SGMCMCJax: a lightweight JAX library for stochastic gradient Markov chain Monte Carlo algorithms

Coullon, J. & Nemeth, C., 18/04/2022, In: Journal of Open Source Software. 7, 72, 2 p., 4113.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Influence of sex, season and environmental air quality on experimental human pneumococcal carriage acquisition: a retrospective cohort analysis

Cheliotis, K. S., Jewell, C. P., Solórzano, C., Urban, B., Collins, A. M., Mitsi, E., Pojar, S., Nikolaou, E., German, E. L., Reiné, J., Gordon, S. B., Jochems, S. P., Rylance, J. & Ferreira, D. M., 11/04/2022, In: ERJ open research. 8, 2, 10 p., 00586-2021.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Efficient computation of the volume of a polytope in high-dimensions using Piecewise Deterministic Markov Processes

Chevallier, A., Cazals, F. & Fearnhead, P., 28/03/2022, In: Proceedings of Machine Learning Research. 151, p. 10146-10160 15 p.

Research output: Contribution to Journal/Magazine › Conference article › peer-review

Enhancing epidemiological surveillance of the emergence of the SARS-CoV-2 Omicron variant using spike gene target failure data, England, 15 November to 31 December 2021

Blomquist, P. B., Bridgen, J., Bray, N., O’Connell, A. M., West, D., Groves, N., Gallagher, E., Utsi, L., Jarvis, C. I., Hardstaff, J. L., Byers, C., Metelmann, S., Simons, D., Zaidi, A., Twohig, K. A., Savagar, B., Løchen, A., Wrenn, K., Saavedra-Campos, M. & Abedin, Z. & 5 others, Florence, I., Cleary, P., Elson, R., Vivancos, R. & Lake, I. R., 17/03/2022, In: Eurosurveillance. 27, 11, 5 p., 2200143.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Chronic obstructive pulmonary disease in sub-Saharan Africa

Awokola, B. I., Amusa, G. A., Jewell, C. P., Okello, G., Stobrink, M., Finney, L. J., Mohammed, N., Erhart, A. & Mortimer, K. J., 1/03/2022, In: International Journal of Tuberculosis and Lung Disease. 26, 3, p. 232-242 11 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Risk factor targeting for vaccine prioritization during the COVID-19 pandemic

Chapman, L. A. C., Shukla, P., Rodríguez-Barraquer, I., Shete, P. B., León, T. M., Bibbins-Domingo, K., Rutherford, G. W., Schechter, R. & Lo, N. C., 23/02/2022, In: Scientific Reports. 12, 12 p., 3055.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Augmented pseudo-marginal Metropolis-Hastings for partially observed diffusion processes

Golightly, A. & Sherlock, C., 15/02/2022, In: Statistics and Computing. 32, 18 p., 21.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Drivers of Resistance in Uganda and Malawi (DRUM): a protocol for the evaluation of One-Health drivers of Extended Spectrum Beta Lactamase (ESBL) resistance in Low-Middle Income Countries (LMICs)

Cocker, D., Sammarro, M., Chidziwisano, K., Elviss, N., Jacob, S. T., Kajumbula, H., Mugisha, L., Musoke, D., Musicha, P., Roberts, A. P., Rowlingson, B., Singer, A. C., Byrne, R. L., Edwards, T., Lester, R., Wilson, C., Hollihead, B., Thomson, N., Jewell, C. P. & Morse, T. & 1 others, Feasey, N., 15/02/2022, (E-pub ahead of print) In: Wellcome Open Research. 7, 13 p., 55.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Innovative and Additive Outlier Robust Kalman Filtering with a Robust Particle Filter

Fisch, A., Eckley, I. & Fearnhead, P., 31/01/2022, In: IEEE Transactions on Signal Processing. 70, p. 47-56 10 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Unexposed populations and potential COVID-19 hospitalisations and deaths in European countries as per data up to 21 November 2021

Chapman, L. A. C., Barnard, R. C., Russell, T. W., Abbott, S., Zandvoort, K. V., Davies, N. G. & Kucharski, A. J., 6/01/2022, In: Eurosurveillance. 27, 1, 8 p., 2101038.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Direct statistical inference for finite Markov jump processes via the matrix exponential

Sherlock, C., 31/12/2021, In: Computational Statistics. 36, 4, p. 2863-2887 25 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Trends, relationships and case attribution of antibiotic resistance between children and environmental sources in rural India

Mitchell, J., Purohit, M., Jewell, C. P., Read, J. M., Marrone, G., Diwan, V. & Stålsby Lundborg, C., 19/11/2021, In: Scientific Reports. 11, 1, 11 p., 22599.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Frequency of Routine Testing for Coronavirus Disease 2019 (COVID-19) in High-risk Healthcare Environments to Reduce Outbreaks

Chin, E. T., Huynh, B. Q., Chapman, L. A. C., Murrill, M., Basu, S. & Lo, N. C., 1/11/2021, In: Clinical Infectious Diseases. 73, 9, p. E3127-E3129 3 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing

Howerton, E., Ferrari, M. J., Bjørnstad, O. N., Bogich, T. L., Borchering, R. K., Jewell, C. P., Nichols, J. D., Probert, W. J. M., Runge, M. C., Tildesley, M. J., Viboud, C. & Shea, K., 28/10/2021, In: PLoS Computational Biology. 17, 10, 19 p., e1009518.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Tuberculosis in badgers where the bovine tuberculosis epidemic is expanding in cattle in England

Swift, B. M. C., Barron, E. S., Christley, R., Corbetta, D., Grau-Roma, L., Jewell, C., O’Cathail, C., Mitchell, A., Phoenix, J., Prosser, A., Rees, C., Sorley, M., Verin, R. & Bennett, M., 25/10/2021, In: Scientific Reports. 11, 1, 10 p., 20995.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Efficiency of delayed-acceptance random walk Metropolis algorithms

Sherlock, C., Thiery, A. & Golightly, A., 15/10/2021, In: Annals of Statistics. 49, 5, p. 2972-2990 19 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Routine asymptomatic testing strategies for airline travel during the COVID-19 pandemic: a simulation study

Kiang, M. V., Chin, E. T., Huynh, B. Q., Chapman, L. A. C., Rodríguez-Barraquer, I., Greenhouse, B., Rutherford, G. W., Bibbins-Domingo, K., Havlir, D., Basu, S. & Lo, N. C., 31/07/2021, In: The Lancet Infectious Diseases. 21, 7, p. 929-938 10 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Novel coronavirus 2019-nCoV (COVID-19): Early estimation of epidemiological parameters and epidemic size estimates

Read, J. M., Bridgen, J. R. E., Cummings, D. A. T., Ho, A. & Jewell, C. P., 19/07/2021, In: Philosophical Transactions of the Royal Society B: Biological Sciences. 376, 1829, 9 p., 20200265.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Modelling the impact of respiratory syncytial virus (RSV) vaccine and immunoprophylaxis strategies in New Zealand

Prasad, N., Read, J. M., Jewell, C., Waite, B., Trenholme, A. A., Huang, Q. S., Grant, C. C., Newbern, E. C. & Hogan, A. B., 13/07/2021, In: Vaccine. 39, 31, p. 4383-4390 8 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Pan-African evolution of within- And between-country COVID-19 dynamics

Ssentongo, P., Fronterre, C., Geronimo, A., Greybush, S. J., Mbabazi, P. K., Muvawala, J., Nahalamba, S. B., Omadi, P. O., Opar, B. T., Sinnar, S. A., Wang, Y., Whalen, A. J., Held, L., Jewell, C., Muwanguzi, A. J. B., Greatrex, H., Norton, M. M., Diggle, P. J. & Schiff, S. J., 13/07/2021, In: Proceedings of the National Academy of Sciences of the United States of America. 118, 28, 10 p., e2026664118.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Strategic testing approaches for targeted disease monitoring can be used to inform pandemic decision-making

Nichols, J. D., Bogich, T. L., Howerton, E., Bjørnstad, O. N., Borchering, R. K., Ferrari, M., Haran, M., Jewell, C., Pepin, K. M., Probert, W. J. M., Pulliam, J. R. C., Runge, M. C., Tildesley, M., Viboud, C. & Shea, K., 17/06/2021, In: Plos Biology. 19, 6, 9 p., e3001307.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

An enhanced care package to improve asthma management in Malawian children: A randomised controlled trial

Rylance, S., Chinoko, B., Mnesa, B., Jewell, C., Grigg, J. & Mortimer, K., 31/05/2021, In: Thorax. 76, 5, p. 434-440 7 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Comparison of infection control strategies to reduce COVID-19 outbreaks in homeless shelters in the United States: a simulation study

Chapman, L. A. C., Kushel, M., Cox, S. N., Scarborough, A., Cawley, C., Nguyen, T. Q., Rodriguez-Barraquer, I., Greenhouse, B., Imbert, E. & Lo, N. C., 7/05/2021, In: BMC Medicine. 19, 13 p., 116.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Developments in statistical inference when assessing spatiotemporal disease clustering with the tau statistic

Pollington, T. M., Tildesley, M. J., Hollingsworth, T. D. & Chapman, L. A. C., 30/04/2021, In: Spatial Statistics. 42, 15 p., 100438.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Stochastic gradient Markov chain Monte Carlo

Nemeth, C. & Fearnhead, P., 30/03/2021, In: Journal of the American Statistical Association. 1116, 533, p. 433-450 18 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Bayesian additive regression trees with model trees

Batista Do Prado, E., Parnell, A. C. & de Andrade Moral, R., 3/03/2021, In: Statistics and Computing. 31, 3, p. 1-13 13 p., 20.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Outbreak of severe vomiting in dogs associated with a canine enteric coronavirus, United Kingdom

Radford, A. D., Singleton, D. A., Jewell, C., Appleton, C., Rowlingson, B., Hale, A. C., Cuartero, C. T., Newton, R., Sánchez-Vizcaíno, F., Greenberg, D., Brant, B., Bentley, E. G., Stewart, J. P., Smith, S., Haldenby, S., Noble, P.-J. & Pinchbeck, G. L., 1/02/2021, In: Emerging Infectious Diseases. 27, 2, p. 517-528 12 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Anticipating future learning affects current control decisions: A comparison between passive and active adaptive management in an epidemiological setting

Atkins, B. D., Jewell, C. P., Runge, M. C., Ferrari, M. J., Shea, K., Probert, W. J. M. & Tildesley, M. J., 7/12/2020, In: Journal of Theoretical Biology. 506, 23 p., 110380.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Quasi-stationary Monte Carlo and the ScaLE Algorithm

Pollock, M., Fearnhead, P., Johansen, A. M. & Roberts, G. O., 1/12/2020, In: Journal of the Royal Statistical Society: Series B (Statistical Methodology). 82, 5, p. 1167-1221 55 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post-kala-azar dermal leishmaniasis

Chapman, L. A. C., Spencer, S. E. F., Pollington, T. M., Jewell, C. P., Mondal, D., Alvar, J., Hollingsworth, T. D., Cameron, M. M., Bern, C. & Medley, G. F., 13/10/2020, In: Proceedings of the National Academy of Sciences of the United States of America. 117, 41, p. 25742-25750 9 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Measuring air quality for advocacy in Africa (MA3): Feasibility and practicality of longitudinal ambient PM2.5 measurement using low-cost sensors

Awokola, B. I., Okello, G., Mortimer, K. J., Jewell, C. P., Erhart, A. & Semple, S., 3/10/2020, In: International Journal of Environmental Research and Public Health. 17, 19, 17 p., 7243.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Discussion of "Bayesian Regression Tree Models for Causal Inference: Regularization, Confounding, and Heterogeneous Effects"

Batista Do Prado, E., O'Neill, E., Hernandez, B., Parnell, A. C. & de Andrade Moral, R., 1/09/2020, In: Bayesian Analysis. 15, 3, p. 965-1056

Research output: Contribution to Journal/Magazine › Journal article › peer-review

A spatio-temporal approach to short-term prediction of visceral leishmaniasis diagnoses in India

Nightingale, E. S., Chapman, L. A. C., Srikantiah, S., Subramanian, S., Jambulingam, P., Bracher, J., Cameron, M. M. & Medley, G. F., 9/07/2020, In: PLoS Neglected Tropical Diseases.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Estimating the burden of antimicrobial resistance in Malawi: protocol for a prospective observational study of the morbidity, mortality and economic cost of third-generation cephalosporin resistant bloodstream infection

Lester, R., Maheswaran, H., Jewell, C. P., Lalloo, D. G. & Feasey, N. A., 1/06/2020, In: Wellcome Open Research. 5, 29.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Estimating the burden of antimicrobial resistance in Malawi: protocol for a prospective observational study of the morbidity, mortality and economic cost of third-generation cephalosporin resistant bloodstream infection [version 2; peer review: 2 approved]

Lester, R., Maheswaran, H., Jewell, C. P., Lalloo, D. G. & Feasey, N. A., 1/06/2020, In: Wellcome Open Research. 5, 29

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Motor unit number estimation via sequential Monte Carlo

Taylor, S., Sherlock, C., Ridall, G. & Fearnhead, P., 1/04/2020, In: Computational Statistics and Data Analysis. 144, 16 p., 106845.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Constrained Dynamic Programming and Supervised Penalty Learning Algorithms for Peak Detection in Genomic Data

Hocking, T. D., Rigaill, G., Fearnhead, P. & Bourque, G., 31/03/2020, In: Journal of Machine Learning Research. 21, p. 1-40 40 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Air pollution interventions and respiratory health: a systematic review

Saleh, S., Shepherd, W., Jewell, C., Lam, N. L., Balmes, J., Bates, M. N., Lai, P. S., Ochieng, C. A., Chinouya, M. & Mortimer, K., 1/02/2020, In: The International Journal of Tuberculosis and Lung Disease . 24, 2, p. 150-164 15 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Lung health and exposure to air pollution in Malawian children (CAPS): a cross-sectional study

Rylance, S., Nightingale, R., Naunje, A., Mbalume, F., Jewell, C., Balmes, J. R., Grigg, J. & Mortimer, K., 1/11/2019, In: Thorax. 74, 11, p. 1070-1077 8 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

sgmcmc: An R Package for Stochastic Gradient Markov Chain Monte Carlo

Baker, J., Fearnhead, P., Fox, E. B. & Nemeth, C. J., 31/10/2019, In: Journal of Statistical Software. 91, 3, p. 1-27 27 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Small animal disease surveillance 2019: Pruritus, pharmacosurveillance, skin tumours and flea infestations

Singleton, D. A., McGarry, J., Torres, J. R., Killick, D., Jewell, C., Smyth, S., Brant, B., Sánchez-Vizcaíno, F., Dawson, S., Pinchbeck, G. L., Noble, P. J. M. & Radford, A. D., 19/10/2019, In: Veterinary Record. 185, 15, p. 470-475 6 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Detecting changes in slope with an L₀ penalty

Fearnhead, P., Maidstone, R. & Letchford, A., 1/06/2019, In: Journal of Computational and Graphical Statistics. 28, 2, p. 265-275 11 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review

Small animal disease surveillance 2019: Respiratory disease, antibiotic prescription and canine infectious respiratory disease complex

Singleton, D. A., Stavisky, J., Jewell, C., Smyth, S., Brant, B., Sánchez-Vizcaíno, F., Dawson, S., Pinchbeck, G. L., Noble, P. J. M. & Radford, A. D., 23/05/2019, In: Veterinary Record. 184, 21, p. 640-645 6 p.

Research output: Contribution to Journal/Magazine › Journal article › peer-review