Submitted publications

• Brown, A., Richardson, S., Whittaker, J., (2010) Application of the Lasso to expression Quantitative Trait Loci mapping, submitted, PDF abstract
• Papathomas, M., Dellaportas, P., Vasdekis, V. G. S. (2010) A novel proposal construction for reversible jump MCMC, PDF (to appear in Biometrika)

Invited papers

Refereed journal publications

2011

• Turro E, Su S-Y, Goncalves A, Coin LJM, Richardson S and Lewin A (2011). Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biology. 12:R13. journal page.

2010

• Blangiardo M; Cassese A; Richardson S. (2010). sdef: an R package to synthesize lists of significant features in related experiments. BMC Bioinformatics. 11:270.journal page
• Bottolo L; Richardson S. (2010). Evolutionary Stochastic Search for Bayesian Model Exploration. BAYESIAN ANAL. 5:583-618. journal page.
• Papathomas M, Molitor J, Richardson S, Riboli E and Vineis P (2010), Examining the Joint Effect of Multiple Risk Factors Using Exposure Risk Profiles: Lung Cancer in Non-Smokers. Environmental Health Perspectives, journal page.
• Molitor J; Papathomas M; Jerrett M; Richardson S. (Jul 2010). Bayesian profile regression with an application to the National Survey of Children's Health. Biostatistics. 11:484-498, journal page
• Paige AJ; Zucknick M; Janczar S; Paul J; Mein CA; Taylor KJ; Stewart M; Gourley C; et al. (Mar 2010). WWOX tumour suppressor gene polymorphisms and ovarian cancer pathology and prognosis. Eur J Cancer. 46:818-825, jorunal page
• Petretto E; Bottolo L; Langley SR; Heinig M; McDermott-Roe C; Sarwar R; Pravenec M; Hubner N; et al. (Apr 2010). New insights into the genetic control of gene expression using a Bayesian multi-tissue approach. PLoS Comput Biol. 6:e1000737. journal page.
• Turro E, Lewin A, Rose A, Dallman M and Richardson S (2010), MMBGX: a method for estimating isoform and gene-level expression from whole transcript Affymetrix arrays that accounts for and exploits multi-match probes. Nucleic Acids Research Vol. 38, No. 1 e4. journal page

2009

• Broet P; Tan P; Alifano M; Camilleri-Broet S; Richardson S. (2009). Finding exclusively deleted or amplified genomic areas in lung cancer adenocarcinomas using a novel chromosomal pattern analysis. BMC Medical Genomics. 2:43. journal page
• Kulinskaya E and Lewin A (2009), On fuzzy familywise error rate and false discovery rate procedures for discrete distributions. Biometrika. 96:201-211. journal page
• Kulinskaya E and Lewin A (2009), Testing for linkage and Hardy-Weinberg disequilibrium. Ann Hum Genet. 73:253-262.
• Ratmann O; Andrieu C; Wiuf C; Richardson S. (30 Jun 2009). Model criticism based on likelihood-free inference, with an application to protein network evolution. Proc Natl Acad Sci U S A. 106:10576-10581.journal page

2008

• Blangiardo M; Richardson S. (2008). A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips. BMC Bioinformatics. 9:512.journal page
• 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
• Lau, J. W. and Green P. J. (2007) Bayesian Model Based Clustering Procedures Journal of Computational and Graphical Statistics vol: 16 , Pages: 525 - 558, journal page
• 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)
• Ratmann O; Jorgensen O; Hinkley T; Stumpf M; Richardson S; Wiuf C. (Nov 2007). Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum. PLOS COMPUT BIOL. 3:2266-2278, journal page
• 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

Technical reports and discussion contributions

• Richardson, S. (2010). Discussion of Meinshausen, N. and Buhlmann, P. Stablity selection. J ROY STAT SOC B. 72:448-451. publisher page
• Richardson, S. and Bottolo, L. (Nov 2008). Contribution to the discussion of Fan, J. and Lv, J. Sure independence screening for ultrahigh dimensional feature space. J ROY STAT SOC B. 70:891-892. publisher page

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