# Publications

**2015**

Aslett, L. J., Esperança, P. M., and Holmes, C. C. (2015a). Encrypted statistical machine learning: new privacy preserving methods. *arXiv preprint arXiv:1508.06845.*

Aslett, L. J., Esperança, P. M., and Holmes, C. C. (2015b). A review of homomorphic encryption and software tools for encrypted statistical machine learning. *arXiv preprint arXiv:1508.06574.*

Bardenet, R., Doucet, A., and Holmes, C. (2015). On Markov Chain Monte Carlo methods for tall data. *arXiv preprint arXiv:1505.02827.*

Daly, A. C., Gavaghan, D. J., Holmes, C., and Cooper, J. (2015). Hodgkin-Huxley revisited: Reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods. *Royal Society Open Science*, 2(12):150499.

de Angelis, M. H., et al. (2015). Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics. *Nature genetics*, 47(9), pp. 969-978.

Drovandi, C. C., et al. (2015). A principled experimental design approach to big data analysis.

Filippi. S., and Holmes, C. (2015). A Bayesian nonparametric approach to quantifying dependence between random variables. *arXiv preprint, arXiv:1506.00829*.

Gray-Davies, T., Holmes, C., and Caron, F. (2015). Scalable Bayesian nonparametric regression via a Plackett-Luce model for conditional ranks. *arXiv preprint, arXiv:1506.07412*.

Holmes, C. C., et al. (2015). Two-sample Bayesian nonparametric hypothesis testing. *Bayesian Analysis*, 10(2), pp. 297-320.

Rantalainen, M., Lindgren, C. M., and Holmes, C. C. (2015). Robust linear models for CIS-EQTL analysis. *PLoS One*, 10(5).

Taylor, J. C., et al. (2015). Factors influencing success of clinical genome sequencing across a broad spectrum of disorders. *Nature Genetics*.

Titsias, M. K., Holmes, C. C., Yau, C. (2015). Statistical inference in hidden Markov models using k-segment constraints. *Journal of the American Statistical Association* (just accepted).

van Stiphout, R. G., et al. (2015). Abstract b1-56: Distinct roles of copy number and loss-of-heterozygosity in predicting prognosis for breast cancer patients. *Cancer Research*, 5(22, Supplement 2), pp. B1-56.

**2014**

Bardenet, R., Doucet, A., and Holmes, C. (2014a). An adaptive subsampling approach for MCMC inference in large datasets. *Proceedings of the 31st International Conference on Machine Learning*, pp. 405-413.

Bardenet, R., Doucet, A., and Holmes, C. (2014b). Towards scaling up Markov Chain Monte Carlo: An adaptive subsampling approach. In *Proceedings of the 31st International Conference on Machine Learning* (ICML-14), pp. 405-413.

Clifford, R. M., et al. (2014). Towards response prediction using integrated genomics in chronic lymphocytic leukaemia: Results on the 250 first-line FCR treated patients from UK clinical trials. *Blood*, 124(21), p. 1942.

Knight, S. J., et al. (2014). The identification of further minimal regions of overlap in chronic lymphocytic leukemia using high-resolution SNP arrays. Blood, 124(21), p. 3315.

Pinnick, K. E., et al. (2014). Distinct developmental profile of lower-body adipose tissue defines resistance against obesity-associated metabolic complications. *Diabetes*, 63(11), pp. 3785-3797.

Taylor, A. R., et al. (2014). Estimation of malaria haplotype and genotype frequencies: A statistical approach to overcome the challenge associated with mulitclonal infections. *Malaria Journal*, 13(1), p. 102.

Watson, J., and Holmes, C. (2014). Approximate models and robust decisions. *arXiv preprint arXiv: 1402.6118*.

Watson, J., Nieto-Barajas, L., and Holmes, C. (2014). Characterising variation of nonparametric random probability measures using the Kullback-Leibler divergence. *arXiv preprint arXiv:1411.6578.*

**2013**

Becker, J., Yau, C., Hancock, J. M., and Holmes, C. C. (2013). NucleoFinder: a statistical approach for the detection of nucleosome positions. *Bioinformatics,* 29(6), pp. 711-716.

Bissiri, P., Holmes, C., and Walker, S. (2013). A general framework for updating belief distributions. *arXiv preprint arXIv :1306.6430.*

Denison, D. D., et al. (2013). *Nonlinear estimation and classification*, volume 171. Springer Science and Business Media.

Domingo, E., et al. (2013). Use of multivariate analysis to suggest a new molecular classification of colorectal cancer. *The Journal of Pathology*, 229(3), pp. 441-448.

Livak, K. J., et al. (2013). Methods for QPCR gene expression profiling applied to 1440 lymphoblastoid single cells. *Methods*, 59(1), pp. 71-79.

Mouradov, D., et al. (2013). Survival in stage II/III colorectal cancer is independently predicted by chromosomal and microsatellite instability but not by specific driver mutations. *The American Journal of Gastroenterology*, 108(11), pp. 1785-1793.

Palles, C., et al. (2013). Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. *Nature Genetics*, 45(2), pp. 136-144.

Taylor, A., et al. (2013). Statistical estimation of malaria genotype frequencies: A Bayesian approach. *Tropical Medicine and International Health*, 18, p. 67.

Wang, W., et al. (2013). Integrative network-based Bayesian analysis of diverse genomics data. *BMC Bioinformatics*, 14(Supplement 13): S8.

Wills, Q. F., et al. (2013). Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments. *Nature Biotechnology* 31(8), pp. 748-752.

Yau, C., and Holmes, C. C. (2013). A decision-theoretic approach for segmental classification. *Annals of Applied Statistics*, 7(3), pp. 1814-1835.

**2012**

Caron, F., Holmes, C., and Rio, E. (2012). On the sampling of distribution of an *l ^{2}* distance between empirical distribution functions with applications to nonparametric testing.

Cazier, J-B., Holmes, C. C., and Broxholme, J. (2012). GREVE: Genomic recurrent event viewer to assist the identification of patterns across individual cancer samples.

*Bioinformatics,*28(22), pp. 2981-2982.

Chittenden, T. W., et al. (2012). Nease: a method for gene ontology sub-classification of high throughput gene expression data.

*Bioinformatics*, 28(5), pp. 726-728.

Davies, J. L., et al. (2012). A novel test for gene-ancestry Interactions in genome-wide association data.

*PLoS One*, 7(12):e48687.

Knight, S., et al. (2012). Quantification of subclonal distributions of recurrent genomic aberrations in paired pre-treatment and relapse samples from patients with B-cell chronic lymphocytic leukemia.

*Leukemia*, 26(7).

Lee, A., Caron, F., Doucet, A., and Holmes, C. (2012). Bayesian sparsity-path-analysis of genetic association signal using generalized t priors.

*Statistical Applications in Genetics and Molecular Biology*, 11(2).

Min, J. L., et al. (2012). Coexpression network analysis in abdominal and gluteal adipose tissue reveals regulatory genetic loci for metabolic syndrome and related phenotypes.

*PLoS Genetics*, 8(2):e1002505.

Palle, C., et al. (2012). Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas. Nature Genetics doi:10.1038/mg.2503.

Rantalainen, M., and Holmes, C. (2012). Robust statistical methods for genome-wide EQTL analysis.

*Genetic Epidemiology*, 36, p. 140.

Taylor, A. R., et al. (2012). A Bayesian model for estimating with-in host p. falciparum haplotype frequencies.

*Malaria Journal*, 11(supp 1), p.36.

Valdar, W., Sabourin, J., Nobel, A., and Holmes, C. C. (2012). Reprioritizing genetic associations in hit regions using lasso-based resample model averaging.

*Genetic Epidemiology*, 36(5), pp. 451-462

**2011**

Cardin, N., Holmes, C., Donnelly, P., Marchini, J., and the Wellcome Trust Case Control Consortium. (2011). Bayesian hierarchical mixture modelling to assign copy number from a targeted CNV array. *Genetic Epidemiology*, 35(6), pp. 536-548.

Ciampa, J., et al. (2011). Application of novel score test for genetic association incorporating gene-gene interaction suggests functionality for prostate cancer susceptibility regions. *Human Heredity*, 72(3), pp. 182–193.

Drong, A., et al. (2011). The presence of methylation quantitative trait loci indicate a direct genetic influence on the level of methylation in adipose tissue. *Diabetologia*, 54, pp. S163-S164.

Holmes, C., and Held, L. (2011). Response to van de Lans. *Bayesian Analysis,* 6(2), pp. 357-358.

Holmes, C., (2011). Invited Discussion of *Regression shrinkage and selection via the lasso: a retrospective* by Robert Tibshirani. *Journal of the Royal Statistical Society B* 73, Part 3, pp. 273-282.

Jasra, A., and Holmes, C. (2011). Stochastic boosting algorithms. *Statistics and Computing*, 21(3), pp. 335-347.

Kato, B., et al. (2011). Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model. *Proteome Science*, 9, p. 73.

Nicholson, G., et al. (2011a). A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. *PLoS Genetics*, 7(9):e1002270.

Nicholson, G., et al. (2011b). Human metabolic profiles are stably controlled by genetic and environmental variation. *Molecular Systems Biology*, 7(1), p. 525.

Rantalainen, M., et al. (2011). MicroRNA expression in abdominal and gluteal adipose tissue is associated with mRNA expression levels and partly genetically driven. *PLos ONE*, 6(11):e27338.

Rantalainen, M., and Holmes, C. (2011). Accounting for control mislabeling in case-control biomarker studies. *Journal of Proteome Research*, 10(12), pp. 5562-5567.

Yau, C., and Holmes, C. (2011). Hierarchical Bayesian nonparametric mixture models for clustering with variable relevance determination. *Bayesian Analysis* (Online), 6(2), pp. 329-352.

Yau, C., Papaspiliopoulos, O., Roberts, G. O., and Holmes, C. (2011). Bayesian non-parametric hidden Markov models with applications in genomics. *Journal of the Royal Statistical Society*, Series B, 73(1), pp. 33-57.

**2010**

Agam, A., et al. (2010). Elusive copy number variation in the mouse genome. *PLoS ONE*, 5(9):e12839.

Chittenden, T., et al. (2010). Therapeutic implications of GIPC1 silencing in cancer. *PloS ONE*, 5(12):e15581.

Clark, T., et al. (2010). A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals. *Bioinformatics*, 26(16), pp. 1999-2003.

Davies, J. L., Hein, J., and Holmes, C. C. (2010). Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unknown. *Genetic Epidemiology*, 34(4), pp. 299-308.

Griffin, J., and Holmes, C. (2010). Computational issues arising in Bayesian nonparametric hierarchical models. *Bayesian Nonparametrics*, 28: p. 208.

Heid, I., et al. (2010). Meta-analysis identifies 13 new loci associated with waist-hip ratio and reveals sexual dimorphism in the genetic basis of fat distribution. *Nature Genetics*, 42(11), pp. 949-960.

Hjort, N. L., Holmes, C., Müller, P., and Walker, S. G. (2010a). *Bayesian non-parametrics*, volume 28, Cambridge University Press.

Hjort, N. L., Holmes, C., Müller, P., and Walker, S. G. (2010b). An invitation to Bayesian nonparametrics. *Bayesian Nonparametrics*, 28, p.1.

Lee, A., Caron, F., Doucet, A., and Holmes, C. (2010a). A hierarchical Bayesian framework for constructing sparsity-inducing priors. arXiv preprint arXiv:1009.1914.

Lee, A., Yau, C., Giles, M. B., Doucet, A., and Holmes, C. (2010b). On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. *Journal of Computational and Graphical Statistics*, 19(4), pp. 769-789.

Rantalainen, A., et al. (2010). Microribonucleic acid expression profiling and expression quantitative trait loci analysis in human gluteal abdominal adipose tissue. *Diabetologia*, 53.

Suchard, M. A., Holmes, C., and West, M. (2010). Some of the what?, why?, how?, who? and where? of graphics processing unit computing for Bayesian analysis. *Bulletin of the International Society for Bayesian Analysis*, 17, pp. 12-16.

Timbs, A., et al. (2010). Quantitative whole genome analysis of sequential samples from patients with b-cell identifies novel recurrent copy number alterations involving critical b-cell transcription factors. *Blood*, 116, p. 1478.

Wellcome Trust Case Consortium, Craddock, N., et al. (2010). Genome-wide association study of CNVs in 16,000 cases of eight common diseases and 3,000 shared controls. *Nature*, 464(7289), pp. 713-720.

Yau, C., Holmes, C. C. (2010). A decision theoretic approach for segmental classification using hidden Markov models. ArXiv preprint ArXiv:1007.4532.

Yau, C., et al. (2010). A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. *Genome Biology*, 11(9):R92.

**2009**

Anjum, S., Doucet, A., and Holmes, C. (2009). A boosting approach to structure learning of graphs with and without prior knowledge. *Bioinformatics*, 25(22), pp. 2929-2936.

Antonyuk, A., and Holmes, C. (2009). On testing for genetic association in case-control studies when population allele frequencies are known. *Genetic Epidemiology*, 33(5), pp. 371-378.

Feller, A., and Holmes, C. (2009). Beyond toplines: Heterogeneous treatment effects in randomized experiements. Unpublished manuscript, University of Oxford.

Holmes, C., and Jasra A. (2009). Antithetic methods for Gibbs samplers. *Journal of Computational and Graphical Statistics*, 18(2), pp. 401-414.

Holmes, C. C., Caron, F., Griffin, J. E., and Stephens, D. A. (2009). Two-sample Bayesian nonparametric hypothesis testing. arXiv preprint arXiv:0910.5060.

Klingelhoefer, J. W., Moutsianas, L., and Holmes, C. (2009). Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency. *Bioinformatics*, 25(13), pp. 1594-1601.

Lemieux, J. E., Feller, A., Holmes, C. C., and Newbold, C. I. (2009a). Reply to Wirth et al.: In viro profiles show continuous variation between 2 cellular populations. *Proceedings of the National Academy of Sciences*, 106(27): E71-E72.

Lemieux, J., et al. (2009b). Statistical estimation of cell-cycle progression and lineage commitment in plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture. Proceedings of the National Academy of Sciences, 106(18), pp. 7559-7564.

Mackenzie, F., et al. (2009). Analysis of the mouse mutant cloth-ears shows a role for the voltage-gated sodium channel Scn8a in peripheral neural hearing loss. *Genes, Brain and Behaviour*, 8(7), pp. 699-713.

Valdar, W., Holmes, C., Mott, R., and Flint, J. (2009). Mapping in structured populations by resample model averaging. *Genetics*, 182(4), pp. 1263-1277.

Webb, A., Hancock, J. M., and Holmes, C. C. (2009). Phylogenetic inference under recombination using Bayesian stochastic topology selection. *Bioinformatics*, 25(2), pp. 197-203.

**2008**

Chittenden, T. W., et al. (2008). Functional classification analysis of somatically mutated genes in human breast and colorectal cancers. *Genomics*, 91(6), pp.508-511.

Giannoulatou, E., Yau, C., Colella, S., Ragoussis, J., and Holmes, C. (2008). GenoSNP: a variational Bayes within-sample SNP genotyping algorithm that does not require a reference population. *Bioinformatics*, 24(19), pp. 2209-2214.

Jasra, J., Doucet, A., Stephens, D., and Holmes, C. (2008). Interacting sequential Monte Carlo samplers for trans-dimensional simulation. *Computational Statstics and Data Analysis*, 52(4), pp. 1765-1791.

Ramasamy, A., Mondry, A., Holmes, C., and Altman, D. G. (2008). Key issues in conducting a meta-analysis of gene expression microarray datasets. *PLos Med*, 5(9):e184.

Yau, C., and Holmes, C. (2008). CNV discovery using SNP genotyping arrays. *Cytogenetic and Genome Research*, 123(1-4), pp. 307-312.

**2007**

Colella, S., et al. (2007). QuantiSNP: an objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. *Nucleic Acids Research*, 35(6), pp. 2013-2025.

Dellaportas, P., Dennison, D. G., and Holmes, C. (2007). Flexible threshold models for modelling interest rate volatility. *Econometric Reviews*: Special Issue on Bayesian Dynamic Econometrics. 26(2-4), pp. 419-437.

Gallagher, K., Stephenson, J., Brown, R., and Holmes, C. (2007). Integrating 3D information from thermochronological data over unknown spatial scales. *Geophysical Research Abstracts*, 9:09015.

Griffin, J., and Holmes, C. (2007). Bayesian nonparametric calibration with applications in spatial epidemiology. Technical Report, *Institute of Mathematics, Statistics and Actuarial Science*, University of Kent.

Holmes, C. C., and Pintore, A. (2007). Bayesian Statistics 8, pp. 253-282. Bernardo, J. M., et al. (eds.), Oxford University Press. Bayesian Statistics 8: *Proceedings of the Eighth Valencia International Meeting, 2-6 June*. (2006), 8:253.

Jasra, A., Stephens, D., and Holmes, C. (2007). Population-based reversible jump Markov Chain Monte Carlo. *Biometrika*, 94(4), pp. 787-807.

Jasra, A., Stephens, D., and Holmes, C. (2007). On population based simulation for static inference. *Statistics and Computing*, 17(3), pp. 263-279.

**2006**

Baladandayuthapani, V., Holmes, C., Mallick, B., and Carroll, R. (2006a). Modeling nonlinear gene interactions using Bayesian MARS. *Bayesian Inference for Gene Expression and Proteomics*, Cambridge University Press.

Baladandayuthapani, V., Holmes, C., Mallick, B., and Carroll, R. (2006b). Bayesian Inference for Gene Expression and Proteomics: Modeling nonlinear gene interactions using Bayesian MARS.

De Wet, H., et al. (2006). Modulation of the BK channel by estrogens: examination at single channel level. *Molecular Membrane Biology*, 23(5), pp. 420-429.

Gallagher, K., Jasra, A., Stephens, D., and Holmes, C. (2006a). A new approach to mixture modelling for geochronology. *Geochimica et Cosmochimica Acta*, 70(18):A190.

Gallagher, K., Stephenson, J., Holmes, C., and Brown, R. (2006b). Putting the data to work strategies for modelling multiple samples in multiple dimensions. *Geochimica et Cosmochimica Acta*, 70(18):A190.

Heard, N., Holmes, C., and Stephens, D. (2006). A quantitative study of gene regulation involved in the immune response of anopheline mosquitoes: An application of Bayesian hierarchical clustering of curves. *Journal of the American Statistical Association*, 101(473), pp.18-29.

Holmes, C. C., and Held, L. (2006). Bayesian auxiliary variable models for binary and multinominal regression. *Bayesian Analysis*, 1(1), pp. 145-168.

Jasra, A., Stephens, D. A., Gallagher, K., and Holmes, C. (2006a). Analysis of geochronological data with measurement error using Bayesian mixtures. *Mathematical Geology*, 38, pp. 269-300.

Jasra, A., Stephens, D., Gallagher, K., and Holmes, C. (2006b). Bayesian mixture modelling in geochronology via Markov chain Monte Carlo. *Mathematical Geology*, 38(3), pp. 269-300.

Pintore, A., and Holmes, C. (2006). Non-stationary covariance functions via spatially adaptive spectra. *Journal of the American Statistical Association*.

Pintore, A., Speckman, P., and Holmes, C. (2006). Spatially adaptive smoothing splines. *Biometrika*, 93(1), pp. 113-125.

Stephenson, J., Gallagher, K., and Holmes, C. (2006a). A Bayesian approach to calibrating apatite fission track annealing models for laboratory and geological timescales. *Geochimica et Cosmochimica Acta*, 70(20), pp.5183-5200.

Stephenson, J., Gallagher, K., and Holmes, C. (2006b). Low temperature thermochronology and strategies for multiple samples 2: Partition modelling for 2D/3D distributions with discontinuities. *Earth and Planetary Science Letters*, 241(3), pp. 557- 570.

**2005**

Gallagher, K., Stephenson, J., Brown, R., Holmes, C., and Ballester, P. (2005). Exploiting 3D spatial sampling in inverse modeling of thermochronological data. *Reviews in Mineralogy and Geochemistry*, 58(1), pp. 375-387.

Gallagher, K., Stephenson, J., Brown, R., Holmes, C., and Fitzgerald, P. (2005b). Low temperature thermochronology and modeling strategies for multiple samples 1: Vertical profiles. Earth and Planetary Science Letters, 237(1), pp. 193-208.

Heard, N. A., Holmes, C., Stephens, D. A., Hand, D. J., and Dimopoulos, G. (2005). Bayesian co-clustering of anopheles gene expression time series: A study of immune defense response to multiple experimental challenges. *Proceedings of the National Academy of Science USA*, 102(47), pp. 16939-16944.

Holmes, C., and Brown, S. (2005). All systems GO for understanding mouse gene function. *The Scientist*, 19(1), pp. 20-21.

Holmes, C., and Held, K. (2005), Bayesian auxiliary variable models for binary and polychotomous regression. *Bayesian Analysis*, 1(1), pp. 145-168.

Holmes, C., Denison, D., Ray, S., and Mallick, B. K. (2005). Bayesian prediction via partitioning. *Journal of Computational and Graphical Statistics*, 14(4), pp. 811-830.

Jasra, A., Holmes, C., and Stephens, D. (2005). Markov Chain Monte Carlo methods and the label switching problem in Bayesian mixture modeling. *Statistical Science*, 20(1), pp. 50-67.

Kim, H.-M., Mallick, B., and Holmes, C. (2005). Analyzing nonstationary spatial data using a piecewise Gaussian process. *Journal of the American Statistical Association*, 100(470), pp. 653-658.

Pintore, A., Holmes, C. (2005). A dimension-reduction approach for spectral tempering using empirical orthogonal functions. *Geostatistics Banff 2004*, Springer, Netherlands, pp. 1007-1015.

Stephenson, J., Holmes, C., Gallagher, K., and Pintore, A. (2005). A statistical technique for modelling non-stationary spatial processes. *Geostatistics Banff 2004*, pp. 125-134.

**2004**

Holmes, C., and Brown, S. (2004). All systems GO for understanding mouse gene function. Invited discussion in *Journal of Biology*, 3(5), p. 20.

Pintore, A., and Holmes, C. (2004). Spatially adaptive non-stationary covariance functions via spatially adaptive spectra.

Stephenson, J., Gallagher, K., and Holmes, C. (2004). Beyong Kringing: Dealing with discontinuous spatial data fields using adaptive prior information and Bayesian partition modelling. *Geological Society*, London, Special Publications, 239(1), pp. 195-209.

**2003**

Denison, D., Hansen, M., Holmes, C., Mallick, B., and Yu, B. (2003). Introduction. In *Nonlinear Estimation and Classification,* pp. 1-5. Springer, New York.

Holmes, C., and Adams, N. M. (2003). Likelihood based inference in nearest-neighbor classification models. *Biometrika*, 90(1), pp. 99-112.

Holmes, C., Denison, D. (2003). Classification with Bayesian MARS. *Machine Learning*, 50(1-2), pp. 159-173.

Holmes, C., and Heard, N. (2003). Generalised monotonic regression using random change points. *Statistics in Medicine*, 22(4), pp. 623-638.

Holmes, C., and Held, L. (2003). On the simulation of Bayesian binary and polychotomous regression models using auxiliary variables. Technical report.

Holmes, C., and Knorr-Held, L. (2003). Efficient simulation of Bayesian logistic regression models. Technical report, *Discussion papers/Sonderforschungsbereich* 386, der Ludwig-Maximilians-Universität, München.

Holmes, C., and Mallick, B. K. (2003). Generalised nonlinear modelling with multivariate free-knot regression splines. *Journal of the American Statistical Association*, 98(462), pp. 352-368.

**2002**

Denison, D., Adams, N., Holmes, C., and Hand, D. (2002). Bayesian partitioning modelling. Computational Statististics and Data Analysis, 38(4), pp. 475-485.

Denison, D. G., Holmes, C., Mallick, B., and Smith, A. (2002). *Bayesian methods for nonlinear classification and regression*, volume 386. John Wiley and Sons.

Ferreira, J., Denison, D., and Holmes, C. (2002). Partition modelling.

Guglielmi, A., Holmes, C., and Walker, S. (2002). Perfect simulation involving functionals of a dirichlet process. *Journal of Computational and Graphical Statistics*, 11(2), pp. 306-310.

Holmes, C. (2002). Comment-spline adaptation in extended linear models. *Statistical Science*, 17(1), pp. 22-23.

Holmes, C. (2002). Probabilistic free-knots splines. Invited discussant on gSpline adaptation in extended linear models'', by Hansen, M H and Kooperberg C, *Statistical Science*, 17, pp. 1-51.

Holmes, C., and Adams, N. A. (2002). A probabilistic nearest-neighbor method for statistical pattern recognition. *Journal of the Royal Statistical Society, Series B*, 64(2), pp. 295-306.

Holmes, C., Denison, D., and Mallick, B. K. (2002a). Bayesian model order determination and basis selection for seemingly unrelated regressions. *Journal of Computational and Graphical Statistics*, 11, pp. 533-551.

Holmes, C., Denison, D., and Mallick, B. K. (2002b). Accounting for model uncertainty in seemingly unrelated regressions. *Journal of Computational and Graphical Statisitics*, 11(3), pp. 533-551.

Holmes, C., and Denison, D. (2002). A Bayesian multivariate adaptive regression spline classifier. *Machine Learning*, 50(1-2), pp. 159-173.

Holmes, C., and Denison, D. G. (2002). Perfect sampling for the wavelet reconstruction of signals. *IEEE Transactions on Signal Processing*, 50(2), pp. 337-344.

**2001**

Denison, D., and Holmes, C. (2001). Bayesian partitioning for estimating disease risk. *Biometrics*, 57(1), pp. 143-149.

Holmes, C., and Mallick, B. K. (2001). Bayesian regression with multivariate linear splines. *Journal of the Royal Statistical Society, Series B*, 63(1), pp. 3-17.

Roberts, S., Holmes, C., and Denison, D. (2001). Minimum-entropy data partitioning using reversible jump Markov Chain Monte Carlo. *IEEE Transactions on Pattern Analysis and Machine Intelligence*, 23(8), pp. 909-914.

**2000**

Holmes, C., and Mallick, B. K. (2000). Bayesian wavelet networks for nonparametric regression.

*IEEE Transactions on Neural Networks*, 11(1), pp. 27-35.

**1999**

Gugliemi, A., Holmes, C., and Walker, S. (1999). Perfect simulation involving a continuous and unbounded state space. Preprint.

Holmes, C., and Denison, D. (1999). Bayesian wavelet analysis with a model complexity prior. *Bayesian Statistics 6*, pp. 972-978.

Holmes, C., Denison, D., and Mallick, B. (1999). Bayesian partitioning for classification and regression. Manuscipt, Imperial College, London.

Holmes, C., and Mallick, B. (1999a). Generalised nonlinear modelling with multivariate smoothing splines. Unpublished manuscript, Statistics Section, Department of Mathematics, Imperial College, London.

Holmes, C., and Mallick, B. (1999b). Perfect simulation for Bayesian curve and surface fitting. Technical Report, Imperial College, London.

**1998**

Holmes, C., and Mallick, B. K. (1998a). Bayesian radial basis functions of variable dimension. *Neural Computation*, 10(5), pp. 1217-1233.

Holmes, C., and Mallick, B. (1998b). Parallel Markov Chain Monte Carlo sampling: An evolutionary based approach. Imperial College, London.

Holmes, C., and Mallick, B. (1998c). Perfect simulation for orthogonal model mixing. Department of Mathematics, Technical Report, Imperial College, London.

Webster, R., et al. (1998). Model-based geostatistics discussion.

**1997**

Holmes, C., and Mallick, B. (1997). Bayesian radical basis functions of unknown dimension. Imperial College Report.