Publications (2022).

Didelot, X; Parkhill, J (2022) A scalable analytical approach from bacterial genomes to epidemiology PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 377 20210246

Carson, J; Ledda, A; Ferretti, L; Keeling, M; Didelot, X (2022) The bounded coalescent model: Conditioning a genealogy on a minimum root date JOURNAL OF THEORETICAL BIOLOGY 548 111186

Kaye, AR; Hart, WS; Bromiley, J; Iwami, S; Thompson, RN (2022) A direct comparison of methods for assessing the threat from emerging infectious diseases in seasonally varying environments JOURNAL OF THEORETICAL BIOLOGY 548 111195

Althobaity, Y; Wu, JH; Tildesley, MJ (2022) Non-pharmaceutical interventions and their relevance in the COVID-19 vaccine rollout in Saudi Arabia and Arab Gulf countries INFECTIOUS DISEASE MODELLING 7 545-560

Dankwa, EA; Lambert, S; Hayes, S; Thompson, RN; Donnelly, CA (2022) Stochastic modelling of African swine fever in wild boar and domestic pigs: Epidemic forecasting and comparison of disease management strategies EPIDEMICS 40 100622

Ezanno, P et al. (2022) The African swine fever modelling challenge: Model comparison and lessons learnt EPIDEMICS 40 100615

Althobaity, Y; Wu, JH; Tildesley, MJ (2022) A comparative analysis of epidemiological characteristics of MERS-CoV and SARS-CoV-2 in Saudi Arabia br INFECTIOUS DISEASE MODELLING 7 473-485

Keeling, MJ; Dyson, L; Tildesley, MJ; Hill, EM; Moore, S (2022) Comparison of the 2021 COVID-19 roadmap projections against public health data in England NATURE COMMUNICATIONS 13 4924

Tildesley, MJ; Vassall, A; Riley, S; Jit, M; Sandmann, F; Hill, EM; Thompson, RN; Atkins, BD; Edmunds, J; Dyson, L; Keeling, MJ (2022) Optimal health and economic impact of non-pharmaceutical intervention measures prior and post vaccination in England: a mathematical modelling study ROYAL SOCIETY OPEN SCIENCE 9 211746

Castrogiovanni, C; Inchingolo, AV; Harrison, JU; Dudka, D; Sen, O; Burroughs, NJ; McAinsh, AD; Meraldi, P (2022) Evidence for a HURP/EB free mixed-nucleotide zone in kinetochore-microtubules NATURE COMMUNICATIONS 13 4704

Orangi, S et al. (2022) Epidemiological impact and cost-effectiveness analysis of COVID-19 vaccination in Kenya BMJ GLOBAL HEALTH 7 e009430

Agoti, CN; Curran, MD; Murunga, N; Ngari, M; Muthumbi, E; Lambisia, AW; Frost, SDW; Blacklaws, BA; Nokes, DJ; Drumright, LN (2022) Differences in epidemiology of enteropathogens in children pre- and post-rotavirus vaccine introduction in Kilifi, coastal Kenya GUT PATHOGENS 14 32

Prosser, NS; Hill, EM; Armstrong, D; Gow, L; Tildesley, MJ; Keeling, MJ; Kaler, J; Ferguson, E; Green, MJ (2022) Descriptive analysis of national bovine viral diarrhoea test data in England (2016-2020) VETERINARY RECORD 191 e1854

Willgert, K et al. (2022) Transmission history of SARS-CoV-2 in humans and white-tailed deer SCIENTIFIC REPORTS 12 12094

Dyson, L (2022) Modelling results on the impact of COVID-19 testing in schools LANCET INFECTIOUS DISEASES 22 915-916

Whittles, LK; Didelot, X; White, PJ (2022) Public health impact and cost-effectiveness of gonorrhoea vaccination: an integrated transmission-dynamic health-economic modelling analysis LANCET INFECTIOUS DISEASES 22 1030-1041

Mendonca, PRF; Tagliatti, E; Langley, H; Kotzadimitriou, D; Zamora-Chimal, CG; Timofeeva, Y; Volynski, KE (2022) Asynchronous glutamate release is enhanced in low release efficacy synapses and dispersed across the active zone NATURE COMMUNICATIONS 13 3497

Agoti, CN et al. (2022) Transmission networks of SARS-CoV-2 in Coastal Kenya during the first two waves: A retrospective genomic study ELIFE 11 e71703

Saez, M; Briscoe, J; Rand, DA (2022) Dynamical landscapes of cell fate decisions INTERFACE FOCUS 12 20220002

Volk, D; Yang-Turner, F; Didelot, X; Crook, DW; Wyllie, D (2022) Catwalk: identifying closely related sequences in large microbial sequence databases MICROBIAL GENOMICS 8 850

Touloupou, P; Retkute, R; Hollingsworth, TD; Spencer, SEF (2022) Statistical methods for linking geostatistical maps and transmission models: Application to lymphatic filariasis in East Africa SPATIAL AND SPATIO-TEMPORAL EPIDEMIOLOGY 41 100391

Morobe, JM et al. (2022) Genomic Epidemiology of SARS-CoV-2 in Seychelles, 2020-2021 VIRUSES-BASEL 14 1318

Fairbanks, EL; Baylis, M; Daly, JM; Tildesley, MJ (2022) Inference for a spatio-temporal model with partial spatial data: African horse sickness virus in Morocco EPIDEMICS 39 100566

Lozano, DCP; Jones, HE; Gavard, R; Thomas, MJ; Ramirez, CX; Wootton, CA; Chaparro, JAS; O'Connor, PB; Spencer, SEF; Rossell, D; Mejia-Ospino, E; Witt, M; Barrow, MP (2022) Revealing the Reactivity of Individual Chemical Entities in Complex Mixtures: the Chemistry Behind Bio-Oil Upgrading ANALYTICAL CHEMISTRY 94 7536-7544

Introini, V; Marin-Menendez, A; Nettesheim, G; Lin, YC; Kariuki, SN; Smith, AL; Jean, L; Brewin, JN; Rees, DC; Cicuta, P; Rayner, JC; Penman, BS (2022) The erythrocyte membrane properties of beta thalassaemia heterozygotes and their consequences for Plasmodium falciparum invasion SCIENTIFIC REPORTS 12 8934

Keeling, MJ; Moore, SE (2022) An assessment of the vaccination of school-aged children in England against SARS-CoV-2 BMC MEDICINE 20 196

Hart, WS; Miller, E; Andrews, NJ; Waight, P; Maini, PK; Funk, S; Thompson, RN (2022) Generation time of the alpha and delta SARS-CoV-2 variants: an epidemiological analysis LANCET INFECTIOUS DISEASES 22 603-610

Prosser, NS; Green, MJ; Ferguson, E; Tildesley, MJ; Hill, EM; Keeling, MJ; Kaler, J (2022) Cattle farmer psychosocial profiles and their association with control strategies for bovine viral diarrhea JOURNAL OF DAIRY SCIENCE 105 3559-3573

Ledda, A; Cummins, M; Shaw, LP; Jauneikaite, E; Cole, K; Lasalle, F; Barry, D; Turton, J; Rosmarin, C; Anaraki, S; Wareham, D; Stoesser, N; Paul, J; Manuel, R; Cherian, BP; Didelot, X (2022) Hospital outbreak of carbapenem- resistant Enterobacterales associated with a bla( OXA-48) plasmid carried mostly by Escherichia coli ST399 MICROBIAL GENOMICS 8 675

Lipecki, J; Mitchell, AE; Muter, J; Lucas, ES; Makwana, K; Fishwick, K; Odendaal, J; Hawkes, A; Vrljicak, P; Brosens, JJ; Ott, S (2022) EndoTime: non-categorical timing estimates for luteal endometrium HUMAN REPRODUCTION 37 747-761

Huang, CI; Crump, RE; Brown, PE; Spencer, SEF; Miaka, EM; Shampa, C; Keeling, MJ; Rock, KS (2022) Identifying regions for enhanced control of gambiense sleeping sickness in the Democratic Republic of Congo NATURE COMMUNICATIONS 13 1448

Xi, XY; Spencer, SEF; Hall, M; Grabowski, MK; Kagaayi, J; Ratmann, O (2022) Inferring the sources of HIV infection in Africa from deep-sequence data with semi-parametric Bayesian Poisson flow models JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS 71 517-540

Wang, L; Didelot, X; Bi, YH; Gao, GF (2022) SARS-CoV-2 transmissibility compared between variants of concern and vaccination status BRIEFINGS IN BIOINFORMATICS 23 bbab594

Kretzschmar, ME; Ashby, B; Fearon, E; Overton, CE; Panovska-Griffiths, J; Pellis, L; Quaife, M; Rozhnova, G; Scarabel, F; Stage, HB; Swallow, B; Thompson, RN; Tildesley, MJ; Villela, D (2022) Challenges for modelling interventions for future pandemics EPIDEMICS 38 100546

Leng, T; Hill, EM; Holmes, A; Southall, E; Thompson, RN; Tildesley, MJ; Keeling, MJ; Dyson, L (2022) Quantifying pupil-to-pupil SARS-CoV-2 transmission and the impact of lateral flow testing in English secondary schools NATURE COMMUNICATIONS 13 1106

Antillon, M; Huang, CI; Crump, RE; Brown, PE; Snijders, R; Miaka, EM; Keeling, MJ; Rock, KS; Tediosi, F (2022) Cost-effectiveness of sleeping sickness elimination campaigns in five settings of the Democratic Republic of Congo NATURE COMMUNICATIONS 13 1051

Achom, M et al. (2022) Plant circadian clock control of Medicago truncatula nodulation via regulation of nodule cysteine-rich peptides JOURNAL OF EXPERIMENTAL BOTANY 73 2142-2156

Lovell-Read, FA; Shen, S; Thompson, RN (2022) Estimating local outbreak risks and the effects of non-pharmaceutical interventions in age-structured populations: SARS-CoV-2 as a case study JOURNAL OF THEORETICAL BIOLOGY 535 110983

Lambisia, AW; Mohammed, KS; Makori, TO; Ndwiga, L; Mburu, MW; Morobe, JM; Moraa, EO; Musyoki, J; Murunga, N; Mwangi, JN; Nokes, DJ; Agoti, CN; Ochola-Oyier, LI; Githinji, G (2022) Optimization of the SARS-CoV-2 ARTIC Network V4 Primers and Whole Genome Sequencing Protocol FRONTIERS IN MEDICINE 9 836728

Singer, BJ; Thompson, RN; Bonsall, MB (2022) Evaluating strategies for spatial allocation of vaccines based on risk and centrality JOURNAL OF THE ROYAL SOCIETY INTERFACE 19 20210709

Hart, WS; Abbott, S; Endo, A; Hellewell, J; Miller, E; Andrews, N; Maini, PK; Funk, S; Thompson, RN (2022) Inference of the SARS-CoV-2 generation time using UK household data ELIFE 11 e70767

Holmes, A; Tildesley, M; Dyson, L (2022) Approximating steady state distributions for household structured epidemic models JOURNAL OF THEORETICAL BIOLOGY 534 110974

Fountain-Jones, NM et al. (2022) Hunting alters viral transmission and evolution in a large carnivore NATURE ECOLOGY & EVOLUTION 6 174

Rock, KS; Huang, CI; Crump, RE; Bessell, PR; Brown, PE; Tirados, I; Solano, P; Antillon, M; Picado, A; Mbainda, S; Darnas, J; Crowley, EH; Torr, SJ; Peka, M (2022) Update of transmission modelling and projections of gambiense human African trypanosomiasis in the Mandoul focus, Chad INFECTIOUS DISEASES OF POVERTY 11 11

Keeling, MJ; Dyson, L; Guyver-Fletcher, G; Holmes, A; Semple, MG; Tildesley, MJ; Hill, EM (2022) Fitting to the UK COVID-19 outbreak, short-term forecasts and estimating the reproductive number STATISTICAL METHODS IN MEDICAL RESEARCH 31 1716-1737

Fairbanks, EL; Brennan, ML; Mertens, PPC; Tildesley, MJ; Daly, JM (2022) Re-parameterization of a mathematical model of African horse sickness virus using data from a systematic literature search TRANSBOUNDARY AND EMERGING DISEASES 69 E671-E681

Phan, MVT; Agoti, CN; Munywoki, PK; Otieno, GP; Ngama, M; Kellam, P; Cotten, M; Nokes, DJ (2022) Identification of missed viruses by metagenomic sequencing of clinical respiratory samples from Kenya SCIENTIFIC REPORTS 12 202

Larsen, J et al. (2022) Emergence of methicillin resistance predates the clinical use of antibiotics NATURE 602 135

Linton, NM; Lovell-Read, FA; Southall, E; Lee, H; Akhmetzhanov, AR; Thompson, RN; Nishiura, H (2022) When Do Epidemics End? Scientific Insights from Mathematical Modelling Studies CENTAURUS 64 31-59

Altmeyer, R; Bretschneider, T; Janak, J; Reiss, M (2022) Parameter Estimation in an SPDE Model for Cell Repolarization SIAM-ASA JOURNAL ON UNCERTAINTY QUANTIFICATION 10 179-199

Pratt, HG; Steinberger, KJ; Mihalik, NE; Ott, S; Whalley, T; Szomolay, B; Boone, BA; Eubank, TD (2022) Macrophage and Neutrophil Interactions in the Pancreatic Tumor Microenvironment Drive the Pathogenesis of Pancreatic Cancer CANCERS 14 194

Willen, L; Milton, P; Hamley, JID; Walker, M; Osei-Atweneboana, M; Volf, P; Basanez, MG; Courtenay, O (2022) Demographic patterns of human antibody levels to Simulium damnosum s.l. saliva in onchocerciasis-endemic areas: An indicator of exposure to vector bites PLOS NEGLECTED TROPICAL DISEASES 16 e0010108

Guyver-Fletcher, G; Gorsich, EE; Tildesley, MJ (2022) A model exploration of carrier and movement transmission as potential explanatory causes for the persistence of foot-and-mouth disease in endemic regions TRANSBOUNDARY AND EMERGING DISEASES 69 2712-2726