Publications (2023).

Lovell-Read, FA; Parnell, S; Cunniffe, NJ; Thompson, RN (2023) Using 'sentinel' plants to improve early detection of invasive plant pathogens PLOS COMPUTATIONAL BIOLOGY 19 e1010884

Southall, E; Ogi-Gittins, Z; Kaye, AR; Hart, WS; Lovell-Read, FA; Thompson, RN (2023) A practical guide to mathematical methods for estimating infectious disease outbreak risks JOURNAL OF THEORETICAL BIOLOGY 562 111417

Huang, CI; Crump, RE; Crowley, EH; Hope, A; Bessell, PR; Shampa, C; Miaka, EM; Rock, KS (2023) A modelling assessment of short- and medium-term risks of programme interruptions for gambiense human African trypanosomiasis in the DRC PLOS NEGLECTED TROPICAL DISEASES 17 e0011299

Platt, A; Lutton, EJ; Offord, E; Bretschneider, T (2023) MiCellAnnGELo: annotate microscopy time series of complex cell surfaces with 3D virtual reality BIOINFORMATICS 39 btad013

Thompson, RN; Southall, E; Daon, Y; Lovell-Read, FA; Iwami, S; Thompson, CP; Obolski, U (2023) The impact of cross-reactive immunity on the emergence of SARS-CoV-2 variants FRONTIERS IN IMMUNOLOGY 13 1049458

Althobaity, Y; Tildesley, MJ (2023) Modelling the impact of non-pharmaceutical interventions on the spread of COVID-19 in Saudi Arabia SCIENTIFIC REPORTS 13

Hill, EM (2023) Modelling the epidemiological implications for SARS-CoV-2 of Christmas household bubbles in England JOURNAL OF THEORETICAL BIOLOGY 557 111331

Marinho, JF; Monteiro, JFCLS; de Carvalho, AWS; de Carvalho, FG; Cavalcanti, MD; Shaw, J; Courtenay, O; Brandao, SP (2023) High levels of infectiousness of asymptomatic Leishmania (Viannia) braziliensis infections in wild rodents highlights their importance in the epidemiology of American Tegumentary Leishmaniasis in Brazil PLOS NEGLECTED TROPICAL DISEASES 17 e0010996

Beck-Johnson, LM; Gorsich, EE; Hallman, C; Tildesley, MJ; Miller, RS; Webb, CT (2023) An exploration of within-herd dynamics of a transboundary livestock disease: A foot and mouth disease case EPIDEMICS 42 100668

van den Bosch, F; McRoberts, N; Bourhis, Y; Parnell, S; Hassall, KL (2023) The value of volunteer surveillance for the early detection of biological invaders JOURNAL OF THEORETICAL BIOLOGY 560 111385

Didelot, X; Franceschi, V; Frost, SDW; Dennis, A; Volz, EM (2023) Model design for nonparametric phylodynamic inference and applications to pathogen surveillance VIRUS EVOLUTION 9 vead028

Gomez, LRE; Savin, C; Andrianaivoarimanana, V; Rahajandraibe, S; Randriantseheno, LN; Zhou, ZM; Kocher, A; Didelot, X; Rajerison, M; Kuhnert, D (2023) Phylogenetic analysis of the origin and spread of plague in Madagascar PLOS NEGLECTED TROPICAL DISEASES 17 e0010362

Ashby, B; Smith, CA; Thompson, RN (2023) Non-pharmaceutical interventions and the emergence of pathogen variants EVOLUTION MEDICINE AND PUBLIC HEALTH 11 80-89

Sachak-Patwa, R; Lafferty, EI; Schmit, CJ; Thompson, RN; Byrne, HM (2023) A target-cell limited model can reproduce influenza infection dynamics in hosts with differing immune responses JOURNAL OF THEORETICAL BIOLOGY 567 111491

Nyagwange, J et al. (2023) Serum immunoglobulin G and mucosal immunoglobulin A antibodies from prepandemic samples collected in Kilifi, Kenya, neutralize SARS-CoV-2 in vitro INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES 127 11-16

Lambisia, AW; Makori, TO; Mutunga, M; Cheruiyot, R; Murunga, N; Quick, J; Githinji, G; Nokes, DJ; Houldcroft, CJ; Agoti, CN (2023) Genomic epidemiology of human adenovirus F40 and F41 in coastal Kenya: A retrospective hospital-based surveillance study (2013-2022) VIRUS EVOLUTION 9 vead023

Eames, KTD; Tang, ML; Hill, EM; Tildesley, MJ; Read, JM; Keeling, MJ; Gog, JR (2023) Coughs, colds and ?freshers? flu?survey in the University of Cambridge, 2007-2008 EPIDEMICS 42 100659

Dingle, KE; Freeman, J; Didelot, X; Quan, TP; Eyre, DW; Swann, J; Spittal, WD; Clark, EV; Jolley, KA; Walker, AS; Wilcox, MH; Crook, DW (2023) Penicillin Binding Protein Substitutions Cooccur with Fluoroquinolone Resistance in Epidemic Lineages of Multidrug-Resistant Clostridioides difficile MBIO

Mughal, SR; Niazi, SA; Do, T; Gilbert, SC; Didelot, X; Radford, DR; Beighton, D (2023) Genomic Diversity among Actinomyces naeslundii Strains and Closely Related Species MICROORGANISMS 11 254

Wambua, J; Munywoki, PK; Coletti, P; Nyawanda, BO; Murunga, N; Nokes, DJ; Hens, N (2022) Drivers of respiratory syncytial virus seasonal epidemics in children under 5 years in Kilifi, coastal Kenya PLOS ONE 17 e0278066

Guarido, MM; Fourie, I; Meno, K; Mendes, A; Riddin, MA; MacIntyre, C; Manyana, S; Johnson, T; Schrama, M; Gorsich, EE; Brooke, BD; Almeida, APG; Venter, M (2023) Alphaviruses Detected in Mosquitoes in the North-Eastern Regions of South Africa, 2014 to 2018 VIRUSES-BASEL 15 414

Makori, TO; Bargul, JL; Lambisia, AW; Mwanga, MJ; Murunga, N; de Laurent, ZR; Lewa, CS; Mutunga, M; Kellam, P; Cotten, M; Nokes, DJ; Phan, M; Agoti, CN (2023) Genomic epidemiology of the rotavirus G2P[4] strains in coastal Kenya pre- and post-rotavirus vaccine introduction, 2012-8 VIRUS EVOLUTION 9 vead025

Abdel-Glil, MY; Hotzel, H; Tomaso, H; Didelot, X; Brandt, C; Seyboldt, C; Linde, J; Schwarz, S; Neubauer, H; El-Adawy, H (2023) Genomic epidemiology of Campylobacter fetus subsp. venerealis from Germany FRONTIERS IN VETERINARY SCIENCE 9 1069062

Koltai, M; Moyes, J; Nyawanda, B; Nyiro, J; Munywoki, PK; Tempia, S; Li, X; Antillon, M; Bilcke, J; Flasche, S; Beutels, P; Nokes, DJ; Cohen, C; Jit, M (2023) Estimating the cost-effectiveness of maternal vaccination and monoclonal antibodies for respiratory syncytial virus in Kenya and South Africa BMC MEDICINE 21 120

Nabakooza, G; Owuor, DC; de Laurent, ZR; Galiwango, R; Owor, N; Kayiwa, JT; Jjingo, D; Agoti, CN; Nokes, DJ; Kateete, DP; Kitayimbwa, JM; Frost, SDW; Lutwama, JJ (2023) Phylogenomic analysis uncovers a 9-year variation of Uganda influenza type-A strains from the WHO-recommended vaccines and other Africa strains SCIENTIFIC REPORTS 13

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