School of Mathematics, Statistics and Physics

Publications by Professor Richard Boys

This page lists my working papers (currently in submission or in preparation) and my published Statistics papers and Consultancy papers in reverse chronological order.

Working papers

Boys, R. J. and Gillespie, C. S. (2017). Construction of Bayes optimal designs for stochastic kinetic models using emulators. In preparation.

Anuta, O., Barteczko-Hibbert, C., Boys, R. J. and Wade, N. (2017). Probabilistic evaluation of current and emerging demand and generation on existing distribution networks. In preparation.

Ainsworth, H. F., Boys, R. J., Gillespie, C. S. and Proctor, C. J. (2017). Parameter inference for a stochastic kinetic model of expanded polyglutamine proteins. In preparation.

Heaps, S. E., Boys, R. J. and Farrow, M. (2017). Building substantive beliefs into a prior distribution for the covariance matrix of a spatial multivariate normal distribution. In preparation.

Johnson, S. R., Henderson, D. A. and Boys, R. J. (2017). Revealing subgroup structure in ranked data using a Bayesian WAND. In preparation.

Gillespie, C. S. and Boys, R. J. (2017). Fast and efficient construction of Bayes optimal designs for stochastic models using cloud computing. In preparation.

Heaps, S. E., Nye, T. M. W., Boys, R. J., Williams, T. W., Cherlin, S. and Embley, T. M. (2017). Generalising rate heterogeneity across sites in statistical phylogenetics. In submission.

Boys, R. J. and Philipson, P. M. (2017). On the ranking of Test match batsmen. Under review.

Statistics papers

Cherlin, S., Nye, T. M. W., Boys, R. J., Heaps, S. E., Williams, T. W. and Embley, T. M. (2017). The effect of non-reversibility on inferring rooted phylogenies. Mol. Biol. Evol., to appear.

Boys, R. J., Ainsworth, H. F. and Gillespie, C. S. (2017). Bayesian inference for a partially observed birth-death process using data on proportions. Aust. N. Z. J. Stat., to appear.

Garbe, M., Nye, T. M. W. and Boys, R. J. (2017). Probabilistic distances between trees. Syst. Biol., to appear.

Drovandi, C. C., Moores, M. T. and Boys, R. J. (2018). Accelerating pseudo-marginal MCMC using Gaussian processes. Comput. Statist. Data Anal., 118, 1-17.

Whitaker, G. A., Golightly, A., Boys, R. J. and Sherlock, C. (2016). Bayesian inference for diffusion-driven mixed-effects models. Bayesian Analysis, 12, 435-463.

Whitaker, G. A., Golightly, A., Boys, R. J. and Sherlock, C. (2016). Improved simulation of conditioned diffusion processes. Statist. Comp., 27, 885-900.

Williams, T. W., Heaps, S. E., Cherlin, S., Nye, T. M. W., Boys, R. J. and Embley, T. M. (2015). New substitution models for rooting phylogenetic trees. Phil. Trans. Roy. Soc. B, 370, 20140336.

Heaps, S. E., Boys, R. J. and Farrow, M. (2015). Bayesian modelling of rainfall data using non-homogeneous hidden Markov models and latent Gaussian variables. Appl. Statist., 64, 543-568.

Heaps, S. E., Nye, T. M. W., Boys, R. J., Williams, T. W. and Embley, T. M. (2014). Bayesian modelling of compositional heterogeneity in molecular phylogenetics. Statist. Appl. Gen. Mol. Biol., 13, 589-609.

Henderson, D. A., Baggaley, A. W., Shukurov, A., Boys, R. J., Sarson, G. R. and Golightly, A. (2014). Regional variations in the European Neolithic dispersal: role of the coastlines. Antiquity, 88, 1291-1302.

Jow, H., Boys, R. J. and Wilkinson, D. J. (2014). Bayesian identification of differential expression in multi-group isobaric labelled mass spectrometry data. Statist. Appl. Gen. Mol. Biol., 13, 531-551.

Heaps, S. E., Boys, R. J. and Farrow, M. (2014). Computation of marginal likelihoods with data-dependent support for latent variables. Comput. Statist. Data Anal., 71, 392-401.

Baggaley, A. W., Boys, R. J., Golightly, A., Sarson, G. R. and Shukurov, A. (2012). Inference for population dynamics in the Neolithic period. Ann. Appl. Statist., 6, 1352-1376.

Golightly, A., Boys, R. J., Cameron, K. and von Zglinicki, T. (2012). The effect of late onset, short term caloric restriction on the core temperature and physical activity in mice. Appl. Statist., 61, 733-751.

Baggaley, A. W., Sarson, G. R., Shukurov, A., Boys, R. J. and Golightly, A. (2012). Bayesian inference for a wavefront model of the Neolithisation of Europe. Phys. Rev. E, 86, 016105 (doi: 10.1103/PhysRevE.86.016105).

Lei, G., Boys, R. J., Gillespie, C. S., Greenall, A. J. and Wilkinson, D. J. (2011). Bayesian inference for sparse VAR(1) models, with application to time course microarray data. J. Biom. Biostatist., 2, 127 (doi: 10.4172/2155-6180.1000127).

Jow, H., Boys, R. J. and Wilkinson, D. J. (2011). A comparative genomics approach to the identification of QTL candidate genes. Revstat, 9, 1-17.

Spagnolia, A., Henderson, R., Boys, R. J. and Houwing-Duistermaat, J. J. (2011). A hidden Markov model for informative dropout in longitudinal response data with crisis states. Statist. Probab. Letters, 81, 730-738.

Golightly, A. and Boys, R. J. (2011). Discussion of "Riemann manifold Langevin and Hamiltonian Monte Carlo methods" by M. Girolami and B. Calderhead. J. Roy. Statist. Soc. B, 73, 181-2.

Boys, R. J., Farrow, M. and Germain, S. E. (2011). Discussion of "Modelling multivariate counts varying continuously in space" by A. M. Schmidt and M. A. Rodriguez. In Bayesian Statistics 9 (Eds. J. M. Bernardo et al.), O.U.P., pp. 628-630.

Gillespie, C. S., Lei, G., Boys, R. J., Greenall, A. J. and Wilkinson, D. J. (2010). Analysing time course microarray data using BioConductor: a case study using yeast2 Affymetrix arrays. BMC Research Notes, 3, 81 (doi:10.1186/1756-0500-3-81)

Chen, Y., Lawless, C., Gillespie, C. S., Boys, R. J., Greenall, A. J., Wu, J. and Wilkinson, D. J. (2010). CaliBayes and BASIS: integrated tools for the calibration, simulation and storage of biological simulation models. Briefings in Bioinformatics (published on-line, doi:10.1093/bib/bbp072)

Jow, H., Bhattacharjee, M., Boys, R. J. and Wilkinson, D. J. (2010). The integration of genetic maps using Bayesian inference. J. Comp. Biol., 17, 825-840.

Henderson, D. A., Boys, R. J. and Wilkinson, D. J. (2010). Bayesian calibration of a stochastic kinetic computer model using multiple data sources. Biometrics, 66, 249-56.

Henderson, D. A., Boys, R. J., Proctor, C. J. and Wilkinson, D. J. (2010). Linking systems biology models to data: a stochastic kinetic model of p53 oscillations. In The Oxford Handbook of Applied Bayesian Analysis (Eds. A. O'Hagan and M. West): O.U.P., pp. 155-87.

Henderson, D. A., Boys, R. J., Krishnan, K. J., Lawless, C. and Wilkinson, D. J. (2009). Bayesian emulation and calibration of a stochastic computer model of mitochondrial DNA deletions in substantia nigra neurons. J. Amer. Statist. Assoc., 104, 76-87.

Boys, R. J., Wilkinson, D. J. and Kirkwood, T. B. L. (2008). Bayesian inference for a discretely observed stochastic kinetic model. Statistics & Computing, 18, 125-135

Boys, R. J. and Giles, P. R. (2007). Bayesian inference for SEIR epidemic models with time-inhomogeneous removal rates. J. Math. Biol., 55, 223-247.

Boys, R. J., Dolton, P. J. and Walker, N. R. (2007). Adapting the optimal job search model for active labour market policy. J. Roy. Statist. Soc. A, 178, 759-779.

Proctor, C. J., Lydall, D. A., Boys, R. J., Gillespie, C. S., Shanley, D. P., Wilkinson, D. J. and Kirkwood, T. B. L. (2007). Modelling the checkpoint response to telomere uncapping in budding yeast. J. Roy. Soc. Interface, 4, 73-90.

Gillespie, C. S., Wilkinson, D. J., Shanley, D. P., Proctor, C. J., Boys, R. J. and Kirkwood, T. B. L. (2006). BASIS: An internet resource for network modelling. Journal of Integrative Bioinformatics, 3, 26.

Gillespie, C. S., Wilkinson, D. J., Proctor, C. J., Shanley, D. P., Boys, R. J. and Kirkwood, T. B. L. (2006). Tools for the SBML community. Bioinformatics, 22, 628-629.

Kirkwood, T. B. L., Boys, R. J., Gillespie, C. S., Proctor C. J., Shanley D. P., Wilkinson, D. J. (2005). Computer Modeling in the Study of Aging. In Handbook of the Biology of Aging, Sixth Edition (Eds. E. J. Masoro and S. N. Austad) Elsevier Inc., pp. 334-357.

Boys, R. J. and Henderson, D. A. (2005). Discussion of "A Bayesian approach to DNA sequence segmentation by R. J. Boys and D. A. Henderson" by H. S. Booth, C. J. Burden, J. H. Maindonald, L. Santoso, M. J. Wakefield and S. R. Wilson. Biometrics, 61, 635-639.

Gillespie, C. S., Proctor, C. J., Shanley, D. P., Wilkinson, D. J., Boys, R. J. and Kirkwood, T. B. L. (2005). Web-services for the biology community: the BASIS project. Proceedings of the UK e-Science All Hands Meeting, Nottingham, UK, 491-493.

Proctor, C. J., Soti, C., Boys, R. J., Gillespie, C. S., Shanley, D. P., Wilkinson, D. J. and Kirkwood, T. B. L. (2005). Modelling the actions of chaperones and their role in ageing. Mechanisms of Ageing and Development, 126, 119-131.

Boys, R. J. (2005). Discussion of "Bayesian analysis of single-molecule experimental data" by S. C. Kou, X. S. Xie and J. S. Liu. Appl. Statist., 54, 503-504.

Aitkin, M., Boys, R. J. and Chadwick, T. J. (2005). Bayesian point null hypothesis testing via the posterior likelihood ratio. Statistics & Computing 15, 217-230.

Boys, R. J. and Henderson, D. A. (2004). A Bayesian approach to DNA sequence segmentation (with discussion). Biometrics, 60, 573-588.

Gillespie, C. S., Proctor, C. J., Boys, R. J., Shanley, D. P., Wilkinson, D. J. and Kirkwood, T. B. L. (2004). A mathematical model of ageing in yeast. J. Theor. Biol., 229, 189-196.

Samuels, D. C., Boys, R. J., Henderson, D. A. and Chinnery, P. F. (2003). A compositional segmentation of the human mitochondrial genome is related to heterogeneities in the guanine mutation rate. Nucleic Acids Research, 31, 6043-6052.

Kirkwood, T. B. L. , Boys, R. J., Gillespie, C. S., Proctor, C. J., Shanley, D. P. and Wilkinson, D. J. (2003). Towards an e-biology of ageing: integrating theory and data. Nature Reviews Molecular Cell Biology, 4, 243-249.

Boys, R. J. and Henderson, D. A. (2002). On determining the order of Markov dependence of an observed process governed by a hidden Markov model. Special Issue of Scientific Programming, 10, 241-251.

Boys, R. J. and Henderson, D. A. (2001). A comparison of reversible jump MCMC algorithms for DNA sequence segmentation using hidden Markov models. Comp. Sci. and Statist., 33, 35-49.

Boys, R. J., Henderson, D. A. and Wilkinson, D. J. (2000). Detecting homogeneous segments in DNA sequences by using hidden Markov models. Appl. Statist., 49, 269-285.

Boys, R. J., Glazebrook, K. D. and Laws, D. J. (1999). On the economic design of a sequential screen. Sequential Anal., 18, 1-21.

Boys, R. J., Glazebrook, K. D. and McCrone, C. M. (1997). Single machine scheduling when processing times are correlated normal random variables. Eur. J. Oper. Res., 102, 111-123.

Boys, R. J., Glazebrook, K. D. and Laws, D. J. (1996). A class of Bayes-optimal two-stage screens. Naval Res. Logist., 43, 1109-1125.

Boys, R. J., Glazebrook, K. D. and McCrone, C. M. (1996). A Bayesian model for the optimal ordering of a collection of screens. Biometrika, 83, 472-476.

Laws, D. J., Boys, R. J. and Glazebrook, K. D. (1996). A Bayes decision-theoretic approach to dimensionality reduction in screen design. In Bayesian Statistics 5 (Eds. J. M. Bernardo, D. V. Lindley, A. P. Dawid and A. F. M. Smith), New York: Oxford Univ. Press, pp. 653-660.

Glazebrook, K. D. and Boys, R. J. (1995). A class of Bayesian models for optimal exploration. J. Roy. Statist. Soc. Ser. B, 57, 705-720.

Boys, R. J. (1992). On a kernel approach to a screening problem. J. Roy. Statist. Soc. Ser. B, 54, 157-169.

Boys, R. J. and Glazebrook, K. D. (1992). A robust design of a screen for a binary response. Biometrika, 79, 643-650.

Glazebrook, K. D., Boys, R. J. and Fay, N. A. (1991). On the evaluation of strategies for branching bandit processes. Ann. Oper. Res., 30, 299-319.

Boys, R. J. (1989). Algorithm AS R80 - A remark on Algorithm AS76: An integral useful in calculating noncentral-t and bivariate normal probabilities. Appl. Statist., 38, 580-582.

Boys, R. J. (1989). A predictive approach to screening. In Multivariate Statistical Analysis, Calcutta: Ind. Statist. Inst., pp. 69-81.

Dunsmore, I. R. and Boys, R. J. (1988). Global v local screening. In Bayesian Statistics 3 (Eds. J. M. Bernardo, M. H. DeGroot, D. V. Lindley and A. F. M. Smith), New York: Oxford Univ. Press, pp. 593-599.

Boys, R. J. and Dunsmore, I. R. (1987). Diagnostic and sampling models in screening. Biometrika, 74, 365-374.

Dunsmore, I. R. and Boys, R. J. (1987). Predictive screening methods in binary response models. In Probability and Bayesian Statistics (Ed. R. Viertl), New York: Plenum, pp. 151-158.

Boys, R. J. and Dunsmore, I. R. (1986). Screening in a normal model. J. Roy. Statist. Soc. Ser. B, 48, 60-69.

Consultancy papers

Jennings, D. J., Boys, R. J. and Gammell, M. P. (2017). Weapon damage is associated with contest dynamics but not mating success in fallow deer (Dama dama). Biology Letters, 13, 20170565.

Jennings, D. J., Boys, R. J. and Gammell, M. P. (2016). Investigating variation in third-party intervention behavior during a fallow deer (Dama dama) rut. Behavioral Ecology, 28, 288-293.

Cameron K. M., Golightly A., Miwa S., Speakman J., Boys R. J. and von Zglinicki T. (2012). Gross energy metabolism in mice under late onset, short term caloric restriction. Mech. Ageing and Development, 132, 202-209.

Venchard, G. R., Thomson, P. J. and Boys, R. J. (2006). Improved sedation for oral surgery by combining nitrous oxide and intravenous Midazolam: a randomized, controlled trial Int. J. Oral Maxillofac. Surg., 35, 522-527.

Anumba, D. O. C., Robson, S. C., Boys, R. J. and Ford, G. A. (1999). Nitric oxide activity in the peripheral vasculature during normotensive and preeclamptic pregnancy. Amer. J. Physiol., 46, H848-H854.

Anumba, D. O. C., Ford, G. A., Boys, R. J. and Robson, S. C. (1999). Stimulated nitric oxide release and nitric oxide sensitivity in forearm arterial vasculature during normotensive and preeclamptic pregnancy. Amer. J. Obst. Gynecol., 181, 1479-1485.

Anumba, D. O. C., Ford, G. A., Boys, R. J. and Robson, S. C. (1996). The role of nitric oxide in the modulation of vascular tone in normal pregnancy. Brit. J. Obst. Gynaecol., 103, 1169-1170.

Majmudar, N. G., Anumba, D., Robson, S. C., Boys, R. and Ford, G. A. (1996). The role of nitric oxide in beta(2)-adrenoceptor-mediated vasodilatation in forearm arterial vasculature. Brit. J. Clin. Pharm., 42, P652-P653.

Skinner, J. R., Boys, R. J., Heads, A., Hey, E. N. and Hunter, S. (1996). Estimation of pulmonary arterial pressure in the newborn: Study of the repeatability of four Doppler echocardiographic techniques. Pediatr. Cardiol., 17, 360-369.

Sturgiss, S. N., Anumba, D., Ford, G., Boys, R. and Robson, S. C. (1996). The role of prostanoids in the modulation of vascular tone in normal human pregnancy. Brit. J. Obst. Gynaecol., 103, 1170.

Thomas, D. G., Robson, S. C., Redfern, N., Hughes, D. and Boys, R. J. (1996). Randomized trial of bolus phenylephrine or ephedrine for maintenance of arterial pressure during spinal anaesthesia for Caesarean section. Brit. J. Anaesth., 76, 61-65.

Thomas, L. H., McColl, E., Priest, J., Bond, S. and Boys, R. J. (1996). Newcastle satisfaction with nursing scales: An instrument for quality assessments of nursing care. Quality Health Care, 5, 67-72.

Robson, S. C., Samsoon, G., Boys, R. J., Rodeck, C. and Morgan, B. (1993). Incremental spinal anesthesia for elective Cesarean section: maternal and fetal hemodynamic effects. Brit. J. Anaesth., 70, 634-638.

Skinner, J. R., Stuart, A. G., O'Sullivan, J., Heads, A., Boys, R. J. and Hunter, S. (1993). Right heart pressure determination by Doppler in infants with tricuspid regurgitation. Arch. Dis. Child., 69, 216-220.

Chang, T. C., Robson, S. C., Boys, R. J. and Spencer, J. A. D. (1992). Prediction of the small-for-gestational-age infant: which ultrasonic measurement is best? Obstet. Gynecol., 80, 1030-1038.

Proctor, S. J., Taylor, P., MacKie, M. J., Donnan, P., Boys, R., Lennard, A., Prescott, R. J., Allan, N. C., Das, S. N., Dawson, A. A., Hepplestone, A., Leonard, R. C. F., Lucraft, H. H., MacLaren, K. S., Parker, A. C., Ritchie, G. L., Sarkar, T. K., Scott, J. S., White, J., Angus, B., Curtis, M. and McGillavray, J. B. (1992). A numerical prognostic index for clinical use in identification of poor-risk patients with Hodgkin's disease at diagnosis. Leukemia & Lymphoma, 7, 17-20.

Robson, S. C., Boys, R. J., Rodeck, C. and Morgan, B. (1992). Maternal and fetal hemodynamic effects of spinal and extradural anesthesia for elective Cesarean section. Brit. J. Anaesth., 68, 54-59.

Robson, S. C., Richley, D., Boys, R. J. and Hunter, S. (1992). Incidence of Doppler regurgitant flow velocities during normal pregnancy. Eur. Heart J., 13, 84-87.

Scott, J., Eccleston, D. and Boys, R. (1992). Can we predict the persistence of depression? Brit. J. Psych., 161, 633-637.

Skinner, J. R., Boys, R. J., Hunter, S. and Hey, E. N. (1992). Pulmonary and systemic arterial pressure in hyaline membrane disease. Arch. Dis. Child., 67, 366-373.

Boys, R. J., Forster, D. P. and Jozan, P. (1991). Mortality from causes amenable and non-amenable to medical care: the experience of Eastern Europe. Brit. Med. J., 303, 879-883.

Coleman, S. A., McCrory, J. W., Vallis, C. J. and Boys, R. J. (1991). Inhalation induction of anesthesia with Isoflurane: effect of added carbon dioxide. Brit. J. Anaesth., 67, 257-261.

Proctor, S. J., Taylor, P., Donnan, P., Boys, R., Lennard, A. and Prescott, R. J. (1991). A numerical prognostic index for clinical use in identification of poor-risk patients with Hodgkin's disease at diagnosis. Eur. J. Cancer, 27, 624-629.

Robson, S. C., Hunter, S., Boys, R. J. and Dunlop, W. (1991). Serial changes in pulmonary hemodynamics during human pregnancy: a noninvasive study using Doppler echocardiography. Clin. Sci., 80, 113-117.

Skinner, J. R., Boys, R. J., Hunter, S. and Hey, E. N. (1991). Non-invasive assessment of pulmonary arterial pressure in healthy neonates. Arch. Dis. Child., 66, 386-390.

Myhre, U., Gorey, T. F., Boys, R. J., Osborne, D. H. and Browne, H. (1990). Pre-operative nutritional assessment predicts surgical morbidity. J. Irish Coll. Phys. Surg., 19, 295-297.

Robson, S. C., Mutch, E., Boys, R. J. and Woodhouse, K. W. (1990). Apparent liver blood flow during pregnancy: a serial study using indocyanine green clearance. Brit. J. Obstet. Gynaecol., 97, 720-724.

Bateman, D. N., Darling, W. M., Boys, R. and Rawlins, M. D. (1989). Extrapyramidal reactions to metoclopramide and prochlorperazine. Quart. J. Med., 71, 307-311.

Robson, S. C., Boys, R. J., Hunter, S. and Dunlop, W. (1989). Maternal hemodynamics after normal delivery and delivery complicated by postpartum hemorrhage. Obstet. Gynecol., 74, 234-239.

Robson, S. C., Dunlop, W., Boys, R. J. and Hunter, S. (1989). Hemodynamic effects of breast-feeding. Brit. J. Obstet. Gynaecol., 96, 1106-1108.

Robson, S. C., Dunlop, W., Hunter, S., Boys, R. and Bryson, M. (1989). Hemodynamic changes associated with Cesarean section under epidural anesthesia. Brit. J. Obstet. Gynaecol., 96, 642-647.

Robson, S. C., Furniss, S. S., Heads, A., Boys, R. J., McGregor, C. and Bexton, R. S. (1989). Isometric exercise in the denervated heart: a Doppler echocardiographic study. Brit. Heart J., 61, 224-230.

Robson, S. C., Hunter, S., Boys, R. J. and Dunlop, W. (1989). Hemodynamic changes during twin pregnancy: a Doppler and M-mode echocardiographic study. Amer. J. Obstet. Gynecol., 161, 1273-1278.

Robson, S. C., Hunter, S., Boys, R. J. and Dunlop, W. (1989). Serial study of factors influencing changes in cardiac output during human pregnancy. Amer. J. Physiol., 256, H1060-H1065.

Robson, S., Hunter, S., Boys, R., Dunlop, W. and Bryson, M. (1989). Changes in cardiac output during epidural anesthesia for Cesarean section. Anaesth., 44, 475-479.

Bateman, D. N., Rawlins, M. D., Darling, W. M. and Boys, R. J. (1988). Extrapyramidal reactions to metoclopramide and prochlorperazine in general practice. Brit. J. Clin. Pharm., 26, P202.

Boys, R. J., Dunlop, W., Hunter, S. and Robson, S. C. (1988). Serial changes in maternal cardiac dimensions and function before and during normal human pregnancy. J. Physiol., 403, P84.

Robson, S. C., Boys, R. J. and Hunter, S. (1988). Doppler echocardiographic estimation of cardiac output: analysis of temporal variability. Eur. Heart J., 9, 313-318.

Robson, S. C., Furniss, S. S., Heads, A., Boys, R. J. and Bexton, R. S. (1988). Isometric exercise in the denervated human heart: a Doppler echocardiographic study. Brit. Heart J., 59, 116.

Proctor, S. J., Donnan, P. T. and Boys, R. (1987). Prognostic index for Hodgkin's disease. Scot. Med. J., 32, 63.

Robson, S. C., Boys, R. J., Dunlop, W. and Hunter, S. (1987). Haemodynamic changes during early human pregnancy: an M-mode and Doppler echocardiographic study. Brit. Heart J., 57, 584-585.

Robson, S. C., Dunlop, W., Boys, R. J. and Hunter, S. (1987). Cardiac output during labour. Brit. Med. J., 295, 1169-1172.