2010
Lin H, Shin S, Blaya JA, Zhang Z, Cegielski P, Contreras C, Asencios L, Bonilla C, Bayona J, Paciorek CJ, Cohen T.
Assessing spatiotemporal patterns of multidrug-resistant and drug-sensitive tuberculosis in a South American setting.
Epidemiol Infect. 2010 Dec 23:1-10. [Epub ahead of print]
Shi P, Keskinocak P, Swann JL, Lee BY.
The impact of mass gatherings and holiday traveling on the course of an influenza pandemic: a computational model.
BMC Public Health. 2010 Dec 21;10:778.
Lee BY, Bacon KM, Connor DL, Willig AM, Bailey RR.
The potential economic value of a Trypanosoma cruzi (Chagas disease) vaccine in Latin America.
PLoS Negl Trop Dis. 2010 Dec 14;4(12):e916.
Levine B, Wilcosky T, Wagener D, Cooley P.
Mass commuting and influenza vaccination prevalence in New York City: protection in a mixing environment.
Epidemics. 2010 Dec;2(4):183-8.
Yang Y, Halloran ME, Daniels MJ, Longini IM Jr.
Modeling Competing Infectious Pathogens from a Bayesian Perspective: Application to Influenza Studies with Incomplete Laboratory Results.
J Am Stat Assoc. 2010 Dec;105(492):1310-1322.
Lee I, Agarwal RK, Lee BY, Fishman NO, Umscheid CA.
Systematic review and cost analysis comparing use of chlorhexidine with use of iodine for preoperative skin antisepsis to prevent surgical site infection.
Infect Control Hosp Epidemiol. 2010 Dec;31(12):1219-29. Epub 2010 Oct 22.
Lee BY, Wateska AR, Bailey RR, Tai JH, Bacon KM, Smith KJ.
Forecasting the economic value of an Enterovirus 71 (EV71) vaccine.
Vaccine. 2010 Nov 16;28(49):7731-6. Epub 2010 Oct 16.
Wu JT, Ma ES, Lee CK, Chu DK, Ho PL, Shen AL, Ho A, Hung IF, Riley S, Ho LM, Lin CK, Tsang T, Lo SV, Lau YL, Leung GM, Cowling BJ, Malik Peiris JS.
The infection attack rate and severity of 2009 pandemic H1N1 influenza in Hong Kong.
Clin Infect Dis. 2010 Nov 15;51:1184-1191.
Matrajt L Jr, Longini IM.
Optimizing vaccine allocation at different points in time during an epidemic.
PLoS One. 2010 Nov 11;5(11):e13767.
Smith KJ, Lee BY, Nowalk MP, Raymund M, Zimmerman RK.
Cost-effectiveness of dual influenza and pneumococcal vaccination in 50-year-olds.
Vaccine.2010 Nov 10;28(48):7620-5. Epub 2010 Sep 29.
Huang SS, Avery TR, Song Y, Elkins KR, Nguyen CC, Nutter SK, Nafday AA, Condon CJ, Chang MT, Chrest D, Boos J, Bobashev G, Wheaton W, Frank SA, Platt R, Lipsitch M, Bush RM, Eubank S, Burke DS, Lee BY.
Quantifying Interhospital Patient Sharing as a Mechanism for Infectious Disease Spread.
Infect Control Hosp Epidemiol. 2010 Nov; 31(11):1160-9.
Lee BY, Wiringa AE, Bailey RR, Goyal V, Tsui B, Lewis GJ, Muder RR, Harrison LH..
The economic effect of screening orthopedic surgery patients preoperatively for methicillin-resistant Staphylococcus aureus.
Infect Control Hosp Epidemiol. 2010 Nov;31(11):1130-8.
Cowling BJ, Lau MS, Ho LM, Chuang SK, Tsang T, Liu SH, Leung PY, Lo SV, Lau EH.
The effective reproduction number of pandemic influenza: prospective estimation.
Epidemiology. 2010 Nov;21:842-846.
Lee BY, Brown ST, Cooley P, Grefenstette JJ, Zimmerman RK, Zimmer SM, Potter MA, Rosenfeld R, Wheaton WD, Wiringa AE, Bacon KM, Burke DS.
Vaccination deep into a pandemic wave potential mechanisms for a "third wave" and the impact of vaccination.
Am J Prev Med. 2010 Nov;39(5):e21-9.
Ibuka Y, Chapman GB, Meyers LA, Li M, Galvani AP.
The dynamics of risk perceptions and precautionary behavior in response to 2009 (H1N1) pandemic influenza.
BMC Infect Dis. 2010 Oct 14;10:296.
Liao Q, Cowling B, Lam WT, Ng MW, Fielding R.
Situational awareness and health protective responses to pandemic influenza A (H1N1) in Hong Kong: a cross-sectional study.
PLoS One. 2010 Oct 12;5:13350-13350.
Lee BY, McGlone SM, Doi Y, Bailey RR, Harrison LH.
Economic impact of Acinetobacter baumannii infection in the intensive care unit.
Infect Control Hosp Epidemiol. 2010 Oct;31(10):1087-9.
Shi P, Keskinocak P, Swann JL, Lee BY.
Modelling seasonality and viral mutation to predict the course of an influenza pandemic.
Epidemiol Infect. 2010 Oct;138(10):1472-81. Epub 2010 Feb 17.
Chao DL, Halloran ME, Longini IM Jr.
School opening dates predict pandemic influenza A(H1N1) outbreaks in the United States.
J Infect Dis. 2010 Sep 15;202(6):877-80.
Zimmerman RK, Lauderdale DS, Tan SM, Wagener DK.
Prevalence of high-risk indications for influenza vaccine varies by age, race, and income.
Vaccine. 2010 Sep 7;28(39):6470-7. Epub 2010 Jul 30.
Eubank S, Barrett C, Beckman R, Bisset K, Durbeck L, Kuhlman C, Lewis B, Marathe A, Marathe M, Stretz P.
Detail in Network Models of Epidemiology: are we there yet?.
J Biol Dyn. 2010 Sep 1;4(5):446-455.
Cajka JC, Cooley PC, Wheaton WD.
Attribute Assignment to a Synthetic Population in Support of Agent-Based Disease Modeling.
RTI Press. 2010 Sep; publication No. MR-0019-1009. Research Triangle Park, NC: RTI
Lessler J, dos Santos T, Aguilera X, Brookmeyer R; PAHO Influenza Technical Working Group, Cummings DA.
H1N1pdm in the Americas.
Epidemics. 2010 Sep;2(3):132-8.
Lajous M, Danon L, López-Ridaura R, Astley CM, Miller JC, Dowell SF, O’Hagan JJ, Goldstein E, Lipsitch M. 
Mobile messaging as surveillance tool during pandemic (H1N1) 2009, Mexico [letter].
Emerg Infect Dis. 2010 Sep;16(9):1488-9.
Taylor C, Marathe A, Beckman R.
Same influenza vaccination strategies but different outcomes across US cities?.
Int J Infect Dis. 2010 Sep;14(9):e792-5.
Lee BY, Bailey RR, Wiringa AE, Afriyie A, Wateska AR, Smith KJ, Zimmerman RK.
Economics of employer-sponsored workplace vaccination to prevent pandemic and seasonal influenza.
Vaccine. 2010 Aug 23;28(37):5952-5959. Epub 2010 Jul 8.
Zhang Y, Lee BY, Donohue JM.
Ambulatory antibiotic use and prescription drug coverage in older adults.
Arch Intern Med. 2010 Aug 9;170(15):1308-14.
Rorres C, Pelletier ST, Keeling MJ, Smith G.
Estimating the kernel parameters of premises-based stochastic models of farmed animal infectious disease epidemics using limited, incomplete, or ongoing data.
Theor Popul Biol. 2010 Aug;78(1):46-53. Epub 2010 May 7.
Lee BY, McGlone SM.
Pricing of new vaccines.
Hum Vaccin. 2010 Aug;6(8):619-26. Review.
Zimmerman RK, Lauderdale DS, Tan SM, Wagener DK.
Prevalence of high-risk indications for influenza vaccine varies by age, race, and income.
Vaccine. 2010 Jul 29. [Epub ahead of print]
Roberts DJ.
Distributed Agent Based Modeling.
Linux Journal. Epub 2010 July 21.
Goldstein E, Cowling BJ, O’Hagan JJ, Danon L, Fang VJ, Hagy A, Miller JC, Reshef D, Robins J, Paul Biedrzycki P, Lipsitch M.
Oseltamivir for treatment and prevention of pandemic influenza A/H1N1 virus infection in households, Milwaukee, 2009.
BMC Infect Dis. 2010 Jul 20;10(1):211. [Epub ahead of print]
Zimmer SM, Crevar CJ, Carter DM, Stark JH, Giles BM, Zimmerman RK, Ostroff SM, Lee BY, Burke DS, Ross TM.
Seroprevalence following the second wave of Pandemic 2009 H1N1 influenza in Pittsburgh, PA, USA.
PLoS One. 2010 Jul 14;5(7):e11601.
Lee BY, Brown ST, Korch GW, Cooley PC, Zimmerman RK, Wheaton WD, Zimmer SM, Grefenstette JJ, Bailey RR, Assi TM, Burke DS.
A computer simulation of vaccine prioritization, allocation, and rationing during the 2009 H1N1 influenza pandemic.
Vaccine. 2010 Jul 12;28(31):4875-9. Epub 2010 May 16.
Lee BY, Wiringa AE, Bailey RR, Goyal V, Lewis GJ, Tsui BY, Smith KJ, Muder RR.
Screening cardiac surgery patients for MRSA: an economic computer model.
Am J Manag Care. 2010 Jul 1;16(7):e163-73.
Eggo RM, Cauchemez S, Ferguson NM.
Spatial dynamics of the 1918 influenza pandemic in England, Wales and the United States.
J R Soc Interface. 2010 Jun 23. [Epub ahead of print]
Lee BY, Ufberg PJ, Bailey RR, Wiringa AE, Smith KJ, Nowalk AJ, Higgins C, Wateska AR, Muder RR.
The potential economic value of a Staphylococcus aureus vaccine for neonates.
Vaccine. 2010 Jun 23;28(29):4653-60. Epub 2010 May 14.
Lee BY, McGlone SM, Bailey RR, Wiringa AE, Zimmer SM, Smith KJ, Zimmerman RK.
To test or to treat? An analysis of influenza testing and antiviral treatment strategies using economic computer modeling.
PLoS One. 2010 Jun 23; 5(6): e11284.
Wendelsdorf K, Bassaganya-Riera J, Hontecillas R, Eubank S.
Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease.
J Theor Biol. 2010 Jun 21;264(4):1225-39. Epub 2010 Apr 1.
Cohen T, Hedt BL, Pagano M.
Estimating the magnitude and direction of bias in tuberculosis drug resistance surveys conducted only in the public sector: a simulation study.
BMC Public Health. 2010 Jun 21;10:355-355.
Lee BY, Popovich MJ, Tian Y, Bailey RR, Ufberg PJ, Wiringa AE, Muder RR.
The potential value of Clostridium difficile vaccine: An economic computer simulation model.
Vaccine. 2010 Jun 10. [Epub ahead of print]
Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M.
What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae?.
J R Soc Interface. 2010 Jun 6;7(47):905-19. Epub 2009 Nov 25.
Lee BY, Norman BA, Assi TM, Chen SI, Bailey RR, Rajgopal J, Brown ST, Wiringa AE, Burke DS.
Single versus multi-dose vaccine vials: An economic computational model.
Vaccine. 2010 Jun 3. [Epub ahead of print]
Van Kerkhove MD, Asikainen T, Becker NG, Bjorge S, Desenclos JC, dos Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM Jr, McBryde ES, Roth CE, Shay DK, Smith DJ, Wallinga J, White PJ, Ferguson NM, Riley S; WHO Informal Network for Mathematical Modelling for Pandemic Influenza H1N1 2009 (Working Group on Data Needs).
Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling.
PLoS Med. 2010 Jun 1;7(6):e1000275.
Stelling J, Yih WK, Galas M, Kulldorff M, Pichel M, Terragno R, Tuduri E, Espetxe S, Binsztein N, O'Brien TF, Platt R; Collaborative Group WHONET-Argentina.
Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes.
Epidemiol Infect. 2010 Jun;138(6):873-83. Epub 2009 Oct 2.
Cohen T, Hedt BL, Pagano M.
Estimating the magnitude and direction of bias in tuberculosis drug resistance surveys conducted only in the public sector: a simulation study.
BMC Public Health. 2010 Jun; 10: 355.
Lee BY, Bailey RR, Smith KJ, Muder RR, Strotmeyer ES, Lewis GJ, Ufberg PJ, Song Y, Harrison LH.
Universal methicillin-resistant Staphylococcus aureus (MRSA) surveillance for adults at hospital admission: an economic model and analysis.
Infect Control Hosp Epidemiol. 2010 Jun;31(6):598-606.
Lau LL, Cowling BJ, Fang VJ, Chan KH, Lau EH, Lipsitch M, Cheng CK, Houck PM, Uyeki TM, Peiris JS, Leung GM.
Viral Shedding and Clinical Illness in Naturally Acquired Influenza Virus Infections.
J Infect Dis. 2010 May 15;201(10):1509-16.
Rorres C, Pelletier ST, Keeling MJ, Smith G.
Estimating the kernel parameters of premises-based stochastic models of farmed animal infectious disease epidemics using limited, incomplete, or ongoing data.
Theor Popul Biol. 2010 May 7. [Epub ahead of print]
Goldstein E, Apolloni A, Lewis B, Miller JC, Macauley M, Eubank S, Lipsitch M, Wallinga J.
Distribution of vaccine/antivirals and the 'least spread line' in a stratified population.
J R Soc Interface. 2010 May 6;7(46):755-64.
Miller JC, Danon L, O'Hagan JJ, Goldstein E, Lajous M, Lipsitch M.
Student behavior during a school closure caused by pandemic influenza A/H1N1.
PLoS One. 2010 May 5;5(5):e10425.
Wu P, Lau E, Cowling BJ, Leung CC, Tam CM, Leung G.
The transmission dynamics of tuberculosis in a recently developed Chinese city.
PLoS One. 2010 May 3;5(5):e10468.
Lipsitch M, Tchetgen Tchetgen E, Cohen T.
Negative controls: a tool for detecting confounding and bias in observational studies.
Epidemiology. 2010 May;21:383-388.
Barrett C, Bisset K, Leidig J, Marathe A, Marathe M. 
An integrated modeling environment to study the co-evolution of networks, individual behavior and epidemics.
Al Magazine. Spring 2010; 31 (1); 75-87.
Cowling BJ, Lau LL, Wu P, Wong HW, Fang VJ, Riley S, Nishiura H.
Entry screening to delay local transmission of 2009 pandemic influenza A (H1N1).
BMC Infect Dis. 2010 Mar 30;10(1):82. [Epub ahead of print]
Lee BY, Wiringa AE, Bailey RR, Lewis GJ, Feura J, Muder RR.
Staphylococcus aureus vaccine for orthopedic patients: an economic model and analysis.
Vaccine. 2010 Mar 11;28(12):2465-71. Epub 2010 Jan 9.
Beres SB, Carroll RK, Shea PR, Sitkiewicz I, Martinez-Gutierrez JC, Low DE, McGeer A, Willey BM, Green K, Tyrrell GJ, Goldman TD, Feldgarden M, Birren BW, Fofanov Y, Boos J, Wheaton WD, Honisch C, Musser JM.
Molecular complexity of successive bacterial epidemics deconvoluted by comparative pathogenomics.
Proc Natl Acad Sci U S A. 2010 Mar 2;107:4371-4376.
Fried JR, Gibbons RV, Kalayanarooj S, Thomas SJ, Srikiatkhachorn A, Yoon IK, Jarman RG, Green S, Rothman AL, Cummings DA.
Serotyrpe-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. 2010 Mar 2;4(3):e617.
Ng S, Cowling BJ, Fang VJ, Chan KH, Ip DK, Cheng CK, Uyeki TM, Houck PM, Malik Peiris JS, Leung GM.
Effects of oseltamivir treatment on duration of clinical illness and viral shedding and household transmission of influenza virus.
Clin Infect Dis. 2010 Mar 1;50(5):707-14.
Lee BY, Tai JH, Bailey RR, Smith KJ, Nowalk AJ.
Economics of influenza vaccine administration timing for children.
Am J Manag Care. 2010 Mar;16(3):e75-e85.
Goldstein E, Miller JC, O’Hagan J, Lipsitch M.
Predispensing of antivirals to high-risk individuals in an influenza pandemic.
Influenza Other Respi Viruses. 2010 Mar; 4(2):101-112.
Cooley P, Lee BY, Brown S, Cajka J, Chasteen B, Ganapathi L, Stark JH, Wheaton WD, Wagener DK, Burke DS.
Protecting health care workers: a pandemic simulation based on Allegheny County.
Influenza Other Respi Viruses. 2010 Mar;4(2):61-72.
Wu JT, Cowling BJ, Lau EH, M Ip DK, Ho LM, Tsang T, Chuang SK, Leung PY, Lo SV, Liu SH, Riley S.
School Closure and Mitigation of Pandemic (H1N1) 2009, Hong Kong.
Emerg Infect Dis. 2010 Mar;16(3):538-41.
Bansal S, Pourbohloul B, Hupert N, Grenfell B, Meyers LA.
The shifting demographic landscape of pandemic influenza.
PLoS One. 2010 Feb 26;5(2):e9360.
Huang SS, Yokoe DS, Stelling J, Placzek H, Kulldorff M, Kleinman K, O'Brien TF, Calderwood MS, Vostok J, Dunn J, Platt R.
Automated detection of infectious disease outbreaks in hospitals: a retrospective cohort study.
PLoS Med. 2010 Feb 23;7(2):e1000238.
Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M.
Absolute humidity and the seasonal onset of influenza in the continental United States.
PLoS Biol. 2010 Feb 23;8(2): e1000316.
Yih WK, Deshpande S, Fuller C, Heisey-Grove D, Hsu J, Kruskal BA, Kulldorff M, Leach M, Nordin J, Patton-Levine J, Puga E, Sherwood E, Shui I, Platt R.
Evaluating real-time syndromic surveillance signals from ambulatory care data in four states.
PLoS Med. 2010 Feb 23;7(2):e1000238.
Wu JT, Lee CK, Cowling BJ, Yuen KY.
Logistical feasibility and potential benefits of a population-wide passive-immunotherapy program during an influenza pandemic.
Proc Natl Acad Sci U S A. 2010 Feb 16;107(7):3269-74.
Chao DL, Halloran ME, Obenchain VJ, Longini IM Jr.
FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model.
PLoS Comput Biol. 2010 Jan 29;6(1):e1000656.
Rosvall M, Bergstrom CT.
Mapping change in large networks.
PLoS One. 2010 Jan 27;5(1):e8694.
Althouse BM, Bergstrom TC, Bergstrom CT.
Evolution in health and medicine Sackler colloquium: a public choice framework for controlling transmissible and evolving diseases.
Proc Natl Acad Sci U S A. 2010 Jan 26;107(S1):1696-1701.
Frank, S. A.
Somatic evolutionary genomics: Mutations during development cause highly variable genetic mosaicism with risk of cancer and neurodegeneration.
Proc Natl Acad Sci U S A. 2010 Jan 26;107 Suppl 1:1725-30. Epub 2009 Sep 23.
Riley S.
Coping without farm location data during a foot-and-mouth outbreak.
Proc Natl Acad Sci U S A. 2010 Jan 19;107:957-958.
Tildesley MJ, House TA, Bruhn MC, Curry RJ, O'Neil M, Allpress JL, Smith G, Keeling MJ.
Impact of spatial clustering on disease transmission and optimal control.
Proc Natl Acad Sci U S A. 2010 Jan 19;107(3):1041-6. Epub 2009 Dec 1.
Wallinga J, van Boven M, Lipsitch M.
Optimizing infectious disease interventions during an emerging epidemic.
Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):923-8. Epub 2009 Dec 28.
Handel A, Longini IM Jr, Antia R.
Towards a quantitative understanding of the within-host dynamics of influenza A infections.
J R Soc Interface. 2010 Jan 6;7(42):35-47.
Frank S. A.
Demography and the tragedy of the commons.
J Evol Biol. 2010 Jan;23(1):32-9. Epub 2009 Nov 13.
Levine B, Wilcosky T, Wagener D, Cooley P.
Mass commuting and influenza vaccination prevalence in New York City: protection in a mixing environment.
Epidemics. 2010;2:183-188.
Liao Q, Cowling BJ, Lam WT, Ng MW, Fielding R.
Situational awareness and health protective responses to pandemic influenza A (H1N1) in Hong Kong: a cross-sectional study.
PLoS ONE, 2010; 5:e13350.
Wu JT, Ma ESK, Lee CK, Chu DKW, Ho PL, Shen AL, Ho A, Hung IFN, Riley S, Ho LM, Lin CK, Tsang T, Lo SV, Lau YL, Leung GM, Cowling BJ, Peiris JSM.
The infection attack rate and severity of 2009 pandemic H1N1 influenza in Hong Kong.
Clinical Infectious Diseases, 2010; 51:1184-91.
2009
Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, Finelli L, Ferguson NM.
Household Transmission of 2009 Pandemic Influenza A (H1N1) Virus in the United States.
N Engl J Med 2009 Dec 31;361(27):2619-2627.
Lessler, J., Reich, NG, Cummings, DA, Nair, HP, Jordan, HT, & Thompson, N.
Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school.
N Engl J Med. 2009 Dec 31;361(27):2628-2636.
Lee BY, Brown ST, Cooley PC, Zimmerman RK, Wheaton WD, Zimmer SM, Grefenstette JJ, Assi TM, Furphy TJ, Wagener DK, Burke DS.
A Computer Simulation of Employee Vaccination to Mitigate an Influenza Epidemic.
Am J Prev Med. 2009 Dec 29. [Epub ahead of print]
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.
Simulating School Closure Strategies to Mitigate an Influenza Epidemic.
J Public Health Manag Pract. 2009 Dec 23. [Epub ahead of print]
Goldstein E, Dushoff J, Ma J, Plotkin JB, Earn DJ, Lipsitch M.
Reconstructing influenza incidence by deconvolution of daily mortality time series.
Proc Natl Acad Sci U S A. 2009 Dec 22;106(51):21825-9. Epub 2009 Dec 18.
The WHO Informal Network for Mathematical Modelling for Pandemic Influenza H1N1 2009 (Working Group on Data Needs).
Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling.
PLoS Curr Influenza. 2009 Dec 16:RRN1135.
Beigi RH, Wiringa AE, Bailey RR, Assi TM, Lee BY.
Economic value of seasonal and pandemic influenza vaccination during pregnancy.
Clin Infect Dis. 2009 Dec 15;49(12):1784-92.
Reed C, Angulo FJ, Swerdlow DL, Lipsitch M, Meltzer MI, Jernigan D, Finelli L.
Estimates of the prevalence of pandemic (H1N1) 2009, United States, April–July 2009.
Emerg Infect Dis. 2009 Dec;15(12):2004-7.
Medlock J, Meyers LA.
Optimizing allocation for a delayed influenza vaccination campaign.
PLoS Curr Influenza. 2009 Dec 9:RRN1134.
Lee BY, Tsui BY, Bailey RR, Smith KJ, Muder RR, Lewis GJ, Harrison LH.
Should vascular surgery patients be screened preoperatively for methicillin-resistant Staphylococcus aureus?
Infect Control Hosp Epidemiol. 2009 Dec;30(12):1158-65.
Presanis AM, De Angelis D; New York City Swine Flu Investigation Team, Hagy A, Reed C, Riley S, Cooper BS, Finelli L, Biedrzycki P, Lipsitch M.
The severity of pandemic H1N1 influenza in the United States, from April to July 2009: a Bayesian analysis.
PLoS Med. 2009 Dec;6(12):e1000207. Epub 2009 Dec 8. PubMed PMID: 19997612; PubMed Central PMCID: PMC2784967.
Jung I, Kulldorff M, Kleinman KP, Yih WK, Platt R.
Using encounters versus episodes in syndromic surveillance.
J Public Health (Oxf). 2009 Dec;31(4):566-72. Epub 2009 May 13.
Goldstein E and Lipsitch M.
H1N1 vaccination and adults with underlying health conditions in the US.
PLoS Curr Influenza. 2009 Nov 23;1:RRN1132.
Lee BY, Tai JH, Bailey RR, Smith KJ.
The timing of influenza vaccination for older adults (65 years and older).
Vaccine. 2009 Nov 23;27(50):7110-5. Epub 2009 Sep 26.
Ghani AC, Baguelin M, Griffin J, Flasche S, Pebody R, van Hoek AJ, Cauchemez S, Hall IM, Donnelly C, Robertson C, White MT, Barrass I, Fraser C, Bermingham A, Truscott J, Ellis J, Jenkins H, Kafatos G, Garske T, Harris R, McMenamin J, Hawkins C, Phin N, Charlett A, Zambon M, Edmonds WJ, Catchpole M, Leach S, White P, Ferguson NM, Cooper B.
The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom.
PLoS Curr Influenza. 2009 Nov 16:RRN1130.
Dimitrov N, Goll S, Meyers LA, Pourbohloul B, Hupert N.
Optimizing Tactics for use of the U.S. Antiviral Strategic National Stockpile for Pandemic (H1N1) Influenza, 2009.
PLoS Curr Influenza. 2009 Nov 4:RRN1127.
Lee BY, Bailey RR, Wiringa AE, Assi TM, Beigi RH.
Antiviral medications for pregnant women for pandemic and seasonal influenza: an economic computer model.
Obstet Gynecol. 2009 Nov;114(5):971-80.
White LF, Wallinga J, Finelli L, Reed C, Riley S, Lipsitch M, Pagano M.
Estimation of the reproductive number and the serial interval in early phase of the 2009 influenza A/H1N1 pandemic in the USA.
Influenza Other Respi Viruses. 2009 Nov;3(6):267-76.
Goldstein E and Lipsitch M.
Antiviral usage for H1N1 treatment: pros, cons and an argument for broader prescribing guidelines in the United States. Version 2.
PLoS Curr Influenza. 2009 October 29 [revised 2009 November 11 ]: RRN1122.
Lipsitch M, Hayden FG, Cowling BJ, Leung GM.
How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count.
Lancet. 2009 Oct 3;374(9696):1209-11.
Stelling J, Yih WK, Galas M, Kulldorff M, Pichel M, Terragno R, Tuduri E, Espetxe S, Binsztein N, O'Brien TF, Platt R.
Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes.
Epidemiol Infect. 2009 Oct 2:1-11.
Bansal S, Pourbohloul B, Grenfell B, Meyers LA.
The shifting demographic landscape of influenza.
PLoS Currents: Influenza. 2009 Oct 2; RRN1047.
Lempel H, Epstein JM, Hammond RA.
Economic cost and health care workforce effects of school closures in the U.S.
PLoS Currents: Influenza. 2009 Oct 1; RRN1048.
Tildesley MJ, Bessell PR, Keeling MJ, Woolhouse ME.
The role of pre-emptive culling in the control of foot-and-mouth disease.
Proc Biol Sci. 2009 Sep 22;276(1671):3239-48. Epub 2009 Jul 1.
Pitzer VE, Lipsitch M.
Exploring the relationship between incidence and the average age of infection during seasonal epidemics.
J Theor Biol. 2009 Sep 21;260(2):175-85. Epub 2009 Jun 13.
Basta, N., Chao D.L., Halloran, M.E., Matrajt, L. and Longini, I.M.
Strategies for pandemic and seasonal influenza vaccination of school children in the United States.
Am J Epidemiol. 2009 Sep 15; 170(6):679–686.
Handel A, Longini IM Jr, Antia R.
Intervention strategies for an influenza pandemic taking into account secondary bacterial infections.
Epidemics, 2009 Sep 10;1(3):185-195.
Yang Y, Sugimoto JD, Halloran ME, Basta NE, Chao DL, Matrajt L, Potter G, Kenah E, Longini IM Jr.
The transmissibility and control of pandemic influenza A (H1N1) virus.
Science. 2009 Sep 10. [Epub ahead of print]
Lipsitch M, Lajous M, O'Hagan JJ, Cohen T, Miller JC, Goldstein E, Danon L, Wallinga J, Riley S, Dowell SF, Reed C, McCarron M.
Use of cumulative incidence of novel influenza A/H1N1 in foreign travelers to estimate lower bounds on cumulative incidence in Mexico.
PLoS One. 2009 Sep 9;4(9):e6895.
Pourbohloul B, Ahued A, Davoudi B, Meza R, Meyers LA, Skowronski DM, et al.
Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America.
Influenza Other Respi Viruses. 2009 Sep;3(5):215-22.
Goldstein E, Paur K, Fraser C, Kenah E, Wallinga J, Lipstich M.
Reproductive numbers, epidemic spread and control in a community of households.
Math Biosci. 2009 Sep;221(1):11-25.
Bisset K and Marathe M.
A CYBER environment to PANDEMIC.
SciDAC Review, Number 13, Summer 2009, 36-47.
Basta NE, Chao DL, Halloran ME, Matrajt L, Longini IM Jr.
Strategies for pandemic and seasonal influenza vaccination of schoolchildren in the United States.
Am J Epidemiol. 2009 Aug 13; [Epub ahead of print]
Epstein JM.
Modelling to contain pandemics.
Nature. 2009 Aug 6;460(7256):687.
McCaw JM, Wood JG, McBryde ES, Nolan TM, Wu JT, Lipsitch M, McVernon J.
Understanding Australia's influenza pandemic policy on the strategic use of the antiviral drug stockpile.
Med J Aust. 2009 Aug 3;191(3):136-7.
Frank S. A.
The common patterns of nature.
J Evol Biol. 2009 Aug;22(8):1563-85. Epub 2009 Jun 17. Review.
Bardach NS, Huang J, Brand R, Hsu J.
Evolving health information technology and the timely availability of visit diagnoses from ambulatory visits: a natural experiment in an integrated delivery system.
BMC Med Inform Decis Mak. 2009 Jul 17;9:35.
Zimmer SM, Burke DS.
Historical perspective - Emergence of Influenza A (H1N1) Viruses.
N Engl J Med. 2009 Jul 16;361(3):279-285.
Lee, BY, Mehrotra, A, Burns, RM, Harris, KM.
Alternative vaccination locations: who uses them and can they increase flu vaccination rates?
Vaccine. 2009 Jul 9;27(32):4252-4256.
Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM.
Managing and reducing uncertainty in an emerging influenza pandemic.
N Engl J Med. 2009 Jul 9;361(2):112-5.
Fraser, C, Donnelly, CA, Cauchemez, S, Hanage, WP, Van Kerkhove, MD, Hollingsworth, TD, et al.
Pandemic potential of a strain of influenza A (H1N1): early findings.
Science. 2009 Jun 19;324(5934):1557-1561.
Handel A, Longini IM Jr, Antia R.
Towards a quantitative understanding of the within-host dynamics of influenza A infections.
J R Soc Interface. 2009 May 27. [Epub ahead of print]
Wu JT, Leung GM, Lipsitch M, Cooper BS, Riley S.
Hedging against antiviral resistance during the next influenza pandemic using small stockpiles of an alternative chemotherapy.
PLoS Med. 2009 May 19;6(5):e1000085.
Cowling BJ, Fang VJ, Riley S, Malik Peiris JS, Leung GM.
Estimation of the serial interval of influenza.
Epidemiology. 2009 May;20(3):344-7.
Wheaton WD, Cajka JC, Chasteen BM, Wagener DK, Cooley PC, Ganapathi L, et al.
Synthesized population databases: A US geospatial database for agent-based models.
RTI Press Publication No. MR-0010-0905. 2009 May.
Lee, BY, Ercius, AK, & Smith, KJ.
A predictive model of the economic effects of an influenza vaccine adjuvant for the older adult (age 65 and over) population.
Vaccine. 2009 Apr 6;27(16):2251-2257.
Yang Y, Halloran ME, Longini IM Jr.
A Bayesian model for evaluating influenza antiviral efficacy in household studies with asymptomatic infections.
Biostatistics. 2009 Apr; 10(2):390-403.
Regev-Yochay G, Lipsitch M, Basset A, Rubinstein E, Dagan R, Raz M, Malley R.
The pneumococcal pilus predicts the absence of Staphylococcus aureus co-colonization in pneumococcal carriers.
Clin Infect Dis. 2009 Mar 15;48(6):760-3.
Lipsitch M, Viboud C.
Influenza seasonality: lifting the fog.
Proc Natl Acad Sci U S A. 2009 Mar 10;106(10):3645-6.
Handel A, Longini IM, and Antia R.
Antiviral resistance and the control of pandemic influenza: the roles of stochasticity, evolution and model details.
J Theor Biol. 2009 Jan 7;256:117-125.
Barrett C, Bisset K, Leidig J, Marathe A, Marathe M.
Estimating the economic impact of public strategies for controlling an epidemic: a multi-agent approach.
In Proceedings of the Twenty-First Innovative Applications of Artificial Intelligence Conference (2009): Pasadena, CA
Johansson MA, Dominici F, Glass GE.
Local and global effects of climate on dengue transmission in Puerto Rico.
PLoS Negl Trop Dis. 2009;3(2):e382.
Yih WK, Teates KS, Abrams A, Kleinman K, Kulldorff M, Pinner R, Harmon R, Wang S, Platt R.
Telephone triage service data for detection of influenza-like illness.
PLoS One. 2009;4(4):e5260. Epub 2009 Apr 17.
2008
Epstein JM, Parker J, Cummings D, Hammond RA.
Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations.
PLoS One. 2008 Dec 16;3(12): e3955.
Basta NE, Halloran ME, Matrajt L, Longini IM Jr.
Estimating influenza vaccine efficacy from challenge and community-based study data.
Am J Epidemiol. 2008 Dec 15;168(12):1343-52.
Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C.
No coexistence for free: neutral null models for multistrain pathogens.
Epidemics, 2008 Nov 4; [Epub ahead of print]
Bobashev G, Morris RJ, Goedecke DM.
Sampling for global epidemic models and the topology of an international airport network.
PLoS One. 2008 Sep;3:3154-3154.
Cooley PC, Roberts D, Bakalov VD, Bikmal S, Cantor S, Costandine T, Ganapathi L, Golla BJ, Grubbs G, Hollingsworth C, Li S, Qin Y, Savage W, Simoni D, Solano E, Wagener D.
The model repository of the models of infectious disease agent study.
IEEE Trans Inf Technol Biomed. 2008 Jul;12:513-522.
Tildesley MJ, Keeling MJ.
Is R(0) a good predictor of final epidemic size: foot-and-mouth disease in the UK.
J Theor Biol. 2009 Jun 21;258(4):623-9. Epub 2009 Mar 6.
Kenah E, Lipsitch M, Robins JM.
Generation interval contraction and epidemic data analysis.
Math Biosci. 2008 May;213(1):71-9.
Takahashi K, Kulldorff M, Tango T, Yih K.
A flexibly shaped space-time scan statistic for disease outbreak detection and monitoring.
Int J Health Geogr. 2008 Apr 11;7:14.
Cauchemez S, Valleron AJ, Boëlle PY, Flahault A, Ferguson NM.
Estimating the impact of school closure on influenza transmission from Sentinel data.
Nature. 2008 Apr 10;452(7188):750-4.
Halloran ME, Ferguson NM, Eubank S, Longini IM Jr, Cummings DAT, Lewis B, Xu S, Fraser C, Vullikanti A, Germann TC, Wagener D, Beckman R, Kadau K, Barrett C, Macken CA, Burke DS, Cooley P.
Modeling targeted layered containment of an influenza pandemic in the United States.
Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4639-44.
Rosvall M, Bergstrom CT.
Maps of random walks on complex networks reveal community structure.
Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1118-23.
Yang Y, Gilbert P, Longini IM, and Halloran ME.
A Bayesian framework for estimating vaccine efficacy per infectious contact.
Annals of Applied Statistics. 2008;2:1409-1431.
Cooley P, Ganapathi L, Ghneim G, Holmberg S, Wheaton W.
Using influenza-like illness data to reconstruct an influenza outbreak.
Mathematical and Computer Modeling. 2008;48:929-939.
2007
Kenah E, Robins JM.
Network-based analysis of stochastic SIR epidemic models with random and proportionate mixing.
J Theor Biol. 2007 Dec 21;249(4):706-22.
Longini IM Jr, Nizam A, Ali M, Yunus M, Shenvi N, Clemens JD.
Controlling endemic cholera with oral vaccines.
PLoS Med. 2007 Nov 27;4(11):e336.
Frank SA, Bush RM.
Barriers to antigenic escape by pathogens: trade-off between reproductive rate and antigenic mutability.
BMC Evol Biol. 2007 Nov 15;7:229-229.
Lipsitch M, O’Hagan JJ.
Patterns of antigenic diversity and the mechanisms that maintain them.
J R Soc Interface. 2007 Oct 22;4(16):787-802.
Schmid-Hempel P, Frank SA.
Pathogenesis, virulence, and infective dose.
PLoS Pathog. 2007 Oct;3(10):e147.
Yang Y, Halloran ME, Sugimoto JD, Longini IM.
Detecting human-to-human transmission of avian influenza A (H5N1).
Emerg Infect Dis. 2007 Sep;13(9):1348-53.
Kenah E, Robins JM.
Second look at the spread of epidemics on networks.
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Sep;76(3 Pt 2):036113.
Pitzer VE, Leung GM, Lipsitch M.
Estimating variability in the transmission of severe acute respiratory syndrome to household contacts in Hong Kong, China.
Am J Epidemiol. 2007 Aug 1;166(3):355-63.
Pitzer VE, Olsen SJ, Bergstrom CT, Dowell SF, Lipsitch M.
Little evidence for genetic susceptibility to influenza A (H5N1) from family clustering data.
Emerg Infect Dis. 2007 Jul;13(7):1074-6.
Yang Y, Longini IM, Halloran ME.
A resampling-based test to detect person-to-person transmission of infectious disease.
Annals of Applied Statistics. 2007 Jun 1;1:211-228.
Halloran ME, Piedra PA, Longini IM Jr, Gaglani MJ, Schmotzer B, Fewlass C, Herschler GB, Glezen WP.
Efficacy of trivalent, cold-adapted, influenza virus vaccine against influenza A (Fujian), a drift variant, during 2003-2004.
Vaccine. 2007 May 16;25(20):4038-45.
Billings L, Schwartz IB, Shaw LB, McCrary M, Burke DS, Cummings DAT.
Instabilities in multiserotype disease models with antibody-dependent enhancement.
J Theor Biol. 2007 May 7;246(1):18-27.
Epstein JM, Goedecke DM, Yu F, Morris RJ, Wagener DK, Bobashev GV.
Controlling pandemic flu: the value of international air travel restrictions.
PLoS ONE. 2007 May 2; 2:e401.
Rosvall M, Bergstrom CT.
An information-theoretic framework for resolving community structure in complex networks.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7327-31.
Hatchett RJ, Mecher CE, Lipsitch M.
Public health interventions and epidemic intensity during the 1918 influenza pandemic.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7582-7.
Bootsma MC, Ferguson NM.
The effect of public health measures on the 1918 influenza pandemic in US cities.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7588-93.
Lessler J, Cummings DA, Fishman S, Vora A, Burke DS.
Transmissibility of swine flu at Fort Dix, 1976.
J R Soc Interface. 2007 Apr 3; [Epub ahead of print]
Handel A, Longini IM Jr., Antia R.
What is the best control strategy for multiple infectious disease outbreaks?
P Roy Soc B-Biol Sci. 2007 Mar 22;274(1611):833-7.
Longini IM Jr, Halloran ME, Nizam A, Yang Y, Xu S, Burke DS, Cummings DA, Epstein JM.
Containing a large bioterrorist smallpox attack: a computer simulation approach.
Int J Infect Dis. 2007 Mar;11(2):98-108.
Wallinga J, Lipsitch M.
How generation intervals shape the relationship between growth rates and reproductive numbers.
Proc Biol Sci. 2007 Feb 22;274(1609):599-604.
Lipsitch M, Cohen T, Murray M, Levin BR.
Antiviral resistance and the control of pandemic influenza.
PLoS Med. 2007 Jan 23;4(1):e15.
Halloran ME, Hayden FG, Yang Y, Longini IM Jr, Monto AS.
Antiviral effects on influenza viral transmission and pathogenicity: observations from household-based trials.
Am J Epidemiol. 2007 Jan 15;165(2):212-21.
2006
Yates A, Antia R, Regoes RR.
How do pathogen evolution and host heterogeneity interact in disease emergence?
Proc Biol Sci. 2006 Dec 22;273(1605):3075-83.
Barbour AG, Dai Q, Restrepo BI, Stoenner HG, Frank SA.
Pathogen escape from host immunity by a genome program for antigenic variation.
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18290-5.
Halloran ME.
Invited commentary: challenges of using contact data to understand acute respiratory disease transmission.
Am J Epidemiol. 2006 Nov 15;164(10):945-6.
Burke DS, Epstein JM, Cummings DA, Parker JI, Cline KC, Singa RM, Chakravarty S.
Individual-based computational modeling of smallpox epidemic control strategies.
Acad Emerg Med. 2006 Nov;13(11):1142-9.
Scharfstein DO, Halloran ME, Chu H, Daniels MJ.
On estimation of vaccine efficacy using validation samples with selection bias.
Biostatistics. 2006 Oct;7(4):615-29.
Handel A, Regoes RR, Antia R.
The role of compensatory mutations in the emergence of drug resistance.
PLoS Comput Biol. 2006 Oct;2(10):e137.
Holmberg SD, Layton CM, Ghneim GS, Wagener DK.
State plans for containment of pandemic influenza.
Emerg Infect Dis. 2006 Sep;12(9):1414-17.
Ferguson NM, Cummings DA, Fraser C, Cajka JC, Cooley PC, Burke DS.
Strategies for mitigating an influenza pandemic.
Nature. 2006 Jul 27;442(7101):448-52.
Mills CE, Robins JM, Bergstrom CT, Lipsitch M.
Pandemic influenza: risk of multiple introductions and the need to prepare for them.
PLoS Med. 2006 Jun;3(6):e135.
Lipsitch M, Robins JM, Mills CE, Bergstrom CT.
Multiple outbreaks and flu containment plans
Science. 2006 May 12;312(5775):845.
Yang Y, Longini IM Jr, Halloran ME.
Design and evaluation of prophylactic interventions using infectious disease incidence data from close contact groups.
Applied Statistics. 2006 May;55(3):317-30.
Germann TC, Kadau K, Longini IM Jr, Macken CA.
Mitigation strategies for pandemic influenza in the United States.
Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5935-40.
Halloran ME, Longini IM Jr.
Public health. Community studies for vaccinating schoolchildren against influenza.
Science. 2006 Feb 3;311(5761):615-6.
Dibble C.
Computational laboratories for spatial agent-based models.
In: Tesfatsion L, Judd KL, eds. Handbook of computational economics, vol 2: Agent-based computational economics. North-Holland: 2006.
2005
Schwartz IB, Shaw LB, Cummings DA, Billings L, McCrary M, Burke DS.
Chaotic desynchronization of multistrain diseases.
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec 1;72(6 Pt 2):066201.
Eubank S.
Network based models of infectious disease spread.
Jpn J Infect Dis. 2005 Dec;58(6):S9-13.
Cummings DA, Schwartz IB, Billings L, Shaw LB, Burke DS.
Dynamic effects of antibody-dependent enhancement on the fitness of viruses.
PNAS. 2005 Oct 18;102(42):15259-64.
Ferguson NM, Cummings DA, Cauchemez S, Fraser C, Riley S, Meeyai A, Iamsirithaworn S, Burke DS.
Strategies for containing an emerging influenza pandemic in Southeast Asia.
Nature. 2005 Sep 8;437(7056):209-14.
Longini IM Jr., Nizam A, Xu S, Ungchusak K, Hanshaoworakul W, Cummings DA, Halloran ME.
Containing pandemic influenza at the source.
Science. 2005 Aug 12;309(5737):1083-7.
Ganusov VV, Antia R.
Pathology during acute infections: contributions of intracellular pathogens and the CTL response.
Biol Lett. 2005 Jun 22;1(2):239-42.
Kulldorff M, Heffernan R, Hartman J, Assunção R, Mostashari F.
A space-time permutation scan statistic for disease outbreak detection.
PLoS Med. 2005 Mar;2(3):e59. Epub 2005 Feb 15.
Barrett CL, Eubank SG, Smith JP.
If smallpox strikes Portland....
Sci Am. 2005 Mar;292(3):42-9.
Longini IM Jr., Halloran ME.
Strategy for distribution of influenza vaccine to high-risk groups and children.
Am J Epidemiol. 2005 Feb 15;161(4):303-6.
2004
Ferguson NM, Fraser C, Donnelly CA, Ghani AC, Anderson RM.
Public health. Public health risks from the avian H5N1 influenza epidemic.
Science. 2004 May 14;304(5673):968-9.