List of Publications for Simon E.F. Spencer: (for pre-prints see WRAP)
Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models.
Xiaoyue Xi, Simon E.F. Spencer, Matthew Hall, M. Kate Grabowski, Joseph Kagaayi and Oliver Ratmann (2022).
Journal of the Royal Statistical Society: Series C (Applied Statistics). arXiv
- Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape.
Warren Tennant, Eric Cardinale, Catherine Cetre-Sossah, Youssouf Moutroifi, Gilles Le Godais, Davide Colombi, Simon E.F. Spencer, Michael Tildesley, Matt Keeling, Onzade Charafouddine, Vittoria Colizza, W. John Edmunds and Raphaelle Metras (2021).
Nature Communications. Full text BioRXiv
- Accelerating adaptation in the adaptive Metropolis-Hastings random walk algorithm.
Simon E.F. Spencer (2021).
Australian and New Zealand Journal of Statistics, 63, 468-484. Full text
- Modelling the impact of fexinidazole use on human African trypanosomiasis transmission in the Democratic Republic of Congo.
Aatreyee M. Das, Nakul Chitnis, Christian Burri, Daniel H. Paris, Swati Patel, Simon E.F. Spencer, Erick M. Miaka, M. Soledad Castaño (2021).
PLOS Neglected Tropical Diseases. Full text MedRXiv
- Estimating HIV, HCV and HSV2 incidence from emergency department serosurvey.
Simon E.F. Spencer, Oliver Laeyendecker, Louise Dyson, Yu-Hsiang Hsieh, Eshan U. Patel, Richard E. Rothman, Gabor D. Kelen, Thomas C. Quinn and T. Deirdre Hollingsworth (2021).
Gates Open Research. Full text
- Integrating geostatistical maps and infectious disease transmission models using adaptive multiple importance sampling.
Renata Retkute, Panayiota Touloupou, María-Gloria Basáñez, T. Deirdre Hollingsworth and Simon E.F. Spencer (2021).
Annals of Applied Statistics. Full text MedRXiv
- Still 'Dairy Farm Fever'? A Bayesian model for Leptospirosis notification data in New Zealand.
Jackie Benschop, Shahista Nisa and Simon E.F. Spencer (2021).
Journal of the Royal Society Interface, 18 (175), 20200964. Full text
- Modelling to quantify the likelihood that local elimination of transmission has occurred using routine gambiense human African trypanosomiasis surveillance data.
Christopher N. Davis, Maria Soledad Castaño, Maryam Aliee, Swati Patel, Erick Mwamba Miaka, Matt J. Keeling, Simon E.F. Spencer, Nakul Chitnis and Kat S. Rock (2021).
Clinical Infectious Diseases, 72 (S3), S146-151. Full text
- Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo.
Maryam Aliee, María Soledad Castaño, Christopher Davis, Swati Patel, Erick Mwamba Miaka, Simon E.F. Spencer, Matt Keeling, Nakul Chitnis and Kat Rock (2021).
Transactions of the Royal Society of Tropical Medicine and Hygiene, 115 (3), 245-252. Full text MedRXiv
- Statistical methods for linking geostatistical maps and transmission models: Application to lymphatic filariasis in East Africa.
Panayiota Touloupou, Renata Retkute, T. Déirdre Hollingsworth and Simon E.F. Spencer (2020).
Spatial and Spatio-temporal Epidemiology. Full text arXiv
- Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo.
Ronald E. Crump, Ching-I Huang, Ed Knock, Simon E.F. Spencer, Paul Brown, Erick Mwamba Miaka, Chansy Shampa, Matt J. Keeling and Kat S. Rock (2020).
PLOS Computational Biology, 17 (1): e1008532. Full text medRXiv
- Bayesian inference assessment of protein secondary structure analysis using circular dichroism data – how much structural information is contained in protein circular dichroism spectra?
Simon E.F. Spencer and Alison Rodger (2020) [with contribution from Jacopo Franco]
Analytical Methods, 13 (3), 359-368 . Full text
- An epidemic model for an evolving pathogen with strain-dependent immunity.
Adam Griffin, Gareth O. Roberts and Simon E.F. Spencer (2020).
Mathematical Biosciences, 330, 108480. Journal arXiv
- Bayesian inference for multi-strain epidemics with application to Escherichia coli O157:H7 in feedlot cattle.
Panayiota Touloupou, Bärbel Finkenstädt, Thomas E. Besser, Nigel P. French and Simon E.F. Spencer (2020).
Annals of Applied Statistics, 14 (4), 1925-1944. Journal Full text
- Climate drivers of plague epidemiology in British India, 1898–1949.
Warren Tennant, Michael Tildesley, Simon E.F. Spencer and Matt Keeling (2020).
Proceedings of the Royal Society B, 287 (1928) 20200538. Full text
- Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post-kala-azar dermal leishmaniasis.
Lloyd A.C. Chapman, Simon E.F. Spencer, Timothy M. Pollington, Chris P. Jewell, Dinesh Mondal, Jorge Alvar, T. Deirdre Hollingsworth, Mary M. Cameron, Caryn Bern and Graham F. Medley (2020).
PNAS, . Full text medRXiv
- Predicted impact of COVID-19 on neglected tropical disease programs and the opportunity for innovation.
Jaspreet Toor, T. Deirdre Hollingsworth and the Neglected Tropical Disease (NTD) Modelling Consortium (2020).
Clinical Infectious Diseases, 72 (8), 1463-1466. Full text
- Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda.
Oliver Ratmann, Joseph Kagaayi, Matthew Hall, Tanya Golubchick, Godfrey Kigozi, Xiaoyue Xi, Chris Wymant, Gertrude Nakigozi, Lucie Abeler-Dörner, David Bonsall, Astrid Gall, Anne Hoppe, Paul Kellam, Jeremiah Bazaale, Sarah Kalibbala, Oliver Laeyendecker, Justin Lessler, Fred Nalugoda, Larry W. Chang, Tulio de Oliveira, Deenan Pillay, Thomas C. Quinn, Steven J. Reynolds, Simon E.F. Spencer, Robert Ssekubugu, David Serwadda, Maria J. Wawer, Ronald H. Gray, Christophe Fraser, M. Kate Grabowski, the Rakai Health Sciences Program and the Pangea HIV Consortium (2020).
The Lancet HIV, 7 (3), e173-e183. Full text Commentary
- KairosMS: A new solution for the processing of hyphenated ultrahigh resolution mass spectrometry data.
Remy Gavard, Hugh Jones, Diana Palacio Lozano, Mary Thomas, David Rossell, Simon E.F. Spencer and Mark Barrow (2020).
Analytical Chemistry, 92 (5), 3775-3786. Full text
- Scalable Bayesian inference for coupled hidden Markov and semi-Markov models.
Panayiota Touloupou, Bärbel Finkenstädt and Simon E.F. Spencer (2019).
Journal of Computational and Graphical Statistics, 29 (2), 238-249. Full text
- Efficient Bayesian model choice for partially observed processes: with application to an experimental transmission study of an infectious disease.
Trevelyan J. McKinley, Peter Neal, Simon E.F. Spencer, Andrew J.K. Conlan and Laurence Tiley (2019).
Bayesian Analysis, 15, (3), 839-870. Full text
- Assessing the impact of aggregating disease stage data in model predictions of human African trypanosomiasis transmission and control activities in Bandundu province (DRC).
Maria Soledad Castano, Martial L. Ndeffo-Mbah, Kat S. Rock, Cody Palmer, Edward Knock, Erick Mwamba Miaka, Joseph M. Ndung'u, Steve Torr, Paul
Verle, Simon E.F. Spencer, Alison Galvani, Caitlin Bever, Matt J. Keeling and Nakul Chitnis (2019).
PLOS Neglected Tropical Diseases, 14 (1), e0007976. Full text
- Rhapso: Automatic stitching of mass segments from Fourier transform ion cyclotron resonance mass spectra.
Remy Gavard, Diana Palacio Lozano, Alexander Guzman, David Rossell, Simon E.F. Spencer and Mark Barrow (2019).
Analytical Chemistry, 91 (23), 15130-15137. Full text
- Pushing the analytical limits: new insights into complex mixtures using mass spectra segments of constant ultrahigh resolving power.
Diana Catalina Palacio Lozano, Remy Gavard, Juan P. Arenas-Diaz, Mary J. Thomas, David D. Stranz, Enrique Mejía-Ospino, Alexander Guzman, Simon E.F. Spencer, David Rossell and Mark P. Barrow (2019).
Chemical Science, 10, 6966-6978. Full text
- Model selection for time series of count data.
Naif Alzahrani, Peter Neal, Simon E.F. Spencer, Trevelyan J. McKinley and Panayiota Touloupou (2018).
Computational Statistics and Data Analysis, 122, 33-44. Full text
- The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh.
Lloyd A.C. Chapman, Chris P. Jewell, Simon E.F. Spencer, Lorenzo Pellis, Samik Datta, Rajib Chowdhury, Caryn Bern, Graham F. Medley and T. Deirdre Hollingsworth (2018).
PLOS Neglected Tropical Diseases, 12 (10), e0006453. Full text
- Processing of discharge summaries in general practice: A retrospective record review.
Rachel A. Spencer, Simon E.F. Spencer, Sarah Rodgers, Stephen Campbell and Anthony J. Avery (2018).
British Journal of General Practice, 68 (673), e576-e585. Full text
- Efficient model comparison techniques for models requiring large scale data augmentation.
Panayiota Touloupou, Naif Alzahrani, Peter Neal, Simon E.F. Spencer and Trevelyan J. McKinley (2018).
Bayesian Analysis, 13 (2), 437-459. Full text
- Inferring source attribution from a multi-year multi-source dataset of Salmonella in Minnesota.
Christina Ahlstrom, Petra Muellner Simon E.F. Spencer, Samuel Hong, Amy Saupe, Albert Rovira, Craig Hedberg, Andres Perez, Ulrich Muellner and Julio Alvarez (2017).
Zoonoses and Public Health, 64 (8), 589-598. Journal
- Simulation from quasi-stationary distributions on reducible state spaces.
Adam Griffin, Paul A. Jenkins, Gareth O. Roberts and Simon E.F. Spencer (2017).
Advances in Applied Probability, 49 (3), 960-980. Journal arXiv
- Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling.
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).
Cell Systems, 4 (1), 73-83. Journal bioRXiv
- Themis: Batch preprocessing for ultrahigh-resolution mass spectra of complex mixtures.
Remy Gavard, David Rossell, Simon E. F. Spencer, and Mark P. Barrow (2017).
Analytical Chemistry, 89 (21), 11383-11390. Full text
- Model comparison with missing data using MCMC and importance sampling.
Panayiota Touloupou, Naif Alzahrani, Peter Neal, Simon E.F. Spencer, Trevelyan J. McKinley (2015).
- 'Super' or just 'above average'? Supershedders and the transmission of Escherichia coli O157:H7 among feedlot cattle.
Simon E.F. Spencer, Thomas E. Besser, Rowland N. Cobbold and Nigel P. French (2015).
Journal of the Royal Society Interface, 12 (110), 20150446. Journal Supplement
- Inferring network structure from interventional time-course experiments.
Simon E.F. Spencer, Steven M. Hill and Sach Mukherjee (2015).
Annals of Applied Statistics, 9 (1), 507-524. Journal arXiv Supplement
- Real-time growth rate for general stochastic SIR epidemics on unclustered networks.
Lorenzo Pellis, Thomas House and Simon E.F. Spencer (2015).
Mathematical Biosciences, 265, 65-81. Journal arXiv
- Osmium atoms and Os2 molecules move faster on Selenium-doped compared to Sulfur-doped Boronic graphenic surfaces.
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).
Chemistry of Materials, 27 (14), 5100-5105. Full text
- Quantifying the multi-scale performance of network inference algorithms.
Chris J. Oates, Richard Amos and Simon E.F. Spencer (2014).
Statistical Applications in Genetics and Molecular Biology, 13 (5), 611-631. Journal arXiv Supplement
- Assessing the impact of intervention delays on stochastic epidemics.
Simon E.F. Spencer and Philip D. O'Neill (2013).
Methodology and Computing in Applied Probability, 15 (4), 803-820. Journal Pre-print
- Dynamic Bayesian networks for interventional data.
Simon E.F. Spencer, Steven M. Hill and Sach Mukherjee (2012).
CRiSM pre-print 12-24.
- The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001–2007.
Simon E.F. Spencer, Jonathan Marshall, Ruth Pirie, Donald Campbell, Michael G. Baker and Nigel P. French (2012).
Epidemiology and Infection, 140 (9), 1663-1677. Journal
- The probability of containment for multitype branching process models for emerging epidemics.
Simon E.F. Spencer and Philip D. O'Neill (2011).
Journal of Applied Probability, 48 (1), 173-188. Journal
- The detection of spatially localised outbreaks in campylobacteriosis notification data.
Simon E.F. Spencer, Jonathan Marshall, Ruth Pirie, Donald Campbell and Nigel P. French (2011).
Spatial and Spatio-temporal Epidemiology, 2 (3), 173-183. Journal
- The integration of molecular tools into veterinary and spatial epidemiology.
Petra Mullner, Ruth N. Zadoks, Andres M. Perez, Simon E.F. Spencer, Ynte H. Schukken and Nigel P. French (2011).
Spatial and Spatio-temporal Epidemiology, 2 (3), 159-171. Journal
- Utilising a combination of molecular and spatial tools to assess the effect of a public health intervention.
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).
Preventive Veterinary Medicine, 102 (3), 242-253. Journal
- Bayesian zero-inflated predictive modelling of herd-level Salmonella prevalence for risk-based surveillance.
Jackie Benschop, Simon E.F. Spencer, Liz Alban, Mark Stevenson and Nigel P. French (2010).
Zoonoses and Public Health, 57, 60-70. Full text
- Molecular and spatial epidemiology of human campylobacteriosis - source association and genotype-related risk factors.
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).
Epidemiology and Infection, 138 (10), 1372-1383. Journal
- Molecular epidemiology of Campylobacter jejuni in a geographically isolated country with a uniquely structured poultry industry.
Petra Mullner, Julie Collins-Emerson, Anne Midwinter, Philip Carter, Simon E.F. Spencer, Peter van der Logt, Steve Hathaway and Nigel P. French (2010).
Applied and Environmental Microbiology, 76 (7), 2145-2154. Full text
- Assigning the source of human campylobacteriosis in New Zealand: A comparative genetic and epidemiological approach.
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).
Infection, Genetics and Evolution, 9 (6), 1311-1319. Journal
- Source attribution of food borne zoonoses in New Zealand: A modified Hald model.
Petra Mullner, Geoff Jones, Alisdair Noble, Simon E.F. Spencer, Steve Hathaway and Nigel P. French (2009).
Risk Analysis, 29 (7), 970-984. Journal
- Stochastic Epidemic Models for Emerging Diseases.
Simon E.F. Spencer (2008).
PhD thesis, University of Nottingham. Full text