Publications
Lee A, Caron F, Doucet A and Holmes C (2012) Bayesian sparsity-path-analysis of genetic association signal using generalized t prior. Statistical Applications in Genetics and Molecular Biology 11(2)
Chittenden T, Howe E, Taylor J, Mar J, Aryee M, Gómez H, Sultana R, Braisted J, Nair S, Quackenbush J and Holmes C (2012) nEASE: a Method for Gene Ontology Sub-Classification of High Throughput Gene Expression Data. Bioinformatics Advance Access published January 13
Ciampa J, Yeager M, Jacobs K, Thun M, Gapstur S, Albanes D, Virtamo J, Weinstein S, Giovannucci E, Willett W, Cancel-Tassin G, Cussenot O, Valeri A, Hunter D, Hoover R, Thomas G, Chanock S, Holmes C and Chatterjee N (2011). Application of a novel score test for genetic association incorporating gene-gene interaction suggests functionality for prostate cancer susceptibility regions. Hum Hered 72(3), 182-93
Kato B, Nicholson G, Neiman M, Rantalainen M, Holmes C, Barrett A, Uhlen M, Nilsson P, Spector T and Schwenk J (2011) Variance decomposition of protein profiles from antibody arrays using a longitudial twin model. Proteome Science 9, 73
Rantalainen 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
Jasra A and Holmes C (2011) Stochastic boosting algorithms. Stat Comput 21(3), 335-347
Nicholson G, Rantalainen M, Li J, Maher A, Malmodin D, Ahmadi K, Faber J, Barrett A, Min J, Rayner N, Toft H, Krestyaninova M, Viksna J, Guha Neogi S, Dumas M-E, Sarkans U, MolPAGE Consortium, Donnelly P, Illig T, Adamski J, Suhre K, Allen M, Zondervan K, Spector T, Nicholson J, Lindon J, Baunsgaard D, Holmes, E, McCarthy and Holmes C (2011) A genome-wide metabolic QTL analysis in Europeans implicates two loci shaped by recent positive selection. PLoS Genet 7
Nicholson G, Rantalainen M, Maher A, Li J, Malmodin D, Ahmadi K, Faber J, Hallgrimsdottir I, Barrett A, Toft H, Krestyaninova M, Viksna J, Guha Neogi S, Dumas M-E, Sarkans U, MolPAGE Consortium, Silverman B, Donnelly P, Nicholson J, Allen M, Zondervan K, Lindon J, Spector T, McCarthy M, Holmes E, Baunsgaard D and Holmes C (2011) Human metabolic profiles are stably controlled by genetic and environmental variation. Mol Syst Biol 7, 525
Ciampa J, Yeager M, Jacbos K, Thun M, Gapstur S, Albanes D, Virtamo J, Weinstein J, Giovannucci E, Willett W, Cancel-Tassin G, Cussenot O, Valeri A, Hunter D, Hoover R, Thomas G, Chanock S, Holmes C, Chatterjee N (2011) Application of novel score test for genetic association incorporating gene-gene interaction suggests functionality for prostate cancer susceptibility regions. Hum Herid: in press
Cardin N, Holmes C, The Wellcome Trust Case Control Consortium, Donnelly P, Marchini J (2011) Bayesian hierarchical mixture modelling to assign copy number from a targeted CNV array. Genetic Epidemiology 35, 1-13
Holmes C (2011) invited discussion of Regression shrinkage and selection via the lasso: a retrospective by Robert Tibshirani J R Statist Soc B 73, Part 3, 273-282
Yau C and Holmes C (2011) Hierarchical Bayesian nonparametric mixture models for clustering with variable relevance determination. Bayesian Analysis 6(2), 329-352
Yau C, Papaspiliopoulos O, Roberts G and Holmes C (2011) Bayesian non-parametric hidden Markov models with applications in genomics. J Royal Stat Soc, Series B 73 (Part 1), 33-57
Lee A, Yau C, Giles M, Doucet A and Holmes C (2010) On the utility of graphics cards to perform massively parallel simulation of advanced Monte Carlo methods. J Comp & Graph Stats 19(4), 769-789
Chittenden, T et al. (2010) Therapeutic implications of GIPC1 silencing in cancer. PloS ONE 5(12)
Hjort N, Holmes C, Muller P and Walker S (2010) Bayesian non-parametrics. CUP
Agam A, Yalcin B, Bhomra A, Cubin M, Webber C et al (2010) Elusive copy number variation in the mouse genome. PLoS ONE 5(9), e12839
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 April 1, 464(7289), 713-720
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. Nat Genet 42(11), 949-960
Yau C, Mouradov D, Jorissen N, Colella S, Mirza G, Steers G, Harris A, Ragoussis J, Sieber O and Holmes C (2010) A statistical approach for detecting genomic aberrations in heterogeneous tumor samples from single nucleotide polymorphism genotyping data. Genome Biol 11(9), (R12)
Clark T, Campino S, Anastasi E, Auburn S, Teo Y, Small K, Rockett K, Kwiatkowski D and Holmes C (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), 1999-2003
Davies J, Hein J and Holmes C (2010) Detecting interacting genetic loci with effects on quantitative traits where the nature and order of the interaction are unkonwn. Genetic Epidemiology 34, 299-308
Mackenzie F, Parker A, Parkinson N, Oliver P, Brooker D, Underhill P, Lukashkina C, Lukashkin A, Holmes C and Brown S (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 Behav 8(7), 699-713, Epub, 2009 Jun 22
Anjum S, Doucet A and Holmes C (2009) A boosting approach to structure learning of graphs with and without prior knowledge. Bioinformatics 25(22), 2929-2936
Holmes C and Jasra J (2009) Antithetic methods for Gibbs samplers. J Comp & Graph Stats 18(2), 401-414
Lemieux J, Gomez-Escobar N, Feller A, Carret C, Amambua-Ngwa A, Pinches R, Day F, Kyes S, Conway D, Holmes C and Newbold C (2009) 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), 7559-7564
Klingelhoefer J, 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), 1594-1601
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), 371-378
Webb A, Hancock J and Holmes C (2009) Phylogenetic inference under recombination using Bayesian stochastic topology selection. Bioinformatics 25(2), 197-203
Valdar W, Holmes C, Mott R and Flint J (2009) Mapping in structured populations by resample model averaging. Genetics 182(4), 1263-1277
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 2, 5(9) e184
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), 2209-2214
Jasra J, Doucet A, Stephens D and Holmes C (2008) Interacting sequential Monte Carlo samplers for trans-dimensional simulation. Comp Stats & Data Analysis 52(4), 1765-1791
Colella S, Yau C, Taylor J M, Mirza G, Butler H, Clouston P, Bassett A S, Seller A, Holmes C and Ragoussis J (2007) QuantiSNP: an objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data. Nucleic Acids Res 35(6), 2013-2025
Yau C and Holmes C (2008) CNV discovery using SNP genotyping arrays. Cytogenet Genome Res 123(1-4), 307-312
Jasra A, Stephens D and Holmes C (2007) Population-based Reversible Jump Markov Chain Monte Carlo. Biometrika 94(4) 787-807
Jasra A, Stephens D and Holmes C (2007) On population based simulation for static inference. Stat Comput 17, 263-279
Dellaportas P, Dennison D and Holmes C (2007) Flexible threshold models for modelling interest rate volatility. Econometric Reviews. Special Issue on Bayesian Dynamic Econometrics. 26(2). 419-437
De Wet H, Allen M, Holmes C, Stobbart M, Lippiat J and Callaghan R (2006) Modulation of the BK channel by estrogens: examination at single channel level. Molecular Membrane Biology 23(5), 420-429
Pintore A and Holmes C (2006) Non-stationary covariance functions via spatially adaptive spectra. Journal of the American Statistical Association. To appear
Pintore A, Speckman P and Holmes C (2006) Spatially adaptive smoothing splines. Biometrika 93, 113-125
Stephenson J, Gallagher K, Holmes C (2006) A Bayesian approach to calibrating apatite fission track annealing models for laboratory and geological timescales. Geochimica Cosmochimica Acta 70(20), 5183-5200
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, 473,18-29
Jasra A, Stephens D, Gallagher K and Holmes C (2006) Bayesian mixture modelling in geochronology via Markov chain Monte Carlo. Mathematical Geology 38(3), 269-300
Stephenson J, Gallagher K and Holmes C (2006) Low temperature thermochronology and strategies for multiple samples 2: partition modelling for 2D/3D distributions with discontinuities. Earth and Planetary Science Letters 241, 557- 570
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, 16939-16944
Holmes C and Brown S (2005) All systems GO for understanding Mouse gene function. Invited discussion in Journal of Biology 3(5), 20
Gallagher K, Stephenson J, Brown R, Holmes C and Fitzgerald P (2005) Low temperature thermochronology and modeling strategies for multiple samples 1: Vertical profiles, Earth and Planetary Science Letters, 237, 193-208
Gallagher K, Stephenson J, Brown R, Holmes C and Ballester P (2005) Exploiting 3D spatial sampling in inverse modeling of thermochronological data. Low-Temperature Thermochronology: Techniques, Interpretations, and Applications 58, 375-387
Holmes C and Held K (2005) Bayesian auxiliary variable models for binary and polychotomous regression. Bayesian Analysis 1(1), 145-168
Kim H-M, Mallick B and Holmes C (2005) Analyzing nonstationary spatial data using a piecewise Gaussian process. Journal of the American Statistical Association 470, 653-658
Holmes C, Denison D, Ray S and Mallick B K (2005) Bayesian partitioning for classification and regression. Journal of Computation and Graphical Statistics 14(4), 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), 50-67
Holmes C and Mallick B K (2003) Generalised nonlinear modelling with multivariate free-knot regression splines. J Amer Statist Assoc 98(462), 352-368
Holmes C and Adams N A (2003) Likelihood based inference in nearest-neighbor classification models. Biometrika 90(1), 99-112
Holmes C and Heard N (2003) Generalised isotonic regression using random change points. Statistics in Medicine 22(4), 623-638
Holmes C, Denison D and Mallick B K (2002) Accounting for model uncertainty in seemingly unrelated regressions. J Comput Graph Stat 11(3), 533-551
Holmes C and Denison D (2002) A Bayesian multivariate adaptive regression spline classifier. Machine Learning 50(1-2), 159-173
Holmes C (2002) Probabilistic free-knots splines. Invited discussant on “Spline adaptation in extended linear models'', by Hansen, M H and Kooperberg C, Statistical Science 17, 1-51
Holmes C and Adams N A (2002) A probabilistic nearest-neighbor method for statistical pattern recognition. J Roy Statist Soc Series B, 64, Part 2, 295-306
Holmes C and Denison D (2002) Perfect sampling for the wavelet reconstruction of signals. IEEE Trans Signal Processing 50(2) 337-344
Guglielmi A, Holmes C and Walker S (2002) Perfect simulation involving a continuous and unbounded state space. J Comp Graph Stats 11(2), 306-310
Denison D, Adams N, Holmes C and Hand D (2002) Bayesian partitioning modelling. Comp Statist Data Anal 38, 475-485
Holmes C and Mallick B K (2001) Bayesian regression with multivariate linear splines. J Roy Statist Soc Series B, 63, 3-19
Denison D and Holmes C (2001) Bayesian partitioning for estimating disease risk. Biometrics 57, 143-149
Roberts S, Holmes C and Denison D (2001) Minimum-entropy data partitioning. IEEE Trans. on Pattern Analysis and Machine Intelligence 23, 909-914
Holmes C and Mallick B K (2000) Bayesian wavelet networks for nonparametric regression. IEEE Trans. Neural Networks 11, 27-35
Holmes C and Denison D (1999) Bayesian wavelet analysis with a model complexity prior. Bayesian Statistics 6. Eds. J M Bernardo, J O Berger, A P Dawid and A F M Smith. Oxford: Oxford University Press. pp 972-978
Holmes C and Mallick B K (1998) Bayesian radial basis functions of variable dimension. Neural Computation 10, 1217-1233
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