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Publications

2013
 
 
Assi TM, Brown ST, Kone S, Norman BA, Djibo A, Connor DL, Wateska AR, Rajgopal J, Slayton RB, Lee BY. (2013). Removing the regional level from the Niger vaccine supply chain.  Vaccine, Apr 16. doi:pii: S0264-410X(13)00430-1.
 
Bejon P, White MT, Olutu A, Bojang K, Lusingu JPA, Salim N, Otsyula, NN, Agnandji S, Asante KP, Owusu-Agyei S, Abdulla S, Ghani AC. (2013). Efficacy of RTS,S malaria vaccines: individual-participant pooled analysis of phase 2 data.  Lancet Infect Dis, 13(4):319-327.
 
Cauchemez S, Epperson S, Biggerstaff M, Swerdlow D, Finelli L, Ferguson NM. (2013). 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:e1001399.
 
Ferrari MJ, Grenfell BT, Strebel PM. (2013). Think globally, act locally: the role of local demographics and vaccination coverage in the dynamic response of measles infection to control. Phil Trans R Soc B, 24 Jun: 368(1623):20120141.
 
Garske T, Ferguson NM, Ghani AC. (2013).  Estimating air temperature and its influence on malaria transmission across Africa.  PLoS One, Feb; 8(2):e56487.
 
Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, Schmitz MM, Paul P, Rajgopal J, Welling JS, Leonard J, Chen S, Lee BY. (2013). Augmenting transport versus increasing cold storage to improve vaccine supply chains. PLoS One, 8(5):e64303.  doi:10.1371/journal.pone.0064303

Metcalf CJE, Hampson K, Tatem AJ, Grenfell BT, Bjørnstad ON. (2013). Persistence in epidemic metapopulations: Quantifying the rescue effects for measles, mumps, rubella and whooping cough.  PLoS One, 8(9):e74696.  doi: 10.1371/journal.pone.0074696
 
Metcalf CJE, Cohen C, Lessler J, McAnerney JM, Ntshoe GM, Puren A, Klepac P, Tatem A, Grenfell BT, Bjørnstad. (2013). Implications of spatially heterogeneous vaccination coverage for the risk of congenital rubella syndrome in South Africa.  J R Soc Interface, 10(78), 20120756.
 
Patel MM, Pitzer VE, Alonso WJ, Vera D, Lopman BA, Tate J, Viboud C, Parashar UD. (2013). Global seasonality of rotavirus disease. Pediatr Infect Dis J, Apr; 32(4): e134-47.
 
Reich NG, Shrestha S, King AA, Rohani P, Lessler J, Kalayanarooj S, Yoon I-K, Gibbons RV, Burke DS, Cummings DAT. (2013). Interactions between serotypes of dengue highlight epidemiological impact of cross-immunityJ R Soc Interface, 10: 20130414. doi: 10.1098/rsif.2013.0414
 
Rozhnova G, Metcalf CJE, Grenfell BT. (2013). Characterizing the dynamics of rubella relative to measles: the role of stochasticity. J R Soc Interface, Sep 11, 10:20130643.
 
Storms A, Van Kerkhove MD, Azziz-Baumgartner, Wing-Kei Lee D, Widdowson MA, Ferguson NM, Mounts AW. (2013). Worldwide transmission and seasonal variation of pandemic influenza A(H1N1)2009 virus activity during the 2009-2010 pandemic.  Influenza Other Respi Viruses, 30 Mar. doi: 10.1111/irv.12106 [Epub ahead of print]
 
Van Kerkhove MD, Hirve S, Koukounari A, Mounts AW; H1N1pdm serology working group. (2013). Estimating age-specific cumulative incidence for the 2009 influenza pandemic: a meta-analysis of A(H1N1)pdm09 serological studies from 19 countries.  Influenza Other Respi Viruses, Jan 21. doi:10.1111/irv.12074
 
White MT, Bejon P, Olutu A, Griffin JT, Riley EM, Kester K, Ockenhouse C, Ghani AC. (2013). The relationship between RTS,S vaccine-induced antibody levels, T cell mediated responses and protection against Plasmodium falciparum infection in malaria-naive adults.  PLoS One, 8(4): e61395.
 
Zelner JL, Lopman BA, Hall AJ, Ballesteros S, Grenfell BT. (2013). Linking time-varying symptomatology and intensity of infectiousness to patterns of norovirus transmission.   PLoS One, July, 8(7):e68413.
 
 
 
2012

 
Arinaminpathy N, Ratmann O, Koelle K, Epstein SL, Price GE, Viboud C, Miller MA, Grenfell BT. (2012). Impact of cross-protective vaccines on epidemiological and evolutionary dynamics of influenza. PNAS, 21 Feb;109(8):3173-3177. doi: 10.1073/pnas.1113342109
 
Arinaminpathy N, Lavine JS, Grenfell BT. (2012). Self-boosting vaccines and their implications for herd immunity.  PNAS, 4 Dec;109(49):20154-20159.  doi: 10.1073/pnas.1209683109
 
Assi TM, Rookkapan K, Rajgopal J, Sornsrivichai V, Brown ST, Welling JS, Norman BA, Connor DL, Chen SI, Slayton RB, Laosiritaworn Y, Wateska AR, Wisniewski SR, Lee BY. (2012).  How influenza vaccination policy may affect vaccine logistics.  Vaccine, Jun 22; 30(30): 4517-23. doi: 10.1016/j.vaccine.2012.04.041
 
Atkins KE, Shim E, Pitzer VE, Galvani AP. (2012). The impact of rotavirus vaccination on epidemiological dynamics in England and Wales. Vaccine, 30(3):552-64.
 
Blackwood JC, Cummings DAT, Broutin H, Iamsirithaworn S, Rohani P. (2012). The population ecology of infectious diseases: pertussis in Thailand as a case studyParasitology, 139:1888-1898.

Blanford J, Kumar S, Luo W, MacEachran A. (2012). It's a long, long walk: accessibility to hospitals, maternity and integrated health centers in Niger. Int J Health Geogr, 27 Jun;11:24. doi:10.1186/1476-072X-11-24

Bousema T, Griffin JT, Sauerwein RW, Smith DL, Churcher TS, Takken W, Ghani A, Drakeley C, Gosling R. (2012). Hitting Hotspots: Spatial Targeting of Malaria for Control and Elimination. PLoS Med, 31 Jan. 9(1): e1001165. doi: 10.1371/journal.pmed.1001165

Cairns M, Roca-Feltrer A, Garske T, Wilson AL, Diallo D, Milligan PJ, Ghani AC, Greenwood BM. (2012). Estimating the potential public health impact of seasonal malaria chemoprevention in African children.  Nat Commun, 3:881.  doi:  10.1038/ncomms1879

Cummings DAT, Boni M, WHO-VMI Dengue Vaccine Modeling Group. (2012). Assessing the potential of a candidate dengue vaccine with mathematical modeling. PLoS Negl Trop Dis, Mar;6(3):e1450.

Cutts FT, Metcalf CJ, Lessler J, Grenfell BT. (2012). Rubella vaccination: must not be business as usual.  Lancet, Jul 21;380(9838):217-8. doi: 10.1016/S0140-6736(12)61215-X.

de Silva E, Ferguson NM, Fraser C. (2012). Inferring pandemic growth rates from sequence data. J R Soc Interface, [epub ahead of print].

Dorigatti I, Cauchemez S, Pugliese A, Ferguson NM. (2012). A new approach to characterising infectious disease transmission dynamics from sentinel surveillance: application to the Italian 2009-2010 A/H1N1 influenza pandemic.  Epidemics, March; 4(1):9-21.

Grassly NC, Jafari H, Bahl S, Sethi R, Deshpande JM, Wolff C, Sutter RW, Aylward RB. (2012). Waning intestinal immunity following vaccination with oral poliovirus vaccines in India. J Infect Dis, 205:1554-1561.

Hird TR, Grassly NC. (2012). Systematic review of mucosal immunity induced by oral and inactivated poliovirus vaccines against virus shedding following oral poliovirus challenge. PLoS Pathog, 8(4):e1002599.

Killingley B, Enstone JE, Greatorex J, Gilbert AS, Lambkin-Williams R, Cauchemez S, Katz JM, Booy R, Hayward A, Oxford J, Bridges CB, Ferguson NM, Van-Tam JSN. (2012). Use of a human influenza challenge model to assess person-to-person transmission: proof-of-concept study. J Infect Dis, 205(1):35-43.

Klepac P, Bjørnstad ON, Metcalf CJE, Grenfell BT. (2012). Optimizing reactive responses to outbreaks of immunizing infections: balancing case management and vaccination.  PLoS One, 7(8):e41428.  doi: 10.1371/journal.pone.0041428

Laurie KL, Huston P, Riley S, Katz JM, Willison DJ, Tam JS, Mounts AW, Hoschler K, Miller E, Vandemaele K, Broberg E, Van Kerkhove MD, Nicoll A. (2012). Influenza serological studies to inform public health action: best practices to optimise timing, quality and reporting. Influenza Other Respir Viruses, April 30, [epub ahead of print].

Lee BY, Assi TM, Rajgopal J, Norman BA, Chen SI, Brown ST, Slayton RB, Kone S, Kenea H, Welling JS, Connor DL, Wateska AR, Jana A, Wiringa AE, Van Panhuis WG, Burke DS. (2012). Impact of Introducing the Pneumococcal and Rotavirus Vaccines into the Routine Immunization Program in Niger. Am J Public Health, Feb; 102(2): 269-76. doi:10.2105/AJPH.2011.300218

Lee BY, Cakouros BE, Assi TM, Connor DL, Welling J, Kone S, Djibo A, Wateska AR, Pierre L, Brown ST. (2012). The impact of making vaccines thermostable in Niger's vaccine supply chain.  Vaccine, Aug 17; 30(38): 5637-43.  doi: 10.1016/j.vaccine.2012.06.087

Lessler J, Metcalf CJE, Grenfell BT. (2012). Measurement of vaccine-derived immunity: how do we use all the data?  Expert Rev Vaccines, 11(7):747-749.  doi: 10.1586/ERV.12.47

Lopman BA, Pitzer VE, Sarkar R, Gladstone B, Patel M, Glasser J, Gambhir M, Atchison C, Grenfell BT, Edmunds WJ, Kang G, Parashar UD. (2012). Understanding reduced rotavirus vaccine efficacy in low socio-economic settings.  PLoS One, August; 7(8):e41720.

Metcalf CJ, Lessler J, Klepac P, Cutts F, Grenfell BT. (2012). Impact of birth rate, seasonality and transmission rate on minimum levels of coverage needed for rubella vaccination.  Epidemiol Infect, Dec; 140(12):2290-301.  doi: 10.1017/S0950268812000131

Metcalf CJ, Lessler J, Klepac P, Morice A, Grenfell BT, Bjørnstad ON. (2012). Structured models of infectious disease: inference with discrete data. Theor Popul Biol, Dec; 82(4):275-82.  doi: 10.1016/j.tpb.2011.12.001

Metcalf CJE, Long GH, Mideo N, Forester JD, Bjørnstad ON, Graham AL. (2012). Revealing mechanisms underlying variation in malaria virulence: effective propagation and host control of uninfected red blood cell supply.  J R Soc Interface, June; 9:2804-2813. doi: 10.1098/rsif.2012.0340 

Nicoll A, Ciancio BC, Chavarrias VL, Mølbak K, Pebody R, Pedzinski B, Penttinen P, van der Sande M, Snacken R, Van Kerkhove MD. (2012). Influenza-related deaths - available methods for estimating numbers and detecting patterns for seasonal and pandemic influenza in Europe.   Euro Surveill, 3 May; 17(18). pii:20162

Okell LC, Bousema T, Griffin JT, Ouédraogo AL, Ghani AC, Drakeley CJ. (2012). Factors determining the occurrence of submicroscopic malaria infections and their relevance for control.  Nat Commun, 3:1237. doi: 10.1038/ncomms2241

O'Reilly KM, Durry E, ul Islam O, Quddus A, Abid NM, Mir TP, Tangermann RH, Aylward RB, Grassly NC. (2012). The effect of mass immunisation campaigns and new oral poliovirus vaccines on the incidence of poliomyelitis in Pakistan and Afghanistan, 2001-11: a retrospective analysis. Lancet, 4 Aug; 380(9840): 491-498.

Pitzer VE, Atkins KE, Freisleben de Blasio B, Van Effelterre T, Atchison CJ, Harris JP, Shim E, Galvani AP, Edmunds WJ, Viboud C, Patel MM, Grenfell BT, Parashar UD, Lopman BA. (2012). Direct and indirect effects of rotavirus vaccination: comparing predictions from transmission dynamic  models.  PLoS One, Aug; 7(8):342320. 

Rainwater-Lovett K, Rodriguez-Barraquer I, Cummings DAT, Lessler J.  (2012).  Variation in dengue virus plaque reduction neutralization testing: systematic review and pooled analysis. BMC Infect Dis, Sep 28;12:233.  doi: 10.1186/1471-2334-12-233

Reich NG, Lessler J, Cummings DAT, Brookmeyer R. (2012). Estimating absolute and relative case fatality ratios from infectious disease surveillance data. Biometrics, June; 68(2):598-606. doi: 10.1111/j.1541-0420.2011.01709.x

Salje H, Lessler J, Endy TP, Curriero FC, Gibbons RV, Nisalak A, Nimmannitya S, Kalayanarooj S, Jarman RG, Thomas SJ, Burke DS, Cummings DAT. (2012). Revealing the microscale spatial signature of dengue transmission and immunity in an urban population. PNAS, May 29. [Epub ahead of print]

Simons E, Ferrari M, Fricks J, Wannemuehler K, Anand A, Burton A, Strebel P. (2012). Assessment of the 2010 global measles mortality reduction goal: results from a model of surveillance data.  The Lancet, Apr;379:2173-78. doi: 10:1016/S0140-6736(12)60522-4

Tatem AJ, Adamo S, Bharti N, Burgert CR, Castro M, Dorelien A, Fink G, Linard C, John M, Montana L, Montgomery MR, Nelson A, Noor AM, Pindolia D, Yetman G, Balk D. (2012). Mapping populations at risk: improving spatial demographic data for infectious disease modeling and metric derivation.  Popul Health Metr, 10:8.

Truscott J, Fraser C, Cauchemez S, Meeyai A, Hinsley W, Donnelly CA, Ghani AC, Ferguson NM. (2012). Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza. J R Soc Interface, 9:304-312.

Van Kerkhove MD, Ferguson NM. (2012). Epidemic and intervention modelling - a scientific rationale for policy decisions? Lessons from the 2009 influenza pandemic. Bull World Health Organ, 90:306-310.

Van Kerkhove MD, Riley S, Lipsitch M, Guan Y, Monto AS, Webster RG, Zambon M, Nicoll A, Malik Peiris JS, Ferguson NM. (2012). Comment on "Seroevidence for H5N1 Influenza Infections in Humans: Meta-Analysis." Science, 22 June;336:1506. doi: 10.1126/science.1221434

Van Kerkhove MD, Broberg E, Engelhardt OG, Wood J, Nicoll A on behalf of the CONSISE steering committee. (2012). The Consortium for the Standardization of Influenza Seroepidemiology (CONSISE): a global partnership to develop influenza investigation protocols and standardize seroepidemiology to inform public health policy.  Influenza Other Respi Viruses. Published online 26 Dec. DOI: 10_1111/irv.12068.

Word DP, Cummings DAT, Burke DS, Iamsirithaworn S, Laird CD. (2012). A nonlinear programming approach for estimation of transmission parameters in childhood infectious disease using a continuous time model. J R Soc Interface, 9:1983-1997.

Yu H, Cauchemez S, Donnelly CA, Zhou L, Feng L, Xiang N, Zheng J, Ye M, Huai Y, Liao Q, Peng Z, Feng Y, Jiang H, Yang W, Wang Y, Ferguson NM, Feng Z. (2012). Transmission dynamics, border entry screening, and school holidays during the 2009 influenza A (H1N1) pandemic, China. Emerg Infect Dis, May;18(5):758-766.

 

2011

 

Althouse BM, Ng YY, Cummings DAT. (2011). Prediction of dengue incidence using search query surveillance. PLoS Negl Trop Dis, August; 5(8):e1258.

Assi TM, Brown ST, Djibo A, Norman BA, Rajgopal J, Welling JS, Chen SI, Bailey RR, Kone S, Kenea H, Connor DL, Wateska AR, Jana A, Wisniewski SR, Van Panhuis WG, Burke DS, Lee BY. (2011). Impact of changing the measles vaccine vial size on Niger's vaccine supply chain. BMC Public Health, 11(1):425.

Bharti N, Broutin H, Grais RF, Ferrari MJ, Djibo A, Tatem AJ, Grenfell BT. (2011). Spatial dynamics of meningococcal meningitis in Niger: observed patterns in comparison with measles.  Epidemiol Infect, 5:1-10.

Bharti N, Tatem AJ, Ferrari MJ, Grais RF, Djibo A, Grenfell BT. (2011). Explaining Seasonal Fluctuations of Measles in Niger Using Nighttime Lights Imagery. Science, 9 Dec, 334(6061):1424-1427. DOI: 10.1126/science.1210554.

Brown S, Tai J, Bailey R, Cooley P, Wheaton W, Potter M, Voorhees RE, LeJune M, Grefenstette JJ, Burke DS, McGlone SM, Lee B. (2011). Would school closure for the 2009 H1N1 influenza epidemic have been worth the cost?: A computational simulation of Pennsylvania. BMC Public Health, 11(1):353.

Cairns M, Ghani A, Okell L, Gosling R, Carneiro I, Anto F, Asoala V, Owusu-Agyei S, Greenwood B, Chandramohan D, Milligan P. (2011). Modelling the protective efficacy of alternative delivery schedules for intermittent preventive treatment of malaria in infants and children. PLoS One, 6(4), e18947. doi:10.1371/journal.pone.0018947

Cauchemez S, Bhattarai A, Marchbanks TL, Fagan RP, Ostroff S, Ferguson NM, Swerdlow D, and the Pennsylvania H1N1 working group. (2011). Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza. PNAS USA, 108:2825-2830

Donnelly CA, Finelli L, Cauchemez S, Olsen SJ, Doshi S, Jackson ML, Kennedy ED, Kamimoto L, Marchbanks TL, Morgan OW, Patel M, Swerdlow DL, Ferguson NM, and the pH1N1 Household Investigations working group. (2011). Serial intervals and the temporal distribution of secondary infections within households of 2009 pandemic influenza A (H1N1): implications for influenza control recommendations. Clin Infect Dis, 1 Jan;52:S123-S130.

Eggo RM, Cauchemez S, Ferguson NM. (2011). Spatial dynamics of the 1918 influenza pandemic in England, Wales and the United States. J R Soc Interface, 6 Feb;8:233-243.

Ferrari MJ, Perkins SE, Pomeroy LW, Bjørnstad ON. (2011). Pathogens, social networks, and the paradox of transmission scaling.Interdiscip Perspect Infect Dis,2011(2011); 267049. doi:10.1155/2011/267049

Fraser C, Cummings DA, Klinkenberg D, Burke DS, Ferguson NM. (2011). Influenza transmission in households during the 1918 pandemic. Am J Epidemiol, Sep 1;174(5):505-514.

Garske T, Yu H, Peng Z, Ye M, Zhou H, Cheng X, Wu J, Ferguson NM. (2011). Travel patterns in China. PloS One, 6(2), e16364. doi:10.1371/journal.pone.0016364

Gosling RD, Okell L, Mosha J, Chandramohan D. (2011). The role of antimalarial treatment in the elimination of malaria. Clin Microbiol Infect, 17(11):1617-1623.

Grenfell B. (2011). Boosting understanding of pertussis outbreaks.  PNAS, May 3, 108(18): 7279-7280.  doi: 10.1073/pnas.1103408108

Griffin JT, Garske T, Ghani AC, Clarke PS. (2011). Joint estimation of the basic reproduction number and generation time parameters for infectious disease outbreaks.Biostatistics (Oxford, England), 12(2):303-312. doi:10.1093/biostatistics/kxq058

Johansson M, Hombach J, Cummings DAT. (2011). Models of the impact of dengue vaccines: a review of current research and potential approaches. Vaccine, 29:5860-8.

Killingley B, Enstone J, Booy R, Hayward A, Oxford J, Ferguson N, Van-Tam JN, on behalf of the influenza transmission strategy development group. (2011). Potential role of human challenge studies for investigation of influenza transmission. Lancet Infect Dis, November;11:879-886.

Klepac P, Laxminarayan R, Grenfell BT. (2011). Synthesizing epidemiological and economic optima for control of immunizing infections.  PNAS, August 23; 108(34):14366-14370.

Lavine JS, King AA, Bjørnstad ON. (2011). Natural immune boosting in pertussis dynamics and the potential for long-term vaccine failure. PNAS, Apr 26; 108(17): 7259-7264.  doi: 10.1073/pnas.1014394108/-/DCSupplemental

Lee BY, Assi TM, Rookkapan K, Wateska AR, Rajgopal J, Sornsrivichai V, Chen SI, Brown ST, Welling J, Norman BA, Connor DL, Bailey RR, Jana A, Van Panhuis WG, Burke DS. (2011). Maintaining Vaccine Delivery Following the Introduction of the Rotavirus and Pneumococcal Vaccines in Thailand. PLoS One, 6((9):e24673. doi:10.1371/journal.pone.0024673

Lee BY, Assi T, Rookkapan K, Connor DL, Rajgopal J, Sornsrivichai V, Brown ST, Welling J, Norman BA, Chen S, Bailey RR, Wiringa AE, Wateska AR, Jana A, Van Panhuis WA, Burke DS. (2011). Replacing the measles ten-dose vaccine presentation with the single-dose presentation in Thailand.Vaccine, 29(21):3811-3817.

Lee BY, Brown ST, Bailey RR, Zimmerman RK, Potter MA, McGlone SM, Cooley P, Grefenstette JJ, Zimmer SM, Wheaton WD, Quinn SC, Voorhees R, Burke DS. (2011). The benefits to all of ensuring equal and timely access to influenza vaccines in poor communities. Health Affairs, 30(6):1141-50

Lee BY, Connor DL, Kitchen SB, Bacon KM, Shah M, Brown ST, Bailey RR, Laosiritaworn Y, Burke DS, Cummings DA. (2011). Economic value of dengue vaccine in Thailand. Am J Trop Med Hyg, 84(5):764-772. doi:10.4269/ajtmh.2011.10-0624

Lee BY, Tai JH, McGlone SM, Bailey RR, Wateska AR, Zimmer SM, Zimmerman RK, Wagner MM. (2011). The potential economic value of a ‘universal’ (multi-year) influenza vaccine. Influenza Other Respi Viruses, Sep 21. doi: 10.1111/j.1750-2659.2011.00288x

Lee BY, Wiringa AE. (2011). The 2009 H1N1 influenza pandemic: a case study of how modeling can assist all stages of vaccine decision-making. Hum Vaccin, Jan 1;7(1):115-119.

Lessler J, Metcalf CJE, Grais RF, Luquero FJ, Cummings DAT, Grenfell BT. (2011). Measuring the performance of vaccination programs using cross-sectional surveys: A likelihood framework and retrospective analysis. PLoS Med, 8(10):  e1001110. doi: 10.1371/journal.pmed.1001110

Lessler J, Cummings DAT, Read JM, Wang S, Zhu H, Smith GJD, Guan Y, Jiang CQ, Riley S. (2011). Location-specific patterns of exposure to recent pre-pandemic strains of influenza A in southern China. Nat Commun, 2:423.

Manjurano A, Okell L, Lukindo T, Reyburn H, Olomi R, Roger C, Clark TG, Joseph S, Riley EM, Drakeley C. (2011). Association of sub-microscopic malaria parasite carriage with transmission intensity in north-eastern Tanzania. Malaria Journal, 10:370.

Merler S, Ajelli M, Pugliese A, Ferguson NM. (2011). Determinants of the spatiotemporal dynamics of the 2009 H1N1 pandemic in Europe: implications for real-time modelling. PLoS Comput Biol, Sep;7(9):e1002205.

Metcalf CJ, Klepac P, Ferrari M, Grais RF, Djibo A, Grenfell BT. (2011). Modelling the first dose of measles vaccination: the role of maternal immunity, demographic factors, and delivery systems Epidemiol Infect, Feb; 139(2):265-74.  doi: 10.1017/S0950268810001329

Metcalf CJE, Graham AL, Huijben S, Barclay VC, Long GH, Grenfell BT, Read AF, Bjørnstad ON. (2011). Partitioning regulatory mechanisms of within-host malaria dynamics using the effective propagation number Science, Aug 19; 333:984-988.

Metcalf CJE, Munayco CV, Chowell G, Grenfell B, Bjørnstad ON. (2011). Rubella metapopulation dynamics and importance of spatial coupling to the risk of Congenital Rubella Syndrome in Peru. J R Soc Interface,8(56):369-376. doi:10.1098/rsif.2010.0320

Metcalf CJE, Bjørnstad ON, Ferrari M, Klepac P, Bharti N, Lopez-Gatell H, Grenfell BT. (2011). The epidemiology of rubella in Mexico: seasonality, stochasticity and regional variation. Epidemiol Infect,139(7):1029-1038doi:10.1017/S0950268810002165

Okell LC, Griffin JT, Kleinschmidt I, Hollingsworth TD, Churcher TS, White MJ, Bousema T, Drakeley CJ, Ghani AC. (2011). The Potential Contribution of Mass Treatment to the Control of Plasmodium falciparum Malaria. PLoS One, May;6(5):e20179.

Opatowski L, Fraser C, Griffin J, de Silva E, Van Kerkhove MD, Lyons EJ, Cauchemez S, Ferguson NM. (2011). Transmission characteristics of the 2009 H1N1 influenza pandemic: comparison of 8 Southern hemisphere countries. PLoS Pathog, Sep;7(9):e1002225.

O'Reilly KM, Chauvin C, Aylward RB, Maher C, Okiror S, Wolff C, Nshmirimana D, Donnelly CA, Grassly NC. (2011). A statistical model of the international spread of wild poliovirus in Africa used to predict and prevent outbreaks. PLoS Med, Oct;8(10):e1001109.

Pitzer VE, Patel MM, Lopman BA, Viboud C, Parashar UD, Grenfell BT. (2011). Modeling Rotavirus Strain Dynamics in Developed Countries to Understand the Potential Impact of Vaccination on Genotype Distributions. PNAS, 29 Nov, 108(48):19353-19358. doi:10.1073/pnas.1110507108
 
Pitzer VE, Viboud C, Lopman BA, Patel MM, Parashar UD, Grenfell BT. (2011). Influence of birth rates and transmission rates on the global seasonality of rotavirus incidence. J R Soc Interface. [Epub ahead of print]. doi:10.1098/rsif.2011.0062

Rajgopal J, Connor DL, Assi TM, Norman BA, Chen S, Bailey RR, Long AR, Wateska AR, Bacon KM, Brown ST, Burke DS, Lee BY. (2011). The optimal number of routine vaccines to order at health clinics in low or middle income countries. Vaccine, July;29(33):5512-5518.

Rodriguez-Barraquer I, Cordeiro MT, Braga C, de Souza WV, Marques ET, Cummings DAT. (2011). From re-emergence to hyperendemicity: The natural history of the dengue epidemic in Brazil.PLoS Negl Trop Dis, 5(1), e935. doi:10.1371/journal.pntd.0000935

Shekalaghe SA, Drakeley C, van den Bosch S, ter Braak R, van den Bijllaardt W, Mwanziva C, Semvua S, Masokoto A, Mosha F, Teelen K, Hermsen R, Okell L, Gosling R, Sauerwein R, Bousema T. (2011). A cluster-randomized trial of mass drug administration with a gametocytocidal drug combination to interrupt malaria transmission in a low endemic area in Tanzania. Malar J, Aug;10:247. doi: 10.1186/1475-2875-10-247

The malERA Consultative Group on Modeling. (2011). A research agenda for malaria eradication: modeling. PLoS Med, 8(1):e1000403. doi:10.1371/journal.pmed.1000403

Tomaszewski B, Blanford J, Ross K, Pezanowski S, MacEachren, AM (2011). Supporting geographically-aware web document foraging and sensemaking. Computers, Environment and Urban Systems, May;35(3):192-207. doi:doi:10.1016/j.compenvurbsys.2011.01.003

Van Kerkhove MD, et al. for the WHO Southern Hemisphere Influenza Comparison Study Working Group. (2011). Epidemiologic and virologic assessment of the 2009 influenza A (H1N1) pandemic on selected temperate countries in the Southern Hemisphere: Argentina, Australia, Chile, New Zealand and South Africa. Influenza Other Respi Viruses, 5:no. doi:10.1111/j.1750-2659.2011.00249x

Van Kerkhove MD, Mumford E, Mounts A, Bresee J, Ly S, Bridges CB, Otte J. (2011). Highly pathogenic avian influenza (H5N1): pathways of exposure at the animal-human interface, a systematic review. PLoS One, 6(1):e14582.

Van Kerkhove MD, Mounts AW. (2011). 2009 versus 2010 comparison of influenza activity in southern hemisphere temperate countries. Influenza Other Respi Viruses, doi:10.1111/j.1750-2659.2011.00241

Van Kerkhove MD, Vandemaele KAH, Shinde V, Jaramillo-Gutierrez G, Koukounari A, et al. (2011). Risk Factors for Severe Outcomes Following 2009 Influenza A (H1N1) Infection: A Global Pooled Analysis. PLoS Med, 8(7).

Van Panhuis W, Luxemburger C, Pengsaa K, Limkittikul K, Sabchareon A, Lang J, Durbin A, Cummings DAT. (2011). Decay and persistence of maternal dengue antibodies among infants in Bangkok.   Am J Trop Med Hyg, Aug;85:355-62.

White MT, Conteh L, Cibulskis R, Ghani AC. (2011). Costs and cost-effectiveness of malaria control interventions: a systematic review.  Malar J, 10:337.

White MT, Griffin, JT, Churcher TS, Ferguson NM, Basanez MG, Ghani AC. (2011). Modelling the impact of vector control interventions on Anopheles gambiae population dynamics. Parasites & Vectors, July 28; 4(1):153.

White MT, Griffin JT, Riley EM, Drakeley CJ, Moorman AM, Odada Sumba P, Kazura JW, Ghani A, John CC. (2011). Efficacy model for antibody-mediated pre-erythrocytic malaria vaccines. Proc R Soc B, May 7;278(1710):1298-1305.

 

2010

 

Bharti N, Djibo A, Ferrari MJ, Grais RF, Tatem A, McCabe C, Bjørnstad ON, Grenfell BT. (2010). Measles hotspots and epidemiological connectivity. Epidemiol Infect, 138(9):1308-1316. doi:10.1017/S09502688099913851

Bousema T, Okell LC, Shekalaghe S, Griffin JT, Omar S, Sawa P, Sutherland C, Sauerwein R, Ghani AC, Drakeley CJ. (2010). Revisiting the circulation time of Plasmodium falciparum gametocytes: molecular detection methods to estimate the duration of gametocyte carriage and the effect of gametocytocidal drugs. Malaria Journal, 9:136.
 
Broutin H, Viboud C, Grenfell BT, Miller MA, Rohani P. (2010). Impact of vaccination and birth rate on the epidemiology of pertussis: a comparative study in 64 countries.  Proc R Soc B, 277(1698): 3239-3245. doi:10.1098/rspb.2010.0994

Cooley P, Lee BY, Brown S, Cajka J, Chasteen B, Ganapathi L, Stark JH, Wheaton WD, Wagener DK, Burke DS. (2010) Protecting health care workers: a pandemic simulation based on Allegheny County. Influenza Other Respi Viruses, March;4(2):61-72.

Cummings DAT. Temporal and Spatial Dynamics of Dengue Virus Transmission.” Frontiers in Dengue Virus Research. Eds. Kathryn Hanley and Scott Weaver. Norwich UK: Caister Academic Press, 2010.
 
Ferrari MJ, Djibo A, Grais RF, Grenfell BT, Bjørnstad ON. (2010). Episodic outbreaks bias estimates of age-specific force of infection: a corrected method using measles as an example. Epidemiol Infect, 138(1):108-116. doi:10.1017/S0950268809990173
 
Ferrari MJ, Djibo A, Grais RF, Bharti N, Grenfell BT, Bjørnstad ON. (2010). Rural-urban gradient in seasonal forcing of measles transmission in Niger. Proc.R Soc B, Sept;277(1695):2775-2782. doi:10.1098/rspb.2010.0536
 
Fried J, Gibbons RV, Kalayanarooj S, Thomas S, Srikiatkhachorn A, Yoon IK, Jarman RG, Greene S, Rothman AL, Cummings DAT. (2010). Serotype-specific differences in the risk of dengue hemorrhagic fever: An analysis of data collected in Bangkok, Thailand from 1994 to 2006. PLoS Negl Trop Dis,4(3), e617. doi:10.1371/journal.pntd.0000617
 
Grassly NC, Jafari H, Bahl S, Durrani S, Wenger J, Sutter RW, Aylward RB. (2010). Asymptomatic wild-type poliovirus infection in India among children with previous oral poliovirus vaccination. J Infect Dis, 201(10), 1535-1543. doi:10.1086/651952
 
Griffin JT, Cairns M, Ghani AC, Roper C, Schellenberg D, Carneiro I, Newman RD, Grobusch MP, Greenwood B, Chandramohan D, Gosling RD. (2010). Protective efficacy of intermittent preventive treatment of malaria in infants (IPTi) using sulfadoxine-pyrimethamine and parasite resistance.PloS One, 5(9), e12618. doi:10.1371/journal.pone.0012618
 
Griffin JT, Hollingsworth TD, Okell LC, Churcher TS, White M, Hinsley W, Bousema T, Drakeley CJ, Ferguson NM, Basáñez MG, Ghani AC. (2010). Reducing Plasmodium falciparum malaria transmission in Africa: a model-based evaluation of intervention strategies. PLoS Med, August;7(8):e1000324.
 
Lavine J, Broutin H, Harvill ET, Bjørnstad ON. (2010). Imperfect vaccine-induced immunity and whooping cough transmission to infants. Vaccine, Dec;29(1):11-16.
 
Lee BY, Brown ST, Cooley P, Grefenstette JJ, Zimmerman RK, Zimmer SM, Potter MA, Rosenfeld R, Wheaton WD, Wiringa AE, Bacon KM, Burke DS. (2010). Vaccination deep into a pandemic wave: potential mechanisms for a "third wave" and the impact of vaccination. Am J Prev Med, Nov;39(5):e21-29.
 
Lee BY, Brown ST, Cooley P, Potter MA, Wheaton WD, Voorhees RE, Stebbins S, Grefenstette JJ, Zimmer SM, Zimmerman RK, Assi TM, Bailey RR, Wagener DK, Burke DS. (2010). Simulating school closure strategies to mitigate an influenza epidemic. J Public Health Manag Pract, 16(3):252-261.
 
Lee BY, Brown ST, Korch GW, Cooley PC, Zimmerman RK, Wheaton WD, Zimmer SM, Grefenstette JJ, Bailey RR, Assi TM, Burke DS. (2010). A computer simulation of vaccine prioritization, allocation and rationing during the 2009 H1N1 influenza pandemic. Vaccine, July;28(31):4875-4879.
 
Lee BY, Burke DS. (2010). Constructing target product profiles (TPPs) to help vaccines overcome post-approval obstaclesVaccine,28(16):2806-2809. doi:10.1016/j.vaccine.2009.09.047
 
Lee BY, Norman BA, Assi TM, Chen SI, Bailey RR, Rajgopal J, Brown ST, Wiringa AS, Burke, DS. (2010). Single versus multi-dose vaccine vials: An economic computational model. Vaccine, July;28(32): 5292-5300. doi:10.1016/j.vaccine.2010.05.048

Lessler J, dos Santos T, Aguilera X, Brookmeyer R, PAHO Influenza Technical Working Group, Cummings DT. (2010). H1N1pdm in the Americas. Epidemics, Sep 1;2(3):132-138.  doi: 10.1016/j.epidem.2010.07.001

Lessler J, Moss WJ, Lowther SA, Cummings DAT. (2010). Maintaining high rates of measles immunization in Africa. Epidemiol Infect, 139(7):1039-1049. doi:10.1017/S0950268810002232 

Long GH, Sinha D, Read AF, Pritt S, Kline B, Harvill ET, Hudson PJ, Bjørnstad ON. (2010). Identifying the age cohort responsible for transmission in a natural outbreak of Bordetella bronchiseptica. PLoS Pathogens, 6(12):e1001224.
 
Luis AD, Douglass RJ, Mills JN, Bjørnstad ON. (2010). The effect of seasonality, density and climate on the population dynamics of Montana deer mice, important reservoir hosts for Sin Nombre hantavirus. J Animal Ecology, 79(2):462-470. doi:10.1111/j.1365-2656.2009.01646x
 
Mantilla-Beniers NB, Bjørnstad ON, Grenfell BT, Rohani P. (2010). Decreasing stochasticity through enhanced seasonality in measles epidemics. J R Soc Interface, 7(46):727-739. doi:10.1098/rsif.2009.0317
 

Rohani P, Zhong X, King AA. (2010). Contact network structure explains the changing epidemiology of pertussis. Science, 12 Nov;330:982-985.

Stack JC, Welch JD, Ferrari MJ, Shapiro BU, Grenfell BT. (2010). Protocols for sampling viral sequences to study epidemic dynamics.  J R Soc Interface, 7:1119-1127.  doi:10.1098/rsif2009.0530

Steenkeste N, Rogers WO, Okell L, Jeanne I, Incardona S, Duval L, Chy S, Hewitt S, Chou M, Socheat D, Babin FX, Ariey F, Rogier C. (2010). Sub-microscopic malaria cases and mixed malaria infection in a remote area of high malaria endemicity in Rattanakiri province, Cambodia: implication for malaria elimination. Malaria Journal, 9:108.

Van Kerkhove MD, et al. for the WHO Informal Network for Mathematical Modelling for Pandemic Influenza H1N1 2009 (Working Group on Data Needs). (2010). Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS Med, June;7(6):e1000275.

Van Panhuis WG, Gibbons RV, Endy TP, Rothman AL, Srikiatkhachorn A, Nisalak A, Burke DS, Cummings DAT. (2010). Inferring the serotype associated with dengue virus infections on the basis of pre- and post-infection neutralizing antibody titers. J Infect Dis, 202(7):1002-1010. doi:10.1086/656141
 
White MT, Griffin JT, Drakeley CJ, Ghani AC. (2010). Heterogeneity in malaria exposure and vaccine response: implications for the interpretation of vaccine efficacy trials. Malaria Journal, 9:82. doi:10.1186/1475-2875-9-82
 
  
2009

 

Cummings DAT, Iamsirithaworn S, Lessler JT, McDermott A, Prasanthong R, Nisalak A, Jarman RG, Burke, DS, Gibbons RV. (2009).  The impact of the demographic transition on dengue in Thailand: insights from a statistical analysis and mathematical modeling. PLoS Med, 6(9), e1000139. doi:10.1371/journal.pmed.1000139

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, et al. and the WHO Rapid Pandemic Assessment Collaboration. (2009). Pandemic potential of a strain of influenza A (H1N1): early findings. Science,324(5934):1557-1561. doi:10.1126/science.1176062

Garske T, Legrand J, Donnelly CA, Ward H, Cauchemez S, Fraser C, Ferguson NM, Ghani AC. (2009). Assessing the severity of the novel influenza A/H1N1 pandemic. BMJ (Clinical Research Ed.), 339,b2840. doi:10.1136/bmj.b2840

Ghani, AC, Baguelin M, Griffin JT, et al. (2009). The early transmission dynamics of H1N1pdm Influenza in the United Kingdom. PLoS Currents, 2:RRN1130. doi:10.1371/currents.RRN1130

Ghani AC, Sutherland CJ, Riley EM, Drakeley CJ, Griffin JT, Gosling R, Filipe JAN. (2009). Loss of population levels of immunity to malaria as a result of exposure-reducing interventions: consequences for interpretation of disease trends. PloS One,4(2), e4383. doi:10.1371/journal.pone.0004383

Grassly NC, Jafari H, Bahl S, Durrani S, Wenger J, Sutter RW, Aylward RB. (2009). Mucosal immunity after vaccination with monovalent and trivalent oral poliovirus vaccine in India. J Infect Dis, 200(5), 794-801. doi:10.1086/605330

Johansson M, Cummings DAT, Glass G. (2009). Multiyear climate variability and dengue-El Niño southern oscillation, weather, and dengue incidence in Puerto Rico, Mexico, and Thailand: a longitudinal data analysisPLoS Med, 6(11), e1000168. doi:10.1371/journal.pmed.1000168

King AA, Shrestha S. Harvill ET, Bjørnstad ON. (2009). Evolution of acute infections and the invasion-persistence trade-off. American Nauralist, 173(4):446-455.

Klepac P, Pomeroy LW, Bjørnstad ON, Kuiken T, Osterhaus ADME, Riijks JM. (2009). Stage-structured transmission of phocine distemper virus in the Dutch 2002 outbreak. Proc R Soc B, 276:2469-2476.

Lee BY, Ercius AK, Smith KJ. (2009). A predictive model of the economic effects of an influenza vaccine adjuvant for the older adult (age 65 and over) population.Vaccine, 27(16):2251-7.

Lee BY, Mehrotra A, Burns RM, Harris KM. (2009). Alternative vaccination locations: who uses them and can they increase flu vaccination rates? Vaccine, 27(32):4252-4256.

Lee BY, Tai JH, Bailey RR, Smith KJ. (2009). The timing of influenza vaccination for older adults (65 years and older). Vaccine, 27(50):7110-7115. doi:10.1016/j.vaccine.2009.09.056

Lessler J, Reich NG, Cummings DAT, and the New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team. (2009). Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school.  NEJM, 361(27):2628-2636. doi:10.1056/NEJMoa0906089

Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM. (2009). Managing and reducing uncertainty in an emerging Influenza pandemic. NEJM. 361(2):112-115. doi:10.1056/NEJMp0904380

Metcalf CJE, Bjørnstad ON, Grenfell BT, Andreasen V. (2009). Seasonality and comparative dynamics of six childhood infections in pre-vaccination Copenhagen. Proc R Soc B, 7 Dec; 276:4111-4118.

Okell LC, Ghani AC, Lyons E, Drakeley CJ. (2009). Sub-microscopic infection in Plasmodium falciparum-endemic populations: a systematic review and meta-analysis. J Infect Dis,200(10):1509-1517. doi:10.1086/644781

Park AW, Daly JM, Lewis NS, Smith DJ, Wood JLN, Grenfell BT. (2009). Quantifying the impact of immune escape on transmission dynamics of influenza. Science, 326(5953):726-728. doi:10.1126/science.1175980

Pitzer VE, Viboud C, Simonsen L, Steiner C, Panozzo CA, Alonso WJ, Miller MA, Glass RI, Glasser JW, Parashar UD, Grenfell BT. (2009). Demographic variability, vaccination, and the spatiotemporal dynamics of rotavirus epidemics. Science,325(5938): 290-294. doi:10.1126/science.1172330

Shaman J, Pitzer VE, Viboud C, Lipsitch M, Grenfell BT. (2009). Absolute humidity and the seasonal onset of influenza in the continental US. PLoS Currents, 2:RRN1138.

Van Kerkhove MD, Ly S, Guitian J, Holl D, San S, Mangtani P, Ghani A, Vong S. (2009). Changes in poultry handling behavior and poultry mortality reporting among rural Cambodians in areas affected by HPAI/H5N1. PLoS One,4(7), e6466. doi:10.1371/journal.pone.0006466

Van Kerkhove MD, Vong S, Guitian J, Holl D, Mangtani P, San S, Ghani AC. (2009).  Poultry movement networks in Cambodia: implications for surveillance and control of highly pathogenic avian influenza (HPAI/H5N1). Vaccine,27(45):6345-6352. doi:10.1016/j.vaccine.2009.05.004

Zimmer SM, Burke DS. (2009). Historical perspective-Emergence of influenza A (H1N1) viruses. NEJM,361(3):279-285. doi:10.1056/NEJMra0904322

 

2008

 

Bjørnstad ON, Grenfell BT. (2008). Hazards, spatial transmission and timing of outbreaks in epidemic metapopulations. Environ Ecol Stat,15(3):265-277. doi:10.1007/s10651-007-0059-3

Ferrari MJ, Grais RF, Bharti N, Conlan AJK, Bjørnstad ON, Wolfson LJ, Guerin PJ, Djibo A, Grenfell BT. (2008). The dynamics of measles in sub-Saharan Africa. Nature, 451(7179):679-684. doi:10.1038/nature06509

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