Newcastle University

Roles and Responsibilities

• Research Group Leader for Statistical Bioinformatics and Systems Biology (SB^2)

• Member, EPSRC Peer Review College

• Chairman, RSS Graduate Training Programme Committee

Research Interests

• Bayesian statistics: computationally intensive methods; inference for partially observed stochastic processes; applications mainly in science, social science and medicine.

• Statistical bioinformatics and stochastic systems biology: stochastic models in molecular biology, hidden Markov models for DNA sequences, phylogenetic inference

• Inference for mathematical models of population dynamics in the Neolithic period

• Econometric models for duration data

• Screening problems
  

• Spagnoli A, Henderson R, Boys RJ, Houwing-Duistermaat JJ. A hidden Markov model for informative dropout in longitudinal response data with crisis states. Statistics and Probability Letters 2011, 81(7), 730-738.
• Golightly A, Boys RJ. Discussion to "Riemann manifold Langevin and Hamiltonian Monte Carlo methods" by Girolami and Calderhead. Journal of the Royal Statistical Society, Series B: Statistical Methodology 2011, 73(2), 181-182.
• Jow H, Boys RJ, Wilkinson DJ. A comparative genomics approach to the identification of QTL candidate genes. Revstat Statistical Journal 2011, 9(1), 1-17.
• Henderson DA, Boys RJ, Proctor CJ, Wilkinson DJ. Linking systems biology models to data: a stochastic kinetic model of p53 oscillations. In: A. O'Hagan and M. West, ed. The Oxford Handbook of Applied Bayesian Analysis. Oxford University Press, 2010, pp. 155-187.
• Henderson DA, Boys RJ, Wilkinson DJ. Bayesian calibration of a stochastic kinetic computer model using multiple data sources. Biometrics 2010, 66(1), 249-256.
• Jow H, Bhattacharjee M, Boys RJ, Wilkinson DJ. The integration of genetic maps using Bayesian inference. Journal of Computational Biology 2010, 17(6), 825-840.
• 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).
• 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.
• Henderson DA, Boys RJ, Krishnan KJ, Lawless C, Wilkinson DJ. Bayesian emulation and calibration of a stochastic computer model of mitochondrial DNA deletions in substantia nigra neurons. Journal of the American Statistical Association 2009, 104(485), 76-87.
• Boys RJ, Wilkinson DJ, Kirkwood TBL. Bayesian inference for a discretely observed stochastic kinetic model. Statistics and Computing 2008, 18(2), 125-135.
• Boys RJ, Giles PR. Bayesian inference for stochastic epidemic models with time-inhomogeneous removal rates. Journal of Mathematical Biology 2007, 55(2), 223-247.
• Boys RJ, Dolton PJ, Walker NR. Adapting the optimal job search model for active labour market policy. Journal of the Royal Statistical Society. Series A: Statistics in Society 2007, 170(3), 759-779.
• 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.
• Venchard GR, Thomson PJ, Boys R. Improved sedation for oral surgery by combining nitrous oxide and intravenous Midazolam: a randomized, controlled trial. International Journal of Oral and Maxillofacial Surgery 2006, 35(6), 522-527.
• Gillespie C, Wilkinson D, Proctor CJ, Shanley D, Boys RJ, Kirkwood TBL. Tools for the SBML community. Bioinformatics 2006, 22(5), 628-629.
• Hawkes AG, Steel M, Sherlock C, Papaspiliopoulos O, Jacobsen M, Sorensen M, Boys RJ. Bayesian analysis of single-molecule experimental data - Discussion. Journal of the Royal Statistical Society Series C: Applied Statistics 2005. Oxford, UK:Wiley-Blackwell Publishing Ltd.,54 496-506.
• Aitkin M, Boys RJ, Chadwick T. Bayesian point null hypothesis testing via the posterior likelihood ratio. Statistics and Computing 2005, 15(3), 217-230.
• 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.
• Aitkin M, Boys RJ, Chadwick TJ. Bayesian point null hypothesis testing via the posterior likelihood ratio. Statistics and Computing 2005, 15(3), 217-230.
• 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.
• Boys RJ. Discussion of "Bayesian analysis of single-molecule experimental data" by Kou, Xie and Liu. Royal Statistical Society. Journal. Series C: Applied Statistics 2005,54 3 503-504.
• 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
• Boys RJ, Henderson DA. Rejoinder to "Discussion of "A Bayesian approach to DNA segmentation by R. J. Boys and D. A. Henderson" by Booth, Burden, Maindonald, Santoso, Wakefield and Wilson". Biometrics 2005,61 2 635-639.
• Boys RJ, Henderson DA. Discussion of "A Bayesian approach to DNA sequence segmentation": Commentary. Biometrics 2005. ,61 2 637-639.
• Boys RJ, Henderson DA. A Bayesian Approach to DNA Sequence Segmentation. Biometrics 2004,60 3 573-581.
• 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.
• Samuels DC, Boys RJ, Henderson DA, Chinnery PF. A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate. Nucleic Acids Research 2003,31 20 6043-6052.
• 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.
• Boys RJ, Henderson DA. A comparison of reversible jump MCMC algorithms for DNA sequence segmentation using hidden Markov models. In: Frontiers in data mining and bioformatics : 33rd Symposium on the Interface. 2001, Costa Mesa, Orange County, California, USA: Interface Foundation of North America.
• Boys RJ, Henderson DA, Wilkinson DJ. Detecting homogeneous segments in DNA sequences by using hidden Markov models. Journal of the Royal Statistical Society. Series C: Applied Statistics 2000, 49(2), 269-285.
• 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).
• Cameron KM, Golightly A, Miwa S, Speakman J, Boys R, von Zglinicki T. Gross energy metabolism in mice under late onset, short term caloric restriction. Mechanisms of Ageing and Development 2011, 132(4), 202-209.
• Boys RJ, Henderson DA. On determining the order of Markov dependence of an observed process governed by a hidden Markov model. Scientific Programming 2002, 10(3), 241-251.