- Room No :
**30.35 Oxford Centre for Gene Function** - Telephone No. :
**+44 (0)1865 285 873** - E-Mail Address :
**cholmes@stats.ox.ac.uk**

My statistical research interests surround the theory, methods and applications of probabalistic data modelling and the use of subjective probability theory as a unified framework for coherent inference. This has lead me to investigate Bayesian methods, particuarly for nonlinear systems.

My main application areas are in statistical genomics and genetic epidemiology. I'm based in the Oxford Centre for Gene Function, see the link from here. I hold a Programmes Leader's award in "Statistical Genomics" from the Medical Research Council through a joint appointment with the MRC Mammalian Genetics Unit at Harwell. I am co-director of the graduate doctoral programme in Genomic Medicine and Statistics held at the Wellcome Trust Centre for Human Genetics where I am a member of the statistical genetics group. This is a four year PhD programme that combines (in the first year) formal training in genetics, genomics, experimental genetics, and statistics; after which students spend 3 years following a PhD research project in one of these fields. I am a member of the Oxford-Man Institute where I research issues in computational statistics, especially surrounding the use of Graphics Cards (GPUs) for advanced Monte Carlo methods (see links below). I serve as an (inaugural) Associate Editor for the Annals of Applied Statistics, and previously as an Associate Editor for the Annals of Statistics. From 2011 I will be serving on Council for the Royal Statistical Society and for the Board of the International Society for Bayesian Analysis (ISBA).

We have been investigating the potential of graphics cards to implement highly parallel stochastic simulation algorithms (such as MCMC and SMC). We have set up a web page as a resource for researchers in statistics and related disciplines who are interested in exploring this technology. Follow the link here.

I have recently edited a volume on Bayesian Nonparametrics with Nils Hjort, Peter Muller and Stephen Walker.

I have an older monograph, co-authored with Dave Denison, Bani Mallick and Adrian Smith, that brings together current work in the area of Bayesian approaches to nonlinear data modelling. Further details can be found here.

We co-organised organised a meeting on ``Statistical Challenges Arising from Genome Resequencing'' held at the Isaac Newton Institute for Mathematical Sciences, Cambridge, in Summer 2010.

I co-organised a workshop on Nonlinear estimation and classification which was held at the Mathmatical Science Research Institute , Berkeley, California in the Spring of 2001. The conference brought together leading researchers in statistical data modelling from the fields of computer science, statistics and engineering. A book of the proceedings should be appearing sometime in 2002. All of the talks are available as on-line video at this page (March 19-29, 2001).

- Pintore, A., Speckman, P. and Holmes, C.C. (2004)
Spatially adaptive smoothing splines.
A revised version to appear in
*Biometrika* - Pintore, A. and Holmes, C.C. (2004)
Non-stationary covariance functions via spatially adaptive spectra.
A revised version "tentatively accepted" in
*J. Amer. Statist. Assoc.* - Holmes, C.C. and Held, K. (2004)
Bayesian auxiliary variable models for binary and polychotomous regression.
A revised version to appear in
*Bayesian Analysis.* - Heard, N., Holmes, C.C. and Stephens, D. (submitted 2002)
A quantitative study of gene regulation involved in the
immune response of Anopheline Mosquuitoes: An application
of Bayesian Hierarchical Clustering of Curves. A revised version to appear in
*J. Amer. Statist. Assoc.* - Holmes, C.C. and Brown, S. (2004)
All systems GO for understanding Mouse gene function.
*Journal of Biology*. Invited review of The functional landscape of Mouse gene expression. - Kim, H-M., Mallick, B. and Holmes, C.C. (2004)
Ananlyzing nonstationary spatial data using a piecewise Gaussian process.
A revised version to appear in
*J. Amer. Statist. Assoc.* - Jasra, A., Holmes, C.C. and Stephens, D. (2004)
MCMC and the label switching problem in Bayesian Mixture Models.
A revised version to appear in
*Statistical Science.* - Holmes, C.C. and Mallick, B.K. (2003) Bayesian regression with multivariate
linear splines.
A revised version to appear in
*J. Amer. Statist. Assoc.* - Holmes, C.C. and Heard, N.A. (2003) Generalised monotonic regression using random change points.
A revised version has appeared in
*Stats. in Medicine*22, pp 623--638. - Holmes, C.C. and Adams. (2003)
Likelihood inference in nearest-neighbour classification models.
A revised version to appear in
*Biometrika.* - Holmes, C.C. and Adams. (2002)
A probabilistic nearest-neighbour algorithm for
statistical pattern recognition.
A revised version has now appeared in
*J. Roy. Statist. Soc.*Series B., vol. 64. part 2, pp 295-306. - Holmes, C.C. and Denison, D. (2002)
Pefect sampling for wavelet reconstruction of signals.
A revised version is found in
*IEEE Trans. Signal Processing.*50, pp 237--244. - Holmes, C.C. and Denison, D. (2002)
Classification with Bayesian MARS.
A revised version (including a couple of extra examples) to appear in
*Machine Learning.* - Guglielmi, A., Holmes, C.C. and Walker, S.G. (2002)
Perfect simulation involving a continuous and unbounded
state space.
A revised version to appear in
*J. Comp. Graph. Stats.* - Holmes, C.C. and Mallick, B.K. (2001) Bayesian regression with multivariate
linear splines.
A revised version has now appeared in
*J. Roy. Statist. Soc.*Series B., vol. 63, no. 1, pp 3-18. - Denison, D.G.T. and Holmes, C.C. (2001)
Bayesian partitioning for estimating
disease risk.
A revised version has now appeared in
*Biometrics*, vol. 57, no. 1, pp 143-149. - Roberts, S., Holmes, C.C. and Denison, D. (2001).
Minimum entropy data partitioning using reversible jump Markov chain Monte Carlo.
*IEEE Trans. Pattern analysis and Machine Intelligence*, vol. 23, June. - Holmes, C.C. and Mallick, B.K. (2000). Bayesian wavelet networks for nonparametric regression.
A revised version has now appeared in
*IEEE. Trans. Neural Networks*, vol. 11, no. 1, pp 27-35. - Holmes, C.C. and Denison, D.G.T. (1999). Bayesian wavelet analysis with a model complexity prior.
A revised version has now appeared in
*Bayesian Statistics 6*: Oxford University Press - Holmes, C.C. and Mallick, B.K. (1998). Bayesian radial basis functions of variable dimension.
*Neural Computation*, vol. 10, pp 1217-1233.

- Bayesian Co-clustering of Anopheles Gene Expression Time Series: A Study of Immune Defense Response To Multiple Experimental Challenges. (2005) (joint work with Nick Heard, Dave Stephens, George Dimopoulos and David Hand)
- Bayesian model order determination and basis selection for seemingly unrelated regressions. (2001) (joint work with Bani Mallick and Dave Denison)
- Bayesian partitioning for classification and regression. (2001) (joint work with Bani Mallick and Dave Denison)
- Perfect simulation for Bayesian curve and surface fitting. (2001) (joint work with Bani Mallick). This paper on "coupled Markov chains from the past" is a revised version of an older paper. Perfect simulation for orthogonal model mixing.