Honorary Fellow

I am an amateur beekeeper and statistician working with David Evans, Eugene Ryabov, Nigel Burroughs and Jim Bull on the BBSRC "Saving the Bees" project. The initial aim is to understand, at a genetic level, the effect that the mite varroa is having on honeybee populations in Europe, North America and New Zealand. The longer term aim is to inform the rational breeding of pathogen-resistant honeybees.

This project has lead recently to the development of methodology and software (MosaicSolver) for finding viral recombinants, made possible using data arising from next generation sequencing technology. Matlab software (MosaicSolver) is available (free for academic use). Methods for correcting and assessing nucleotide diversity in a viral metagenome have also been developed, available in Matlab or Excel (Diversity).

Recent Publications

(with Eugene V Ryabov​, Jessica M Fannon, Jonathan D Moore and David J Evans) “The Iflaviruses Sacbrood virus and Deformed wing virus evoke different transcriptional responses in the honeybee which may facilitate horizontal or vertical transmission of these viruses”, PeerJ (2016), doi: 10.7717/peerj.1591.

(with Nigel Burroughs, David J Evans and Eugene V Ryabov) "Error correction and diversity analysis of population mixtures determined by NGS", PeerJ (2014), doi:10.7717/peerj.645, preprint also available at Diversity paper.

(with Eugene V. Ryabov, Jessica M. Fannon, Jonathan D. Moore, David J. Evans and Nigel Burroughs) "MosaicSolver: a tool for determining recombinants of viral genomes from pileup data", Nucleic Acids Research (2014) doi:10.1093/nar/gku524.

(with Eugene V. Ryabov, Jessica M. Fannon, Jonathan D. Moore, James C. Bull, Dave Chandler, Andrew Mead, Nigel Burroughs and David J. Evans) "A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmision", PLoS Pathogens (2014) doi:10.1371/journal.ppat.1004230.

(with D.J. Saville) "A geometric examination of linear model assumptions", Australian and New Zealand Journal of Statistics 55 (2013) 285-303.

(with P.C.H. Morel and D. Sirisatien) "Effect of pig type, ingredient cost and price schedule on dietary nutrient specification for maximum profitability in grower-finisher pigs: a theoretical approach", Livestock Science 148 (3) (2012) 255-267.

(with Yumi Patton and David Fisher) "Global energy minimisation and cotranslational protein folding of HP models", Journal of Global Optimization (Reiner Horst Special Issue) 52 (2012) 575-590.

(with Masanori Honda, Jiraporn Chompikul, Cheerawit Rattanapan and Somprattana Klungboonkrong) "Sharps Injuries among Nurses in a Thai Regional Hospital: Prevalence and Risk Factors", The International Journal of Occupational and Environmental Medicine 2 (4) (2011) 215-223.

(with Yumi Patton, Sheenal Srivastava and David Fisher) "Cotranslational protein folding and terminus hydrophobicity", Advances in Bioinformatics (2011), Article ID 176813, 8 pp., doi:10.1155/2011/176813.

(with Shane Turner, Tim Hughes and Rohit Singh) "Safety performance functions for bicycle crashes in New Zealand and Australia", Transportation Research Record (2011) (http://trid.trb.org/view.aspx?id=1092877).

(with P.C.H. Morel, D.L.J. Alexander, R.L. Sherriff and D. Sirisatien) "A new development in pig growth modelling”, Modelling Nutrient Digestion and Utilisation in Farm Animals, Eds. D. Sauvant, J. van Milgen, P. Faverdin, N. Friggens, Wageningen Academic Publishers, (D. Sauvant, J. Van Milgen, P. Faverdin and N. Friggens, eds.), Wageningen Academic Publishers, 2011.

(with J. Ma and S. Gudlaugsdottir) "Generalized EM estimation for semi-parametric mixture distributions with discretized non-parametric component", Statistics and Computing, 21 (2011) 601-612, doi:10.1007/s11222-010-9195-y.

(with Shane Turner, Tim Hughes, Tracy Allatt and Qingwei Luo) "Cycle safety - measuring the crash risk", Road and Transport Research, 19(2) (2010) 20-31.

(with Braddon K. Lance and Charlotte M. Deane) "Exploring the potential of template-based modelling", Bioinformatics, 26(15) (2010) 1849-1856 doi:10.1093/bioinformatics/btq294.

(with Shane Turner, Qingwei Luo, Rohit Singh and Tracy Allatt) "Crash prediction models and the factors that influence cycle safety", Journal of the Australasian College of Road Safety, 21(3) (2010) 26-36.

(with Jonathan J. Ellis, Fabien P.E. Huard, Charlotte M. Deane and Sheenal Srivastava) "Directionality in protein fold prediction", BMC Bioinformatics 11 (2010) 172.

Full list of publications 

I retain a link with Macquarie University in Sydney. I am generally happy and content (see last line of Nigel's page). Sarah Davis is thanked for the picture.