Technical reports & submitted publications

• Blangiardo M., Richardson S. (2007) A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips, submitted, PDF, supplementary material, WinBUGS code
• Bottolo L., Richardson S. (2007) Fully Bayesian variable selection using g-priors, submitted, PDF abstract
• Brown A., Richardson, S., Petretto, E., Whittaker J, (2008) A multivariate shrinkage approach to expression Quantitative Trait Loci mapping, submitted, PDF abstract
• Ambler, G. K. and Green P. J. (2007) Bayesian two-way clustering with applications to gene expression microarray data, Technical report, School of Mathematics, University of Bristol
• Green P. J. (2007) The coloured Dirichlet process: a probability model for clustering heterogeneously, in preparation.
• Lau, J. W. and Green P. J. (2007), Bayesian Model Based Clustering Procedures. To appear in Journal of Computational and Graphical Statistics. Technical report (PDF).
• Lau, J. W. and Green P. J. (2007) Bayesian clustering using a heterogeneous Dirichlet process, with application to parametric gene expression profiles, in final preparation.

Refereed journal publications

2008

• Zucknick, Manuela; Richardson, Sylvia; and Stronach, Euan A. (2008) "Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods" Statistical Applications in Genetics and Molecular Biology: Vol. 7 : Iss. 1, Article 7. journal page

2007

• Blangiardo M., Richardson S. (2007) Statistical tools for synthesizing lists of differentially expressed features in related experiments Genome Biology, 8, R54 journal page , with BGcom R package
• Bochkina N., Richardson S. (2007) Tail posterior probability for inference in pairwise and multiclass gene expression data, Biometrics, journal page, with supplementary material
• Lewin, A., Bochkina, N. and Richardson, S (2007) Fully Bayesian mixture model for differential gene expression: simulations and model checks. Statistical Applications in Genetics and Molecular Biology Vol. 6 : Iss. 1, Article 36. journal page BGmix software
• Lewin, A., Richardson, S. (2007) Bayesian methods for microarray data, to appear in the Handbook of Statistical Genetics, eds D. Balding, M. Bishop and C. Cannings, Wiley (draft PDF)
• Turro, E., Bochkina, N. Hein, A.-M.K., and Richardson, S. (2007) BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips, BMC Bioinformatics 2007, 8:439 (journal page).

2006

• Broët, P. and Richardson S. (2006), Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model. Bioinformatics 2006 22(8):911-918; doi:10.1093/bioinformatics/btl035   journal page   supplementary material    CGHmix WinBUGS code
• Hein, A.-M.K., Lewin, A. and Richardson, S. (2006) Bayesian hierarchical models for inference in microarray data. In Do KA, Muller, P, and Vanucci M (eds). Bayesian inference for gene expression and proteomics. Cambridge University Press. p. 53-70
• Hein A.-M. and Richardson S. (2006), A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates. BMC Bioinformatics 2006, 7:353 doi:10.1186/1471-2105-7-353  journal page
• Lewin, A. and Grieve, I. (2006), Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data. BMC Bioinformatics 2006 7:426 doi:10.1186/1471-2105-7-426   journal page
• Lewin, A., Richardson, S., Marshall, C., Glazier, A. and Aitman, T. (2006), Bayesian Modelling of Differential Gene Expression.   Biometrics 2006 62: 10 doi:10.1111/j.1541-0420.2005.00394.x   journal page   supplementary material, including WinBUGS code

2005

• Hein, A.-M.K., Richardson, S., Causton, H.C., Ambler, G.K., Green, P.J. (2005), BGX: a fully Bayesian gene expression index for Affymetrix GeneChip data.   Biostatistics, 2005 6(3):349-373; doi:10.1093/biostatistics/kxi016.   journal page   Software

2004

• Broët, P., Lewin, A., Richardson, S., Dalmasso, C. and Magdelenat, H. (2004), A mixture model based strategy for selecting sets of genes in multiclass response microarray experiments.   Bioinformatics 2004 20(16):2562-2571; doi:10.1093/bioinformatics/bth285. journal page   journal TOC   software

2002

• Broët, P., Richardson, S. and Radvanyi, F. (2002), Bayesian Hierarchical Model for Identifying Changes in Gene Expression from Microarray Experiments Journal of Computational Biology 9, 671-683.   journal page

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