OxCSML : People : Chris Holmes

I am Professor of Biostatistics and MRC Programme Leader in Statistical Genomics. I hold a joint appointment in the Department of Statistics and the Nuffield Department of Medicine, University of Oxford. I am a Faculty Fellow of the Alan Turing Institute. I have broad research interests in the theory, methods, and applications of decision analysis, probabilistic modelling, and statistical machine learning in medical research.

Publications

2020

E. Fong , C. Holmes , On the marginal likelihood and cross-validation, Biometrika, vol. 107, no. 2, 489–496, 2020.

@article{Fong2020,
  title = {On the marginal likelihood and cross-validation},
  author = {Fong, Edwin and Holmes, CC},
  journal = {Biometrika},
  volume = {107},
  number = {2},
  pages = {489--496},
  year = {2020},
  publisher = {Oxford University Press}
}

2017

J. Watson , L. Nieto-Barajas , C. C. Holmes , Characterizing variation of nonparametric random probability measures using the Kullback–Leibler divergence, Statistics, vol. 51, no. 3, 558–571, 2017.

@article{watson2017characterizing,
  title = {Characterizing variation of nonparametric random probability measures using the Kullback--Leibler divergence},
  author = {Watson, James and Nieto-Barajas, Luis and Holmes, Chris C.},
  journal = {Statistics},
  volume = {51},
  number = {3},
  pages = {558--571},
  year = {2017},
  publisher = {Taylor \& Francis}
}

S. Filippi , C. C. Holmes , . others , A Bayesian nonparametric approach to testing for dependence between random variables, Bayesian Analysis, 2017.

@article{filippi2017bayesian,
  title = {A Bayesian nonparametric approach to testing for dependence between random variables},
  author = {Filippi, Sarah and Holmes, Chris C and others},
  journal = {Bayesian Analysis},
  year = {2017},
  publisher = {International Society for Bayesian Analysis}
}

A. R. Taylor , J. A. Flegg , C. C. Holmes , P. J. Guérin , C. H. Sibley , M. D. Conrad , G. Dorsey , P. J. Rosenthal , Artemether-Lumefantrine and Dihydroartemisinin-Piperaquine Exert Inverse Selective Pressure on Plasmodium Falciparum Drug Sensitivity-Associated Haplotypes in Uganda, in Open forum infectious diseases, 2017, vol. 4, no. 1.

@inproceedings{taylor2017artemether,
  title = {Artemether-Lumefantrine and Dihydroartemisinin-Piperaquine Exert Inverse Selective Pressure on Plasmodium Falciparum Drug Sensitivity-Associated Haplotypes in Uganda},
  author = {Taylor, Aimee R and Flegg, Jennifer A and Holmes, Chris C and Gu{\'e}rin, Philippe J and Sibley, Carol H and Conrad, Melissa D and Dorsey, Grant and Rosenthal, Philip J},
  booktitle = {Open forum infectious diseases},
  volume = {4},
  number = {1},
  year = {2017},
  organization = {Oxford University Press}
}

G. Nicholson , C. C. Holmes , A note on statistical repeatability and study design for high-throughput assays, Statistics in medicine, vol. 36, no. 5, 790–798, 2017.

@article{nicholson2017note,
  title = {A note on statistical repeatability and study design for high-throughput assays},
  author = {Nicholson, George and Holmes, Chris C.},
  journal = {Statistics in medicine},
  volume = {36},
  number = {5},
  pages = {790--798},
  year = {2017},
  publisher = {John Wiley \& Sons, Ltd}
}

C. Holmes , S. Walker , Assigning a value to a power likelihood in a general Bayesian model, Biometrika, vol. 104, no. 2, 497–503, 2017.

@article{holmes2017assigning,
  title = {Assigning a value to a power likelihood in a general Bayesian model},
  author = {Holmes, CC and Walker, SG},
  journal = {Biometrika},
  volume = {104},
  number = {2},
  pages = {497--503},
  year = {2017},
  publisher = {Oxford University Press}
}

T. Rukat , C. C. Holmes , M. K. Titsias , C. Yau , Bayesian Boolean Matrix Factorisation, arXiv preprint arXiv:1702.06166, 2017.

@article{rukat2017bayesian,
  title = {Bayesian Boolean Matrix Factorisation},
  author = {Rukat, Tammo and Holmes, Chris C and Titsias, Michalis K and Yau, Christopher},
  journal = {arXiv preprint arXiv:1702.06166},
  year = {2017}
}

C. C. Drovandi , C. C. Holmes , J. McGree , K. Mengersen , S. Richardson , E. Ryan , Principles of experimental design for Big Data analysis, Statistical Science, 2017.

@article{drovandi2017principles,
  title = {Principles of experimental design for Big Data analysis},
  author = {Drovandi, Christopher C and Holmes, Chris C and McGree, James and Mengersen, Kerrie and Richardson, Sylvia and Ryan, Elizabeth},
  journal = {Statistical Science},
  year = {2017},
  publisher = {Institute of Mathematical Statistics}
}

I. Roxanis , R. Colling , E. A. Rakha , A. Green , J. Rittscher , R. C. Conceicao , A. Ross , G. Nicholson , C. C. Holmes , Digital Analysis of Tumour Microarchitecture as an Independent Prognostic Tool in Breast Cancer, in LABORATORY INVESTIGATION, 2017, vol. 97, 68A–68A.

@inproceedings{roxanis2017digital,
  title = {Digital Analysis of Tumour Microarchitecture as an Independent Prognostic Tool in Breast Cancer},
  author = {Roxanis, Ioannis and Colling, Richard and Rakha, Emad A and Green, Andrew and Rittscher, Jens and Conceicao, Raquel C and Ross, Aidan and Nicholson, George and Holmes, Chris C.},
  booktitle = {LABORATORY INVESTIGATION},
  volume = {97},
  pages = {68A--68A},
  year = {2017},
  organization = {NATURE PUBLISHING GROUP 75 VARICK ST, 9TH FLR, NEW YORK, NY 10013-1917 USA}
}

A. Doucet , C. Holmes , R. Bardenet , On Markov chain Monte Carlo Methods for Tall Data, 2017.

@article{doucet2017markov,
  title = {On Markov chain Monte Carlo Methods for Tall Data},
  author = {Doucet, A and Holmes, CC and Bardenet, R},
  year = {2017}
}

T. Rukat , C. C. Holmes , M. K. Titsias , C. Yau , Bayesian Boolean Matrix Factorisation, 2017.
Boolean matrix factorisation aims to decompose a binary data matrix into an approximate Boolean product of two low rank, binary matrices: one containing meaningful patterns, the other quantifying how the observations can be expressed as a combination of these patterns. We introduce the OrMachine, a probabilistic generative model for Boolean matrix factorisation and derive a Metropolised Gibbs sampler that facilitates efficient parallel posterior inference. On real world and simulated data, our method outperforms all currently existing approaches for Boolean matrix factorisation and completion. This is the first method to provide full posterior inference for Boolean Matrix factorisation which is relevant in applications, e.g. for controlling false positive rates in collaborative filtering and, crucially, improves the interpretability of the inferred patterns. The proposed algorithm scales to large datasets as we demonstrate by analysing single cell gene expression data in 1.3 million mouse brain cells across 11 thousand genes on commodity hardware.
```
@article{rukat2017_bayes-boolean,
  title = {Bayesian Boolean Matrix Factorisation},
  author = {Rukat, Tammo and Holmes, Chris C. and Titsias, Michalis K. and Yau, Christopher},
  archiveprefix = {arXiv},
  year = {2017},
  eprint = {1702.06166},
  primaryclass = {stat.ML}
}
```

2016

S. Filippi , C. C. Holmes , L. E. Nieto-Barajas , Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures, Electronic Journal of Statistics, 2016.

@article{Filippi:2016kg,
  author = {Filippi, Sarah and Holmes, Chris C and Nieto-Barajas, Luis E.},
  title = {{Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures}},
  journal = {Electronic Journal of Statistics},
  year = {2016}
}

P. G. Bissiri , C. Holmes , S. G. Walker , A general framework for updating belief distributions, Journal of the Royal Statistical Society: Series B (Statistical Methodology), 2016.

@article{bissiri2016general,
  title = {A general framework for updating belief distributions},
  author = {Bissiri, Pier Giovanni and Holmes, CC and Walker, Stephen G},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2016}
}

M. K. Titsias , C. C. Holmes , C. Yau , Statistical inference in hidden Markov models using k-segment constraints, Journal of the American Statistical Association, vol. 111, no. 513, 200–215, 2016.

@article{titsias2016statistical,
  title = {Statistical inference in hidden Markov models using k-segment constraints},
  author = {Titsias, Michalis K and Holmes, Chris C and Yau, Christopher},
  journal = {Journal of the American Statistical Association},
  volume = {111},
  number = {513},
  pages = {200--215},
  year = {2016},
  publisher = {Taylor \& Francis}
}

J. Watson , C. C. Holmes , . others , Approximate models and robust decisions, Statistical Science, vol. 31, no. 4, 465–489, 2016.

@article{watson2016approximate,
  title = {Approximate models and robust decisions},
  author = {Watson, James and Holmes, Chris C. and others},
  journal = {Statistical Science},
  volume = {31},
  number = {4},
  pages = {465--489},
  year = {2016},
  publisher = {Institute of Mathematical Statistics}
}

T. Gray-Davies , C. C. Holmes , F. Caron , . others , Scalable Bayesian nonparametric regression via a Plackett-Luce model for conditional ranks, Electronic Journal of Statistics, vol. 10, no. 2, 1807–1828, 2016.

@article{gray2016scalable,
  title = {Scalable Bayesian nonparametric regression via a Plackett-Luce model for conditional ranks},
  author = {Gray-Davies, Tristan and Holmes, Chris C and Caron, Fran{\c{c}}ois and others},
  journal = {Electronic Journal of Statistics},
  volume = {10},
  number = {2},
  pages = {1807--1828},
  year = {2016},
  publisher = {The Institute of Mathematical Statistics and the Bernoulli Society}
}

S. Filippi , C. C. Holmes , L. E. Nieto-Barajas , . others , Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures, Electronic Journal of Statistics, vol. 10, no. 2, 3338–3354, 2016.

@article{filippi2016scalable,
  title = {Scalable Bayesian nonparametric measures for exploring pairwise dependence via Dirichlet Process Mixtures},
  author = {Filippi, Sarah and Holmes, Chris C and Nieto-Barajas, Luis E and others},
  journal = {Electronic Journal of Statistics},
  volume = {10},
  number = {2},
  pages = {3338--3354},
  year = {2016},
  publisher = {The Institute of Mathematical Statistics and the Bernoulli Society}
}

Z. Wang , J. S. Morris , C. C. Holmes , J. Ahn , B. Li , W. Lu , X. Tang , I. I. Wistuba , W. Wang , Cell type-specific deconvolution of heterogeneous tumor samples with immune infiltration using expression data. American Association for Cancer Research, 2016.

@misc{wang2016cell,
  title = {Cell type-specific deconvolution of heterogeneous tumor samples with immune infiltration using expression data},
  author = {Wang, Zeya and Morris, Jeffrey S and Holmes, Chris C and Ahn, Jaeil and Li, Bo and Lu, Wei and Tang, Ximing and Wistuba, Ignacio I and Wang, Wenyi},
  year = {2016},
  publisher = {American Association for Cancer Research}
}

M. Behr , C. C. Holmes , A. Munk , Multiscale Blind Source Separation, arXiv preprint arXiv:1608.07173, 2016.

@article{behr2016multiscale,
  title = {Multiscale Blind Source Separation},
  author = {Behr, Merle and Holmes, Chris C. and Munk, Axel},
  journal = {arXiv preprint arXiv:1608.07173},
  year = {2016}
}

J. Watson , C. C. Holmes , . others , Rejoinder: Approximate Models and Robust Decisions, Statistical Science, vol. 31, no. 4, 516–520, 2016.

@article{watson2016rejoinder,
  title = {Rejoinder: Approximate Models and Robust Decisions},
  author = {Watson, James and Holmes, Chris C. and others},
  journal = {Statistical Science},
  volume = {31},
  number = {4},
  pages = {516--520},
  year = {2016},
  publisher = {Institute of Mathematical Statistics}
}

2015

C. C. Holmes , F. Caron , J. E. Griffin , D. A. Stephens , Two-sample Bayesian nonparametric hypothesis testing, Bayesian Analysis, vol. 10, no. 2, 297–320, 2015.

@article{Holmes2015,
  title = {Two-sample Bayesian nonparametric hypothesis testing},
  author = {Holmes, C. C. and Caron, F. and Griffin, J. E. and Stephens, D. A.},
  journal = {Bayesian Analysis},
  year = {2015},
  number = {2},
  pages = {297--320},
  volume = {10},
  file = {1422884976:https\://projecteuclid.org/download/pdfview_1/euclid.ba/1422884976:PDF},
  publisher = {International Society for Bayesian Analysis}
}

C. C. Holmes , F. Caron , J. E. Griffin , D. A. Stephens , . others , Two-sample Bayesian nonparametric hypothesis testing, Bayesian Analysis, vol. 10, no. 2, 297–320, 2015.

@article{holmes2015two,
  title = {Two-sample Bayesian nonparametric hypothesis testing},
  author = {Holmes, Chris C and Caron, Fran{\c{c}}ois and Griffin, Jim E and Stephens, David A and others},
  journal = {Bayesian Analysis},
  volume = {10},
  number = {2},
  pages = {297--320},
  year = {2015},
  publisher = {International Society for Bayesian Analysis}
}

R. Bardenet , A. Doucet , C. C. Holmes , On Markov chain Monte Carlo methods for tall data, arXiv preprint arXiv:1505.02827, 2015.

@article{bardenet2015markov,
  title = {On Markov chain Monte Carlo methods for tall data},
  author = {Bardenet, R{\'e}mi and Doucet, Arnaud and Holmes, Chris C.},
  journal = {arXiv preprint arXiv:1505.02827},
  year = {2015}
}

C. C. Drovandi , C. C. Holmes , J. McGree , K. Mengersen , S. Richardson , E. Ryan , A principled experimental design approach to Big Data analysis, 2015.

@article{drovandi2015principled,
  title = {A principled experimental design approach to Big Data analysis},
  author = {Drovandi, Christopher C and Holmes, Chris C and McGree, James and Mengersen, Kerrie and Richardson, Sylvia and Ryan, Elizabeth},
  year = {2015}
}

R. G. Stiphout , L. Winchester , S. A. Haider , J. Ragoussis , A. L. Harris , C. C. Holmes , F. M. Buffa , . others , Abstract B1-56: Distinct roles of copy number and loss-of-heterozygosity in predicting prognosis for breast cancer patients. American Association for Cancer Research, 2015.

@misc{van2015abstract,
  title = {Abstract B1-56: Distinct roles of copy number and loss-of-heterozygosity in predicting prognosis for breast cancer patients},
  author = {van Stiphout, Ruud GPM and Winchester, Laura and Haider, Syed A and Ragoussis, Jiannis and Harris, Adrian L and Holmes, Chris C. and Buffa, Francesca M and others},
  year = {2015},
  publisher = {American Association for Cancer Research}
}

A. C. Daly , D. J. Gavaghan , C. C. Holmes , J. Cooper , Hodgkin–Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods, Royal Society open science, vol. 2, no. 12, 150499, 2015.

@article{daly2015hodgkin,
  title = {Hodgkin--Huxley revisited: reparametrization and identifiability analysis of the classic action potential model with approximate Bayesian methods},
  author = {Daly, Aidan C and Gavaghan, David J and Holmes, Chris C. and Cooper, Jonathan},
  journal = {Royal Society open science},
  volume = {2},
  number = {12},
  pages = {150499},
  year = {2015},
  publisher = {The Royal Society}
}

C. Holmes , P. Bissiri , S. Walker , A general framework for updating belief distributions, Journal of the Royal Statistical Society Series B: Statistical Methodology, 2015.

@article{holmes2015general,
  title = {A general framework for updating belief distributions},
  author = {Holmes, CC and Bissiri, PG and Walker, SG},
  journal = {Journal of the Royal Statistical Society Series B: Statistical Methodology},
  year = {2015},
  publisher = {Wiley: 12 months}
}

2014

R. Bardenet , A. Doucet , C. C. Holmes , Towards scaling up Markov chain Monte Carlo: an adaptive subsampling approach, in Proceedings of the 31st International Conference on Machine Learning (ICML-14), 2014, 405–413.

@inproceedings{bardenet2014towards,
  title = {Towards scaling up Markov chain Monte Carlo: an adaptive subsampling approach},
  author = {Bardenet, R{\'e}mi and Doucet, Arnaud and Holmes, Chris C.},
  booktitle = {Proceedings of the 31st International Conference on Machine Learning (ICML-14)},
  pages = {405--413},
  year = {2014}
}

R. Bardenet , A. Doucet , C. C. Holmes , An adaptive subsampling approach for MCMC inference in large datasets, in Proceedings of The 31st International Conference on Machine Learning, 2014, 405–413.

@inproceedings{bardenet2014adaptive,
  title = {An adaptive subsampling approach for MCMC inference in large datasets},
  author = {Bardenet, R{\'e}mi and Doucet, Arnaud and Holmes, Chris C.},
  booktitle = {Proceedings of The 31st International Conference on Machine Learning},
  pages = {405--413},
  year = {2014}
}

2013

D. D. Denison , M. H. Hansen , C. C. Holmes , B. Mallick , B. Yu , Nonlinear estimation and classification. Springer Science & Business Media, 2013.

@misc{denison2013nonlinear,
  title = {Nonlinear estimation and classification},
  author = {Denison, David D and Hansen, Mark H and Holmes, Chris C and Mallick, Bani and Yu, Bin},
  year = {2013},
  publisher = {Springer Science \& Business Media}
}

Q. F. Wills , K. J. Livak , A. J. Tipping , T. Enver , A. J. Goldson , D. W. Sexton , C. C. Holmes , Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments, Nature biotechnology, vol. 31, no. 8, 748–752, 2013.

@article{wills2013single,
  title = {Single-cell gene expression analysis reveals genetic associations masked in whole-tissue experiments},
  author = {Wills, Quin F and Livak, Kenneth J and Tipping, Alex J and Enver, Tariq and Goldson, Andrew J and Sexton, Darren W and Holmes, Chris C.},
  journal = {Nature biotechnology},
  volume = {31},
  number = {8},
  pages = {748--752},
  year = {2013},
  publisher = {Nature Publishing Group}
}

W. Wang , V. Baladandayuthapani , C. C. Holmes , K. Do , Integrative network-based Bayesian analysis of diverse genomics data, BMC bioinformatics, vol. 14, no. 13, S8, 2013.

@article{wang2013integrative,
  title = {Integrative network-based Bayesian analysis of diverse genomics data},
  author = {Wang, Wenting and Baladandayuthapani, Veerabhadran and Holmes, Chris C and Do, Kim-Anh},
  journal = {BMC bioinformatics},
  volume = {14},
  number = {13},
  pages = {S8},
  year = {2013},
  publisher = {BioMed Central}
}

2012

A. Lee , F. Caron , A. Doucet , C. C. Holmes , . others , Bayesian sparsity-path-analysis of genetic association signal using generalized t priors, Statistical applications in genetics and molecular biology, vol. 11, no. 2, 1–29, 2012.

@article{lee2012bayesian,
  title = {Bayesian sparsity-path-analysis of genetic association signal using generalized t priors},
  author = {Lee, Anthony and Caron, Francois and Doucet, Arnaud and Holmes, Chris C. and others},
  journal = {Statistical applications in genetics and molecular biology},
  volume = {11},
  number = {2},
  pages = {1--29},
  year = {2012},
  publisher = {Walter de Gruyter GmbH \& Co. KG}
}

F. Caron , C. C. Holmes , E. Rio , On the sampling distribution of an $\backslash ell\^ 2$ distance between Empirical Distribution Functions with applications to nonparametric testing, PhD thesis, INRIA, 2012.

@phdthesis{caron2012sampling,
  title = {On the sampling distribution of an $$\backslash$ ell\^{} 2$ distance between Empirical Distribution Functions with applications to nonparametric testing},
  author = {Caron, Francois and Holmes, Chris C. and Rio, Emmanuel},
  year = {2012},
  school = {INRIA}
}

J. Cazier , C. C. Holmes , J. Broxholme , GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples, Bioinformatics, vol. 28, no. 22, 2981–2982, 2012.

@article{cazier2012greve,
  title = {GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples},
  author = {Cazier, Jean-Baptiste and Holmes, Chris C and Broxholme, John},
  journal = {Bioinformatics},
  volume = {28},
  number = {22},
  pages = {2981--2982},
  year = {2012},
  publisher = {Oxford University Press}
}

A. R. Taylor , J. A. Flegg , P. J. Guerin , C. Roper , C. C. Holmes , A Bayesian model for estimating with-in host P. falciparum haplotype frequencies, Malaria Journal, vol. 11, no. S1, P36, 2012.

@article{taylor2012bayesian,
  title = {A Bayesian model for estimating with-in host P. falciparum haplotype frequencies},
  author = {Taylor, Aimee R and Flegg, Jennifer A and Guerin, Philippe J and Roper, Cally and Holmes, Chris C.},
  journal = {Malaria Journal},
  volume = {11},
  number = {S1},
  pages = {P36},
  year = {2012},
  publisher = {BioMed Central}
}

M. Rantalainen , C. C. Holmes , Robust Statistical Methods For Genome-Wide Eqtl Analysis, 2012.

@inproceedings{rantalainen2012robust,
  title = {Robust Statistical Methods For Genome-Wide Eqtl Analysis},
  author = {Rantalainen, Mattias and Holmes, Chris C.},
  year = {2012}
}

F. Caron , C. C. Holmes , E. Rio , On the sampling distribution of an l2 norm of the Empirical Distribution Function, with applications to two-sample nonparametric testing, 2012.

@article{caron2012samplinh,
  title = {On the sampling distribution of an l2 norm of the Empirical Distribution Function, with applications to two-sample nonparametric testing},
  author = {Caron, Francois and Holmes, Chris C. and Rio, Emmanuel},
  year = {2012}
}

C. C. Holmes , Auxiliary Counting Variables for Posterior Decoding of Hidden Markov Models with Applications to Cancer Genomics, in ISBA Regional Meeting and International Workshop/Conference on Bayesian Theory and Applications (IWCBTA), 2012.

@inproceedings{holmes2012auxiliary,
  title = {Auxiliary Counting Variables for Posterior Decoding of Hidden Markov Models with Applications to Cancer Genomics},
  author = {Holmes, Chris C.},
  booktitle = {ISBA Regional Meeting and International Workshop/Conference on Bayesian Theory and Applications (IWCBTA)},
  year = {2012}
}

C. C. Holmes , Large-scale genetic analysis of quantitative traits, PhD thesis, University of Oxford, 2012.

@phdthesis{holmes2012large,
  title = {Large-scale genetic analysis of quantitative traits},
  author = {Holmes, Chris C.},
  year = {2012},
  school = {University of Oxford}
}

C. C. Holmes , Extensions of the case-control design in genome-wide association studies, PhD thesis, University of Oxford, 2012.

@phdthesis{holmes2012extensions,
  title = {Extensions of the case-control design in genome-wide association studies},
  author = {Holmes, Chris C.},
  year = {2012},
  school = {University of Oxford}
}

2011

C. Yau , C. C. Holmes , Hierarchical Bayesian nonparametric mixture models for clustering with variable relevance determination, Bayesian analysis (Online), vol. 6, no. 2, 329, 2011.

@article{yau2011hierarchical,
  title = {Hierarchical Bayesian nonparametric mixture models for clustering with variable relevance determination},
  author = {Yau, Christopher and Holmes, Chris C.},
  journal = {Bayesian analysis (Online)},
  volume = {6},
  number = {2},
  pages = {329},
  year = {2011},
  publisher = {Europe PMC Funders}
}

B. S. Kato , G. Nicholson , M. Neiman , M. Rantalainen , C. C. Holmes , A. Barrett , M. Uhlén , P. Nilsson , T. D. Spector , J. M. Schwenk , Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model, Proteome science, vol. 9, no. 1, 73, 2011.

@article{kato2011variance,
  title = {Variance decomposition of protein profiles from antibody arrays using a longitudinal twin model},
  author = {Kato, Bernet S and Nicholson, George and Neiman, Maja and Rantalainen, Mattias and Holmes, Chris C and Barrett, Amy and Uhl{\'e}n, Mathias and Nilsson, Peter and Spector, Tim D and Schwenk, Jochen M},
  journal = {Proteome science},
  volume = {9},
  number = {1},
  pages = {73},
  year = {2011},
  publisher = {BioMed Central}
}

N. Cardin , C. C. Holmes , P. Donnelly , J. Marchini , Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array, Genetic epidemiology, vol. 35, no. 6, 536–548, 2011.

@article{cardin2011bayesian,
  title = {Bayesian hierarchical mixture modeling to assign copy number from a targeted CNV array},
  author = {Cardin, Niall and Holmes, Chris C. and Donnelly, Peter and Marchini, Jonathan},
  journal = {Genetic epidemiology},
  volume = {35},
  number = {6},
  pages = {536--548},
  year = {2011},
  publisher = {Wiley Subscription Services, Inc., A Wiley Company}
}

C. C. Holmes , L. Held , . others , Response to van der Lans, Bayesian Analysis, vol. 6, no. 2, 357–358, 2011.

@article{holmes2011response,
  title = {Response to van der Lans},
  author = {Holmes, Chris C. and Held, Leonhard and others},
  journal = {Bayesian Analysis},
  volume = {6},
  number = {2},
  pages = {357--358},
  year = {2011},
  publisher = {International Society for Bayesian Analysis}
}

A. Drong , G. Nicholson , M. Schuster , F. Karpe , M. McCarthy , C. Holmes , M. Rantalainen , C. Lindgren , M. Consortia , The presence of methylation quantitative trait loci indicate a direct genetic influence on the level of methylation in adipose tissue, 2011.

@inproceedings{drong2011presence,
  title = {The presence of methylation quantitative trait loci indicate a direct genetic influence on the level of methylation in adipose tissue},
  author = {Drong, A and Nicholson, G and Schuster, M and Karpe, F and McCarthy, MI and Holmes, CC and Rantalainen, M and Lindgren, CM and Consortia, M},
  year = {2011}
}

J. G. Ciampa , C. C. Holmes , N. Chatterjee , Application of a novel multi-locus test for genetic association incorporating gene-gene interaction suggests functionality for multiple susceptibility loci for prostate cancer. American Association for Cancer Research, 2011.

@misc{ciampa2011applicatioo,
  title = {Application of a novel multi-locus test for genetic association incorporating gene-gene interaction suggests functionality for multiple susceptibility loci for prostate cancer},
  author = {Ciampa, Julia G and Holmes, Chris C. and Chatterjee, Nilanjan},
  year = {2011},
  publisher = {American Association for Cancer Research}
}

2010

N. L. Hjort , C. C. Holmes , P. Müller , S. G. Walker , Bayesian nonparametrics. Cambridge University Press, 2010.

@misc{hjort2010bayesian,
  title = {Bayesian nonparametrics},
  author = {Hjort, Nils Lid and Holmes, Chris C. and M{\"u}ller, Peter and Walker, Stephen G},
  year = {2010},
  publisher = {Cambridge University Press}
}

M. A. Suchard , C. C. Holmes , M. West , 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, vol. 17, no. 1, 12–16, 2010.

@article{suchard2010some,
  title = {Some of the what?, why?, how?, who? and where? of graphics processing unit computing for Bayesian analysis},
  author = {Suchard, Marc A and Holmes, Chris C. and West, Mike},
  journal = {Bulletin of the International Society for Bayesian Analysis},
  volume = {17},
  number = {1},
  pages = {12--16},
  year = {2010}
}

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

@article{lee2010hierarchical,
  title = {A hierarchical Bayesian framework for constructing sparsity-inducing priors},
  author = {Lee, Anthony and Caron, Francois and Doucet, Arnaud and Holmes, Chris C.},
  journal = {arXiv preprint arXiv:1009.1914},
  year = {2010}
}

N. L. Hjort , C. C. Holmes , P. Müller , S. G. Walker , An invitation to Bayesian nonparametrics, Bayesian Nonparametrics, vol. 28, 1, 2010.

@article{hjort2010invitation,
  title = {An invitation to Bayesian nonparametrics},
  author = {Hjort, Nils Lid and Holmes, Chris C. and M{\"u}ller, Peter and Walker, Stephen G},
  journal = {Bayesian Nonparametrics},
  volume = {28},
  pages = {1},
  year = {2010},
  publisher = {Cambridge University Press}
}

J. Griffin , C. C. Holmes , Computational issues arising in Bayesian nonparametric hierarchical models, Bayesian Nonparametrics, vol. 28, 208, 2010.

@article{griffin2010computational,
  title = {Computational issues arising in Bayesian nonparametric hierarchical models},
  author = {Griffin, Jim and Holmes, Chris C.},
  journal = {Bayesian Nonparametrics},
  volume = {28},
  pages = {208},
  year = {2010},
  publisher = {Cambridge University Press}
}

C. Yau , D. Mouradov , R. N. Jorissen , S. Colella , G. Mirza , G. Steers , A. Harris , J. Ragoussis , O. Sieber , C. C. Holmes , . others , A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data, Genome biology, vol. 11, no. 9, R92, 2010.

@article{yau2010statistical,
  title = {A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data},
  author = {Yau, Christopher and Mouradov, Dmitri and Jorissen, Robert N and Colella, Stefano and Mirza, Ghazala and Steers, Graham and Harris, Adrian and Ragoussis, Jiannis and Sieber, Oliver and Holmes, Chris C and others},
  journal = {Genome biology},
  volume = {11},
  number = {9},
  pages = {R92},
  year = {2010},
  publisher = {BioMed Central Ltd}
}

A. Agam , B. Yalcin , A. Bhomra , M. Cubin , C. Webber , C. C. Holmes , J. Flint , R. Mott , Elusive copy number variation in the mouse genome, PLoS One, vol. 5, no. 9, e12839, 2010.

@article{agam2010elusive,
  title = {Elusive copy number variation in the mouse genome},
  author = {Agam, Avigail and Yalcin, Binnaz and Bhomra, Amarjit and Cubin, Matthew and Webber, Caleb and Holmes, Chris C and Flint, Jonathan and Mott, Richard},
  journal = {PLoS One},
  volume = {5},
  number = {9},
  pages = {e12839},
  year = {2010},
  publisher = {Public Library of Science}
}

N. L. Hjort , C. C. Holmes , P. Müller , S. G. Walker , Bayesian nonparametrics. Cambridge series in statistical and probabilistic mathematics, Cambridge: Cambridge Univ. Press. Mathematical Reviews (MathSciNet): MR2722987, 2010.

@article{hjort2010bayesiao,
  title = {Bayesian nonparametrics. Cambridge series in statistical and probabilistic mathematics},
  author = {Hjort, Nils Lid and Holmes, Chris C. and M{\"u}ller, Peter and Walker, Stephen G},
  journal = {Cambridge: Cambridge Univ. Press. Mathematical Reviews (MathSciNet): MR2722987},
  year = {2010}
}

A. Timbs , S. Knight , E. SadighiAkha , A. Burns , H. Dreau , A. Hewitt , C. Hatton , C. Yau , C. C. Holmes , J. Taylor , . others , Quantitative Whole Genome Analysis of Sequential Samples From Patients with B-CLL Identifies Novel Recurrent Copy Number Alterations Involving Critical B-Cell Transcription Factors, Blood, vol. 116, no. 21, 3590–3590, 2010.

@article{timbs2010quantitative,
  title = {Quantitative Whole Genome Analysis of Sequential Samples From Patients with B-CLL Identifies Novel Recurrent Copy Number Alterations Involving Critical B-Cell Transcription Factors},
  author = {Timbs, Adele and Knight, Sam and SadighiAkha, Elham and Burns, Adam and Dreau, Helene and Hewitt, Anne-Marie and Hatton, Chris and Yau, Chris and Holmes, Chris C. and Taylor, Jenny and others},
  journal = {Blood},
  volume = {116},
  number = {21},
  pages = {3590--3590},
  year = {2010},
  publisher = {American Society of Hematology}
}

Q. Zhou , A. K. Ching , W. K. Leung , C. Szeto , S. Ho , C. C. Holmes , Y. Yuan , P. B. Lai , W. Yeo , N. Wong , Novel therapeutic potential in targeting the microtubules by nanoparticle albumin-bound paclitaxel in hepatocellular carcinoma. American Association for Cancer Research, 2010.

@misc{zhou2010novel,
  title = {Novel therapeutic potential in targeting the microtubules by nanoparticle albumin-bound paclitaxel in hepatocellular carcinoma},
  author = {Zhou, Qian and Ching, Arthur KK and Leung, Wilson KC and Szeto, Carol and Ho, Shuk-Mei and Holmes, Chris C and Yuan, Yun-fei and Lai, Paul BS and Yeo, Winnie and Wong, Nathalie},
  year = {2010},
  publisher = {American Association for Cancer Research}
}

2009

J. E. Lemieux , N. Gomez-Escobar , A. Feller , C. Carret , A. Amambua-Ngwa , R. Pinches , F. Day , S. A. Kyes , D. J. Conway , C. C. Holmes , . others , 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, vol. 106, no. 18, 7559–7564, 2009.

@article{lemieux2009statistical,
  title = {Statistical estimation of cell-cycle progression and lineage commitment in Plasmodium falciparum reveals a homogeneous pattern of transcription in ex vivo culture},
  author = {Lemieux, Jacob E and Gomez-Escobar, Natalia and Feller, Avi and Carret, Celine and Amambua-Ngwa, Alfred and Pinches, Robert and Day, Felix and Kyes, Sue A and Conway, David J and Holmes, Chris C and others},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {106},
  number = {18},
  pages = {7559--7564},
  year = {2009},
  publisher = {National Acad Sciences}
}

J. W. Klingelhoefer , L. Moutsianas , C. C. Holmes , Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency, Bioinformatics, vol. 25, no. 13, 1594–1601, 2009.

@article{klingelhoefer2009approximate,
  title = {Approximate Bayesian feature selection on a large meta-dataset offers novel insights on factors that effect siRNA potency},
  author = {Klingelhoefer, Jochen W and Moutsianas, Loukas and Holmes, Chris C.},
  journal = {Bioinformatics},
  volume = {25},
  number = {13},
  pages = {1594--1601},
  year = {2009},
  publisher = {Oxford Univ Press}
}

C. C. Holmes , A. Jasra , Antithetic methods for gibbs samplers, Journal of Computational and Graphical Statistics, vol. 18, no. 2, 401–414, 2009.

@article{holmes2009antithetic,
  title = {Antithetic methods for gibbs samplers},
  author = {Holmes, Chris C. and Jasra, Ajay},
  journal = {Journal of Computational and Graphical Statistics},
  volume = {18},
  number = {2},
  pages = {401--414},
  year = {2009},
  publisher = {Taylor \& Francis}
}

W. Valdar , C. C. Holmes , R. Mott , J. Flint , Mapping in structured populations by resample model averaging, Genetics, vol. 182, no. 4, 1263–1277, 2009.

@article{valdar2009mapping,
  title = {Mapping in structured populations by resample model averaging},
  author = {Valdar, William and Holmes, Chris C and Mott, Richard and Flint, Jonathan},
  journal = {Genetics},
  volume = {182},
  number = {4},
  pages = {1263--1277},
  year = {2009},
  publisher = {Genetics}
}

J. E. Lemieux , A. Feller , C. C. Holmes , C. I. Newbold , Reply to Wirth et al.: In vivo profiles show continuous variation between 2 cellular populations, Proceedings of the National Academy of Sciences, vol. 106, no. 27, E71–E72, 2009.

@article{lemieux2009reply,
  title = {Reply to Wirth et al.: In vivo profiles show continuous variation between 2 cellular populations},
  author = {Lemieux, Jacob E and Feller, Avi and Holmes, Chris C and Newbold, Chris I},
  journal = {Proceedings of the National Academy of Sciences},
  volume = {106},
  number = {27},
  pages = {E71--E72},
  year = {2009},
  publisher = {National Acad Sciences}
}

C. C. Holmes , Increasing statistical power and generalizability in genomics microarray research, PhD thesis, University of Oxford, 2009.

@phdthesis{holmes2009increasing,
  title = {Increasing statistical power and generalizability in genomics microarray research},
  author = {Holmes, Chris C.},
  year = {2009},
  school = {University of Oxford}
}

2008

A. Ramasamy , A. Mondry , C. C. Holmes , D. G. Altman , Key issues in conducting a meta-analysis of gene expression microarray datasets, PLoS Med, vol. 5, no. 9, e184, 2008.

@article{ramasamy2008key,
  title = {Key issues in conducting a meta-analysis of gene expression microarray datasets},
  author = {Ramasamy, Adaikalavan and Mondry, Adrian and Holmes, Chris C and Altman, Douglas G},
  journal = {PLoS Med},
  volume = {5},
  number = {9},
  pages = {e184},
  year = {2008},
  publisher = {Public Library of Science}
}

T. W. Chittenden , E. A. Howe , A. C. Culhane , R. Sultana , J. M. Taylor , C. C. Holmes , J. Quackenbush , Functional classification analysis of somatically mutated genes in human breast and colorectal cancers, Genomics, vol. 91, no. 6, 508–511, 2008.

@article{chittenden2008functional,
  title = {Functional classification analysis of somatically mutated genes in human breast and colorectal cancers},
  author = {Chittenden, Thomas W and Howe, Eleanor A and Culhane, Aedin C and Sultana, Razvan and Taylor, Jennifer M and Holmes, Chris C. and Quackenbush, John},
  journal = {Genomics},
  volume = {91},
  number = {6},
  pages = {508--511},
  year = {2008},
  publisher = {Elsevier}
}

C. Yau , C. Holmes , CNV discovery using SNP genotyping arrays, Cytogenetic and genome research, vol. 123, no. 1-4, 307–312, 2008.

@article{yau2008cnv,
  title = {CNV discovery using SNP genotyping arrays},
  author = {Yau, C and Holmes, CC},
  journal = {Cytogenetic and genome research},
  volume = {123},
  number = {1-4},
  pages = {307--312},
  year = {2008},
  publisher = {Karger Publishers}
}

2007

P. Dellaportas , D. G. Denison , C. C. Holmes , Flexible threshold models for modelling interest rate volatility, Econometric reviews, vol. 26, no. 2-4, 419–437, 2007.

@article{dellaportas2007flexible,
  title = {Flexible threshold models for modelling interest rate volatility},
  author = {Dellaportas, Petros and Denison, David GT and Holmes, Chris C.},
  journal = {Econometric reviews},
  volume = {26},
  number = {2-4},
  pages = {419--437},
  year = {2007},
  publisher = {Taylor \& Francis}
}

C. C. Holmes , A. Pintore , BAYESIAN STATISTICS 8, pp. 253-282. JM Bernardo, MJ Bayarri, JO Berger, AP Dawid, D. Heckerman, AFM Smith and M. West (Eds.)\copyright Oxford University Press, 2007, in Bayesian statistics 8: proceedings of the eighth Valencia International Meeting, June 2-6, 2006, 2007, vol. 8, 253.

@inproceedings{holmes2007bayesian,
  title = {BAYESIAN STATISTICS 8, pp. 253-282. JM Bernardo, MJ Bayarri, JO Berger, AP Dawid, D. Heckerman, AFM Smith and M. West (Eds.){\copyright} Oxford University Press, 2007},
  author = {Holmes, Chris C and Pintore, Alexandre},
  booktitle = {Bayesian statistics 8: proceedings of the eighth Valencia International Meeting, June 2-6, 2006},
  volume = {8},
  pages = {253},
  year = {2007},
  organization = {Oxford University Press, USA}
}

L. Astle , C. Holmes , D. Balding , Turbo Genomic Control, 2007.

@inproceedings{astle2007turbo,
  title = {Turbo Genomic Control},
  author = {Astle, LJ and Holmes, CC and Balding, DJ},
  year = {2007},
  organization = {WILEY-LISS}
}

S. Colella , C. Yau , J. M. Taylor , G. Mirza , H. Butler , P. Clouston , A. S. Bassett , A. Seller , C. C. Holmes , J. Ragoussis , QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data, Nucleic Acids Research, vol. 35, no. 6, 2013–2025, 2007.

@article{colella2007quantisnp,
  title = {QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data},
  author = {Colella, Stefano and Yau, Christopher and Taylor, Jennifer M and Mirza, Ghazala and Butler, Helen and Clouston, Penny and Bassett, Anne S and Seller, Anneke and Holmes, Chris C and Ragoussis, Jiannis},
  journal = {Nucleic Acids Research},
  volume = {35},
  number = {6},
  pages = {2013--2025},
  year = {2007},
  publisher = {Oxford Univ Press}
}

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

@techreport{griffin2007bayesian,
  title = {Bayesian nonparametric calibration with applications in spatial epidemiology},
  author = {Griffin, JE and Holmes, CC},
  year = {2007},
  institution = {Technical Report, Institute of Mathematics, Statistics and Actuarial Science, University of Kent}
}

M. Zucknick , C. C. Holmes , S. Richardson , Mcmc Methods for Bayesian Variable Selection in Large-scale Genomic Applications, Annals of Human Genetics, vol. 71, no. 4, 558–559, 2007.

@article{zucknick2007mcmc,
  title = {Mcmc Methods for Bayesian Variable Selection in Large-scale Genomic Applications},
  author = {Zucknick, Manuela and Holmes, Chris C. and Richardson, Sylvia},
  journal = {Annals of Human Genetics},
  volume = {71},
  number = {4},
  pages = {558--559},
  year = {2007}
}

2006

C. C. Holmes , L. Held , . others , Bayesian auxiliary variable models for binary and multinomial regression, Bayesian analysis, vol. 1, no. 1, 145–168, 2006.

@article{holmes2006bayesian,
  title = {Bayesian auxiliary variable models for binary and multinomial regression},
  author = {Holmes, Chris C and Held, Leonhard and others},
  journal = {Bayesian analysis},
  volume = {1},
  number = {1},
  pages = {145--168},
  year = {2006},
  publisher = {International Society for Bayesian Analysis}
}

J. Stephenson , K. Gallagher , C. C. Holmes , A Bayesian approach to calibrating apatite fission track annealing models for laboratory and geological timescales, Geochimica et Cosmochimica Acta, vol. 70, no. 20, 5183–5200, 2006.

@article{stephenson2006bayesian,
  title = {A Bayesian approach to calibrating apatite fission track annealing models for laboratory and geological timescales},
  author = {Stephenson, John and Gallagher, Kerry and Holmes, Chris C.},
  journal = {Geochimica et Cosmochimica Acta},
  volume = {70},
  number = {20},
  pages = {5183--5200},
  year = {2006},
  publisher = {Pergamon}
}

H. De Wet , M. Allen , C. C. Holmes , M. Stobbart , J. D. Lippiat , H. De Wet , M. Allen , C. C. Holmes , M. Stobbart , J. D. Lippiat , . others , Modulation of the BK channel by estrogens: examination at single channel level, Molecular membrane biology, vol. 23, no. 5, 420–429, 2006.

@article{de2006modulation,
  title = {Modulation of the BK channel by estrogens: examination at single channel level},
  author = {De Wet, Heidi and Allen, Marcus and Holmes, Chris C. and Stobbart, Michelle and Lippiat, Jonathan D and De Wet, Heidi and Allen, Marcus and Holmes, Chris C. and Stobbart, Michelle and Lippiat, Jonathan D and others},
  journal = {Molecular membrane biology},
  volume = {23},
  number = {5},
  pages = {420--429},
  year = {2006},
  publisher = {Taylor \& Francis}
}

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

@misc{baladandayuthapani2006modeling,
  title = {Modeling nonlinear gene interactions using Bayesian MARS},
  author = {Baladandayuthapani, Veerabhadran and Holmes, Chris C and Mallick, BK and Carroll, RJ},
  year = {2006},
  publisher = {Bayesian Inference for Gene Expression and Proteomics. Cambridge University Press}
}

K. Gallagher , A. Jasra , D. Stephens , C. C. Holmes , A new approach to mixture modelling for geochronology, Geochimica et Cosmochimica Acta, vol. 70, no. 18, A190, 2006.

@article{gallagher2006new,
  title = {A new approach to mixture modelling for geochronology},
  author = {Gallagher, Kerry and Jasra, Ajay and Stephens, David and Holmes, Chris C.},
  journal = {Geochimica et Cosmochimica Acta},
  volume = {70},
  number = {18},
  pages = {A190},
  year = {2006},
  publisher = {Pergamon}
}

A. Jasra , D. Stephens , K. Gallagher , C. Holmes , Analysis of geochronological data with measurement error using Bayesian mixtures, Mathematical Geology, vol. 38, 269–300, 2006.

@article{jasra2006analysis,
  title = {Analysis of geochronological data with measurement error using Bayesian mixtures},
  author = {Jasra, A and Stephens, DA and Gallagher, K and Holmes, CC},
  journal = {Mathematical Geology},
  volume = {38},
  pages = {269--300},
  year = {2006}
}

N. A. Heard , C. C. Holmes , D. A. Stephens , A quantitative study of gene regulation involved in the immune response of anopheline mosquitoes, Journal of the American Statistical Association, vol. 101, no. 473, 18–29, 2006.

@article{heard2006quantitative,
  title = {A quantitative study of gene regulation involved in the immune response of anopheline mosquitoes},
  author = {Heard, Nicholas A and Holmes, Chris C and Stephens, David A},
  journal = {Journal of the American Statistical Association},
  volume = {101},
  number = {473},
  pages = {18--29},
  year = {2006},
  publisher = {ASA}
}

J. Stephenson , K. Gallagher , C. Holmes , Low temperature thermochronology and strategies for multiple samples: 2: Partition modelling for 2d/3d distributions with discontinuities, Earth and Planetary Science Letters, vol. 241, no. 3, 557–570, 2006.

@article{stephenson2006low,
  title = {Low temperature thermochronology and strategies for multiple samples: 2: Partition modelling for 2d/3d distributions with discontinuities},
  author = {Stephenson, John and Gallagher, K and Holmes, CC},
  journal = {Earth and Planetary Science Letters},
  volume = {241},
  number = {3},
  pages = {557--570},
  year = {2006},
  publisher = {Elsevier}
}

V. Baladandayuthapani , C. C. Holmes , B. K. Mallick , R. J. Carroll , Bayesian Inference for Gene Expression and Proteomics: Modeling Nonlinear Gene Interactions Using Bayesian MARS, 2006.

@article{baladandayuthapani2006bayesian,
  title = {Bayesian Inference for Gene Expression and Proteomics: Modeling Nonlinear Gene Interactions Using Bayesian MARS},
  author = {Baladandayuthapani, Veerabhadran and Holmes, Chris C and Mallick, Bani K and Carroll, Raymond J},
  year = {2006}
}

2005

K. Gallagher , J. Stephenson , R. Brown , C. C. Holmes , P. Ballester , Exploiting 3D spatial sampling in inverse modeling of thermochronological data, Reviews in mineralogy and geochemistry, vol. 58, no. 1, 375–387, 2005.

@article{gallagher2005exploiting,
  title = {Exploiting 3D spatial sampling in inverse modeling of thermochronological data},
  author = {Gallagher, Kerry and Stephenson, John and Brown, Roderick and Holmes, Chris C. and Ballester, Pedro},
  journal = {Reviews in mineralogy and geochemistry},
  volume = {58},
  number = {1},
  pages = {375--387},
  year = {2005},
  publisher = {Mineral Soc America}
}

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

@article{stephenson2005statistical,
  title = {A statistical technique for modelling non-stationary spatial processes},
  author = {Stephenson, John and Holmes, Chris C. and Gallagher, Kerry and Pintore, Alexandre},
  journal = {Geostatistics Banff 2004},
  pages = {125--134},
  year = {2005},
  publisher = {Springer Netherlands}
}

K. Gallagher , J. Stephenson , R. Brown , C. C. Holmes , P. Fitzgerald , Low temperature thermochronology and modeling strategies for multiple samples 1: Vertical profiles, Earth and Planetary Science Letters, vol. 237, no. 1, 193–208, 2005.

@article{gallagher2005low,
  title = {Low temperature thermochronology and modeling strategies for multiple samples 1: Vertical profiles},
  author = {Gallagher, Kerry and Stephenson, John and Brown, Roderick and Holmes, Chris C. and Fitzgerald, Paul},
  journal = {Earth and Planetary Science Letters},
  volume = {237},
  number = {1},
  pages = {193--208},
  year = {2005},
  publisher = {Elsevier}
}

A. Jasra , C. C. Holmes , D. A. Stephens , Markov chain Monte Carlo methods and the label switching problem in Bayesian mixture modeling, Statistical Science, 50–67, 2005.

@article{jasra2005markov,
  title = {Markov chain Monte Carlo methods and the label switching problem in Bayesian mixture modeling},
  author = {Jasra, Ajay and Holmes, Chris C and Stephens, David A},
  journal = {Statistical Science},
  pages = {50--67},
  year = {2005},
  publisher = {Institute of Mathematical Statistics}
}

N. A. Heard , C. C. Holmes , D. A. Stephens , D. J. Hand , G. Dimopoulos , Bayesian coclustering of Anopheles gene expression time series: study of immune defense response to multiple experimental challenges, Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 47, 16939, 2005.

@article{heard2005bayesian,
  title = {Bayesian coclustering of Anopheles gene expression time series: study of immune defense response to multiple experimental challenges},
  author = {Heard, Nicholas A and Holmes, Chris C and Stephens, David A and Hand, David J and Dimopoulos, George},
  journal = {Proceedings of the National Academy of Sciences of the United States of America},
  volume = {102},
  number = {47},
  pages = {16939},
  year = {2005},
  publisher = {National Acad Sciences}
}

C. Holmes , D. T. Denison , S. Ray , B. Mallick , Bayesian prediction via partitioning, Journal of Computational and Graphical Statistics, vol. 14, no. 4, 811–830, 2005.

@article{holmes2005bayesian,
  title = {Bayesian prediction via partitioning},
  author = {Holmes, CC and Denison, DG T and Ray, S and Mallick, BK},
  journal = {Journal of Computational and Graphical Statistics},
  volume = {14},
  number = {4},
  pages = {811--830},
  year = {2005},
  publisher = {Taylor \& Francis}
}

C. C. Holmes , S. D. Brown , All systems GO for understanding mouse gene function, The Scientist, vol. 19, no. 1, 20–1, 2005.

@article{holmes2005all,
  title = {All systems GO for understanding mouse gene function},
  author = {Holmes, Chris C. and Brown, Steve DM},
  journal = {The Scientist},
  volume = {19},
  number = {1},
  pages = {20--1},
  year = {2005},
  publisher = {Scientist Inc.}
}

2004

C. C. Holmes , S. D. Brown , All systems GO for understanding mouse gene function, Journal of biology, vol. 3, no. 5, 20, 2004.

@article{holmes2004all,
  title = {All systems GO for understanding mouse gene function},
  author = {Holmes, Chris C. and Brown, Steve DM},
  journal = {Journal of biology},
  volume = {3},
  number = {5},
  pages = {20},
  year = {2004},
  publisher = {BioMed Central}
}

J. Stephenson , K. Gallagher , C. Holmes , Beyond kriging: dealing with discontinuous spatial data fields using adaptive prior information and Bayesian partition modelling, Geological Society, London, Special Publications, vol. 239, no. 1, 195–209, 2004.

@article{stephenson2004beyond,
  title = {Beyond kriging: dealing with discontinuous spatial data fields using adaptive prior information and Bayesian partition modelling},
  author = {Stephenson, John and Gallagher, K and Holmes, CC},
  journal = {Geological Society, London, Special Publications},
  volume = {239},
  number = {1},
  pages = {195--209},
  year = {2004},
  publisher = {Geological Society of London}
}

2003

C. Holmes , L. Held , On the simulation of Bayesian binary and polychotomous regression models using auxiliary variables, Technical report. Available at: http://www. stat. uni-muenchen. de/\\~ leo, 2003.

@techreport{holmes2003simulation,
  title = {On the simulation of Bayesian binary and polychotomous regression models using auxiliary variables},
  author = {Holmes, CC and Held, L},
  year = {2003},
  institution = {Technical report. Available at: http://www. stat. uni-muenchen. de/\\\~{}{} leo}
}

C. Holmes , N. Heard , Generalized monotonic regression using random change points, Statistics in Medicine, vol. 22, no. 4, 623–638, 2003.

@article{holmes2003generalized,
  title = {Generalized monotonic regression using random change points},
  author = {Holmes, CC and Heard, NA},
  journal = {Statistics in Medicine},
  volume = {22},
  number = {4},
  pages = {623--638},
  year = {2003},
  publisher = {Wiley Online Library}
}

C. Holmes , B. Mallick , Generalized nonlinear modeling with multivariate free-knot regression splines, Journal of the American Statistical Association, vol. 98, no. 462, 352–368, 2003.

@article{holmes2003generalizee,
  title = {Generalized nonlinear modeling with multivariate free-knot regression splines},
  author = {Holmes, CC and Mallick, BK},
  journal = {Journal of the American Statistical Association},
  volume = {98},
  number = {462},
  pages = {352--368},
  year = {2003},
  publisher = {Taylor \& Francis}
}

C. C. Holmes , N. M. Adams , Likelihood inference in nearest-neighbour classification models, Biometrika, 99–112, 2003.

@article{holmes2003likelihood,
  title = {Likelihood inference in nearest-neighbour classification models},
  author = {Holmes, Chris C and Adams, Niall M},
  journal = {Biometrika},
  pages = {99--112},
  year = {2003},
  publisher = {Biometrika Trust, University College London}
}

C. Holmes , D. Denison , Classification with bayesian MARS, Machine Learning, vol. 50, no. 1, 159–173, 2003.

@article{holmes2003classification,
  title = {Classification with bayesian MARS},
  author = {Holmes, CC and Denison, DGT},
  journal = {Machine Learning},
  volume = {50},
  number = {1},
  pages = {159--173},
  year = {2003},
  publisher = {Springer Netherlands}
}

C. Holmes , B. Mallick , Perfect simulation for Bayesian curve and surface fitting, Preprint from www. stat. tamu. edu/\\~ bmallick/papers/perf. ps, 2003.

@article{holmes2003perfect,
  title = {Perfect simulation for Bayesian curve and surface fitting},
  author = {Holmes, CC and Mallick, BK},
  journal = {Preprint from www. stat. tamu. edu/\\\~{}{} bmallick/papers/perf. ps},
  year = {2003}
}

R. Graziani , C. C. Holmes , Bayesian free knot polynomial splines of random order. Università commerciale Luigi Bocconi, 2003.

@misc{graziani2003bayesian,
  title = {Bayesian free knot polynomial splines of random order},
  author = {Graziani, Rebecca and Holmes, Chris C.},
  year = {2003},
  publisher = {Universit{\`a} commerciale Luigi Bocconi}
}

R. M. Gray , D. Denison , M. Hansen , C. Holmes , B. Mallick , B. Yu , Gauss mixture quantization: clustering Gauss mixtures, in Nonlinear Estimation and Classification, 2003, vol. 1003, 189–212.

@inproceedings{gray2003gauss,
  title = {Gauss mixture quantization: clustering Gauss mixtures},
  author = {Gray, Robert M and Denison, DD and Hansen, MH and Holmes, CC and Mallick, B and Yu, B},
  booktitle = {Nonlinear Estimation and Classification},
  volume = {1003},
  pages = {189--212},
  year = {2003},
  organization = {Springer, New York}
}

C. Holmes , D. Denison , Stochastic search algorithms inspired by physical and biological systems are applied to the problem of learning directed graphical probability models in the presence of missing observations and hidden variables. For this class of problems, deterministic search algorithms tend to halt at local optima, requiring random restarts to obtain solutions of acceptable quality. We compare three stochastic search..., Machine Learning, vol. 50, no. 3, 279–301, 2003.

@article{holmes2003stochastic,
  title = {Stochastic search algorithms inspired by physical and biological systems are applied to the problem of learning directed graphical probability models in the presence of missing observations and hidden variables. For this class of problems, deterministic search algorithms tend to halt at local optima, requiring random restarts to obtain solutions of acceptable quality. We compare three stochastic search...},
  author = {Holmes, CC and Denison, DGT},
  journal = {Machine Learning},
  volume = {50},
  number = {3},
  pages = {279--301},
  year = {2003}
}

2002

C. C. Holmes , D. G. Denison , Perfect sampling for the wavelet reconstruction of signals, IEEE Transactions on Signal Processing, vol. 50, no. 2, 337–344, 2002.

@article{holmes2002perfect,
  title = {Perfect sampling for the wavelet reconstruction of signals},
  author = {Holmes, Chris C. and Denison, David GT},
  journal = {IEEE Transactions on Signal Processing},
  volume = {50},
  number = {2},
  pages = {337--344},
  year = {2002},
  publisher = {IEEE}
}

A. Guglielmi , C. C. Holmes , S. G. Walker , Perfect simulation involving functionals of a Dirichlet process, Journal of Computational and Graphical Statistics, vol. 11, no. 2, 306–310, 2002.

@article{guglielmi2002perfect,
  title = {Perfect simulation involving functionals of a Dirichlet process},
  author = {Guglielmi, Alessandra and Holmes, Chris C and Walker, Stephen G},
  journal = {Journal of Computational and Graphical Statistics},
  volume = {11},
  number = {2},
  pages = {306--310},
  year = {2002},
  publisher = {Taylor \& Francis}
}

D. Denison , N. Adams , C. Holmes , D. Hand , Bayesian partition modelling, Computational statistics & data analysis, vol. 38, no. 4, 475–485, 2002.

@article{denison2002bayesian,
  title = {Bayesian partition modelling},
  author = {Denison, DGT and Adams, NM and Holmes, CC and Hand, DJ},
  journal = {Computational statistics \& data analysis},
  volume = {38},
  number = {4},
  pages = {475--485},
  year = {2002},
  publisher = {Elsevier}
}

J. Ferreira , D. Denison , C. Holmes , Partition modelling, 2002.

@article{ferreira2002partition,
  title = {Partition modelling},
  author = {Ferreira, JTAS and Denison, DGT and Holmes, CC},
  year = {2002}
}

C. Holmes , N. Adams , A probabilistic nearest neighbour method for statistical pattern recognition, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol. 64, no. 2, 295–306, 2002.

@article{holmes2002probabilistic,
  title = {A probabilistic nearest neighbour method for statistical pattern recognition},
  author = {Holmes, CC and Adams, NM},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume = {64},
  number = {2},
  pages = {295--306},
  year = {2002},
  publisher = {Wiley Online Library}
}

C. Holmes , D. T. Denison , B. Mallick , Accounting for model uncertainty in seemingly unrelated regressions, Journal of Computational and Graphical Statistics, vol. 11, no. 3, 533–551, 2002.

@article{holmes2002accounting,
  title = {Accounting for model uncertainty in seemingly unrelated regressions},
  author = {Holmes, CC and Denison, DG T and Mallick, BK},
  journal = {Journal of Computational and Graphical Statistics},
  volume = {11},
  number = {3},
  pages = {533--551},
  year = {2002},
  publisher = {Taylor \& Francis}
}

C. Holmes , [Spline Adaptation in Extended Linear Models]: Comment, Statistical Science, vol. 17, no. 1, 22–24, 2002.

@article{holmes2002spline,
  title = {[Spline Adaptation in Extended Linear Models]: Comment},
  author = {Holmes, CC},
  journal = {Statistical Science},
  volume = {17},
  number = {1},
  pages = {22--24},
  year = {2002},
  publisher = {Institute of Mathematical Statistics}
}

2001

C. Holmes , B. Mallick , Bayesian regression with multivariate linear splines, Journal of the Royal Statistical Society: Series B (Statistical Methodology), vol. 63, no. 1, 3–17, 2001.

@article{holmes2001bayesian,
  title = {Bayesian regression with multivariate linear splines},
  author = {Holmes, CC and Mallick, BK},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  volume = {63},
  number = {1},
  pages = {3--17},
  year = {2001},
  publisher = {Wiley Online Library}
}

D. Denison , C. Holmes , Bayesian partitioning for estimating disease risk, Biometrics, vol. 57, no. 1, 143–149, 2001.

@article{denison2001bayesian,
  title = {Bayesian partitioning for estimating disease risk},
  author = {Denison, DGT and Holmes, CC},
  journal = {Biometrics},
  volume = {57},
  number = {1},
  pages = {143--149},
  year = {2001},
  publisher = {Blackwell Publishing Ltd}
}

S. J. Roberts , C. C. Holmes , D. Denison , Minimum-entropy data partitioning using reversible jump Markov chain Monte Carlo, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 23, no. 8, 909–914, 2001.

@article{roberts2001minimum,
  title = {Minimum-entropy data partitioning using reversible jump Markov chain Monte Carlo},
  author = {Roberts, Stephen J. and Holmes, Chris C and Denison, Dave},
  journal = {IEEE Transactions on Pattern Analysis and Machine Intelligence},
  volume = {23},
  number = {8},
  pages = {909--914},
  year = {2001},
  publisher = {IEEE}
}

S. Roberts , C. C. Holmes , D. Denison , Minimum-entropy data clustering using reversible jump markov chain monte carlo, Artificial Neural Networks—ICANN 2001, 103–110, 2001.

@article{roberts2001minimun,
  title = {Minimum-entropy data clustering using reversible jump markov chain monte carlo},
  author = {Roberts, Stephen and Holmes, Chris C and Denison, Dave},
  journal = {Artificial Neural Networks—ICANN 2001},
  pages = {103--110},
  year = {2001},
  publisher = {Springer Berlin/Heidelberg}
}

C. C. D. L. Holmes , Bayesian methods for nonlinear classification and regression, PhD thesis, Department of Mathematics, Imperial College, 2001.

@phdthesis{holmes2001bayesiao,
  title = {Bayesian methods for nonlinear classification and regression},
  author = {Holmes, Chris C De Lance},
  year = {2001},
  school = {Department of Mathematics, Imperial College}
}

2000

C. C. Holmes , B. K. Mallick , Bayesian wavelet networks for nonparametric regression, IEEE transactions on neural networks, vol. 11, no. 1, 27–35, 2000.

@article{holmes2000bayesian,
  title = {Bayesian wavelet networks for nonparametric regression},
  author = {Holmes, Chris C and Mallick, Bani K},
  journal = {IEEE transactions on neural networks},
  volume = {11},
  number = {1},
  pages = {27--35},
  year = {2000},
  publisher = {IEEE}
}

1999

A. Guglielmi , C. C. Holmes , S. G. Walker , Perfect simulation involving a continuous and unbounded state space, Preprint, 1999.

@article{guglielmi1999perfect,
  title = {Perfect simulation involving a continuous and unbounded state space},
  author = {Guglielmi, Alessandra and Holmes, Chris C and Walker, Stephen G},
  journal = {Preprint},
  year = {1999},
  publisher = {Citeseer}
}

C. Holmes , D. Denison , Bayesian wavelet analysis with a model complexity prior, Bayesian statistics, vol. 6, 769–776, 1999.

@article{holmes1999bayesian,
  title = {Bayesian wavelet analysis with a model complexity prior},
  author = {Holmes, CC and Denison, DGT},
  journal = {Bayesian statistics},
  volume = {6},
  pages = {769--776},
  year = {1999},
  publisher = {Citeseer}
}

C. Holmes , D. Denison , B. Mallick , Bayesian partitioning for classification and regression, Manuscript, Imperial College, 1999.

@article{holmes1999bayesiao,
  title = {Bayesian partitioning for classification and regression},
  author = {Holmes, CC and Denison, DGT and Mallick, BK},
  journal = {Manuscript, Imperial College},
  year = {1999}
}

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

@article{holmes1999generalised,
  title = {Generalised nonlinear modelling with multivariate smoothing splines},
  author = {Holmes, CC and Mallick, BK},
  journal = {Unpublished manuscript, Statistics Section, Department of Mathematics, Imperial College of London},
  year = {1999}
}

1998

C. Holmes , B. Mallick , Bayesian radial basis functions of variable dimension, Neural Computation, vol. 10, no. 5, 1217–1233, 1998.

@article{holmes1998bayesian,
  title = {Bayesian radial basis functions of variable dimension},
  author = {Holmes, CC and Mallick, BK},
  journal = {Neural Computation},
  volume = {10},
  number = {5},
  pages = {1217--1233},
  year = {1998},
  publisher = {MIT Press}
}

C. Holmes , B. Mallick , Parallel Markov chain Monte Carlo sampling: an evolutionary based approach, London, Imperial College, 1998.

@article{holmes1998parallel,
  title = {Parallel Markov chain Monte Carlo sampling: an evolutionary based approach},
  author = {Holmes, CC and Mallick, BK},
  journal = {London, Imperial College},
  year = {1998}
}

1997

C. Holmes , B. Mallick , Bayesian radial basis functions of unknown dimension, Imperial College Report, 1997.

@article{holmes1997bayesian,
  title = {Bayesian radial basis functions of unknown dimension},
  author = {Holmes, CC and Mallick, BK},
  journal = {Imperial College Report},
  year = {1997}
}