Newcastle University

Roles and Responsibilities

Postgraduate Tutor/selector in Statistics

 Research Interests

• Parallel computing;
• Bayesian statistics;
• Moment closure;
• Stochastic kinetic models. 

Projects

• The Biology of Ageing e-Science Integration and Simulation system (BASIS)
  Project Leader(s): Darren Wilkinson

Undergraduate Teaching (2012-13)

• MAS1343: Computational statistics with R;
• MAS2316: Introduction to Regression and Modelling.

Postgraduate Teaching (2012-13)

• Advanced R programming.      

MMathStat Projects

• Analysis of mobile phone data, 2011, Seb Mellor; 
• Bayesian inference for stochastic population processes, 2010, Nina Wilkinson.

• Cockell S, Bashton M, Gillespie CS. Bioconductor tools for microarray analysis. In: Microarray Image and Data Analysis: Theory and Practice. CRC Press, 2013. Submitted.
• Milner P, Gillespie CS, Wilkinson DJ. Moment closure based parameter inference of stochastic kinetic models. Statistics and Computing 2013, 23(2), 287-295.
• Golighty A, Gillespie CS. Simulation of stochastic kinetic models. In: Schneider, M.V, ed. In-silico Systems Biology: A systems-based approach to understanding biological processes. Humana Press, 2013. In Press.
• Lawless C, Jurk D, Gillespie CS, Shanley D, Saretzki G, von Zglinicki T, Passos JF. A Stochastic Step Model of Replicative Senescence Explains ROS Production Rate in Ageing Cell Populations. PLoS One 2012, 7(2), e32117.
• Bell MJ, Gillespie CS, Swan D, Lord P. An approach to describing and analysing bulk annotation quality: a case study using UniprotKB. Bioinformatics 2012, 28(18), i562-i568.
• Bell MJ, Gillespie CS, Swan D, Lord P. An approach to describing and analysing bulk biological annotation quality: A case study using UniProtKB. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2012. School of Computing Science Technical Report Series 1336.
• Gillespie CS, Golightly A. Bayesian inference for the chemical master equation using approximate models. In: 9th International Workshop on Computational Systems Biology (WCSB). 2012, Ulm, Germany.
• Gillespie CS. Stochastic simulation of chemically reacting systems using multi-core processors. Journal of Chemical Physics 2012, 136(1), 014101.
• 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, 2(127).
• Pohl S, Tu WY, Aldridge PD, Gillespie C, Hahne H, Mäder U, Read TD, Harwood CR. Combined proteomic and transcriptomic analysis of the response of Bacillus anthracis to oxidative stress. Proteomics 2011, 11(15), 3036-3055.
• Milner P, Gillespie CS, Wilkinson DJ. Moment closure approximations for stochastic kinetic models with rational rate laws. Mathematical Biosciences 2011, 231(2), 99-104.
• Caldwell GS, Fitzer S, Gillespie CS, Pickavance G, Turnbull E, Bentley MG. Ocean acidification takes sperm back in time. Invertebrate Reproduction and Development 2011, 55(4), 217-221.
• Wockenforth R, Gillespie CS, Jaffray B. Survival of children following Nissen fundoplication. British Journal of Surgery 2011, 98(5), 680-685.
• Dall'Olio GM, Marino J, Schubert M, Keys KL, Stefan MI, Gillespie CS, Poulain P, Shameer K, Sugar R, Invergo BM, Jensen LJ, Bertranpetit J, Laayouni H. Ten Simple Rules for Getting Help from Online Scientific Communities. PLoS Computational Biology 2011, 7(9), e1002202.
• Gillespie CS, Lei G, Boys RJ, Greenall AJ, Wilkinson DJ. Analysing time course microarray data using Bioconductor: a case study using yeast2 Affymetrix arrays. BMC Research Notes 2010, 3(81).
• Gillespie CS, Golightly A. Bayesian inference for generalized stochastic population growth models with application to aphids. Journal of the Royal Statistical Society: Series C (Applied Statistics) 2010, 59(2), 341-357.
• Chen YH, Lawless C, Gillespie CS, Wu J, Boys RJ, Wilkinson DJ. CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. Briefings in Bioinformatics 2010, 11(3), 278-289.
• Gillespie CS. Moment-closure approximations for mass-action models. IET Systems Biology 2009, 3(1), 52-58.
• Hong M, Ryan KR, Arkwright P, Gennery A, Costigan C, Denning D, Cant AJ, Abinun M, Young DA, McConnell V, Spickett GP, Swan DC, Gillespie CS, Lilac D, Dominguez M. Pattern recognition receptor expression is not impaired in patients with chronic mucocutanous candidiasis with or without autoimmune polyendocrinopathy candidiasis ectodermal dystrophy. Clinical and Experimental Immunology 2009, 156(1), 40-51.
• Gillespie CS, Renshaw E. The evolution of a single-paired immigration death process. Journal of Physics A: Mathematical and Theoretical 2008, 41(35), -.
• Evans TW, Gillespie CS, Wilkinson DJ. The SBML discrete stochastic models test suite. Bioinformatics 2008, 24(2), 285-286.
• Gillespie CS, Renshaw E. An improved saddlepoint approximation. Mathematical Biosciences 2007, 208(2), 359-374.
• Proctor CJ, Lydall D, Boys RJ, Gillespie CS, Shanley D, Wilkinson DJ, Kirkwood TBL. Modelling the checkpoint response to telomere uncapping in budding yeast. Journal of the Royal Society Interface 2007, 4(12), 73-90.
• Gillespie CS, Wilkinson DJ, Shanley DP, Proctor CJ, Boys RJ, Kirkwood TBL. BASIS: an internet resource for network modelling. Journal of Integrative Bioinformatics 2006, 3(2), [12].
• Kirkwood TBL, Boys RJ, Gillespie CS, Proctor CJ, Shanley DP, Wilkinson DJ. Computer modeling in the study of aging. In: Masoro, E.J., Austad, S.N, ed. Handbook of The Biology of Aging. London, UK: Academic Press, 2006, pp.334-356.
• Gillespie C, Wilkinson D, Proctor CJ, Shanley D, Boys RJ, Kirkwood TBL. Tools for the SBML community. Bioinformatics 2006, 22(5), 628-629.
• Kirkwood TBL, Boys RJ, Gillespie CS, Proctor CJ, Shanley DP, Wilkinson DJ. Computer Modeling in the Study of Aging. In: Austad, S.N., Masoro, E.J, ed. Handbook of the Biology of Aging. Amsterdam; Boston: Academic Press, 2005, pp.334-359.
• Proctor CJ, Soti C, Boys RJ, Gillespie CS, Shanley DP, Wilkinson DJ, Kirkwood TBL. Modelling the actions of chaperones and their role in ageing. Mechanisms of Ageing and Development 2005, 126(1), 119-131.
• Gillespie CS, Renshaw E. The evolution of a batch-immigration death process subject to counts. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 2005, 461(2057), 1563-1581.
• Gillespie CS, Proctor CJ, Shanley DP, Wilkinson DJ, Boys RJ, Kirkwood TBL. Web-services for the biology community: the BASIS project. In: UK e-Science All Hands Meeting. 2005, Nottingham, UK.
• Gillespie C, Proctor CJ, Boys R, Shanley D, Wilkinson D, Kirkwood T. A mathematical model of ageing in yeast. Journal of Theoretical Biology 2004, 229(2), 189-196.
• Kirkwood TBL, Boys RJ, Gillespie CJ, Proctor CJ, Shanley DP, Wilkinson DJ. Towards an e-biology of ageing: Integrating theory and data. Nature Reviews Molecular Cell Biology 2003, 4(3), 243-249.