BioSS Publications 2005-2006

Methodology

Bierman, S. , Elston, D.A. , Lambin, X., Fairbairn, J.P., Tidhar, D. & Petty, S.J. 2006. Changes over time in the spatiotemporal dynamics of field voles ( Microtus agrestis L.). American Naturalist 167 , 583-590.

Brewer, M.J. , Filipe, J.A.N., Elston, D.A. , Dawson ,  L.A. , Mayes, R.W., Soulsby, C. & Dunn, S.M. 2005. A hierarchical model for compositional data analysis. Journal of Agricultural, Biological, and Environmental Statistics 10 , 19-34.

Coe, J.B. & Mao, X. 2005. Gompertz mortality law and scaling behavior of the Penna model. Physical Review E 72 , 051925.

Durban , J.W. & Elston, D.A. 2005. Mark-recapture with occasion and individual effects: abundance estimation through Bayesian model selection in a fixed dimensional parameter space. Journal of Agricultural, Biological, and Environmental Statistics 10 , 291-305.

Durban , J.W., Elston, D.A. , Ellifrit, D.K., Dickson, E., Hammond , P.S. & Thompson, P.M. 2005. Multisite mark-recaupture for cetaceans: population estimates with Bayesian model averaging. Marine Mammal Science 21 , 80-92.

Gibson, G., Otten, W., Filipe, J.A.N., Cook, A. , Marion ,  G. & Gilligan ,  C.A. 2006. Bayesian estimation for percolation models of disease spread in plant populations. Statistics and Computing 16 , 391-402.

Glasbey ,  C.A. 2006. Warping of electrophoresis gels using generalisations of dynamic programming. In Interdisciplinary Statistics and Bioinformatics , Eds. S. Barber, P.D. Baxter, K.V. Mardia and R.E. Walls, 71-74. Leeds University Press, Leeds .

Glasbey ,  C.A. & Khondoker, M.R. 2005. Correction for pixel censoring in cDNA microarrays. In Statistical Solutions to Modern Problems: Proceedings of the 20th International Workshop on Statistical Modelling , Eds. A.R. Francis, K.M. Matawie, A. Oshlack, G.K. Smyth, 17-31. University of Western Australia , Sydney , Australia .

Glasbey ,  C.A. , Vali, L. & Gustafsson, J.S. 2005. A statistical model for unwarping of 1-D electrophoresis gels. Electrophoresis 26 , 4237-4242.

Holtrop, G. , Petrie, J., McElhiney, J. & Dennison, N. 2006. Can general anaesthesia be used for the Paralytic Shellfish Poison bioassay? Toxicon 47 , 336-347.

Horgan, G.W. 2005. Interpretation of two-stage experiments. Laboratory Animals 39 , 75-79.

Horgan, G.W. 2005. Optimising two-dye microarray designs for estimation. Journal of Biotechnology 118 , 1-8.

Horgan, G.W. & Ball, B.C. 2005. Modelling the effect of water distribution and hysteresis on air-filled pore space. European Journal of Soil Science 56 , 647-654.

Horgan, G.W. , Travis, A.J. & Liang, J. 2005. Automatic recognition of maize cell types using context information. Micron 36 , 163-167.

Hudson ,  I. , Keatley, M. & Roberts, A.M.I. 2005. Statistical methods in phenological research. In Statistical Solutions to Modern Problems: Proceedings of the 20th International Workshop on Statistical Modelling , Eds. A.R. Francis, K.M. Matawie, A. Oshlack, G.K. Smyth, 259-270. University of Western Sydney , Sydney , Australia .

Husmeier, D. 2005. Discriminating between rate heterogeneity and interspecific recombination in DNA sequence alignments with phylogenetic factorial hidden Markov models. Bioinformatics 21 , ii166-ii172.

Husmeier, D. 2006. Detecting mosaic structures in DNA sequence alignments. In Biomathematics: Modelling and Simulation , Eds. Misra, J.C. 1-35, ISBN 981-238-110-4. World Scientific, London .

Husmeier, D. & Wright, F. 2005. Detecting recombination in DNA sequence alignments. In Probabilistic Modeling in Bioinformatics and Medical Informatics , Eds. Husmeier, D., Dybowski, R. & Roberts, S., 147-190. Springer Verlag.

Husmeier, D. , Wright, F. & Milne,  I. 2005. Detecting interspecific recombination with a pruned probabilistic divergence measure. Bioinformatics 21 , 1797-1806.

Kedzierska, A. & Husmeier, D. 2006. A heuristic Bayesian method for segmenting DNA sequence alignments and detecting evidence for recombination and gene conversion. Statistical Applications in Genetics and Molecular Biology 5 , Article 27.

Khondoker, M.R. , Glasbey ,  C.A. & Worton, B.J. 2006. Statistical estimation of gene expression using multiple laser scans of microarrays. Bioinformatics 22 , 215-219.

Krishnarajah, I. , Cook, A. , Marion , G. & Gibson, G. 2005. Novel moment closure approximations in stochastic epidemics. Bulletin of Mathematical Biology 67 , 855-873.

Kühn, I., Bierman, S. , Durka, W. & Klotz, S. 2006. Relating geographical variation in pollination types to environmental and spatial factors using novel statistical methods. New Phytologist 72 , 127 - 139.

Lehrach, W.P. , Husmeier, D. & Williams, C.K.I. 2006. A regularized discriminative model for the prediction of protein-peptide interactions. Bioinformatics 22 , 532-540.

Lehrach, W.P. , Husmeier, D. & Williams, C.K.I. 2006. Probabilistic in silico prediction of protein-peptide interactions. In Systems Biology and Regulatory Genomics , Eds. Eskin E., Ideker T., Raphael B. and Workman C, 188-197. Springer Verlag, San Diego, USA.

Marion, G. , Swain, D.L. & Hutchings, M.R. 2005. Understanding foraging behaviour in spatialy heterogenous environments. Journal of Theoretical Biology 232 , 127-142.

Mayer, C-D. & Glasbey, C.A. 2005. Statistical methods in microarray data analysis. In Probabilistic Modelling in Bioinformatics and Medical Informatics , Eds. D. Husmeier, R. Dybowski and S. Roberts, 211-238. Springer Verlag, London.

Paulo, M.J., van der Voet, H., Wood, J.C. , Marion, G. & van Klaveren, J.D. 2006. Analysis of multivariate extreme intakes of food chemicals. Food and Chemical Toxicology 44 , 994-1005.

Sims, M. , Wanless, S., Harris, M.P., Mitchell, I. & Elston, D.A. 2006. Evaluating the power of monitoring plot designs for detecting long-term trends in the numbers of common guillemots. Journal of Applied Ecology 43 , 537-546.

Small, M., Tse, C.K. & Walker, D.M. 2006. Super-spreaders and the rate of transmission of the SARS virus. Physica D 215 , 146-158.

Theobald, C.M. , Roberts, A.M.I. , Talbot, M. & Spink, J.H. 2006. Estimation of economically optimum seed rates for winter wheat from series of trials. Journal of Agricultural Science 144 , 303-316.

Walker, D.M. 2006. Parameter estimation using Kalman filters with constraints. International Journal of Bifurcation and Chaos 16 , 1067-1078.

Walker, D.M. & Marion, G. 2006. Selecting nonlinear stochastic process rate models using information criteria. Physica D 213 , 190-196.

Walker, D.M. , Perez-Barberia, F.J. & Marion, G. 2006. Stochastic modelling of ecological processes using hybrid Gibbs samplers. Ecological Modelling 198 , 40-52.

Walker, D.M. & Small, M. 2006. Detecting unstable fixed points using Kalman filters with constraints. IEEE Transactions on Circuits and Systems I 53 , 2818-2827.

Webster, R., Welham, S.J., Potts, J.M. & Oliver, M.A. 2006. Estimating the spatial scales of regionalized variables by nested sampling, hierarchical analysis of variance and residual maximum likelihood. Computers and Geosciences 32 , 1320-1333.

Werhli, A.V. , Grzegorczyk, M., Chiang, M.T. & Husmeier, D. 2006. Improved Gibbs sampling for detecting mosaic structures in DNA sequence alignments. In Statistics in Genomics and Proteomics , Eds. Urfer W. and Turkman M. A, 23-34. Centro Internacional de Matematica, Coimbra, Portugal.

Werhli, A.V. , Grzegorczyk, M. & Husmeier, D. 2006. Comparative evaluation of reverse engineering gene regulatory networks with relevance networks, graphical Gaussian models and Bayesian networks. Bioinformatics 22 , 2523-2531.

Wood, J.C. , McKendrick, I.J. & Gettinby, G. 2006. A simulation model for the study of the within-animal infection dynamics of E. coli O157. Preventive Veterinary Medicine 74 , 180-193.

Wood, J.C. , McKendrick, I.J. & Gettinby, G. 2006. Assessing the efficacy of within-animal control strategies against E. coli O157: a simulation study. Preventive Veterinary Medicine 74 , 194-211.

Wood, J.C. , Spiers, D.C., Naylor, S.W., Gettinby, G. & McKendrick, I.J. 2006. A continuum model of the within-animal population dynamics of E. coli O157. Journal of Biological Systems 14 , 425-443.

Wood, M. , Jolliffe, I. & Horgan, G.W. 2005. Variable selection for discriminant analysis of fish sounds. Journal of Agricultural, Biological, and Environmental Statistics 10 , 321-336.

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