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Publications

List of Publications for Simon E.F. Spencer: (for pre-prints see WRAP)

Naif Alzahrani, Peter Neal, Simon E.F. Spencer, Trevelyan J. McKinley and Panayiota Touloupou (2018).
Model selection for time series of count data.
Computational Statistics and Data Analysis, 122, 33-44. Journal

Lloyd A.C. Chapman, Chris P. Jewell, Simon E.F. Spencer, Lorenzo Pellis, Samik Datta, Rajib Chowdhury, Caryn Bern, Graham F. Medley, T. Deirdre Hollingsworth (2018).
The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh.
PLOS Neglected Tropical Diseases.

Rachel A. Spencer, Simon E.F. Spencer, Sarah Rodgers, Stephen Campbell, Anthony J. Avery (2018).
Processing of discharge summaries in general practice: A retrospective record review.
British Journal of General Practice, 68 (673): e576-e585. Full text

Panayiota Touloupou, Naif Alzahrani, Peter Neal, Simon E.F. Spencer, and Trevelyan J. McKinley (2017).
Efficient model comparison techniques for models requiring large scale data augmentation.
Bayesian Analysis, 13 (2), 437-459. Full text

Christina Ahlstrom, Petra Muellner Simon E.F. Spencer, Samuel Hong, Amy Saupe, Albert Rovira, Craig Hedberg, Andres Perez, Ulrich Muellner and Julio Alvarez (2017).
Inferring source attribution from a multi-year multi-source dataset of Salmonella in Minnesota.
Zoonoses and Public Health, 64 (8), 589-598. Journal

Adam Griffin, Paul A. Jenkins, Gareth O. Roberts and Simon E.F. Spencer (2017).
Simulation from quasi-stationary distributions on reducible state spaces.
Advances in Applied Probability, 49 (3), 960-980. Journal arXiv

Steven M. Hill, Nicole K. Nesser, Katie Johnson-Camacho, Mara Jeffress, Aimee Johnson, Chris Boniface, Simon E.F. Spencer, Yiling Lu, Laura M. Heiser, Yancey Lawrence, Nupur T. Pande, James E. Korkola, Joe W. Gray, Gordon B. Mills, Sach Mukherjee and Paul T. Spellman (2017).
Context-specificity in causal signaling networks revealed by phosphoprotein profiling.
Cell Systems, 4 (1), 73-83. View on-line bioRXiv

Remy Gavard, David Rossell, Simon E. F. Spencer, and Mark P. Barrow (2017).
Themis: Batch preprocessing for ultrahigh-resolution mass spectra of complex mixtures.
Analytical Chemistry, 89 (21), 11383-11390. Full text

Panayiota Touloupou, Naif Alzahrani, Peter Neal, Simon E.F. Spencer, Trevelyan J. McKinley (2015).
Model comparison with missing data using MCMC and importance sampling.
arXiv

Simon E.F. Spencer, Thomas E. Besser, Rowland N. Cobbold and Nigel P. French (2015).
'Super' or just 'above average'? Supershedders and the transmission of Escherichia coli O157:H7 among feedlot cattle.
Journal of the Royal Society Interface, 12 (110), 20150446. Journal Supplement

Simon E.F. Spencer, Steven M. Hill and Sach Mukherjee (2015).
Inferring network structure from interventional time-course experiments.
Annals of Applied Statistics, 9 (1), 507-524. Journal arXiv Supplement

Lorenzo Pellis, Thomas House and Simon E.F. Spencer (2015).
Real-time growth rate for general stochastic SIR epidemics on unclustered networks.
Mathematical Biosciences, 265, 65-81. Journal arXiv

Nicolas P.E. Barry, Anaïs Pitto-Barry, Johanna Tran, Simon E.F. Spencer, Adam Johansen, Ana M. Sanchez, Andrew P. Dove, Rachel K. O’Reilly, Robert J. Deeth, Richard Beanland and Peter J. Sadler (2015).
Osmium atoms and Os2 molecules move faster on Selenium-doped compared to Sulfur-doped Boronic graphenic surfaces.
Chemistry of Materials, 27 (14), 5100-5105. Full text

Chris J. Oates, Richard Amos and Simon E.F. Spencer (2014).
Quantifying the multi-scale performance of network inference algorithms.
Statistical Applications in Genetics and Molecular Biology, 13 (5), 611-631. Journal arXiv Supplement

Simon E.F. Spencer and Philip D. O'Neill (2013).
Assessing the impact of intervention delays on stochastic epidemics.
Methodology and Computing in Applied Probability, 15​ (4), 803-820. Journal Pre-print

Simon E.F. Spencer, Steven M. Hill and Sach Mukherjee (2012).
Dynamic Bayesian networks for interventional data.
CRiSM pre-print 12-24.

Simon E.F. Spencer, Jonathan Marshall, Ruth Pirie, Donald Campbell, Michael G. Baker and Nigel P. French (2012).
The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001–2007.
Epidemiology and Infection, 140 (9), 1663-1677. Journal

Simon E.F. Spencer and Philip D. O'Neill (2011).
The probability of containment for multitype branching process models for emerging epidemics.
Journal of Applied Probability, 48 (1), 173-188. Journal

Simon E.F. Spencer, Jonathan Marshall, Ruth Pirie, Donald Campbell and Nigel P. French (2011).
The detection of spatially localised outbreaks in campylobacteriosis notification data.
Spatial and Spatio-temporal Epidemiology, 2 (3), 173-183. Journal

Petra Mullner, Ruth N. Zadoks, Andres M. Perez, Simon E.F. Spencer, Ynte H. Schukken and Nigel P. French (2011).
The integration of molecular tools into veterinary and spatial epidemiology.
Spatial and Spatio-temporal Epidemiology, 2 (3), 159-171. Journal

Petra Mullner, Jonathan Marshall, Simon E.F. Spencer, Alisdair Noble, Tui Shadbolt, Julie M. Collins-Emerson, Anne C. Midwinter, Philip E. Carter, Ruth Pirie, Daniel Wilson, Donald Campbell, Mark Stevenson and Nigel P. French (2011).
Utilising a combination of molecular and spatial tools to assess the effect of a public health intervention.
Preventive Veterinary Medicine, 102 (3), 242-253. Journal

Jackie Benschop, Simon E.F. Spencer, Liz Alban, Mark Stevenson and Nigel P. French (2010).
Bayesian zero-inflated predictive modelling of herd-level Salmonella prevalence for risk-based surveillance.
Zoonoses and Public Health, 57, 60-70. Full text

Petra Mullner, Tui Shadbolt, Julie M. Collins-Emerson, Anne C. Midwinter, Simon E.F. Spencer, Jonathan Marshall, Philip E. Carter, Donald M. Campbell, Daniel J. Wilson, Steve Hathaway, Ruth Pirie and Nigel P. French (2010).
Molecular and spatial epidemiology of human campylobacteriosis - source association and genotype-related risk factors.
Epidemiology and Infection, 138 (10), 1372-1383. Journal

Petra Mullner, Julie Collins-Emerson, Anne Midwinter, Philip Carter, Simon E.F. Spencer, Peter van der Logt, Steve Hathaway and Nigel P. French (2010).
Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry.
Applied and Environmental Microbiology, 76 (7), 2145-2154. Full text

Petra Mullner, Simon E.F. Spencer, Daniel Wilson, Geoff Jones, Alisdair Noble, Anne Midwinter, Julie Collins-Emerson, Philip Carter, Steve Hathaway and Nigel P. French (2009).
Assigning the source of human campylobacteriosis in New Zealand: A comparative genetic and epidemiological approach.
Infection, Genetics and Evolution, 9 (6), 1311-1319. Journal

Petra Mullner, Geoff Jones, Alisdair Noble, Simon E.F. Spencer, Steve Hathaway and Nigel P. French (2009).
Source attribution of food borne zoonoses in New Zealand: A modified Hald model.
Risk Analysis, 29 (7), 970-984. Journal

Simon E.F. Spencer (2008).
Stochastic Epidemic Models for Emerging Diseases.
PhD thesis, University of Nottingham. Full text