Publications

  • David Hoyle and Tariq M. Aslam. Generative mathematical modelling to demonstrate virtual simulations of neovascular age related macular degeneration. PLoS One 12(12):e0189053, 2017
  • David C. Hoyle and Andrew Brass. Statistical Mechanics of ontology-based annotations. Physica A 442:284-299, 2016
  • David C. HoyleBenford’s Law in the Natural Sciences. In Theory and Applications of Benford’s Law, pp290-303, S. J. Miller(Ed). Princeton University Press, 2015.
  • H. M. Davey, E. J. M. Cross, C. L. Davey,  K. Gkargkas, D. Delneri, D. C. Hoyle,  S. G. Oliver,  D. B. Kell and Gareth W. Griffith. Genome-wide analysis of longevity in nutrient-deprived Saccharomyces cerevisiae reveals importance ofrecycling in maintaining cell viability. Environmental Microbiology 14 :1249-1260, 2012
  • David. C. Hoyle. Accuracy of Pseudo-Inverse Covariance Learning – A Random Matrix Theory Analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence 33:1479-1481, 2011.
  • David. C. Hoyle. Statistical mechanics of learning orthogonal signals for general covariance models. Journal of Statistical Mechanics, 2010. doi:10.1088/1742-5468/2010/04/P04009 
  • D.C. Hoyle, M. Delderfield, L. Kitching, G. Smith and I. Buchan. Shared Genomics: Developing an Accessible Integrated Analysis Platform for Genome-wide Association Studies. In proceedings of AMIA 2010 Summit on Translational Bioinformatics
  • N. Bivi, M. Romanello, R. Harrison, I. Clarke, David. C. Hoyle, L. Moro, F. Ortolani, A. Bonetti, F. Quadrifoglio, G. Tell and D. Delneri. Identification of secondary targets of N-containing bisphosphonates in mammalian cells via parallel competition analysis of the barcoded yeast deletion collection. Genome Biology 10:R93, 2009
  • D.C. Hoyle, M. Delderfield, L. Kitching, G. Smith and I. Buchan. Shared Genomics: A Platform for emerging interpretation of genetic epidemiology. In proceedings of IEEE conference on Computer Based Medical Systems 2009.
  • D.C. Hoyle, M. Delderfield, L. Kitching, G. Smith and I. Buchan. Shared Genomics: High Performance Computing for distributed insights in genomic medical research. Studies in Health Technology & Informatics 147:232-241, 2009.
  • D.C. Hoyle. Automatic PCA Dimension Selection for High Dimensional Data and Small Sample Size. Journal of Machine Learning Research 9:2733-2759, 2008
  • C. Rennie, H.A. Noyes, S.J. Kemp, H. Hulme, A. Brass and D.C. Hoyle. Strong position-dependent effects of sequence mismatches on signal ratios measured using long   oligonucleotide microarrays. BMC Genomics 9:317, 2008.
  • D. Delneri, D. C. Hoyle, K. Gkargkas, E. J. M. Cross, B. Rash, L. Zeef, H.-S. Leong, H. M. Davey, A. Hayes, D. B. Kell, G. W. Griffith and S. G. Oliver. Identification and characterization of high-flux-control genes of yeast through competition analyses in continuous cultures. Nature Genetics 40(1):113-117, 2008
  • S. Holland, E. Lodwig, T. Sideri, T. Reader, I. Clarke, K. Gkargkas, D.C. Hoyle, D. Delneri, S.G. Oliver, S.V. Avery. Application of the comprehensive set of heterozygous yeast deletion mutants to elucidate the molecular basis of cellular chromium toxicity. Genome Biology 8(12):R268, 2007
  • J. I. Castrillo, L. A. Zeef, D. C. Hoyle, N. Zhang, A. Hayes, D. C. J. Gardner, M. J. Cornell, J. Petty, L. Hakes, L. Wardleworth, M. Brown,W. B. Dunn, D. Broadhurst, S. R. Hart , C. S. Jackson, K. O’Donoghue, S. Hester, T. Dunkley, S. J. Gaskell, N. W. Paton, K.S. Lilley, D. B. Kell and S.G. Oliver. Growth control of the eukaryote cell: A systems biology study in yeast. Journal of Biology 6:4, 2007.
  • L. Edwards-Ingram, P. Gitsham, N. Burton, G. Warhurst, I. Clarke, D. Hoyle, S. G. Oliver and L.Stateva. Genotypic and physiological characterization of Saccharomyces boulardii, the probiotic strain of Saccharomyces cerevisiae. Applied and Environmental Biology 73:2458-2467, 2007
  • D.C. Hoyle and M. Rattray. Statistical mechanics of learning multiple orthogonal signals: Asymptotic theory and fluctuation effects. Physical Review E 75:016101, 2007
  • H. Bhaskar, D.C. Hoyle & S. Singh. Machine Learning in Bioinformatics : A Brief Survey and Recommendations for Practitioners. Computers in Biology and Medicine 36:1104-1125, 2006.
  • R. Bishop, T. Shah, R. Pelle, D. Hoyle, T. Pearson, L. Haines, A. Brass, H. Hulme, P. Graham, E. L. N. Taracha, S. Kanga, C. Lu, B. Hass, J. Wortman, O. White, M. J. Gardner, Nene and E. P. de Villiers. Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage, Nucleic Acids Research 33:5503-55011, 2005
  • J.D. Spalding & D.C. Hoyle. Accuracy of String kernels for protein sequence classification. Proceedings of ICAPR 2005, 3rd International Conference on Advances in Pattern Recognition, Bath, UK, August 2005. Lecture Notes in Computer Science 3686, S. Singh et al. (Eds.) pp.454-460, Springer-Verlag, 2005.
  • M. Cornell, I. Alam, N. Alpdemir, D. Soanes, H.M. Wong, M. Rattray, S. Hubbard, N.J. Talbot, Lings, D.C. Hoyle, S.G. Oliver & N.W. Paton. e-Fungi: An e-Science Infrastructure for Comparative Functional Genomics in Fungal Species. In proceedings of UK e-Science Programme All Hands Meeting 2005, Nottingham September 2005.
  • D. C. Hoyle & M. Rattray. A Statistical Mechanics Analysis of Gram Matrix Eigenvalue Spectra. In Learning Theory, Proceedings of COLT 2004 Banff, Canada. Lecture Notes in Artificial Intelligence, J. Shawe-Taylor and Y. Singer  (Eds)., pp. 579-593, Springer-Verlag, 2004.
  • D.C. Hoyle &  M. Rattray. Principal Component Analysis Eigenvalue Spectra from Data with Symmetry Breaking Structure.Physical Review E 69, 026124 (2004).
  • D.L. Jones, J. Pretty, D.C. Hoyle, A. Hayes, S.G. Oliver, I. Riba-Garcia, S. J. Gaskell & L. Stateva. Genome-wide analysis of the effects of heat shock on a Saccharomyces cerevisiae mutant with a constitutively activated cAMP-dependent pathway. Comparative and Functional Genomics 5:419-431 (2004).
  • L.C. Edwards-Ingram, M.E. Gent, D.C. Hoyle, A. Hayes, L.I. Stateva & S.G. Oliver. Comparative Genomic Hybridization Provides New Insights Into the Molecular Taxonomy of the Saccharomyces Sensu Stricto Complex. Genome Research 14:1043-1051 (2004).
  • A. H. Sims, G. D. Robson, D. C. Hoyle, S. G. Oliver, G. Turner, R. A. Prade, H. H. Russell, N. S. Dunn-Coleman & M. E. Gent. Use of expressed sequence tag (EST) analysis and cDNA microarrays of the filamentous fungus Aspergillus nidulans. Fungal Genetics and Biology 41: 199-212 (2004)
  • A. Hayes & D.C. Hoyle. Book Review of MicroArray Gene Expression Data Analysis : A Beginners Guide by A. Brazma, H. Causton and J. Quackenbush.Yeast 21: 973-974 (2004).
  • D.L. Jones,  J. Petty,  D.C. Hoyle,  A. Hayes,  S.G. Oliver &  L. I. Stateva. Transcriptome profiling of a Saccharomyces cerevisiae mutant with a constitutively activated  Ras/cAMP-dependent pathway. Physiological Genomics 16(1) : 107-118 (2003)
  • D. C. Hoyle & M. Rattray. Limiting form of the sample covariance matrix eigenspectrum in PCA and kernel PCA. In Advances in Neural Information Processing Systems 16, edited by Sebastian Thrun, Lawrence Saul, and Bernhard Schölkopf, Proceedings of Neural Information Processing Systems conference, 2003.
  • Y. Fang, A. Brass, D. C. Hoyle, A. Hayes, A. Bashein, S.G. Oliver, D. Waddington & M. Rattray. A model-based analysis of microarray experimental error and normalisation. Nucleic Acids Research (methods) 31(16) e96 (2003).
  • D.C. Hoyle & M. Rattray. PCA Learning for Sparse High-dimensional data. Europhysics Letters  62(1): 117-123 (2003).
  • D.C. Hoyle & P.G. Higgs. Factors Affecting the Errors in the Estimation of Evolutionary Distances Between Sequences. Molecular Biology and Evolution 20(1): 1-9 (2003).
  • N. Morrison & D. C. Hoyle. Normalization: Concepts and Methods for Normalizing Microarray Data. In A Practical Approach to MicroArray Data Analysis,  D.P. Berrar, W. Dubitzky & M. Granzow (eds.), Kluwer Academic Publishers, Boston, 2003.
  • D. C. Hoyle, M. Rattray, R. Jupp & A. Brass. Making Sense of MicroArray Data Distributions. Bioinformatics 18(4): 576-584 (2002)
  • N. J. Savill, D. C. Hoyle & P. G. Higgs. RNA Sequence Evolution with Secondary Structure Constraints : Comparison of Substitution Rate Models. Genetics 157: 399-411 (2001).
  • R.J.F. Leote de Carvalho, R. Evans, D.C. Hoyle & J.R. Henderson.The decay of the pair correlation function in simple fluids : long versus short-ranged potentials. Journal of Physics C : Condensed Matter 6: 9275 (1994).
  • R. Evans, R.J.F. Leote de Carvalho, J.R. Henderson & D.C. Hoyle. Asymptotic decay of correlations in liquids and their mixtures. Journal of Chemical Physics 100: 591 (1994).
  • R. Evans, J.R. Henderson, D.C. Hoyle, A.O. Parry & Z.A. Sabeur. Asymptotic decay of liquid structure : oscillatory liquid-vapour density profiles and the Fisher-Widom line. Molecular Physics 80: 755 (1993).
  • R. Evans, D.C. Hoyle & A.O. Parry. Length scales for wetting transitions : Beyond the continuum Landau approximation for the interfacial binding  potential. Physical Review. A45: 3823 (1992).