BioSS Publications 2007-2008

Methodology

Allcroft, D.J.Glasbey, C.A. & Paulo, M.J. 2007. A latent Gaussian model for multivariate consumption data. Food Quality and Preference 18, 508-516.

Blanchet, J. & Vignes, M. 2007. Combined expression data with missing values and gene interaction network analysis: a Markovian integrated approach. In Proceedings of the 7th IEEE Symposium on Bioinformatics and Bioengineering, 366-373. IEEE Computer Society, Boston, Massachusetts, USA. ISBN 978-1-4244-1509-0.

Braga, R., Horgan, G.W., Enes, A.M., Miron, D., Rabelo, G. & Filho, J.B.B. 2007. Biological feature isolation by wavelets in biospeckle laser images. Computers and Electronics in Agriculture 58, 123-132.

Braga, R., Silva, B.O., Rabelo, G., Costa, R.M., Enes, A.M., Cap, N., Rabal, H., Arizaga, R., Trivi, M. & Horgan, G.W. 2007. Reliability of biospeckle image analysis. Optics and Laser in Engineering 45, 390-395.

Brewer, M.J. & Nolan, A.J. 2007. Variable smoothing in Bayesian intrinsic autoregressions. Environmetrics 18, 841-857.

Brewer, M.J., Tetzlaff, D., Malcolm, I.A. & Soulsby, C. 2008. A temporal compositional analysis of water quality monitoring data. In International Workshop on Spatio-Temporal Modelling (METMA4), Eds. Cocchi, D., Mateu, J., Montes, F., Otranto, E. Porcu, E. and Usai, U, 135-140. Editrice Democratica Sarda (EDES), Sassari, Sardinia. ISBN 88-6025-098-6.

Brewer, M.J., Tetzlaff, D., Waldron, S. & Soulsby, C. 2007. Temporal smoothing of compositional data on water quality. In Proceedings of the 22nd International Workshop on Statistical Modelling, Eds. del Castillo, J., Espinal, A. and Puig, P, 121-125. l'Institut d'Estadistica de Catalunya, Barcelona, Spain. ISBN 9788469059432.

Butler, A. & Glasbey, C.A. 2008. A latent Gaussian model for compositional data with zeros (with publisher's corrigendum). Journal of the Royal Statistical Society, Series C - Applied Statistics 57, 505-520.

Butler, A., Heffernan, J.E., Tawn, J.A. & Flather, R.A. 2007. Trend estimation in extremes of synthetic North Sea surges. Journal of the Royal Statistical Society, Series C - Applied Statistics 56, 395-414.

Butler, A., Heffernan, J.E., Tawn, J.A., Flather, R.A. & Horsburgh, K.J. 2007. Extreme value analysis of decadal variations in storm surge elevations. Journal of Marine Systems 67, 189-200.

Chatterjee, A.Horgan, G.W. & Theobald, C.M. 2008. Exposure assessment for pesticide intake from multiple food products: a Bayesian latent-variable approach. Risk Analysis 28, 1727-1736.

Cook, A., Marion, G., Butler, A. & Gibson, G. 2007. Bayesian inference for the spatio-temporal invasion of alien species. Bulletin of Mathematical Biology 69, 2005-2025.

Cook, A., Otten, W., Marion, G., Gibson, G. & Gilligan, C.A. 2007. Estimation of multiple transmission rates for epidemics in heterogeneous populations. Proceedings of the National Academy of Sciences USA 104, 20392-20397.

Davidson, R.S., Marion, G. & Hutchings, M.R. 2008. Effects of host social hierarchy on disease persistence. Journal of Theoretical Biology 253, 424-433.

deOliviera, R., Braga, R., Neto, A.E.D.R., Trinidade, N., Mori, F.A. & Horgan, G.W. 2008. Reliability of wood grain orientation by laser illumination. Biosystems Engineering 100, 479-483.

Glasbey, C.A. & Allcroft, D.J. 2008. A spatiotemporal auto-regressive moving average model for solar radiation. Applied Statistics 57, 343-355.

Glasbey, C.A., Forster, T. & Ghazal, P. 2007. Estimation of expression levels in spotted microarrays with saturated pixels. Statistical Applications in Genetics and Molecular Biology 6, 34.

Glasbey, C.A. & van der Heijden, G.W.A.M. 2007. Alignment and sub-pixel interpolation of images using Fourier methods. Journal of Applied Statistics 34, 217-230.

Glasbey, C.A., van der Heijden, G.W.A.M., Toh, V. & Gray, A.J. 2007. Colour displays for categorical images. Color Research and Application 32, 304-309.

Grzegorczyk, M. & Husmeier, D. 2008. Improving the structure MCMC sampler for Bayesian networks by introducing a new edge reversal move. Machine Learning 71, 265-305.

Grzegorczyk, M., Husmeier, D., Edwards, K., Ghazal, P. & Millar, A.J. 2008. Modelling non-stationary gene regulatory processes with a non-homogeneous Bayesian network and the allocation sampler. Bioinformatics 24, 2071-2078.

Grzegorczyk, M., Husmeier, D. & Werhli, A.V. 2008. Reverse engineering gene regulatory networks with various machine learning methods. In Analysis of Microarray Data: Network based Approaches, Eds. F. Emmert-Streibl and M. Dehmer, 101-142. Wiley, Weinheim. ISBN 978-3-527-31822-3.

Hackett, C.A.Milne, I., Bradshaw, J.E. & Luo, Z.W. 2007. TetraploidMap for Windows: linkage map construction and QTL mapping in autotetraploid species. Journal of Heredity 98, 727-729.

Horgan, G.W. 2007. Sample size and replication in 2D gel electrophoresis studies. Journal of Proteome Research 6, 2884-2887.

Horgan, G.W., Molchanov, I., Scherbakov, V. & Zuyev, S. 2007. Approximate models for bacteria leaching. Applied Mathematics and Computation 188, 1941-1954.

Husmeier, D. & Mantzaris, A.V. 2008. Addressing the shortcomings of three recent Bayesian methods for detecting interspecific recombination in DNA sequence alignments. Statistical Applications in Genetics and Molecular Biology 7, Article34.

Husmeier, D. & Werhli, A.V. 2007. Bayesian integration of biological prior knowledge into the reconstruction of gene networks with Bayesian networks. In CSB - Conference on Computational Systems Bioinformatics, Eds. Y. Xin Tan, 85-95. Imperial College Press, London. ISBN 10:1-86094-872-3.

Khondoker, M.R., Glasbey, C.A. & Worton, B.J. 2007. A comparison of parametric and nonparametric methods for normalising cDNA microarray data. Biometrical Journal 49, 815-823.

Krishnarajah, I., Marion, G. & Gibson, G. 2007. Novel bivariate moment-closure approximations. Mathematical Biosciences 208, 621-643.

Kvarnstrom, M. & Glasbey, C.A. 2007. Estimation of centres and radial intensity profiles of spherical particles in digital microscopy. Biometrical Journal 49, 300-311.

Lawson, D.J. & Jensen, H.J. 2008. Understanding clustering in type space using field theoretic techniques. Bulletin of Mathematical Biology 70, 1065-81.

Lawson, D.J. & Jensen, H.J. 2007. Neutral evolution as diffusion in phenotype space: reproduction with mutation but without selection. Physics Review Letters 98, 098102.

Marion, G., Smith, L., Swain, D.L., Davidson, R.S. & Hutchings, M.R. 2008. Understanding the impact of foraging behaviour on disease risks from faeces in spatially heterogeneous systems. Journal of Agricultural Science 146, 507-520.

Marion, G., Walker, D.M., Cook, A., Swain, D.L. & Hutchings, M.R. 2007. Towards an integrated approach to a stochastic process-based modelling: with applications to behaviour and spatio-temporal spread. In Redesigning Animal Agriculture, Eds. Swain, D. L., Charmley, E., Steel, J. & Coffey, S, 144-170. CABI, Oxford, UK. ISBN 13:978 1 84593 223 7.

Nath, M., Woolliams, J.A. & Bishop, S.C. 2008. Assessment of the dynamics of microparasite infections in genetically homogeneous and heterogeneous populations using a stochastic epidemic model. Journal of Animal Science 86, 1747-1757.

Nonyane, A. & Theobald, C.M. 2008. Multiplicative models for combining information from several sensory experiments: a Bayesian analysis. Food Quality and Preference 19, 260-266.

Nonyane, A. & Theobald, C.M. 2007. Design sequences for sensory studies: achieving balance for carry-over and position effects. British Journal of Mathematical and Statistical Psychology 60, 339-349.

Roberts, A.M.I. 2008. Exploring relationships between phenological and weather data using smoothing. International Journal of Biometeorology 52, 463-470.

Roberts, A.M.I., Theobald, C.M. & McNeil, M. 2007. Calibration of quantitative PCR assays. Journal of Agricultural, Biological, and Environmental Statistics 12, 364-378.

Sales, J., Vali, L., Hoyle, D., Yates, C., Amyes, S.G.B. & McKendrick, I.J. 2007. The interaction between dam methylation sites and Xba1 restriction digest sites in Escherichia coli O157:H7 EDL933. Journal of Applied Microbiology 102, 820-825.

Sims, M., Elston, D.A., Harris, M.P. & Wanless, S. 2007. Incorporating variance uncertainty into a power analysis of monitoring designs. Journal of Agricultural, Biological, and Environmental Statistics 12, 236-249.

Sims, M., Elston, D.A., Larkham, A., Nussey, D.H. & Albon, S.D. 2007. Identifying when weather influences life history traits of grazing herbivores. Journal of Animal Ecology 76, 761-770.

Storch, D., Šizling, A., Reiff, J., Polechova, J., Šizlingová, E. & Gaston, K J. 2008. The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales. Ecology Letters 11, 771-794.

Werhli, A.V. & Husmeier, D. 2008. Gene regulatory network reconstruction by Bayesian integration of prior knowledge and/or different experimental conditions. Journal of Bioinformatics and Computational Biology 6, 543-572.

Werhli, A.V. & Husmeier, D. 2007. Reconstructing gene regulatory networks with Bayesian networks by combining expression data with multiple sources of prior knowledge. Statistical Applications in Genetics and Molecular Biology 6, Article 15.

Wood, A.J. & Coe, J.B. 2007. A fitness based analysis of Daisyworld. Journal of Theoretical Biology 249, 190-197.

Wood, J.C., McKendrick, I.J. & Gettinby, G. 2007. A simulation model to assess herd-level intervention strategies against E. coli O157. Epidemiology and Infection 135, 749-764.

Swain, D.L., Hutchings, M.R. & Marion, G. 2007. Using a spatially explicit model to understand the impact of search rate and search distance on spatial heterogeneity within an herbivore grazing system. Ecological Modelling 203, 319-326.

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