Publications (2024).

Davis, CN; Crump, RE; Sutherland, SA; Spencer, SEF; Corbella, A; Chansy, S; Lebuki, J; Miaka, EM; Rock, KS (2024) Comparison of stochastic and deterministic models for gambiense sleeping sickness at different spatial scales: A health area analysis in the DRC PLOS COMPUTATIONAL BIOLOGY 20 e1011993

Crump, RE; Aliee, M; Sutherland, SA; Huang, C; Crowley, EH; Spencer, SEF; Keeling, MJ; Shampa, C; Miaka, EM; Rock, KS (2024) Modelling timelines to elimination of sleeping sickness in the Democratic Republic of Congo, accounting for possible cryptic human and animal transmission PARASITES & VECTORS 17 332

Richardson, MJE (2024) Linear and nonlinear integrate-and-fire neurons driven by synaptic shot noise with reversal potentials PHYSICAL REVIEW E 109 24407

Asplin, P; Keeling, MJ; Mancy, R; Hill, EM (2024) Epidemiological and health economic implications of symptom propagation in respiratory pathogens: A mathematical modelling investigation PLOS COMPUTATIONAL BIOLOGY 20 e1012096

Cant, S; Shanks, GD; Keeling, MJ; Penman, BS (2024) Extreme mortality during a historical measles outbreak on Rotuma is consistent with measles immunosuppression EPIDEMIOLOGY & INFECTION 152 e85

Davis, EL; Hollingsworth, TD; Keeling, MJ (2024) An analytically tractable, age-structured model of the impact of vector control on mosquito-transmitted infections PLOS COMPUTATIONAL BIOLOGY 20 e1011440

Vlachou, D; Veretennikova, M; Usselmann, L; Vasilyev, V; Ott, S; Bjarnason, GA; Dallmann, R; Levi, F; Rand, DA (2024) TimeTeller: A tool to probe the circadian clock as a multigene dynamical system PLOS COMPUTATIONAL BIOLOGY 20 e1011779

Asplin, P; Mancy, R; Finnie, T; Cumming, F; Keeling, MJ; Hill, EM (2024) Symptom propagation in respiratory pathogens of public health concern: a review of the evidence JOURNAL OF THE ROYAL SOCIETY INTERFACE 21 20240009

Moore, MP; Laager, M; Ribeca, P; Didelot, X (2024) KmerAperture: Retaining k-mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes PLOS GENETICS 20 e1011184

Carson, J; Keeling, M; Wyllie, D; Ribeca, P; Didelot, X (2024) Inference of Infectious Disease Transmission through a Relaxed Bottleneck Using Multiple Genomes Per Host MOLECULAR BIOLOGY AND EVOLUTION 41 msad288

Rawlings, NN; Bailey, M; Craig, P; Courtenay, O (2024) Cutaneous leishmaniasis in British troops following jungle training in Belize: Cumulative incidence and potential risk practices PARASITE EPIDEMIOLOGY AND CONTROL 27 e00385

Eigentler, L; Sensi, M (2024) Delayed loss of stability of periodic travelling waves: Insights from the analysis of essential spectra JOURNAL OF THEORETICAL BIOLOGY 595 111945

Medina-Aguayo, FJ; Didelot, X; Everitt, R (2024) Speeding up Inference of Homologous Recombination in Bacteria BAYESIAN ANALYSIS 19 1245-1275

Bouros, I; Hill, EM; Keeling, MJ; Moore, S; Thompson, RN (2024) Prioritising older individuals for COVID-19 booster vaccination leads to optimal public health outcomes in a range of socio-economic settings PLOS COMPUTATIONAL BIOLOGY 20 e1012309

Burroughs, NJ; Leuridan, MLC (2024) Optimising the tumour elimination payoff in cancer therapy IET CONTROL THEORY AND APPLICATIONS 18 1621-1637

Doyle, NJ; Cumming, F; Thompson, RN; Tildesley, MJ (2024) When should lockdown be implemented? Devising cost-effective strategies for managing epidemics amid vaccine uncertainty PLOS COMPUTATIONAL BIOLOGY 20 e1012010

Nair, S; Barker, CR; Bird, M; Greig, DR; Collins, C; Painset, A; Chattaway, M; Pickard, D; Larkin, L; Gharbia, S; Didelot, X; Ribeca, P (2024) Presence of phage- plasmids in multiple serovars of Salmonella enterica MICROBIAL GENOMICS 10 1247

Moro, S; Spencer, SEF; Lester, DW; Nübling, F; Sommer, M; Costantini, G (2024) Molecular-Scale Imaging Enables Direct Visualization of Molecular Defects and Chain Structure of Conjugated Polymers ACS NANO 18 11655-11664

Keeling, MJ; Dyson, L (2024) A retrospective assessment of forecasting the peak of the SARS-CoV-2 Omicron BA.1 wave in England PLOS COMPUTATIONAL BIOLOGY 20 e1012452

Cartes, JA; Bonizzoni, P; Ciccolella, S; Della Vedova, G; Denti, L; Didelot, X; Monti, DC; Pirola, Y (2024) RecGraph: recombination-aware alignment of sequences to variation graphs BIOINFORMATICS 40 btae292

Fairbanks, EL; Daly, JM; Tildesley, MJ (2024) Modelling the Influence of Climate and Vector Control Interventions on Arbovirus Transmission VIRUSES-BASEL 16 1221

Vasconcelos, A et al. (2024) Accelerating Progress Towards the 2030 Neglected Tropical Diseases Targets: How Can Quantitative Modeling Support Programmatic Decisions? CLINICAL INFECTIOUS DISEASES 78 S83-S92

Reinhold, K; Eigentler, L; Kikuchi, DW (2024) Evolution of individual variation in a competitive trait: a theoretical analysis JOURNAL OF EVOLUTIONARY BIOLOGY 37 538-547

Roberts, GO; Rosenthal, JS (2024) Football group draw probabilities and corrections CANADIAN JOURNAL OF STATISTICS-REVUE CANADIENNE DE STATISTIQUE 52 659-677

Lambisia, AW; Murunga, N; Mutunga, M; Cheruiyot, R; Maina, G; Makori, TO; Nokes, DJ; Agoti, CN (2024) Temporal changes in the positivity rate of common enteric viruses among paediatric admissions in coastal Kenya, during the COVID-19 pandemic, 2019-2022 GUT PATHOGENS 16 2

Osman, R; Dema, E; David, A; Hughes, G; Field, N; Cole, M; Didelot, X; Saunders, J (2024) Understanding the potential role of whole genome sequencing (WGS) in managing patients with gonorrhoea: A systematic review of WGS use on human pathogens in individual patient care JOURNAL OF INFECTION 88 106168

Rosazza, T; Earl, C; Eigentler, L; Davidson, FA; Stanley-Wall, NR (2024) Reciprocal sharing of extracellular proteases and extracellular matrix molecules facilitates Bacillus subtilis biofilm formation MOLECULAR MICROBIOLOGY 122 184-200

Kay, RR; Lutton, JE; King, JS; Bretschneider, T (2024) Making cups and rings: the 'stalled-wave ' model for macropinocytosis BIOCHEMICAL SOCIETY TRANSACTIONS 52 1785-1794

Courson, J; Quoy, M; Timofeeva, Y; Manos, T (2024) An exploratory computational analysis in mice brain networks of widespread epileptic seizure onset locations along with potential strategies for effective intervention and propagation control FRONTIERS IN COMPUTATIONAL NEUROSCIENCE 18 1360009

Owuor, DC; Ngoi, JM; Nyasimi, FM; Murunga, N; Nyiro, JU; Chaves, SS; Nokes, DJ; Agoti, CN (2024) Local patterns of spread of influenza A H3N2 virus in coastal Kenya over a 1-year period revealed through virus sequence data SCIENTIFIC REPORTS 14 23426

Ogi-Gittins, I; Hart, WS; Song, J; Nash, RK; Polonsky, J; Cori, A; Hill, EM; Thompson, RN (2024) A simulation-based approach for estimating the time-dependent reproduction number from temporally aggregated disease incidence time series data EPIDEMICS 47 100773

Kendall, M; Ferretti, L; Wymant, C; Tsallis, D; Petrie, J; Di Francia, A; Di Lauro, F; Abeler-Dörner, L; Manley, H; Panovska-Griffiths, J; Ledda, A; Didelot, X; Fraser, C (2024) Drivers of epidemic dynamics in real time from daily digital COVID-19 measurements SCIENCE 385 eadm8103

Fotopoulou, ET; Jenkins, C; Barker, CR; Painset, A; Didelot, X; Simbo, A; Douglas, A; Godbole, G; Jorgensen, F; Gharbia, S; McLauchlin, J (2024) Genomic epidemiology of the clinically dominant clonal complex 1 in the Listeria monocytogenes population in the UK MICROBIAL GENOMICS 10 1155

Owuor, DC; de Laurent, ZR; Oketch, JW; Murunga, N; Otieno, JR; Nabakooza, G; Chaves, SS; Nokes, DJ; Agoti, CN (2024) Phylogeography and reassortment patterns of human influenza A viruses in sub-Saharan Africa SCIENTIFIC REPORTS 14 18987

MacDonald, JC; Gulbudak, H; Beechler, B; Gorsich, EE; Gubbins, S; Pérez-Martin, E; Jolles, AE (2024) Within-Host Viral Growth and Immune Response Rates Predict Foot-and-Mouth Disease Virus Transmission Dynamics for African Buffalo AMERICAN NATURALIST 204 133-146

Fielder, H; Beale, T; Jeger, MJ; Oliver, G; Parnell, S; Szyniszewska, AM; Taylor, P; Cunniffe, NJ (2024) A Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2022 PHYTOPATHOLOGY 114 1717-1732

Li, H et al. (2024) Centralized industrialization of pork in Europe and America contributes to the global spread of Salmonella enterica NATURE FOOD 5

Nyiro, JU et al. (2024) The cost of care for children hospitalized with respiratory syncytial virus (RSV) associated lower respiratory infection in Kenya BMC PUBLIC HEALTH 24 2410

Rock, KS; Chapman, LAC; Dobson, AP; Adams, ER; Hollingsworth, TD (2024) The Hidden Hand of Asymptomatic Infection Hinders Control of Neglected Tropical Diseases: A Modeling Analysis CLINICAL INFECTIOUS DISEASES 78 S175-S182

Pratt, HG; Ma, L; Dziadowicz, SA; Ott, S; Whalley, T; Szomolay, B; Eubank, TD; Hu, GQ; Boone, BA (2024) Analysis of single nuclear chromatin accessibility reveals unique myeloid populations in human pancreatic ductal adenocarcinoma CLINICAL AND TRANSLATIONAL MEDICINE 14 e1595

Croft, W; Pounds, R; Jeevan, D; Singh, K; Balega, J; Sundar, S; Williams, A; Ganesan, R; Kehoe, S; Ott, S; Zuo, J; Yap, J; Moss, P (2024) The chromatin landscape of high-grade serous ovarian cancer metastasis identifies regulatory drivers in post-chemotherapy residual tumour cells COMMUNICATIONS BIOLOGY 7 1211

Carvalho, BM; Maia, C; Courtenay, O; Llabrés-Brustenga, A; Batista, M; Moirano, G; van Daalen, KR; Semenza, JC; Lowe, R (2024) A climatic suitability indicator to support Leishmania infantum surveillance in Europe: a modelling study LANCET REGIONAL HEALTH-EUROPE 43 100971

Katsamba, P; Butler, MD; Koens, L; Montenegro-Johnson, TD (2024) Slender phoretic loops and knots PHYSICAL REVIEW FLUIDS 9 54201

Nimmo, C; Ortiz, AT; Tan, CCS; Pang, J; Acman, M; Millard, J; Padayatchi, N; Grant, AD; O'Donnell, M; Pym, A; Brynildsrud, OB; Eldholm, V; Grandjean, L; Didelot, X; Balloux, F; van Dorp, L (2024) Detection of a historic reservoir of bedaquiline/clofazimine resistance-associated variants in Mycobacterium tuberculosis GENOME MEDICINE 16 34

Vieira, A et al. (2024) Rapid expansion and international spread of M1UK in the post-pandemic UK upsurge of Streptococcus pyogenes NATURE COMMUNICATIONS 15 3916

Oliver, MCA; Graham, M; Gass, KM; Medley, GF; Clark, J; Davis, EL; Reimer, LJ; King, JD; Pouwels, KB; Hollingsworth, TD (2024) Reducing the Antigen Prevalence Target Threshold for Stopping and Restarting Mass Drug Administration for Lymphatic Filariasis Elimination: A Model-Based Cost-effectiveness Simulation in Tanzania, India and Haiti CLINICAL INFECTIOUS DISEASES 78 S160-S168

Gordon, NS; Mcguigan, EK; Ondasova, M; Knight, J; Baxter, LA; Ott, S; Hastings, RK; Zeegers, MP; James, ND; Cheng, KK; Goel, A; Yu, MH; Arnold, R; Bryan, RT; Ward, DG (2024) Comparison and combination of mutation and methylation-based urine tests for bladder cancer detection BIOMARKER RESEARCH 12 133

Barquera, R et al. (2024) Ancient genomes reveal insights into ritual life at Chichén Itzá NATURE 630 568-569

Taylor, AJ et al. (2024) Epistasis, core-genome disharmony, and adaptation in recombining bacteria MBIO 15

van Daalen, KR et al. (2024) The 2024 Europe report of the Lancet Countdown on health and climate change: unprecedented warming demands unprecedented action LANCET PUBLIC HEALTH 9 e495-e522

Touloupou, P et al. (2024) An Ensemble Framework for Projecting the Impact of Lymphatic Filariasis Interventions Across Sub-Saharan Africa at a Fine Spatial Scale CLINICAL INFECTIOUS DISEASES 78 S108-S116

Dyer, NP; Päuker, B; Baxter, L; Gupta, A; Bunk, B; Overmann, J; Diricks, M; Dreyer, V; Niemann, S; Holt, KE; Rahman, M; Brown, PE; Stark, R; Zhou, ZM; Ott, S; Nübel, U (2024) EnteroBase in 2025: exploring the genomic epidemiology of bacterial pathogens NUCLEIC ACIDS RESEARCH

Prada, JM et al. (2024) Subnational Projections of Lymphatic Filariasis Elimination Targets in Ethiopia to Support National Level Policy CLINICAL INFECTIOUS DISEASES 78 S117-S125

Monod, M et al. (2024) Longitudinal population-level HIV epidemiologic and genomic surveillance highlights growing gender disparity of HIV transmission in Uganda NATURE MICROBIOLOGY 9

Cong, BB et al. (2024) Changes in the global hospitalisation burden of respiratory syncytial virus in young children during the COVID-19 pandemic: a systematic analysis LANCET INFECTIOUS DISEASES 24 361-374