots from polymorphism data reveals multiple hotspots in human genes. P Fearnhead and N G C Smith (2005). American Journal of Human Genetics, 77 781-794.
  [List of Hotspots][Software]
• Analysis of Recombination in Campylobacter jejuni from MLST Population Data. P Fearnhead, N G C Smith, M Barrigas, A Fox and N French (2005). Journal of Molecular Evolution, 61 333-340.
• Direct Simulation for Discrete Mixture Distributions. P. Fearnhead. (2005) Statistics and Computing, 15 , 125-133.
  [Software]
• Exact Bayesian Curve Fitting and Signal Segmentation. P. Fearnhead. (2005) IEEE Transactions on Signal Processsing, 53, 2160--2166.
  [Software]
• Spatial epidemiology and natural population structure of Campylobacter jejuni colonizing a farmland ecosystem. Nigel French, Mishele Barrigas, Patrick Brown, Paulo Ribiero, Nicola Williams, Howard Leatherbarrow, Richard Birtles, Eric Bolton, Paul Fearnhead and Andrew Fox. (2005) Environmental Microbiology, 7 , 1116-1126.

2004

• Application of coalescent methods to reveal fine scale rate variation and recombination hotspots. P. Fearnhead, Rosalind M. Harding, Julie A. Schneider, Simon Myers, Peter Donnelly (2004). Genetics, 167, 2067--2081.
  [Software]
• Particle filters for mixture models with an unknown number of components. P. Fearnhead. (2004) Statistics and Computing, 14 , 11-21.
• Exact filtering for partially-observed continuous-time models. P. Fearnhead and L. Meligkotsidou. (2004) JRSS Series B , 66, 771-789.
• Exact filtering for partially-observed queues. P. Fearnhead. (2004) Statistics and Computing 14, 261--266.
• A second order approximation to the log-likelihood surface for mixture models, with application to the EM algorithm. P. Fearnhead. (2004) Journal of Computational and Graphical Statistics , 13, 739-754.

2003

• Consistency of estimators of the population-scaled recombination rate. P. Fearnhead (2003). Theoretical Population Biology, 64 , 67-79.
• Ancestral Processes for non-neutral models of complex diseases. P. Fearnhead (2003). Theoretical Population Biology, 63 , 115-130.
  [Software]
• Haplotypes: the joint distribution of alleles at linked loci. P. Fearnhead (2003) Journal of Applied Probability, 40 , 505-512.
• Online inference for hidden Markov models via particle filters. P. Fearnhead and P. Clifford. (2003) JRSS Series B , 65, 887-899.

2002

• Approximate likelihood methods for estimating local recombination rates. P. Fearnhead and P. Donnelly (2002). JRSS Series B , 64, 657-680.
  [Software]
• A coalescent-based method for detecting and estimating recombination from gene sequences. G. McVean, P. Awadalla and P. Fearnhead (2002). Genetics 160 , 1231-1241.
• MCMC, sufficient statistics and particle filters. P. Fearnhead. (2002) Journal of Computational and Graphical Statistics , 11, 848-862 .
• The common ancestor at a non-neutral locus. P. Fearnhead (2002). Journal of Applied Probability, 39

2001

• Estimating recombination rates from population genetic data. P. Fearnhead and P. Donnelly (2001). Genetics , 159, 1299-1318.
  [Software]
• Perfect simulation of population genetic models with selection. P. Fearnhead (2001). Theoretical Population Biology, 59 , 263-279.
  [Software]

1999

• An improved particle filter for non-linear problems. J. Carpenter, P. Clifford and P. Fearnhead (1999). IEE proceedings - Radar, Sonar and Navigation, 146, 2-7.

1998

• Sequential Monte Carlo methods in filter theory. P. Fearnhead. (1998) PhD Thesis, University of Oxford
  [abstract]