Publications
My publications can be grouped into four main areas: modelling, stochastic processes, computing and statistical consultancy. Obviously there is considerable overlap between research areas. Please contact me if you wish copies or have questions about the articles below.
Work in progress
Golightly, A. and Gillespie, CS, 2012. Bayesian Inference for Hybrid Discrete-Continuous Systems Biology Models, in preparation.
Bell, MJ, Gillespie, CS, Swan, D, Lord, P, 2012. An approach to describing and analysing bulk biological annotation quality: A case study using UniProtKB, in submission.
Published work
Milner, P, Gillespie, CS and Wilkinson, DJ. Moment closure based parameter inference of stochastic kinetic models. Statistics and Computing, in press (pdf).
Gillespie, CS Stochastic simulation of chemically reacting systems using multi-core CPUs. Journal of Chemical Physics 2012, 36, 014101 (pdf).
Lawless C, et al. A Stochastic Step Model of Replicative Senescence Explains ROS Production Rate in Ageing Cell Populations. PLoS ONE 2012, 7(2): e32117.
Pohl, S. et al., Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress. Protemics 2011, 11(15) 3036-55.
Caldwell, GS. et al., Ocean acidification takes sperm back in time. Invertebrate Reproduction and Development 2011, 55(4), 217-221.
Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, et al. Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology 2011, 7(9): e1002202.
Milner, P, Gillespie, CS and Wilkinson, DJ. Moment closure approximations for stochastic kinetic models with rational rate laws. Mathematical Biosciences 2011, 231, 99-104 (pdf).
Wockenforth, R, Gillespie, CS, and Jaffray, B. Survival of children following Nissen fundoplication: a case series. British Journal of Surgery 2011, 5, 680-685.
Lei, G, Boys, RJ, Gillespie, CS, Greenall, AJ, Wilkinson, DJ. Bayesian inference for sparse VAR(1) models, with application to time course microarray data. Journal of Biometrics and Biostatistics 2011, in press.
Gillespie, C. S., Lei, G., Boys, R. J., Greenall, A. J., Wilkinson, D. J.
Analysing yeast
time course microarray data using BioConductor: a case study using yeast2
Affymetrix arrays. BMC Research Notes 2010, 3:81
(bibtex, website).
Chen, Y., Lawless, C., Gillespie, C. S., Wu, J., Boys, R. J., and Wilkinson, D. J. CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. Briefings in Bioinformatics, 2010, 11, 278-289 (bibtex, pdf).
Gillespie, CS and Golightly, A. Bayesian inference for generalized stochastic population growth models with application to aphids. Journal of the Royal Statistical Society, Series C, 2010, 59, 341-357 (bibtex, pdf).
Gillespie, CS. Moment closure approximations for mass-action models. IET Systems Biology 2009, 3, 52-58 (pdf, bibtex, software).
Hong, M. et al. Pattern recognition receptors expression is not impaired in patients with chronic Mucocutaneous Candidiasis with or without Autoimmune Polyendocrinopathy Candidiasis Ectodermal Dystrophy (APECED). Clinical and Experimental Immunology 2009, 156, 40-51.
Chen, Y. et al. CaliBayes and BASIS: e-Science applications for Systems Biology research. In: All Hands Meeting 2009, Oxford.
Gillespie, CS and Renshaw, E. The evolution of a single-paired immigration death process. Journal of Physics A: Mathematical and Theoretical 2008, 41, 355002 (pdf, bibtex).
Evans, TW, Gillespie, CS and Wilkinson, DJ. The SBML Discrete Stochastic Models Test Suite. Bioinformatics 2008, 24, 285-286 (website, bibtex).
Gillespie, C.S. and Renshaw, E. An improved saddlepoint approximation. Mathematical Biosciences 2007, 208, 359-374 (bibtex, pdf).
Proctor, C.J., Lydall, D.A., Boys, R.J., Gillespie, C.S., Shanley, D.P., Wilkinson, D.J., and Kirkwood, T.B.L. Modelling the checkpoint response to telomere uncapping in budding yeast. Journal of the Royal Society Interface 2007, 4, 73-90 (bibtex).
Lawson, S.E.M., and Gillespie, C.S. Three dimensional customisation: effect of statistical technique on HJC prediction equation in children. Journal of Biomechanics 2007, 40(2), S321 (bibtex).
Gillespie, C.S., Wilkinson, D.J., Shanley D.P, Proctor, C.J., Boys, R.J. and Kirkwood, T.B.L. BASIS: an internet resource for network modelling. Journal of Integrative Bioinformatics 2006, 3(2) (bibtex, pdf).
Gillespie, C.S., Proctor, C.J., Shanley, D.P., Wilkinson, D.J., Boys, R.J. and Kirkwood, T.B.L. Tools for the SBML community Bioinformatics 2006, 22, 628-629 (bibtex, pdf).
Gillespie, C.S. and Renshaw, E. The evolution of a batch-immigration death process subject to counts. Proceedings of the Royal Society of London Series A 2005, 461, 1563-1581 (bibtex).
Kirkwood, T.B.L., Boys, R.J., Gillespie, C.S., Proctor, C.J., Shanley, D.P. and Wilkinson, D.J. Computer Modeling in the Study of Aging. In: Austad, S.N. and Masoro, E.J., ed. Handbook of the Biology of Aging. Academic Press, 2005.
Proctor, C.J., Csaba, S., Boys, R.J., Gillespie, C.S., Shanley, D.P., Wilkinson, D.J., Kirkwood, T.B.L. Modelling the actions of chaperones and their role in ageing. Mechanisms of Ageing and Development 2005, 126(1), 119-131 (bibtex, SBML model).
Gillespie, C.S., Proctor, C.J., Shanley, D.P., Wilkinson, D.J., Boys, R.J. and Kirkwood, T.B.L. Web-services for the biology community: the BASIS project. In: All Hands Meeting 2005, Nottingham (pdf).
Gillespie, C.S., Proctor, C.J., Boys, R.J., Shanley, D.P., Wilkinson, D.J. and Kirkwood, T.B.L. A mathematical model of ageing in yeast. Journal of Theoretical Biology 2004, 229(2), 189-196 (bibtex, R code).
Kirkwood, T.B.L., Boys, R.J., Gillespie, C.S., Proctor, C.J., Shanley, D.P. and Wilkinson, D.J. Towards an e-biology of ageing: integrating theory and data. Nature Reviews Molecular Cell Biology 2003, 4, 243-249 (bibtex).