ALL PUBLICATIONS
Aguas R, Ferguson NM
Feature selection methods for identifying genetic determinants of host species in RNA viruses PLoS Comput Biol.. 2013;9(10):e1003254-null
 
Ali ST, Kadi AS, Ferguson NM.
Transmission dynamics of the 2009 influenza A (H1N1) pandemic in India: The impact of holiday-related school closure. Epidemics.. 2013;Dec;5(4):157-63.:null-null
 
Althouse BM, Ng YY, Cummings DA.
Prediction of dengue incidence using search query surveillance PLoS Negl Trop Dis.. 2011;5(8):null-null
 
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;107(1):1696-1701
 
Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM.
Mechanism of 150-cavity formation in influenza neuraminidase Nat Commun.. 2011;2:388-null
 
Andrews JR, Noubary F, Walensky RP, Cerda R, Losina E, Horsburgh CR.
Risk of progression to active tuberculosis following reinfection with Mycobacterium tuberculosis Clin Infect Dis. 2012;54(6):784-791
 
Andrews JR, Wood R, Bekker LG, Middelkoop K, Walensky RP
Projecting the benefits of antiretroviral therapy for HIV prevention: the impact of population mobility and linkage to care J Infect Dis. 2012;206(4):543-551
 
Andrews JR, Lawn SD, Rusu C, Wood R, Noubary F, Bender MA, Horsburgh CR, Losina E, Freedberg KA, Walensky RP.
The cost-effectiveness of routine tuberculosis screening with Xpert MTB/RIF prior to initiation of antiretroviral therapy: a model-based analysis. AIDS. 2012;26(8):987-995
 
Andrews JR, Basu S
Transmission dynamics and control of cholera in Haiti: an epidemic model Lancet. 2011;377(9773):1248-1255
 
Araz OM, Damien P, Paltiel DA, Burke S, Geijn BV, Galvani A, Meyers LA.
Simulating school closure policies for cost effective pandemic decision making BMC Public Health.. 2012;12(1):449-null
 
Araz OM, Galvani A, Meyers LA.
Geographic prioritization of distributing pandemic influenza vaccines Health Care Manag Sci.. 2012;15(3):175-187
 
Archer BN, Tempia S, White LF, Pagano M, Cohen C.
Reproductive number and serial interval of the first wave of influenza A(H1N1)pdm09 virus in South Africa PLoS One. 2012;7(11):e49482-null
 
Assi TM, Brown ST, Kone S, Norman BA, Djibo A, Connor DL, Wateska AR, Rajgopal J, Slayton RB, Lee BY.
Removing the regional level from the Niger vaccine supply chain. Vaccine. 2013;31(26):2828-2834
 
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.
How influenza vaccination policy may affect vaccine logistics. Vaccine. . 2012;30(30):4517-4523
 
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.
Impact of changing the measles vaccine vial size on Niger's vaccine supply chain: a computational model BMC Public Health.. 2011;11(1):425-null
 
Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, Cummings DA, Alabdullatif ZN, Assad M, Almulhim A, Makhdoom H, Madani H, Alhakeem R, Al-Tawfiq JA, Cotten M, Watson SJ, Kellam P, Zumla AI, Memish ZA; the KSA MERS-CoV Investigation Team.
Hospital Outbreak of Middle East Respiratory Syndrome Coronavirus N Engl J Med. . 2013;369(5):407-416
 
Atkins KE, Shim E, Pitzer VE, Galvani AP.
Impact of rotavirus vaccination on epidemiological dynamics in England and Wales. Vaccine. . 2012;30(3):552-564
 
Azman AS, Rudolph KE, Cummings DA, Lessler J.
The incubation period of cholera: a systematic review J Infect.. 2013;66(5):432-438
 
Bacon KM, Hotez PJ, Kruchten SD, Kamhawi S, Bottazzi ME, Valenzuela JG, Lee BY.
The potential economic value of a cutaneous leishmaniasis vaccine in seven endemic countries in the Americas. Vaccine.. 2013;31(3):480-486
 
Bailey RR, Stuckey DR, Norman BA, Duggan AP, Bacon KM, Connor DL, Lee I, Muder RR, Lee BY
Economic value of dispensing home-based preoperative chlorhexidine bathing cloths to prevent surgical site infection Infect Control Hosp Epidemiol.. 2011;32(5):465-471
 
Bansal S, Pourbohloul B, Grenfell B, Meyers LA.
The shifting demographic landscape of influenza. PLoS Currents: Influenza.. 2009;RRN1047:1-1
 
Barbour A.G., Q. Dai, B.I. Restrepo, H.G. Stoenner, and S.A. Frank.
Pathogen Escape from Host Immunity by a Genome Program for Antigenic Variation. Proc Natl Acad Sci U S A.. 2006;103(48):18290-18295
 
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;9:35-35
 
Barrett C, Channakeshava K, Huang F, Kim J, Marathe A, Marathe MV, Pei G, Saha S, Subbiah BS, Vullikanti AK.
Human initiated cascading failures in societal infrastructures PLoS One. . 2012;7(10):e45406-null
 
Barrett C, Beckman R, Bisset K, Chen J, Dubois T, Eubank S, Anil Kumar V, Lewis B, Marathe M, Srinivasan A,and Stretz P
Optimizing Epidemic Protection for Socially Essential Workers 2nd ACM SIGHIT International Health Informatics Symposium, Miami, FL. 2012;(IHI 2012):31-40
 
Barrett CL, Channakeshava K, Eubank S, Anil Kumar VS, Marathe MV.
From biological and social network metaphors to coupled bio-social wireless networks Int J Auton Adapt Commun Syst.. 2011;4(2):122-144
 
Barrett CL, Eubank S, Marathe A, Marathe MV, Pan Z, Swarup S.
Information Integration to Support Model-Based Policy Informatics Innov J. . 2011;16(1):pii: v16i1a2-null
 
Barrett C, Bisset K, Leidig J, Marathe A, Marathe M.
Economic and social impact of influenza mitigation strategies by demographic class. Epidemics. . 2011;3(1):19-31
 
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. 2010;31(1):75-87
 
Barrett CL, Eubank SG, Smith JP
If smallpox strikes Portland.... Scientific American. 2005;292(3):54-61
 
Bartsch SM, Umscheid CA, Fishman N, Lee BY.
Is fidaxomicin worth the cost? An economic analysis. Clin Infect Dis.. 2013;57(4):555-561
 
Basta NE, Chao DL, Halloran ME, Matrajt L, Longini Jr IM
Strategies for pandemic and seasonal influenza vaccination of schoolchildren in the United States American Journal of Epidemiology. 2009;170(6):679-686
 
Basta N, Halloran ME, Matrajt L and Longini IM.
Estimating influenza vaccine efficacy from challenge and community-based study data Am J of Epidemiol. 2008;168(12):1343-1352
 
Beigi RH, Wiringa AE, Bailey RR, Assi TM, Lee BY.
Economic value of seasonal and pandemic influenza vaccination during pregnancy Clin Infect Dis. 2009;49(12):1784-1792
 
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;107(9):4371-4376
 
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;246(1):18-27
 
Bisset K, Marathe M
A CYBER environment to PANDEMIC SciDAC Review. 2009;13:36-47
 
Bobashev G, Morris RJ, Goedecke DM.
Sampling for Global Epidemic Models and the Topology of an International Airport Network PLoS ONE. 2008;3(9):3154-3154
 
Bootsma MC, Ferguson NM.
The effect of public health measures on the 1918 influenza pandemic in U.S. cities. Proc Natl Acad Sci U S A. . 2007;104(18):7588-7593
 
Brown ST, Tai JH, Bailey RR, Cooley PC, Wheaton WD, Potter MA, Voorhees RE, Lejeune M, Grefenstette JJ, Burke DS, McGlone SM, Lee BY
Would school closure for the 2009 H1N1 influenza epidemic have been worth the cost?: a computational simulation of Pennsylvania. BMC Public Health.. 2011;11:353-null
 
Bryant SP, Solano E, Cantor S, Cooley PC, Wagener DK
Sharing Research Models: Using Software Engineering Practices for Facilitation Methods Rep RTI Press.. 2011;Mar:1-16
 
Buckee CO, Wesolowski A, Eagle NN, Hansen E, Snow RW.
Mobile phones and malaria: modeling human and parasite travel Travel Med Infect Dis.. 2013;11(1):15-22
 
Buckee CO, Recker M.
Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum PLoS Comput Biol. . 2012;8(4):e1002451-null
 
Burke DS, Grefenstette JJ
Toward an Integrated Meta-model of Public Health Dynamics for Preparedness Decision Support J Public Health Manag Pract. . 2013;19 Suppl 5:S12-S15
 
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;13(11):1142-1149
 
Cajka, JC, Cooley, PC, Wheaton, WD.
Attribute assignment to a synthetic population in support of agent-based disease modeling RTI Press. 2010;publication No. MR-0019-1009:null-null
 
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 Euro Surveill.. 2013;18(24):pii 20503-null
 
Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, Enouf V, van der Werf S, Ferguson NM.
Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. Lancet Infect Dis.. 2013;Nov 12. pii: S1473-3099(13)70304-9.:null-null
 
Cauchemez S, Epperson S, Biggerstaff M, Swerdlow D, Finelli L, Ferguson NM.
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.. 2013;10(3):e1001399-null
 
Cauchemez S, Horby P, Fox A, Mai le Q, Thanh le T, Thai PQ, Hoa le NM, Hien NT, Ferguson NM.
Influenza infection rates, measurement errors and the interpretation of paired serology. PLoS Pathog.. 2012;8(12):e1003061-null
 
Cauchemez S, Bhattarai A, Marchbanks TL, Fagan RP, Ostroff S, Ferguson NM, Swerdlow D; the Pennsylvania H1N1 working group.
Role of social networks in shaping disease transmission during a community outbreak of 2009 H1N1 pandemic influenza Proc Natl Acad Sci U S A. . 2011;108(7):2825-2830
 
Cauchemez S, Ferguson NM.
Methods to infer transmission risk factors in complex outbreak data J R Soc Interface.. 2011;[Epub ahead of print]:null-null
 
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;361(27):2619-2627
 
Cauchemez S, Valleron AJ, Boelle PY, Flahault A, Ferguson NM
Estimating the impact of school closure on influenza transmission from Sentinel data Nature. 2008;452(7188):750-754
 
Chao DL, Matrajt L, Basta NE, Sugimoto JD, Dean B, Bagwell DA, Oiulfstad B, Halloran ME, Longini IM Jr.
Planning for the Control of Pandemic Influenza A (H1N1) in Los Angeles County and the United States. Am J Epidemiol. . 2011;173(10):1121-1130
 
Chao DL, Bloom JD, Kochin BF, Antia R, Longini IM Jr.
The global spread of drug-resistant influenza J R Soc Interface. 2011;2011 Aug 24 [Epub ahead of print]:1-9
 
Chao DL, Halloran ME, Longini IM Jr
Vaccination strategies for epidemic cholera in Haiti with implications for the developing world Proc Natl Acad Sci U S A.. 2011;108(17):7081-7085
 
Chao DL, Halloran ME, Obenchain VJ, Longini IM Jr.
FluTE, a Publicly Available Stochastic Influenza Epidemic Simulation Model PLoS Comput Biol. 2010;6(1):null-null
 
Chao DL, Halloran ME, Longini IM Jr.
School opening dates predict pandemic influenza A(H1N1) outbreaks in the United States J Infect Dis. 2010;202(6):877-880
 
Chasteen BM, Wheaton WD, Cooley PC, Ganapathi L, Wagener DK.
Including the Group Quarters Population in the US Synthesized Population Database Methods Rep RTI Press. . 2011;20(1102):1-26
 
Cheng CK, Ip DK, Cowling BJ, Ho LM, Leung GM, Lau EH.
Digital dashboard design using multiple data streams for disease surveillance with influenza surveillance as an example J Med Internet Res.. 2011;13(4):e85-null
 
Chrest DP, Wheaton WD.
Using Geographic Information Systems to Define and Map Commuting Patterns as Inputs to Agent-Based Models. Methods Rep RTI Press.. 2009;2009(12):906-930
 
Cobey S, Lipsitch M.
Pathogen diversity and hidden regimes of apparent competition Am Nat. 2013;181(1):12-24
 
Cobey S, Lipsitch M.
Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes Science. 2012;335(6074):1376-1380
 
Cohen T, Manjourides J, Hedt-Gauthier B.
Linking Surveillance with Action against Drug-resistant Tuberculosis Am J Respir Crit Care Med.. 2012;186(5):399-401
 
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;10:355-355
 
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;7(47):905-919
 
Connor TR, Corander J, Hanage WP.
Population subdivision and the detection of recombination in non-typable Haemophilus influenzae Microbiology. . 2012;158(Pt 12):2958-2964
 
Cooley P, Brown S, Cajka J, Chasteen B, Ganapathi L, Grefenstette J, Hollingsworth CR, Lee BY, Levine B, Wheaton WD, Wagener DK
The role of subway travel in an influenza epidemic: a new york city simulation J Urban Health. . 2011;88(5):982-995
 
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;4(2):61-72
 
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(5):929-939
 
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;12(4):513-522
 
Corander J, Connor TR, O'Dwyer CA, Kroll JS, Hanage WP.
Population structure in the Neisseria, and the biological significance of fuzzy species. J R Soc Interface. . 2012;9(71):1208-1215
 
Cornforth DM, Reluga TC, Shim E, Bauch CT, Galvani AP, Meyers LA
Erratic flu vaccination emerges from short-sighted behavior in contact networks PLoS Comput Biol. 2011;7(1):1-10
 
Cowan NJ, Chastain EJ, Vilhena DA, Freudenberg JS, Bergstrom CT.
Nodal dynamics, not degree distributions, determine the structural controllability of complex networks PLoS One.. 2012;7(6):e38398-null
 
Cowling BJ, Freeman G, Wong JY, Wu P, Liao Q, Lau EH, Wu JT, Fielding R, Leung GM.
Preliminary inferences on the age-specific seriousness of human disease caused by avian influenza A(H7N9) infections in China, March to April 2013 Euro Surveill.. 2013;18(19):20475-null
 
Cowling BJ, Ip DK, Fang VJ, Suntarattiwong P, Olsen SJ, Levy J, Uyeki TM, Leung GM, Malik Peiris JS, Chotpitayasunondh T, Nishiura H, Mark Simmerman J.
Aerosol transmission is an important mode of influenza A virus spread. Nat Commun. . 2013;4:1935-null
 
Cowling BJ, Jin L, Lau EH, Liao Q, Wu P, Jiang H, Tsang TK, Zheng J, Fang VJ, Chang Z, Ni MY, Zhang Q, Ip DK, Yu J, Li Y, Wang L, Tu W, Meng L, Wu JT, Luo H, Li Q, Shu Y, Li Z, Feng Z, Yang W, Wang Y, Leung GM, Yu H.
Comparative epidemiology of human infections with avian influenza A H7N9 and H5N1 viruses in China: a population-based study of laboratory-confirmed cases Lancet.. 2013;382(9887):129-137
 
Cowling BJ, Fang VJ, Nishiura H, Chan KH, Ng S, Ip DK, Chiu SS, Leung GM, Peiris JS.
Increased risk of non-influenza respiratory virus infections associated with receipt of inactivated influenza vaccine Clin Infect Dis. . 2012;54(12):1778-1783
 
Cowling BJ, Nishiura H.
Virus interference and estimates of influenza vaccine effectiveness from test-negative studies Epidemiology. . 2012;23(6):930-931
 
Cowling BJ.
Editorial commentary: airborne transmission of influenza: implications for control in healthcare and community settings Clin Infect Dis.. 2012;54(11):1578-1580
 
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;16(3):538-541
 
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;21(6):842-846
 
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;10:82-82
 
Cowling BJ, Fang VJ, Riley S, Malik Peiris JS, Leung GM.
Estimation of the serial interval of influenza Epidemiology. . 2009;20(3):344-347
 
Croucher NJ, Harris SR, Grad YH, Hanage WP.
Bacterial genomes in epidemiology--present and future Philos Trans R Soc Lond B Biol Sci. . 2013;368(1614):20120202-null
 
Cummings DA, Schwartz IB, Billings L, Shaw LB, Burke DS.
Dynamic effects of antibody-dependent enhancement on the fitness of viruses PNAS. 2005;102(42):15259-15264
 
Deodhar S, Bisset K, Chen J, Ma Y, Marathe M
Enhancing User-Productivity and Capability Through Integration of Distinct Software in Epidemiological Systems In 2nd ACM SIGHIT International Health Informatics Symposium, (IHI 2012) Miami, FL. 2012;(IHI 2012):171-180
 
Dimitrov NB, Meyers LA
Mathematical Approaches to Infectious Disease Prediction and Control INFORMS. 2010;isbn 978-0-9843378-0-4:null-null
 
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;RRN1127.:1-1
 
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; pH1N1 Household Investigations Working Group.
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.. 2011;52 Suppl 1:S123-S130
 
Dorigatti I, Cauchemez S, Ferguson NM.
Increased transmissibility explains the third wave of infection by the 2009 H1N1 pandemic virus in England. Proc Natl Acad Sci U S A. . 2013;110(33):13422-13427
 
Dukic VM, David MZ, Lauderdale DS.
Internet queries and methicillin-resistant Staphylococcus aureus surveillance Emerg Infect Dis. 2011;17(6):null-null
 
Durham DP, Casman EA, Albert SM.
Deriving behavior model parameters from survey data: self-protective behavior adoption during the 2009-2010 influenza A(H1N1) pandemic Risk Anal. . 2012;32(12):2020-2031
 
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;[epub ahead of print 2010 Jun 23]:233-243
 
Ejima K, Aihara K, Nishiura H.
Modeling the obesity epidemic: social contagion and its implications for control Theor Biol Med Model.. 2013;10:17-null
 
Ejima K, Omori R, Aihara K, Nishiura H.
Real-time Investigation of Measles Epidemics with Estimate of Vaccine Efficacy Int J Biol Sci. . 2012;8(5):620-629
 
Ejima K, Omori R, Cowling BJ, Aihara K, Nishiura H.
The time required to estimate the case fatality ratio of influenza using only the tip of an iceberg: joint estimation of the virulence and the transmission potential. Comput Math Methods Med.. 2012;2012:978901-null
 
Epstein JM, Pankajakshan R, Hammond RA
Combining Computational Fluid Dynamics and Agent-Based Modeling: a new approach to evacuation planning PLoS One.. 2011;6(5):e20139-null
 
Epstein JM
Modelling to contain pandemics Nature. 2009;460(7256):687-687
 
Epstein JM, Parker J, Cummings D, Hammond RA.
Coupled Contagion Dynamics of Fear and Disease: Mathematical and Computational Explorations. PLoS One. 2008;3(12):3955-3955
 
Epstein JM, D. Goedecke M, Yu F, Morris RJ, Wagener DK, Bobashev GV.
Controlling Pandemic Flu: The Value of International Air Travel Restrictions. PLoS ONE. 2007;2(5):401-401
 
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;4(5):446-455
 
Eubank S.
Network based models of infectious disease spread. Jpn J Infect Dis. 2005;58(6):9-13
 
Everett KH, Potter MA, Wheaton WD, Gleason SM, Brown ST, Lee BY.
Geospatial Analytics to Evaluate Point-of-Dispensing Sites for Mass Immunizations in Allegheny County, Pennsylvania. J Public Health Manag Pract.. 2013;19 Suppl 5:s31-s36
 
Ferguson NM, Cummings DAT, Fraser C, Cajka CC, Cooley PC, Burke DS
Strategies for mitigating an influenza pandemic Nature . 2006;442:448-452
 
Ferguson NM, Cummings DAT, Cauchemez S, Fraser C, Riley S, Meeyai A, Iamsirithaworn S, Burke DS
Strategies for containing an emerging influenza pandemic in Southeast Asia Nature. 2005;437(7056):209-214
 
Ferguson NM, Fraser C, Donnelly CA, Ghani AC, Anderson RM.
Public health. Public health risks from the avian H5N1 influenza epidemic. Science. 2004;304:968-969
 
Fitzpatrick MC, Hampson K, Cleaveland S, Meyers LA, Townsend JP, Galvani AP.
Potential for Rabies Control through Dog Vaccination in Wildlife-Abundant Communities of Tanzania PLoS Negl Trop Dis. . 2012;6(8):e1796-null
 
Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis Nat Genet.. 2013;45(7):784-790
 
Ford CB, Lin PL, Chase MR, Shah RR, Iartchouk O, Galagan J, Mohaideen N, Ioerger TR, Sacchettini JC, Lipsitch M, Flynn JL, Fortune SM.
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection Nat Genet.. 2011;43(5):482-486
 
Frank SA
Demography and the tragedy of the commons J Evol Biol.. 2010;23(1):32-39
 
Frank SA
Evolution in health and medicine Sackler colloquium: 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;107 Suppl 1:1725-1730
 
Frank SA.
The common patterns of nature J Evol Biol.. 2009;22(8):1563-1585
 
Frank SA, Bush RM.
Barriers to antigenic escape by pathogens: trade-off between reproductive rate and antigenic mutability. BMC Evol Biol. 2007;7:229-229
 
Fraser C, Cummings DA, Klinkenberg D, Burke DS, Ferguson NM.
Influenza transmission in households during the 1918 pandemic Am J Epidemiol. . 2011;174(5):505-514
 
Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, Griffin J, Baggaley RF, Jenkins HE, Lyons EJ, Jombart T, Hinsley WR, Grassly NC, Balloux F, Ghani AC, Ferguson NM, Rambaut A, Pybus OG, Lopez-Gatell H, Alpuche-Aranda CM, Chapela IB, Zavala EP, Guevara DM, Checchi F, Garcia E, Hugonnet S, Roth C; WHO Rapid Pandemic Assessment Collaboration.
Pandemic potential of a strain of influenza A (H1N1): early findings Science. 2009;324(5934):1557-1561
 
Fried JR, Gibbons RV, Kalayanarooj S, Thomas SJ, Srikiatkhachorn A, Yoon IK, Jarman RG, Green S, Rothman AL, Cummings DA
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. . 2010;4(3):e617-null
 
Gambhir M, Swerdlow DL, Finelli L, Van Kerkhove MD, Biggerstaff M, Cauchemez S, Ferguson NM.
Multiple contributory factors to the age distribution of disease cases: a modeling study in the context of influenza A(H3N2v) Clin Infect Dis.. 2013;57 Suppl 1:S23-S27
 
Ganusov VV, Antia R.
Pathology during acute infections: contributions of intracellular pathogens and the CTL response Biol Lett.. 2005;1(2):239-242
 
Garske T, Ferguson NM, Ghani AC.
Estimating air temperature and its influence on malaria transmission across Africa PLoS One.. 2013;8(2):e56487-null
 
Gegia M, Jenkins HE, Kalandadze I, Furin J.
Outcomes of children treated for tuberculosis with second-line medications in Georgia, 2009-2011 Int J Tuberc Lung Dis.. 2013;17(5):624-629
 
Germann TC, Kadau K, Longini IM Jr, Macken CA
Mitigation strategies for pandemic influenza in the United States Proc Natl Acad Sci . 2006;103(15):5935-5940
 
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. 2009;RRN1130:1-1
 
Gluckman PD, Bergstrom CT.
Evolutionary biology within medicine: a perspective of growing value BMJ.. 2011;343:d7671-null
 
Goldstein E, Wallinga J, Lipsitch M.
Vaccine allocation in a declining epidemic J R Soc Interface.. 2012;9(76):null-null
 
Goldstein E, Viboud C, Charu V, Lipsitch M.
Improving the estimation of influenza-related mortality over a seasonal baseline Epidemiology. . 2012;23(6):829-838
 
Goldstein E, Kirkcaldy RD, Reshef D, Berman S, Weinstock H, Sabeti P, Del Rio C, Hall G, Hook EW, Lipsitch M.
Factors Related to Increasing Prevalence of Resistance to Ciprofloxacin and Other Antimicrobial Drugs in Neisseria gonorrhoeae, United States. Emerg Infect Dis.. 2012;18(8):1290-1297
 
Goldstein E, Cobey S, Takahashi S, Miller JC, Lipsitch M.
Predicting the Epidemic Sizes of Influenza A/H1N1, A/H3N2, and B: A Statistical Method. PLoS Med. . 2011;8(7):e1001051-null
 
Goldstein E, Cowling BJ, Aiello AE, Takahashi S, King G, Lu Y, Lipsitch M.
Estimating incidence curves of several infections using symptom surveillance data PLoS One. . 2011;6(8):e23380-null
 
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;7(46):755-764
 
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;10(1):211-211
 
Goldstein E, Miller JC, O'Hagan J, Lipsitch M.
Predispensing of antivirals to high-risk individuals in an influenza pandemic. Influenza and Other Respiratory Viruses. 2010;4(2):101-112
 
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;221(1):11-25
 
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;RRN1122.:1-1
 
Goldstein E and Lipsitch M.
H1N1 vaccination and adults with underlying health conditions in the US. Version 2. PLoS Curr Influenza. . 2009;RRN1132.:1-1
 
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;106(51):21825-21829
 
Grad YH, Godfrey P, Cerquiera GC, Mariani-Kurkdjian P, Gouali M, Bingen E, Shea TP, Haas BJ, Griggs A, Young S, Zeng Q, Lipsitch M, Waldor MK, Weill FX, Wortman JR, Hanage WP.
Comparative genomics of recent Shiga toxin-producing Escherichia coli O104:H4: short-term evolution of an emerging pathogen MBio. 2013;4(1):e00452-12-null
 
Grad YH, Lipsitch M, Aiello AE.
Secular Trends in Helicobacter pylori Seroprevalence in Adults in the United States: Evidence for Sustained Race/Ethnic Disparities Am J Epidemiol. . 2012;175(1):54-59
 
Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP.
Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany. Proc Natl Acad Sci U S A.. 2012;109(52):E3629-E3630
 
Grad YH, Miller JC, Lipsitch M.
Cholera modeling: challenges to quantitative analysis and predicting the impact of interventions. Epidemiology. . 2012;23(4):523-530
 
Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-M┐ller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP.
Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011. Proc Natl Acad Sci U S A.. 2012;109(8):3065-3070
 
Greene SK, Kulldorff M, Huang J, Brand RJ, Kleinman KP, Hsu J, Platt R.
Timely detection of localized excess influenza activity in Northern California across patient care, prescription, and laboratory data. Stat Med.. 2011;30(5):549-559
 
Grefenstette JJ, Brown ST, Rosenfeld R, Depasse J, Stone NT, Cooley PC, Wheaton WD, Fyshe A, Galloway DD, Sriram A, Guclu H, Abraham T, Burke DS
FRED (A Framework for Reconstructing Epidemic Dynamics): an open-source software system for modeling infectious diseases and control strategies using census-based populations. BMC Public Health.. 2013;13(1):940-null
 
Grim P, Thomas SB, Fisher S, Reade C, Singer DJ, Garza MA, Fryer Cs, Chatman J.
Polarization and Belief Dynamics in the Black and WHite Communities: An Agent-Based Network Model from the Data Artifical Life. 2013;13:186-193
 
Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, Schmitz MM, Paul P, Rajgopal J, Welling JS, Leonard J, Chen SI, Lee BY.
Augmenting transport versus increasing cold storage to improve vaccine supply chains PLoS One. . 2013;8(5):e64303-null
 
Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, Schmitz MM, Paul P, Rajgopal J, Welling JS, Leonard J, Claypool EG, Weng Y, Chen S, Lee BY.
Only Adding Stationary Storage to Vaccine Supply Chains May Create and Worsen Transport Bottlenecks J Public Health Manag Pract.. 2013;19 Suppl 5:S65-S67
 
Halloran ME, Ferguson NM, Eubank S, Longini IM Jr, Cummings DA, 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;105(12):4639-4644
 
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 (CAIV T) against influenza A (Fujian) during 2003-2004 using surveillance cultures. Vaccine. 2007;25(20):4038-4045
 
Halloran ME, Hayden FG, Yang Y, Longini IM Jr., Monto AS
Antiviral effects on influenza viral transmission and pathogenicity: observations from household-based trials AJE. 2007;165:212-221
 
Halloran ME, Longini IM Jr.
Community studies for vaccinating schoolchildren against influenza Science. 2006;311:615-616
 
Halloran ME.
Invited commentary: Challenges of using contact data to understand acute respiratory disease transmission. Am J Epidemiol. 2006;164(10):945-946
 
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;7(42):35-47
 
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;256(1):117-125
 
Handel A, Longini IM Jr, Antia R
Intervention strategies for an influenza pandemic taking into account secondary bacterial infections. Epidemics. 2009;1(3):185-195
 
Handel A, Longini IM, Antia R.
What is the best control strategy for multiple infectious disease outbreaks? Proc R Soc B. 2007;274(1611):833-837
 
Handel A, Regoes RR, Antia R.
The role of compensatory mutations in the emergence of drug resistance PLoS Comput Biol. 2006;2(10):137-137
 
Hansen E, Buckee CO
Modeling the human infectious reservoir for malaria control: does heterogeneity matter? Trends Parasitol.. 2013;29(6):270-275
 
Hatchett RJ, Mecher CE, Lipsitch M.
Public health interventions and epidemic intensity during the 1918 influenza pandemic. Proc Natl Acad Sci USA. 2007;104(18):7582-7587
 
Hedt BL, van Leth F, Zignol M, Cobelens F, van Gemert W, Nhung NV, Lyepshina S, Egwaga S, Cohen T.
Multidrug Resistance Among New Tuberculosis Cases: Detecting Local Variation Through Lot Quality-assurance Sampling Epidemiology. 2012;23(2):293-300
 
Hedt BL, Laufer MK, Cohen T.
Drug resistance surveillance in resource-poor settings: current methods and considerations for TB, HIV, and malaria. Am J Trop Med Hyg. . 2011;84(2):192-199
 
Hernan MA, Lipsitch M
Oseltamivir and Risk of Lower Respiratory Tract Complications in Patients With Flu Symptoms: A Meta-analysis of Eleven Randomized Clinical Trials Clin Infect Dis.. 2011;53(3):277-279
 
Hernan MA, Lipsitch M.
Reply to cochrane neuraminidase inhibitors review team Clin Infect Dis. 2011;53(12):1303-1304
 
Hladish TJ, Melamud E, Barrera LA, Galvani A, Meyers LA.
EpiFire: An open source C++ library and application for contact network epidemiology BMC Bioinformatics.. 2012;13(17):76-null
 
Holmberg SD, Layton CM, Ghneim GS, Wagener DK.
State plans for containment of pandemic influenza Emerg Infect Dis. 2006;12(9):1414-1417
 
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;7(2):1-10
 
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;31(11):1160-1169
 
Hwang GM, Mahoney PJ, James JH, Lin GC, Berro AD, Keybl MA, Goedecke DM, Mathieu JJ, Wilson T
A model-based tool to predict the propagation of infectious disease via airports Travel Med Infect Dis.. 2012;10(1):32-41
 
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;10(296):1-11
 
Ip DK, Liao Q, Wu P, Gao Z, Cao B, Feng L, Xu X, Jiang H, Li M, Bao J, Zheng J, Zhang Q, Chang Z, Li Y, Yu J, Liu F, Ni MY, Wu JT, Cowling BJ, Yang W, Leung GM, Yu H.
Detection of mild to moderate influenza A/H7N9 infection by China┐s national sentinel surveillance system for influenza-like illness: case series BMJ. 2013;346:f3693-null
 
Ip DK, Schutten M, Fang VJ, Fung RO, Dutkowski RT, Chan KH, Leung GM, Peiris JS, Cowling BJ.
Validation of self-swab for virologic confirmation of influenza virus infections in a community setting J Infect Dis.. 2012;205(4):631-634
 
Izu A, Cohen T, Degruttola V.
Bayesian estimation of mixture models with prespecified elements to compare drug resistance in treatment-na┐ve and experienced tuberculosis cases PLoS Comput Biol.. 2013;9(3):e1002973-null
 
Izu A, Cohen T, Mitnick C, Murray M, Gruttola VD
Bayesian methods for fitting mixture models that characterize branching tree processes: An application to development of resistant TB strains. Stat Med.. 2011;30(22):2708-2720
 
Jacobs JH, Archer BN, Baker MG, Cowling BJ, Heffernan RT, Mercer G, Uez O, Hanshaoworakul W, Viboud C, Schwartz J, Tchetgen Tchetgen E, Lipsitch M
Searching for Sharp Drops in the Incidence of Pandemic A/H1N1 Influenza by Single Year of Age PLoS One.. 2012;7(8):e42328-null
 
Jenkins HE, Ciobanu A, Plesca V, Crudu V, Galusca I, Soltan V, Cohen T.
Risk factors and timing of default from treatment for non-multidrug-resistant tuberculosis in Moldova Int J Tuberc Lung Dis.. 2013;17(3):373-380
 
Jenkins HE, Plesca V, Ciobanu A, Crudu V, Galusca I, Soltan V, Serbulenco A, Zignol M, Dadu A, Dara M, Cohen T.
Assessing spatial heterogeneity of MDR-TB in a high burden country Eur Respir J. 2012;[Epub ahead of print]:null-null
 
Jenkins HE, Zignol M, Cohen T.
Quantifying the burden and trends of isoniazid resistant tuberculosis, 1994-2009. PLoS One. . 2011;6(7):e22927-null
 
Johansson MA, Hombach J, Cummings DA.
Models of the impact of dengue vaccines: a review of current research and potential approaches Vaccine.. 2011;29(35):5860-5868
 
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):1-1
 
Joice R, Lipsitch M
Targeting Imperfect Vaccines against Drug-Resistance Determinants: A Strategy for Countering the Rise of Drug Resistance PLoS One.. 2013;8(7):e68940-null
 
Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N
Bayesian reconstruction of disease outbreaks by combining epidemiologic and genomic data PLoS Comput Biol.. 2014;10(1):null-null
 
Jombart T, Eggo RM, Dodd PJ, Balloux F.
Reconstructing disease outbreaks from genetic data: a graph approach Heredity (Edinb). . 2011;106(2):383-390
 
Jombart T, Ahmed I.
adegenet 1.3-1: new tools for the analysis of genome-wide SNP data Bioinformatics.. 2011;27(21):3070-3071
 
Jung I, Kulldorff M, Kleinman KP, Yih WK, Platt R
Using encounters versus episodes in syndromic surveillance J Public Health (Oxf).. 2009;31(4):566-572
 
Katz LS, Petkau A, Beaulaurier J, Tyler S, Antonova ES, Turnsek MA, Guo Y, Wang S, Paxinos EE, Orata F, Gladney LM, Stroika S, Folster JP, Rowe L, Freeman MM, Knox N, Frace M, Boncy J, Graham M, Hammer BK, Boucher Y, Bashir A, Hanage WP, Van Domselaar G, Tarr CL.
Evolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti MBio. 2013;4(4):e00398-13
 
Ke W, Huang SS, Hudson LO, Elkins KR, Nguyen CC, Spratt BG, Murphy CR, Avery TR, Lipsitch M.
Patient sharing and population genetic structure of methicillin-resistant Staphylococcus aureus Proc Natl Acad Sci U S A.. 2012;109(17):6763-6768
 
Kelly H, Cowling B
Insights from Europe related to pandemic influenza A(H1N1)2009 have international relevance Euro Surveill.. 2011;16(26):pii 19899-null
 
Kenah E, Miller JC.
Epidemic percolation networks, epidemic outcomes, and interventions. Interdiscip Perspect Infect Dis. 2011;2011:543520-null
 
Kenah E, Chao DL, Matrajt L, Halloran ME, Longini IM Jr.
The global transmission and control of influenza PLoS One. . 2011;6(5):e19515-null
 
Kenah E, Lipsitch M, Robins JM.
Generation interval contraction and epidemic data analysis Math Biosci. 2008;213(1):71-79
 
Kenah E, Robins JM.
Second look at the spread of epidemics on networks. Phys Rev E Stat Nonlin Soft Matter Phys.. 2007;76(3):36113-36113
 
Kenah E, Robins JM.
Network-based analysis of stochastic SIR epidemic models with random and proportionate mixing. J Theor Biol. 2007;249(4):706-722
 
Klein EY
The impact of heterogeneous transmission on the establishment and spread of antimalarial drug resistance J Theor Biol. 2014;340:null-null
 
Klick B, Nishiura H, Leung GM, Cowling BJ.
Optimal design of studies of influenza transmission in households. II: Comparison between cohort and case-ascertained studies Epidemiol Infect.. 2013;[Epub ahead of print]:1281-9
 
Klick B, Leung GM, Cowling BJ
Optimal design of studies of influenza transmission in households. I: Case-ascertained studies Epidemiol Infect.. 2012;140(1):106-114
 
Klick B, Nishiura H, Cowling BJ.
Optimal design of intervention studies to prevent influenza in healthy cohorts PLoS One.. 2012;7(4):e35166-null
 
Klick B, Nishiura H, Ng S, Fang VJ, Leung GM, Peiris JS, Cowling BJ.
Transmissibility of seasonal and pandemic influenza in a cohort of households in Hong Kong in 2009 Epidemiology.. 2011;22(6):793-796
 
Koep TH, Enders FT, Pierret C, Ekker SC, Krageschmidt D, Neff KL, Lipsitch M, Shaman J, Huskins WC.
Predictors of indoor absolute humidity and estimated effects on influenza virus survival in grade schools BMC Infect Dis.. 2013;13:71-null
 
Kouyos R, Klein E, Grenfell B.
Hospital-community interactions foster coexistence between methicillin-resistant strains of Staphylococcus aureus PLoS Pathog. . 2013;9(2):e1003134-null
 
Kuhlman C, Kumar VSA, Marathe M, Mortveit H, Swarup S, Tuli G, Ravi SS, Rosenkrantz D
A General-Purpose Graph Dynamical System Modeling Framework Proceedings of the 2011 Winter Simulation Conference (WSC 2011). Phoenix, Arizona, USA. 2011;(WSC 2011):296-308
 
Kulldorff M, Heffernan R, Hartman J, Assun┐┐o R, Mostashari F
A space-time permutation scan statistic for disease outbreak detection PLoS Med.. 2005;2(3):e59-null
 
Kumar S, Grefenstette JJ, Galloway D, Albert SM, Burke DS
Kumar et al. respond Am J Public Health. 2014;104(1):null-null
 
Kumar S, Grefenstette JJ, Galloway D, Albert SM, Burke DS.
. Policies to reduce influenza in the workplace: impact assessments using an agent-based model. Am J Public Health. . 2013;103(8):1406-1411
 
Kwok KO, Leung GM, Riley S.
Modelling the proportion of influenza infections within households during pandemic and non-pandemic years. PLoS One.. 2011;6(7):e22089-null
 
Lajous M, Danon L, Lopez-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 Emerg Infect Dis. 2010;16(9):1488-1499
 
Lam EH, Cowling BJ, Cook AR, Wong JY, Lau MS, Nishiura H.
The feasibility of age-specific travel restrictions during influenza pandemics Theor Biol Med Model. . 2011;8:44-null
 
Lau LL, Ip DK, Nishiura H, Fang VJ, Chan KH, Peiris JS, Leung GM, Cowling BJ.
Heterogeneity in viral shedding among individuals with medically attended influenza A virus infection J Infect Dis.. 2013;207(8):1281-1285
 
Lau LL, Nishiura H, Kelly H, Ip DK, Leung GM, Cowling BJ.
Household Transmission of 2009 Pandemic Influenza A(H1N1): A Systematic Review and Meta-analysis Epidemiology. 2012;23(4):531-542
 
Lau EH, Cheng CK, Ip DK, Cowling BJ
Situational awareness of influenza activity based on multiple streams of surveillance data using multivariate dynamic linear model PLoS One. 2012;7(5):e38346-null
 
Lau EH, Nishiura H, Cowling BJ, Ip DK, Wu JT.
Scarlet fever outbreak, Hong Kong, 2011 Emerg Infect Dis. 2012;18(10):1700-1702
 
Lau L, Cowling BJ, Fang VJ, Chan KH, Lau E, Lipsitch M, Cheng C, Houck PM, Uyeki TM, Peiris J, Leung GM
Viral shedding and clinical illness in naturally acquired influenza virus infections. J Infect Dis. 2010;201(10):1509-1516
 
Lee BY, Bartsch SM, Wong KF, Singh A, Avery TR, Kim DS, Brown ST, Murphy CR, Yilmaz SL, Potter MA, Huang SS.
. The importance of nursing homes in the spread of methicillin-resistant Staphylococcus aureus (MRSA) among hospitals Med Care.. 2013;51(3):205-215
 
Lee BY, Singh A, David MZ, Bartsch SM, Slayton RB, Huang SS, Zimmer SM, Potter MA, Macal CM, Lauderdale DS, Miller LG, Daum RS.
The economic burden of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA). Clin Microbiol Infect.. 2013;19(6):528-536
 
Lee BY, Singh A, Bartsch SM, Wong KF, Kim DS, Avery TR, Brown ST, Murphy CR, Yilmaz SL, Huang SS.
The Potential Regional Impact of Contact Precaution Use in Nursing Homes to Control Methicillin-Resistant Staphylococcus aureus Infect Control Hosp Epidemiol. . 2013;34(2):151-160
 
Lee BY, Bacon KM, Bottazzi ME, Hotez PJ.
Global economic burden of Chagas disease: a computational simulation model. Lancet Infect Dis.. 2013;13(4):342-348
 
Lee BY, Wong KF, Bartsch SM, Yilmaz SL, Avery TR, Brown ST, Song Y, Singh A, Kim DS, Huang SS.
The Regional Healthcare Ecosystem Analyst (RHEA): a simulation modeling tool to assist infectious disease control in a health system. J Am Med Inform Assoc.. 2013;20(e1):e139-e146
 
Lee BY, Yilmaz SL, Wong KF, Bartsch SM, Eubank S, Song Y, Avery TR, Christie R, Brown ST, Epstein JM, Parker JI, Huang SS.
Modeling the regional spread and control of vancomycin-resistant enterococci Am J Infect Control. . 2013;41(8):668-673
 
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
Impact of Introducing the Pneumococcal and Rotavirus Vaccines Into the Routine Immunization Program in Niger Am J Public Health.. 2012;102(2):269-276
 
Lee BY, Bartsch SM, Wong KF, Yilmaz SL, Avery TR, Singh A, Song Y, Kim DS, Brown ST, Potter MA, Platt R, Huang SS.
Simulation shows hospitals that cooperate on infection control obtain better results than hospitals acting alone. Health Aff (Millwood).. 2012;31(10):2295-2303
 
Lee BY, Cakouros BE, Assi TM, Connor DL, Welling J, Kone S, Djibo A, Wateska AR, Pierre L, Brown ST.
The impact of making vaccines thermostable in Niger's vaccine supply chain. Vaccine. . 2012;30(38):5637-5643
 
Lee BY, Bacon KM, Shah M, Kitchen SB, Connor DL, Slayton RB.
The economic value of a visceral leishmaniasis vaccine in Bihar state, India Am J Trop Med Hyg.. 2012;86(3):417-425
 
Lee BY, Brown ST, Bailey RR, Zimmerman RK, Potter MA, McGlone SM, Cooley PC, Grefenstette JJ, Zimmer SM, Wheaton WD, Quinn SC, Voorhees RE, Burke DS.
The benefits to all of ensuring equal and timely access to influenza vaccines in poor communities. Health Aff (Millwood).. 2011;30(6):1141-1150
 
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.
Maintaining vaccine delivery following the introduction of the rotavirus and pneumococcal vaccines in Thailand PLoS One. . 2011;6(9):e24673-null
 
Lee BY, McGlone SM, Doi Y, Bailey RR, Harrison LH.
Economic value of Acinetobacter baumannii screening in the intensive care unit Clin Microbiol Infect. . 2011;17(11):1691-1697
 
Lee BY, Wiringa AE, Mitgang EA, McGlone SM, Afriyie AN, Song Y, Beigi RH.
Routine pre-cesarean Staphylococcus aureus screening and decolonization: a cost-effectiveness analysis Am J Manag Care.. 2011;17(10):693-700
 
Lee BY, Tai JH, McGlone SM, Bailey RR, Wateska AR, Zimmer SM, Zimmerman RK, Wagner MM.
The potential economic value of a 'universal' (multi-year) influenza vaccine Influenza Other Respi Viruses.. 2011; [Epub ahead of print]:doi: 10.1111/j.1750-2659.2011.00288.x-null
 
Lee BY, Song Y, Bartsch SM, Kim DS, Singh A, Avery TR, Brown ST, Yilmaz SL, Wong KF, Potter MA, Burke DS, Platt R, Huang SS.
Long-term care facilities: important participants of the acute care facility social network? PLoS One. . 2011;6(12):e29342-null
 
Lee BY, Stalter RM, Bacon KM, Tai JH, Bailey RR, Zimmer SM, Wagner MM.
Cost-effectiveness of adjuvanted versus nonadjuvanted influenza vaccine in adult hemodialysis patients Am J Kidney Dis. . 2011;57(5):724-732
 
Lee BY, Connor DL, Kitchen SB, Bacon KM, Shah M, Brown ST, Bailey RR, Laosiritaworn Y, Burke DS, Cummings DA
Economic value of dengue vaccine in Thailand. Am J Trop Med Hyg.. 2011;84(5):764-772
 
Lee BY, Assi TM, Rookkapan K, Connor DL, Rajgopal J, Sornsrivichai V, Brown ST, Welling JS, Norman BA, Chen SI, Bailey RR, Wiringa AE, Wateska AR, Jana A, Van Panhuis WG, Burke DS.
Replacing the measles ten-dose vaccine presentation with the single-dose presentation in Thailand. Vaccine. 2011;29(21):3811-3817
 
Lee BY, Wiringa AE.
The 2009 H1N1 influenza pandemic: a case study of how modeling can assist all stages of vaccine decision-making Hum Vaccin. . 2011;7(1):115-119
 
Lee BY, Bacon KM, Donohue JM, Wiringa AE, Bailey RR, Zimmerman RK
From the patient perspective: the economic value of seasonal and H1N1 influenza vaccination Vaccine. 2011;29(11):2149-2158
 
Lee BY, McGlone SM, Song Y, Avery TR, Eubank S, Chang CC, Bailey RR, Wagener DK, Burke DS, Platt R, Huang SS
Social network analysis of patient sharing among hospitals in Orange County, California Am J Public Health. . 2011;101(4):707-713
 
Lee BY, Wettstein ZS, McGlone SM, Bailey RR, Umscheid CA, Smith KJ, Muder RR.
Economic value of norovirus outbreak control measures in healthcare settings. Clin Microbiol Infect. 2011;17(4):640-646
 
Lee BY, Song Y, McGlone SM, Bailey RR, Feura JM, Tai JH, Lewis GJ, Wiringa AE, Smith KJ, Muder RR, Harrison LH, Piraino B.
The economic value of screening haemodialysis patients for methicillin-resistant Staphylococcus aureus in the USA. Clin Microbiol Infect. 2011;17(11):1717-1726
 
Lee BY, Tai JH, Bailey RR, McGlone SM, Wiringa AE, Zimmer SM, Smith KJ, Zimmerman RK.
Economic model for emergency use authorization of intravenous peramivir. Am J Manag Care.. 2011;17(1):e1-9
 
Lee BY, McGlone SM, Wong KF, Yilmaz SL, Avery TR, Song Y, Christie R, Eubank S, Brown ST, Epstein JM, Parker JI, Burke DS, Platt R, Huang SS.
Modeling the Spread of Methicillin-Resistant Staphylococcus aureus (MRSA) Outbreaks throughout the Hospitals in Orange County, California. Infect Control Hosp Epidemiol. . 2011;32(6):562-572
 
Lee BY, McGlone SM, Doi Y, Bailey RR, Harrison LH.
Economic value of Acinetobacter baumannii screening in the intensive care unit. Clin Microbiol Infect.. 2011;17(11):1691-1698
 
Lee BY, McGlone SM, Bailey RR, Wettstein ZS, Umscheid CA, Muder RR.
Economic impact of outbreaks of norovirus infection in hospitals Infect Control Hosp Epidemiol.. 2011;32(2):191-193
 
Lee BY, Bacon KM, Bailey R, Wiringa AE, Smith KJ.
The potential economic value of a hookworm vaccine Vaccine. 2011;29(6):1201-1210
 
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;28(37):5952-5959
 
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;31(10):1087-1089
 
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;31(11):1130-1138
 
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;16(7):e163-e173
 
Lee BY, McGlone SM
Pricing of new vaccines Hum Vaccin. . 2010;6(8):619-626
 
Lee BY, Tai JH, Bailey RR, Smith KJ, Nowalk AJ.
Economics of influenza vaccine administration timing for children Am J Manag Care. . 2010;16(3):e75-e85
 
Lee BY, Wateska AR, Bailey RR, Tai JH, Bacon KM, Smith KJ.
Forecasting the economic value of an Enterovirus 71 (EV71) vaccine. Vaccine. 2010;28(49):7731-7736
 
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;4(12):e916-null
 
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;31(12):1219-1229
 
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;39(5):21-29
 
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;28(29):4653-4660
 
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;28(32):5292-5300
 
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;28(32):5245-5253
 
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;5(6):1-1
 
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;31(6):598-606
 
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;28(31):4875-4879
 
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;28(12):2465-2471
 
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. 2010;16(3):252-261
 
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. 2010;38(3):247-257
 
Lee BY, Mehrotra A, Burns RM, Harris KM.
Alternative vaccination locations: who uses them and can they increase flu vaccination rates? Vaccine. 2009;27(32):4252-4256
 
Lee BY, Tai JH, Bailey RR, Smith KJ.
The timing of influenza vaccination for older adults (65 years and older). Vaccine. 2009;27(50):7110-7115
 
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;114(5):971-980
 
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;30(12):1158-1165
 
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;27(16):2251-2257
 
Lempel H, Epstein JM, Hammond RA.
Economic cost and health care workforce effects of school closures in the U.S. PLoS Currents: Influenza. 2009;RRN1051:1-1
 
Lessler J, Cummings DA, Read JM, Wang S, Zhu H, Smith GJ, Guan Y, Jiang CQ, Riley S.
Location-specific patterns of exposure to recent pre-pandemic strains of influenza A in southern China Nat Commun.. 2011;2:423-null
 
Lessler J, Metcalf CJ, Grais RF, Luquero FJ, Cummings DA, Grenfell BT.
Measuring the performance of vaccination programs using cross-sectional surveys: a likelihood framework and retrospective analysis PLoS Med.. 2011;8(10):e1001110-null
 
Lessler J, dos Santos T, Aguilera X, Brookmeyer R; PAHO Influenza Technical Working Group, Cummings DA
H1N1pdm in the Americas Epidemics.. 2010;2(3):132-138
 
Lessler J, Reich NG, Cummings DA; New York City Department of Health and Mental Hygiene Swine Influenza Investigation Team, Nair HP, Jordan HT, Thompson N.
Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school N Engl J Med. 2009;361(27):2628-2636
 
Lessler J, Cummings DA, Fishman S, Vora A, Burke DS.
Transmissibility of swine flu at Fort Dix, 1976. J R Soc Interface. . 2007;4(15):755-762
 
Levine B, Wilcosky T, Wagener D, Cooley P.
Mass commuting and influenza vaccination prevalence in New York City: Protection in a mixing environment Epidemics. doi:10.1016/j.epidem.2010.07.002. 2010;2(4):183-188
 
Levy JW, Cowling BJ, Simmerman JM, Olsen SJ, Fang VJ, Suntarattiwong P, Jarman RG, Klick B, Chotipitayasunondh T.
. The serial intervals of seasonal and pandemic influenza viruses in households in Bangkok, Thailand Am J Epidemiol. . 2013;177(12):1443-1451
 
Lewis B, Eubank S, Abrams AM, Kleinman K.
In silico surveillance: evaluating outbreak detection with simulation models BMC Med Inform Decis Mak. . 2013;13(1):12-null
 
Li M, Chapman GB, Ibuka Y, Meyers LA, Galvani A
Who got vaccinated against H1N1 pandemic influenza? - A longitudinal study in four US cities. Psychol Health. 2012;27(1):101-115
 
Liao Q, Cowling BJ, Lam WW, Fielding R.
The Influence of Social-Cognitive Factors on Personal Hygiene Practices to Protect Against Influenzas: Using Modelling to Compare Avian A/H5N1 and 2009 Pandemic A/H1N1 Influenzas in Hong Kong. Int J Behav Med. . 2011;18(2):93-104
 
Liao Q, Cowling BJ, Lam WW, Fielding R.
Factors Affecting Intention to Receive and Self-Reported Receipt of 2009 Pandemic (H1N1) Vaccine in Hong Kong: A Longitudinal Study. PLoS One. 2011;6(3):e17713. -null
 
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;5(10):13350-13350
 
Lim C, Hansen E, DeSimone TM, Moreno Y, Junker K, Bei A, Brugnara C, Buckee CO, Duraisingh MT.
Expansion of host cellular niche can drive adaptation of a zoonotic malaria parasite to humans Nat Commun. . 2013;4:1638-null
 
Lin HH, Shin SS, Contreras C, Asencios L, Paciorek CJ, Cohen T.
Use of spatial information to predict multidrug resistance in tuberculosis patients, Peru Emerg Infect Dis. . 2012;18(5):811-813
 
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. . 2011;139(11):1784-1793
 
Link-Gelles R, Thomas A, Lynfield R, Petit S, Schaffner W, Harrison L, Farley MM, Aragon D, Nicols M, Kirley PD, Zansky S, Jorgensen J, Juni BA, Jackson D, Moore MR, Lipsitch M.
Geographic and Temporal Trends in Antimicrobial Nonsusceptibility in Streptococcus pneumoniae in the Post-vaccine era in the United States J Infect Dis. . 2013;208(8):1266-1273
 
Lipsitch M, Hernan MA.
Oseltamivir Effect on Antibiotic-Treated Lower Respiratory Tract Complications in Virologically Positive Randomized Trial Participants Clin Infect Dis.. 2013;[Epub ahead of print]:null-null
 
Lipsitch M, Bloom BR.
Rethinking biosafety in research on potential pandemic pathogens MBio.. 2012;3(5):null-null
 
Lipsitch M, Plotkin JB, Simonsen L, Bloom B.
Evolution, safety, and highly pathogenic influenza viruses. Science. 2012;336(6088):1529-1531
 
Lipsitch M, Finelli L, Heffernan RT, Leung GM, Redd For The 2009 H1n1 Surveillance Group SC.
Improving the Evidence Base for Decision Making During a Pandemic: The Example of 2009 Influenza A/H1N1 Biosecur Bioterror.. 2011;9(2):89-115
 
Lipsitch M, Tchetgen Tchetgen E, Cohen T.
Negative controls: a tool for detecting confounding and bias in observational studies. Epidemiology. 2010;21(3):383-388
 
Lipsitch M and Vlboud C
Influenza seasonality: lifting the fog PNAS. 2009;106(10):3645-3646
 
Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM.
Managing and reducing uncertainty in an emerging influenza pandemic N Engl J Med. 2009;361(2):112-115
 
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;4(9):6895-6895
 
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;374(9696):1209-1211
 
Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C.
No coexistence for free: Neutral null models for multistrain pathogens. Epidemics. doi:10.1016/j.epidem.2008.07.001 .. 2008;1(1):2-13
 
Lipsitch M, O'hagan JJ
Patterns of antigenic diversity and the mechanisms that maintain them J R Soc Interface. 2007;4(16):787-802
 
Lipsitch M., Cohen T., Murray M., Levin B.R.
Antiviral resistance and the control of pandemic influenza PLoS Med.. 2007;4(1):15-15
 
Lipsitch M, Mills C, Robins J.
Estimates of the basic reproductive number for 1918 pandemic influenza in the United States: implications for policy. none- online only. 2007;0:1-1
 
Lipsitch M., Robins J. M., Mills C. E. and Bergstrom C. T.
Multiple outbreaks and flu containment plans. Science. 2006;312(5775):845-845
 
Liu F, Enanoria WT, Ray KJ, Coffee MP, Gordon A, Aragon TJ, Yu G, Cowling BJ, Porco TC
Effect of the one-child policy on influenza transmission in China: a stochastic transmission model PLoS ONE. 2014;In Press:null-null
 
Liu SH, Brotman RM, Zenilman JM, Gravitt PE, Cummings DA
Menstrual Cycle and Detectable Human Papillomavirus in Reproductive-age Women: A Time Series Study J Infect Dis.. 2013;[Epub ahead of print]:null-null
 
Longini IM Jr
A theoretic framework to consider the effect of immunizing schoolchildren against influenza: implications for research Pediatrics.. 2012;129 Suppl 2:S63-S67
 
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. International Journal of Infectious Diseases. 2007;11:98-108
 
Longini IM Jr, Nizam A, Ali M, Yunus M, Shenvi N, Clemens JD.
Controlling endemic cholera with oral vaccines PLoS Med. 2007;4(11):336-null
 
Longini IM Jr., Nizam A, Xu S, Ungchusak K, Hanshaoworakul W, Cummings DAT, Halloran ME
Containing pandemic influenza at the source Science. 2005;309:1083-1087
 
Longini IM and Halloran ME
Strategy for distribution of Influenca Vaccine in High Risk Groups and Children Am J Epidemiol. 2005;161(4):303-306
 
Luangkesorn KL, Ghiasabadi F, Chhatwal J
A Sequential Experimental Design Method to Evaluate a Combination of School Closure and Vaccination Policies to Control an H1N1-Like Pandemic J Public Health Manag Pract.. 2013;19 Suppl 5:S37-S41
 
Luz PM, Vanni T, Medlock J, Paltiel AD, Galvani AP.
Dengue vector control strategies in an urban setting: an economic modelling assessment Lancet.. 2011;377(9778):1673-1680
 
Maher MC, Alemayehu W, Lakew T, Gaynor BD, Haug S, Cevallos V, Keenan JD, Lietman TM, Porco TC.
The fitness cost of antibiotic resistance in Streptococcus pneumoniae: insight from the field PLoS One.. 2012;7(1):e29407-null
 
Manjourides J, Lin HH, Shin S, Jeffery C, Contreras C, Cruz JS, Jave O, Yagui M, Asencios L, Pagano M, Cohen T.
Identifying multidrug resistant tuberculosis transmission hotspots using routinely collected data Tuberculosis (Edinb).. 2012;92(3):273-279
 
Marathe A, Lewis B, Chen J, Eubank S.
Sensitivity of Household Transmission to Household Contact Structure and Size PLoS ONE. 2011;6(8):e22461-null
 
Marathe A, Lewis B, Barrett C, Chen J, Marathe M, Eubank S, Ma Y
Comparing effectiveness of top-down and bottom-up strategies in containing Influenza PLoS ONE. 2011;6(9):e25149-null
 
Marchbanks TL, Bhattarai A, Fagan RP, Ostroff S, Sodha SV, Moll ME, Lee BY, Chang CC, Ennis B, Britz P, Fiore A, Nguyen M, Palekar R, Archer WR, Gift TL, Leap R, Nygren BL, Cauchemez S, Angulo FJ, Swerdlow D; Pennsylvania Working Group
An outbreak of 2009 pandemic influenza A (H1N1) virus infection in an elementary school in Pennsylvania Clin Infect Dis.. 2011;52 Suppl 1:S154-S160
 
Marttinen P, Hanage WP, Croucher NJ, Connor TR, Harris SR, Bentley SD, Corander J.
Detection of recombination events in bacterial genomes from large population samples Nucleic Acids Res.. 2012;40(1):e6-null
 
Matrajt L, Longini IM Jr.
Critical immune and vaccination thresholds for determining multiple influenza epidemic waves Epidemics. 2012;4(1):22-32
 
Matrajt L Jr, Longini IM
Optimizing vaccine allocation at different points in time during an epidemic PLoS One.. 2010;5(11):e13767-null
 
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;191(3):136-137
 
McGlone SM, Bailey RR, Zimmer SM, Popovich MJ, Tian Y, Ufberg P, Muder RR, Lee BY.
The economic burden of Clostridium difficile Clin Microbiol Infect. 2011;[Epub ahead of print]:doi: 10.1111/j.1469-0691.2011.03571.x. -null
 
Medlock J, Meyers LA.
Optimizing allocation for a delayed influenza vaccination campaign. PLoS Curr Influenza. 2009;RRN1134.:1-1
 
Menzies NA, Cohen T, Lin HH, Murray M, Salomon JA.
Population health impact and cost-effectiveness of tuberculosis diagnosis with Xpert MTB/RIF: a dynamic simulation and economic evaluation PLoS Med.. 2012;9(11):e1001347-null
 
Merler S, Ajelli M, Pugliese A, Ferguson NM.
Determinants of the spatiotemporal dynamics of the 2009 H1N1 pandemic in europe: Implications for real-time modelling PLoS Comput Biol.. 2011;7(9):e1002205-null
 
Mier-y-Teran-Romero L, Schwartz IB, Cummings DA.
Breaking the symmetry: immune enhancement increases persistence of dengue viruses in the presence of asymmetric transmission rates J Theor Biol.. 2013;332:203-210
 
Miller JC.
Cocirculation of infectious diseases on networks Phys Rev E Stat Nonlin Soft Matter Phys.. 2013;87(6):060801-null
 
Miller JC, Slim AC, Volz EM.
Edge-based compartmental modelling for infectious disease spread J R Soc Interface.. 2012;9(70):890-906
 
Miller JC, Volz EM.
Model hierarchies in edge-based compartmental modeling for infectious disease spread J Math Biol. . 2012;67(4):869-899
 
Miller JC.
A note on the derivation of epidemic final sizes Bull Math Biol. . 2012;74(9):2125-2141
 
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;5(5):1-7
 
Mills HL, Cohen T, Colijn C.
Community-wide isoniazid preventive therapy drives Sci Transl Med.. 2013;5(180):180ra49-null
 
Mills HL, Cohen T, Colijn C
Modelling the performance of isoniazid preventive therapy for reducing tuberculosis in HIV endemic settings: the effects of network structure J R Soc Interface.. 2011;8(63):1510-1520
 
Mills CE, Robins JM, Bergstrom CT, Lipsitch M.
Pandemic influenza: risk of multiple introductions and the need to prepare for them PLoS Med. 2006;3(6):135-null
 
Min JY, Santos C, Fitch A, Twaddle A, Toyoda Y, DePasse JV, Ghedin E, Subbarao K
Mammalian adaptation in the PB2 gene of avian H5N1 influenza virus J Virol. . 2013;87(19):10884-10888
 
Mitchell SA, Pagano M.
Effective classification of the prevalence of Schistosoma mansoni Trop Med Int Health. 2012;[Epub ahead of print]:null-null
 
Mitchell S, Pagano M.
Pooled testing for effective estimation of the prevalence of Schistosoma mansoni. Am J Trop Med Hyg.. 2012;87(5):850-861
 
Mizumoto K, Ejima K, Yamamoto T, Nishiura H.
Vaccination and clinical severity: is the effectiveness of contact tracing and case isolation hampered by past vaccination? Int J Environ Res Public Health.. 2013;10(3):816-829
 
Mizumoto K, Yamamoto T, Nishiura H.
Age-dependent estimates of the epidemiological impact of pandemic influenza (H1N1-2009) in Japan Comput Math Methods Med. . 2013;2013:637064-null
 
Mizumoto K, Nishiura H, Yamamoto T.
Effectiveness of antiviral prophylaxis coupled with contact tracing in reducing the transmission of the influenza A (H1N1-2009): a systematic review Theor Biol Med Model. . 2013;10:4-null
 
Mostofsky E, Lipsitch M, Regev-Yochay G.
Is methicillin-resistant Staphylococcus aureus replacing methicillin-susceptible S. aureus? J Antimicrob Chemother. . 2011;66(10):2199-2214
 
Ndeffo Mbah ML, Liu J, Bauch CT, Tekel YI, Medlock J, Meyers LA, Galvani AP.
The impact of imitation on vaccination behavior in social contact networks PLoS Comput Biol. . 2012;86(4):e1002469-null
 
Ng S, Fang VJ, Ip DK, Chan KH, Leung GM, Peiris JS, Cowling BJ.
. Estimation of the Association Between Antibody Titers and Protection Against Confirmed Influenza Virus Infection in Children J Infect Dis.. 2013;208(8):1320-1324
 
Ng S, Ip DK, Fang VJ, Chan KH, Chiu SS, Leung GM, Peiris JS, Cowling BJ.
The effect of age and recent influenza vaccination history on the immunogenicity and efficacy of 2009-10 seasonal trivalent inactivated influenza vaccination in children PLoS One.. 2013;8(3):e59077-null
 
Ng S, Fang VJ, Ip DK, Chiu SS, Leung GM, Peiris JS, Cowling BJ.
Humoral antibody response after receipt of inactivated seasonal influenza vaccinations one year apart in children Pediatr Infect Dis J. 2012;31(9):964-969
 
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;50(5):707-714
 
Nishiura H, Mizumoto K.
Epidemiological determinants of successful vaccine development Int J Med Sci.. 2013;10(4):382-384
 
Nishiura H, Yen HL, Cowling BJ
Sample size considerations for one-to-one animal transmission studies of the influenza A viruses PLoS One.. 2013;8(1):e55358-null
 
Nishiura H, Yan P, Sleeman CK, Mode CJ.
Estimating the transmission potential of supercritical processes based on the final size distribution of minor outbreaks J Theor Biol. . 2012;294:48-55
 
Nishiura H, Mizumoto K, Ejima K, Zhong Y, Cowling B, Omori R.
Incubation period as part of the case definition of severe respiratory illness caused by a novel coronavirus Euro Surveill. 2012;17(42):pii: 20296-null
 
Nishiura H, Cook AR, Cowling BJ
Assortativity and the Probability of Epidemic Extinction: A Case Study of Pandemic Influenza A (H1N1-2009). Interdiscip Perspect Infect Dis. . 2011;2011:194507-null
 
Nsoesie EO, Beckman RJ, Marathe MV
Sensitivity Analysis of an Individual-Based Model for Simulation of Influenza Epidemics PLos One. 2012;7(10):e45414-null
 
Nsoesie EO, Beckman R, Marathe M, Bryan L.
Prediction of an Epidemic Curve: A Supervised Classification Approach Stat Commun Infect Dis. 2011;3(1):null-null
 
O'Hagan JJ, Hernan MA, Walensky RP, Lipsitch M.
Apparent declining efficacy in randomized trials: examples of the Thai RV144 HIV vaccine and South African CAPRISA 004 microbicide trials AIDS. . 2012;26(2):123-126
 
Oei W, Nishiura H.
The relationship between tuberculosis and influenza death during the influenza (H1N1) pandemic from 1918-19 Comput Math Methods Med.. 2012;2012:124861-null
 
Omori R, Cowling BJ, Nishiura H.
How is vaccine effectiveness scaled by the transmission dynamics of interacting pathogen strains with cross-protective immunity? PLoS One. 2012;7(11):e50751-null
 
Opatowski L, Fraser C, Griffin J, de Silva E, Van Kerkhove MD, Lyons EJ, Cauchemez S, Ferguson NM.
Transmission characteristics of the 2009 H1N1 influenza pandemic: Comparison of 8 southern hemisphere countries PLoS Pathog.. 2011;7(9):e1002225-null
 
Palmer ME, Lipsitch M, Moxon ER, Bayliss CD.
Broad conditions favor the evolution of phase-variable loci MBio. 2013;4(1):e00430-12-null
 
Pellis L, Ferguson NM, Fraser C.
Epidemic growth rate and household reproduction number in communities of households, schools and workplaces J Math Biol. . 2011;63(4):691-734
 
Pitzer VE, Burgner D, Viboud C, Simonsen L, Andreasen V, Steiner CA, Lipsitch M.
Modelling seasonal variations in the age and incidence of Kawasaki disease to explore possible infectious aetiologies Proc Biol Sci.. 2012;[Epub ahead of print]:null-null
 
Pitzer VE, Atkins KE, de Blasio BF, Van Effelterre T, Atchison CJ, Harris JP, Shim E, Galvani AP, Edmunds WJ, Viboud C, Patel MM, Grenfell BT, Parashar UD, Lopman BA.
Direct and indirect effects of rotavirus vaccination: Comparing predictions from transmission dynamic models PLoS One.. 2012;7(8):e42320-null
 
Pitzer VE, Lipsitch M.
Exploring the relationship between incidence and the average age of infection during seasonal epidemics J Theor Biol.. 2009;260(2):175-185
 
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;166(3):355-363
 
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;13(7):1074-1076
 
Polz MF, Alm EJ, Hanage WP
Horizontal gene transfer and the evolution of bacterial and archaeal population structure Trends Genet.. 2013;29(3):170-175
 
Poon LL, Chan KH, Chu DK, Fung CC, Cheng CK, Ip DK, Leung GM, Peiris JS, Cowling BJ.
Viral genetic sequence variations in pandemic H1N1/2009 and seasonal H3N2 influenza viruses within an individual, a household and a community J Clin Virol. . 2011;52(2):146-150
 
Porco TC, Oh P, Flood JM.
Antituberculosis Drug Resistance Acquired During Treatment: An Analysis of Cases Reported in California, 1994-2006. Clin Infect Dis. . 2012;[Epub ahead of print]:null-null
 
Potter MA.
Dynamics of Preparedness: Systems and Impacts J Public Health Manag Pract.. 2013;19 Suppl 5:s1-s2
 
Potter MA, Brown ST, Lee BY, Grefenstette J, Keane CR, Lin CJ, Quinn SC, Stebbins S, Sweeney PM, Burke DS.
Preparedness for pandemics: does variation among states affect the nation as a whole? J Public Health Manag Pract. . 2012;18(3):233-240
 
Potter GE, Handcock MS, Longini IM Jr, Halloran ME
Estimating within-school contact networks to understand influenza transmission Ann Appl Stat.. 2012;6(1):1-26
 
Potter MA, Brown ST, Cooley PC, Sweeney PM, Hershey TB, Gleason SM, Lee BY, Keane CR, Grefenstette J, Burke DS.
School closure as an influenza mitigation strategy: how variations in legal authority and plan criteria can alter the impact. BMC Public Health.. 2012;12:977-null
 
Potter GE, Handcock MS, Longini IM Jr, Halloran ME.
ESTIMATING WITHIN-HOUSEHOLD CONTACT NETWORKS FROM EGOCENTRIC DATA Ann Appl Stat.. 2011;5(3):1816-1838
 
Pourbohloul B, Ahued A, Davoudi B, Meza R, Meyers LA, Skowronski DM, Villasenor I, Galvan F, Cravioto P, Earn DJ, Dushoff J, Fisman D, Edmunds WJ, Hupert N, Scarpino SV, Trujillo J, Lutzow M, Morales J, Contreras A, Chavez C, Patrick DM, Brunham RC.
Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America Influenza and Other Respiratory Viruses. 2009;3:215-222
 
Presanis AM, Pebody RG, Paterson BJ, Tom BD, Birrell PJ, Charlett A, Lipsitch M, De Angelis D.
Changes in severity of 2009 pandemic A/H1N1 influenza in England: a Bayesian evidence synthesis BMJ. 2011;343:d5408-null
 
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;6(12):null-null
 
Presanis AM, Lipsitch M, Daniela De Angelis; Swine Flu Investigation Team, New York City Department of Health and Mental Hygiene, Hagy A, Reed C, Riley S, Cooper B.
The severity of pandemic H1N1 influenza in the United States, April - July 2009. PLoS Currents: Influenza. 2009;RRN1042:null-null
 
Rajgopal J, Connor DL, Assi TM, Norman BA, Chen SI, Bailey RR, Long AR, Wateska AR, Bacon KM, Brown ST, Burke DS, Lee BY.
The optimal number of routine vaccines to order at health clinics in low or middle income countries. Vaccine. 2011;29(33):5512-5518
 
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;15(12):2004-2007
 
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;48(6):760-763
 
Reich NG, Perl TM, Cummings DA, Lessler J
Visualizing clinical evidence: citation networks for the incubation periods of respiratory viral infections. PLoS One. . 2011;6(4):e19496-null
 
Reshef DN, Reshef YA, Finucane HK, Grossman SR, McVean G, Turnbaugh PJ, Lander ES, Mitzenmacher M, Sabeti PC.
Detecting novel associations in large data sets Science.. 2011;334(6062):1518-1524
 
Riley S, Kwok KO, Wu KM, Ning DY, Cowling BJ, Wu JT, Ho LM, Tsang T, Lo SV, Chu DK, Ma ES, Peiris JS
Epidemiological Characteristics of 2009 (H1N1) Pandemic Influenza Based on Paired Sera from a Longitudinal Community Cohort Study. PloS Med. 2011;8(6):e1000442-null
 
Riley S
Coping without farm location data during a foot-and-mouth outbreak. Proc Natl Acad Sci U S A. 2010;107(3):957-958
 
Rivers C, Lum K, Lewis B, Eubank S
Estimating Human Cases of Avian Influenza A(H7N9) from Poultry Exposure PLOS Currents Outbreaks. 2013;doi: 10.1371/currents.outbreaks.264e737b489bef383fbcbaba60daf928:1-8
 
Roberts DJ
Distributed Agent Based Modeling. Linux Journal. 2010;[Epub only July 21]:null-null
 
Robinson K, Fyson N, Cohen T, Fraser C, Colijn C.
How the dynamics and structure of sexual contact networks shape pathogen phylogenies PLoS Comput Biol. . 2013;9(6):e1003105-null
 
Robinson K, Cohen T, Colijn C.
The Dynamics of Sexual Contact Networks: Effects on Disease Spread and Control Theor Popul Biol. . 2012;81(2):89-96
 
Rodriguez-Barraquer I, Buathong R, Iamsirithaworn S, Nisalak A, Lessler J, Jarman RG, Gibbons RV, Cummings DA.
Revisiting Rayong: Shifting Seroprofiles of Dengue in Thailand and Their Implications for Transmission and Control. Am J Epidemiol.. 2013;[Epub ahead of print]:null-null
 
Rodriguez-Barraquer I, Mier-Y-Teran-Romero L, Schwartz IB, Burke DS, Cummings DA.
Potential opportunities and perils of imperfect dengue vaccines. Vaccine.. 2013;Nov 19. pii: S0264-410X(13)01537-5. :null-null
 
Rodriguez-Barraquer I, Cordeiro MT, Braga C, de Souza WV, Marques ET, Cummings DA
From re-emergence to hyperendemicity: the natural history of the dengue epidemic in Brazil. PLoS Negl Trop Dis.. 2011;5(1):e935-null
 
Rorres C, Pelletier STK, Smith G
Stochastic modeling of animal epidemics using data collected over three different spatial scales Epidemics. 2011;3:61-70
 
Rorres C, Pelletier STK, Bruhn MC, Smith G
Ongoing Estimation of the Epidemic Parameters of a Stochastic, Spatial, Discrete-Time Model for a 1983-84 Avian Influenza Epidemic Avian Diseases . 2011;55(1):35-42
 
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;78(1):46-53
 
Rosvall M, Bergstrom CT
Multilevel compression of random walks on networks reveals hierarchical organization in large integrated systems PLoS One.. 2011;6(4):e18209-null
 
Rosvall M, Bergstrom CT
Mapping change in large networks PLoS One.. 2010;5(1):e8694-null
 
Rosvall M, Bergstrom CT.
Maps of random walks on complex networks reveal community structure Proc Natl Acad Sci U S A. 2008;105(4):1118-1123
 
Rosvall M, CT Bergstrom
An Information-theoretic Framework for Resolving Community Structure in Complex Networks. Proc Natl Acad Sci U S A. 2007;104(18):7327-7331
 
Salje H, Lessler J, Endy TP, Curriero FC, Gibbons RV, Nisalak A, Nimmannitya S, Kalayanarooj S, Jarman RG, Thomas SJ, Burke DS, Cummings DA.
Revealing the microscale spatial signature of dengue transmission and immunity in an urban population Proc Natl Acad Sci U S A.. 2012;109(24):9535-9538
 
Salter SJ, Hinds J, Gould KA, Lambertsen L, Hanage WP, Antonio M, Turner P, Hermans PW, Bootsma HJ, O'Brien KL, Bentley SD.
Variation at the capsule locus, cps, of mistyped and non-typable Streptococcus pneumoniae isolates Microbiology.. 2012;158(Pt 6):1560-1569
 
Sander B, Nizam A, Garrison LP Jr, Postma MJ, Halloran ME, Longini IM Jr
Economic evaluation of influenza pandemic mitigation strategies in the United States using a stochastic microsimulation transmission model Value Health. 2009;12(2):226-233
 
Scharfstein DO, Halloran ME, Chu H, Daniels MJ
On estimation of vaccine efficacy using validation samples with selection bias. Biostatistics. 2006;7(4):615-629
 
Schmid-Hempel P, Frank SA.
Pathogenesis, virulence, and infective dose. PLoS Pathog. 2007;3(10):1372-1373
 
Schuh RG, Tony Eichelberger R, Stebbins S, Pomer B, Duran L, Mahoney JF, Keane C, Lin CJ, Potter MA.
Developing a measure of local agency adaptation to emergencies: a metric Eval Program Plann.. 2012;35(4):473-480
 
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;72(6):66201-66201
 
Scott JR, Hinds J, Gould KA, Millar EV, Reid R, Santosham M, O'Brien KL, Hanage WP.
Nontypeable pneumococcal isolates among navajo and white mountain apache communities: are these really a cause of invasive disease? J Infect Dis.. 2012;206(1):73-80
 
Sergeev R, Colijn C, Murray M, Cohen T.
Modeling the dynamic relationship between HIV and the risk of drug-resistant tuberculosis Sci Transl Med. 2012;4(135):135ra67-null
 
Sergeev R, Colijn C, Cohen T
Models to understand the population-level impact of mixed strain M. tuberculosis infections J Theor Biol. . 2011;280(1):88-100
 
Seto WH, Cowling BJ, Lam HS, Ching PT, To ML, Pittet D.
Clinical and nonclinical health care workers faced a similar risk of acquiring 2009 pandemic H1N1 infection Clin Infect Dis. . 2011;53(3):280-283
 
Shaman J, Lipsitch M.
The El Nino-Southern Oscillation (ENSO)-pandemic Influenza connection: Coincident or causal? Proc Natl Acad Sci U S A. . 2012;[Epub ahead of print]:null-null
 
Shaman J, Karspeck A.
Forecasting seasonal outbreaks of influenza Proc Natl Acad Sci U S A.. 2012;109(50):20425-20430
 
Shaman J, Goldstein E, Lipsitch M.
Absolute humidity and pandemic versus epidemic influenza Am J Epidemiol.. 2011;173(2):127-135
 
Shaman J, Jeon CY, Giovannucci E, Lipsitch M.
Shortcomings of vitamin D-based model simulations of seasonal influenza PLoS One.. 2011;6(6):e20743-null
 
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;8(2):1-1
 
Shaman J, Pitzer VE, Viboud C, Grenfell BT, Lipsitch M.
Absolute Humidity and the Seasonal Onset of Influenza in the Continental United States PLoS Curr. 2009;null(RRN1138):1-13
 
Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szab┐ G, Polz MF, Alm EJ.
Population genomics of early events in the ecological differentiation of bacteria Science. 2012;336(6077):48-51
 
Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, Hanage WP.
Historical Zoonoses and Other Changes in Host Tropism of Staphylococcus PLoS One. 2013;8(5):E62369-null
 
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;10:778-null
 
Shi P, Keskinocak P, Swann JL, Lee BY
Modelling seasonality and viral mutation to predict the course of an influenza pandemic Epidemiol Infect.. 2010;138(10):1472-1481
 
Shim E, Chapman GB, Townsend JP, Galvani AP.
The influence of altruism on influenza vaccination decisions J R Soc Interface.. 2012;9(74):2234-2243
 
Shim E, Feng Z, Castillo-Chavez C.
Differential impact of sickle cell trait on symptomatic and asymptomatic malaria Math Biosci Eng. . 2012;9(4):877-898
 
Shim E, Galvani AP.
Distinguishing vaccine efficacy and effectiveness Vaccine. . 2012;30(47):6700-6705
 
Shim E, Grefenstette JJ, Albert SM, Cakouros BE, Burke DS.
A game dynamic model for vaccine skeptics and vaccine believers: measles as an example J Theor Biol. . 2012;295:194-203
 
Shim E, Meyers LA, Galvani AP.
Optimal H1N1 vaccination strategies based on self-interest versus group interest BMC Public Health.. 2011;11(Suppl 1):S4-null
 
Shim E
Prioritization of delayed vaccination for pandemic influenza Math Biosci Eng.. 2011;8(1):95-112
 
Sir┐n J, Hanage WP, Corander J.
Inference on population histories by approximating infinite alleles diffusion Mol Biol Evol. 2013;30(2):457-468
 
Smith G
Food- and water-borne disease: Using case control studies to estimate the force of infection that accounts for primary, sporadic cases. Epidemics. 2013;5(2):77-84
 
Smith G, Dunipace.S.
How backyard poultry flocks influence the effort required to curtail avian influenza epidemics in commercial poultry flocks. Epidemics. 2011;3:71-75
 
Smith J, Lipsitch M, Almond JW
Vaccine production, distribution, access, and uptake Lancet. 2011;378(9789):428-438
 
Smith KJ, Lee BY, Nowalk MP, Raymund M, Zimmerman RK
Cost-effectiveness of dual influenza and pneumococcal vaccination in 50-year-olds Vaccine.. 2010;28(48):7620-7625
 
Song Y, Tai JH, Bartsch SM, Zimmerman RK, Muder RR, Lee BY.
The potential economic value of a Staphylococcus aureus vaccine among hemodialysis patients Vaccine. . 2012;30(24):3675-3682
 
Stark JH, Sharma R, Ostroff S, Cummings DA, Ermentrout B, Stebbins S, Burke DS, Wisniewski SR.
Local spatial and temporal processes of influenza in Pennsylvania, USA: 2003-2009 PLoS One.. 2012;7(3):e34245-null
 
Stark JH, Cummings DA, Ermentrout B, Ostroff S, Sharma R, Stebbins S, Burke DS, Wisniewski SR.
Local variations in spatial synchrony of influenza epidemics PLoS One. . 2012;7(8):e43528-null
 
Stebbins S, Cummings DA, Stark JH, Vukotich C, Mitruka K, Thompson W, Rinaldo C, Roth L, Wagner M, Wisniewski SR, Dato V, Eng H, Burke DS.
Reduction in the incidence of influenza A but not influenza B associated with use of hand sanitizer and cough hygiene in schools: a randomized controlled trial Pediatr Infect Dis J.. 2011;30(11):921-926
 
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. 2010;138(6):873-883
 
Stromberg SP, Antia R.
Vaccination by delayed treatment of infection Vaccine.. 2011;29(52):9624-9631
 
Sugimoto JD, Borse NN, Ta ML, Stockman LJ, Fischer GE, Yang Y, Halloran ME, Longini IM Jr, Duchin JS
The effect of age on transmission of 2009 pandemic influenza A (H1N1) in a camp and associated households Epidemiology.. 2011;22(2):180-187
 
Sweeney PM, Bjerke EF, Guclu H, Keane CR, Galvan J, Gleason SM, Potter MA.
Social network analysis: a novel approach to legal research on emergency public health systems J Public Health Manag Pract.. 2013;19(6):e38-e40
 
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;7:14-14
 
Tamerius JD, Shaman J, Alonso WJ, Bloom-Feshbach K, Uejio CK, Comrie A, Viboud C.
Environmental predictors of seasonal influenza epidemics across temperate and tropical climates PLoS Pathog.. 2013;9(3):e1003194-null
 
Tamerius, J. D., M. S. Perzanowski, L. M. Acosta, J. S. Jacobson, I. F. Goldstein, J. W. Quinn, A. G. Rundle, J. Shaman
Socioeconomic and Outdoor Meteorological Determinants of Indoor Temperature and Humidity in New York City Dwellings Weather, Climate, and Society. 2013;5(2):168-179
 
Taylor C, Marathe A, Beckman R
Same influenza vaccination strategies but different outcomes across US cities? Int J Infect Dis.. 2010;14(9):e792-e795
 
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;107(3):1041-1046
 
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;258(4):623-629
 
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;276(1671):3239-3248
 
Tracht SM, Del Valle SY, Edwards BK
Economic analysis of the use of facemasks during pandemic (H1N1) 2009 J Theor Biol.. 2012;300:161-172
 
Travis C. Porco, Daozhou Gao, James C. Scott, Eunha Shim, Wayne T. Enanoria, Alison P. Galvani, Thomas M. Lietman
When Does Overuse of Antibiotics Become a Tragedy of the Commons? PLoS One.. 2012;7(12):e46505-null
 
Tuli G, Kuhlman C, Marathe M, Ravi S, Swarup S
Addiction dynamics may explain the slow decline of smoking prevalence Proceedings of International Conference on Social Computing, Behavioral Modeling, and Prediction . 2012;(SBP12), :114-122
 
van Panhuis WG, Grefenstette J, Jung SY, Chok NS, Cross A, Eng H, Lee BY, Zadorozhny V, Brown S, Cummings D, Burke DS.
Contagious diseases in the United States from 1888 to the present. N Engl J Med.. 2013;369(22):2152-2158
 
Van Kerkhove MD, Riley S, Lipsitch M, Guan Y, Monto AS, Webster RG, Zambon M, Nicoll A, Peiris JS, Ferguson NM.
Comment on "Seroevidence for H5N1 influenza infections in humans: meta-analysis". Science. 2012;336(6088):1506-null
 
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;7(6):1-6
 
Volz EM, Miller JC, Galvani A, Ancel Meyers L.
Effects of heterogeneous and clustered contact patterns on infectious disease dynamics PLoS Comput Biol.. 2011;7(6):e1002042-null
 
Wallinga J, van Boven M, Lipsitch M.
Optimizing infectious disease interventions during an emerging epidemic. Proc Natl Acad Sci U S A. 2010;107(2):923-928
 
Wallinga J, Lipsitch M.
How generation intervals shape the relationship between growth rates and reproductive numbers Proc Biol Sci. 2007;274(1609):599-604
 
Wang Y, Feng Z, Yang Y, Self S, Gao Y, Longini IM, Wakefield J, Zhang J, Wang L, Chen X, Yao L, Stanaway JD, Wang Z, Yang W.
Hand, foot, and mouth disease in China: patterns of spread and transmissibility Epidemiology.. 2011;22(6):781-792
 
Warren-Gash C, Bhaskaran K, Hayward A, Leung GM, Lo SV, Wong CM, Ellis J, Pebody R, Smeeth L, Cowling BJ.
Circulating influenza virus, climatic factors, and acute myocardial infarction: a time series study in England and Wales and Hong Kong. J Infect Dis.. 2011;203(12):1710-1718
 
Welch H, Steenhoff AP, Chakalisa U, Arscott-Mills T, Mazhani L, Mokomane M, Foster-Fabiano S, Wirth KE, Skinn A, Pernica JM, Smieja M, Goldfarb DM
Hospital-based surveillance for rotavirus gastroenteritis using molecular testing and immunoassay during the 2011 season in Botswana. Pediatr Infect Dis J.. 2013;32(5):570-572
 
Wells CR, Tchuenche JM, Meyers LA, Galvani AP, Bauch CT
Impact of Imitation Processes on the Effectiveness of Ring Vaccination Bull Math Biol.. 2011;73(11):2748-2772
 
Wendelsdorf KV, Alam M, Bassaganya-Riera J, Bisset K, Eubank S, Hontecillas R, Hoops S, Marathe M.
ENteric Immunity SImulator: A Tool for In Silico Study of Gastroenteric Infections IEEE Trans Nanobioscience. . 2012;11(3):273-288
 
Wendelsdorf K, Bassaganya-Riera J, Hontecillas R, Eubank S
Model of colonic inflammation: immune modulatory mechanisms in inflammatory bowel disease J Theor Biol. . 2010;264(4):1225-1239
 
Wesolowski A, Eagle N, Noor AM, Snow RW, Buckee CO.
The impact of biases in mobile phone ownership on estimates of human mobility. J R Soc Interface.. 2013;10(81):20120986-null
 
Wesolowski A, Buckee CO, Pindolia DK, Eagle N, Smith DL, Garcia AJ, Tatem AJ.
The use of census migration data to approximate human movement patterns across temporal scales PLoS One. 2013;8(12):e52971-null
 
Wesolowski A, Eagle N, Noor AM, Snow RW, Buckee CO.
Heterogeneous mobile phone ownership and usage patterns in Kenya. PLoS One.. 2012;7(4):e35319-null
 
Wesolowski A, Eagle N, Tatem AJ, Smith DL, Noor AM, Snow RW, Buckee CO.
Quantifying the impact of human mobility on malaria Science. 2012;338(6104):267-270
 
Wheaton WD, Cajka JC, Chasteen BM, Wagener DK, Cooley PC, Ganapathi L, Roberts DJ, Allpress JL
Synthesized population databases: A US geospatial database for agent-based models RTI Press. 2009;MR-0010-0905:2-16
 
White LF, Archer B, Pagano M.
Estimating the reproductive number in the presence of spatial heterogeneity of transmission patterns Int J Health Geogr.. 2013;12:35-null
 
White MT, Griffin JT, Churcher TS, Ferguson NM, Bas┐┐ez MG, Ghani AC.
Modelling the impact of vector control interventions on anopheles gambiae population dynamics Parasit Vectors.. 2011;4(153):null-null
 
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;3(6):267-276
 
WHO-VMI Dengue Vaccine Modeling Group, Beatty M, Boni MF, Brown S, Buathong R, Burke D, Coudeville L, Cummings DA, Edelman R, Farrar J, Focks DA, Gomes MG, Guignard A, Halstead S, Hombach J, Knerer G, Koelle K, Lam FC, Lang J, Longini I, Medlock J, Namgyal P, Powell M, Recker M, Rohani P, Standaert B, Struchiner C, Teyssou R, Wearing H.
Assessing the potential of a candidate dengue vaccine with mathematical modeling PLoS Negl Trop Dis.. 2012;6(3):e1450-null
 
Willems RJ, Top J, van Schaik W, Leavis H, Bonten M, Sir┐n J, Hanage WP, Corander J.
Restricted gene flow among hospital subpopulations of Enterococcus faecium MBio. . 2012;3(4):e00151-12-null
 
Willems RJ, Hanage WP, Bessen DE, Feil EJ.
Population biology of Gram-positive pathogens: high-risk clones for dissemination of antibiotic resistance FEMS Microbiol Rev. . 2011;35(5):872-900
 
Wirth KE, Tchetgen Tchetgen EJ, Silverman JG, Murray MB.
How does sex trafficking increase the risk of HIV Infection? An observational study from Southern India. Am J Epidemiol.. 2013;177(3):232-241
 
Wong JY, Wu P, Nishiura H, Goldstein E, Lau EH, Yang L, Chuang SK, Tsang T, Peiris JS, Wu JT, Cowling BJ.
Infection fatality risk of the pandemic A(H1N1)2009 virus in Hong Kong Am J Epidemiol. . 2013;177(8):834-840
 
Wong IO, Cowling BJ, Leung GM, Schooling CM.
Trends in mortality from septicaemia and pneumonia with economic development: an age-period-cohort analysis PLoS One. 2012;7(6):e38988-null
 
Word DP, Cummings DA, Burke DS, Iamsirithaworn S, Laird CD.
A nonlinear programming approach for estimation of transmission parameters in childhood infectious disease using a continuous time model. J R Soc Interface.. 2012;9(73):1983-1997
 
Wu P, Cowling BJ, Wu JT, Lau EH, Ip DK, Nishiura H.
The epidemiological and public health research response to 2009 pandemic influenza A(H1N1): experiences from Hong Kong. Influenza Other Respi Viruses. 2013;7(3):367-382
 
Wu P, Goldstein E, Ho LM, Yang L, Nishiura H, Wu JT, Ip DK, Chuang SK, Tsang T, Cowling BJ.
Excess mortality associated with influenza A and B virus in Hong Kong, 1998-2009 J Infect Dis.. 2012;206(12):1862-1871
 
Wu F, Guclu H.
Aflatoxin regulations in a network of global maize trade. PLoS One. . 2012;7(9):e45151-null
 
Wu JT, Lee CK, Cowling BJ, Yuen KY
Logistical feasibility and potential benefits of a population-wide passive immunotherapy program during an influenza pandemic Influenza Other Respi Viruses.. 2011;5 suppl 1:226-229
 
Wu JT, Ho A, Ma ES, Lee CK, Chu DK, Ho PL, Hung IF, Ho LM, Lin CK, Tsang T, Lo SV, Lau YL, Leung GM, Cowling BJ, Peiris JS
Estimating Infection Attack Rates and Severity in Real Time during an Influenza Pandemic: Analysis of Serial Cross-Sectional Serologic Surveillance Data PLoS Med. . 2011;8(10):e1001103-null
 
Wu JT, Cowling BJ.
The use of mathematical models to inform influenza pandemic preparedness and response Exp Biol Med (Maywood). . 2011;236(8):955-961
 
Wu P, Lau EH, Cowling BJ, Leung CC, Tam CM, Leung GM
The Transmission Dynamics of Tuberculosis in a Recently Developed Chinese City PLoS ONE . 2010;5(5):1-9
 
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;51(10):1184-1191
 
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;107(7):3269-3274
 
Wu JT, Cowling B, 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;16(3):538-541
 
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. doi:10.1371/journal.pmed.1000085. 2009;6:1-1
 
Yaesoubi R, Cohen T
Identifying dynamic tuberculosis case-finding policies for HIV/TB coepidemics Proc Natl Acad Sci U S A. . 2013;110(23):9457-9462
 
Yaesoubi R, Cohen T
Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies Eur J Oper Res.. 2011;215(3):679-687
 
Yaesoubi R, Cohen T.
Dynamic health policies for controlling the spread of emerging infections: influenza as an example PLoS One. . 2011;6(9):e24043-null
 
Yang Y, Longini Jr IM, Halloran ME, Obenchain V.
A Hybrid EM and Monte Carlo EM Algorithm and Its Application to Analysis of Transmission of Infectious Diseases. Biometrics. . 2012;[Epub ahead of print]:null-null
 
Yang Y, Atkinson PM, Ettema D.
Analysis of CDC social control measures using an agent-based simulation of an influenza epidemic in a city BMC Infect Dis. . 2011;11:199-null
 
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;105(492):1310-1322
 
Yang Y, Halloran ME, Longini IM Jr.
A Bayesian model for evaluating influenza antiviral efficacy in household studies with asymptomatic infections Biostatistics. 2009;10(2):390-403
 
Yang Y, Sugimoto JD, Halloran ME, Basta NE, Chao DL, Matrajt L, Potter G, Kenah E, Longini Jr IM
The transmissibility and control of pandemic influenza A (H1N1) virus Science. 2009;326(5953):729-733
 
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(4):1409-1431
 
Yang Y, Longini IM, Halloran ME
A resampling-based test to detect person-to-person transmission of infectious disease Annals of Applied Statistics. 2007;1(1):211-228
 
Yang Y, Halloran ME, Sugimoto J, Longini Jr IM.
Detecting human-to-human transmission of avian influenza A (H5N1) Emerg Infect Dis. 2007;13(9):1348-1353
 
Yang Y, Longini IM, Halloran ME
Design and evaluation of prophylactic interventions using infectious disease incidence data from close contact groups Applied Statistics. 2006;55:317-330
 
Yates A, Antia R, Regoes RR.
How do pathogen evolution and host heterogeneity interact in disease emergence? Proc Biol Sci. 2006;273(1605):3075-3083
 
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 Public Health Rep.. 2010;125(1):111-120
 
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-null
 
Yu H, Cowling BJ, Feng L, Lau EH, Liao Q, Tsang TK, Peng Z, Wu P, Liu F, Fang VJ, Zhang H, Li M, Zeng L, Xu Z, Li Z, Luo H, Li Q, Feng Z, Cao B, Yang W, Wu JT, Wang Y, Leung GM.
Human infection with avian influenza A H7N9 virus: an assessment of clinical severity Lancet.. 2013;382(9887):138-145
 
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.
Transmission dynamics, border entry screening, and school holidays during the 2009 influenza A (H1N1) pandemic, China Emerg Infect Dis. . 2012;18(5):758-766
 
Yuen CM, Tolman AW, Cohen T, Parr JB, Keshavjee S, Becerra MC.
Isoniazid-Resistant Tuberculosis in Children: A Systematic Review Pediatr Infect Dis J. . 2013;[Epub ahead of print]:null-null
 
Zhang Y, Lee BY, Donohue JM.
Ambulatory antibiotic use and prescription drug coverage in older adults Arch Intern Med.. 2010;170(15):1308-1314
 
Zhao Z, Wang G, Butt A, Khan M, Kumar VS Anil, Marathe M
SAHad: Subgraph analysis in massive networks using hadoop. Proc. 26th IEEE International Parallel & Distributed Processing Symposium,. 2012;(IPDPS 2012). :390-401
 
Zhou Y, Lau EH, Ip DK, Nishiura H, Leung GM, Seto WH, Cowling BJ.
Years of Life Lost in the First Wave of the 2009 Influenza A(H1N1) Pandemic in Hong Kong Am J Epidemiol.. 2013;[Epub ahead of print]:null-null
 
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;5(7):e11601-null
 
Zimmer SM, Burke DS.
Historical perspective - Emergence of Influenza A (H1N1) Viruses. N Engl J Med. 2009;361(3):279-285
 
Zimmerman RK, Lauderdale DS, Tan SM, Wagener DK.
Prevalence of high-risk indications for influenza vaccine varies by age, race, and income. Vaccine . 2010;28(39):6470-6477