School of Public Health

MRC Centre for Outbreak Analysis and Modelling

coam smallerOur mission is to be an international resource and centre of excellence for research on the epidemiological analysis and modelling of novel infectious disease outbreaks. (more information)

Recent Publications

27 Oct 2013
Aguas R., N.M Ferguson “Feature selection methods for identifying genetic determinants of host species in RNA viruses.” PLoS Comput Biol 9(10):e1003254 (2013) (pdf)

07 Oct 2013
Mangal T.D. Aylward R.B., N.C. Grassly "The Potential Impact of Routine Immunization with Inactivated Poliovirus Vaccine on Wild-type or Vaccine-derived Poliovirus Outbreaks in a Post eradication Setting." Am J Epidemiol DOI: 10.1093/aje/kwt20 (2013) (pdf)

26 Sep 2013

Eyre D.W., Cule M.L., Wilson D.J., Griffiths D., Vaughan A., O'Connor L., Ip C.L., Golubchik T., Batty E.M., Finney J.M., Wyllie D.H., Didelot X., Piazza P., Bowden R., Dingle K.E., Harding R.M., Crook D.W., Wilcox M.H., Peto T.E., A.S. Walker “Diverse sources of C. difficile infection identified on whole-genome sequencing.” N Engl J Med 369(13):1195-1205 (2013) (pdf)

15 Sep 2013
Cori A., Ferguson N.M., Fraser C., S. Cauchemez “A New Framework and Software to Estimate Time-Varying Reproduction Numbers During Epidemics” Am J Epidemiol doi:10.1093/aje/kwt133 (2013) (pdf)

01 Sep 2013
M.D. Van Kerkhove, “Brief literature review for the WHO global influenza research agenda - highly pathogenic avian influenza H5N1 risk in humans.” Influenza Other Respi Viruses 7 Suppl 2:26-33 ( 2013)

Aug 23, Aug 2013
Marshall J.M.White M.T.Ghani A.C., Schlein Y., Muller G.C., J.C. Beier ”Quantifying the mosquito's sweet tooth: modelling the effectiveness of attractive toxic sugar baits (ATSB) for malaria vector control.” Malar J 12(1):291 (2013) (pdf)

Aug 14, 2013
Beshir K.B., Sutherland C.J., Sawa P., Drakeley C.J., Okell L., Mweresa C.K., Omar S.A., Shekalaghe S.A., Kaur H., Ndaro A., Chilongola J., Schallig H.D., Sauerwein R.W., Hallett R.L., T. Bousema “Residual Plasmodium falciparum parasitemia in Kenyan children after artemisinin-combination therapy is associated with increased transmission to mosquitoes and parasite recurrence.” J Infect Dis [Epub ahead of print] (2013) (pdf)

Aug 01, 2013
Doddington B.J., Bosch J., Oliver J.A., Grassly N.C., Garcia G., Schmidt B.R., Garner T.W.J, M.C. Fisher “Context-dependent amphibian host population response to an invading pathogen“ Ecology94(8):1795-1804 (2013) (pdf)

Aug 08, 2013
White M.T.Griffin J.T.A.C. Ghani “The design and statistical power of treatment re-infection studies of the association between pre-erythrocytic immunity and infection with Plasmodium falciparum.” Malar J 12(1):278 (2013) (pdf)

July 23, 2013

Dorigatti I.Cauchemez S.N.M Ferguson “Increased transmissibility explains the third wave of infection by the 2009 H1N1 pandemic virus in England.” Proc Natl Acad Sci (2013) (abstract and pdf)

July 15, 2013
Gambhir M., Swerdlow D.L., Finelli L., Van Kerkhove M.D., Biggerstaff M., Cauchemez S.N.M Ferguson “Multiple Contributory Factors to the Age Distribution of Disease Cases: A Modeling Study in the Context of Influenza A(H3N2v)” CLINICAL INFECTIOUS DISEASES 57:S23-S27 (2013) (abstract)

July 15, 2013
Celum C., Hallett T.B., J.M Baeten “HIV-1 Prevention With ART and PrEP: Mathematical Modeling Insights Into Resistance, Effectiveness, and Public Health Impact” JOURNAL OF INFECTIOUS DISEASES 208(2):189-191 (2013) (pdf)

July 08. 2013
Behrens W., Schweinitzer T., Bal J., Dorsch M., Bleich A., Kops F., Brenneke B., Didelot X., Suerbaum S., C. Josenhans "Role of energy sensor TlpD of Helicobacter pylori in gerbil colonization and genome analyses after adaptation in the gerbil" Infect Immun [e-pub ahead of print] (pdf)

July 01, 2013
Sheppard S.K., Didelot X., Meric G., Torralbo A., Jolley K.A., Kelly D.J., Bentley S.D., Maiden M.C., Parkhill J., D. Falush “Genome-wide association study identifies vitamin B5 biosynthesis as a host specificity factor in Campylobacter.” Proc Natl Acad Sci U S A 01 (2013) (pdf)

July 01, 2013
Hallett T.B.J.W Eaton “A Side Door Into Care Cascade for HIV-Infected Patients?” J Acquir Immune Defic Syndr 63 Suppl (2013) (abstract)

Jun 04, 2013
Walker P.G., Jost C., Ghani A.C.Cauchemez S., Bett B., Azhar M., Murahman J., Widiastuti T., Daju D., J. Mariner "Estimating the Transmissibility of H5N1 and the Effect of Vaccination in Indonesia." Transbound Emerg Dis (2013) (pdf)

Jun 01, 2013
Robinson K., Fyson N., Cohen T., Fraser C., C. Colijn “How the dynamics and structure of sexual contact networks shape pathogen phylogenies.” PLoS Comput Biol 9(6):e1003105 (2013) (pdf)

Jun 01, 2013

Cowling B.J., Ho L.M., Riley S., G.M. Leung “Statistical algorithms for early detection of the annual influenza peak season in Hong Kong using sentinel surveillance data.” Hong Kong Med J 19 Suppl 4:4-5 (2013) (pdf)

Jun 01, 2013
Riley S., Cowling B.J., Chan K.H., Peiris J.S., G.M.  Leung “Viral evolution from one generation of human influenza infection to the next.” Hong Kong Med J 19 Suppl 4:6-10 (2013) (pdf)

Jun 01, 2013
Kwok KO, Leung G.M., Mak P., S. Riley "Antiviral stockpiles for influenza pandemics from the household perspective: Treatment alone versus treatment with prophylaxis." Epidemics 5(2):92-97 (2013) (pdf)

May 28, 2013
Fournié G., Guitian J., Desvaux S., Cuong V.C., Dung D.O.H., Pfeiffer D.U., Mangtani P., A.C. Ghani"Interventions for avian influenza A (H5N1) risk management in live bird market networks" Proc Natl Acad Sci U S A 110(22):9177-9182 28 May 2013 (pdf)

May 07, 2013
Shepheard M.A., Fleming V.M., Connor T.R., Corander J., Feil E.J., Fraser C., W.P. Hanage "Historical Zoonoses and Other Changes in Host Tropism of Staphylococcus aureus, Identified by Phylogenetic Analysis of a Population Dataset." PLoS One 8(5):e62369 (2013) (open access pdf)

May 02, 2013
Alizon S., C. Fraser. "Within-host and between-host evolutionary rates across the HIV-1 genome" Retrovirology. 10(1):49 (2013) (provisional pdf)

May 01, 2013
Riley P, Ben-Nun M, Armenta R, Linker JA, Eick AA, Sanchez JL, George D, Bacon DP, S. Riley"Multiple Estimates of Transmissibility for the 2009 Influenza Pandemic Based on Influenza-like-Illness Data from Small US Military Populations" PLoS Computational Biology 9(5):9 (2013) (open access pdf)

April 22, 2013
Nouvellet P.Donnelly C.A., De Nardi M., Rhodes C.J., De Benedictis P., Citterio C., Obber F., Lorenzetto M., Pozza M.D., Cauchemez S., G. Cattoli. "Rabies and canine distemper virus epidemics in the red fox population of northern Italy (2006-2010)" PLoS ONE 8(4):e61588 (2013) (open access pdf)

April 22, 2013
Rao V.B, Schellenberg D., A.C. Ghani. "Overcoming health systems barriers to successful malaria treatment".Trends Parasitol. 29 (4) 164–180 (2013) (pdf)

April 16, 2013
White M.T., Bejon P., Olotu A., Griffin J.T., Riley E.M., Kester K.E., Ockenhouse C.F., A.C. Ghani. " The Relationship between RTS,S Vaccine-Induced Antibodies, CD4(+) T Cell Responses and Protection against Plasmodium falciparum Infection." PLoS ONE 8(4):e61395 (2013) (open access pdf)

April 05, 2013
Balabanova .D, Mills .A, Conteh .L, Akkazieva .B, Banteyerga .H, Dash .U, Gilson .L, Harmer .A, Ibraimova .A, et al. "Good Health at Low Cost 25 years on: lessons for the future of health systems strengthening." The Lancet [Epub ahead of print] (pdf)

April 01, 2013
Didelot X "Genomic analysis to improve the management of outbreaks of bacterial infection." Expert Rev Anti Infect Ther 11(4):335-337 (2013) (pdf)

April 01, 2013
Koukounari A., Moustaki I., Grassly N.C.Blake I.M., Basáñez M.G., Gambhir M., Mabey D.C., Bailey R.L., Burton M.J.,Solomon A.W., C.A. Donnelly, "Using a Nonparametric Multilevel Latent Markov Model to Evaluate Diagnostics for Trachoma" Am J Epidemiol [Epub ahead of print] (pdf)

April 01, 2013
Gatton M.L, Chitnis N., Churcher T., Donnelly M.J, Ghani A.C., Godfray H.C., Gould F., Hastings I., Marshall J., H. Ranson, "The importance of mosquito behavioural adaptations to malaria control in Africa", Evolution 67 (4) 1218-1230 (2013) (pdf)

March 23, 2013
Cauchemez S., S. Epperson, M. Biggerstaff, D. Swerdlow,L Finelli, N.M. Ferguson "Using Routine Surveillance Data to Estimate the Epidemic Potential of Emerging Zoonoses: Application to the Emergence of US Swine Origin Influenza A H3N2v Virus." PLoS Med 10(3):e1001399 (2013) (open-access pdf)

March 19, 2013
Walker P.G. , J.T. Griffin, M. Cairns, S.J. Rogerson, A.M. van Eijk ,F. Ter Kuile, A.C. Ghani. "A model of parity-dependent immunity to placental malaria." Nat Commun 4:1609 19 (2013) (open-access pdf)

March 04, 2013
Estill J., M. Egger, N. Blaser, L.S. Vizcaya, D. Garone, R. Wood, J.Campbell, T.B. Hallett, O. Keiser. "Cost-effectiveness of point-of-care viral load monitoring of ART in resource-limited settings: Mathematical modelling study." AIDS (2013) (abstract) (pdf)

March 01, 2013
Zhang X.S.,D. De Angelis, P.J. White, A Charlett, R.G. Pebody,J. McCauley. "Co-circulation of influenza A virus strains and emergence of pandemic via reassortment: The role of cross-immunity." Epidemics 5(1):20-33 (2013) (abstract) (pdf)

February 28, 2013
Estill J., Egger M., Johnson L.F., Gsponer T., Wandeler G., Davies M-A., Boulle A., Wood R, Garone D., Stringer J.S.A., Hallett T.B., O Keiser, "Monitoring of Antiretroviral Therapy and Mortality in HIV Programmes in Malawi, South Africa and Zambia: Mathematical Modelling Study" PLoS ONE, 8 (2) (2103) (open-access pdf)

February 28, 2013
Bejon, P., M.T. White, A.Olutu, K. Bojang, J.P.A. Lusingu, N. Salim, N. N. Otsyula, S.T. Agnandji, K. P. Asante, S. Owusu-Agyei, S. Abdulla, and A. Ghani.,"Efficacy of RTS,S malaria vaccines: individual-participant pooled analysis of phase 2 data" The Lancet Infectious Diseases, (in-press) (pdf)

February 07, 2013
Pepin K.M, J. Wang, C.T. Webb, J.A. Hoeting, M. Poss, P.J. Hudson, W. Hong, H. Zhu, Y. Guan, S. Riley., "Anticipating the Prevalence of Avian Influenza Subtypes H9 and H5 in Live-Bird Markets"PLoS ONE 8(2):8 pages (open-access pdf)

February 07, 2013
Pepin K.M., S. Riley, B.T. Grenfell, "Effects of influenza antivirals on individual and population immunity over many epidemic waves." Epidemiology and Infection 141(2):366-376 (2013) (pdf)

February 05, 2013
de Muinck, E. J., K. Lagesen, J. E. Afset, X. Didelot, K. S. Ronningen, K. Rudi, N. C. Stenseth, and P. Trosvik. "Comparisons of Infant Escherichia Coli Isolates Link Genomic Profiles with Adaptation to the Ecological Niche." BMC Genomics 14, no. 1 (2013): 81. (abstract) (open access pdf)

January 28, 2013
Cremin I., R. Alsallaq, M. Dybul, P. Piot, G. Garnett, T.B. Hallett. "The new role of antiretrovirals in combination HIV prevention: a mathematical modelling analysis." AIDS 27(3):447-458 (2013) (pdf)

January 01, 2013
Godfray H.C., Donnelly C.A., Kao R.R., Macdonald D.W., McDonald R.A., Petrokofsky G., Wood J.L., Woodroffe R., Young D.B., A.R McLean “A restatement of the natural science evidence base relevant to the control of bovine tuberculosis in Great Britain” Proc Biol Sci 280(1768):20131634 (2013)

January 01, 2013

Magiorkinis G., Sypsa V., Magiorkinis E., Paraskevis D., Katsoulidou A., Belshaw R., Fraser C., Pybus O.G., A. Hatzakis "Integrating phylodynamics and epidemiology to estimate transmission diversity in viral epidemics." PLoS Comput Biol 9 (1) e1002876 (2013)

January 01, 2013
Pybus O.G., C. Fraser., A. Rambaut, "Evolutionary epidemiology: preparing for an age of genomic plenty" Philos Trans R Soc Lond B Biol Sci 368 (1614): 20120193 (2013) (full text and pdf)

January 01, 2013
Strelioff C.C., Vijaykrishna D., Riley S., Guan Y., Peiris J.S., J.O. Lloyd-Smith "Inferring patterns of influenza transmission in swine from multiple streams of surveillance data." Proc Biol Sci280(1762):20130872 (2013) (pdf)

January 01, 2013 
Price, J. R., X. Didelot, D.W. Crook, M. J. Llewelyn, and J. Paul. "Whole Genome Sequencing in the Prevention and Control of Staphylococcus Aureus Infection." J Hosp Infect 83, no. 1 (2013): 14-21 (abstract)

December 28, 2012 
Roddy, P., N. Howard, M.D. Van Kerkhove, J. Lutwama, J. Wamala, Z. Yoti, R. Colebunders, P.P. Palma, E. Sterk, and B. Jeffs. "Clinical Manifestations and Case Management of Ebola Haemorrhagic Fever Caused by a Newly Identified Virus Strain, Bundibugyo, Uganda, 2007–2008."PLoS One 7, no. 12 (2012):  (open access full text) (pdf)

December 26, 2012 
Van Kerkhove, M. D., E. Broberg, O. G. Engelhardt, J. Wood, and A. Nicoll. "The Consortium for the Standardization of Influenza Seroepidemiology (Consise): A Global Partnership to Standardize Influenza Seroepidemiology and Develop Influenza Investigation Protocols to Inform Public Health Policy." Influenza Other Respi Viruses,  (2012) (wiley online library - full text) (wiley online library - pdf)

December 21, 2012 
Didelot, X., D. Eyre, M. Cule, C. Ip, A. Ansari, D. Griffiths, A. Vaughan, L. O'Connor, T. Golubchik, E. Batty, P. Piazza, D. Wilson, R. Bowden, P. Donnelly, K. Dingle, M. Wilcox, S. Walker, D. Crook, T. Peto, and R. Harding. "Microevolutionary Analysis of Clostridium Difficile Genomes to Investigate Transmission." Genome Biol 13, no. 12 (2012): R118. (abstract) (open-access pdf)

December 20, 2012 
Sheppard, S. K., X. Didelot, K. A. Jolley, A. E. Darling, B. Pascoe, G. Meric, D. J. Kelly, A. Cody, F. M. Colles, N. J. Strachan, I. D. Ogden, K. Forbes, N. P. French, P. Carter, W. G. Miller, N. D. McCarthy, R. Owen, E. Litrup, M. Egholm, J. P. Affourtit, S. D. Bentley, J. Parkhill, M. C. Maiden, and D. Falush. "Progressive Genome-Wide Introgression in Agricultural Campylobacter Coli." Mol Ecol,  (2012). (abstract)

December 13, 2012 
Cauchemez, S., P. Horby, A. Fox, Q. Mai le, T. Thanh le, P. Q. Thai, N. M. Hoa le, N. T. Hien, and N. M. Ferguson. "Influenza Infection Rates, Measurement Errors and the Interpretation of Paired Serology." PLoS Pathog 8, no. 12 (2012): e1003061. (open access full text) (pdf)

December 07, 2012 
Karolemeas, K., C. A. Donnelly, A. J. K. Conlan, A. P. Mitchell, R. S. Clifton-Hadley, P. Upton, J. L. N. Wood, and T. J. McKinley. "The Effect of Badger Culling on Breakdown Prolongation and Recurrence of Bovine Tuberculosis in Cattle Herds in Great Britain." PLoS One 7, no. 12 (2012). (open access full text) (pdf)

December 04, 2012 
Okell, L. C., T. Bousema, J. T. Griffin, A. L. Ouedraogo, A. C. Ghani, and C. J. Drakeley. "Factors Determining the Occurrence of Submicroscopic Malaria Infections and Their Relevance for Control." Nat Commun 3,  (2012): 1237. (open access full text) (pdf)

December 01, 2012 
Ratmann, O., G. Donker, A. Meijer, C. Fraser, and K. Koelle. "Phylodynamic Inference and Model Assessment with Approximate Bayesian Computation: Influenza as a Case Study." PLoS Comput Biol 8, no. 12 (2012) (open access full text) (pdf)

December 2012

(first published online June 12, 2012)
Read, J. M., W. J. Edmunds, S. Riley, J. Lessler, and D. A. Cummings. "Close Encounters of the Infectious Kind: Methods to Measure Social Mixing Behaviour." Epidemiol Infect 140, no. 12 (2012): 2117-30. (abstract)

November 29, 2012
Dingle, K. E., X. Didelot, M. A. Ansari, D. W. Eyre, A. Vaughan, D. Griffiths, C. L. Ip, E. M. Batty, T. Golubchik, R. Bowden, K. A. Jolley, D. W. Hood, W. N. Fawley, A. S. Walker, T. E. Peto, M. H. Wilcox, and D. W. Crook. "Recombinational Switching of the Clostridium Difficile S-Layer and a Novel Glycosylation Gene Cluster Revealed by Large Scale Whole Genome Sequencing." J Infect Dis,  (2012) (abstract)

November 01, 2012 
Wolbers, M., I. Kleinschmidt, C. P. Simmons, and C. A. Donnelly. "Considerations in the Design of Clinical Trials to Test Novel Entomological Approaches to Dengue Control." PLoS Negl Trop Dis 6, no. 11 (2012): e1937 (open access full text) (pdf)

Principal Investigators

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