BioSS Publications 2009-2010

Methodology

Beale C.M., Lennon J.J., Yearsley J.M., Brewer M.J. & Elston D.A. 2010. Regression analysis of spatial data. Ecology Letters 13, 246-264.

Bierman S. & Glasbey C.A. 2009. A graphical method for dating chicks using bivariate body measurements. Journal of Agricultural, Biological, and Environmental Statistics 14, 443-451.

Bierman S., Butler A., Marion G. & Kühn I. 2010. Bayesian image restoration models for combining expert knowledge on recording activity with species distribution data. Ecography 33, 451-460.

Blanchet J. & Vignes M. 2009. A model-based approach to gene clustering with missing observation reconstruction in a Markov random field framework. Journal of Computational Biology 16, 475-486.

Braga R., Horgan G.W. & Glasbey C.A. 2010. Optical metrology in agriculture. In Agriculture Research and Technology, Eds. K. Bundgaard & L. Isaksen, 303-329. Nova Science Publishers. ISBN 1607418509.

Brewer M.J., Beale C.M., Baker N.E. & Lennon J.J. 2010. Modelling observer effort in spatiotemporal modelling of Tanzanian bird data. In International Workshop on Spatio-Temporal Modelling (METMA V), Eds. W. González-Manteiga et al., 38-41. Unidixital. ISBN 978-84-934272-8-3.

Butler A., Doherty R. & Marion G. 2009. Model averaging to combine simulations of future global vegetation carbon stocks. Environmetrics 20, 791-811.

Davidson R.S., Marion G., White P.C.L. & Hutchings M.R. 2009. Use of host population reduction to control wildlife infection: rabbits and paratuberculosis. Epidemiology and Infection 137, 131-138.

Dondelinger F., Lebre S. & Husmeier D. 2010. Heterogeneous continuous dynamic Bayesian networks with flexible structure and inter-time segment information sharing. In Proceedings of the International Conference on Machine Learning (ICML 2010), Eds. J. Furnkranz & T. Joachims, 303- 310. Omnipress. ISBN 978-1-60558-907-7.

Faisal M.A., Dondelinger F., Husmeier D. & Beale C. 2010. Inferring species interaction networks from species abundance data: a comparative evaluation of various statistical and machine learning methods. Ecological Informatics 5, 451-464.

Glasbey C.A. & Khondoker M.R. 2009. Efficiency of functional regression estimators for combining multiple laser scans of cDNA microarrays. Biometrical Journal 51, 45-55.

Glasbey C.A. 2009. Two-dimensional generalisations of dynamic programming for image analysis. Statistics and Computing 19, 49-56.

Grzegorczyk M. & Husmeier D. 2009. Avoiding spurious feedback loops in the reconstruction of gene regulatory networks with dynamic Bayesian networks. In Pattern Recognition in Bioinformatics, Eds. V. Kadirkamanathan et al., 113-124. Springer Verlag. ISBN 978-3-642-04030-6.

Grzegorczyk M. & Husmeier D. 2009. Modelling non-stationary gene regulatory processes with a non-homogeneous dynamic Bayesian network and the change point process. In Proceedings of the Sixth International Workshop on Computational Systems Biology (WCSB 2009), Eds. T. Manninen (et al)., 51- 54. Tampere International Center for Signal Processing, Finland. ISBN 978-952-15-2160-7.

Grzegorczyk M. & Husmeier D. 2009. Non-stationary continuous dynamic Bayesian networks. In Advances in Neural Information Processing Systems (NIPS), Eds. Bengio et al., 682-690. Curran Associates. ISBN 9781605603520.

Grzegorczyk M., Husmeier D. & Rahnenfuehrer J. 2010. Modelling non-stationary gene regulatory processes. Advances in Bioinformatics 2010, ID 749848.

Hackett C.A., Russell J.R., Jorgensen L., Gordon S. & Brennan R.M. 2010. Multi-environment QTL mapping in blackcurrant (Ribes nigrum L.) using mixed models. Theoretical and Applied Genetics 121, 1483-1488.

Lawson D.J. & Jensen H.J. 2009. The role of weak selection and high mutation rates in nearly neutral evolution. Journal of Theoretical Biology 257, 696-703.

Lehrach W.P. & Husmeier D. 2009. Segmenting bacterial and viral DNA sequence alignments with a transdimensional phylogenetic factorial hidden Markov model. Applied Statistics 58, 307-327.

Lewis F.I., Gunn G.J., McKendrick I.J. & Murray F.M. 2009. Bayesian inference for within-herd prevalence of Leptospira interrogans serovar Hardjo using bulk milk antibody testing. Biostatistics 10, 719-728.

Lin K. & Husmeier D. 2009. Modelling transcriptional regulation with a mixture of factor analyzers and variational Bayesian expectation maximization. EURASIP Journal on Bioinformatics and Systems Biology 2009, ID 601068.

Lin K. & Husmeier D. 2010. Mixtures of factor analyzers for modelling transcriptional regulation. In Learning and Inference in Computational Systems Biology, Eds. N. Lawrence (et al), 153-200. MIT Press. ISBN 978 0 262 01386 4.

Magurran A.E., Baillie S.R., Buckland S.T., Dick J.McP., Elston D.A., Scott E.M., Smith R.I., Somerfield P.J. & Watt A.D. 2010. Long-term datasets in biodiversity research and monitoring: assessing change in ecological communities through time. Trends in Ecology and Evolution 25, 574-582.

Mantzaris A.V. & Husmeier D. 2009. Distinguishing regional from within-codon rate heterogeneity in DNA sequence alignments. In Pattern Recognition in Bioinformatics, Eds. V. Kadirkamanathan et al., 187-198. Springer Verlag. ISBN 978-3-642-04030-6.

Marion G., Bierman S., Butler A., Catterall S., Cook A., Doherty R., Kuhn I., Reineking B., Schweiger O. & Hulme P. 2010. Statistical aspects of biodiversity risk assessment. In Atlas of Biodiversity Risk, Eds. J. Settele et al., 58-61. Pensoft, Sofia & Moscow. ISBN 978-954-642-446-4.

Marion G., Grabaum R., Bierman S., Butler A., Grescho V., Spangenberg J., Kuhn I., Hammen V., Hickler T., Hulme P., Douguet J.M., Peterson K., Potts S., Reginster I., Maxim L., Omann I. & Settele J. 2010. Biodiversity risk assessment for Europe - putting it all together. In Atlas of Biodiversity Risk, Eds. J. Settele et al., 252-253. Pensoft, Sofia & Moscow. ISBN 978-954-642-446-4.

Marot G. & Mayer C-D. 2009. Sequential analysis for microarray data based on sensitivity and metaanalysis. Statistical Applications in Genetics and Molecular Biology 8.

Marot G., Foulley J.L., Mayer C-D. & Jaffrezic F. 2009. Moderated effect size and p-value combinations for microarray meta-analyses. Bioinformatics 25, 2692-2699.

Milne I., Bayer M.M., Cardle L., Shaw P., Stephen G., Wright F. & Marshall D.F. 2010. Tablet - next generation sequence assembly visualization. Bioinformatics 26, 401-402.

Milne I., Lindner D., Bayer M.M., Husmeier D., McGuire G., Marshall D.F. & Wright F. 2009. TOPALi v2: a rich graphical interface for evolutionary analyses of multiple alignments on HPC clusters and multi-core desktops. Bioinformatics 25, 126-127.

Navajas E., Glasbey C.A., Fisher A.V., Ross D., Hyslop J.J., Richardson R.I., Simm G. & Roehe R. 2010. Assessing beef carcass composition using computed tomography spirals of primal cuts. Meat Science 84, 30-38.

Paroli R. & Spezia L. 2010. Reversible jump MCMC methods and segmentation algorithms in hidden Markov models. Australian & New Zealand Journal of Statistics 52, 151-166.

Polechova J., Barton N. & Marion G. 2009. Species range: adaptation in space and time. American Naturalist 174, E186-204.

Potts J.M., Chapman S.J., Towers W. & Campbell C.D. 2009. Comments on ‘Baseline values and change in the soil, and implications for monitoring’ by R.M. Lark, P.H. Bellamy and G.J.D. Kirk. European Journal of Soil Science 60, 481-483.

Reginster I., Rounsevell M., Butler A. & Dendoncker N. 2010. Land use change scenarios for ALARM. In Atlas of Biodiversity Risk, Eds. J. Settele (et al)., 100-105. Pensoft, Sofia & Moscow. ISBN 978-954-642-446-4.

Roberts A.M.I. 2009. Smoothing methods. In Phenological Research: Methods for Environmental and Climate Change Analysis, Eds. M.R. Keatley & I.L. Hudson, 255-269. Springer Verlag. ISBN 978-90- 481-3334-5.

Spangenberg J., Fronzek S., Hammen V., Hickler T., Hulme P., Jäger J., Jylhä K., Kühn I., Marion G., Maxim L., Monterroso I., O’Connor M., Omann I., Reginster I., Rodríguez-Labajos B., Rounsevell M., Sykes M. & Vighi M. 2010. The ALARM scenarios: storylines and simulations for assessing biodiversity risks in Europe. In Atlas of Biodiversity Risk, Eds. J. Settele et al., 10-15. Pensoft, Sofia & Moscow. ISBN 978-954-642-446-4.

Spezia L. 2009. Reversible jump and the label switching problem in hidden Markov models. Journal of Statistical Planning and Inference 139, 2305-2315.

Spezia L. 2010. Bayesian analysis of multivariate Gaussian hidden Markov models with an unknown number of components. Journal of Time Series Analysis 31, 1-11.

Zhang X-S., Chase-Topping M.E., McKendrick I.J., Savill N.J. & Woolhouse M.E.J. 2010. Spread of E. coli O157 infection among Scottish cattle farms: stochastic models and model selection. Epidemics 2, 11-20.

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