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

2023

Guzmán-Rincón, LM; Hill, EM; Dyson, L; Tildesley, MJ; Keeling, MJ (2023) Bayesian estimation of real-time epidemic growth rates using Gaussian processes: local dynamics of SARS-CoV-2 in England JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS 72 1413-1434

Cavallaro, M; Dyson, L; Tildesley, MJ; Todkill, D; Keeling, MJ (2023) Spatio-temporal surveillance and early detection of SARS-CoV-2 variants of concern: a retrospective analysis JOURNAL OF THE ROYAL SOCIETY INTERFACE 20 20230410

Keeling, MJ; Moore, S; Penman, BS; Hill, EM (2023) The impacts of SARS-CoV-2 vaccine dose separation and targeting on the COVID-19 epidemic in England NATURE COMMUNICATIONS 14 740

Helekal, D; Keeling, M; Grad, YH; Didelot, X (2023) Estimating the fitness cost and benefit of antimicrobial resistance from pathogen genomic data JOURNAL OF THE ROYAL SOCIETY INTERFACE 20 20230074

McKendrick, JQ; Tennant, WSD; Tildesley, MJ (2023) Modelling seasonality of Lassa fever incidences and vector dynamics in Nigeria PLOS NEGLECTED TROPICAL DISEASES 17 e0011543

Gowers, RP; Richardson, MJE (2023) Upcrossing-rate dynamics for a minimal neuron model receiving spatially distributed synaptic drive PHYSICAL REVIEW RESEARCH 5 23095

Tomás, RMF; Dallman, R; Congdon, TR; Gibson, MI (2023) Cryopreservation of assay-ready hepatocyte monolayers by chemically-induced ice nucleation: preservation of hepatic function and hepatotoxicity screening capabilities BIOMATERIALS SCIENCE 11 7639-7654

Lagunas, B; Richards, L; Sergaki, C; Burgess, J; Pardal, AJ; Hussain, RMF; Richmond, BL; Baxter, L; Roy, P; Pakidi, A; Stovold, G; Vázquez, S; Ott, S; Schäfer, P; Gifford, ML (2023) Rhizobial nitrogen fixation efficiency shapes endosphere bacterial communities and Medicago truncatula host growth MICROBIOME 11 146

Hill, EM; Prosser, NS; Brown, PE; Ferguson, E; Green, MJ; Kaler, J; Keeling, MJ; Tildesley, MJ (2023) Incorporating heterogeneity in farmer disease control behaviour into a livestock disease transmission model PREVENTIVE VETERINARY MEDICINE 219 106019

Vasdekis, G; Roberts, GO (2023) SPEED UP ZIG-ZAG ANNALS OF APPLIED PROBABILITY 33 4693-4746

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

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

Jeger, MJ; Fielder, H; Beale, T; Szyniszewska, AM; Parnell, S; Cunniffe, NJ (2023) What Can Be Learned by a Synoptic Review of Plant Disease Epidemics and Outbreaks Published in 2021? PHYTOPATHOLOGY 113 1141-1158

Didelot, X; Helekal, D; Kendall, M; Ribeca, P (2023) Distinguishing imported cases from locally acquired cases within a geographically limited genomic sample of an infectious disease BIOINFORMATICS 39

Vrljicak, P; Lucas, ES; Tryfonos, M; Muter, J; Ott, S; Brosens, JJ (2023) Dynamic chromatin remodeling in cycling human endometrium at single-cell level CELL REPORTS 42 113525

Brand, SPC; Cavallaro, M; Cumming, F; Turner, C; Florence, I; Blomquist, P; Hilton, J; Guzman-Rincon, LM; House, T; Nokes, DJ; Keeling, MJ (2023) The role of vaccination and public awareness in forecasts of Mpox incidence in the United Kingdom NATURE COMMUNICATIONS 14

Althobaity, Y; Tildesley, MJ (2023) Modelling the impact of non-pharmaceutical interventions on the spread of COVID-19 in Saudi Arabia SCIENTIFIC REPORTS 13 843

Offord, E; Lutton, JE; Bretschneider, T (2023) CELL MEMBRANE FEATURE DETECTION USING GRAPH NEURAL NETWORKS 2023 IEEE 20TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING, ISBI

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 Jr; 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

Courtenay, O; Marinho, JF Jr; Brito, MEF; Monteiro, JFCLS; Shaw, JJ; Brandao, SP (2023) Incidence of Human and Free-Ranging Wild Rodent Infections with Leishmania (Viannia) braziliensis, Aetiological Agent of Cutaneous Leishmaniasis PATHOGENS 12 1395

Jenkins, PA; Pollock, M; Roberts, GO (2023) Flexible Bayesian Inference for Diffusion Processesusing Splines METHODOLOGY AND COMPUTING IN APPLIED PROBABILITY 25 83

Corbella, A; Presanis, AM; Birrell, PJ; De Angelis, D (2023) Alice Corbella, Anne M Presanis, Paul J Birrell and Daniela De Angelis's contribution to the Discussion of 'The Second Discussion Meeting on Statistical aspects of the Covid-19 Pandemic' JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES A-STATISTICS IN SOCIETY 186

Rysava, K; Tildesley, MJ (2023) Identification of dynamical changes of rabies transmission under quarantine: Community-based measures towards rabies elimination PLOS COMPUTATIONAL BIOLOGY 19 e1011187

Lutton, JE; Coker, HLE; Paschke, P; Munn, CJ; King, JS; Bretschneider, T; Kay, RR (2023) Formation and closure of macropinocytic cups in Dictyostelium CURRENT BIOLOGY 33 3083

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

Keeling, MJ (2023) Patterns of reported infection and reinfection of SARS-CoV-2 in England JOURNAL OF THEORETICAL BIOLOGY 556 111299

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

Reid, D et al. (2023) Feasibility and acceptability of longitudinal sample and data collection: learning from the sexually transmissible enteric infections in men who have sex with men (STEIM) pilot study SEXUALLY TRANSMITTED INFECTIONS 99 A99-A100

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

Mahony, CB; Copper, L; Vrljicak, P; Noyvert, B; Constantinidou, C; Browne, S; Pan, Y; Palles, C; Ott, S; Higgs, MR; Monteiro, R (2023) Lineage skewing and genome instability underlie marrow failure in a zebrafish model of GATA2 deficiency CELL REPORTS 42 112571

Kaba, D et al. (2023) Towards the sustainable elimination of gambiense human African trypanosomiasis in Cote d'Ivoire using an integrated approach PLOS NEGLECTED TROPICAL DISEASES 17 e0011514

Antillon, M et al. (2023) Health economic evaluation of strategies to eliminate gambiense human African trypanosomiasis in the Mandoul disease focus of Chad PLOS NEGLECTED TROPICAL DISEASES 17 e0011396

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

Gonçalves, FB; Latuszynski, KG; Roberts, GO (2023) Exact Bayesian Inference for Diffusion-Driven Cox Processes JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

Agrawal, S; Vats, D; Latuszynski, K; Roberts, GO (2023) OPTIMAL SCALING OF MCMC BEYOND METROPOLIS ADVANCES IN APPLIED PROBABILITY 55 492-509

Davis, EL; Crump, RE; Medley, GF; Solomon, AW; Pemmaraju, VRR; Hollingsworth, TD (2023) A modelling analysis of a new multi-stage pathway for classifying achievement of public health milestones for leprosy PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 378 20220408

Chase-Topping, M et al. (2023) Analysis of Escherichia coli O157 strains in cattle and humans between Scotland and England & Wales: implications for human health MICROBIAL GENOMICS 9 1090

Gallagher, KE et al. (2023) Symptom prevalence and secondary attack rate of SARS-CoV-2 in rural Kenyan households: A prospective cohort study INFLUENZA AND OTHER RESPIRATORY VIRUSES 17 e13185

Norman, CA; Krishnakumar, SS; Timofeeva, Y; Volynski, KE (2023) The release of inhibition model reproduces kinetics and plasticity of neurotransmitter release in central synapses COMMUNICATIONS BIOLOGY 6 1091

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

Roberts, GO; Rosenthal, JS (2023) Polynomial Convergence Rates of Piecewise Deterministic Markov Processes METHODOLOGY AND COMPUTING IN APPLIED PROBABILITY 25 6

Kendall, M; Tsallis, D; Wymant, C; Di Francia, A; Balogun, Y; Didelot, X; Ferretti, L; Fraser, C (2023) Epidemiological impacts of the NHS COVID-19 app in England and Wales throughout its first year NATURE COMMUNICATIONS 14 858

Gonçalves, FB; Latuszynski, K; Roberts, GO (2023) Exact Monte Carlo likelihood-based inference for jump-diffusion processes JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY 85 732-756

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

Mwanga, MJ et al. (2023) New SARS-CoV-2 Omicron Variant with Spike Protein Mutation Y451H, Kilifi, Kenya, March-May 2023 EMERGING INFECTIOUS DISEASES 29 2376-2379

Owuor, DC; de Laurent, ZR; Nyawanda, BO; Emukule, GO; Kondor, R; Barnes, JR; Nokes, DJ; Agoti, CN; Chaves, SS (2023) Genetic and potential antigenic evolution of influenza A(H1N1)pdm09 viruses circulating in Kenya during 2009-2018 influenza seasons SCIENTIFIC REPORTS 13 22342

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

Rushmore, J; Beechler, BR; Tavalire, H; Gorsich, EE; Charleston, B; Devan-Song, A; Glidden, CK; Jolles, AE (2023) The heterogeneous herd: Drivers of close-contact variation in African buffalo and implications for pathogen invasion ECOLOGY AND EVOLUTION 13 e10447

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

Chan, YLE; Irvine, MA; Prystajecky, N; Sbihi, H; Taylor, M; Joffres, Y; Schertzer, A; Rose, C; Dyson, L; Hill, EM; Tildesley, M; Tyson, JR; Hoang, LMN; Galanis, E (2023) Emergence of SARS-CoV-2 Delta Variant and Effect of Nonpharmaceutical Interventions, British Columbia, Canada EMERGING INFECTIOUS DISEASES 29 1999-2007

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 14

Yenew, B et al. (2023) A smooth tubercle bacillus from Ethiopia phylogenetically close to the Mycobacterium tuberculosis complex NATURE COMMUNICATIONS 14 7519

Shaw, JJ; Marinho, JF Jr; Courtenay, O; Brandao, SP (2023) Assessing reservoir host status in leishmaniasis with special reference to the infectiousness of Leishmania (Viannia) braziliensis infections in wild rodents REVISTA DA SOCIEDADE BRASILEIRA DE MEDICINA TROPICAL 56 e05032023

Dai, HS; Pollock, M; Roberts, GO (2023) Bayesian fusion: scalable unification of distributed statistical analyses JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-STATISTICAL METHODOLOGY 85 84-107

Ward, DG; Baxter, L; Ott, S; Gordon, NS; Wang, JH; Patel, P; Piechocki, K; Silcock, L; Sale, C; Zeegers, MP; Cheng, K; James, ND; Bryan, RT (2023) Highly Sensitive and Specific Detection of Bladder Cancer via Targeted Ultra-deep Sequencing of Urinary DNA EUROPEAN UROLOGY ONCOLOGY 6 67-75

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

Baxter, L et al. (2023) Properties of non-coding mutation hotspots as urinary biomarkers for bladder cancer detection SCIENTIFIC REPORTS 13 1060

Ortiz, AT; Kendall, M; Storey, N; Hatcher, J; Dunn, H; Roy, S; Williams, R; Williams, C; Goldstein, RA; Didelot, X; Harris, K; Breuer, J; Grandjean, L (2023) Within-host diversity improves phylogenetic and transmission reconstruction of SARS-CoV-2 outbreaks ELIFE 12 e84384

Jibreel, T et al. (2023) Host preference and human blood index of Phlebotomus orientalis, an exophilic sand fly vector of visceral leishmaniasis in eastern Sudan MEDICAL AND VETERINARY ENTOMOLOGY 37 782-792

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 5516

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

Shea, K et al. (2023) Multiple models for outbreak decision support in the face of uncertainty PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 120 e2207537120

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

2021

Ortiz, AT; Coronel, J; Vidal, JR; Bonilla, C; Moore, DAJ; Gilman, RH; Balloux, F; Kon, OM; Didelot, X; Grandjean, L (2021) Genomic signatures of pre-resistance in Mycobacterium tuberculosis NATURE COMMUNICATIONS 12 7312

Antillon, M; Huang, CI; Rock, KS; Tediosi, F (2021) Economic evaluation of disease elimination: An extension to the net-benefit framework and application to human African trypanosomiasis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 e2026797118

Keeling, MJ; Guyver-Fletcher, G; Dyson, L; Tildesley, MJ; Hill, EM; Medley, GF (2021) Precautionary breaks: Planned, limited duration circuit breaks to control the prevalence of SARS-CoV2 and the burden of COVID-19 disease EPIDEMICS 37 100526

Retkute, R; Touloupou, P; Basanez, MG; Hollingsworth, TD; Spencer, SEF (2021) INTEGRATING GEOSTATISTICAL MAPS AND INFECTIOUS DISEASE TRANSMISSION MODELS USING ADAPTIVE MULTIPLE IMPORTANCE SAMPLING ANNALS OF APPLIED STATISTICS 15 1980-1998

Guarido, MM; Motlou, T; Riddin, MA; MacIntyre, C; Manyana, SC; Johnson, T; Schrama, M; Gorsich, EE; Brooke, BD; Almeida, APG; Venter, M (2021) Potential Mosquito Vectors for Shuni Virus, South Africa, 2014-2018 EMERGING INFECTIOUS DISEASES 27 3142-3146

Mousa, A et al. (2021) Social contact patterns and implications for infectious disease transmission - a systematic review and meta-analysis of contact surveys ELIFE 10 e70294

Sen, O; Harrison, JU; Burroughs, NJ; McAinsh, AD (2021) Kinetochore life histories reveal an Aurora-B-dependent error correction mechanism in anaphase DEVELOPMENTAL CELL 56 3082

Syrimi, E et al. (2021) The immune landscape of SARS-CoV-2-associated Multisystem Inflammatory Syndrome in Children (MIS-C) from acute disease to recovery ISCIENCE 24 103215

Brand, SPC et al. (2021) COVID-19 transmission dynamics underlying epidemic waves in Kenya SCIENCE 374 989

Morobe, JM; Kamau, E; Murunga, N; Gatua, W; Luka, MM; Lewa, C; Cheruiyot, R; Mutunga, M; Odundo, C; Nokes, DJ; Agoti, CN (2021) Trends and Intensity of Rhinovirus Invasions in Kilifi, Coastal Kenya, Over a 12-Year Period, 2007-2018 OPEN FORUM INFECTIOUS DISEASES 8 ofab571

Glennon, EE; Bruijning, M; Lessler, J; Miller, IF; Rice, BL; Thompson, RN; Wells, K; Metcalf, CJE (2021) Challenges in modeling the emergence of novel pathogens EPIDEMICS 37 100516

Del Fava, E; Adema, I; Kiti, MC; Poletti, P; Merler, S; Nokes, DJ; Manfredi, P; Melegaro, A (2021) Individual's daily behaviour and intergenerational mixing in different social contexts of Kenya SCIENTIFIC REPORTS 11 21589

Spencer, SEF (2021) Accelerating adaptation in the adaptive Metropolis-Hastings random walk algorithm AUSTRALIAN & NEW ZEALAND JOURNAL OF STATISTICS 63 468-484

Geerts, M; Van Reet, N; Leyten, S; Berghmans, R; Rock, KS; Coetzer, THT; Eyssen, LEA; Buscher, P (2021) Trypanosoma brucei gambiense-iELISA: A Promising New Test for the Post-Elimination Monitoring of Human African Trypanosomiasis CLINICAL INFECTIOUS DISEASES 73 E2477-E2483

Das, AM; Chitnis, N; Burri, C; Paris, DH; Patel, S; Spencer, SEF; Miaka, EM; Castano, MS (2021) Modelling the impact of fexinidazole use on human African trypanosomiasis (HAT) transmission in the Democratic Republic of the Congo PLOS NEGLECTED TROPICAL DISEASES 15 e0009992

Guarido, MM; Govender, K; Riddin, MA; Schrama, M; Gorsich, EE; Brooke, BD; Almeida, APG; Venter, M (2021) Detection of Insect-Specific Flaviviruses in Mosquitoes (Diptera: Culicidae) in Northeastern Regions of South Africa VIRUSES-BASEL 13 2148

Bottomley, C; Otiende, M; Uyoga, S; Gallagher, K; Kagucia, EW; Etyang, AO; Mugo, D; Gitonga, J; Karanja, H; Nyagwange, J; Adetifa, IMO; Agweyu, A; Nokes, DJ; Warimwe, GM; Scott, JAG (2021) Quantifying previous SARS-CoV-2 infection through mixture modelling of antibody levels NATURE COMMUNICATIONS 12 6196

Wilkinson, E et al. (2021) A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa SCIENCE 374 423

Davis, CN; Keeling, MJ; Rock, KS (2021) Modelling gambiense human African trypanosomiasis infection in villages of the Democratic Republic of Congo using Kolmogorov forward equations JOURNAL OF THE ROYAL SOCIETY INTERFACE 18 20210419

Howerton, E; Ferrari, MJ; Bjornstad, ON; Bogich, TL; Borchering, RK; Jewell, CP; Nichols, JD; Probert, WJM; Runge, MC; Tildesley, MJ; Viboud, C; Shea, K (2021) Synergistic interventions to control COVID-19: Mass testing and isolation mitigates reliance on distancing PLOS COMPUTATIONAL BIOLOGY 17 e1009518

Dyson, L; Hill, EM; Moore, S; Curran-Sebastian, J; Tildesley, MJ; Lythgoe, KA; House, T; Pellis, L; Keeling, MJ (2021) Possible future waves of SARS-CoV-2 infection generated by variants of concern with a range of characteristics NATURE COMMUNICATIONS 12 5730

Southall, E; Brett, TS; Tildesley, MJ; Dyson, L (2021) Early warning signals of infectious disease transitions: a review JOURNAL OF THE ROYAL SOCIETY INTERFACE 18 20210555

Vegvari, C et al. (2022) Commentary on the use of the reproduction number R during the COVID-19 pandemic STATISTICAL METHODS IN MEDICAL RESEARCH 31 1675-1685

Tennant, WSD; Cardinale, E; Cetre-Sossah, C; Moutroifi, Y; Le Godais, G; Colombi, D; Spencer, SEF; Tildesley, MJ; Keeling, MJ; Charafouddine, O; Colizza, V; Edmunds, WJ; Metras, R (2021) Modelling the persistence and control of Rift Valley fever virus in a spatially heterogeneous landscape NATURE COMMUNICATIONS 12 5593

Rand, DA; Raju, A; Saez, M; Corson, F; Siggia, ED (2021) Geometry of gene regulatory dynamics PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 118 e2109729118

Awori, JO et al. (2021) The Etiology of Pneumonia in HIV-uninfected Children in Kilifi, Kenya Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study PEDIATRIC INFECTIOUS DISEASE JOURNAL 40 S29-S39

Aliee, M; Keeling, MJ; Rock, KS (2021) Modelling to explore the potential impact of asymptomatic human infections on transmission and dynamics of African sleeping sickness PLOS COMPUTATIONAL BIOLOGY 17 e1009367

Hill, EM; Keeling, MJ (2021) Comparison between one and two dose SARS-CoV-2 vaccine prioritization for a fixed number of vaccine doses JOURNAL OF THE ROYAL SOCIETY INTERFACE 18 20210214

Monaghan, EM; Prosser, NS; Witt, J; Lewis, KE; Nabb, E; Keeling, MJ; Purdy, KJ; Green, LE (2021) Impact of Strain Variation of Dichelobacter nodosus on Disease Severity and Presence in Sheep Flocks in England FRONTIERS IN VETERINARY SCIENCE 8 713927

Githinji, G et al. (2021) Tracking the introduction and spread of SARS-CoV-2 in coastal Kenya NATURE COMMUNICATIONS 12 4809

Enright, J; Hill, EM; Stage, HB; Bolton, KJ; Nixon, EJ; Fairbanks, EL; Tang, ML; Brooks-Pollock, E; Dyson, L; Budd, CJ; Hoyle, RB; Schewe, L; Gog, JR; Tildesley, MJ (2021) SARS-CoV-2 infection in UK university students: lessons from September-December 2020 and modelling insights for future student return ROYAL SOCIETY OPEN SCIENCE 8 210310

Brooks-Pollock, E; Read, JM; McLean, AR; Keeling, MJ; Danon, L (2021) Mapping social distancing measures to the reproduction number for COVID-19 PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 376 20200276

Brooks-Pollock, E; Read, JM; House, T; Medley, GF; Keeling, MJ; Danon, L (2021) The population attributable fraction of cases due to gatherings and groups with relevance to COVID-19 mitigation strategies PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 376 20200273

Keeling, MJ; Tildesley, MJ; Atkins, BD; Penman, B; Southall, E; Guyver-Fletcher, G; Holmes, A; McKimm, H; Gorsich, EE; Hill, EM; Dyson, L (2021) The impact of school reopening on the spread of COVID-19 in England PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 376 20200261

Akhmetzhanov, AR; Jung, SM; Cheng, HY; Thompson, RN (2021) A hospital-related outbreak of SARS-CoV-2 associated with variant Epsilon (B.1.429) in Taiwan: transmission potential and outbreak containment under intensified contact tracing, January-February 2021 INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES 110 15-20

Gog, JR; Hill, EM; Danon, L; Thompson, RN (2021) Vaccine escape in a heterogeneous population: insights for SARS-CoV-2 from a simple model ROYAL SOCIETY OPEN SCIENCE 8 210530

Hale, T; Angrist, N; Hale, AJ; Kira, B; Majumdar, S; Petherick, A; Phillips, T; Sridhar, D; Thompson, RN; Webster, S; Zhang, YX (2021) Government responses and COVID-19 deaths: Global evidence across multiple pandemic waves PLOS ONE 16 e0253116

Hill, EM; Atkins, BD; Keeling, MJ; Tildesley, MJ; Dyson, L (2021) Modelling SARS-CoV-2 transmission in a UK university setting EPIDEMICS 36 100476

Parisi, A; Brand, SPC; Hilton, J; Aziza, R; Keeling, MJ; Nokes, DJ (2021) Spatially resolved simulations of the spread of COVID-19 in three European countries PLOS COMPUTATIONAL BIOLOGY 17 e1009090

Iwanami, S et al. (2021) Detection of significant antiviral drug effects on COVID-19 with reasonable sample sizes in randomized controlled trials: A modeling study PLOS MEDICINE 18 e1003660

Goncalves, R; Landivar, D; Liendo, EGS; Fernandez, JM; Ismail, HM; Paine, MJI; Courtenay, O; Bern, C (2021) Improving houses in the Bolivian Chaco increases effectiveness of residual insecticide spraying against infestation with Triatoma infestans, vector of Chagas disease TROPICAL MEDICINE & INTERNATIONAL HEALTH 26 1127-1138

Guarido, MM; Riddin, MA; Johnson, T; Braack, LEO; Schrama, M; Gorsich, EE; Brooke, BD; Almeida, APG; Venter, M (2021) Aedes species (Diptera: Culicidae) ecological and host feeding patterns in the north-eastern parts of South Africa, 2014-2018 PARASITES & VECTORS 14 339

Thompson, RN; Hill, EM; Gog, JR (2021) SARS-CoV-2 incidence and vaccine escape LANCET INFECTIOUS DISEASES 21 913-914

Wang, L; Didelot, X; Bi, YH; Gao, GF (2021) Assessing the extent of community spread caused by mink-derived SARS-CoV-2 variants INNOVATION 2

Goncalves, R; Logan, RAE; Ismail, HM; Paine, MJI; Bern, C; Courtenay, O (2021) Indoor residual spraying practices against Triatoma infestans in the Bolivian Chaco: contributing factors to suboptimal insecticide delivery to treated households PARASITES & VECTORS 14 327

Davis, CN; Castano, MS; Aliee, M; Patel, S; Miaka, EM; Keeling, MJ; Spencer, SEF; Chitnis, N; Rock, KS (2021) Modelling to Quantify the Likelihood that Local Elimination of Transmission has Occurred Using Routine Gambiense Human African Trypanosomiasis Surveillance Data CLINICAL INFECTIOUS DISEASES 72 S146-S151

Knight, DR; Imwattana, K; Kullin, B; Guerrero-Araya, E; Paredes-Sabja, D; Didelot, X; Dingle, KE; Eyre, DW; Rodriguez, C; Riley, TV (2021) Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy ELIFE 10 e64325

Southall, E; Holmes, A; Hill, EM; Atkins, BD; Leng, T; Thompson, RN; Dyson, L; Keeling, MJ; Tildesley, MJ (2021) An analysis of school absences in England during the COVID-19 pandemic BMC MEDICINE 19 137

Willen, L; Basanez, MG; Dvorak, V; Veriegh, FBD; Aboagye, FT; Idun, B; Osman, ME; Osei-Atweneboana, MY; Courtenay, O; Volf, P (2021) Human immune response against salivary antigens of Simulium damnosum s.l.: A new epidemiological marker for exposure to blackfly bites in onchocerciasis endemic areas PLOS NEGLECTED TROPICAL DISEASES 15 e0009512

Cavallaro, M; Moiz, H; Keeling, MJ; McCarthy, ND (2021) Contrasting factors associated with COVID-19-related ICU admission and death outcomes in hospitalised patients by means of Shapley values PLOS COMPUTATIONAL BIOLOGY 17 e1009121

Hill, EM; Atkins, BD; Keeling, MJ; Dyson, L; Tildesley, MJ (2021) A network modelling approach to assess non-pharmaceutical disease controls in a worker population: An application to SARS-CoV-2 PLOS COMPUTATIONAL BIOLOGY 17 e1009058

Camacho-Aguilar, E; Warmflash, A; Rand, DA (2021) Quantifying cell transitions in C. elegans with data-fitted landscape models PLOS COMPUTATIONAL BIOLOGY 17 e1009034

Oketch, JW; Kamau, E; Otieno, JR; Mwema, A; Lewa, C; Isoe, E; Nokes, DJ; Agoti, CN (2021) Comparative analysis of spatial-temporal patterns of human metapneumovirus and respiratory syncytial virus in Africa using genetic data, 2011-2014 VIROLOGY JOURNAL 18 104

Moore, S; Hill, EM; Tildesley, MJ; Dyson, L; Keeling, MJ (2021) Vaccination and non-pharmaceutical interventions for COVID-19: a mathematical modelling study LANCET INFECTIOUS DISEASES 21 793-802

Lovell-Read, FA; Funk, S; Obolski, U; Donnelly, CA; Thompson, RN (2021) Interventions targeting non-symptomatic cases can be important to prevent local outbreaks: SARS-CoV-2 as a case study JOURNAL OF THE ROYAL SOCIETY INTERFACE 18 20201014

Moore, S; Hill, EM; Dyson, L; Tildesley, MJ; Keeling, MJ (2021) Modelling optimal vaccination strategy for SARS-CoV-2 in the UK PLOS COMPUTATIONAL BIOLOGY 17 e1008849

Lowe-Power, T; Dyson, L; Polter, AM (2021) A generation of junior faculty is at risk from the impacts of COVID-19 PLOS BIOLOGY 19 e3001266

Hart, WS; Maini, PK; Thompson, RN (2021) High infectiousness immediately before COVID-19 symptom onset highlights the importance of continued contact tracing ELIFE 10 e65534

Boeri, J; Meunier, C; Le Corronc, H; Branchereau, P; Timofeeva, Y; Lejeune, FX; Mouffle, C; Arulkandarajah, H; Mangin, JM; Legendre, P; Czarnecki, A (2021) Two opposite voltage-dependent currents control the unusual early development pattern of embryonic Renshaw cell electrical activity ELIFE 10 e62639

Toor, J et al. (2021) Predicted Impact of COVID-19 on Neglected Tropical Disease Programs and the Opportunity for Innovation CLINICAL INFECTIOUS DISEASES 72 1463-1466

Lambisia, AW; Phan, MVT; de Laurent, ZR; Cotten, M; Nokes, DJ; Agoti, CN (2021) Near-Complete Genome Sequences of Eight Human Astroviruses Recovered from Diarrheal Stool Samples of Hospitalized Children in Coastal Kenya in 2019 MICROBIOLOGY RESOURCE ANNOUNCEMENTS 10 e00162-21

Davis, CN; Rock, KS; Antillon, M; Miaka, EM; Keeling, MJ (2021) Cost-effectiveness modelling to optimise active screening strategy for gambiense human African trypanosomiasis in endemic areas of the Democratic Republic of Congo BMC MEDICINE 19 86

Diniz-da-Costa, M; Kong, CS; Fishwick, KJ; Rawlings, T; Brighton, PJ; Hawkes, A; Odendaal, J; Quenby, S; Ott, S; Lucas, ES; Vrljicak, P; Brosens, JJ (2021) Characterization of highly proliferative decidual precursor cells during the window of implantation in human endometrium STEM CELLS 39 1067-1080

Pollington, TM; Tildesley, MJ; Hollingsworth, TD; Chapman, LAC (2021) Developments in statistical inference when assessing spatiotemporal disease clustering with the tau statistic SPATIAL STATISTICS 42 100438

Challen, R; Brooks-Pollock, E; Read, JM; Dyson, L; Tsaneva-Atanasova, K; Danon, L (2021) Risk of mortality in patients infected with SARS-CoV-2 variant of concern 202012/1: matched cohort study BMJ-BRITISH MEDICAL JOURNAL 372 n579

Sachak-Patwa, R; Byrne, HM; Thompson, RN (2021) Accounting for cross-immunity can improve forecast accuracy during influenza epidemics EPIDEMICS 34 100432

Kim, KS et al. (2021) A quantitative model used to compare within-host SARS-CoV-2, MERS-CoV, and SARS-CoV dynamics provides insights into the pathogenesis and treatment of SARS-CoV-2 PLOS BIOLOGY 19 e3001128

Retkute, R; Dilger, E; Hamilton, JGC; Keeling, MJ; Courtenay, O (2021) Modelling Sand Fly Lutzomyia longipalpis Attraction to Host Odour: Synthetic Sex-Aggregation Pheromone Dominates the Response MICROORGANISMS 9 602

Aliee, M; Castano, S; Davis, CN; Patel, S; Miaka, EM; Spencer, SEF; Keeling, MJ; Chitnis, N; Rock, KS (2021) Predicting the impact of COVID-19 interruptions on transmission of gambiense human African trypanosomiasis in two health zones of the Democratic Republic of Congo TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE 115 245-252

Benschop, J; Nisa, S; Spencer, SEF (2021) Still 'dairy farm fever'? A Bayesian model for leptospirosis notification data in New Zealand JOURNAL OF THE ROYAL SOCIETY INTERFACE 18 20200964

Staniszewska, S; Hill, EM; Grant, R; Grove, P; Porter, J; Shiri, T; Tulip, S; Whitehurst, J; Wright, C; Datta, S; Petrou, S; Keeling, M (2021) Developing a Framework for Public Involvement in Mathematical and Economic Modelling: Bringing New Dynamism to Vaccination Policy Recommendations (Jan, 10.1007/s40271-020-00476-x, 2021) PATIENT-PATIENT CENTERED OUTCOMES RESEARCH 14 447-447

MacPherson, A; Keeling, MJ; Otto, SP (2021) Coevolution fails to maintain genetic variation in a host-parasite model with constant finite population size THEORETICAL POPULATION BIOLOGY 137 10-21

Mburu, CN et al. (2021) The importance of supplementary immunisation activities to prevent measles outbreaks during the COVID-19 pandemic in Kenya BMC MEDICINE 19 35

Nimmo, C; van Dorp, L; Ortiz, AT; Pang, J; Acman, M; Millard, J; Padayatchi, N; Grant, A; O'Donnell, M; Brynildsrud, O; Eldholm, V; Grandjean, L; Didelot, X; Balloux, F (2021) BEDAQUILINE RESISTANCE IN MYCOBACTERIUM TUBERCULOSIS PREDATES ITS CLINICAL USE THORAX 76 A51-A52

Goncalves, R; de Souza, CF; Rontani, RB; Pereira, A; Farnes, KB; Gorsich, EE; Silva, RA; Brazil, RP; Hamilton, JGC; Courtenay, O (2021) Community deployment of a synthetic pheromone of the sand fly Lutzomyia longipalpis co-located with insecticide reduces vector abundance in treated and neighbouring untreated houses: Implications for control of Leishmania infantum PLOS NEGLECTED TROPICAL DISEASES 15 e0009080

Lutton, EJ; Collier, S; Bretschneider, T (2021) A Curvature-Enhanced Random Walker Segmentation Method for Detailed Capture of 3D Cell Surface Membranes IEEE TRANSACTIONS ON MEDICAL IMAGING 40 514-526

MacPherson, A; Keeling, MJ; Otto, SP (2021) Feedback between coevolution and epidemiology can help or hinder the maintenance of genetic variation in host-parasite models EVOLUTION 75 582-599

Mohlmann, TWR; Keeling, MJ; Wennergren, U; Favia, G; Santman-Berends, I; Takken, W; Koenraadt, CJM; Brand, SPC (2021) Biting midge dynamics and bluetongue transmission: a multiscale model linking catch data with climate and disease outbreaks SCIENTIFIC REPORTS 11 1892

Spencer, SEF; Rodger, A (2021) Bayesian inference assessment of protein secondary structure analysis using circular dichroism data - how much structural information is contained in protein circular dichroism spectra? ANALYTICAL METHODS 13 359-368

Staniszewska, S; Hill, EM; Grant, R; Grove, P; Porter, J; Shiri, T; Tulip, S; Whitehurst, J; Wright, C; Datta, S; Petrou, S; Keeling, M (2021) Developing a Framework for Public Involvement in Mathematical and Economic Modelling: Bringing New Dynamism to Vaccination Policy Recommendations PATIENT-PATIENT CENTERED OUTCOMES RESEARCH 14 435-445

Kombe, IK; Agoti, CN; Munywoki, PK; Baguelin, M; Nokes, DJ; Medley, GF (2021) Integrating epidemiological and genetic data with different sampling intensities into a dynamic model of respiratory syncytial virus transmission SCIENTIFIC REPORTS 11 1463

Rodwell, EV; Vishram, B; Smith, R; Browning, L; Smith-Palmer, A; Allison, L; Holmes, A; Godbole, G; McCarthy, N; Dallman, TJ; Jenkins, C (2021) Epidemiology and genomic analysis of Shiga toxin-producing Escherichia coli clonal complex 165 in the UK JOURNAL OF MEDICAL MICROBIOLOGY 70 1471

Grove, A; Osokogu, O; Al-Khudairy, L; Mehrabian, A; Zanganeh, M; Brown, A; Court, R; Taylor-Phillips, S; Uthman, OA; McCarthy, N; Kumar, S; Clarke, A (2021) Association between vitamin D supplementation or serum vitamin D level and susceptibility to SARS-CoV-2 infection or COVID-19 including clinical course, morbidity and mortality outcomes? A systematic review BMJ OPEN 11 e043737

Hill, E; Gowers, R; Richardson, MJE; Wall, MJ (2021) alpha-Synuclein Aggregates Increase the Conductance of Substantia Nigra Dopamine Neurons, an Effect Partly Reversed by the KATP Channel Inhibitor Glibenclamide ENEURO 8 0330-20.2020

Crump, RE; Huang, CI; Knock, ES; Spencer, SEF; Brown, PE; Miaka, EM; Shampa, C; Keeling, MJ; Rock, KS (2021) Quantifying epidemiological drivers of gambiense human African Trypanosomiasis across the Democratic Republic of Congo PLOS COMPUTATIONAL BIOLOGY 17 e1008532

Keeling, MJ; Hill, EM; Gorsich, EE; Penman, B; Guyver-Fletcher, G; Holmes, A; Leng, T; McKimm, H; Tamborrino, M; Dyson, L; Tildesley, MJ (2021) Predictions of COVID-19 dynamics in the UK: Short-term forecasting and analysis of potential exit strategies PLOS COMPUTATIONAL BIOLOGY 17 e1008619

Lassalle, F; Dastgheib, SMM; Zhao, FJ; Zhang, J; Verbarg, S; Fruhling, A; Brinkmann, H; Osborne, TH; Sikorski, J; Balloux, F; Didelot, X; Santini, JM; Petersen, J (2021) Phylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus SYSTEMATIC AND APPLIED MICROBIOLOGY 44 126165

Didelot, X; Siveroni, I; Volz, EM (2021) Additive Uncorrelated Relaxed Clock Models for the Dating of Genomic Epidemiology Phylogenies MOLECULAR BIOLOGY AND EVOLUTION 38 307-317

2020

Atkins, BD; Jewell, CP; Runge, MC; Ferrari, MJ; Shea, K; Probert, WJM; Tildesley, MJ (2020) Anticipating future learning affects current control decisions: A comparison between passive and active adaptive management in an epidemiological setting JOURNAL OF THEORETICAL BIOLOGY 506 110380

Kamau, E; Otieno, JR; Lewa, CS; Mwema, A; Murunga, N; Nokes, DJ; Agoti, CN (2020) Evolution of respiratory syncytial virus genotype BA in Kilifi, Kenya, 15 years on SCIENTIFIC REPORTS 10 21176

Touloupou, P; Finkenstadt, B; Besser, TE; French, NP; Spencer, SEF (2020) BAYESIAN INFERENCE FOR MULTISTRAIN EPIDEMICS WITH APPLICATION TO ESCHERICHIA COLI O157:H7 IN FEEDLOT CATTLE ANNALS OF APPLIED STATISTICS 14 1925-1944

Mwanga, MJ; Verani, JR; Omore, R; Tate, JE; Parashar, UD; Murunga, N; Gicheru, E; Breiman, RF; Nokes, DJ; Agoti, CN (2020) Multiple Introductions and Predominance of Rotavirus Group A Genotype G3P[8] in Kilifi, Coastal Kenya, 4 Years after Nationwide Vaccine Introduction PATHOGENS 9 981

Griffin, A; Roberts, GO; Spencer, SEF (2020) An epidemic model for an evolving pathogen with strain-dependent immunity MATHEMATICAL BIOSCIENCES 330 108480

Gorsich, EE; Webb, CT; Merton, AA; Hoeting, JA; Miller, RS; Farnsworth, ML; Swafford, SR; DeLiberto, TJ; Pedersen, K; Franklin, AB; McLean, RG; Wilson, KR; Doherty, PF (2021) Continental-scale dynamics of avian influenza in US waterfowl are driven by demography, migration, and temperature ECOLOGICAL APPLICATIONS 31 e02245

Nyiro, JU; Bukusi, E; Mwaengo, D; Walumbe, D; Nyaguara, A; Nyawanda, B; Otieno, N; Berkley, JA; Munywoki, P; Nokes, DJ (2020) Implications of gestational age at antenatal care attendance on the successful implementation of a maternal respiratory syncytial virus (RSV) vaccine program in coastal Kenya BMC PUBLIC HEALTH 20 1723

Gonzalez, MA; Dilger, E; Ronderos, MM; Spinelli, GR; Courtenay, O; Hamilton, JGC (2020) Significant reduction in abundance of peridomestic mosquitoes (Culicidae) and Culicoides midges (Ceratopogonidae) after chemical intervention in western SAo Paulo, Brazil PARASITES & VECTORS 13 549

Osnes, MN; Didelot, X; de Korne-Elenbaas, J; Alfsnes, K; Brynildsrud, OB; Syversen, G; Nilsen, OJ; De Blasio, BF; Caugant, DA; Eldholm, V (2020) Sudden emergence of a Neisseria gonorrhoeae Glade with reduced susceptibility to extended-spectrum cephalosporins, Norway MICROBIAL GENOMICS 6 480

Zhao, L; Chen, HY; Didelot, X; Li, ZP; Li, YH; Chen, ML; Du, Y; Zhao, HQ; Li, J; Hu, QH; Kan, B; Chen, M; Pang, B (2020) Co-existence of multiple distinct lineages in Vibrio parahaemolyticus serotype O4:K12 MICROBIAL GENOMICS 6 287

Holmes, A; Tildesley, MJ; Solomon, AW; Mabey, DCW; Sokana, O; Marks, M; Dyson, L (2020) Modeling Treatment Strategies to Inform Yaws Eradication EMERGING INFECTIOUS DISEASES 26 2685-2693

Vegvari, C; Grad, YH; White, PJ; Didelot, X; Whittles, LK; Scangarella-Oman, NE; Mitrani-Gold, FS; Dumont, E; Perry, CR; Gilchrist, K; Hossain, M; Mortimer, TD; Anderson, RM; Gardiner, D (2020) Using rapid point-of-care tests to inform antibiotic choice to mitigate drug resistance in gonorrhoea EUROSURVEILLANCE 25 1900210

Thompson, CP et al. (2020) Detection of neutralising antibodies to SARS-CoV-2 to determine population exposure in Scottish blood donors between March and May 2020 EUROSURVEILLANCE 25 33-41

Whittles, LK; White, PJ; Didelot, X (2020) Assessment of the Potential of Vaccination to Combat Antibiotic Resistance in Gonorrhea: A Modeling Analysis to Determine Preferred Product Characteristics CLINICAL INFECTIOUS DISEASES 71 1912-1919

van Andel, M; Tildesley, MJ; Gates, MC (2021) Challenges and opportunities for using national animal datasets to support foot-and-mouth disease control TRANSBOUNDARY AND EMERGING DISEASES 68 1800-1813

Chapman, LAC; Spencer, SEF; Pollington, TM; Jewell, CP; Mondal, D; Alvar, J; Hollingsworth, TD; Cameron, MM; Bern, C; Medley, GF (2020) Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post-kala-azar dermal leishmaniasis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 117 25742-25750

Wang, L; Didelot, X; Yang, J; Wong, G; Shi, Y; Liu, WJ; Gao, GF; Bi, YH (2020) Inference of person-to-person transmission of COVID-19 reveals hidden super-spreading events during the early outbreak phase NATURE COMMUNICATIONS 11 5006

Luka, MM; Kamau, E; Adema, I; Munywoki, PK; Otieno, GP; Gicheru, E; Gichuki, A; Kibinge, N; Agoti, CN; Nokes, DJ (2020) Molecular Epidemiology of Human Rhinovirus From 1-Year Surveillance Within a School Setting in Rural Coastal Kenya OPEN FORUM INFECTIOUS DISEASES 7 ofaa385

Keeling, MJ; Hollingsworth, TD; Read, JM (2020) Efficacy of contact tracing for the containment of the 2019 novel coronavirus (COVID-19) JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH 74 861-866

Elnaiem, DEA; Dakein, O; Alawad, AMA; Alsharif, B; Khogali, A; Jibreel, T; Osman, OF; Has'san, H; Atia, AM; Elhag, M; Den Boer, M; Ritmeijer, K; Bern, C; Alvar, J; Khalid, N; Courtenay, O (2020) Outdoor Residual Insecticide Spraying (ODRS), a New Approach for the Control of the Exophilic Vectors of Human Visceral Leishmaniasis:Phlebotomus orientalisin East Africa PLOS NEGLECTED TROPICAL DISEASES 14 e0008774

Janezic, S; Dingle, K; Alvin, J; Accetto, T; Didelot, X; Crook, DW; Lacy, DB; Rupnik, M (2020) Comparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution MICROBIAL GENOMICS 6 449

Penman, BS; Gandon, S (2020) Adaptive immunity selects against malaria infection blocking mutations PLOS COMPUTATIONAL BIOLOGY 16 e1008181

Hill, EM; Petrou, S; Forster, H; de Lusignan, S; Yonova, I; Keeling, MJ (2020) Optimising age coverage of seasonal influenza vaccination in England: A mathematical and health economic evaluation PLOS COMPUTATIONAL BIOLOGY 16 e1008278

Gonzalez, MA; Bell, M; Souza, CF; Maciel-de-Freitas, R; Brazil, RP; Courtenay, O; Hamilton, JGC (2020) Synthetic sex-aggregation pheromone of Lutzomyia longipalpis, the South American sand fly vector of Leishmania infantum, attracts males and females over long-distance PLOS NEGLECTED TROPICAL DISEASES 14 e0008798

Leng, T; Keeling, MJ (2020) Improving pairwise approximations for network models with susceptible-infected-susceptible dynamics JOURNAL OF THEORETICAL BIOLOGY 500 110328

Volz, EM; Carsten, W; Grad, YH; Frost, SDW; Dennis, AM; Didelot, X (2020) Identification of Hidden Population Structure in Time-Scaled Phylogenies SYSTEMATIC BIOLOGY 69 884-896

Rich-Griffin, C; Eichmann, R; Reitz, MU; Hermann, S; Woolley-Allen, K; Brown, PE; Wiwatdirekkul, K; Esteban, E; Pasha, A; Kogel, KH; Provart, NJ; Ott, S; Schafer, P (2020) Regulation of Cell Type-Specific Immunity Networks in Arabidopsis Roots([CC-BY]) PLANT CELL 32 2742-2762

Southall, E; Tildesley, MJ; Dyson, L (2020) Prospects for detecting early warning signals in discrete event sequence data: Application to epidemiological incidence data PLOS COMPUTATIONAL BIOLOGY 16 e1007836

Lucciola, R; Vrljicak, P; Gurung, S; Filby, C; Darzi, S; Muter, J; Ott, S; Brosens, JJ; Gargett, CE (2020) Impact of Sustained Transforming Growth Factor-beta Receptor Inhibition on Chromatin Accessibility and Gene Expression in Cultured Human Endometrial MSC FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY 8 567610

McKinley, TJ; Neal, P; Spencer, SEF; Conlan, AJK; Tiley, L (2020) Efficient Bayesian Model Choice for Partially Observed Processes: With Application to an Experimental Transmission Study of an Infectious Disease BAYESIAN ANALYSIS 15 839-870

White, CF; Pellis, L; Keeling, MJ; Penman, BS (2020) Detecting HLA-infectious disease associations for multi -strain pathogens INFECTION GENETICS AND EVOLUTION 83 104344

Thompson, RN et al. (2020) Key questions for modelling COVID-19 exit strategies PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 287 20201405

Schrama, M; Hunting, ER; Beechler, BR; Guarido, MM; Govender, D; Nijland, W; Zelfde, MV; Venter, M; van Bodegom, PM; Gorsich, EE (2020) Human practices promote presence and abundance of disease-transmitting mosquito species SCIENTIFIC REPORTS 10 13543

Minas, G; Woodcock, DJ; Ashall, L; Harper, CV; White, MRH; Rand, DA (2020) Multiplexing information flow through dynamic signalling systems PLOS COMPUTATIONAL BIOLOGY 16 e1008076

Esan, OB; Perera, R; McCarthy, N; Violato, M; Fanshawe, TR (2020) Incidence, risk factors, and health service burden of sequelae of campylobacter and non-typhoidal salmonella infections in England, 2000-2015: A retrospective cohort study using linked electronic health records JOURNAL OF INFECTION 81 221-230

Mwanga, MJ et al. (2020) Rotavirus group A genotype circulation patterns across Kenya before and after nationwide vaccine introduction, 2010-2018 BMC INFECTIOUS DISEASES 20 504

Aanensen, DM et al. (2020) An integrated national scale SARS-CoV-2 genomic surveillance network LANCET MICROBE 1 E99-E100

Fountain-Jones, NM; Appaw, RC; Carver, S; Didelot, X; Volz, E; Charleston, M (2020) Emerging phylogenetic structure of the SARS-CoV-2 pandemic VIRUS EVOLUTION 6 veaa082

Kamau, E; Otieno, JR; Murunga, N; Oketch, JW; Ngoi, JM; de Laurent, ZR; Mwema, A; Nyiro, JU; Agoti, CN; Nokes, DJ (2020) Genomic epidemiology and evolutionary dynamics of respiratory syncytial virus group B in Kilifi, Kenya, 2015-17 VIRUS EVOLUTION 6 veaa050

Nyasimi, FM; Owuor, DC; Ngoi, JM; Mwihuri, AG; Otieno, GP; Otieno, JR; Githinji, G; Nyiro, JU; Nokes, DJ; Agoti, CN (2020) Epidemiological and evolutionary dynamics of influenza B virus in coastal Kenya as revealed by genomic analysis of strains sampled over a single season VIRUS EVOLUTION 6 veaa045

Hilton, J; Keeling, MJ (2020) Estimation of country-level basic reproductive ratios for novel Coronavirus (SARS-CoV-2/COVID-19) using synthetic contact matrices PLOS COMPUTATIONAL BIOLOGY 16 e1008031

Tennant, WSD; Tildesley, MJ; Spencer, SEF; Keeling, MJ (2020) Climate drivers of plague epidemiology in British India, 1898-1949 PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 287 20200538

Kura, K; Collyer, BS; Toor, J; Truscott, JE; Hollingsworth, TD; Keeling, MJ; Anderson, RM (2020) Policy implications of the potential use of a novel vaccine to prevent infection with Schistosoma mansoni with or without mass drug administration VACCINE 38 4379-4386

Khagayi, S et al. (2020) Effectiveness of Monovalent Rotavirus Vaccine Against Hospitalization With Acute Rotavirus Gastroenteritis in Kenyan Children CLINICAL INFECTIOUS DISEASES 70 2298-2305

Otieno, GP et al. (2020) Impact of the Introduction of Rotavirus Vaccine on Hospital Admissions for Diarrhea Among Children in Kenya: A Controlled Interrupted Time-Series Analysis CLINICAL INFECTIOUS DISEASES 70 2306-2313

Rodriguez-Manzano, J; Moser, N; Malpartida-Cardenas, K; Moniri, A; Fisarova, L; Pennisi, I; Boonyasiri, A; Jauneikaite, E; Abdolrasouli, A; Otter, JA; Bolt, F; Davies, F; Didelot, X; Holmes, A; Georgiou, P (2020) Rapid Detection of Mobilized Colistin Resistance using a Nucleic Acid Based Lab-on-a-Chip Diagnostic System SCIENTIFIC REPORTS 10 8448

Owuor, DC; Ngoi, JM; Otieno, JR; Otieno, GP; Nyasimi, FM; Nyiro, JU; Agoti, CN; Chaves, SS; Nokes, DJ (2020) Genetic characterization of influenza A(H3N2) viruses circulating in coastal Kenya, 2009-2017 INFLUENZA AND OTHER RESPIRATORY VIRUSES 14 320-330

Roscioli, E; Germanova, TE; Smith, CA; Embacher, PA; Erent, M; Thompson, AI; Burroughs, NJ; McAinsh, AD (2020) Ensemble-Level Organization of Human Kinetochores and Evidence for Distinct Tension and Attachment Sensors CELL REPORTS 31 107535

Kinyanjui, T; Pan-Ngum, W; Saralamba, S; Taylor, S; White, L; Nokes, DJ (2020) Model evaluation of target product profiles of an infant vaccine against respiratory syncytial virus (RSV) in a developed country setting VACCINE: X 4 100055

Touloupou, P; Finkenstadt, B; Spencer, SEF (2020) Scalable Bayesian Inference for Coupled Hidden Markov and Semi-Markov Models JOURNAL OF COMPUTATIONAL AND GRAPHICAL STATISTICS 29 238-249

Gowers, RP; Timofeeva, Y; Richardson, MJE (2020) Low-rate firing limit for neurons with axon, soma and dendrites driven by spatially distributed stochastic synapses PLOS COMPUTATIONAL BIOLOGY 16 e1007175

Stinner, B; Bretschneider, T (2020) Mathematical modelling in cell migration: tackling biochemistry in changing geometries BIOCHEMICAL SOCIETY TRANSACTIONS 48 419-428

Brand, SPC; Munywoki, P; Walumbe, D; Keeling, MJ; Nokes, DJ (2020) Reducing respiratory syncytial virus (RSV) hospitalization in a lower-income country by vaccinating mothers-to-be and their households ELIFE 9 e47003

Gavard, R; Jones, HE; Lozano, DCP; Thomas, MJ; Rossell, D; Spencer, SEF; Barrow, MP (2020) KairosMS: A New Solution for the Processing of Hyphenated Ultrahigh Resolution Mass Spectrometry Data ANALYTICAL CHEMISTRY 92 3775-3786

Dantas-Torres, F et al. (2020) Vaccination against canine leishmaniasis in Brazil INTERNATIONAL JOURNAL FOR PARASITOLOGY 50 171-176

Ratmann, O et al. (2020) Quantifying HIV transmission flow between high-prevalence hotspots and surrounding communities: a population-based study in Rakai, Uganda LANCET HIV 7 E173-E183

Lang, S; Loving, S; McCarthy, ND; Ramsay, ME; Salisbury, D; Pollard, AJ (2020) Two centuries of immunisation in the UK (part II) ARCHIVES OF DISEASE IN CHILDHOOD 105 216-222

Barquera, R et al. (2020) Diversity of HLA Class I and Class II blocks and conserved extended haplotypes in Lacandon Mayans SCIENTIFIC REPORTS 10 3248

Tsao, K; Sellman, S; Beck-Johnson, LM; Murrieta, DJ; Hallman, C; Lindstrom, T; Miller, RS; Portacci, K; Tildesley, MJ; Webb, CT (2020) Effects of regional differences and demography in modelling foot-and-mouth disease in cattle at the national scale INTERFACE FOCUS 10 20190054

Wang, HQ; Yang, C; Sun, Z; Zheng, W; Zhang, W; Yu, H; Wu, YR; Didelot, X; Yang, RF; Pan, JC; Cui, YJ (2020) Genomic epidemiology of Vibrio cholerae reveals the regional and global spread of two epidemic non-toxigenic lineages PLOS NEGLECTED TROPICAL DISEASES 14 e0008046

Sellman, S; Tildesley, MJ; Burdett, CL; Miller, RS; Hallman, C; Webb, CT; Wennergren, U; Portacci, K; Lindstrom, T (2020) Realistic assumptions about spatial locations and clustering of premises matter for models of foot-and-mouth disease spread in the United States PLOS COMPUTATIONAL BIOLOGY 16 e1007641

Lang, S; Loving, S; McCarthy, ND; Ramsay, ME; Salisbury, D; Pollard, AJ (2020) Two centuries of immunisation in the UK (part 1) ARCHIVES OF DISEASE IN CHILDHOOD 105 115-121

Yusuf, AA; Figueiredo, IP; Afsar, A; Burroughs, NJ; Pinto, AA; Oliveira, BMPM (2020) The Effect of a Linear Tuning between the Antigenic Stimulations of CD4(+) T Cells and CD4(+) Tregs MATHEMATICS 8 293

Rich-Griffin, C; Stechemesser, A; Finch, J; Lucas, E; Ott, S; Schafer, P (2020) Single-Cell Transcriptomics: A High-Resolution Avenue for Plant Functional Genomics TRENDS IN PLANT SCIENCE 25 186-197

Kamau, E; Oketch, JW; de Laurent, ZR; Phan, MVT; Agoti, CN; Nokes, DJ; Cotten, M (2020) Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia (vol 21, 5, 2020) BMC GENOMICS 21 83

Lucas, ES; Vrljicak, P; Muter, J; Diniz-da-Costa, MM; Brighton, PJ; Kong, CS; Lipecki, J; Fishwick, KJ; Odendaal, J; Ewington, LJ; Quenby, S; Ott, S; Brosens, JJ (2020) Recurrent pregnancy loss is associated with a pro-senescent decidual response during the peri-implantation window COMMUNICATIONS BIOLOGY 3 37

Kamau, E; Oketch, JW; de Laurent, ZR; Phan, MVT; Agoti, CN; Nokes, DJ; Cotten, M (2020) Whole genome sequencing and phylogenetic analysis of human metapneumovirus strains from Kenya and Zambia BMC GENOMICS 21

Castano, MS; Ndeffo-Mbah, ML; Rock, KS; Palmer, C; Knock, E; Miaka, EM; Ndung'u, JM; Torr, S; Verle, P; Spencer, SEF; Galvani, A; Bever, C; Keeling, MJ; Chitnis, N (2020) Assessing the impact of aggregating disease stage data in model predictions of human African trypanosomiasis transmission and control activities in Bandundu province (DRC) PLOS NEGLECTED TROPICAL DISEASES 14 e0007976

Wilson, AL; Courtenay, O; Kelly-Hope, LA; Scott, TW; Takken, W; Torr, SJ; Lindsay, SW (2020) The importance of vector control for the control and elimination of vector-borne diseases PLOS NEGLECTED TROPICAL DISEASES 14 e0007831

Abidha, CA; Nyiro, J; Kamau, E; Abdullahi, O; Nokes, DJ; Agoti, CN (2020) Transmission and evolutionary dynamics of human coronavirus OC43 strains in coastal Kenya investigated by partial spike sequence analysis, 2015-16 VIRUS EVOLUTION 6 veaa031

Lucas, TCD; Pollington, TM; Davis, EL; Hollingsworth, TD (2020) Responsible modelling: Unit testing for infectious disease epidemiology EPIDEMICS 33 100425

Mansfield, LA; Nowack, PJ; Kasoar, M; Everitt, RG; Collins, WJ; Voulgarakis, A (2020) Predicting global patterns of long-term climate change from short-term simulations using machine learning NPJ CLIMATE AND ATMOSPHERIC SCIENCE 3 44

Chapman, LAC; Spencer, SEF; Pollington, TM; Jewell, CP; Mondal, D; Alvar, J; Hollingsworth, TD; Cameron, MM; Bern, C; Medley, GF (2020) Inferring transmission trees to guide targeting of interventions against visceral leishmaniasis and post-kala-azar dermal leishmaniasis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 117 25742-25750

Levi, F; Komarzynski, S; Huang, Q; Young, T; Ang, Y; Fuller, C; Bolborea, M; Brettschneider, J; Fursse, J; Finkenstadt, B; White, DP; Innominato, P (2020) Tele-Monitoring of Cancer Patients' Rhythms during Daily Life Identifies Actionable Determinants of Circadian and Sleep Disruption CANCERS 12 1938

Chamberland, S; Timofeeva, Y; Evstratova, A; Norman, CA; Volynski, K; Toth, K (2020) Slow-decaying presynaptic calcium dynamics gate long-lasting asynchronous release at the hippocampal mossy fiber to CA3 pyramidal cell synapse SYNAPSE 74 e22178

Tyurikova, O; Zheng, KY; Nicholson, E; Timofeeva, Y; Semyanov, A; Volynski, KE; Rusakov, DA (2021) Fluorescence lifetime imaging reveals regulation of presynaptic Ca2+ by glutamate uptake and mGluRs, but not somatic voltage in cortical neurons JOURNAL OF NEUROCHEMISTRY 156 48-58

Cunningham, N; Griffin, JE; Wild, DL (2020) ParticleMDI: particle Monte Carlo methods for the cluster analysis of multiple datasets with applications to cancer subtype identification ADVANCES IN DATA ANALYSIS AND CLASSIFICATION 14 463-484

Gowers, RP; Timofeeva, Y; Richardson, MJE (2020) Low-rate firing limit for neurons with axon, soma and dendrites driven by spatially distributed stochastic synapses PLOS COMPUTATIONAL BIOLOGY 16 e1007175

Birrell, PJ; Wernisch, L; Tom, BDM; Held, L; Roberts, GO; Pebody, RG; De Angelis, D (2020) EFFICIENT REAL-TIME MONITORING OF AN EMERGING INFLUENZA PANDEMIC: HOW FEASIBLE? ANNALS OF APPLIED STATISTICS 14 74-93

Davis, CN; Hollingsworth, TD; Caudron, Q; Irvine, MA (2020) The use of mixture density networks in the emulation of complex epidemiological individual-based models PLOS COMPUTATIONAL BIOLOGY 16 e1006869

Tagliatti, E; Bello, OD; Mendonca, PRF; Kotzadimitriou, D; Nicholson, E; Coleman, J; Timofeeva, Y; Rothman, JE; Krishnakumar, SS; Volynski, KE (2020) Synaptotagmin 1 oligomers clamp and regulate different modes of neurotransmitter release PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 117 3819-3827

Lu, YH; Timofeeva, Y (2020) Exact solutions to cable equations in branching neurons with tapering dendrites JOURNAL OF MATHEMATICAL NEUROSCIENCE 10 1

2019

Meakin, SR; Keeling, MJ (2019) Correlations between stochastic endemic infection in multiple interacting subpopulations JOURNAL OF THEORETICAL BIOLOGY 483 109991

Gavard, R; Lozano, DCP; Guzman, A; Rossell, D; Spencer, SEF; Barrow, MP (2019) Rhapso: Automatic Stitching of Mass Segments from Fourier Transform Ion Cyclotron Resonance Mass Spectra ANALYTICAL CHEMISTRY 91 15130-15137

Baniukiewicz, P; Lutton, EJ; Collier, S; Bretschneider, T (2019) Generative Adversarial Networks for Augmenting Training Data of Microscopic Cell Images FRONTIERS IN COMPUTER SCIENCE 1 10

Dessavre, AG; Southall, E; Tildesley, MJ; Dyson, L (2019) The problem of detrending when analysing potential indicators of disease elimination JOURNAL OF THEORETICAL BIOLOGY 481 183-193

Auguste, P; Madan, J; Tsertsvadze, A; Court, R; McCarthy, N; Sutcliffe, P; Taylor-Phillips, S; Pink, J; Clarke, A (2019) Identifying latent tuberculosis in high-risk populations: systematic review and meta-analysis of test accuracy INTERNATIONAL JOURNAL OF TUBERCULOSIS AND LUNG DISEASE 23 1178-1190

Shiri, T; Khan, K; Keaney, K; Mukherjee, G; McCarthy, ND; Petrou, S (2019) Pneumococcal Disease: A Systematic Review of Health Utilities, Resource Use, Costs, and Economic Evaluations of Interventions VALUE IN HEALTH 22 1329-1344

Kintz, E; Byrne, L; Jenkins, C; Mccarthy, N; Vivancos, R; Hunter, P (2019) Outbreaks of Shiga Toxin-Producing Escherichia coli Linked to Sprouted Seeds, Salad, and Leafy Greens: A Systematic Review JOURNAL OF FOOD PROTECTION 82 1950-1958

Kamau, E; Luka, MM; de Laurent, ZR; Adema, I; Agoti, CN; Nokes, DJ (2019) Genome Sequences of Human Coronavirus OC43 and NL63, Associated with Respiratory Infections in Kilifi, Kenya MICROBIOLOGY RESOURCE ANNOUNCEMENTS 8 e00730-19

Codys, AJ; Maiden, MCJ; Strachan, NJC; McCarthy, ND (2019) A systematic review of source attribution of human campylobacteriosis using multilocus sequence typing EUROSURVEILLANCE 24 8-15

Collyer, BS; Turner, HC; Hollingsworth, TD; Keeling, MJ (2019) Vaccination or mass drug administration against schistosomiasis: a hypothetical cost-effectiveness modelling comparison PARASITES & VECTORS 12 499

Gorsich, EE; Beechler, BR; van Bodegom, PM; Govender, D; Guarido, MM; Venter, M; Schrama, M (2019) A comparative assessment of adult mosquito trapping methods to estimate spatial patterns of abundance and community composition in southern Africa PARASITES & VECTORS 12 462

Hill, EM; Petrou, S; de Lusignan, S; Yonova, I; Keeling, MJ (2019) Seasonal influenza: Modelling approaches to capture immunity propagation PLOS COMPUTATIONAL BIOLOGY 15 e1007096

Courtenay, O; Dilger, E; Calvo-Bado, LA; Kravar-Garde, L; Carter, V; Bell, MJ; Alves, GB; Goncalves, R; Makhdoomi, MM; Gonzalez, MA; Nunes, CM; Bray, DP; Brazil, RP; Hamilton, JGC (2019) Sand fly synthetic sex-aggregation pheromone co-located with insecticide reduces the incidence of infection in the canine reservoir of visceral leishmaniasis: A stratified cluster randomised trial PLOS NEGLECTED TROPICAL DISEASES 13 e0007767

Davis, CN; Rock, KS; Miaka, EM; Keeling, MJ (2019) Village-scale persistence and elimination of gambiense human African trypanosomiasis PLOS NEGLECTED TROPICAL DISEASES 13 e0007838

Awofisayo-Okuyelu, A; Pratt, A; McCarthy, N; Hall, I (2019) Within-host mathematical modelling of the incubation period of Salmonella Typhi ROYAL SOCIETY OPEN SCIENCE 6 182143

Hill, E; Karikari, TK; Moffat, KG; Richardson, MJE; Wall, MJ (2019) Introduction of Tau Oligomers into Cortical Neurons Alters Action Potential Dynamics and Disrupts Synaptic Transmission and Plasticity ENEURO 6 0166-19.2019

Juric, I; Hibberd, JM; Blatt, M; Burroughs, NJ (2019) Computational modelling predicts substantial carbon assimilation gains for C-3 plants with a single-celled C-4 biochemical pump PLOS COMPUTATIONAL BIOLOGY 15 e1007373

Noufaily, A; Morbey, RA; Colon-Gonzalez, FJ; Elliot, AJ; Smith, GE; Lake, IR; McCarthy, N (2019) Comparison of statistical algorithms for daily syndromic surveillance aberration detection BIOINFORMATICS 35 3110-3118

Tildesley, MJ; Brand, S; Pollock, EB; Bradbury, NV; Werkman, M; Keeling, MJ (2019) The role of movement restrictions in limiting the economic impact of livestock infections NATURE SUSTAINABILITY 2 834-840

Hopkins, T; Goncalves, R; Mamani, J; Courtenay, O; Bern, C (2019) Chagas disease in the Bolivian Chaco: Persistent transmission indicated by childhood seroscreening study INTERNATIONAL JOURNAL OF INFECTIOUS DISEASES 86 175-177

Ward, DG et al. (2019) Targeted deep sequencing of urothelial bladder cancers and associated urinary DNA: a 23-gene panel with utility for non-invasive diagnosis and risk stratification BJU INTERNATIONAL 124 532-544

Oketch, JW; Kamau, E; Otieno, GP; Otieno, JR; Agoti, CN; Nokes, DJ (2019) Human metapneumovirus prevalence and patterns of subgroup persistence identified through surveillance of pediatric pneumonia hospital admissions in coastal Kenya, 2007-2016 BMC INFECTIOUS DISEASES 19 757

Lozano, DCP; Gavard, R; Arenas-Diaz, JP; Thomas, MJ; Stranz, DD; Mejia-Ospino, E; Guzman, A; Spencer, SEF; Rossell, D; Barrow, MP (2019) Pushing the analytical limits: new insights into complex mixtures using mass spectra segments of constant ultrahigh resolving power CHEMICAL SCIENCE 10 6966-6978

Hilton, J; Keeling, MJ (2019) Incorporating household structure and demography into models of endemic disease JOURNAL OF THE ROYAL SOCIETY INTERFACE 16 20190317

Criscuolo, A; Issenhuth-Jeanjean, S; Didelot, X; Thorell, K; Hale, J; Parkhill, J; Thomson, NR; Weill, FX; Falush, D; Brisse, S (2019) The speciation and hybridization history of the genus Salmonella MICROBIAL GENOMICS 5 284

Li, Y et al. (2019) Global patterns in monthly activity of influenza virus, respiratory syncytial virus, parainfluenza virus, and metapneumovirus: a systematic analysis LANCET GLOBAL HEALTH 7 E1031-E1045

Sande, CJ; Njunge, JM; Ngoi, JM; Mutunga, MN; Chege, T; Gicheru, ET; Gardiner, EM; Gwela, A; Green, CA; Drysdale, SB; Berkley, JA; Nokes, DJ; Pollard, AJ (2019) Airway response to respiratory syncytial virus has incidental antibacterial effects (vol 10, 2218, 2019) NATURE COMMUNICATIONS 10 3291

Beechler, BR; Boersma, KS; Buss, PE; Coon, CAC; Gorsich, EE; Henrichs, BS; Siepielski, AM; Spaan, JM; Spaan, RS; Ezenwa, VO; Jolles, AE (2019) Bovine tuberculosis disturbs parasite functional trait composition in African buffalo PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 116 14645-14650

Agoti, CN; Phan, MVT; Munywoki, PK; Githinji, G; Medley, GF; Canes, PA; Kellam, P; Cotten, M; Nokes, DJ (2019) Genomic analysis of respiratory syncytial virus infections in households and utility in inferring who infects the infant SCIENTIFIC REPORTS 9 10076

Krol, L; Van der Hoorn, B; Gorsich, EE; Trimbos, K; van Bodegom, PM; Schrama, M (2019) How Does eDNA Compare to Traditional Trapping? Detecting Mosquito Communities in South-African Freshwater Ponds FRONTIERS IN ECOLOGY AND EVOLUTION 7 260

Probert, WJM; Lakkur, S; Fonnesbeck, CJ; Shea, K; Runge, MC; Tildesley, MJ; Ferrari, MJ (2019) Context matters: using reinforcement learning to develop human-readable, state-dependent outbreak response policies PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 374 20180277

Whittles, L; White, P; Didelot, X (2019) ESTIMATING THE POTENTIAL IMPACT OF REALISTIC VACCINATION STRATEGIES AGAINST ANTIBIOTIC RESISTANT NEISSERIA GONORRHOEAE SEXUALLY TRANSMITTED INFECTIONS 95 A278-A278

Ozer, EA; Nnah, E; Didelot, X; Whitaker, RJ; Hauser, AR (2019) The Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU plus and exoS plus Lineages GENOME BIOLOGY AND EVOLUTION 11 1780-1796

Didelot, X; Pouwels, KB (2019) Machine-learning-assisted selection of antibiotic prescription NATURE MEDICINE 25 1033-1034

Datta, S; Pink, J; Medley, GF; Petrou, S; Staniszewska, S; Underwood, M; Sonnenberg, P; Keeling, MJ (2019) Assessing the cost-effectiveness of HPV vaccination strategies for adolescent girls and boys in the UK BMC INFECTIOUS DISEASES 19 552

Li, SL; Ferrari, MJ; Bjornstad, ON; Runge, MC; Fonnesbeck, CJ; Tildesley, MJ; Pannell, D; Shea, K (2019) Concurrent assessment of epidemiological and operational uncertainties for optimal outbreak control: Ebola as a case study PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 286 20190774

Castano, MS; Aliee, M; Miaka, EM; Keeling, MJ; Chitnis, N; Rock, KS (2019) Screening Strategies for a Sustainable Endpoint for Gambiense Sleeping Sickness JOURNAL OF INFECTIOUS DISEASES 221 S539-S545

Shiri, T; McCarthy, ND; Petrou, S (2019) The impact of childhood pneumococcal vaccination on hospital admissions in England: a whole population observational study BMC INFECTIOUS DISEASES 19 510

Moniri, A; Rodriguez-Manzano, J; Malpartida-Cardenas, K; Yu, LS; Didelot, X; Holmes, A; Georgiou, P (2019) Framework for DNA Quantification and Outlier Detection Using Multidimensional Standard Curves ANALYTICAL CHEMISTRY 91 7426-7434

Lagunas, B; Achom, M; Bonyadi-Pour, R; Pardal, AJ; Richmond, BL; Sergaki, C; Vazquez, S; Schafer, P; Ott, S; Hammond, J; Gifford, ML (2019) Regulation of Resource Partitioning Coordinates Nitrogen and Rhizobia Responses and Autoregulation of Nodulation in Medicago truncatula MOLECULAR PLANT 12 833-846

Momiji, H; Hassall, KL; Featherstone, K; McNamara, AV; Patist, AL; Spiller, DG; Christian, HC; White, MRH; Davis, JRE; Finkenstadt, BF; Rand, DA (2019) Disentangling juxtacrine from paracrine signalling in dynamic tissue PLOS COMPUTATIONAL BIOLOGY 15 e1007030

Kombe, IK; Munywoki, PK; Baguelin, M; Nokes, DJ; Medley, GF (2019) Model-based estimates of transmission of respiratory syncytial virus within households EPIDEMICS 27 1-11

Hockham, C; Ekwattanakit, S; Bhatt, S; Penman, BS; Gupta, S; Viprakasit, V; Piel, FB (2019) Estimating the burden of alpha-thalassaemia in Thailand using a comprehensive prevalence database for Southeast Asia ELIFE 8 e40580

Ailloud, F; Didelot, X; Woltemate, S; Pfaffinger, G; Overmann, J; Bader, RC; Schulz, C; Malfertheiner, P; Suerbaum, S (2019) Within-host evolution of Helicobacter pylori shaped by niche-specific adaptation, intragastric migrations and selective sweeps NATURE COMMUNICATIONS 10 2273

Buckingham-Jeffery, E; Hill, EM; Datta, S; Dilger, E; Courtenay, O (2019) Spatio-temporal modelling of Leishmania infantum infection among domestic dogs: a simulation study and sensitivity analysis applied to rural Brazil PARASITES & VECTORS 12 215

Eyre, DW; Didelot, X; Buckley, AM; Freeman, J; Moura, IB; Crook, DW; Peto, TEA; SarahWalker, A; Wilcox, MH; Dingle, KE (2019) Clostridium difficile trehalose metabolism variants are common and not associated with adverse patient outcomes when variably present in the same lineage EBIOMEDICINE 43 347-355

Gargett, CE; Lucciola, R; Filby, C; Darzi, S; Vrljicak, P; Ott, S; Brosens, JJ (2019) CHROMATIN ARCHITECTURE AND GENE EXPRESSION IN HUMAN ENDOMETRIAL MSC EXPANDED IN CULTURE UNDER TGF beta RECEPTOR INHIBITION FOR CLINICAL TRANSLATION CYTOTHERAPY 21 S72-S72

Krol, L; Gorsich, EE; Hunting, ER; Govender, D; van Bodegom, PM; Schrama, M (2019) Eutrophication governs predator-prey interactions and temperature effects in Aedes aegypti populations PARASITES & VECTORS 12 179

Kamau, E; Onyango, CO; Otieno, GP; Kiyuka, PK; Agoti, CN; Medley, GF; Cane, PA; Nokes, DJ; Munywoki, PK (2019) An Intensive, Active Surveillance Reveals Continuous Invasion and High Diversity of Rhinovirus in Households JOURNAL OF INFECTIOUS DISEASES 219 1049-1057

van Dorp, L; Wang, Q; Shaw, LP; Acman, M; Brynildsrud, OB; Eldholm, V; Wang, RB; Gao, H; Yin, YY; Chen, HB; Ding, CL; Farrer, RA; Didelot, X; Balloux, F; Wang, H (2019) Rapid phenotypic evolution in multidrug-resistant Klebsiella pneumoniae hospital outbreak strains MICROBIAL GENOMICS 5 263

Cheffings, TH; Burroughs, NJ; Balasubramanian, MK (2019) Actin turnover ensures uniform tension distribution during cytokinetic actomyosin ring contraction MOLECULAR BIOLOGY OF THE CELL 30 933-941

Bazarova, A; Nieduszynski, CA; Akerman, I; Burroughs, NJ (2019) Bayesian inference of origin firing time distributions, origin interference and licencing probabilities from Next Generation Sequencing data NUCLEIC ACIDS RESEARCH 47 2229-2243

Gonzalez, MA; Bell, MJ; Bernhardt, SA; Brazil, RP; Dilger, E; Courtenay, O; Hamilton, JGC (2019) Susceptibility of wild-caught Lutzomyia longipalpis (Diptera: Psychodidae) sand flies to insecticide after an extended period of exposure in western SAo Paulo, Brazil PARASITES & VECTORS 12 110

Gorsich, EE; Miller, RS; Mask, HM; Hallman, C; Portacci, K; Webb, CT (2019) Spatio-temporal patterns and characteristics of swine shipments in the US based on Interstate Certificates of Veterinary Inspection SCIENTIFIC REPORTS 9 3915

Dingle, KE et al. (2019) A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078 MBIO 10 e02790-18

Whittles, LK; White, PJ; Didelot, X (2019) A dynamic power-law sexual network model of gonorrhoea outbreaks PLOS COMPUTATIONAL BIOLOGY 15 e1006748

Courtenay, O; Bazmani, A; Parvizi, P; Ready, PD; Cameron, MM (2019) Insecticide-impregnated dog collars reduce infantile clinical visceral leishmaniasis under operational conditions in NW Iran: A community-wide cluster randomised trial PLOS NEGLECTED TROPICAL DISEASES 13 e0007193

Meakin, SR; Keeling, MJ (2019) Correlations between stochastic epidemics in two interacting populations EPIDEMICS 26 58-67

Arzt, J; Branan, MA; Delgado, AH; Yadav, S; Moreno-Torres, KI; Tildesley, MJ; Stenfeldt, C (2019) Quantitative impacts of incubation phase transmission of foot-and-mouth disease virus SCIENTIFIC REPORTS 9 2707

Seedat, F et al. (2019) Universal antenatal screening for group B streptococcus may cause more harm than good BMJ-BRITISH MEDICAL JOURNAL 364 l463

Spensley, KJ; Wikramaratna, PS; Penman, BS; Walker, A; Smith, AL; Pybus, OG; Jean, L; Gupta, S; Lourenco, J (2019) Reverse immunodynamics: a new method for identifying targets of protective immunity SCIENTIFIC REPORTS 9 2164

Awofisayo-Okuyelu, A; Brainard, J; Hall, I; McCarthy, N (2019) Incubation Period of Shiga Toxin-Producing Escherichia coli EPIDEMIOLOGIC REVIEWS 41 121-129

Jeeta, RR; Gordon, NS; Baxter, L; Goel, A; Noyvert, B; Ott, S; Boucher, RH; Humayun-Zakaria, N; Arnold, R; James, ND; Zeegers, MP; Cheng, KK; Bryan, RT; Ward, DG (2019) Non-Coding Mutations in Urothelial Bladder Cancer: Biological and Clinical Relevance and Potential Utility as Biomarkers BLADDER CANCER 5 263-272

Awofisayo-Okuyelu, A; Hall, I; Arnold, E; Byrne, L; McCarthy, N (2019) Analysis of individual patient data to describe the incubation period distribution of Shiga-toxin producing Escherichia coli EPIDEMIOLOGY AND INFECTION 147 e162

Inns, T; Curtis, D; Crook, P; Vivancos, R; Gardiner, D; McCarthy, N; Mook, P (2019) Are food exposures obtained through commercial market panels representative of the general population? Implications for outbreak investigations EPIDEMIOLOGY AND INFECTION 147 e99

Minas, G; Rand, DA (2019) Parameter sensitivity analysis for biochemical reaction networks MATHEMATICAL BIOSCIENCES AND ENGINEERING 16 3965-3987

Kamau, E; Agoti, CN; Ngoi, JM; de Laurent, ZR; Gitonga, J; Cotten, M; Phan, MVT; Nokes, DJ; Delwart, E; Sanders, E; Warimwe, GM (2019) Complete Genome Sequences of Dengue Virus Type 2 Strains from Kilifi, Kenya MICROBIOLOGY RESOURCE ANNOUNCEMENTS 8 e01566-18

Beck-Johnson, LM; Hallman, C; Miller, RS; Portacci, K; Gorsich, EE; Grear, DA; Hartmann, K; Webb, CT (2019) Estimating and exploring the proportions of inter- and intrastate cattle shipments in the United States PREVENTIVE VETERINARY MEDICINE 162 56-66

Davis, EL; Reimer, LJ; Pellis, L; Hollingsworth, TD (2019) Evaluating the Evidence for Lymphatic Filariasis Elimination TRENDS IN PARASITOLOGY 35 860-869

Komarzynski, S; Bolborea, M; Huang, Q; Finkenstadt, B; Levi, F (2019) Predictability of individual circadian phase during daily routine for medical applications of circadian clocks JCI INSIGHT 4 e130423

Momiji, H; Hassall, KL; Featherstone, K; McNamara, AV; Patist, AL; Spiller, DG; Christian, HC; White, MRH; Davis, JRE; Finkenstadt, BF; Rand, DA (2019) Disentangling juxtacrine from paracrine signalling in dynamic tissue PLOS COMPUTATIONAL BIOLOGY 15 e1007030

Calderazzo, S; Brancaccio, M; Finkenstadt, B (2019) Filtering and inference for stochastic oscillators with distributed delays BIOINFORMATICS 35 1380-1387

Pareek, M et al. (2019) Community-based testing of migrants for infectious diseases (COMBAT-ID): impact, acceptability and cost-effectiveness of identifying infectious diseases among migrants in primary care: protocol for an interrupted time-series, qualitative and health economic analysis BMJ OPEN 9 e029188

Prada, JM; Davis, EL; Touloupou, P; Stolk, WA; Kontoroupis, P; Smith, ME; Sharma, S; Michael, E; de Vlas, SJ; Hollingsworth, TD (2019) Elimination or Resurgence: Modelling Lymphatic Filariasis After Reaching the 1% Microfilaremia Prevalence Threshold JOURNAL OF INFECTIOUS DISEASES 221 S503-S509

Nash, A; Kalvala, S (2019) A P system model of swarming and aggregation in a Myxobacterial colony JOURNAL OF MEMBRANE COMPUTING 1 103-111

Chapman, LAC; Morgan, ALK; Adams, ER; Bern, C; Medley, GF; Hollingsworth, TD (2018) Age trends in asymptomatic and symptomatic Leishmania donovani infection in the Indian subcontinent: A review and analysis of data from diagnostic and epidemiological studies PLOS NEGLECTED TROPICAL DISEASES 12 e0006803

2018

Hockham, C; Bhatt, S; Colah, R; Mukherjee, MB; Penman, BS; Gupta, S; Piel, FB (2018) The spatial epidemiology of sickle-cell anaemia in India SCIENTIFIC REPORTS 8 17685

Bell, MJ; Sedda, L; Gonzalez, MA; de Souza, CF; Dilger, E; Brazil, RP; Courtenay, O; Hamilton, JGC (2018) Attraction of Lutzomyia longipalpis to synthetic sex-aggregation pheromone: Effect of release rate and proximity of adjacent pheromone sources PLOS NEGLECTED TROPICAL DISEASES 12 e0007007

Tavalire, HF; Beechler, BR; Buss, PE; Gorsich, EE; Hoal, EG; le Roex, N; Spaan, JM; Spaan, RS; van Helden, PD; Ezenwa, VO; Jolles, AE (2018) Context-dependent costs and benefits of tuberculosis resistance traits in a wild mammalian host ECOLOGY AND EVOLUTION 8 12712-12726

Widlak, MM; Neal, M; Daulton, E; Thomas, CL; Tomkins, C; Singh, B; Harmston, C; Wicaksono, A; Evans, C; Smith, S; Savage, RS; Covington, JA; Arasaradnam, RP (2018) Risk stratification of symptomatic patients suspected of colorectal cancer using faecal and urinary markers COLORECTAL DISEASE 20 O335-O342

Byrne, L; Dallman, TJ; Adams, N; Mikhail, AFW; McCarthy, N; Jenkins, C (2018) Highly Pathogenic Clone of Shiga Toxin-Producing Escherichia coli O157:H7, England and Wales EMERGING INFECTIOUS DISEASES 24 2303-2308

Leng, T; Keeling, MJ (2018) Concurrency of partnerships, consistency with data, and control of sexually transmitted infections EPIDEMICS 25 35-46

Seedat, F; Brown, CS; Stinton, C; Patterson, J; Geppert, J; Freeman, K; Tan, B; Johnson, SA; Fraser, H; Uthman, OA; Robinson, ER; McCarthy, ND; Clarke, A; Taylor-Phillips, S (2018) Bacterial Load and Molecular Markers Associated With Early-onset Group B Streptococcus: A Systematic Review and Meta-analysis PEDIATRIC INFECTIOUS DISEASE JOURNAL 37 E306-E314

Munywoki, PK; Koech, DC; Agoti, CN; Cane, PA; Medley, GF; Nokes, DJ (2018) Continuous Invasion by Respiratory Viruses Observed in Rural Households During a Respiratory Syncytial Virus Seasonal Outbreak in Coastal Kenya CLINICAL INFECTIOUS DISEASES 67 1559-1567

Pandey, A; Cleary, DW; Laver, JR; Gorringe, A; Deasy, AM; Dale, AP; Morris, PD; Didelot, X; Maiden, MCJ; Read, RC (2018) Microevolution of Neisseria lactamica during nasopharyngeal colonisation induced by controlled human infection NATURE COMMUNICATIONS 9 4753

Slator, PJ; Burroughs, NJ (2018) A Hidden Markov Model for Detecting Confinement in Single-Particle Tracking Trajectories BIOPHYSICAL JOURNAL 115 1741-1754

Adams, S; Grundy, J; Veflingstad, SR; Dyer, NP; Hannah, MA; Ott, S; Carre, IA (2018) Circadian control of abscisic acid biosynthesis and signalling pathways revealed by genome-wide analysis of LHY binding targets NEW PHYTOLOGIST 220 893-907

Datta, S; Mercer, CH; Keeling, MJ (2018) Capturing sexual contact patterns in modelling the spread of sexually transmitted infections: Evidence using Natsal-3 PLOS ONE 13 e0206501

Retkute, R; Jewell, CP; Van Boeckel, TP; Zhang, G; Xiao, XM; Thanapongtharm, W; Keeling, M; Gilbert, M; Tildesley, MJ (2018) Dynamics of the 2004 avian influenza H5N1 outbreak in Thailand: The role of duck farming, sequential model fitting and control PREVENTIVE VETERINARY MEDICINE 159 171-181

Richardson, MJE (2018) Spike shape and synaptic-amplitude distribution interact to set the high-frequency firing-rate response of neuronal populations PHYSICAL REVIEW E 98 42405

Chapman, LAC; Jewell, CP; Spencer, SEF; Pellis, L; Datta, S; Chowdhury, R; Bern, C; Medley, GF; Hollingsworth, TD (2018) The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh PLOS NEGLECTED TROPICAL DISEASES 12 e0006453

Duthie, MS; Lison, A; Courtenay, O (2018) Advances toward Diagnostic Tools for Managing Zoonotic Visceral Leishmaniasis TRENDS IN PARASITOLOGY 34 881-890

Martinez-Vernon, AS; Covington, JA; Arasaradnam, RP; Esfahani, S; O'Connell, N; Kyrou, I; Savage, RS (2018) An improved machine learning pipeline for urinary volatiles disease detection: Diagnosing diabetes PLOS ONE 13 e0204425

Awofisayo-Okuyelu, A; McCarthy, N; Mgbakor, I; Hall, I (2018) Incubation period of typhoidal salmonellosis: a systematic review and meta-analysis of outbreaks and experimental studies occurring over the last century BMC INFECTIOUS DISEASES 18 483

Sande, CJ; Mutunga, M; Muteti, J; Berkley, JA; Nokes, DJ; Njunge, J (2018) Untargeted analysis of the airway proteomes of children with respiratory infections using mass spectrometry based proteomics SCIENTIFIC REPORTS 8 13814

Armitage, AD; Taylor, A; Sobczyk, MK; Baxter, L; Greenfield, BPJ; Bates, HJ; Wilson, F; Jackson, AC; Ott, S; Harrison, RJ; Clarkson, JP (2018) Characterisation of pathogen-specific regions and novel effector candidates in Fusarium oxysporum f. sp cepae SCIENTIFIC REPORTS 8 13530

Dyson, L; Holmes, A; Li, A; Kulesa, PM (2018) A chemotactic model of trunk neural crest cell migration GENESIS 56 e23239

Hill, EM; House, T; Dhingra, MS; Kalpravidh, W; Morzaria, S; Osmani, MG; Brum, E; Yamage, M; Kalam, MA; Prosser, DJ; Takekawa, JY; Xiao, XM; Gilbert, M; Tildesley, MJ (2018) The impact of surveillance and control on highly pathogenic avian influenza outbreaks in poultry in Dhaka division, Bangladesh PLOS COMPUTATIONAL BIOLOGY 14 e1006439

Gomez, SA; Chapman, LAC; Dilger, E; Courtenay, O; Picado, A (2018) Estimating the efficacy of community-wide use of systemic insecticides in dogs to control zoonotic visceral leishmaniasis: A modelling study in a Brazilian scenario PLOS NEGLECTED TROPICAL DISEASES 12 e0006797

Mook, P; McCormick, J; Kanagarajah, S; Adak, GK; Cleary, P; Elson, R; Gobin, M; Hawker, J; Inns, T; Sinclair, C; Trienekens, SCM; Vivancos, R; McCarthy, ND (2018) Online market research panel members as controls in case-control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK (vol 146, pg 458, 2018) EPIDEMIOLOGY AND INFECTION 146 1611-1611

Spencer, RA; Spencer, SEF; Rodgers, S; Campbell, SM; Avery, AJ (2018) Processing of discharge summaries in general practice: a retrospective record review BRITISH JOURNAL OF GENERAL PRACTICE 68 E576-E585

Baniukiewicz, P; Collier, S; Bretschneider, T (2018) QuimP: analyzing transmembrane signalling in highly deformable cells BIOINFORMATICS 34 2695-2697

Mook, P; Gardiner, D; Kanagarajah, S; Kerac, M; Hughes, G; Field, N; McCarthy, N; Rawlings, C; Simms, I; Lane, C; Crook, PD (2018) Use of gender distribution in routine surveillance data to detect potential transmission of gastrointestinal infections among men who have sex with men in England EPIDEMIOLOGY AND INFECTION 146 1468-1477

Morpeth, SC; Munywoki, P; Hammitt, LL; Bett, A; Bottomley, C; Onyango, CO; Murdoch, DR; Nokes, DJ; Scott, JAG (2018) Impact of viral upper respiratory tract infection on the concentration of nasopharyngeal pneumococcal carriage among Kenyan children SCIENTIFIC REPORTS 8 11030

Otieno, JR; Kamau, EM; Oketch, JW; Ngoi, JM; Gichuki, AM; Binter, S; Otieno, GP; Ngama, M; Agoti, CN; Cane, PA; Kellam, P; Cotten, M; Lemey, P; Nokes, DJ (2018) Whole genome analysis of local Kenyan and global sequences unravels the epidemiological and molecular evolutionary dynamics of RSV genotype ON1 strains VIRUS EVOLUTION 4 vey027

Dyson, L; Hollingsworth, TD (2018) Diagnosing risk factors alongside mass drug administration using serial diagnostic tests-which test first? TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE 112 342-348

Meadows, AJ; Mundt, CC; Keeling, MJ; Tildesley, MJ (2018) Disentangling the influence of livestock vs. farm density on livestock disease epidemics ECOSPHERE 9 e02294

Probert, WJM; Jewell, CP; Werkman, M; Fonnesbeck, CJ; Goto, Y; Runge, MC; Sekiguchi, S; Shea, K; Keeling, MJ; Ferrari, MJ; Tildesley, MJ (2018) Real-time decision-making during emergency disease outbreaks PLOS COMPUTATIONAL BIOLOGY 14 e1006202

Rock, KS; Ndeffo-Mbah, ML; Castano, S; Palmer, C; Pandey, A; Atkins, KE; Ndung'u, JM; Hollingsworth, TD; Galvani, A; Bever, C; Chitnis, N; Keeling, MJ (2018) Assessing Strategies Against Gambiense Sleeping Sickness Through Mathematical Modeling CLINICAL INFECTIOUS DISEASES 66 S286-S292

Kiyuka, PK; Agoti, CN; Munywoki, PK; Njeru, R; Bett, A; Otieno, JR; Otieno, GP; Kamau, E; Clark, TG; van der Hoek, L; Kellam, P; Nokes, DJ; Cotten, M (2018) Human Coronavirus NL63 Molecular Epidemiology and Evolutionary Patterns in Rural Coastal Kenya JOURNAL OF INFECTIOUS DISEASES 217 1728-1739

Bird, AD; Richardson, MJE (2018) Transmission of temporally correlated spike trains through synapses with short-term depression PLOS COMPUTATIONAL BIOLOGY 14 e1006232

Wedagedera, JR; Burroughs, NJ (2018) COMPARISON OF A DUAL STRATEGY FOR T-CELL ACTIVATION UNDER INHIBITION OF THE CD4 RECEPTOR JOURNAL OF BIOLOGICAL SYSTEMS 26 321-338

Touloupou, P; Alzahrani, N; Neal, P; Spencer, SEF; McKinley, TJ (2018) Efficient Model Comparison Techniques for Models Requiring Large Scale Data Augmentation BAYESIAN ANALYSIS 13 437-459

Alzahrani, N; Neal, P; Spencer, SEF; McKinley, TJ; Touloupou, P (2018) Model selection for time series of count data COMPUTATIONAL STATISTICS & DATA ANALYSIS 122 33-44

Harper, CV; Woodcock, DJ; Lam, C; Garcia-Albornoz, M; Adamson, A; Ashall, L; Rowe, W; Downton, P; Schmidt, L; West, S; Spiller, DG; Rand, DA; White, MRH (2018) Temperature regulates NF-kappa B dynamics and function through timing of A20 transcription PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115 E5243-E5249

Inns, T et al. (2018) Novel application of the matched case-control design to compare food supply chains during an Escherichia coli O157 outbreak, United Kingdom, 2016 EUROSURVEILLANCE 23 20-24

Penman, BS; Gupta, S (2018) Detecting signatures of past pathogen selection on human HLA loci: are there needles in the haystack? PARASITOLOGY 145 731-739

Vrljicak, P; Lucas, ES; Lansdowne, L; Lucciola, R; Muter, J; Dyer, NP; Brosens, JJ; Ott, S (2018) Analysis of chromatin accessibility in decidualizing human endometrial stromal cells FASEB JOURNAL 32 2467-2477

Peet, DR; Burroughs, NJ; Cross, RA (2018) Kinesin expands and stabilizes the GDP-microtubule lattice NATURE NANOTECHNOLOGY 13 386

Hughes, V; Richardson, MJE; Wall, MJ (2018) Acute ethanol exposure has bidirectional actions on the endogenous neuromodulator adenosine in rat hippocampus BRITISH JOURNAL OF PHARMACOLOGY 175 1471-1485

Dyson, L; Marks, M; Crook, OM; Sokana, O; Solomon, AW; Bishop, A; Mabey, DCW; Hollingsworth, TD (2018) Targeted Treatment of Yaws With Household Contact Tracing: How Much Do We Miss? AMERICAN JOURNAL OF EPIDEMIOLOGY 187 837-844

Rius, C; Attaf, M; Tungatt, K; Bianchi, V; Legut, M; Bovay, A; Donia, M; Straten, PT; Peakman, M; Svane, IM; Ott, S; Connor, T; Szomolay, B; Dolton, G; Sewell, AK (2018) Peptide-MHC Class I Tetramers Can Fail To Detect Relevant Functional T Cell Clonotypes and Underestimate Antigen-Reactive T Cell Populations JOURNAL OF IMMUNOLOGY 200 2263-2279

Sellman, S; Tsao, K; Tildesley, MJ; Brommesson, P; Webb, CT; Wennergren, U; Keeling, MJ; Lindstrom, T (2018) Need for speed: An optimized gridding approach for spatially explicit disease simulations PLOS COMPUTATIONAL BIOLOGY 14 e1006086

Chalmers, RM; McCarthy, N; Barlow, KL; Stiff, R (2018) An evaluation of health protection practices for the investigation and management of Cryptosporidium in England and Wales JOURNAL OF PUBLIC HEALTH 40 114-120

Polanski, K; Gao, B; Mason, SA; Brown, P; Ott, S; Denby, KJ; Wild, DL (2018) Bringing numerous methods for expression and promoter analysis to a public cloud computing service BIOINFORMATICS 34 884-886

Ordonez-Mena, JM; McCarthy, ND; Fanshawe, TR (2018) Comparative efficacy of drugs for treating giardiasis: a systematic update of the literature and network meta-analysis of randomized clinical trials JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY 73 596-606

Mook, P; McCormick, J; Kanagarajah, S; Adak, GK; Cleary, P; Elson, R; Gobin, M; Hawker, J; Inns, T; Sinclair, C; Trienekens, SCM; Vivancos, R; McCarthy, ND (2018) Online market research panel members as controls in case-control studies to investigate gastrointestinal disease outbreaks: early experiences and lessons learnt from the UK EPIDEMIOLOGY AND INFECTION 146 458-464

Buscher, P et al. (2018) Do Cryptic Reservoirs Threaten Gambiense-Sleeping Sickness Elimination? TRENDS IN PARASITOLOGY 34 197-207

Feroz, HM; Ferlez, B; Lefoulon, C; Mohammadiarani, H; Rei, T; Baker, CS; Butler, PJ; Huehn, J; Kerfeld, CA; Burroughs, NJ; Vashisth, H; Parak, W; Blatt, M; Golbeck, J; Kumar, M (2018) Measuring Transport Kinetics of Light Driven Membrane Protein, Halorhodopsin BIOPHYSICAL JOURNAL 114 146A-146A

Irvine, MA; Bull, JC; Keeling, MJ (2018) Conservation of pattern as a tool for inference on spatial snapshots in ecological data SCIENTIFIC REPORTS 8

Quinnell, RJ; Soremekun, S; Bates, PA; Rogers, ME; Garcez, LM; Courtenay, O (2018) Antibody response to sand fly saliva is a marker of transmission intensity but not disease progression in dogs naturally infected with Leishmania infantum PARASITES & VECTORS 11 7

Widlak, MM; Neal, M; Daulton, E; Thomas, CL; Tomkins, C; Singh, B; Harmston, C; Wicaksono, A; Evans, C; Smith, S; Savage, RS; Covington, JA; Arasaradnam, RP (2018) Risk stratification of symptomatic patients suspected of colorectal cancer using faecal and urinary markers COLORECTAL DISEASE 20 O335-O342

Fowler, AC; Hollingsworth, TD (2018) The Dynamics of Ascaris lumbricoides Infections (vol 78, pg 815, 2016) BULLETIN OF MATHEMATICAL BIOLOGY 80 2787-2787

Chapman, LAC; Jewell, CP; Spencer, SEF; Pellis, L; Datta, S; Chowdhury, R; Bern, C; Medley, GF; Hollingsworth, TD (2018) The role of case proximity in transmission of visceral leishmaniasis in a highly endemic village in Bangladesh PLOS NEGLECTED TROPICAL DISEASES 12 e0006453

Cooper, AJ; Hollingsworth, TD (2018) The impact of seasonality on the dynamics and control of Ascaris lumbricoides infections JOURNAL OF THEORETICAL BIOLOGY 453 96-107

Tiberi, S; Walsh, M; Cavallaro, M; Hebenstreit, D; Finkenstadt, B (2018) Bayesian inference on stochastic gene transcription from flow cytometry data BIOINFORMATICS 34 647-655

Lepper, HC; Prada, JM; Davis, EL; Gunawardena, SA; Hollingsworth, TD (2018) Complex interactions in soil-transmitted helminth co-infections from a cross-sectional study in Sri Lanka TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE 112 397-404

Le Rutte, EA; Chapman, LAC; Coffeng, LE; Ruiz-Postigo, JA; Olliaro, PL; Adams, ER; Hasker, EC; Boelaert, MC; Hollingsworth, TD; Medley, GF; de Vlas, SJ (2018) Policy Recommendations From Transmission Modeling for the Elimination of Visceral Leishmaniasis in the Indian Subcontinent CLINICAL INFECTIOUS DISEASES 66 S301-S308

Medley, GF; Blok, DJ; Crump, RE; Hollingsworth, TD; Galvani, AP; Ndeffo-Mbah, ML; Porco, TC; Richardus, JH (2018) Policy Lessons From Quantitative Modeling of Leprosy CLINICAL INFECTIOUS DISEASES 66 S281-S285

Stolk, WA; Prada, JM; Smith, ME; Kontoroupis, P; de Vos, AS; Touloupou, P; Irvine, MA; Brown, P; Subramanian, S; Kloek, M; Michael, E; Hollingsworth, TD; de Vlas, SJ (2018) Are Alternative Strategies Required to Accelerate the Global Elimination of Lymphatic Filariasis? Insights From Mathematical Models CLINICAL INFECTIOUS DISEASES 66 S260-S266

Turner, HC; Toor, J; Hollingsworth, TD; Anderson, RM (2018) Economic Evaluations of Mass Drug Administration: The Importance of Economies of Scale and Scope CLINICAL INFECTIOUS DISEASES 66 1298-1303

Gedge, LM; Bettis, AA; Bradley, MH; Hollingsworth, TD; Turner, HC (2018) Economic evaluations of lymphatic filariasis interventions: a systematic review and research needs PARASITES & VECTORS 11 75

Irvine, MA; Kazura, JW; Hollingsworth, TD; Reimer, LJ (2018) Understanding heterogeneities in mosquito-bite exposure and infection distributions for the elimination of lymphatic filariasis PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 285 20172253

Prada, JM; Touloupou, P; Adriko, M; Tukahebwa, EM; Lamberton, PHL; Hollingsworth, TD (2018) Understanding the relationship between egg- and antigen-based diagnostics of Schistosoma mansoni infection pre- and post-treatment in Uganda PARASITES & VECTORS 11 21

Davis, EL; Danon, L; Prada, JM; Gunawardena, SA; Truscott, JE; Vlaminck, J; Anderson, RM; Levecke, B; Morgan, ER; Hollingsworth, TD (2018) Seasonally timed treatment programs for Ascaris lumbricoides to increase impact-An investigation using mathematical models PLOS NEGLECTED TROPICAL DISEASES 12 e0006195

Hope, EC; Crump, RE; Hollingsworth, TD; Smieszek, T; Robotham, JV; Pouwels, KB (2018) Identifying English Practices that Are High Antibiotic Prescribers Accounting for Comorbidities and Other Legitimate Medical Reasons for Variation ECLINICALMEDICINE 6 36-41

Martinez-Vernon, AS; Covington, JA; Arasaradnam, RP; Esfahani, S; O'Connell, N; Kyrou, I; Savage, RS (2018) An improved machine learning pipeline for urinary volatiles disease detection: Diagnosing diabetes PLOS ONE 13 e0204425

Chamberland, S; Timofeeva, Y; Evstratova, A; Volynski, K; Toth, K (2018) Action potential counting at giant mossy fiber terminals gates information transfer in the hippocampus PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 115 7434-7439

Komarzynski, S; Huang, Q; Innominato, PF; Maurice, M; Arbaud, A; Beau, J; Bouchanda, M; Ulusakarya, A; Beaumatin, N; Breda, G; Finkenstadt, B; Levi, F (2018) Relevance of a Mobile Internet Platform for Capturing Inter- and Intrasubject Variabilities in Circadian Coordination During Daily Routine: Pilot Study JOURNAL OF MEDICAL INTERNET RESEARCH 20 e204

Polanski, K; Gao, B; Mason, SA; Brown, P; Ott, S; Denby, KJ; Wild, DL (2018) Bringing numerous methods for expression and promoter analysis to a public cloud computing service BIOINFORMATICS 34 884-886

Huang, Q; Cohen, D; Komarzynski, S; Li, XM; Innominato, P; Levi, F; Finkenstadt, B (2018) Hidden Markov models for monitoring circadian rhythmicity in telemetric activity data JOURNAL OF THE ROYAL SOCIETY INTERFACE 15 20170885

2017

Dunham, LSS; Momiji, H; Harper, CV; Downton, PJ; Hey, K; McNamara, A; Featherstone, K; Spiller, DG; Rand, DA; Finkenstadt, B; White, MRH; Davis, JRE (2017) Asymmetry between Activation and Deactivation during a Transcriptional Pulse CELL SYSTEMS 5 646

Lewis, JM; Savage, RS; Beeching, NJ; Beadsworth, MBJ; Feasey, N; Covington, JA (2017) Identifying volatile metabolite signatures for the diagnosis of bacterial respiratory tract infection using electronic nose technology: A pilot study PLOS ONE 12 e0188879

Brighton, PJ et al. (2017) Clearance of senescent decidual cells by uterine natural killer cells in cycling human endometrium ELIFE 6 e31274

Jervis, S; Chapman, LAC; Dwivedi, S; Karthick, M; Das, A; Le Rutte, EA; Courtenay, O; Medley, GF; Banerjee, I; Mahapatra, T; Chaudhuri, I; Srikantiah, S; Hollingsworth, TD (2017) Variations in visceral leishmaniasis burden, mortality and the pathway to care within Bihar, India PARASITES & VECTORS 10

Gonzalez, MA; Bandi, KK; Bell, MJ; Brazil, RP; Dilger, E; Guerrero, A; Courtenay, O; Hamilton, JGC (2017) A temporal comparison of sex-aggregation pheromone gland content and dynamics of release in three members of the Lutzomyia longipalpis (Diptera: Psychodidae) species complex PLOS NEGLECTED TROPICAL DISEASES 11 e0006071

Keeling, MJ; Broadfoot, KA; Datta, S (2017) The impact of current infection levels on the cost-benefit of vaccination EPIDEMICS 21 56-62

Ahlstrom, C; Muellner, P; Spencer, SEF; Hong, S; Saupe, A; Rovira, A; Hedberg, C; Perez, A; Muellner, U; Alvarez, J (2017) Inferring source attribution from a multiyear multisource data set of Salmonella in Minnesota ZOONOSES AND PUBLIC HEALTH 64 589-598

Gavard, R; Rossell, D; Spencer, SEF; Barrow, MP (2017) Themis: Batch Preprocessing for Ultrahigh-Resolution Mass Spectra of Complex Mixtures ANALYTICAL CHEMISTRY 89 11383-11390

Tusco, R; Jacomin, AC; Jain, A; Penman, BS; Larsen, KB; Johansen, T; Nezis, IP (2017) Kenny mediates selective autophagic degradation of the IKK complex to control innate immune responses NATURE COMMUNICATIONS 8 1264

Adaikalakoteswari, A; Vatish, M; Alam, MT; Ott, S; Kumar, S; Saravanan, P (2017) Low Vitamin B12 in Pregnancy Is Associated With Adipose-Derived Circulating miRs Targeting PPAR gamma and Insulin Resistance JOURNAL OF CLINICAL ENDOCRINOLOGY & METABOLISM 102 4200-4209

Minas, G; Jenkins, DJ; Rand, DA; Finkenstadt, B (2017) Inferring transcriptional logic from multiple dynamic experiments BIOINFORMATICS 33 3437-3444

Pereira-Fonseca, DCM; Oliveira-Rovai, FM; Rodas, LAC; Beloti, CAC; Torrecilha, RBP; Ito, PKRK; Avanco, SV; Cipriano, RS; Utsunomiya, YT; Hiramoto, RM; Calvo-Bado, L; Courtenay, O; Machado, GF; Lima, VMF; Nunes, CM (2017) Dog skin parasite load, TLR-2, IL-10 and TNF-alpha expression and infectiousness PARASITE IMMUNOLOGY 39 e12493

Brignall, R et al. (2017) Integration of Kinase and Calcium Signaling at the Level of Chromatin Underlies Inducible Gene Activation in T Cells JOURNAL OF IMMUNOLOGY 199 2652-2667

Diez, R; Richardson, MJE; Wall, MJ (2017) Reducing Extracellular Ca2+ Induces Adenosine Release via Equilibrative Nucleoside Transporters to Provide Negative Feedback Control of Activity in the Hippocampus FRONTIERS IN NEURAL CIRCUITS 11 75

Salker, MS et al. (2017) Loss of Endometrial Sodium Glucose Cotransporter SGLT1 is Detrimental to Embryo Survival and Fetal Growth in Pregnancy SCIENTIFIC REPORTS 7 12612

Walker, L; Boddington, C; Jenkins, D; Wang, Y; Gronlund, JT; Hulsmans, J; Kumar, S; Patel, D; Moore, JD; Carter, A; Samavedam, S; Bonomo, G; Hersh, DS; Coruzzi, GM; Burroughs, NJ; Gifford, ML (2017) Changes in Gene Expression in Space and Time Orchestrate Environmentally Mediated Shaping of Root Architecture PLANT CELL 29 2393-2412

Courtenay, O; Peters, NC; Rogers, ME; Bern, C (2017) Combining epidemiology with basic biology of sand flies, parasites, and hosts to inform leishmaniasis transmission dynamics and control PLOS PATHOGENS 13 e1006571

Donia, M; Kjeldsen, JW; Andersen, R; Westergaard, MCW; Bianchi, V; Legut, M; Attaf, M; Szomolay, B; Ott, S; Dolton, G; Lyngaa, R; Hadrup, SR; Sewell, AK; Svane, IM (2017) PD-1(+) Polyfunctional T Cells Dominate the Periphery after Tumor-Infiltrating Lymphocyte Therapy for Cancer CLINICAL CANCER RESEARCH 23 5779-5788

Scheltema, NM et al. (2017) Global respiratory syncytial virus-associated mortality in young children (RSV GOLD): a retrospective case series LANCET GLOBAL HEALTH 5 E984-E991

McFarland, N et al. (2017) Recurrent seasonal outbreak of an emerging serotype of Shiga toxin-producing Escherichia coli (STEC O55:H7 Stx2a) in the south west of England, July 2014 to September 2015 EUROSURVEILLANCE 22 8-17

Shi, T et al. (2017) Global, regional, and national disease burden estimates of acute lower respiratory infections due to respiratory syncytial virus in young children in 2015: a systematic review and modelling study LANCET 390 946-958

Seedat, F; Geppert, J; Stinton, C; Patterson, J; Brown, CS; Tan, B; Freeman, K; Uthman, OA; McCarthy, ND; Robinson, ER; Johnson, SA; Fraser, H; Clarke, A; Taylor-Phillips, SA (2017) UNIVERSAL ANTENATAL CULTURE-BASED SCREENING FOR MATERNAL GROUP B STREPTOCOCCUS (GBS) CARRIAGE TO PREVENT EARLY-ONSET GBS DISEASE: A SYSTEMATIC REVIEW FOR THE UK NATIONAL SCREENING COMMITTEE (NSC) JOURNAL OF EPIDEMIOLOGY AND COMMUNITY HEALTH 71 A18-A18

Griffin, A; Jenkins, PA; Roberts, GO; Spencer, SEF (2017) SIMULATION FROM QUASI-STATIONARY DISTRIBUTIONS ON REDUCIBLE STATE SPACES ADVANCES IN APPLIED PROBABILITY 49 960-980

Hill, EM; House, T; Dhingra, MS; Kalpravidh, W; Morzaria, S; Osmani, MG; Yamage, M; Xiao, XM; Gilbert, M; Tildesley, MJ (2017) Modelling H5N1 in Bangladesh across spatial scales: Model complexity and zoonotic transmission risk EPIDEMICS 20 37-55

Duggan, JM; Close, R; Mccann, L; Wright, D; Keys, M; Mccarthy, N; Mannes, T; Walsh, A; Charlett, A; Brooks, TJG (2017) A seroprevalence study to determine the frequency of hantavirus infection in people exposed to wild and pet fancy rats in England EPIDEMIOLOGY AND INFECTION 145 2458-2465

Pascoe, B et al. (2017) Local genes for local bacteria: Evidence of allopatry in the genomes of transatlantic Campylobacter populations MOLECULAR ECOLOGY 26 4497-4508

Awofisayo-Okuyelu, A; Hall, I; Adak, G; Hawker, JI; Abbott, S; McCarthy, N (2017) A systematic review and meta-analysis on the incubation period of Campylobacteriosis EPIDEMIOLOGY AND INFECTION 145 2241-2253

Collier, S; Paschke, P; Kay, RR; Bretschneider, T (2017) Image based modeling of bleb site selection SCIENTIFIC REPORTS 7 6692

Seedat, F; Stinton, C; Patterson, J; Geppert, J; Tan, B; Robinson, ER; McCarthy, ND; Uthman, OA; Freeman, K; Johnson, SA; Fraser, H; Brown, CS; Clarke, A; Taylor-Phillips, S (2017) Adverse events in women and children who have received intrapartum antibiotic prophylaxis treatment: a systematic review BMC PREGNANCY AND CHILDBIRTH 17 247

Keeling, MJ; Franklin, DN; Datta, S; Brown, MA; Budge, GE (2017) Predicting the spread of the Asian hornet (Vespa velutina) following its incursion into Great Britain SCIENTIFIC REPORTS 7 6240

Loza, A; Talaga, A; Herbas, G; Canaviri, RJ; Cahuasiri, T; Luck, L; Guibarra, A; Goncalves, R; Pereira, JA; Gomez, SA; Picado, A; Messenger, LA; Bern, C; Courtenay, O (2017) Systemic insecticide treatment of the canine reservoir of Trypanosoma cruzi induces high levels of lethality in Triatoma infestans, a principal vector of Chagas disease PARASITES & VECTORS 10 344

Mahamat, MH et al. (2017) Adding tsetse control to medical activities contributes to decreasing transmission of sleeping sickness in the Mandoul focus (Chad) PLOS NEGLECTED TROPICAL DISEASES 11 e0005792

Metras, R; Fournie, G; Dommergues, L; Camacho, A; Cavalerie, L; Merot, P; Keeling, MJ; Cetre-Sossah, C; Cardinale, E; Edmunds, WJ (2017) Drivers for Rift Valley fever emergence in Mayotte: A Bayesian modelling approach PLOS NEGLECTED TROPICAL DISEASES 11 e0005767

Minas, G; Rand, DA (2017) Long-time analytic approximation of large stochastic oscillators: Simulation, analysis and inference PLOS COMPUTATIONAL BIOLOGY 13 e1005676

Cody, AJ; Bray, JE; Jolley, KA; McCarthy, ND; Maiden, MCJ (2017) Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C-coli Human Disease Isolates JOURNAL OF CLINICAL MICROBIOLOGY 55 2086-2097

Minas, G; Momiji, H; Jenkins, DJ; Costa, MJ; Rand, DA; Finkenstadt, B (2017) ReTrOS: a MATLAB toolbox for reconstructing transcriptional activity from gene and protein expression data BMC BIOINFORMATICS 18 316

Flasche, S; Ojal, J; de Waroux, OL; Otiende, M; O'Brien, KL; Kiti, M; Nokes, DJ; Edmunds, WJ; Scott, JAG (2017) Assessing the efficiency of catch-up campaigns for the introduction of pneumococcal conjugate vaccine: a modelling study based on data from PCV10 introduction in Kilifi, Kenya BMC MEDICINE 15 113

Adetifa, IMO; Bwanaali, T; Wafula, J; Mutuku, A; Karia, B; Makumi, A; Mwatsuma, P; Bauni, E; Hammitt, LL; Nokes, DJ; Maree, E; Tabu, C; Kamau, T; Mataza, C; Williams, TN; Scott, JAG (2017) Cohort Profile: The Kilifi Vaccine Monitoring Study INTERNATIONAL JOURNAL OF EPIDEMIOLOGY 46

Li, SL; Bjornstad, ON; Ferrari, MJ; Mummah, R; Runge, MC; Fonnesbeck, CJ; Tildesley, MJ; Probert, WJM; Shea, K (2017) Essential information: Uncertainty and optimal control of Ebola outbreaks PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 114 5659-5664

Nyiro, JU; Kombe, IK; Sande, CJ; Kipkoech, J; Kiyuka, PK; Onyango, CO; Munywoki, PK; Kinyanjui, TM; Nokes, DJ (2017) Defining the vaccination window for respiratory syncytial virus (RSV) using age-seroprevalence data for children in Kilifi, Kenya PLOS ONE 12 e0177803

Franklin, DN; Brown, MA; Datta, S; Cuthbertson, AGS; Budge, GE; Keeling, MJ (2017) Invasion dynamics of Asian hornet, Vespa velutina (Hymenoptera: Vespidae): a case study of a commune in south-west France APPLIED ENTOMOLOGY AND ZOOLOGY 52 221-229

Metras, R; Dommergues, L; Ortiz, K; Pannequin, M; Schuler, C; Roux, P; Edmunds, JW; Keeling, MJ; Cetre-Sossah, C; Cardinale, E (2017) Absence of Evidence of Rift Valley Fever Infection in Eulemur fulvus (Brown Lemur) in Mayotte During an Interepidemic Period VECTOR-BORNE AND ZOONOTIC DISEASES 17 358-360

Ngari, MM; Fegan, G; Mwangome, MK; Ngama, MJ; Mturi, N; Scott, JAG; Bauni, E; Nokes, DJ; Berkley, JA (2017) Mortality after Inpatient Treatment for Severe Pneumonia in Children: a Cohort Study PAEDIATRIC AND PERINATAL EPIDEMIOLOGY 31 233-242

Freeman, K; Mistry, H; Tsertsvadze, A; Royle, P; McCarthy, N; Taylor-Phillips, S; Manuel, R; Mason, J (2017) Multiplex tests to identify gastrointestinal bacteria, viruses and parasites in people with suspected infectious gastroenteritis: a systematic review and economic analysis HEALTH TECHNOLOGY ASSESSMENT 21 1

Keeling, MJ; Datta, S; Franklin, DN; Flatman, I; Wattam, A; Brown, M; Budge, GE (2017) Efficient use of sentinel sites: detection of invasive honeybee pests and diseases in the UK JOURNAL OF THE ROYAL SOCIETY INTERFACE 14 20160908

Ballesta, A; Innominato, PF; Dallmann, R; Rand, DA; Levi, FA (2017) Systems Chronotherapeutics PHARMACOLOGICAL REVIEWS 69 161-199

King, HC; Khera-Butler, T; James, P; Oakley, BB; Erenso, G; Aseffa, A; Knight, R; Wellington, EM; Courtenay, O (2017) Environmental reservoirs of pathogenic mycobacteria across the Ethiopian biogeographical landscape PLOS ONE 12 e0173811

Auguste, P; Tsertsvadze, A; Pink, J; Court, R; McCarthy, N; Sutcliffe, P; Clarke, A (2017) Comparing interferon-gamma release assays with tuberculin skin test for identifying latent tuberculosis infection that progresses to active tuberculosis: systematic review and meta-analysis BMC INFECTIOUS DISEASES 17 200

Freeman, K; Tsertsvadze, A; Taylor-Phillips, S; McCarthy, N; Mistry, H; Manuel, R; Mason, J (2017) Agreement between gastrointestinal panel testing and standard microbiology methods for detecting pathogens in suspected infectious gastroenteritis: Test evaluation and meta-analysis in the absence of a reference standard PLOS ONE 12 e0173196

Hill, EM; Tildesley, MJ; House, T (2017) Evidence for history-dependence of influenza pandemic emergence SCIENTIFIC REPORTS 7 43623

Brand, SPC; Keeling, MJ (2017) The impact of temperature changes on vector- borne disease transmission: Culicoides midges and bluetongue virus JOURNAL OF THE ROYAL SOCIETY INTERFACE 14 20160481

Rock, KS; Pandey, A; Ndeffo-Mbah, ML; Atkins, KE; Lumbala, C; Galvani, A; Keeling, MJ (2017) Data-driven models to predict the elimination of sleeping sickness in former Equateur province of DRC EPIDEMICS 18 101-112

Kostalova, T et al. (2017) The recombinant protein rSP03B is a valid antigen for screening dog exposure to Phlebotomus perniciosus across foci of canine leishmaniasis MEDICAL AND VETERINARY ENTOMOLOGY 31 88-93

Dyson, L; Stolk, WA; Farrell, SH; Hollingsworth, TD (2017) Measuring and modelling the effects of systematic non-adherence to mass drug administration EPIDEMICS 18 56-66

Newton, AJH; Wall, MJ; Richardson, MJE (2017) Modeling microelectrode biosensors: free-flow calibration can substantially underestimate tissue concentrations JOURNAL OF NEUROPHYSIOLOGY 117 937-949

Esan, OB; Pearce, M; van Hecke, O; Roberts, N; Collins, DRJ; Violato, M; McCarthy, N; Perera, R; Fanshawe, TR (2017) Factors Associated with Sequelae of Campylobacter and Non-typhoidal Salmonella Infections: A Systematic Review EBIOMEDICINE 15 100-111

Bradbury, NV; Probert, WJM; Shea, K; Runge, MC; Fonnesbeck, CJ; Keeling, MJ; Ferrari, MJ; Tildesley, MJ (2017) Quantifying the Value of Perfect Information in Emergency Vaccination Campaigns PLOS COMPUTATIONAL BIOLOGY 13 e1005318

Otieno, JR; Kamau, EM; Agoti, CN; Lewa, C; Otieno, G; Bett, A; Ngama, M; Cane, PA; Nokes, DJ (2017) Spread and Evolution of Respiratory Syncytial Virus A Genotype ON1, Coastal Kenya, 2010-2015 EMERGING INFECTIOUS DISEASES 23 264-271

Hill, SM; Nesser, NK; Johnson-Camacho, K; Jeffress, M; Johnson, A; Boniface, C; Spencer, SEF; Lu, YL; Heiser, LM; Lawrence, Y; Pande, NT; Korkola, JE; Gray, JW; Mills, GB; Mukherjee, S; Spellman, PT (2017) Context Specificity in Causal Signaling Networks Revealed by Phosphoprotein Profiling CELL SYSTEMS 4 73

Pan-Ngum, W; Kinyanjui, T; Kiti, M; Taylor, S; Toussaint, JF; Saralamba, S; Van Effelterre, T; Nokes, DJ; White, LJ (2017) Predicting the relative impacts of maternal and neonatal respiratory syncytial virus (RSV) vaccine target product profiles: A consensus modelling approach VACCINE 35 403-409

Agoti, CN; Munywoki, PK; Phan, MVT; Otieno, JR; Kamau, E; Bett, A; Kombe, I; Githinji, G; Medley, GF; Cane, PA; Kellam, P; Cotten, M; Nokes, DJ (2017) Transmission patterns and evolution of respiratory syncytial virus in a community outbreak identified by genomic analysis VIRUS EVOLUTION 3 vex006

Rock, KS; Torr, SJ; Lumbala, C; Keeling, MJ (2017) Predicting the Impact of Intervention Strategies for Sleeping Sickness in Two High-Endemicity Health Zones of the Democratic Republic of Congo PLOS NEGLECTED TROPICAL DISEASES 11 e0005162

Yahara, K et al. (2017) Genome-wide association of functional traits linked with Campylobacter jejuni survival from farm to fork ENVIRONMENTAL MICROBIOLOGY 19 361-380

Juric, I; Gonzalez-Perez, V; Hibberd, JM; Edwards, G; Burroughs, NJ (2017) Size matters for single-cell C-4 photosynthesis in Bienertia JOURNAL OF EXPERIMENTAL BOTANY 68 255-267

Shiri, T; Datta, S; Madan, J; Tsertsvadze, A; Royle, P; Keeling, MJ; McCarthy, ND; Petrou, S (2017) Indirect effects of childhood pneumococcal conjugate vaccination on invasive pneumococcal disease: a systematic review and meta-analysis LANCET GLOBAL HEALTH 5 E51-E59

Lewis, JM; Savage, RS; Beeching, NJ; Beadsworth, MBJ; Feasey, N; Covington, JA (2017) Identifying volatile metabolite signatures for the diagnosis of bacterial respiratory tract infection using electronic nose technology: A pilot study PLOS ONE 12 e0188879

Jervis, S; Chapman, LAC; Dwivedi, S; Karthick, M; Das, A; Le Rutte, EA; Courtenay, O; Medley, GF; Banerjee, I; Mahapatra, T; Chaudhuri, I; Srikantiah, S; Hollingsworth, TD (2017) Variations in visceral leishmaniasis burden, mortality and the pathway to care within Bihar, India PARASITES & VECTORS 10

Minas, G; Jenkins, DJ; Rand, DA; Finkenstadt, B (2017) Inferring transcriptional logic from multiple dynamic experiments BIOINFORMATICS 33 3437-3444

Le Doare, K et al. (2017) Intrapartum Antibiotic Chemoprophylaxis Policies for the Prevention of Group B Streptococcal Disease Worldwide: Systematic Review CLINICAL INFECTIOUS DISEASES 65 S143-S151

Steinmann, P; Reed, SG; Mirza, F; Hollingsworth, TD; Richardus, JH (2017) Innovative tools and approaches to end the transmission of Mycobacterium leprae LANCET INFECTIOUS DISEASES 17 E298-E305

Irvine, MA; Stolk, WA; Smith, ME; Subramanian, S; Singh, BK; Weil, GJ; Michael, E; Hollingsworth, TD (2017) Effectiveness of a triple-drug regimen for global elimination of lymphatic filariasis: a modelling study LANCET INFECTIOUS DISEASES 17 451-458

Hollingsworth, TD; Medley, GF (2017) Learning from multi-model comparisons: Collaboration leads to insights, but limitations remain EPIDEMICS 18 1-3

Smith, ME; Singh, BK; Irvine, MA; Stolk, WA; Subramanian, S; Hollingsworth, TD; Michael, E (2017) Predicting lymphatic filariasis transmission and elimination dynamics using a multi-model ensemble framework EPIDEMICS 18 16-28

Dyson, L; Stolk, WA; Farrell, SH; Hollingsworth, TD (2017) Measuring and modelling the effects of systematic non-adherence to mass drug administration EPIDEMICS 18 56-66

Le Rutte, EA; Chapman, LAC; Coffeng, LE; Jervis, S; Hasker, EC; Dwivedi, S; Karthick, M; Das, A; Mahapatra, T; Chaudhuri, I; Boelaert, MC; Medley, GF; Srikantiah, S; Hollingsworth, TD; de Vlas, SJ (2017) Elimination of visceral leishmaniasis in the Indian subcontinent: a comparison of predictions from three transmission models EPIDEMICS 18 67-80

Everitt, RG; Johansen, AM; Rowing, E; Evdemon-Hogan, M (2017) Bayesian model comparison with un-normalised likelihoods STATISTICS AND COMPUTING 27 403-422

Varnai, C; Burkoff, NS; Wild, DL (2017) Improving protein-protein interaction prediction using evolutionary information from low-quality MSAs PLOS ONE 12 e0169356

Irvine, MA; Hollingsworth, TD (2017) Making Transmission Models Accessible to End-Users: The Example of TRANSFIL PLOS NEGLECTED TROPICAL DISEASES 11 e0005206

Koukounari, A; Hollingsworth, TD (2017) A strengthening evidence-base for mass deworming, but questions remain LANCET 389 231-233

2016

Werkman, M; Tildesley, MJ; Brooks-Pollock, E; Keeling, MJ (2016) Preserving privacy whilst maintaining robust epidemiological predictions EPIDEMICS 17 35-41

Keeling, MJ; House, T; Cooper, AJ; Pellis, L (2016) Systematic Approximations to Susceptible-Infectious-Susceptible Dynamics on Networks PLOS COMPUTATIONAL BIOLOGY 12 e1005296

Bird, AD; Wall, MJ; Richardson, MJE (2016) Bayesian Inference of Synaptic Quantal Parameters from Correlated Vesicle Release FRONTIERS IN COMPUTATIONAL NEUROSCIENCE 10 116

Nyiro, JU; Sande, CJ; Mutunga, M; Kiyuka, PK; Munywoki, PK; Scott, JAG; Nokes, DJ (2016) Absence of Association between Cord Specific Antibody Levels and Severe Respiratory Syncytial Virus ( RSV) Disease in Early Infants: A Case Control Study from Coastal Kenya PLOS ONE 11 e0166706

Lucas, ES; Dyer, NP; Fishwick, K; Ott, S; Brosens, JJ (2016) Success after failure: the role of endometrial stem cells in recurrent miscarriage REPRODUCTION 152 R159-R166

Ahmed, U; Anwar, A; Savage, RS; Thornalley, PJ; Rabbani, N (2016) Protein oxidation, nitration and glycation biomarkers for early-stage diagnosis of osteoarthritis of the knee and typing and progression of arthritic disease ARTHRITIS RESEARCH & THERAPY 18

Bretschneider, T; Othmer, HG; Weijer, CJ (2016) Progress and perspectives in signal transduction, actin dynamics, and movement at the cell and tissue level: lessons from Dictyostelium INTERFACE FOCUS 6 20160047

Torrecilha, RBP; Utsunomiya, YT; Bosco, AM; Almeida, BF; Pereira, PP; Narciso, LG; Pereira, DCM; Baptistiolli, L; Calvo-Bado, L; Courtenay, O; Nunes, CM; Ciarlini, PC (2016) Correlations between peripheral parasite load and common clinical and laboratory alterations in dogs with visceral leishmaniasis PREVENTIVE VETERINARY MEDICINE 132 83-87

Smith, CA; McAinsh, AD; Burroughs, NJ (2016) Human kinetochores are swivel joints that mediate microtubule attachments ELIFE 5 e16159

Irvine, MA; Bull, JC; Keeling, MJ (2016) Disease transmission promotes evolution of host spatial patterns JOURNAL OF THE ROYAL SOCIETY INTERFACE 13 20160463

Emukule, GO; Mott, JA; Spreeuwenberg, P; Viboud, C; Commanday, A; Muthoka, P; Munywoki, PK; Nokes, DJ; van Der Velden, K; Paget, JW (2016) Influenza activity in Kenya, 2007-2013: timing, association with climatic factors, and implications for vaccination campaigns INFLUENZA AND OTHER RESPIRATORY VIRUSES 10 375-385

Ford, KJ; Lang, S; Pollard, AJ; McCarthy, ND (2016) A quantitative review of healthcare professionals' questions to a local immunization advice service: 4299 enquiries from 3 years JOURNAL OF PUBLIC HEALTH 38 578-584

Barchinger, SE; Pirbadian, S; Sambles, C; Baker, CS; Leung, KM; Burroughs, NJ; El-Naggar, MY; Golbeck, JH (2016) Regulation of Gene Expression in Shewanella oneidensis MR-1 during Electron Acceptor Limitation and Bacterial Nanowire Formation APPLIED AND ENVIRONMENTAL MICROBIOLOGY 82 5428-5443

Cheffings, TH; Burroughs, NJ; Balasubramanian, MK (2016) Actomyosin Ring Formation and Tension Generation in Eukaryotic Cytokinesis CURRENT BIOLOGY 26 R719-R737

Lafuerza, LF; Dyson, L; Edmonds, B; McKane, AJ (2016) Simplification and analysis of a model of social interaction in voting EUROPEAN PHYSICAL JOURNAL B 89 159

Agoti, CN; Kiyuka, PK; Kamau, E; Munywoki, PK; Bett, A; van der Hoek, L; Kellam, P; Nokes, DJ; Cotten, M (2016) Human Rhinovirus B and C Genomes from Rural Coastal Kenya MICROBIOLOGY RESOURCE ANNOUNCEMENTS 4 e00751-16

Adamson, A; Boddington, C; Downton, P; Rowe, W; Bagnall, J; Lam, C; Maya-Mendoza, A; Schmidt, L; Harper, CV; Spiller, DG; Rand, DA; Jackson, DA; White, MRH; Paszek, P (2016) Signal transduction controls heterogeneous NF-kappa B dynamics and target gene expression through cytokine-specific refractory states NATURE COMMUNICATIONS 7 12057

Sahota, AS; Gowda, R; Arasaradnam, RP; Daulton, E; Savage, RS; Skinner, JR; Adams, E; Ward, SA; Covington, JA (2016) A simple breath test for tuberculosis using ion mobility: A pilot study TUBERCULOSIS 99 143-146

Lafuerza, LF; Dyson, L; Edmonds, B; McKane, AJ (2016) Staged Models for Interdisciplinary Research PLOS ONE 11 e0157261

Owor, BE; Masankwa, GN; Mwango, LC; Njeru, RW; Agoti, CN; Nokes, DJ (2016) Human metapneumovirus epidemiological and evolutionary patterns in Coastal Kenya, 2007-11 BMC INFECTIOUS DISEASES 16 301

Armond, JW; Vladimirou, E; McAinsh, AD; Burroughs, NJ (2016) KiT: a MATLAB package for kinetochore tracking BIOINFORMATICS 32 1917-1919

Kiti, MC; Tizzoni, M; Kinyanjui, TM; Koech, DC; Munywoki, PK; Meriac, M; Cappa, L; Panisson, A; Barrat, A; Cattuto, C; Nokes, DJ (2016) Quantifying social contacts in a household setting of rural Kenya using wearable proximity sensors EPJ DATA SCIENCE 5 21

Metras, R; Cavalerie, L; Dommergues, L; Merot, P; Edmunds, WJ; Keeling, MJ; Cetre-Sossah, C; Cardinale, E (2016) The Epidemiology of Rift Valley Fever in Mayotte: Insights and Perspectives from 11 Years of Data PLOS NEGLECTED TROPICAL DISEASES 10 e0004783

Chalker, VJ; Smith, A; Al-Shahib, A; Botchway, S; Macdonald, E; Daniel, R; Phillips, S; Platt, S; Doumith, M; Tewolde, R; Coelho, J; Jolley, KA; Underwood, A; McCarthy, ND (2016) Integration of Genomic and Other Epidemiologic Data to Investigate and Control a Cross-Institutional Outbreak of Streptococcus pyogenes EMERGING INFECTIOUS DISEASES 22 973-980

Kaufmann, TJ; Harrison, PM; Richardson, MJE; Pinheiro, TJT; Wall, MJ (2016) Intracellular soluble alpha-synuclein oligomers reduce pyramidal cell excitability JOURNAL OF PHYSIOLOGY-LONDON 594 2751-2772

Otieno, JR; Agoti, CN; Gitahi, CW; Bett, A; Ngama, M; Medley, GF; Cane, PA; Nokes, DJ (2016) Molecular Evolutionary Dynamics of Respiratory Syncytial Virus Group A in Recurrent Epidemics in Coastal Kenya JOURNAL OF VIROLOGY 90 4990-5002

Toleman, MS; Herbert, K; McCarthy, N; Church, DN (2016) Vaccination of chemotherapy patients-effect of guideline implementation SUPPORTIVE CARE IN CANCER 24 2317-2321

Atia, J; McCloskey, C; Shmygol, AS; Rand, DA; van den Berg, HA; Blanks, AM (2016) Reconstruction of Cell Surface Densities of Ion Pumps, Exchangers, and Channels from mRNA Expression, Conductance Kinetics, Whole-Cell Calcium, and Current-Clamp Voltage Recordings, with an Application to Human Uterine Smooth Muscle Cells PLOS COMPUTATIONAL BIOLOGY 12 e1004828

Brand, SPC; Rock, KS; Keeling, MJ (2016) The Interaction between Vector Life History and Short Vector Life in Vector-Borne Disease Transmission and Control PLOS COMPUTATIONAL BIOLOGY 12 e1004837

Irvine, MA; Bull, JC; Keeling, MJ (2016) Aggregation dynamics explain vegetation patch-size distributions THEORETICAL POPULATION BIOLOGY 108 70-74

Domijan, M; Brown, PE; Shulgin, BV; Rand, DA (2016) PeTTSy: a computational tool for perturbation analysis of complex systems biology models BMC BIOINFORMATICS 17 124

Arasaradnam, RP; McFarlane, M; Ling, K; Wurie, S; O'Connell, N; Nwokolo, CU; Bardhan, KD; Skinner, J; Savage, RS; Covington, JA (2016) Breathomics-exhaled volatile organic compound analysis to detect hepatic encephalopathy: a pilot study JOURNAL OF BREATH RESEARCH 10 16012

Bevington, SL; Cauchy, P; Piper, J; Bertrand, E; Lalli, N; Jarvis, RC; Gilding, LN; Ott, S; Bonifer, C; Cockerill, PN (2016) Inducible chromatin priming is associated with the establishment of immunological memory in T cells EMBO JOURNAL 35 515-535

Irvine, MA; Jackson, EL; Kenyon, EJ; Cook, KJ; Keeling, MJ; Bull, JC (2016) Fractal measures of spatial pattern as a heuristic for return rate in vegetative systems ROYAL SOCIETY OPEN SCIENCE 3 150519

Ward, DG et al. (2016) Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer PLOS ONE 11 e0149756

Pirbadian, S; Barchinger, SE; Subramanian, P; Sambles, CM; Baker, CS; Burroughs, NJ; Jensen, GJ; Golbeck, JH; El-Naggar, MY (2016) Multiheme Cytochromes and the Bacterial Nanowires of Shewanella oneidensis MR-1: Regulation, Structure, and Extracellular Electron Transport Mechanisms BIOPHYSICAL JOURNAL 110 314A-314A

Featherstone, K; Hey, K; Momiji, H; McNamara, AV; Patist, AL; Woodburn, J; Spiller, DG; Christian, HC; McNeilly, AS; Mullins, JJ; Finkenstadt, BF; Rand, DA; White, MRH; Davis, JRE (2016) Spatially coordinated dynamic gene transcription in living pituitary tissue ELIFE 5 e08494

Bechtold, U et al. (2016) Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis PLANT CELL 28 345-366

Savage, RS; Yuan, YY (2016) Predicting chemoinsensitivity in breast cancer with 'omics/digital pathology data fusion ROYAL SOCIETY OPEN SCIENCE 3 140501

Lucas, ES; Dyer, NP; Murakami, K; Lee, YH; Chan, YW; Grimaldi, G; Muter, J; Brighton, PJ; Moore, JD; Patel, G; Chan, JKY; Takeda, S; Lam, EWF; Quenby, S; Ott, S; Brosens, JJ (2016) Loss of Endometrial Plasticity in Recurrent Pregnancy Loss STEM CELLS 34 346-356

Cameron, MM et al. (2016) Understanding the transmission dynamics of Leishmania donovani to provide robust evidence for interventions to eliminate visceral leishmaniasis in Bihar, India PARASITES & VECTORS 9 25

Rock, KS; Quinnell, RJ; Medley, GF; Courtenay, O (2016) Progress in the Mathematical Modelling of Visceral Leishmaniasis ADVANCES IN PARASITOLOGY, VOL 94: MATHEMATICAL MODELS FOR NEGLECTED TROPICAL DISEASES: ESSENTIAL TOOLS FOR CONTROL AND ELIMINATION, PT B 94 49-131

Dyer, N; Young, L; Ott, S (2016) Artifacts in the data of Hu et al. NATURE GENETICS 48 2-3

Cvijovic, M et al. (2016) Strategies for structuring interdisciplinary education in Systems Biology: an European perspective NPJ SYSTEMS BIOLOGY AND APPLICATIONS 2 16011

Tsertsvadze, A; Royle, P; Seedat, F; Cooper, J; Crosby, R; McCarthy, N (2016) Community-onset sepsis and its public health burden: a systematic review SYSTEMATIC REVIEWS 5 81

Ahmed, U; Anwar, A; Savage, RS; Thornalley, PJ; Rabbani, N (2016) Protein oxidation, nitration and glycation biomarkers for early-stage diagnosis of osteoarthritis of the knee and typing and progression of arthritic disease ARTHRITIS RESEARCH & THERAPY 18

Deol, A; Webster, JP; Walker, M; Basanez, MG; Hollingsworth, TD; Fleming, FM; Montresor, A; French, MD (2016) Development and evaluation of a Markov model to predict changes in schistosomiasis prevalence in response to praziquantel treatment: a case study of Schistosoma mansoni in Uganda and Mali PARASITES & VECTORS 9 543

Lu, YH; Timofeeva, Y (2016) Response functions for electrically coupled neuronal network: a method of local point matching and its applications BIOLOGICAL CYBERNETICS 110 117-133

Sayyid, F; Kalvala, S (2016) On the importance of modelling the internal spatial dynamics of biological cells BIOSYSTEMS 145 53-66

Turner, HC; Truscott, JE; Fleming, FM; Hollingsworth, TD; Brooker, SJ; Anderson, RM (2016) Cost-effectiveness of scaling up mass drug administration for the control of soil-transmitted helminths: a comparison of cost function and constant costs analyses LANCET INFECTIOUS DISEASES 16 838-846

Sahota, AS; Gowda, R; Arasaradnam, RP; Daulton, E; Savage, RS; Skinner, JR; Adams, E; Ward, SA; Covington, JA (2016) A simple breath test for tuberculosis using ion mobility: A pilot study TUBERCULOSIS 99 143-146

Sprague, DA; Jeffery, C; Crossland, N; House, T; Roberts, GO; Vargas, W; Ouma, J; Lwanga, SK; Valadez, JJ (2016) Assessing delivery practices of mothers over time and over space in Uganda, 2003-2012 EMERGING THEMES IN EPIDEMIOLOGY 13 9

Arasaradnam, RP; McFarlane, M; Ling, K; Wurie, S; O'Connell, N; Nwokolo, CU; Bardhan, KD; Skinner, J; Savage, RS; Covington, JA (2016) Breathomics-exhaled volatile organic compound analysis to detect hepatic encephalopathy: a pilot study JOURNAL OF BREATH RESEARCH 10 16012

Pollock, M; Johansen, AM; Roberts, GO (2016) On the exact and epsilon-strong simulation of (jump) diffusions BERNOULLI 22 794-856

Marshall, JM; Toure, M; Ouedraogo, AL; Ndhlovu, M; Kiware, SS; Rezai, A; Nkhama, E; Griffin, JT; Hollingsworth, TD; Doumbia, S; Govella, NJ; Ferguson, NM; Ghani, AC (2016) Key traveller groups of relevance to spatial malaria transmission: a survey of movement patterns in four sub-Saharan African countries MALARIA JOURNAL 15 200

Fowler, AC; Hollingsworth, TD (2016) The Dynamics of Ascaris lumbricoides Infections BULLETIN OF MATHEMATICAL BIOLOGY 78 815-833

Burkoff, NS; Baldock, RJN; Varnai, C; Wild, DL; Csanyi, G (2016) Exploiting molecular dynamics in Nested Sampling simulations of small peptides COMPUTER PHYSICS COMMUNICATIONS 201 8-18

Mason, SA; Sayyid, F; Kirk, PDW; Starr, C; Wild, DL (2016) MDI-GPU: accelerating integrative modelling for genomic-scale data using GP-GPU computing STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY 15 83-86

Ward, DG et al. (2016) Multiplex PCR and Next Generation Sequencing for the Non-Invasive Detection of Bladder Cancer PLOS ONE 11 e0149756

Featherstone, K; Hey, K; Momiji, H; McNamara, AV; Patist, AL; Woodburn, J; Spiller, DG; Christian, HC; McNeilly, AS; Mullins, JJ; Finkenstadt, BF; Rand, DA; White, MRH; Davis, JRE (2016) Spatially coordinated dynamic gene transcription in living pituitary tissue ELIFE 5 e08494

Bechtold, U et al. (2016) Time-Series Transcriptomics Reveals That AGAMOUS-LIKE22 Affects Primary Metabolism and Developmental Processes in Drought-Stressed Arabidopsis PLANT CELL 28 345-366

Savage, RS; Yuan, YY (2016) Predicting chemoinsensitivity in breast cancer with 'omics/digital pathology data fusion ROYAL SOCIETY OPEN SCIENCE 3 140501

Irvine, MA; Njenga, SM; Gunawardena, S; Wamae, CN; Cano, J; Brooker, SJ; Hollingsworth, TD (2016) Understanding the relationship between prevalence of microfilariae and antigenaemia using a model of lymphatic filariasis infection TRANSACTIONS OF THE ROYAL SOCIETY OF TROPICAL MEDICINE AND HYGIENE 110 118-124

Cameron, MM et al. (2016) Understanding the transmission dynamics of Leishmania donovani to provide robust evidence for interventions to eliminate visceral leishmaniasis in Bihar, India PARASITES & VECTORS 9 25

Medley, GF; Turner, HC; Baggaley, RF; Holland, C; Hollingsworth, TD (2016) The Role of More Sensitive Helminth Diagnostics in Mass Drug Administration Campaigns: Elimination and Health Impacts ADVANCES IN PARASITOLOGY, VOL 94: MATHEMATICAL MODELS FOR NEGLECTED TROPICAL DISEASES: ESSENTIAL TOOLS FOR CONTROL AND ELIMINATION, PT B 94 343-392

2015

Hollingsworth, TD et al. (2015) Quantitative analyses and modelling to support achievement of the 2020 goals for nine neglected tropical diseases PARASITES & VECTORS 8 630

Munywoki, PK; Koech, DC; Agoti, CN; Bett, A; Cane, PA; Medley, GF; Nokes, DJ (2015) Frequent Asymptomatic Respiratory Syncytial Virus Infections During an Epidemic in a Rural Kenyan Household Cohort JOURNAL OF INFECTIOUS DISEASES 212 1711-1718

House, T; Read, JM; Danon, L; Keeling, MJ (2015) Testing the hypothesis of preferential attachment in social network formation EPJ DATA SCIENCE 4 13

Geard, N; Glass, K; Mccaw, JM; McBryde, ES; Korb, KB; Keeling, MJ; McVernon, J (2015) The effects of demographic change on disease transmission and vaccine impact in a household structured population EPIDEMICS 13 56-64

Piper, J; Assi, SA; Cauchy, P; Ladroue, C; Cockerill, PN; Bonifer, C; Ott, S (2015) Wellington-bootstrap: differential DNase-seq footprinting identifies cell-type determining transcription factors BMC GENOMICS 16 1000

Field, SL; Dasgupta, T; Cummings, M; Savage, RS; Adebayo, J; McSara, H; Gunawardena, J; Orsi, NM (2015) Bayesian modeling suggests that IL-12(p40), IL-13 and MCP-1 drive murine cytokine networks in vivo BMC SYSTEMS BIOLOGY 9 76

Dyson, L; Yates, CA; Buhl, J; McKane, AJ (2015) Onset of collective motion in locusts is captured by a minimal model PHYSICAL REVIEW E 92 52708

Agoti, CN; Otieno, JR; Ngama, M; Mwihuri, AG; Medley, GF; Cane, PA; Nokes, DJ (2015) Successive Respiratory Syncytial Virus Epidemics in Local Populations Arise from Multiple Variant Introductions, Providing Insights into Virus Persistence JOURNAL OF VIROLOGY 89 11630-11642

Lewis, LA et al. (2015) Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000 PLANT CELL 27 3038-3064

Armond, JW; Harry, EF; McAinsh, AD; Burroughs, NJ (2015) Inferring the Forces Controlling Metaphase Kinetochore Oscillations by Reverse Engineering System Dynamics PLOS COMPUTATIONAL BIOLOGY 11 e1004607

Chapman, LAC; Dyson, L; Courtenay, O; Chowdhury, R; Bern, C; Medley, GF; Hollingsworth, TD (2015) Quantification of the natural history of visceral leishmaniasis and consequences for control PARASITES & VECTORS 8 521

Rock, KS; Torr, SJ; Lumbala, C; Keeling, MJ (2015) Quantitative evaluation of the strategy to eliminate human African trypanosomiasis in the Democratic Republic of Congo PARASITES & VECTORS 8 532

Davies, NJ; Krusche, P; Tauber, E; Ott, S (2015) Analysis of 5 ' gene regions reveals extraordinary conservation of novel non-coding sequences in a wide range of animals BMC EVOLUTIONARY BIOLOGY 15 227

Slator, PJ; Cairo, CW; Burroughs, NJ (2015) Detection of Diffusion Heterogeneity in Single Particle Tracking Trajectories Using a Hidden Markov Model with Measurement Noise Propagation PLOS ONE 10 e0140759

Burroughs, NJ; Harry, EF; McAinsh, AD (2015) Super-resolution kinetochore tracking reveals the mechanisms of human sister kinetochore directional switching ELIFE 4 e09500

Pellis, L; House, T; Keeling, MJ (2015) Exact and approximate moment closures for non-Markovian network epidemics JOURNAL OF THEORETICAL BIOLOGY 382 160-177

Andrade, MS; Courtenay, O; Brito, MEF; Carvalho, FG; Carvalho, AWS; Soares, F; Carvalho, SM; Costa, PL; Zampieri, R; Floeter-Winter, LM; Shaw, JJ; Brandao, SP (2015) Infectiousness of Sylvatic and Synanthropic Small Rodents Implicates a Multi-host Reservoir of Leishmania (Viannia) braziliensis PLOS NEGLECTED TROPICAL DISEASES 9 e0004137

Cody, AJ; McCarthy, ND; Bray, JE; Wimalarathna, HML; Colles, FM; van Rensburg, MJJ; Dingle, KE; Waldenstrom, J; Maiden, MCJ (2015) Wild bird-associated Campylobacter jejuni isolates are a consistent source of human disease, in Oxfordshire, United Kingdom ENVIRONMENTAL MICROBIOLOGY REPORTS 7 782-788

Hey, KL; Momiji, H; Featherstone, K; Davis, JRE; White, MRH; Rand, DA; Finkenstadt, B (2015) A stochastic transcriptional switch model for single cell imaging data BIOSTATISTICS 16 655-669

Kinyanjui, TM; House, TA; Kiti, MC; Cane, PA; Nokes, DJ; Medley, GF (2015) Vaccine Induced Herd Immunity for Control of Respiratory Syncytial Virus Disease in a Low-Income Country Setting PLOS ONE 10 e0138018

Fernandes, AM; Balasegaram, S; Willis, C; Wimalarathna, HML; Maiden, MC; McCarthy, ND (2015) Partial Failure of Milk Pasteurization as a Risk for the Transmission of Campylobacter From Cattle to Humans CLINICAL INFECTIOUS DISEASES 61 903-909

Spencer, SEF; Besser, TE; Cobbold, RN; French, NP (2015) 'Super' or just 'above average'? Supershedders and the transmission of Escherichia coli 0157:H7 among feedlot cattle JOURNAL OF THE ROYAL SOCIETY INTERFACE 12 20150446

Rock, KS; Wood, DA; Keeling, MJ (2015) Age- and bite-structured models for vector-borne diseases EPIDEMICS 12 20-29

Xue, MZ; Momiji, H; Rabbani, N; Barker, G; Bretschneider, T; Shmygol, A; Rand, DA; Thornalley, PJ (2015) Frequency Modulated Translocational Oscillations of Nrf2 Mediate the Antioxidant Response Element Cytoprotective Transcriptional Response ANTIOXIDANTS & REDOX SIGNALING 23 613-629

Vance, KW; Woodcock, DJ; Reid, JE; Bretschneider, T; Ott, S; Koentges, G (2015) Conserved Cis-Regulatory Modules Control Robustness in Msx1 Expression at Single-Cell Resolution GENOME BIOLOGY AND EVOLUTION 7 2762-2778

Eduati, F et al. (2015) Prediction of human population responses to toxic compounds by a collaborative competition NATURE BIOTECHNOLOGY 33 933

Achtman, M; Zhou, ZM; Didelot, X (2015) Formal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence PLOS ONE 10 e0134435

King, HC; Murphy, A; James, P; Travis, E; Porter, D; Hung, YJ; Sawyer, J; Cork, J; Delahay, RJ; Gaze, W; Courtenay, O; Wellington, EM (2015) The variability and seasonality of the environmental reservoir of Mycobacterium bovis shed by wild European badgers SCIENTIFIC REPORTS 5 12318

Cauchy, P et al. (2015) Chronic FLT3-ITD Signaling in Acute Myeloid Leukemia Is Connected to a Specific Chromatin Signature CELL REPORTS 12 821-836

Harrison, PM; Badel, L; Wall, MJ; Richardson, MJE (2015) Experimentally Verified Parameter Sets for Modelling Heterogeneous Neocortical Pyramidal-Cell Populations PLOS COMPUTATIONAL BIOLOGY 11 e1004165

Xue, MZ; Momiji, H; Rabbani, N; Bretschneider, T; Rand, DA; Thornalley, PJ (2015) Frequency modulated translocational oscillations of Nrf2, a transcription factor functioning like a wireless sensor BIOCHEMICAL SOCIETY TRANSACTIONS 43 669-673

Barry, NPE; Pitto-Barry, A; Tran, J; Spencer, SEF; Johansen, AM; Sanchez, AM; Dove, AP; O'Reilly, RK; Deeth, RJ; Beanland, R; Sadler, PJ (2015) Osmium Atoms and Os-2 Molecules Move Faster on Selenium-Doped Compared to Sulfur-Doped Boronic Graphenic Surfaces CHEMISTRY OF MATERIALS 27 5100-5105

Xue, M; Momiji, H; Rabbani, N; Barker, G; Bretschneider, T; Shmygol, A; Rand, DA; Thornalley, PJ (2015) ANTIOXIDANT RESPONSE ELEMENT CYTOPROTECTIVE RESPONSE IN AORTIC ENDOTHELIAL CELLS COORDINATED BY TRANSCRIPTION FACTOR NRF2 IS REGULATED THROUGH FREQUENCY-MODULATED TRANSLOCATIONAL OSCILLATIONS ATHEROSCLEROSIS 241 E2-E2

King, HC; Murphy, A; James, P; Travis, E; Porter, D; Sawyer, J; Cork, J; Delahay, RJ; Gaze, W; Courtenay, O; Wellington, EM (2015) Performance of a Noninvasive Test for Detecting Mycobacterium bovis Shedding in European Badger (Meles meles) Populations JOURNAL OF CLINICAL MICROBIOLOGY 53 2316-2323

Pellis, L; Spencer, SEF; House, T (2015) Real-time growth rate for general stochastic SIR epidemics on unclustered networks MATHEMATICAL BIOSCIENCES 265 65-81

Loftus, FC; Richardson, MJE; Shmygol, A (2015) Single-cell mechanics and calcium signalling in organotypic slices of human myometrium JOURNAL OF BIOMECHANICS 48 1620-1624

Dawson, PM; Werkman, M; Brooks-Pollock, E; Tildesley, MJ (2015) Epidemic predictions in an imperfect world: modelling disease spread with partial data PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 282 20150205

Mook, P; Kanagarajah, S; Gardiner, D; Kerac, M; Hughes, G; Field, N; McCarthy, N; Simms, I; Lane, C; Adak, B; Crook, P (2015) MONITORING GENDER RATIO OF GASTROINTESTINAL INFECTION LABORATORY REPORTS AS A MECHANISM FOR IDENTIFYING POSSIBLE INCREASES AMONG MEN WHO HAVE SEX WITH MEN, ENGLAND, 2003-2013 SEXUALLY TRANSMITTED INFECTIONS 91 A87

Rock, KS; le Rutte, EA; de Vlas, SJ; Adams, ER; Medley, GF; Hollingsworth, TD (2015) Uniting mathematics and biology for control of visceral leishmaniasis TRENDS IN PARASITOLOGY 31 251-259

Lockley, R; Ladds, G; Bretschneider, T (2015) Image based validation of dynamical models for cell reorientation CYTOMETRY PART A 87A 471-480

Keeling, MJ; Ross, JV (2015) Optimal prophylactic vaccination in segregated populations: When can we improve on the equalising strategy? EPIDEMICS 11 7-13

Armond, JW; Vladimirou, E; Erent, M; McAinsh, AD; Burroughs, NJ (2015) Probing microtubule polymerisation state at single kinetochores during metaphase chromosome motion JOURNAL OF CELL SCIENCE 128 1991-2001

Feillet, C; van der Horst, GTJ; Levi, F; Rand, DA; Delaunay, F (2015) Coupling between the circadian clock and cell cycle oscillators: implication for healthy cells and malignant growth FRONTIERS IN NEUROLOGY 6 96

Sacharz, J; Bryan, SJ; Yu, JF; Burroughs, NJ; Spence, EM; Nixon, PJ; Mullineaux, CW (2015) Sub-cellular location of FtsH proteases in the cyanobacterium Synechocystis sp PCC 6803 suggests localised PSII repair zones in the thylakoid membranes MOLECULAR MICROBIOLOGY 96 448-462

Nyiro, JU; Sande, C; Mutunga, M; Kiyuka, PK; Munywoki, PK; Scott, JAG; Nokes, DJ (2015) Quantifying maternally derived respiratory syncytial virus specific neutralising antibodies in a birth cohort from coastal Kenya VACCINE 33 1797-1801

Brand, SPC; Tildesley, MJ; Keeling, MJ (2015) Rapid simulation of spatial epidemics: A spectral method JOURNAL OF THEORETICAL BIOLOGY 370 121-134

Bomers, MK; Menke, FP; Savage, RS; Vandenbroucke-Grauls, CMJE; van Agtmael, MA; Covington, JA; Smulders, YM (2015) Rapid, Accurate, and On-Site Detection of C-difficile in Stool Samples AMERICAN JOURNAL OF GASTROENTEROLOGY 110 588-594

Agoti, CN; Otieno, JR; Munywoki, PK; Mwihuri, AG; Cane, PA; Nokes, DJ; Kellam, P; Cotten, M (2015) Local Evolutionary Patterns of Human Respiratory Syncytial Virus Derived from Whole-Genome Sequencing JOURNAL OF VIROLOGY 89 3444-3454

Ahmed, U; Anwar, A; Savage, RS; Costa, ML; Mackay, N; Filer, A; Raza, K; Watts, RA; Winyard, PG; Tarr, J; Haigh, RC; Thornalley, PJ; Rabbani, N (2015) Biomarkers of early stage osteoarthritis, rheumatoid arthritis and musculoskeletal health SCIENTIFIC REPORTS 5 9259

Lloyd, KL; Cree, IA; Savage, RS (2015) Prediction of resistance to chemotherapy in ovarian cancer: a systematic review BMC CANCER 15

Poletti, P; Merler, S; Ajelli, M; Manfredi, P; Munywoki, PK; Nokes, DJ; Melegaro, A (2015) Evaluating vaccination strategies for reducing infant respiratory syncytial virus infection in low-income settings BMC MEDICINE 13 49

Domijan, M; Rand, DA (2015) Using constraints and their value for optimization of large ODE systems JOURNAL OF THE ROYAL SOCIETY INTERFACE 12 20141303

Munywoki, PK; Koech, DC; Agoti, CN; Kibirige, N; Kipkoech, J; Cane, PA; Medley, GF; Nokes, DJ (2015) Influence of age, severity of infection, and co-infection on the duration of respiratory syncytial virus (RSV) shedding EPIDEMIOLOGY AND INFECTION 143 804-812

Spencer, SEF; Hill, SM; Mukherjee, S (2015) INFERRING NETWORK STRUCTURE FROM INTERVENTIONAL TIME-COURSE EXPERIMENTS ANNALS OF APPLIED STATISTICS 9 507-524

Brooks-Pollock, E; de Jong, MCM; Keeling, MJ; Klinkenberg, D; Wood, JLN (2015) Eight challenges in modelling infectious livestock diseases EPIDEMICS 10 1-5

Didelot, X; Pang, B; Zhou, ZM; McCann, A; Ni, PX; Li, DF; Achtman, M; Kan, B (2015) The Role of China in the Global Spread of the Current Cholera Pandemic PLOS GENETICS 11 e1005072

Wall, MJ; Richardson, MJE (2015) Localized adenosine signaling provides fine-tuned negative feedback over a wide dynamic range of neocortical network activities JOURNAL OF NEUROPHYSIOLOGY 113 871-882

Covington, JA; van der Schee, MP; Edge, ASL; Boyle, B; Savage, RS; Arasaradnam, RP (2015) The application of FAIMS gas analysis in medical diagnostics ANALYST 14 6775-6781

Rock, KS; Stone, CM; Hastings, IM; Keeling, MJ; Torr, SJ; Chitnis, N (2015) Mathematical Models of Human African Trypanosomiasis Epidemiology MATHEMATICAL MODELS FOR NEGLECTED TROPICAL DISEASES: ESSENTIAL TOOLS FOR CONTROL AND ELIMINATION, PT A 87 53-133

Tsertsvadze, A; Chen, YF; Moher, D; Sutcliffe, P; McCarthy, N (2015) How to conduct systematic reviews more expeditiously? SYSTEMATIC REVIEWS 4 160

Tsertsvadze, A; Royle, P; McCarthy, N (2015) Community-onset sepsis and its public health burden: protocol of a systematic review SYSTEMATIC REVIEWS 4 119

Medley, GF; Hollingsworth, TD; Olliaro, PL; Adams, ER (2015) Health-seeking behaviour, diagnostics and transmission dynamics in the control of visceral leishmaniasis in the Indian subcontinent NATURE 528 S102-S108

Field, SL; Dasgupta, T; Cummings, M; Savage, RS; Adebayo, J; McSara, H; Gunawardena, J; Orsi, NM (2015) Bayesian modeling suggests that IL-12(p40), IL-13 and MCP-1 drive murine cytokine networks in vivo BMC SYSTEMS BIOLOGY 9 76

Turner, HC; Truscott, JE; Bettis, AA; Shuford, KV; Dunn, JC; Hollingsworth, TD; Brooker, SJ; Anderson, RM (2015) An economic evaluation of expanding hookworm control strategies to target the whole community PARASITES & VECTORS 8 570

Lewis, LA et al. (2015) Transcriptional Dynamics Driving MAMP-Triggered Immunity and Pathogen Effector-Mediated Immunosuppression in Arabidopsis Leaves Following Infection with Pseudomonas syringae pv tomato DC3000 PLANT CELL 27 3038-3064

Drake, LJ et al. (2015) Bihar's Pioneering School-Based Deworming Programme: Lessons Learned in Deworming over 17 Million Indian School-Age Children in One Sustainable Campaign PLOS NEGLECTED TROPICAL DISEASES 9 e0004106

Moraga, P; Cano, J; Baggaley, RF; Gyapong, JO; Njenga, SM; Nikolay, B; Davies, E; Rebollo, MP; Pullan, RL; Bockarie, MJ; Hollingsworth, TD; Gambhir, M; Brooker, SJ (2015) Modelling the distribution and transmission intensity of lymphatic filariasis in sub-Saharan Africa prior to scaling up interventions: integrated use of geostatistical and mathematical modelling PARASITES & VECTORS 8 560

Chapman, LAC; Dyson, L; Courtenay, O; Chowdhury, R; Bern, C; Medley, GF; Hollingsworth, TD (2015) Quantification of the natural history of visceral leishmaniasis and consequences for control PARASITES & VECTORS 8 521

Irvine, MA; Reimer, LJ; Njenga, SM; Gunawardena, S; Kelly-Hope, L; Bockarie, M; Hollingsworth, TD (2015) Modelling strategies to break transmission of lymphatic filariasis - aggregation, adherence and vector competence greatly alter elimination PARASITES & VECTORS 8 547

Covington, JA; van der Schee, MP; Edge, ASL; Boyle, B; Savage, RS; Arasaradnam, RP (2015) The application of FAIMS gas analysis in medical diagnostics ANALYST 14 6775-6781

Medley, GF; Hollingsworth, TD (2015) MDA helminth control: more questions than answers LANCET GLOBAL HEALTH 3 E583-E584

Eduati, F et al. (2015) Prediction of human population responses to toxic compounds by a collaborative competition NATURE BIOTECHNOLOGY 33 933

Fowler, AC; Hollingsworth, TD (2015) Simple Approximations for Epidemics with Exponential and Fixed Infectious Periods BULLETIN OF MATHEMATICAL BIOLOGY 77 1539-1555

Anderson, RM; Turner, HC; Truscott, JE; Hollingsworth, TD; Brooker, SJ (2015) Should the Goal for the Treatment of Soil Transmitted Helminth (STH) Infections Be Changed from Morbidity Control in Children to Community-Wide Transmission Elimination? PLOS NEGLECTED TROPICAL DISEASES 9 e0003897

Penfold, CA; Millar, JBA; Wild, DL (2015) Inferring orthologous gene regulatory networks using interspecies data fusion BIOINFORMATICS 31 97-105

Turner, HC; Truscott, JE; Hollingsworth, TD; Bettis, AA; Brooker, SJ; Anderson, RM (2015) Cost and cost-effectiveness of soil-transmitted helminth treatment programmes: systematic review and research needs PARASITES & VECTORS 8 355

Timofeeva, Y; Volynski, KE (2015) Calmodulin as a major calcium buffer shaping vesicular release and short-term synaptic plasticity: facilitation through buffer dislocation FRONTIERS IN CELLULAR NEUROSCIENCE 9 239

Hollingsworth, TD; Pilcher, CD; Hecht, FM; Deeks, SG; Fraser, C (2015) High Transmissibility During Early HIV Infection Among Men Who Have Sex With Men-San Francisco, California JOURNAL OF INFECTIOUS DISEASES 211 1757-1760

Penfold, CA; Shifaz, A; Brown, PE; Nicholson, A; Wild, DL (2015) CSI: a nonparametric Bayesian approach to network inference from multiple perturbed time series gene expression data STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY 14 307-310

2014

Bryan, SJ; Burroughs, NJ; Shevela, D; Yu, JF; Rupprecht, E; Liu, LN; Mastroianni, G; Xue, Q; Llorente-Garcia, I; Leake, MC; Eichacker, LA; Schneider, D; Nixon, PJ; Mullineaux, CW (2014) Localisation and interactions of the Vipp1 protein in cyanobacteria MOLECULAR MICROBIOLOGY 94 1179-1195

Wood, GR; Burroughs, NJ; Evans, DJ; Ryabov, EV (2014) Error correction and diversity analysis of population mixtures determined by NGS PEERJ 2 e645

Xue, MZ; Momiji, H; Rabbani, N; Barker, G; Bretschneider, T; Shmygol, A; Rand, D; Thornalley, P (2014) Frequency Modulated Translocational Oscillations of Nrf2 Mediate the ARE Cytoprotective Transcriptional Response FREE RADICAL BIOLOGY AND MEDICINE 76 S74-S74

Burroughs, NJ; Boehm, M; Eckert, C; Mastroianni, G; Spence, EM; Yu, JF; Nixon, PJ; Appel, J; Mullineaux, CW; Bryan, SJ (2014) Solar powered biohydrogen production requires specific localization of the hydrogenase ENERGY & ENVIRONMENTAL SCIENCE 7 3791-3800

Black, AJ; House, T; Keeling, MJ; Ross, JV (2014) The effect of clumped population structure on the variability of spreading dynamics JOURNAL OF THEORETICAL BIOLOGY 359 45-53

Loftus, FC; Shmygol, A; Richardson, MJE (2014) Fine spatiotemporal activity in contracting myometrium revealed by motion-corrected calcium imaging JOURNAL OF PHYSIOLOGY-LONDON 592 4447-4463

Oates, CJ; Amos, R; Spencer, SEF (2014) Quantifying the multi-scale performance of network inference algorithms STATISTICAL APPLICATIONS IN GENETICS AND MOLECULAR BIOLOGY 13 611-631

Wang, Y; Penfold, CA; Hodgson, DA; Gifford, ML; Burroughs, NJ (2014) Correcting for link loss in causal network inference caused by regulator interference BIOINFORMATICS 30 2779-2786

Ptasinska, A et al. (2014) Identification of a Dynamic Core Transcriptional Network in t(8;21) AML that Regulates Differentiation Block and Self-Renewal CELL REPORTS 8 1974-1988

McCloskey, C et al. (2014) The inwardly rectifying K+ channel KIR7.1 controls uterine excitability throughout pregnancy EMBO MOLECULAR MEDICINE 6 1161-1174

Hancock, PA; Rehman, Y; Hall, IM; Edeghere, O; Danon, L; House, TA; Keeling, MJ (2014) Strategies for Controlling Non-Transmissible Infection Outbreaks Using a Large Human Movement Data Set PLOS COMPUTATIONAL BIOLOGY 10 e1003809

Sande, CJ; Cane, PA; Nokes, DJ (2014) The association between age and the development of respiratory syncytial virus neutralising antibody responses following natural infection in infants VACCINE 32 4726-4729

Kiti, MC; Kinyanjui, TM; Koech, DC; Munywoki, PK; Medley, GF; Nokes, DJ (2014) Quantifying Age-Related Rates of Social Contact Using Diaries in a Rural Coastal Population of Kenya PLOS ONE 9 e104786

Tyson, RA; Zatulovskiy, E; Kay, RR; Bretschneider, T (2014) How blebs and pseudopods cooperate during chemotaxis PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 11703-11708

Cabeza, JZ; Cauchy, P; James, S; Piper, J; Ptasinska, A; Imperato, MR; Canestraro, M; Assi, S; Hoogenkamp, M; Westhead, D; Ott, S; Bonifer, C; Cockerill, P (2014) DECLINED PRESENTATION ACTIVATING FLT3-ITD RECEPTOR MUTATIONS IN AML ARE ASSOCIATED WITH A SPECIFIC EPIGENETIC SIGNATURE COMPOSED OF A DISCRETE SUBSET RUNX1-BOUND DNASEI HYPERSENSITIVE SITES ENRICHED FOR AP-1 AND C/EBP MOTIFS EXPERIMENTAL HEMATOLOGY 42 S67-S67

Brooks-Pollock, E; Roberts, GO; Keeling, MJ (2014) A dynamic model of bovine tuberculosis spread and control in Great Britain NATURE 511 228

Feillet, C; Krusche, P; Tamanini, F; Janssens, RC; Downey, MJ; Martin, P; Teboul, M; Saito, S; Levi, FA; Bretschneider, T; van der Horst, GTJ; Delaunay, F; Rand, DA (2014) Phase locking and multiple oscillating attractors for the coupled mammalian clock and cell cycle PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 111 9828-9833

Papanayotou, C; Benhaddou, A; Camus, A; Perea-Gomez, A; Jouneau, A; Mezger, V; Langa, F; Ott, S; Saberan-Djoneidi, D; Collignon, J (2014) A Novel Nodal Enhancer Dependent on Pluripotency Factors and Smad2/3 Signaling Conditions a Regulatory Switch During Epiblast Maturation PLOS BIOLOGY 12 e1001890

Munywoki, PK; Koech, DC; Agoti, CN; Lewa, C; Cane, PA; Medley, GF; Nokes, DJ (2014) The Source of Respiratory Syncytial Virus Infection In Infants: A Household Cohort Study In Rural Kenya JOURNAL OF INFECTIOUS DISEASES 209 1685-1692

Agoti, CN; Otieno, JR; Gitahi, CW; Cane, PA; Nokes, DJ (2014) Rapid Spread and Diversification of Respiratory Syncytial Virus Genotype ON1, Kenya EMERGING INFECTIOUS DISEASES 20 950-959

Brunel, N; Hakim, V; Richardson, MJE (2014) Single neuron dynamics and computation CURRENT OPINION IN NEUROBIOLOGY 25 149-155

Agoti, CN; Mayieka, LM; Otieno, JR; Ahmed, JA; Fields, BS; Waiboci, LW; Nyoka, R; Eidex, RB; Marano, N; Burton, W; Montgomery, JM; Breiman, RF; Nokes, DJ (2014) Examining strain diversity and phylogeography in relation to an unusual epidemic pattern of respiratory syncytial virus (RSV) in a long-term refugee camp in Kenya BMC INFECTIOUS DISEASES 14 178

Polanski, K; Rhodes, J; Hill, C; Zhang, PJ; Jenkins, DJ; Kiddle, SJ; Jironkin, A; Beynon, J; Buchanan-Wollaston, V; Ott, S; Denby, KJ (2014) Wigwams: identifying gene modules co-regulated across multiple biological conditions BIOINFORMATICS 30 962-970

Buhnerkempe, MG; Tildesley, MJ; Lindstrom, T; Grear, DA; Portacci, K; Miller, RS; Lombard, JE; Werkman, M; Keeling, MJ; Wennergren, U; Webb, CT (2014) The Impact of Movements and Animal Density on Continental Scale Cattle Disease Outbreaks in the United States PLOS ONE 9 e91724

Zatulovskiy, E; Tyson, R; Bretschneider, T; Kay, RR (2014) Bleb-driven chemotaxis of Dictyostelium cells JOURNAL OF CELL BIOLOGY 204 1027-1044

Gould, PS; Dyer, NP; Croft, W; Ott, S; Easton, AJ (2014) Cellular mRNAs access second ORFs using a novel amino acid sequence-dependent coupled translation termination-reinitiation mechanism RNA 20 373-381

Ott, S; Hebenstreit, D (2014) Apply market forces to peer review NATURE 506 295-295

Haase, JK; Didelot, X; Lecuit, M; Korkeala, H; Achtman, M (2014) The ubiquitous nature of Listeria monocytogenes clones: a large-scale Multilocus Sequence Typing study ENVIRONMENTAL MICROBIOLOGY 16 405-416

Rock, K; Brand, S; Moir, J; Keeling, MJ (2014) Dynamics of infectious diseases REPORTS ON PROGRESS IN PHYSICS 77 26602

Bird, AD; Richardson, MJE (2014) Long-term plasticity determines the postsynaptic response to correlated afferents with multivesicular short-term synaptic depression FRONTIERS IN COMPUTATIONAL NEUROSCIENCE 8 2

Courtenay, O; Carson, C; Calvo-Bado, L; Garcez, LM; Quinnell, RJ (2014) Heterogeneities in Leishmania infantum Infection: Using Skin Parasite Burdens to Identify Highly Infectious Dogs PLOS NEGLECTED TROPICAL DISEASES 8 e2583

Sidaway-Lee, K; Costa, MJ; Rand, DA; Finkenstadt, B; Penfield, S (2014) Direct measurement of transcription rates reveals multiple mechanisms for configuration of the Arabidopsis ambient temperature response GENOME BIOLOGY 15 R45

2013

Finkenstadt, B; Woodcock, DJ; Komorowski, M; Harper, CV; Davis, JRE; White, MRH; Rand, DA (2013) QUANTIFYING INTRINSIC AND EXTRINSIC NOISE IN GENE TRANSCRIPTION USING THE LINEAR NOISE APPROXIMATION: AN APPLICATION TO SINGLE CELL DATA ANNALS OF APPLIED STATISTICS 7 1960-1982

Robery, S; Tyson, R; Dinh, C; Kuspa, A; Noegel, AA; Bretschneider, T; Andrews, PLR; Williams, RSB (2013) A novel human receptor involved in bitter tastant detection identified using Dictyostelium discoideum JOURNAL OF CELL SCIENCE 126 5465-5476

Datta, S; Bull, JC; Budge, GE; Keeling, MJ (2013) Modelling the spread of American foulbrood in honeybees JOURNAL OF THE ROYAL SOCIETY INTERFACE 10 20130650

Agoti, CN; Gitahi, CW; Medley, GF; Cane, PA; Nokes, DJ (2013) Identification of group B respiratory syncytial viruses that lack the 60-nucleotide duplication after six consecutive epidemics of total BA dominance at coastal Kenya INFLUENZA AND OTHER RESPIRATORY VIRUSES 7 1008-1012

Sande, CJ; Mutunga, MN; Okiro, EA; Medley, GF; Cane, PA; Nokes, DJ (2013) Kinetics of the Neutralizing Antibody Response to Respiratory Syncytial Virus Infections in a Birth Cohort JOURNAL OF MEDICAL VIROLOGY 85 2020-2025

Piper, J; Elze, MC; Cauchy, P; Cockerill, PN; Bonifer, C; Ott, S (2013) Wellington: a novel method for the accurate identification of digital genomic footprints from DNase-seq data NUCLEIC ACIDS RESEARCH 41 e201

Sirinukunwattana, K; Savage, RS; Bari, MF; Snead, DRJ; Rajpoot, NM (2013) Bayesian Hierarchical Clustering for Studying Cancer Gene Expression Data with Unknown Statistics PLOS ONE 8 e75748

Panousopoulou, E; Tyson, RA; Bretschneider, T; Green, JBA (2013) The distribution of Dishevelled in convergently extending mesoderm DEVELOPMENTAL BIOLOGY 382 496-503

Flood, JS; Porphyre, T; Tildesley, MJ; Woolhouse, MEJ (2013) The performance of approximations of farm contiguity compared to contiguity defined using detailed geographical information in two sample areas in Scotland: implications for foot-and-mouth disease modelling BMC VETERINARY RESEARCH 9 198

Porphyre, T; Auty, HK; Tildesley, MJ; Gunn, GJ; Woolhouse, MEJ (2013) Vaccination against Foot-And-Mouth Disease: Do Initial Conditions Affect Its Benefit? PLOS ONE 8 e77616

Du, CJ; Hawkins, PT; Stephens, LR; Bretschneider, T (2013) 3D time series analysis of cell shape using Laplacian approaches BMC BIOINFORMATICS 14 296

Costa, MJ; Finkenstadt, B; Roche, V; Levi, F; Gould, PD; Foreman, J; Halliday, K; Hall, A; Rand, DA (2013) Inference on periodicity of circadian time series BIOSTATISTICS 14 792-806

Danon, L; Read, JM; House, TA; Vernon, MC; Keeling, MJ (2013) Social encounter networks: characterizing Great Britain PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 280 20131037

Bechtold, U et al. (2013) Arabidopsis HEAT SHOCK TRANSCRIPTION FACTORA1b overexpression enhances water productivity, resistance to drought, and infection JOURNAL OF EXPERIMENTAL BOTANY 64 3467-3481

Pontiroli, A; Khera, TT; Oakley, BB; Mason, S; Dowd, SE; Travis, ER; Erenso, G; Aseffa, A; Courtenay, O; Wellington, EMH (2013) Prospecting Environmental Mycobacteria: Combined Molecular Approaches Reveal Unprecedented Diversity PLOS ONE 8 e68648

Kerr, MI; Wall, MJ; Richardson, MJE (2013) Adenosine A(1) receptor activation mediates the developmental shift at layer 5 pyramidal cell synapses and is a determinant of mature synaptic strength JOURNAL OF PHYSIOLOGY-LONDON 591 3371-3380

Brown, P; Baxter, L; Hickman, R; Beynon, J; Moore, JD; Ott, S (2013) MEME-LaB: motif analysis in clusters BIOINFORMATICS 29 1696-1697

Hickman, R; Hill, C; Penfold, CA; Breeze, E; Bowden, L; Moore, JD; Zhang, PJ; Jackson, A; Cooke, E; Bewicke-Copley, F; Mead, A; Beynon, J; Wild, DL; Denby, KJ; Ott, S; Buchanan-Wollaston, V (2013) A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves PLANT JOURNAL 75 26-39

Woodcock, DJ; Vance, KW; Komorowski, M; Koentges, G; Finkenstadt, B; Rand, DA (2013) A hierarchical model of transcriptional dynamics allows robust estimation of transcription rates in populations of single cells with variable gene copy number BIOINFORMATICS 29 1519-1525

Webb, SD; Keeling, MJ; Boots, M (2013) The role of spatial population structure on the evolution of parasites with acquired immunity and demography JOURNAL OF THEORETICAL BIOLOGY 324 21-31

Jenkins, DJ; Finkenstadt, B; Rand, DA (2013) A temporal switch model for estimating transcriptional activity in gene expression BIOINFORMATICS 29 1158-1165

Laranjeiro, R; Tamai, TK; Peyric, E; Krusche, P; Ott, S; Whitmore, D (2013) Cyclin-dependent kinase inhibitor p20 controls circadian cell-cycle timing PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 110 6835-6840

Anderson, LJ; Dormitzer, PR; Nokes, DJ; Rappuoli, R; Roca, A; Graham, BS (2013) Strategic priorities for respiratory syncytial virus (RSV) vaccine development VACCINE 31 B209-B215

Loebel, A; Le Be, JV; Richardson, MJE; Markram, H; Herz, AVM (2013) Matched Pre- and Post-Synaptic Changes Underlie Synaptic Plasticity over Long Time Scales JOURNAL OF NEUROSCIENCE 33 6257-6266

Black, AJ; House, T; Keeling, MJ; Ross, JV (2013) Epidemiological consequences of household-based antiviral prophylaxis for pandemic influenza JOURNAL OF THE ROYAL SOCIETY INTERFACE 10 20121019

Darkins, R; Cooke, EJ; Ghahramani, Z; Kirk, PDW; Wild, DL; Savage, RS (2013) Accelerating Bayesian Hierarchical Clustering of Time Series Data with a Randomised Algorithm PLOS ONE 8 e59795

Bond, M; Croft, W; Tyson, R; Bretschneider, T; Davey, J; Ladds, G (2013) Quantitative analysis of human ras localization and function in the fission yeast Schizosaccharomyces pombe YEAST 30 145-156

Gould, PD; Ugarte, N; Domijan, M; Costa, M; Foreman, J; MacGregor, D; Rose, K; Griffiths, J; Millar, AJ; Finkenstadt, B; Penfield, S; Rand, DA; Halliday, KJ; Hall, AJW (2013) Network balance via CRY signalling controls the Arabidopsis circadian clock over ambient temperatures MOLECULAR SYSTEMS BIOLOGY 9 650

Webb, SD; Keeling, MJ; Boots, M (2013) A theoretical study of the role of spatial population structure in the evolution of parasite virulence THEORETICAL POPULATION BIOLOGY 84 36-45

Fuller, JA et al. (2013) Estimation of the National Disease Burden of Influenza-Associated Severe Acute Respiratory Illness in Kenya and Guatemala: A Novel Methodology PLOS ONE 8 e56882

Sande, CJ; Mutunga, MN; Medley, GF; Cane, PA; Nokes, DJ (2013) Group- and Genotype-Specific Neutralizing Antibody Responses Against Respiratory Syncytial Virus in Infants and Young Children With Severe Pneumonia JOURNAL OF INFECTIOUS DISEASES 207 489-492

Munywoki, PK; Ohuma, EO; Ngama, M; Bauni, E; Scott, JAG; Nokes, DJ (2013) Severe Lower Respiratory Tract Infection in Early Infancy and Pneumonia Hospitalizations among Children, Kenya EMERGING INFECTIOUS DISEASES 19 223-229

Quinnell, RJ; Carson, C; Reithinger, R; Garcez, LM; Courtenay, O (2013) Evaluation of rK39 Rapid Diagnostic Tests for Canine Visceral Leishmaniasis: Longitudinal Study and Meta-Analysis PLOS NEGLECTED TROPICAL DISEASES 7 e1992

Sutherland, WJ et al. (2013) Identification of 100 fundamental ecological questions JOURNAL OF ECOLOGY 101 58-67

2012

Okiro, EA; Ngama, M; Bett, A; Nokes, DJ (2012) The Incidence and Clinical Burden of Respiratory Syncytial Virus Disease Identified through Hospital Outpatient Presentations in Kenyan Children PLOS ONE 7 e52520

Onyango, CO; Njeru, R; Kazungu, S; Achilla, R; Bulimo, W; Welch, SR; Cane, PA; Gunson, RN; Hammitt, LL; Scott, JAG; Berkley, JA; Nokes, DJ (2012) Influenza Surveillance Among Children With Pneumonia Admitted to a District Hospital in Coastal Kenya, 2007-2010 JOURNAL OF INFECTIOUS DISEASES 206 S61-S67

Kirk, P; Griffin, JE; Savage, RS; Ghahramani, Z; Wild, DL (2012) Bayesian correlated clustering to integrate multiple datasets BIOINFORMATICS 28 3290-3297

Agoti, CN; Mwihuri, AG; Sande, CJ; Onyango, CO; Medley, GF; Cane, PA; Nokes, DJ (2012) Genetic Relatedness of Infecting and Reinfecting Respiratory Syncytial Virus Strains Identified in a Birth Cohort From Rural Kenya JOURNAL OF INFECTIOUS DISEASES 206 1532-1541

Danon, L; House, TA; Read, JM; Keeling, MJ (2012) Social encounter networks: collective properties and disease transmission JOURNAL OF THE ROYAL SOCIETY INTERFACE 9 2826-2833

Tildesley, MJ; Ryan, SJ (2012) Disease Prevention versus Data Privacy: Using Landcover Maps to Inform Spatial Epidemic Models PLOS COMPUTATIONAL BIOLOGY 8 e1002723

Ohuma, EO; Okiro, EA; Ochola, R; Sande, CJ; Cane, PA; Medley, GF; Bottomley, C; Nokes, DJ (2012) The Natural History of Respiratory Syncytial Virus in a Birth Cohort: The Influence of Age and Previous Infection on Reinfection and Disease AMERICAN JOURNAL OF EPIDEMIOLOGY 176 794-802

van Hoek, AJ; Ngama, M; Ismail, A; Chuma, J; Cheburet, S; Mutonga, D; Kamau, T; Nokes, DJ (2012) A Cost Effectiveness and Capacity Analysis for the Introduction of Universal Rotavirus Vaccination in Kenya: Comparison between Rotarix and RotaTeq Vaccines PLOS ONE 7 e47511

House, T; Inglis, N; Ross, JV; Wilson, F; Suleman, S; Edeghere, O; Smith, G; Olowokure, B; Keeling, MJ (2012) Estimation of outbreak severity and transmissibility: Influenza A(H1N1)pdm09 in households BMC MEDICINE 10 117

Baxter, L; Jironkin, A; Hickman, R; Moore, J; Barrington, C; Krusche, P; Dyer, NP; Buchanan-Wollaston, V; Tiskin, A; Beynon, J; Denby, K; Ott, S (2012) Conserved Noncoding Sequences Highlight Shared Components of Regulatory Networks in Dicotyledonous Plants PLANT CELL 24 3949-3965

Webb, C; Ngama, M; Ngatia, A; Shebbe, M; Morpeth, S; Mwarumba, S; Bett, A; Nokes, DJ; Seale, AC; Kazungu, S; Munywoki, P; Hammitt, LL; Scott, JAG; Berkley, JA (2012) Treatment Failure Among Kenyan Children With Severe Pneumonia-A Cohort Study PEDIATRIC INFECTIOUS DISEASE JOURNAL 31 E152-E157

Spencer, SEF; Marshall, J; Pirie, R; Campbell, D; Baker, MG; French, NP (2012) The spatial and temporal determinants of campylobacteriosis notifications in New Zealand, 2001-2007 EPIDEMIOLOGY AND INFECTION 140 1663-1677

Xue, M; Momiji, H; Rabbani, N; Barker, G; Rand, DA; Thornalley, PJ (2012) Control of ARE-linked gene expression by cytoplasm-nucleus translocational oscillations of Nrf2 FREE RADICAL BIOLOGY AND MEDICINE 53 S37-S37

Xue, M; Momiji, H; Barker, G; Rand, DA; Rabbani, N; Thornalley, PJ (2012) Multi-tiered protective response of Nrf2 transactivational activity in endothelial cells in vitro FREE RADICAL BIOLOGY AND MEDICINE 53 S233-S233

Xue, M; Shaheen, F; Momiji, H; Barker, G; Rand, DA; Rabbani, N (2012) Effect of nrf2 activators on protein oxidative damage in human endothelial cells in vitro FREE RADICAL BIOLOGY AND MEDICINE 53 S100-S101

Windram, O et al. (2012) Arabidopsis Defense against Botrytis cinerea: Chronology and Regulation Deciphered by High-Resolution Temporal Transcriptomic Analysis PLANT CELL 24 3530-3557

Martin, JF; Santos-Beneit, F; Rodriguez-Garcia, A; Sola-Landa, A; Smith, MCM; Ellingsen, TE; Nieselt, K; Burroughs, NJ; Wellington, EMH (2012) Transcriptomic studies of phosphate control of primary and secondary metabolism in Streptomyces coelicolor APPLIED MICROBIOLOGY AND BIOTECHNOLOGY 95 61-75

Iqbal, M; Mast, Y; Amin, R; Hodgson, DA; Wohlleben, W; Burroughs, NJ (2012) Extracting regulator activity profiles by integration of de novo motifs and expression data: characterizing key regulators of nutrient depletion responses in Streptomyces coelicolor NUCLEIC ACIDS RESEARCH 40 5227-5239

Rock, KS; Keeling, MJ; Wood, DA (2012) Modelling the future of the Hawaiian honeycreeper: An ecological and epidemiological problem ECOLOGICAL MODELLING 235 26-35

Vernon, MC; Keeling, MJ (2012) Impact of regulatory perturbations to disease spread through cattle movements in Great Britain PREVENTIVE VETERINARY MEDICINE 105 110-117

Keeling, MJ; Shattock, A (2012) Optimal but unequitable prophylactic distribution of vaccine EPIDEMICS 4 78-85

Onyango, CO; Welch, SR; Munywoki, PK; Agoti, CN; Bett, A; Ngama, M; Myers, R; Cane, PA; Nokes, DJ (2012) Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya JOURNAL OF MEDICAL VIROLOGY 84 823-831

Tildesley, MJ; Smith, G; Keeling, MJ (2012) Modeling the spread and control of foot-and-mouth disease in Pennsylvania following its discovery and options for control PREVENTIVE VETERINARY MEDICINE 104 224-239

Hammitt, LL; Kazungu, S; Morpeth, SC; Gibson, DG; Mvera, B; Brent, AJ; Mwarumba, S; Onyango, CO; Bett, A; Akech, DO; Murdoch, DR; Nokes, DJ; Scott, JAG (2012) A Preliminary Study of Pneumonia Etiology Among Hospitalized Children in Kenya CLINICAL INFECTIOUS DISEASES 54 S190-S199

Thomas, L; Hodgson, DA; Wentzel, A; Nieselt, K; Ellingsen, TE; Moore, J; Morrissey, ER; Legaie, R; Wohlleben, W; Rodriguez-Garcia, A; Martin, JF; Burroughs, NJ; Wellington, EMH; Smith, MCM (2012) Metabolic Switches and Adaptations Deduced from the Proteomes of Streptomyces coelicolor Wild Type and phoP Mutant Grown in Batch Culture MOLECULAR & CELLULAR PROTEOMICS 11 M111.013797

Du, CJ; Ferguson, JG; Hawkins, PT; Stephens, LR; Bretschneider, T (2012) Local Shape Representation in 3D: from Weighted Spherical Harmonics to Spherical Wavelets PROCEEDINGS OF THE BRITISH MACHINE VISION CONFERENCE 2012

2011

Downey, MJ; Jeziorska, DM; Ott, S; Tamai, TK; Koentges, G; Vance, KW; Bretschneider, T (2011) Extracting Fluorescent Reporter Time Courses of Cell Lineages from High-Throughput Microscopy at Low Temporal Resolution PLOS ONE 6 e27886

Tsibidis, GD; Burroughs, NJ; Gaze, W; Wellington, EMH (2011) Semi-automated Acanthamoeba polyphaga detection and computation of Salmonella typhimurium concentration in spatio-temporal images MICRON 42 911-920

Tildesley, MJ; Volkova, VV; Woolhouse, MEJ (2011) Potential for epidemic take-off from the primary outbreak farm via livestock movements BMC VETERINARY RESEARCH 7 76

Travis, ER et al. (2011) An Inter-Laboratory Validation of a Real Time PCR Assay to Measure Host Excretion of Bacterial Pathogens, Particularly of Mycobacterium bovis PLOS ONE 6 e27369

Cooke, EJ; Savage, RS; Kirk, PDW; Darkins, R; Wild, DL (2011) Bayesian hierarchical clustering for microarray time series data with replicates and outlier measurements BMC BIOINFORMATICS 12 399

Mwambi, H; Ramroop, S; White, LJ; Okiro, EA; Nokes, DJ; Shkedy, Z; Molenberghs, G (2011) A frequentist approach to estimating the force of infection for a respiratory disease using repeated measurement data from a birth cohort STATISTICAL METHODS IN MEDICAL RESEARCH 20 551-570

Morrissey, ER; Juarez, MA; Denby, KJ; Burroughs, NJ (2011) Inferring the time-invariant topology of a nonlinear sparse gene regulatory network using fully Bayesian spline autoregression BIOSTATISTICS 12 682-694

Yuan, YY; Savage, RS; Markowetz, F (2011) Patient-Specific Data Fusion Defines Prognostic Cancer Subtypes PLOS COMPUTATIONAL BIOLOGY 7 e1002227

House, T; Baguelin, M; Van Hoek, AJ; White, PJ; Sadique, Z; Eames, K; Read, JM; Hens, N; Melegaro, A; Edmunds, WJ; Keeling, MJ (2011) Modelling the impact of local reactive school closures on critical care provision during an influenza pandemic PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES 278 2753-2760

Munywoki, PK; Hamid, F; Mutunga, M; Welch, S; Cane, P; Nokes, DJ (2011) Improved Detection of Respiratory Viruses in Pediatric Outpatients with Acute Respiratory Illness by Real-Time PCR Using Nasopharyngeal Flocked Swabs JOURNAL OF CLINICAL MICROBIOLOGY 49 3365-3367

Burroughs, NJ; Kohler, K; Miloserdov, V; Dustin, ML; van der Merwe, PA; Davis, DM (2011) Boltzmann Energy-based Image Analysis Demonstrates that Extracellular Domain Size Differences Explain Protein Segregation at Immune Synapses PLOS COMPUTATIONAL BIOLOGY 7 e1002076

Alijani, AK; Richardson, MJE (2011) Rate response of neurons subject to fast or frozen noise: From stochastic and homogeneous to deterministic and heterogeneous populations PHYSICAL REVIEW E 84 11919

Hammitt, LL; Kazungu, S; Welch, S; Bett, A; Onyango, CO; Gunson, RN; Scott, JAG; Nokes, DJ (2011) Added Value of an Oropharyngeal Swab in Detection of Viruses in Children Hospitalized with Lower Respiratory Tract Infection JOURNAL OF CLINICAL MICROBIOLOGY 49 2318-2320

Nyiro, JU; Sanders, EJ; Ngetsa, C; Wale, S; Awuondo, K; Bukusi, E; Price, MA; Amornkul, PN; Nokes, DJ (2011) Seroprevalence, predictors and estimated incidence of maternal and neonatal Herpes Simplex Virus Type 2 infection in semi-urban women in Kilifi, Kenya BMC INFECTIOUS DISEASES 11 155

Komorowski, M; Costa, MJ; Rand, DA; Stumpf, MPH (2011) Sensitivity, robustness, and identifiability in stochastic chemical kinetics models PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 108 8645-8650

Bryan, SJ; Burroughs, NJ; Evered, C; Sacharz, J; Nenninger, A; Mullineaux, CW; Spence, EM (2011) Loss of the SPHF Homologue Slr1768 Leads to a Catastrophic Failure in the Maintenance of Thylakoid Membranes in Synechocystis sp PCC 6803 PLOS ONE 6 e19625

Keeling, MJ; White, PJ (2011) Targeting vaccination against novel infections: risk, age and spatial structure for pandemic influenza in Great Britain JOURNAL OF THE ROYAL SOCIETY INTERFACE 8 661-670

Burroughs, NJ; Ferreira, M; Oliveira, BMPM; Pinto, AA (2011) Autoimmunity arising from bystander proliferation of T cells in an immune response model MATHEMATICAL AND COMPUTER MODELLING 53 1389-1393

Burroughs, NJ; Oliveira, BMPM; Pinto, AA; Ferreira, M (2011) Immune response dynamics MATHEMATICAL AND COMPUTER MODELLING 53 1410-1419

Harper, CV; Finkenstadt, B; Woodcock, DJ; Friedrichsen, S; Semprini, S; Ashall, L; Spiller, DG; Mullins, JJ; Rand, DA; Davis, JRE; White, MRH (2011) Dynamic Analysis of Stochastic Transcription Cycles PLOS BIOLOGY 9 e1000607

Pontiroli, A; Travis, ER; Sweeney, FP; Porter, D; Gaze, WH; Mason, S; Hibberd, V; Holden, J; Courtenay, O; Wellington, EMH (2011) Pathogen Quantitation in Complex Matrices: A Multi-Operator Comparison of DNA Extraction Methods with a Novel Assessment of PCR Inhibition PLOS ONE 6 e17916

House, T; Keeling, MJ (2011) Epidemic prediction and control in clustered populations JOURNAL OF THEORETICAL BIOLOGY 272 1-7

Spencer, SEF; O'Neill, PD (2011) THE PROBABILITY OF CONTAINMENT FOR MULTITYPE BRANCHING PROCESS MODELS FOR EMERGING EPIDEMICS JOURNAL OF APPLIED PROBABILITY 48 173-188

Breeze, E et al. (2011) High-Resolution Temporal Profiling of Transcripts during Arabidopsis Leaf Senescence Reveals a Distinct Chronology of Processes and Regulation PLANT CELL 23 873-894

Levi, F; Mosekilde, E; Rand, DA (2011) Advancing systems medicine and therapeutics through biosimulation INTRODUCTION INTERFACE FOCUS 1 3-6

Domijan, M; Rand, DA (2011) Balance equations can buffer noisy and sustained environmental perturbations of circadian clocks INTERFACE FOCUS 1 177-186

Klyuch, BP; Richardson, MJE; Dale, N; Wall, MJ (2011) The dynamics of single spike-evoked adenosine release in the cerebellum JOURNAL OF PHYSIOLOGY-LONDON 589 283-295

House, T; Keeling, MJ (2011) Insights from unifying modern approximations to infections on networks JOURNAL OF THE ROYAL SOCIETY INTERFACE 8 67-73

Rand, DA (2011) Network Control Analysis for Time-Dependent Dynamical States DYNAMICS, GAMES AND SCIENCE II 2 1-24

Didelot, X; Everitt, RG; Johansen, AM; Lawson, DJ (2011) Likelihood-free estimation of model evidence BAYESIAN ANALYSIS 6 49-76

Almeida, JP; Fisher, AM; Pinto, AA; Rand, DA (2011) Anosov and Circle Diffeomorphisms DYNAMICS, GAMES AND SCIENCE I 1 11-23

Burroughs, NJ; Ferreira, M; Martins, J; Oliveira, BMPM; Pinto, AA; Stollenwerk, N (2011) Dynamics and Biological Thresholds DYNAMICS, GAMES AND SCIENCE I 1 183-191

Pinto, AA; Rand, DA (2011) Uniformly hyperbolic diffeomorphisms in every surfaces JOURNAL OF DIFFERENCE EQUATIONS AND APPLICATIONS 17 1031-1047

Burroughs, NJ; Ferreira, M; Oliveira, BMPM; Pinto, AA (2011) A transcritical bifurcation in an immune response model JOURNAL OF DIFFERENCE EQUATIONS AND APPLICATIONS 17 1101-1106

2010

Pinto, AA; Burroughs, NJ; Ferreira, M; Oliveira, BMPM (2010) Dynamics of Immunological Models ACTA BIOTHEORETICA 58 391-404

Du, CJ; Marcello, M; Spiller, DG; White, MRH; Bretschneider, T (2010) Interactive Segmentation of Clustered Cells via Geodesic Commute Distance and Constrained Density Weighted Nystrom Method CYTOMETRY PART A 77A 1137-1147

Kohler, K; Xiong, SQ; Brzostek, J; Mehrabi, M; Eissmann, P; Harrison, A; Cordoba, SP; Oddos, S; Miloserdov, V; Gould, K; Burroughs, NJ; van der Merwe, PA; Davis, DM (2010) Matched Sizes of Activating and Inhibitory Receptor/Ligand Pairs Are Required for Optimal Signal Integration by Human Natural Killer Cells PLOS ONE 5 e15374

Edwards, KD; Akman, OE; Knox, K; Lumsden, PJ; Thomson, AW; Brown, PE; Pokhilko, A; Kozma-Bognar, L; Nagy, F; Rand, DA; Millar, AJ (2010) Quantitative analysis of regulatory flexibility under changing environmental conditions MOLECULAR SYSTEMS BIOLOGY 6 424

Richardson, MJE; Swarbrick, R (2010) Firing-Rate Response of a Neuron Receiving Excitatory and Inhibitory Synaptic Shot Noise PHYSICAL REVIEW LETTERS 105 178102

Koohy, H; Dyer, NP; Reid, JE; Koentges, G; Ott, S (2010) An alignment-free model for comparison of regulatory sequences BIOINFORMATICS 26 2391-2397

Agoti, CN; Mbisa, JL; Bett, A; Medley, GF; Nokes, DJ; Cane, PA (2010) Intrapatient Variation of the Respiratory Syncytial Virus Attachment Protein Gene JOURNAL OF VIROLOGY 84 10425-10428

Picot, E; Krusche, P; Tiskin, A; Carre, I; Ott, S (2010) Evolutionary analysis of regulatory sequences (EARS) in plants PLANT JOURNAL 64 165-176

Nair, H; Gessner, BD; Nokes, DJ; Theodoratou, E; Rudan, I; Madhi, SA; Simoes, EAF; Campbell, H (2010) Childhood mortality due to respiratory syncytial virus Reply LANCET 376 872-873

Morrissey, ER; Juarez, MA; Denby, KJ; Burroughs, NJ (2010) On reverse engineering of gene interaction networks using time course data with repeated measurements BIOINFORMATICS 26 2305-2312

Carson, C; Quinnell, RJ; Holden, J; Garcez, LM; Deborggraeve, S; Courtenay, O (2010) Comparison of Leishmania OligoC-TesT PCR with Conventional and Real-Time PCR for Diagnosis of Canine Leishmania Infection JOURNAL OF CLINICAL MICROBIOLOGY 48 3325-3330

Nokes, DJ; Peenze, I; Netshifhefhe, L; Abwao, J; De Beer, MC; Seheri, M; Williams, TN; Page, N; Steele, D (2010) Rotavirus Genetic Diversity, Disease Association, and Temporal Change in Hospitalized Rural Kenyan Children JOURNAL OF INFECTIOUS DISEASES 202 S180-S186

Turner, DA; Paszek, P; Woodcock, DJ; Nelson, DE; Horton, CA; Wang, YJ; Spiller, DG; Rand, DA; White, MRH; Harper, CV (2010) Physiological levels of TNF alpha stimulation induce stochastic dynamics of NF-kappa B responses in single living cells JOURNAL OF CELL SCIENCE 123 2834-2843

Vance, KW; Shaw, HM; Rodriguez, M; Ott, S; Goding, CR (2010) The Retinoblastoma Protein Modulates Tbx2 Functional Specificity MOLECULAR BIOLOGY OF THE CELL 21 2770-2779

Rorres, C; Pelletier, STK; Keeling, MJ; Smith, G (2010) Estimating the kernel parameters of premises-based stochastic models of farmed animal infectious disease epidemics using limited, incomplete, or ongoing data THEORETICAL POPULATION BIOLOGY 78 46-53

Morelli, G; Didelot, X; Kusecek, B; Schwarz, S; Bahlawane, C; Falush, D; Suerbaum, S; Achtman, M (2010) Microevolution of Helicobacter pylori during Prolonged Infection of Single Hosts and within Families PLOS GENETICS 6 e1001036

Didelot, X; Maiden, MCJ (2010) Impact of recombination on bacterial evolution TRENDS IN MICROBIOLOGY 18 315-322

Akman, OE; Rand, DA; Brown, PE; Millar, AJ (2010) Robustness from flexibility in the fungal circadian clock BMC SYSTEMS BIOLOGY 4 88

Paszek, P; Ryan, S; Ashall, L; Sillitoe, K; Harper, CV; Spiller, DG; Rand, DA; White, MRH (2010) Population robustness arising from cellular heterogeneity PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 107 11644-11649

Savage, RS; Ghahramani, Z; Griffin, JE; de la Cruz, BJ; Wild, DL (2010) Discovering transcriptional modules by Bayesian data integration BIOINFORMATICS 26 i158-i167

Spiller, DG; Wood, CD; Rand, DA; White, MRH (2010) Measurement of single-cell dynamics NATURE 465 736-745

Yang, J; Kohler, K; Davis, DM; Burroughs, NJ (2010) An improved strip FRAP method for estimating diffusion coefficients: correcting for the degree of photobleaching JOURNAL OF MICROSCOPY 238 240-253

Berkley, JA; Munywoki, P; Ngama, M; Kazungu, S; Abwao, J; Bett, A; Lassauniere, R; Kresfelder, T; Cane, PA; Venter, M; Scott, JAG; Nokes, DJ (2010) Viral Etiology of Severe Pneumonia Among Kenyan Infants and Children JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION 303 2051-2057

Keeling, MJ; Danon, L; Vernon, MC; House, TA (2010) Individual identity and movement networks for disease metapopulations PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 107 8866-8870

Nair, H et al. (2010) Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis LANCET 375 1545-1555

Sanchez-Romero, MA; Busby, SJW; Dyer, NP; Ott, S; Millard, AD; Grainger, DC (2010) Dynamic Distribution of SeqA Protein across the Chromosome of Escherichia coli K-12 MBIO 1 e00012-10

Ross, JV; House, T; Keeling, MJ (2010) Calculation of Disease Dynamics in a Population of Households PLOS ONE 5 e9666

House, T; Keeling, MJ (2010) The Impact of Contact Tracing in Clustered Populations PLOS COMPUTATIONAL BIOLOGY 6 e1000721

Carson, C; Quinnell, RJ; Day, MJ; Courtenay, O (2010) Comparison of monoclonal and polyclonal antibodies for the detection of canine IgG1 and IgG2, and associations with infection outcome in Leishmania infantum naturally infected dogs VETERINARY IMMUNOLOGY AND IMMUNOPATHOLOGY 133 264-268

House, T; Hall, I; Danon, L; Keeling, MJ (2010) Contingency planning for a deliberate release of smallpox in Great Britain-the role of geographical scale and contact structure BMC INFECTIOUS DISEASES 10 25

Bern, C; Courtenay, O; Alvar, J (2010) Of Cattle, Sand Flies and Men: A Systematic Review of Risk Factor Analyses for South Asian Visceral Leishmaniasis and Implications for Elimination PLOS NEGLECTED TROPICAL DISEASES 4 e599

Okiro, EA; White, LJ; Ngama, M; Cane, PA; Medley, GF; Nokes, DJ (2010) Duration of shedding of respiratory syncytial virus in a community study of Kenyan children BMC INFECTIOUS DISEASES 10 15

Tildesley, MJ; House, TA; Bruhn, MC; Curry, RJ; O'Neil, M; Allpress, JLE; Smith, G; Keeling, MJ (2010) Impact of spatial clustering on disease transmission and optimal control PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 107 1041-1046

Reid, JE; Evans, KJ; Dyer, N; Wernisch, L; Ott, S (2010) Variable structure motifs for transcription factor binding sites BMC GENOMICS 11 30

Nieselt, K et al. (2010) The dynamic architecture of the metabolic switch in Streptomyces coelicolor BMC GENOMICS 11 10

Pinto, AA; Rand, DA; Ferreira, F (2010) Arc exchange systems and renormalization JOURNAL OF DIFFERENCE EQUATIONS AND APPLICATIONS 16 347-371

Pinto, AA; Rand, DA (2010) Train tracks with C1+ self-renormalizable structures JOURNAL OF DIFFERENCE EQUATIONS AND APPLICATIONS 16 945-962

Tyson, RA; Epstein, DBA; Anderson, KI; Bretschneider, T (2010) High Resolution Tracking of Cell Membrane Dynamics in Moving Cells: an Electrifying Approach MATHEMATICAL MODELLING OF NATURAL PHENOMENA 5 34-55