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

24 Jul 2014
Imai N, White MT, Ghani AC, Drakely CJ "Transmission and Contro of Plasmodium knowlesi: A Mathematical Modelling Study" PLoS Negl Trop Dis 8(7) e2978 (2014) (pdf)

22 Jul 2014
Blake IM, Martin R, Goel A, Khetsuriani N, Everts J, Wolff C, Wassilak S, Aylward RB, Grassly NC "The role of older children and adults in wild poliovirus transmissions" Proc Natl Acad Sci USA 111(29) 10604-10609 (2014) (pdf)

19 Jul 2014
Jones A, KIm S, Jay J, Huh J, Dybul M, Cremin I, Hallett T, Abdullah F, ... Piot P "Transformation of HIV from pandemic to low-endemic levels: a public health approach to combination prevention" The Lancet 384(9939) 272-279 (2014) (pdf)

19 July 2014
Anderson SJ, Cremin I, Hallett TB, Fecht D, Cherutich P, Kimanga D et al "Maximising the effect of combination HIV prevention through prioritisation of the people and places in greatest need: a modelling study" The Lancet 384(9939) 249-256 (2014) (pdf)

10 Jul 2014
John J, Giri S, Karthikeyan AS, Iturriza-Gomara M, Muliyil J, Abrahan A, Grassly NC, Kang G "Effect of a single inactivated poliovirus vaccine dose on intestinal immunity against poliovirus in children previously given oral vaccine: an open-label, randomised controlled trial" Lancet (2014) (pdf)

10 Jul 2014
White MT, Bejon P, Olotu A, Griffin JT, Bojang K, Lusingu J, ... Ghani AC "A combined analysis of immunogenicity, antibody kinetics and vaccine efficacy from phase 2 trials of the RTS,S malaria vaccine" BMC Medicine 12(1), 117 (2014) (pdf)

9 Jul 2014
Cao Q, He L, You Y, Gong Y, Liu J, Zhang J, Didelot X, Wu Z, Li Y, et al "Progressive genomic convergence of two Helicobacter pylori strains during mixed infection of a patient with chronic gastritis" Gut 10.1136/gutjnl-2014-307345 (2014) (pdf)

6 Jul 2014
Clapham HE, Tricou V, Nguyen VVC, Simmons CP, Ferguson NM "Within-host viral dynamics of dengue serotype 1 infection" Journal of the Royal Society Interface 11(96):11 pages (2014) (pdf)

20 Jun 2014
Slater HC, Walker PG, Bousema T, Okell LC, Ghani AC "The Potential IMpact of Adding Ivermectin to a Mass Treatment INtervention to Reduce Malaria Transmission: a Modelling Study" Journal of Infectious Diseases (2014) (pdf)

13 Jun 2014
Churcher TS, Cohen JM, Novotny J, Ntschalintschali N, Kunene S, Cauchemez S "Public health. Measuring the path toward malaria elimination" Science 344 (6189) 1230-1232 (2014) (pdf)

9 Jun 2014
Bielby J, Donnelly CA, Pope LC, Burke T, & Woodroffe R (2014). "Badger responses to small-scale culling may compromise targeted control of bovine tuberculosis" Proc Natl Acad Sci U S A 111(25): 9193-9198 (2014) (pdf)

9 Jun 2014
Ferguson NM, Cummings DA "How season and serotype determine dengue transmissibility" Proc Natl Acad Sci U S A 111(25) (2014) (pdf)

1 Jun 2014
Hayward AC, Fragaszy EB, Bermingham A, Wang L, Copas A, Edmunds WJ, Ferguson N, Goonetilleke N, Harvey G, et al "Comparative community burden and severity of seasonal and pandemic influenza: results of the Flu Watch cohort study" Lancet Respiratory Medicine 2(6):445-454 (2014) (pdf)

1 Jun 2014
Jombart T, Collins C, Cori A, Didelot X, Fraser C, Ratmann O, Ferguson N, Baguelin M, Birrell P, et al. "OutbreakTools: A new platform for disease outbreak analysis using the R software" Epidemics (7): 28-34 (2014) (pdf)

23 May 2014
White MT, Griffin JT, Akpogheneta O, Conway DJ, Koram KA, Riley EM, ... Ghani AC "Dynamics of the Antibody Response to Plasmodium falciparum Infection in African Children" Journal of Infectious Diseases (2014) (pdf)

9 May 2014
Parker EP, Kampmann B, Kang G, Grassly NC "Influence of Enteric Infections on Response to Oral Poliovirus Vaccine: A Systematic Review and Meta-analysis" J Infect Dis 210(6) 853-864 (2014) (pdf)

1 May 2014
Garske T, Van Kerkhove MD, Ferguson NM, Yactayo S, Perea W, Ronveaux O, Lewis RF, Staples JE, Burke D, De La Hoz F, et al. "Yellow Fever in Africa: Estimating the Burden of Disease Impact of Mass Vaccination from Outbreak and Serological Data" PLoS Medicine 11(5) (2014) (pdf)

1 May 2014
Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser C "Heterogeneity in the frequency and characteristics of homologous recombination in pneumococcal evolution" PLoS Genet 10(5) (2014) (pdf)

8 Apr 2014
Didelot X, Gardy J, Colijn C "Bayesian Inference of Infectious Disease Transmission from Whole-Genome Sequence Data"  Molecular Biology and Evolution 31(7): 1869-1879 (2014) (pdf)

21 March 2014
Fraser C, Lythgoe K, Leventhal GE, Shirreff G, Hollingsworth TD, Alizon S, Bonhoeffer S "Virulence and Pathogenesis of HIV-1 Infection: An Evolutionary Perspective" Science 343(6177): 1328-+21 (2014) (pdf)

7 Mar 2014
Kucharski A, Mills H, Pinsent A, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S  "Distinguishing Between Reservoir Exposure and Human-to-Human Transmission for Emerging Pathogens Using Case Onset Data" PLoS Curr, 6 (2014) (pdf)

27 Feb 2014
Yahara K, Sheppard SK, Didelot X, Ansari MA, Falush D "Efficient inference of recombination hot regions in bacterial genomes" Molecular Biology and Evolution 31 (6): 1593-1605 (2014) (pdf)

18 Feb 2014
Smith J, Nyamukapa C, Gregson S, Lewis J, Magutshwa S, Schumacher C, Mushati P, Hallett T, Garnett G "The Distribution of Sex Acts and Condom Use within Partnerships in a Rural Sub-Saharan African Population" PLOS ONE 9(2) 12 pages (2014) (pdf)

13 Feb 2014
Winskill P, Harris AF, Morgan SA, Stevenson J, Raduan N, Alphey L, . . . Donnelly CA. "Genetic control of Aedes aegypti: data-driven modelling to assess the effect of releasing different life stages and the potential for long-term suppression" PARASITES & VECTORS, 7, 11 pages (2014) (pdf)

11 Feb 2014
Griffin JT, Ferguson NM, Ghani AC "Estimates of the changing age-burden of Plasmodium falciparum malaria disease in sub-Saharan Africa" Nature Communications 5:10, (2014) (pdf)

1 Feb 2014
Mangal TD, Aylward RB, Mwanza M, Gasasira A, Abanida E, Pate MA, Grassly NC "Key issues in the persistence of poliomyelitis in Nigeria: a case-control study" Lancet Global Health 2(2) e90-e97 (2014) (pdf)

1 Feb 2014
Haase JK, Achtman M, Didelot X, Lecuit M, Korkeala H, Leclercq A, Grant K, Wiedmann M, Apfalter P "The ubiquitous nature of Listeria monocytogenes clones: A large-scale Multilocus Sequence Typing study" Environmental Microbiology 16(2): 405-416 (2014) (pdf)

24 Jan 2014
Blake IM, Donnelly CA, "A Simple Incidence-Based Method to Avoid Misinterpretation of Bovine Tuberculosis Incidence Trends in Great Britain" PLoS Curr, 6 (2014) (pdf)

23 Jan 2014
Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson NM "Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data" PLoS Computational Biology 10(1) (2014) (pdf)

15 Jan 2014
Birger RB, Hallett TB, Sinha A, Grenfell BT, Hodder SL "Modeling the Impact of Interventions Along the HIV Continuum of Care in Newark, New Jersey" Clinical Infectious Diseases 58(2) 274-284 (2014) (pdf)

15 Jan 2014
Cori A, Ayles H, Beyers N, Schaap A, Floyd S, Sabapathy K, Eaton JW, Hauck K, Smith P,...Fraser C "HPTN 071 (PopART): A Cluster-Randomized Trial of the Population Impact of an HIV Combination Prevention Intervention Including Universal Testing and Treatment: Mathematical Model" PLOS ONE 9(1):11 (2014) (pdf)

1 Jan 2014
Pretorius C, Menzies NA, Chindelevitch L, Chen T, Cori A, Eaton JWFraser C, Gopalappa C, Hallett TB, ... Dodd P J "The potential effects of changing HIV treatment policy on tuberculosis outcomes in South Africa: results from three tuberculosis-HIV transmission models" AIDS 28 S25-S34 (2014) (pdf)

1 Jan 2014
Hallett TB, Menzies NA, Revill P, Keebler D, Borquez A, McRobie E, Eaton JW "Using modeling to inform international guidelines for antiretroviral treatment" AIDS 28, S25-S34 (2014) (pdf)

1 Jan 2014
Keebler D, Revill P, Braithwaite S, Phillips A, Blaser N, Borquez A, ... Hallet, TB "Cost-effectiveness of different strategies to monitor adults on antiretroviral treatment: a combined analysis of three mathematical models" Lancet Global Health 2(1) E23-E34 (2014) (pdf)

1 Jan 2014
Braithwaite, RS, Nucifora KA, Toohey C, Kessler J, Uhler LM, Mentor SM, ... Hallet T "How do different eligibility guidelines for antiretroviral therapy affect the cost–effectiveness of routine viral load testing in sub-Saharan Africa?" AIDS 23, S73-S83 (2014) (pdf)

1 Jan 2014
Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enouf V, van der Werf S, Ferguson N.M "Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility" Lancet Infectious Diseases 14(1): 50-56 (2014) (pdf)

1 Jan 2014
O'Brien JD, Didelot X, Iqbal Z, Amenga-Etego L, Ahiska B, Falush D "A Bayesian Approach to Inferring the Phylogenetic Structure of Communities from Metagenomic Data" Genetics doi:10.1534/genetics/114.161299 (2014) (pdf)

1 Jan 2014
Eaton JW, Menzies NA, Stover J, Cambiano V, Chindelevitch L, Cori A, Hontelez JAC, Humair S, Kerr CC, Klein DJ,.... Fraser C "Health benefits, costs, and cost-effectiveness of earlier eligibility for adult antiretroviral therapy and expanded treatment coverage: a combined analysis of 12 mathematical models" Lancet Global Health 2(1): E23-E34 (2014) (pdf)

1 Jan 2014
Cauchemez S, Van Kerkhove MD, Archer BN, Cetron M, Cowling BJ, Grove P, Hunt D, Kojouharova M, Kon P, UNgchusak K, et al. "School closures during the 2009 influenza pandemic: national and local experiences" BMC Infectious Diseases 14:11 (2014) (pdf)

 1 Jan 2014
Ansari MA, Didelot X "Inference of the Properties of the Recombination Process from Whole Bacterial Genomes" Genetics 196(1): 253-+ (2014) (pdf)

1 Jan 2014
Dingle, K. E., Elliott, B., Robinson, E., Griffiths, D., Eyre, D. W., Stoesser, N., . . .  Didelot X. (2014). Evolutionary History of the Clostridium difficile Pathogenicity Locus. GENOME BIOLOGY AND EVOLUTION, 6(1), 36-52 (2014) (pdf)

16 Dec 2013
Vial F, Mitchell A, Donnelly C.A "Bovine Tuberculosis Risk factors for British Herds Before and After the 2001 Foot-And-Mouth Epidemic: What we have learned from the TB99 and CCS2005 Studies" Transbound Emerg Dis 10.1111/tbed.12184 (2013) (pdf)

01 Dec 2013

Ferguson NM, Van Kerkhove MD "Identification of MERS-CoV in dromedary camels" Lancet Infectious Diseases 14(2):93-94 (2014) (pdf)

01 Dec 2013
Ali S.T, Kadi A.S, Ferguson N.M "Transmission Dynamics of the 2009 influenza A (H1N1) pandemic in India: The impact of holiday related school closure" Epidemics 5(4):157-163 (2013) (pdf)

01 Dec 2013
Koukounari A, Donnelly C.A, Moustaki I, Tukahebwa E.M, kabatereine N.B, Wilson S, Webster J.P, Deelder A.M, Vennervald B.J, van Dam G.J  "A Latent Markhove Modelling approach to the Evolution of Circulating Cathodic Antigen Strips for Schistosomiasis Diagnosis Pre- and Post-Praziquantel Treatment in Uganda" Pos Computational Biology 9(12): 10 pages Article number ARTN e1003402 01 (2013) (pdf)

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

01 Nov 2013
Storms AD, Van Kerkhove MD, Azziz-Baumgartner E, Lee W-K, Widdowson M-A, Ferguson NM, Mounts AW "Worldwide transmission and seasonal variation of pandemic influenza A(H1N1)2009 virus activity during the 2009-2010 pandemic" Influenza and Other Respiratory Viruses 7(6): 1328-1335 (2013) (pdf)

01 Nov 2013
Sridhar S, Begom., Bermingham A, Hoschler K, Adamson W, Carman W, Van Kerkhove M.D, Lalvani A "Incidence of Influenza A (H1N1) pdm09 Infection, United Kingdom, 2009-2011" Emerging Infectios Diseases 19(11):1866-1869 (2013) (pdf)

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

10 Oct 2013
Donnelly CA, Nouvellet P "The contribution of badgers to confirmed tuberculosis in cattle in high-incidence areas in England" PLoS Curr 5 (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)

01 Oct 2013
Hontelez JAC, Lurie MN, Baernighausen T, Bakker R, Baltussen R, Tanser F, Hallett TB, Newell M-L, de Vlas SJ "Elimination of HIV in South Africa through Expanded Access to Antiretroviral Therapy: A Model Comparison Study", PLOS Medicine 10(10) 13 pages, (2013) (pdf)

01 Oct 2013
Lythgoe K. A, Pellis L, C Fraser "Is HIV Short-Sighted? Insights from a Multistrain Nested Model" Evolution 67(10):2769-2782 (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)

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,  2013
Marshall JMWhite MTGhani AC, 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 20, 2013
Didelot X, Nell S, Yang I, Woltemate S, van der Merwe S, Suerbaum S "Genomic evolution and transmission of Helicobacterpylori in two South African Families" Proceedings of the National Academy of Science of the United States of America 110(34) 13880-13885 (2013) (pdf) Aug 14, 2013Beshir 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 110(33): 13422-13427 (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 24, 2013
Grassly NC "The final stages of the global eradication of poliomyelitis" Philosophical transactions of the Royal Society B-Biological Sciences 368(1623) 14 pages (2014) (pdf)

Jun 15, 2013
Balabanova D, Mills A, Conteh L, Akkazieva B, Banteyerga H, Dash U, Gilson L, Harmer A, Ibraimova A, Islam Z et al. "Good Health at Low Cost 25 years on: lessons for the future of health systems strengthening" Lancet 381(9883): 2118-2133 (2013) (pdf)

Jun 13, 2013
Cauchemez S, Van Kerkhove MD, Riley S, Donnelly CA, Fraser C, Ferguson NM "Transmission scenarios for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and how to tell them apart" Eurosurveillance 18(24) 7-13 (2014) (pdf)

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 01, 2012
Blake IM, Donnelly CA "Estimating risk over time using data from targeted surveillance systems: Application to bovine tuberculosis in Great Britain" Epidemics  (4) 179-186 (2012) (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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