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Dr Paul Jenkins

I am an Associate Professor of Data Science in Statistics and Computer Science, with interests in Monte Carlo methods, genomic data analysis, inference from stochastic processes, and mathematical population genetics.

Teaching

ST208: Mathematical Methods

ST340: Programming for Data Science

ST343: Topics in Data Science

APTS Computer Intensive Statistics

Preprints

Perrone, V., Jenkins, P. A., Spanò, D., and Teh, Y. W. Poisson random fields for dynamic feature models.
[ arXiv ]

Koskela, J., Spanò, D, and Jenkins, P. A. Consistency of Bayesian nonparametric inference for discretely observed jump diffusions.
[ arXiv ]

Jenkins, P. A. Exact simulation of the sample paths of a diffusion with a finite entrance boundary.
[ arXiv ]

Publications

Griffiths, R., Jenkins, P. A., and Spanò, D. Wright-Fisher diffusion bridges. Theoretical Population Biology, to appear.
[ arXiv ]

Griffin, A., Jenkins, P. A., Roberts, G. O., and Spencer, S. E. F. Simulation from quasi-stationary distributions on reducible state spaces. Advances in Applied Probability, to appear.
[ arXiv ]

Koskela, J., Jenkins, P. A., and Spanò, D. Bayesian non-parametric inference for Λ-coalescents: consistency and a parametric method. Bernoulli, to appear.
[ arXiv ]

Koskela, J., Jenkins, P. A., and Spanò, D. Inference and rare event simulation for stopped Markov processes via reverse-time sequential Monte Carlo. Statistics & Computing, to appear.
[ arXiv ]

Jenkins, P. A., and Spanò, D. (2017). Exact simulation of the Wright-Fisher diffusion. Annals of Applied Probability, 27(3): 1478–1509.
[ Abstract ] [ arXiv ] [ CRiSM Working Paper 14-27 (an earlier version) ]

Griffiths, R. C., Jenkins, P. A., and Lessard, S. (2016). A coalescent dual process for a Wright-Fisher diffusion with recombination and its application to haplotype partitioning. Theoretical Population Biology, 112: 126–138.
[ Abstract ] [ arXiv ]

Dialdestoro, K., Sibbesen, J. A., Maretty, L., Raghwani, J., Gall, A., Kellam, P., Pybus, O. G., Hein, J., and Jenkins, P. A. (2016). Coalescent inference using serially sampled, high-throughput sequencing data from intra-host HIV infection. Genetics, 202 (4): 1449–1472.
[ Abstract ] [ bioRxiv ]

Koskela, J., Jenkins, P., and Spanò, D. (2015). Computational inference beyond Kingman's coalescent. Journal of Applied Probability, 52 (2): 519–537.
[ Abstract ] [ arXiv ]

Jenkins, P. A., Fearnhead, P., and Song, Y. S. (2015). Tractable diffusion and coalescent processes for weakly correlated loci. Electronic Journal of Probability, 20 (58): 1-26. 
[ Abstract & PDF ] [ arXiv ]

Jenkins, P. A., Mueller, J.W, and Song, Y. S. (2014). General triallelic frequency spectrum under demographic models with variable population size. Genetics, 196: 295–311.
[ Abstract ] [ arXiv ]

Chan, A. H., Jenkins, P. A., and Song, Y. S. (2012). Genome-wide fine-scale recombination rate variation in Drosophila melanogaster. PLoS Genetics, 8 (12): e1003090.
[ Abstract & PDF ] [ Software ]

Jenkins, P. A., Song, Y. S., and Brem, R. B. (2012). Genealogy-based methods for inference of historical recombination and gene flow and their application in Saccharomyces cerevisiae. PLoS ONE, 7 (11): e46947.
[ Abstract & PDF ]

Jenkins, P. A. and Song, Y. S. (2012). Padé approximants and exact two-locus sampling distributions. Annals of Applied Probability, 22 (2): 576–607.
(Technical Report #793, Department of Statistics, University of California, Berkeley, 2010.)
[ Abstract ] [ arXiv ] [ Tech Report Version ]

Jenkins, P. A. (2012). Stopping-time resampling and population genetic inference under coalescent models. Statistical Applications in Genetics and Molecular Biology, 11 (1): Article 9.
[ Abstract ] [ PDF ]

Jenkins, P. A. and Song, Y. S. (2011). The effect of recurrent mutation on the frequency spectrum of a segregating site and the age of an allele. Theoretical Population Biology, 80 (2): 158–173.
[ Abstract ] [ Preprint ]

Jenkins, P. A. and Griffiths, R. C. (2011). Inference from samples of DNA sequences using a two-locus model. Journal of Computational Biology, 18 (1): 109–127.
[ Abstract ] [ PDF ]

Jenkins, P. A. and Song, Y. S. (2010). An asymptotic sampling formula for the coalescent with recombination. Annals of Applied Probability, 20 (3): 1005–1028.
(Technical Report #775, Department of Statistics, University of California, Berkeley, 2009.)
[ Abstract ] [ arXiv ] [ Tech Report Version ]

Jenkins, P. A. and Song, Y. S. (2009). Closed-form two-locus sampling distributions: accuracy and universality. Genetics, 183 : 1087–1103.
[ Abstract ] [ PDF ] [ Software ]

Griffiths, R. C., Jenkins, P. A., and Song, Y. S. (2008). Importance sampling and the two-locus model with subdivided population structure. Advances in Applied Probability, 40 (2): 473–500.
[ Abstract ] [ Preprint ]

Jenkins, P., Lyngsø, R., and Hein, J. (2006). How many transcripts does it take to reconstruct the splice graph? In: Proceedings of the Workshop on Algorithms in Bioinformatics, Lecture Notes in Computer Science vol. 4175, pp. 103–114.
[ Abstract ] [ PDF ] [ Supplementary material ]

Thesis

Importance sampling on the coalescent with recombination. University of Oxford, 2008.
[ Abstract ] [ PDF ]

PhD Students

Jere Koskela (2013–2016, with Dario Spanò)
Mathias Cronjäger (2015–, with Jotun Hein)
Valerio Perrone (2015–, with Dario Spanò and Yee Whye Teh)
Marcin Mider (2016–, with Murray Pollock and Gareth Roberts)
photo_pj.png

Contact:

Dr Paul Jenkins
Dept of Statistics
University of Warwick
Coventry, CV4 7AL
United Kingdom

Voice:

024 7657 4856

Email:

p . jenkins at warwick . ac . uk

Office:

Zeeman D0.15.

Term 1 office hours: Mon 14.30-15.30 and Thu 15.30-16.30.