Publications
150 results found
Geneletti S, Richardson S, Best N, 2009, Adjusting for selection bias in retrospective, case-control studies, BIOSTATISTICS, Vol: 10, Pages: 17-31, ISSN: 1465-4644
- Author Web Link
- Cite
- Citations: 92
Molitor N-T, Best N, Jackson C, et al., 2009, Using Bayesian graphical models to model biases in observational studies and to combine multiple sources of data: application to low birth weight and water disinfection by-products, JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY, Vol: 172, Pages: 615-637, ISSN: 0964-1998
- Author Web Link
- Cite
- Citations: 18
Broet P, Tan P, Alifano M, et al., 2009, Finding exclusively deleted or amplified genomic areas in lung cancer adenocarcinomas using a novel chromosomal pattern analysis, BMC Medical Genomics, Vol: 2
Blangiardo M, Richardson S, 2008, A Bayesian calibration model for combining different pre-processing methods in Affymetrix chips, BMC BIOINFORMATICS, Vol: 9, ISSN: 1471-2105
- Author Web Link
- Open Access Link
- Cite
- Citations: 4
Jackson CH, Richardson S, Best NG, 2008, Studying place effects on health by synthesising individual and area-level outcomes, SOCIAL SCIENCE & MEDICINE, Vol: 67, Pages: 1995-2006, ISSN: 0277-9536
- Author Web Link
- Cite
- Citations: 19
Bickel P, Buehlmann P, Yao Q, et al., 2008, Sure independence screening for ultrahigh dimensional feature space Discussion, Publisher: WILEY
- Author Web Link
- Cite
- Citations: 10
Abellan JJ, Richardson S, Best N, 2008, Use of space-time models to investigate the stability of patterns of disease, ENVIRONMENTAL HEALTH PERSPECTIVES, Vol: 116, Pages: 1111-1119, ISSN: 0091-6765
- Author Web Link
- Cite
- Citations: 75
Jackson C, Best N, Richardson S, 2008, Hierarchical related regression for combining aggregate and individual data in studies of socio-economic disease risk factors, JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY, Vol: 171, Pages: 159-178, ISSN: 0964-1998
- Author Web Link
- Cite
- Citations: 60
Zucknick M, Richardson S, Stronach EA, 2008, Comparing the characteristics of gene expression profiles derived by univariate and multivariate classification methods, STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, Vol: 7, ISSN: 2194-6302
- Author Web Link
- Cite
- Citations: 40
Jarup L, Morris S, Richardson S, et al., 2007, Down syndrome in births near landfill sites, PRENATAL DIAGNOSIS, Vol: 27, Pages: 1191-1196, ISSN: 0197-3851
- Author Web Link
- Cite
- Citations: 14
Ratmann O, Jorgensen O, Hinkley T, et al., 2007, Using likelihood-free inference to compare evolutionary dynamics of the protein networks of H. pylori and P. falciparum, PLOS Computational Biology, Vol: 3, ISSN: 1553-734X
Gene duplication with subsequent interaction divergence is one of the primary driving forces in the evolution of genetic systems. Yet little is known about the precise mechanisms and the role of duplication divergence in the evolution of protein networks from the prokaryote and eukaryote domains. We developed a novel, model-based approach for Bayesian inference on biological network data that centres on approximate Bayesian computation, or likelihood-free inference. Instead of computing the intractable likelihood of the protein network topology, our method summarizes key features of the network and, based on these, uses a MCMC algorithm to approximate the posterior distribution of the model parameters. This allowed us to reliably fit a flexible mixture model that captures hallmarks of evolution by gene duplication and subfunctionalization to protein interaction network data of Helicobacter pylori and Plasmodium falciparum. The 80% credible intervals for the duplication–divergence component are [0.64, 0.98] for H. pylori and [0.87, 0.99] for P. falciparum. The remaining parameter estimates are not inconsistent with sequence data. An extensive sensitivity analysis showed that incompleteness of PIN data does not largely affect the analysis of models of protein network evolution, and that the degree sequence alone barely captures the evolutionary footprints of protein networks relative to other statistics. Our likelihood-free inference approach enables a fully Bayesian analysis of a complex and highly stochastic system that is otherwise intractable at present. Modelling the evolutionary history of PIN data, it transpires that only the simultaneous analysis of several global aspects of protein networks enables credible and consistent inference to be made from available datasets. Our results indicate that gene duplication has played a larger part in the network evolution of the eukaryote than in the prokaryote, and suggests that single gene duplications with immedia
Turro E, Bochkina N, Hein A-MK, et al., 2007, BGX: a Bioconductor package for the Bayesian integrated analysis of Affymetrix GeneChips, BMC BIOINFORMATICS, Vol: 8, ISSN: 1471-2105
- Author Web Link
- Cite
- Citations: 17
Abellan JJ, Fecht D, Best N, et al., 2007, Bayesian analysis of the multivariate geographical distribution of the socio-economic environment in England, 3rd International Workshop on Spatio-Temporal Modelling, Publisher: WILEY, Pages: 745-758, ISSN: 1180-4009
- Author Web Link
- Cite
- Citations: 13
Abellan JJ, Richardson S, Best N, 2007, Spatial versus spatiotemporal disease mapping, 19th Annual Conference of the International-Society-for-Environmental-Epidemiology, Publisher: LIPPINCOTT WILLIAMS & WILKINS, Pages: S111-S111, ISSN: 1044-3983
Barton SJ, Richardson S, Perkins DN, et al., 2007, Using statistical models to identify factors that have a role in defining the abundance of ions produced by tandem MS, ANALYTICAL CHEMISTRY, Vol: 79, Pages: 5601-5607, ISSN: 0003-2700
- Author Web Link
- Cite
- Citations: 20
Zucknick M, Holmes C, Richardson S, 2007, MCMC methods for bayesian variable selection in large-scale genomic applications, 35th European Mathematical Genetics Meeting, Publisher: BLACKWELL PUBLISHING, Pages: 558-559, ISSN: 0003-4800
Lewin A, Bochkina N, Richardson S, 2007, Fully bayesian mixture model for differential gene expression: Simulations and model checks, STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY, Vol: 6, ISSN: 2194-6302
- Author Web Link
- Cite
- Citations: 22
Blangiardo M, Richardson S, 2007, Statistical tools for synthesizing lists of differentially expressed features in related experiments, GENOME BIOLOGY, Vol: 8, ISSN: 1474-760X
- Author Web Link
- Open Access Link
- Cite
- Citations: 12
Bochkina N, Richardson S, 2007, Tail posterior probability for Inference in Pairwise and Multiclass Gene Expression Data, Biometrics
Jarup L, Morris S, Richardson S, et al., 2006, Down's syndrome in births near landfill sites, EPIDEMIOLOGY, Vol: 17, Pages: S348-S348, ISSN: 1044-3983
Hein A-MK, Richardson S, 2006, A powerful method for detecting differentially expressed genes from GeneChip arrays that does not require replicates, BMC BIOINFORMATICS, Vol: 7, ISSN: 1471-2105
- Author Web Link
- Cite
- Citations: 10
Jackson C, Best N, Richardson S, 2006, Improving ecological inference using individual-level data, STATISTICS IN MEDICINE, Vol: 25, Pages: 2136-2159, ISSN: 0277-6715
- Author Web Link
- Cite
- Citations: 101
Schischmanoff PO, Naccache J-M, Carrere A, et al., 2006, Progressive pulmonary sarcoidosis is associated with over-expression of TYK2 and p21<SUP>waf1/CiP1</SUP>, SARCOIDOSIS VASCULITIS AND DIFFUSE LUNG DISEASES, Vol: 23, Pages: 101-107, ISSN: 1124-0490
- Author Web Link
- Cite
- Citations: 6
Broët P, Richardson S, 2006, Detection of gene copy number changes in CGH microarrays using a spatially correlated mixture model, BIOINFORMATICS, Vol: 22, Pages: 911-918, ISSN: 1367-4803
- Author Web Link
- Cite
- Citations: 55
Parry S, Hadaschik D, Blancher C, et al., 2006, Glycomics investigation into insulin action, BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, Vol: 1760, Pages: 652-668, ISSN: 0304-4165
- Author Web Link
- Cite
- Citations: 16
Lewin A, Richardson S, Marshall C, et al., 2006, Bayesian modeling of differential gene expression, BIOMETRICS, Vol: 62, Pages: 1-9, ISSN: 0006-341X
- Author Web Link
- Cite
- Citations: 58
Richardson S, Abellan JJ, Best N, 2006, Bayesian spatio-temporal analysis of joint patterns of male and female lung cancer risks in Yorkshire (UK), STATISTICAL METHODS IN MEDICAL RESEARCH, Vol: 15, Pages: 385-407, ISSN: 0962-2802
- Author Web Link
- Cite
- Citations: 94
Richardson S, 2005, Statistics for studies of human welfare - Discussion, INTERNATIONAL STATISTICAL REVIEW, Vol: 73, Pages: 263-264, ISSN: 0306-7734
Hein AMK, Richardson S, Causton HC, et al., 2005, BGX: a fully Bayesian integrated approach to the analysis of Affymetrix GeneChip data, BIOSTATISTICS, Vol: 6, Pages: 349-373, ISSN: 1465-4644
- Author Web Link
- Cite
- Citations: 42
Seaman SR, Richardson S, 2005, Equivalence of prospective and retrospective models in the Bayesian analysis of case-control studies (vol 91, pg 15, 2004), BIOMETRIKA, Vol: 92, Pages: 505-505, ISSN: 0006-3444
This data is extracted from the Web of Science and reproduced under a licence from Thomson Reuters. You may not copy or re-distribute this data in whole or in part without the written consent of the Science business of Thomson Reuters.