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Publications

2016

Balmert LC, Buchanich JM, Pringle JL, Williams KE, Burke DS, Marsh GM. Patterns and Trends in Accidental Poisoning Deaths: Pennsylvania's Experience 1979-2014. PLoS One. Public Library of Science; 2016 Jan 10;11(3):e0151655. URL

Buchanich JM, Balmert LC, Pringle JL, Williams KE, Burke DS, Marsh GM. Patterns and trends in accidental poisoning death rates in the US, 1979-2014. Prev Med (Baltim). 2016 Apr 13. URL

Burke DS. Forecasting the opioid epidemic. Science, 2016 Nov 4; 354(6312):529. DOI: 10.1126/science/aal2943. URL

Dalziel BD, Bjørnstad ON, van Panhuis WG, Burke DS, Metcalf CJE, Grenfell BT. Persistent Chaos of Measles Epidemics in the Prevaccination United States Caused by a Small Change in Seasonal Transmission Patterns. PLoS Comput Biol. 2016 Feb;12(2):e1004655. URL

He T, Li K, Roberts MS, Spaulding AC, Ayer T, Grefenstette JJ, et al. Prevention of Hepatitis C by Screening and Treatment in U.S. Prisons. Ann Intern Med. 2016 Jan 19;164(2):84–92. URL

Lessler J, Cummings DAT. Mechanistic Models of Infectious Disease and Their Impact on Public Health. Am J Epidemiol. 2016 Mar 1;183(5):415–22. URL

Lessler J, Salje H, Van Kerkhove MD, Ferguson NM, Cauchemez S, Rodriquez-Barraquer I, et al. Estimating the Severity and Subclinical Burden of Middle East Respiratory Syndrome Coronavirus Infection in the Kingdom of Saudi Arabia. Am J Epidemiol. 2016 Feb 4;183(7):657–63. URL

Metcalf CJE, Farrar J, Cutts FT, Basta NE, Graham AL, Lessler J, et al. Use of serological surveys to generate key insights into the changing global landscape of infectious disease. Lancet (London, England). 2016 Apr 5. URL

Mochan-Keef E, Swigon D, Ermentrout GB, Clermont G. A Three-Tiered Study of Differences in Murine Intrahost Immune Response to Multiple Pneumococcal Strains. PLoS One. 2015;10(8):e0134012. URL

Nisalak A, Clapham HE, Kalayanarooj S, Klungthong C, Thaisomboonsuk B, Fernandez S, et al. Forty Years of Dengue Surveillance at a Tertiary Pediatric Hospital in Bangkok, Thailand, 1973-2012. Am J Trop Med Hyg. 2016 Mar 28. URL

Poon LLM, Song T, Rosenfeld R, Lin X, Rogers MB, Zhou B, et al. Quantifying influenza virus diversity and transmission in humans. Nat Genet. 2016 Jan 4;48(2):195–200. URL

Rodriguez-Barraquer I, Salje H, Cummings DAT. Dengue Vaccine in Regions of Endemic Disease. N Engl J Med. 2016 Apr 7;374(14):1388. URL

2015

Althouse BM, Hanley KA, Diallo M, Sall AA, Ba Y, Faye O, et al. Impact of climate and mosquito vector abundance on sylvatic arbovirus circulation dynamics in Senegal. Am J Trop Med Hyg. 2015 Jan;92(1):88–97. URL

Braithwaite RS, Roberts MS. Validation Is Necessary but Insufficient. Med Decis Making. 2015 Oct;35(7):815–6. URL

Brooks LC, Farrow DC, Hyun S, Tibshirani RJ, Rosenfeld R. Flexible Modeling of Epidemics with an Empirical Bayes Framework. PLoS Comput Biol. 2015 Aug;11(8):e1004382. URL

Clapham H, Cummings DAT, Nisalak A, Kalayanarooj S, Thaisomboonsuk B, Klungthong C, et al. Epidemiology of Infant Dengue Cases Illuminates Serotype-Specificity in the Interaction between Immunity and Disease, and Changes in Transmission Dynamics. PLoS Negl Trop Dis. 2015 Dec;9(12):e0004262. URL

Farrow DC, Burke DS, Rosenfeld R. Computational Characterization of Transient Strain-Transcending Immunity against Influenza A. PLoS One. 2015 Jan;10(5):e0125047. URL

Grim P, Singer DJ, Reade C, Fisher S. Germs, Genes, and Memes: Function and Fitness Dynamics on Information Networks. Philos Sci. 2015;82(2):219–43. URL

Klein EY, Makowsky M, Orlando M, Hatna E, Braykov NP, Laxminarayan R. Influence of provider and urgent care density across different socioeconomic strata on outpatient antibiotic prescribing in the USA. J Antimicrob Chemother. 2015 May;70(5):1580–7. URL

Klein EY, Smith DL, Cohen JM, Laxminarayan R. Bioeconomic analysis of child-targeted subsidies for artemisinin combination therapies: a cost-effectiveness analysis. J R Soc Interface. 2015 Jun 6;12(107). URL

Kraemer MU, Perkins TA, Cummings DAT, Zakar R, Hay SI, Smith DL, et al. Big city, small world: density, contact rates, and transmission of dengue across Pakistan. J R Soc Interface. 2015 Oct 6;12(111). URL

Kumar S, Piper K, Galloway DD, Hadler JL, Grefenstette JJ. Is population structure sufficient to generate area-level inequalities in influenza rates? An examination using agent-based models. BMC Public Health. 2015 Jan;15(1):947. URL

Price I, Mochan-Keef ED, Swigon D, Ermentrout GB, Lukens S, Toapanta FR, et al. The inflammatory response to influenza A virus (H1N1): An experimental and mathematical study. J Theor Biol. 2015 Jun 7;374:83–93. URL

Reich NG, Cummings DAT, Lauer SA, Zorn M, Robinson C, Nyquist A-C, et al. Triggering Interventions for Influenza: The ALERT Algorithm. Clin Infect Dis. 2015 Feb 15;60(4):499–504. URL

Rodriguez-Barraquer I, Mier-y-Teran-Romero L, Ferguson N, Burke DS, Cummings DAT. Differential efficacy of dengue vaccine by immune status. Lancet. 2015 May 2;385(9979):1726. URL

Rodríguez-Barraquer I, Solomon SS, Kuganantham P, Srikrishnan AK, Vasudevan CK, Iqbal SH, et al. The Hidden Burden of Dengue and Chikungunya in Chennai, India. Kittayapong P, editor. PLoS Negl Trop Dis. 2015 Jul 16;9(7):e0003906. URL

Rogers MB, Song T, Sebra R, Greenbaum BD, Hamelin M-E, Fitch A, et al. Intrahost dynamics of antiviral resistance in influenza A virus reflect complex patterns of segment linkage, reassortment, and natural selection. MBio. 2015 Jan;6(2). URL

Ruberto I, Marques E, Burke DS, Van Panhuis WG. The availability and consistency of dengue surveillance data provided online by the World Health Organization. PLoS Negl Trop Dis. 2015 May;9(4):e0003511. URL

Salje H, Cauchemez S, Theresa Alera M, Rodriguez-Barraquer I, Thaisomboonsuk B, Srikiatkhachorn A, et al. Reconstruction of 60 years of chikungunya epidemiology in the Philippines demonstrates episodic and focal transmission. J Infect Dis. 2015 Sep 25. URL

Shrestha S, Foxman B, Berus J, van Panhuis WG, Steiner C, Viboud C, et al. The role of influenza in the epidemiology of pneumonia. Sci Rep. 2015 Jan;5:15314. URL

van Panhuis WG, Choisy M, Xiong X, Chok NS, Akarasewi P, Iamsirithaworn S, et al. Region-wide synchrony and traveling waves of dengue across eight countries in Southeast Asia. Proc Natl Acad Sci U S A. 2015 Oct 20;112(42):13069–74. URL

2014

Althouse BM, Durbin AP, Hanley KA, Halstead SB, Weaver SC, Cummings DAT. Viral kinetics of primary dengue virus infection in non-human primates: a systematic review and individual pooled analysis. Virology. 2014 Mar;452-453:237–46. URL.

Biggerstaff M, Cauchemez S, Reed C, Gambhir M, Finelli L. Estimates of the reproduction number for seasonal, pandemic, and zoonotic influenza: a systematic review of the literature. BMC Infect Dis. 2014 Jan;14:480. URL.

Burke JG, Lich KH, Neal JW, Meissner HI, Yonas M, Mabry PL. Enhancing Dissemination and Implementation Research Using Systems Science Methods. Int J Behav Med. 2014 May 23. URL.

Cauchemez S, Ledrans M, Poletto C, Quenel P, de Valk H, Colizza V, et al. Local and regional spread of chikungunya fever in the Americas. Euro Surveill. 2014 Jan;19(28). URL.

Cauchemez S, Ferguson NM, Fox A, Mai LQ, Thanh LT, Thai PQ, et al. Determinants of Influenza Transmission in South East Asia: Insights from a Household Cohort Study in Vietnam. PLoS Pathog. 2014 Aug;10(8):e1004310. URL.

Cauchemez S, Fraser C, Van Kerkhove MD, Donnelly CA, Riley S, Rambaut A, et al. Middle East respiratory syndrome coronavirus: quantification of the extent of the epidemic, surveillance biases, and transmissibility. Lancet Infect Dis. 2014 Jan;14(1):50–6. URL.

Cauchemez S, Van Kerkhove MD, Archer BN, Cetron M, Cowling BJ, Grove P, et al. School closures during the 2009 influenza pandemic: national and local experiences. BMC Infect Dis. 2014 Jan;14:207. URL.

Churcher TS, Cohen JM, Novotny J, Ntshalintshali N, Kunene S, Cauchemez S. Public health. Measuring the path toward malaria elimination. Science. 2014 Jun 13;344(6189):1230–2. URL.

Clapham HE, Tricou V, Van Vinh Chau N, Simmons CP, Ferguson NM. Within-host viral dynamics of dengue serotype 1 infection. J R Soc Interface. 2014 Jul 6;11(96). URL.

Ferguson NM, Cummings DAT. How season and serotype determine dengue transmissibility. Proc Natl Acad Sci U S A. 2014 Jul 1;111(26):9370–1. URL.

Gog JR, Ballesteros S, Viboud C, Simonsen L, Bjornstad ON, Shaman J, et al. Spatial Transmission of 2009 Pandemic Influenza in the US. PLoS Comput Biol. 2014 Jun;10(6):e1003635. URL.

Guclu H, Ferrell Bjerke E, Galvan J, Sweeney P, Potter MA. State-level legal preparedness for nuclear and radiological emergencies in the U.S.: a network analysis of state laws and regulations. Public Health Rep. 2014 Jan;129 Suppl:154–65. URL.

Jombart T, Aanensen DM, Baguelin M, Birrell P, Cauchemez S, Camacho A, et al. OutbreakTools: a new platform for disease outbreak analysis using the R software. Epidemics. 2014 Jun;7:28–34. URL.

Jombart T, Cori A, Didelot X, Cauchemez S, Fraser C, Ferguson N. Bayesian Reconstruction of Disease Outbreaks by Combining Epidemiologic and Genomic Data. Tanaka MM, editor. PLoS Comput Biol. 2014 Jan 23;10(1):e1003457. URL.

Klein EY. The impact of heterogeneous transmission on the establishment and spread of antimalarial drug resistance. J Theor Biol. 2014 Jan 7;340:177–85. URL.

Klein EY, Graham AL, Llinás M, Levin S. Cross-reactive immune responses as primary drivers of malaria chronicity. Infect Immun. 2014 Jan;82(1):140–51. URL.

Klein EY, Serohijos AWR, Choi J-M, Shakhnovich EI, Pekosz A. Influenza A H1N1 Pandemic Strain Evolution – Divergence and the Potential for Antigenic Drift Variants. Viboud C, editor. PLoS One. 2014 Apr 3;9(4):e93632. URL.

Kumar S, Grefenstette JJ, Galloway D, Albert SM, Burke DS. Kumar et Al. Respond. Am J Public Health. 2014 Jan;104(1):e1–2. URL.

Lessler J, Rodriguez-Barraquer I, Cummings DAT, Garske T, Van Kerkhove M, Mills H, et al. Estimating Potential Incidence of MERS-CoV Associated with Hajj Pilgrims to Saudi Arabia, 2014. PLoS Curr. 2014 Jan;6. URL

Lukens S, DePasse J, Rosenfeld R, Ghedin E, Mochan E, Brown ST, et al. A large-scale immuno-epidemiological simulation of influenza A epidemics. BMC Public Health. 2014 Jan 29;14(1):1019. URL.

May L, Klein EY, Rothman RE, Laxminarayan R. Trends in antibiotic resistance in coagulase-negative staphylococci in the United States, 1999 to 2012. Antimicrob Agents Chemother. 2014 Mar 1;58(3):1404–9. URL.

Mochan E, Swigon D, Ermentrout GB, Lukens S, Clermont G. A mathematical model of intrahost pneumococcal pneumonia infection dynamics in murine strains. J Theor Biol. 2014 Mar 2;353C:44–54. URL.

Mostowy R, Croucher NJ, Hanage WP, Harris SR, Bentley S, Fraser C. Heterogeneity in the Frequency and Characteristics of Homologous Recombination in Pneumococcal Evolution. PLoS Genet. 2014 May;10(5):e1004300. URL.

Pelat C, Ferguson NM, White PJ, Reed C, Finelli L, Cauchemez S, et al. Optimizing the Precision of Case Fatality Ratio Estimates Under the Surveillance Pyramid Approach. Am J Epidemiol. 2014 Sep 25. URL.

Quinn SC, Kumar S. Health inequalities and infectious disease epidemics: a challenge for global health security. Biosecur Bioterror. 2014;12(5):263–73. URL.

Rodriguez-Barraquer I, Buathong R, Iamsirithaworn S, Nisalak A, Lessler J, Jarman RG, et al. Revisiting rayong: shifting seroprofiles of dengue in Thailand and their implications for transmission and control. Am J Epidemiol. 2014 Feb 1;179(3):353–60. URL.

Rodriguez-Barraquer I, Mier-Y-Teran-Romero L, Schwartz IB, Burke DS, Cummings DAT. Potential opportunities and perils of imperfect dengue vaccines. Vaccine. 2014 Jan 16;32(4):514–20. URL.

Rudolph KE, Lessler J, Moloney RM, Kmush B, Cummings DAT. Incubation periods of mosquito-borne viral infections: a systematic review. Am J Trop Med Hyg. 2014 May;90(5):882–91. URL.

Salje H, Rodríguez-Barraquer I, Rainwater-Lovett K, Nisalak A, Thaisomboonsuk B, Thomas SJ, et al. Variability in dengue titer estimates from plaque reduction neutralization tests poses a challenge to epidemiological studies and vaccine development. PLoS Negl Trop Dis. 2014 Jun;8(6):e2952. URL.

Singh A, Bartsch SM, Muder RR, Lee BY. An economic model: value of antimicrobial-coated sutures to society, hospitals, and third-party payers in preventing abdominal surgical site infections. Infect Control Hosp Epidemiol. 2014 Aug;35(8):1013–20. URL.

Skene KJ, Paltiel AD, Shim E, Galvani AP. A marginal benefit approach for vaccinating influenza “superspreaders”. Med Decis Making. 2014 May;34(4):536–49. URL.

Smith DL, Perkins TA, Reiner RC, Barker CM, Niu T, Chaves LF, et al. Recasting the theory of mosquito-borne pathogen transmission dynamics and control. Trans R Soc Trop Med Hyg. 2014 Apr;108(4):185–97. URL.

van Panhuis WG, Hyun S, Blaney K, Marques ETA, Coelho GE, Siqueira JB, et al. Risk of Dengue for Tourists and Teams during the World Cup 2014 in Brazil. PLoS Negl Trop Dis. 2014 Jan;8(7):e3063. URL.

van Panhuis WG, Paul P, Emerson C, Grefenstette J, Wilder R, Herbst AJ, et al. A systematic review of barriers to data sharing in public health. BMC Public Health. 2014 Jan;14(1):1144. URL.

Wu C, Rosenfeld R, Clermont G. Using data-driven rules to predict mortality in severe community acquired pneumonia. PLoS One. 2014 Jan;9(4):e89053. URL.

Ebola Virus Disease in West Africa - The First 9 Months of the Epidemic and Forward Projections. N Engl J Med. 2014 Sep 22;371(16):1481–95. URL.

Ferguson NM, Van Kerkhove MD. Identification of MERS-CoV in dromedary camels. Lancet Infect Dis. 2014 Feb;14(2):93–4. URL.

Kwok KO, Jiang C, Tan L, Justin L, Read JM, Zhu H, et al. [An international collaborative study on influenza viruses antibody titers and contact patterns of individuals in rural and urban household of Guangzhou]. Zhonghua Liu Xing Bing Xue Za Zhi. 2014 Apr;35(4):433–6. URL.

2013

Aguas R, Ferguson NM. Feature selection methods for identifying genetic determinants of host species in RNA viruses. PLoS Comput Biol. 2013 Oct;9(10):e1003254. URL.

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. URL.

Ampofo WK, Baylor N, Cobey S, Cox NJ, Daves S, Edwards S, et al. Improving influenza vaccine virus selection: report of a WHO informal consultation held at WHO headquarters, Geneva, Switzerland, 14-16 June 2010. Influenza Other Respi Viruses. 2013 Sep;7 Suppl 2:52–3. URL.

Assi T-M, Brown ST, Kone S, Norman BA, Djibo A, Connor DL, et al. Removing the regional level from the Niger vaccine supply chain. Vaccine. 2013 Apr 17. URL.

Assiri A, McGeer A, Perl TM, Price CS, Al Rabeeah AA, Cummings DAT, et al. Hospital outbreak of Middle East respiratory syndrome coronavirus. N Engl J Med. 2013 Aug 1;369(5):407–16. URL.

Azman AS, Rudolph KE, Cummings DAT, Lessler J. The incubation period of cholera: a systematic review. J Infect. 2013 May;66(5):432–8. URL.

Bacon KM, Hotez PJ, Kruchten SD, Kamhawi S, Bottazzi ME, Valenzuela JG, et al. The potential economic value of a cutaneous leishmaniasis vaccine in seven endemic countries in the Americas. Vaccine. 2013 Jan 7;31(3):480–6. URL.

Bartsch SM, Umscheid CA, Fishman N, Lee BY. Is Fidaxomicin worth the cost? An economic analysis. Clin Infect Dis. 2013 May 23. URL.

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 2:S12–5. URL.

Cauchemez S, Van Kerkhove M, Riley S, Donnelly C, Fraser C, Ferguson N. Transmission scenarios for Middle East Respiratory Syndrome Coronavirus (MERS-CoV) and how to tell them apart. Euro Surveill. 2013 Jan;18(24). URL.

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. Peiris JSM, editor. PLoS Med. 2013 Mar 5;10(3):e1001399. URL.

Cori A, Ferguson NM, Fraser C, Cauchemez S. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidemiol. 2013 Nov 1;178(9):1505–12. URL.

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 Jul 23;110(33):13422–7. URL.

Potter MA. Dynamics of preparedness: systems and impacts. J Public Health Manag Pract. 2013 Jan;19:S1–2. URL.

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 2:S31–6. URL.

Gambhir M, Swerdlow DL, Finelli L, Van Kerkhove MD, Biggerstaff M, Cauchemez S, et al. Multiple Contributory Factors to the Age Distribution of Disease Cases: A Modeling Study in the Context of Influenza A(H3N2v). Clin Infect Dis. 2013 Jul;57 Suppl 1:S23–7. URL.

Garske T, Ferguson NM, Ghani AC. Estimating Air Temperature and Its Influence on Malaria Transmission across Africa. PLoS One. 2013 Jan;8(2):e56487. URL.

Grefenstette JJ, Brown ST, Rosenfeld R, Depasse J, Stone NT, Cooley PC, et al. 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 Oct 8;13(1):940. URL

Grim P, Singer DJ, Fisher S, Bramson A, Berger WJ, Reade C, et al. Scientific Networks on Data Landscapes: Question Difficulty, Epistemic Success, and Convergence. Episteme (Edinb). 2013 Dec 1;10(4):441–64. URL

Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, et al. Augmenting transport versus increasing cold storage to improve vaccine supply chains. PLoS One. 2013 Jan;8(5):e64303. URL.

Haidari LA, Connor DL, Wateska AR, Brown ST, Mueller LE, Norman BA, et al. Only adding stationary storage to vaccine supply chains may create and worsen transport bottlenecks. J Public Health Manag Pract. 2013;19 Suppl 2:S65–7. URL.

Klein EY. Antimalarial drug resistance: a review of the biology and strategies to delay emergence and spread. Int J Antimicrob Agents. 2013 Feb 7;41(4):311–7. URL.

Klein EY, Laxminarayan R. The potential impact of age and season on methicillin-resistant Staphylococcus aureus prevalence. Future Microbiol. 2013 Jul;8(7):809–12. URL.

Kouyos R, Klein E, Grenfell B. Hospital-Community Interactions Foster Coexistence between Methicillin-Resistant Strains of Staphylococcus aureus. Levin BR, editor. PLoS Pathog. 2013 Feb 28;9(2):e1003134. URL.

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. American Public Health Association; 2013 Jun 13;e1–6. URL.

Lee BY, Singh A, David MZ, Bartsch SM, Slayton RB, Huang SS, et al. The economic burden of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA). Clin Microbiol Infect. 2013 Jun 21;19(6):528–36. URL.

Lee BY, Bacon KM, Bottazzi ME, Hotez PJ. Global economic burden of Chagas disease: a computational simulation model. Lancet Infect Dis. 2013 Feb 7. URL.

Lee BY, Bartsch SM, Wong KF, Singh A, Avery TR, Kim DS, et al. The Importance of Nursing Homes in the Spread of Methicillin-resistant Staphylococcus aureus (MRSA) Among Hospitals. Med Care. 2013 Jan 25. URL.

Lee BY, Singh A, Bartsch SM, Wong KF, Kim DS, Avery TR, et al. The Potential Regional Impact of Contact Precaution Use in Nursing Homes to Control Methicillin-Resistant Staphylococcus aureus. Infect Control Hosp Epidemiol. 2013 Mar;34(2):151–60. URL.

Lee BY, Wong KF, Bartsch SM, Yilmaz SL, Avery TR, Brown ST, et al. 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 Apr 9. URL.

Lee BY, Yilmaz SL, Wong KF, Bartsch SM, Eubank S, Song Y, et al. Modeling the regional spread and control of vancomycin-resistant enterococci. Am J Infect Control. 2013 Aug;41(8):668–73. URL.

Liu S-H, Brotman RM, Zenilman JM, Gravitt PE, Cummings DAT. Menstrual Cycle and Detectable Human Papillomavirus in Reproductive Women: A Time Series Study. J Infect Dis. 2013 Jul 24. URL.

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 2:S37–41. URL.

Lukens S, Clermont G, Swigon D. Sensitivity of human immune response to influenza a virus infection and its dependence on virus and host phenotypes. J Crit Care. 2013 Feb;28(1):e7–8. URL.

Mier-Y-Teran-Romero L, Schwartz IB, Cummings DAT. Breaking the symmetry: Immune enhancement increases persistence of dengue viruses in the presence of asymmetric transmission rates. J Theor Biol. 2013 May 7;332C:203–10. URL.

Min J-Y, Santos C, Fitch A, Twaddle A, Toyoda Y, Depasse J V, et al. Mammalian adaptation in the PB2 gene of avian H5N1 influenza virus. J Virol. 2013 Jul 17. URL.

Potter MA, Houck OC, Miner K, Shoaf K. Data for preparedness metrics: legal, economic, and operational. J Public Health Manag Pract. 2013;19 Suppl 2:S22–7. URL.

Reich NG, Shrestha S, King AA, Rohani P, Lessler J, Kalayanarooj S, et al. Interactions between serotypes of dengue highlight epidemiological impact of cross-immunity. J R Soc Interface. 2013 Jan;10(86):20130414. URL.

Rodriguez-Barraquer I, Mier-y-Teran-Romero L, Burke DS, Cummings DAT. Challenges in the interpretation of dengue vaccine trial results. PLoS Negl Trop Dis. 2013 Jan;7(8):e2126. URL.

Shepheard MA, Fleming VM, Connor TR, Corander J, Feil EJ, Fraser C, et al. Historical Zoonoses and Other Changes in Host Tropism of Staphylococcus aureus, Identified by Phylogenetic Analysis of a Population Dataset. PLoS One. 2013 Jan;8(5):e62369. URL.

Shim E. Optimal strategies of social distancing and vaccination against seasonal influenza. Math Biosci Eng. 2013;10(5-6):1615–34. URL.

Sweeney PM, Bjerke EF, Guclu H, Keane CR, Galvan J, Gleason SM, et al. Social network analysis: a novel approach to legal research on emergency public health systems. J Public Health Manag Pract. 2013;19(6):E38–40. URL.

Toner ES, Adalja AA, Nuzzo JB, Inglesby T V, Henderson DA, Burke DS. Assessment of serosurveys for H5N1. Clin Infect Dis. 2013 May;56(9):1206–12. URL.

van Panhuis WG, Grefenstette J, Jung SY, Chok NS, Cross A, Eng H, et al. Contagious diseases in the United States from 1888 to the present. N Engl J Med. 2013 Nov 28;369(22):2152–8. URL.

Yonas MA, Burke JG, Brown ST, Borrebach JD, Garland R, Burke DS, et al. Dynamic simulation of crime perpetration and reporting to examine community intervention strategies. Health Educ Behav. 2013 Oct;40(1 Suppl):87S – 97S. URL.

Pepin KM, Wang J, Webb CT, Smith GJD, Poss M, Hudson PJ, et al. Multiannual patterns of influenza A transmission in Chinese live bird market systems. Influenza Other Respi Viruses. 2013 Jan;7(1):97–107. URL.

2012

Albert SM. Time to specify mechanisms of community health benefit or harm. Prev Med (Baltim). 2012 Dec;55(6):563–4. URL.

Albert SM, Duffy J. Differences in risk aversion between young and older adults. Neurosci Neuroeconomics. 2012;1(1):3–9. URL.

Althouse BM, Lessler J, Sall AA, Diallo M, Hanley KA, Watts DM, et al. Synchrony of sylvatic dengue isolations: a multi-host, multi-vector SIR model of dengue virus transmission in Senegal. PLoS Negl Trop Dis. 2012 Nov;6(11):e1928. URL.

Assi T-M, Rookkapan K, Rajgopal J, Sornsrivichai V, Brown ST, Welling JS, et al. How influenza vaccination policy may affect vaccine logistics. Vaccine. 2012 Jun 22;30(30):4517–23. URL.

Atkins KE, Shim E, Pitzer VE, Galvani AP. Impact of rotavirus vaccination on epidemiological dynamics in England and Wales. Vaccine. 2012 Jan 11;30(3):552–64. URL.

Bartsch SM, Curry SR, Harrison LH, Lee BY. The potential economic value of screening hospital admissions for Clostridium difficile. Eur J Clin Microbiol Infect Dis. 2012 Nov;31(11):3163–71. URL.

Bartsch SM, Lopman BA, Hall AJ, Parashar UD, Lee BY. The potential economic value of a human norovirus vaccine for the United States. Vaccine. 2012 Nov 19;30(49):7097–104. URL.

Beutel A, Prakash BA, Rosenfeld R, Faloutsos C. Interacting viruses in networks. Proceedings of the 18th ACM SIGKDD international conference on Knowledge discovery and data mining - KDD ’12. New York, New York, USA: ACM Press; 2012. p. 426–34. URL.

Blackwood JC, Cummings DAT, Broutin H, Iamsirithaworn S, Rohani P. The population ecology of infectious diseases: pertussis in Thailand as a case study. Parasitology. 2012 Dec;139(14):1888–98. URL.

Burton J, Billings L, Cummings DAT, Schwartz IB. Disease persistence in epidemiological models: the interplay between vaccination and migration. Math Biosci. 2012 Sep;239(1):91–6. URL.

Cauchemez S, Horby P, Fox A, Mai LQ, Thanh LT, Thai PQ, et al. Influenza infection rates, measurement errors and the interpretation of paired serology. PLoS Pathog. 2012 Dec;8(12):e1003061. URL.

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

Durham DP, Casman EA. Incorporating individual health-protective decisions into disease transmission models: a mathematical framework. J R Soc Interface. 2012 Mar 7;9(68):562–70. URL.

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 Dec;32(12):2020–31. URL.

Ghedin E, Holmes EC, DePasse J V, Pinilla LT, Fitch A, Hamelin M-E, et al. Presence of oseltamivir-resistant pandemic A/H1N1 minor variants before drug therapy with subsequent selection and transmission. J Infect Dis. 2012 Nov 15;206(10):1504–11. URL.

Grim P. Epistemology of Modeling and Simulation: Variations on a Theme. Philos Technol. 2012 Jun 7;26(1):73–4. URL.

Grim P, Thomas SB, Fisher S, Reade C, Singer DJ, Garza MA, et al. Polarization and Belief Dynamics in the Black and White Communities: An Agent-Based Network Model from the Data. Artificial Life 13. MIT Press; 2012. p. 186–93. URL.

Lee BY, Assi T-M, Rajgopal J, Norman BA, Chen S-I, Brown ST, et al. Impact of introducing the pneumococcal and rotavirus vaccines into the routine immunization program in Niger. Am J Public Health. 2012 Feb;102(2):269–76. URL.

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 Mar 1;86(3):417–25. URL.

Lee BY, Bartsch SM, Willig AM. The economic value of a quadrivalent versus trivalent influenza vaccine. Vaccine. 2012 Dec 14;30(52):7443–6. URL.

Lee BY, Bartsch SM, Wong KF, Yilmaz SL, Avery TR, Singh A, et al. Simulation shows hospitals that cooperate on infection control obtain better results than hospitals acting alone. Health Aff (Millwood). 2012 Oct;31(10):2295–303. URL.

Lee BY, Cakouros BE, Assi T-M, Connor DL, Welling J, Kone S, et al. The impact of making vaccines thermostable in Niger’s vaccine supply chain. Vaccine. 2012 Aug 17;30(38):5637–43. URL.

Lee BY, Tai JHY, McGlone SM, Bailey RR, Wateska AR, Zimmer SM, et al. The potential economic value of a “universal” (multi-year) influenza vaccine. Influenza Other Respi Viruses. 2012 May;6(3):167–75. URL.

Lukens S, DePasse J V., Swigon D, Miller D, Rosenfield R, Ghedin E, et al. Linking population-level and host-level models of influenza A virus. J Crit Care. 2012 Jun;27(3):e12. URL.

Mitchell MD, Hong JA, Lee BY, Umscheid CA, Bartsch SM, Don CW. Systematic review and cost-benefit analysis of radial artery access for coronary angiography and intervention. Circ Cardiovasc Qual Outcomes. 2012 Jul 1;5(4):454–62. URL.

Paparian J, Brown S, Burke D, Grefenstette J. FRED Navigator: An interactive system for visualizing results from large-scale epidemic simulations. 2012 IEEE 8th International Conference on E-Science. IEEE; 2012. p. 1–5. URL.

Porco TC, Gao D, Scott JC, Shim E, Enanoria WT, Galvani AP, et al. When Does Overuse of Antibiotics Become a Tragedy of the Commons? PLoS One. 2012 Jan;7(12):e46505. URL.

Potter MA, Brown ST, Cooley PC, Sweeney PM, Hershey TB, Gleason SM, et al. School closure as an influenza mitigation strategy: how variations in legal authority and plan criteria can alter the impact. BMC Public Health. 2012 Nov;12:977. URL.

Potter MA, Brown ST, Lee BY, Grefenstette J, Keane CR, Lin CJ, et al. Preparedness for pandemics: does variation among states affect the nation as a whole? J Public Health Manag Pract. 2012;18(3):233–40. URL.

Prakash BA, Beutel A, Rosenfeld R, Faloutsos C. Winner takes all. Proceedings of the 21st international conference on World Wide Web - WWW ’12. New York, New York, USA: ACM Press; 2012. p. 1037. URL.

Rainwater-Lovett K, Rodriguez-Barraquer I, Cummings DAT, Lessler J. Variation in dengue virus plaque reduction neutralization testing: systematic review and pooled analysis. BMC Infect Dis. 2012 Jan;12:233. URL.

Salje H, Lessler J, Endy TP, Curriero FC, Gibbons R V, Nisalak A, et al. Revealing the microscale spatial signature of dengue transmission and immunity in an urban population. Proc Natl Acad Sci U S A. 2012 Jun 12;109(24):9535–8. URL.

Shim E, Chapman GB, Townsend JP, Galvani AP. The influence of altruism on influenza vaccination decisions. J R Soc Interface. 2012 Sep 7;9(74):2234–43. URL.

Shim E, Feng Z, Castillo-Chavez C. Differential impact of sickle cell trait on symptomatic and asymptomatic malaria. Math Biosci Eng. 2012 Oct 1;9(4):877–98. URL.

Shim E, Galvani AP. Distinguishing vaccine efficacy and effectiveness. Vaccine. 2012 Oct 19;30(47):6700–5. URL.

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 Feb 21;295:194–203. URL.

Song Y, Tai JHY, Bartsch SM, Zimmerman RK, Muder RR, Lee BY. The potential economic value of a Staphylococcus aureus vaccine among hemodialysis patients. Vaccine. 2012 May 21;30(24):3675–82. URL.

Stark JH, Cummings DAT, Ermentrout B, Ostroff S, Sharma R, Stebbins S, et al. Local variations in spatial synchrony of influenza epidemics. PLoS One. 2012 Jan;7(8):e43528. URL.

Stark JH, Sharma R, Ostroff S, Cummings DAT, Ermentrout B, Stebbins S, et al. Local spatial and temporal processes of influenza in Pennsylvania, USA: 2003-2009. PLoS One. 2012 Jan;7(3):e34245. URL.

Truscott J, Ferguson NM. Evaluating the adequacy of gravity models as a description of human mobility for epidemic modelling. PLoS Comput Biol. 2012 Jan;8(10):e1002699. URL.

Truscott J, Fraser C, Cauchemez S, Meeyai A, Hinsley W, Donnelly CA, et al. Essential epidemiological mechanisms underpinning the transmission dynamics of seasonal influenza. J R Soc Interface. 2012 Feb 7;9(67):304–12. URL.

Wettstein ZS, Fleming M, Chang AY, Copenhaver DJ, Wateska AR, Bartsch SM, et al. Total economic cost and burden of dengue in Nicaragua: 1996-2010. Am J Trop Med Hyg. 2012 Oct;87(4):616–22. URL.

Word DP, Cummings DAT, 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 Aug 7;9(73):1983–97. URL.

Yu H, Cauchemez S, Donnelly CA, Zhou L, Feng L, Xiang N, et al. Transmission dynamics, border entry screening, and school holidays during the 2009 influenza A (H1N1) pandemic, China. Emerg Infect Dis. 2012 May;18(5):758–66. URL.

Grim P, Bramson A, Singer DJ, Fisher S, Flocken C, Berger W. Philosophical Analysis in Modeling Polarization: Notes from a Work in Progress. APA newsletters. 2012 Jan;12(1):7–15. URL.

Klein EY, Smith DL, Laxminarayan R, Levin S. Superinfection and the evolution of resistance to antimalarial drugs. Proc Biol Sci. 2012 Sep 22;279(1743):3834–42. URL.

McGlone SM, Bailey RR, Zimmer SM, Popovich MJ, Tian Y, Ufberg P, et al. The economic burden of Clostridium difficile. Clin Microbiol Infect. 2012 Mar;18(3):282–9. URL.

Reich NG, Lessler J, Cummings DAT, Brookmeyer R. Estimating absolute and relative case fatality ratios from infectious disease surveillance data. Biometrics. 2012 Jun;68(2):598–606. URL.

Song SO, Song SOK, Hogg J, Peng Z-Y, Parker R, Kellum JA, et al. Ensemble models of neutrophil trafficking in severe sepsis. PLoS Comput Biol. 2012 Jan;8(3):e1002422. URL.

Swanson RC, Cattaneo A, Bradley E, Chunharas S, Atun R, Abbas KM, et al. Rethinking health systems strengthening: key systems thinking tools and strategies for transformational change. Health Policy Plan. 2012 Oct;27 Suppl 4:iv54–61. URL.

2011

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

Assi TM, Brown ST, Djibo A, Norman BA, Rajgopal J, Welling JS, et al. Impact of changing the measles vaccine vial size on Niger’s vaccine supply chain: a computational model. BMC Public Health. 2011 Jun;11:425.

Bailey RR, Stuckey DR, Norman BA, Duggan AP, Bacon KM, Connor DL, et al. Economic value of dispensing home-based preoperative chlorhexidine bathing cloths to prevent surgical site infection. Infect Control Hosp Epidemiol. 2011 May;32(5):465–71.

Brown ST, Tai JH, Bailey RR, Cooley PC, Wheaton WD, Potter MA, et al. Would school closure for the 2009 H1N1 influenza epidemic have been worth the cost?: a computational simulation of Pennsylvania. BMC Public Health. 2011 May;11:353.

Cauchemez S, Bhattarai A, Marchbanks TL, Fagan RP, Ostroff S, Ferguson NM, et al. 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 Feb 15;108(7):2825–30. URL.

Cauchemez S, Ferguson NM. Methods to infer transmission risk factors in complex outbreak data. J R Soc Interface. 2011 Mar 7;9(68):456–69. URL.

Cooley P, Brown S, Cajka J, Chasteen B, Ganapathi L, Grefenstette J, et al. The role of subway travel in an influenza epidemic: a new york city simulation. J Urban Health. 2011 Oct;88(5):982–95.

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 Jan;7(1):e1001062. URL.

Donnelly CA, Finelli L, Cauchemez S, Olsen SJ, Doshi S, Jackson ML, et al. 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 Jan 1;52 Suppl 1:S123–30. URL.

Eggo RM, Cauchemez S, Ferguson NM. Spatial dynamics of the 1918 influenza pandemic in England, Wales and the United States. J R Soc Interface. 2011 Feb 6;8(55):233–43. URL.

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.

Fraser C, Cummings DA, Klinkenberg D, Burke DS, Ferguson NM. Influenza transmission in households during the 1918 pandemic. Am J Epidemiol. 2011 Sep;174(5):505–14.

Lee BY, Assi TM, Rajgopal J, Norman BA, Chen SI, Brown ST, et al. Impact of Introducing the Pneumococcal and Rotavirus Vaccines Into the Routine Immunization Program in Niger. Am J Public Health. 2011 Sep;

Lee BY, Assi TM, Rookkapan K, Connor DL, Rajgopal J, Sornsrivichai V, et al. Replacing the measles ten-dose vaccine presentation with the single-dose presentation in Thailand. Vaccine. 2011 May;29(21):3811–7.

Lee BY, Assi TM, Rookkapan K, Wateska AR, Rajgopal J, Sornsrivichai V, et al. Maintaining vaccine delivery following the introduction of the rotavirus and pneumococcal vaccines in Thailand. PLoS One. 2011;6(9):e24673.

Lee BY, Bacon KM, Bailey R, Wiringa AE, Smith KJ. The potential economic value of a hookworm vaccine. Vaccine. 2011 Feb;29(6):1201–10.

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 Mar;29(11):2149–58.

Lee BY, Brown ST, Bailey RR, Zimmerman RK, Potter MA, McGlone SM, et al. The benefits to all of ensuring equal and timely access to influenza vaccines in poor communities. Health Aff (Millwood). 2011 Jun;30(6):1141–50.

Lee BY, Connor DL, Kitchen SB, Bacon KM, Shah M, Brown ST, et al. Economic value of dengue vaccine in Thailand. Am J Trop Med Hyg. 2011 May;84(5):764–72.

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 Feb;32(2):191–3.

Lee BY, McGlone SM, Song Y, Avery TR, Eubank S, Chang CC, et al. Social network analysis of patient sharing among hospitals in Orange County, California. Am J Public Health. 2011 Apr;101(4):707–13.

Lee BY, McGlone SM, Wong KF, Yilmaz SL, Avery TR, Song Y, et al. Modeling the spread of methicillin-resistant Staphylococcus aureus (MRSA) outbreaks throughout the hospitals in Orange County, California. Infect Control Hosp Epidemiol. 2011 Jun;32(6):562–72.

Lee BY, Stalter RM, Bacon KM, Tai JH, Bailey RR, Zimmer SM, et al. Cost-effectiveness of adjuvanted versus nonadjuvanted influenza vaccine in adult hemodialysis patients. Am J Kidney Dis. 2011 May;57(5):724–32.

Lee BY, Tai JH, Bailey RR, McGlone SM, Wiringa AE, Zimmer SM, et al. Economic model for emergency use authorization of intravenous peramivir. Am J Manag Care. 2011 Jan;17(1):e1–9.

Lee BY, Wettstein ZS, McGlone SM, Bailey RR, Umscheid CA, Smith KJ, et al. Economic value of norovirus outbreak control measures in healthcare settings. Clin Microbiol Infect. 2011 Apr;17(4):640–6.

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 Jan;7(1):115–9.

Lee BY, Wiringa AE, Mitgang EA, McGlone SM, Afriyie AN, Song Y, et al. Routine pre-cesarean staphylococcus aureus screening and decolonization: a cost-effectiveness analysis. Am J Manag Care. 2011 Oct;17(10):693–700.

Lee BY, Song Y, Bartsch SM, Kim DS, Singh A, Avery TR, et al. Long-term care facilities: important participants of the acute care facility social network? PLoS One. 2011 Jan;6(12):e29342. URL.

Lessler J, Cummings DA, Read JM, Wang S, Zhu H, Smith GJ, et al. Location-specific patterns of exposure to recent pre-pandemic strains of influenza A in southern China. Nat Commun. 2011 Aug;2:423.

MacIntyre CR, Wang Q, Cauchemez S, Seale H, Dwyer DE, Yang P, et al. A cluster randomized clinical trial comparing fit-tested and non-fit-tested N95 respirators to medical masks to prevent respiratory virus infection in health care workers. Influenza Other Respi Viruses. 2011 May;5(3):170–9. URL.

Marchbanks TL, Bhattarai A, Fagan RP, Ostroff S, Sodha S V, Moll ME, et al. An outbreak of 2009 pandemic influenza A (H1N1) virus infection in an elementary school in Pennsylvania. Clin Infect Dis. 2011 Jan 1;52 Suppl 1:S154–60. URL.

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 Sep;7(9):e1002205.

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

Pellis L, Ferguson NM, Fraser C. Epidemic growth rate and household reproduction number in communities of households, schools and workplaces. J Math Biol. 2011 Oct;63(4):691–734.

Rajgopal J, Connor DL, Assi TM, Norman BA, Chen SI, Bailey RR, et al. The optimal number of routine vaccines to order at health clinics in low or middle income countries. Vaccine. 2011 Jul;29(33):5512–8.

Shim E. Prioritization of delayed vaccination for pandemic influenza. Math Biosci Eng. 2011 Jan;8(1):95–112. URL.

Shim E, Meyers LA, Galvani AP. Optimal H1N1 vaccination strategies based on self-interest versus group interest. BMC Public Health. 2011 Jan;11 Suppl 1:S4. URL.

Souza W V, Marques ET, Cummings DA. From re-emergence to hyperendemicity: the natural history of the dengue epidemic in Brazil. PLoS Negl Trop Dis. 2011 Jan;5(1):e935.

Stebbins S, Cummings DAT, Stark JH, Vukotich C, Mitruka K, Thompson W, et al. 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 Nov;30(11):921–6. URL.

White MT, Griffin JT, Churcher TS, Ferguson NM, Basanez MG, Ghani AC. Modelling the impact of vector control interventions on Anopheles gambiae population dynamics. Parasites {&} vectors. 2011 Jul;4:153.

Luquero FJ, Pham-Orsetti H, Cummings DAT, Ngaunji PE, Nimpa M, Fermon F, et al. A long-lasting measles epidemic in Maroua, Cameroon 2008-2009: mass vaccination as response to the epidemic. J Infect Dis. 2011 Jul;204 Suppl :S243–51. URL.

Reich NG, Perl TM, Cummings DAT, Lessler J. Visualizing clinical evidence: citation networks for the incubation periods of respiratory viral infections. PLoS One. 2011 Jan;6(4):e19496. URL.

van Panhuis WG, Luxemburger C, Pengsaa K, Limkittikul K, Sabchareon A, Lang J, et al. Decay and persistence of maternal dengue antibodies among infants in Bangkok. Am J Trop Med Hyg. 2011 Aug;85(2):355–62. URL.

Wu C, Walsh AS, Rosenfeld R. Genotype phenotype mapping in RNA viruses - disjunctive normal form learning. Pac Symp Biocomput. 2011 Jan;62–73. URL.

2010

Cremin I, Nyamukapa C, Sherr L, Hallett TB, Chawira G, Cauchemez S, et al. Patterns of self-reported behaviour change associated with receiving voluntary counselling and testing in a longitudinal study from Manicaland, Zimbabwe. AIDS Behav. 2010 Jun;14(3):708–15. URL.

Egan JR, Legrand J, Hall IM, Cauchemez S, Ferguson NM, Leach S. Re-assessment of mitigation strategies for deliberate releases of anthrax using a real-time outbreak characterization tool. Epidemics. 2010 Dec;2(4):189–94. URL.

Griffin JT, Hollingsworth TD, Okell LC, Churcher TS, White M, Hinsley W, et al. Reducing Plasmodium falciparum malaria transmission in Africa: a model-based evaluation of intervention strategies. PLoS Med. 2010 Aug;7(8):e1000324.

Huang SS, Avery TR, Song Y, Elkins KR, Nguyen CC, Nutter SK, et al. Quantifying interhospital patient sharing as a mechanism for infectious disease spread. Infect Control Hosp Epidemiol. 2010 Nov;31(11):1160–9.

Lee BY, Bacon KM, Connor DL, Willig AM, Bailey RR. The potential economic value of a Trypanosoma cruzi (Chagas disease) vaccine in Latin America. PLoS Negl Trop Dis. 2010 Dec;4(12):e916.

Lee BY, Bailey RR, Smith KJ, Muder RR, Strotmeyer ES, Lewis GJ, et al. Universal methicillin-resistant Staphylococcus aureus (MRSA) surveillance for adults at hospital admission: an economic model and analysis. Infect Control Hosp Epidemiol. 2010 Jun;31(6):598–606.

Lee BY, Bailey RR, Wiringa AE, Afriyie A, Wateska AR, Smith KJ, et al. Economics of employer-sponsored workplace vaccination to prevent pandemic and seasonal influenza. Vaccine. 2010 Aug;28(37):5952–9.

Lee BY, Brown ST, Cooley PC, Zimmerman RK, Wheaton WD, Zimmer SM, et al. A computer simulation of employee vaccination to mitigate an influenza epidemic. Am J Prev Med. 2010 Mar;38(3):247–57.

Lee BY, Brown ST, Cooley P, Grefenstette JJ, Zimmerman RK, Zimmer SM, et al. Vaccination deep into a pandemic wave potential mechanisms for a third wave and the impact of vaccination. Am J Prev Med. 2010 Nov;39(5):e21–9.

Lee BY, Brown ST, Cooley P, Potter MA, Wheaton WD, Voorhees RE, et al. Simulating school closure strategies to mitigate an influenza epidemic. J Public Health Manag Pract. 2010;16(3):252–61.

Lee BY, Brown ST, Korch GW, Cooley PC, Zimmerman RK, Wheaton WD, et al. A computer simulation of vaccine prioritization, allocation, and rationing during the 2009 H1N1 influenza pandemic. Vaccine. 2010 Jul;28(31):4875–9.

Lee BY, McGlone SM. Pricing of new vaccines. Hum Vaccin. 2010 Aug;6(8):619–26.

Lee BY, McGlone SM, Bailey RR, Wiringa AE, Zimmer SM, Smith KJ, et al. To test or to treat? An analysis of influenza testing and antiviral treatment strategies using economic computer modeling. PLoS One. 2010 Jun;5(6):e11284.

Lee BY, McGlone SM, Doi Y, Bailey RR, Harrison LH. Economic impact of Acinetobacter baumannii infection in the intensive care unit. Infect Control Hosp Epidemiol. 2010 Oct;31(10):1087–9.

Lee BY, Norman BA, Assi TM, Chen SI, Bailey RR, Rajgopal J, et al. Single versus multi-dose vaccine vials: an economic computational model. Vaccine. 2010 Jul;28(32):5292–300.

Lee BY, Popovich MJ, Tian Y, Bailey RR, Ufberg PJ, Wiringa AE, et al. The potential value of Clostridium difficile vaccine: an economic computer simulation model. Vaccine. 2010 Jul;28(32):5245–53.

Lee BY, Tai JH, Bailey RR, Smith KJ, Nowalk AJ. Economics of influenza vaccine administration timing for children. Am J Manag Care. 2010 Mar;16(3):e75–85.

Lee BY, Ufberg PJ, Bailey RR, Wiringa AE, Smith KJ, Nowalk AJ, et al. The potential economic value of a Staphylococcus aureus vaccine for neonates. Vaccine. 2010 Jun;28(29):4653–60.

Lee BY, Wateska AR, Bailey RR, Tai JH, Bacon KM, Smith KJ. Forecasting the economic value of an Enterovirus 71 (EV71) vaccine. Vaccine. 2010 Nov;28(49):7731–6.

Lee BY, Wiringa AE, Bailey RR, Goyal V, Lewis GJ, Tsui BY, et al. Screening cardiac surgery patients for MRSA: an economic computer model. Am J Manag Care. 2010 Jul;16(7):e163–73.

Lee BY, Wiringa AE, Bailey RR, Goyal V, Tsui B, Lewis GJ, et al. The economic effect of screening orthopedic surgery patients preoperatively for methicillin-resistant Staphylococcus aureus. Infect Control Hosp Epidemiol. 2010 Nov;31(11):1130–8.

Lee BY, Wiringa AE, Bailey RR, Lewis GJ, Feura J, Muder RR. Staphylococcus aureus vaccine for orthopedic patients: an economic model and analysis. Vaccine. 2010 Mar;28(12):2465–71.

Lee I, Agarwal RK, Lee BY, Fishman NO, Umscheid CA. Systematic review and cost analysis comparing use of chlorhexidine with use of iodine for preoperative skin antisepsis to prevent surgical site infection. Infect Control Hosp Epidemiol. 2010 Dec;31(12):1219–29.

Lessler J, dos Santos T, Aguilera X, Brookmeyer R, Cummings DAT. H1N1pdm in the Americas. Epidemics. 2010 Sep;2(3):132–8. URL.

Santos T, Fraser C, Leung GM, Lipsitch M, Longini IM Jr, McBryde ES, et al. Studies needed to address public health challenges of the 2009 H1N1 influenza pandemic: insights from modeling. PLoS Med. 2010 Jun;7(6):e1000275.

Shi P, Keskinocak P, Swann JL, Lee BY. The impact of mass gatherings and holiday traveling on the course of an influenza pandemic: a computational model. BMC Public Health. 2010 Dec;10:778.

Shi P, Keskinocak P, Swann JL, Lee BY. Modelling seasonality and viral mutation to predict the course of an influenza pandemic. Epidemiol Infect. 2010 Oct;138(10):1472–81.

Shim E, Chapman GB, Galvani AP. Decision making with regard to antiviral intervention during an influenza pandemic. Med Decis Making. 2010;30(4):E64–81. URL.

Smith KJ, Lee BY, Nowalk MP, Raymund M, Zimmerman RK. Cost-effectiveness of dual influenza and pneumococcal vaccination in 50-year-olds. Vaccine. 2010 Nov;28(48):7620–5.

van Panhuis WG, Gibbons R V, Endy TP, Rothman AL, Srikiatkhachorn A, Nisalak A, et al. Inferring the serotype associated with dengue virus infections on the basis of pre- and postinfection neutralizing antibody titers. J Infect Dis. 2010 Oct 1;202(7):1002–10. URL.

Walker PGT, Cauchemez S, Métras R, Dung DH, Pfeiffer D, Ghani AC. A Bayesian approach to quantifying the effects of mass poultry vaccination upon the spatial and temporal dynamics of H5N1 in Northern Vietnam. PLoS Comput Biol. 2010 Feb;6(2):e1000683. URL.

Zhang Y, Lee BY, Donohue JM. Ambulatory antibiotic use and prescription drug coverage in older adults. Arch Intern Med. 2010 Aug;170(15):1308–14.

Zimmer SM, Crevar CJ, Carter DM, Stark JH, Giles BM, Zimmerman RK, et al. Seroprevalence following the second wave of Pandemic 2009 H1N1 influenza in Pittsburgh, PA USA. PLoS One. 2010 Jul;5(7):e11601.

Fried JR, Gibbons R V, Kalayanarooj S, Thomas SJ, Srikiatkhachorn A, Yoon I-K, et al. 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 Jan;4(3):e617. URL.

Grim P, Reade C, Singer DJ, Fisher S, Majewicz S. What You Believe Travels Differently: Information and Infection Dynamics across Sub-networks. Connect (Tor). 2010 Dec;30(2):50–63. URL.

Morens DM, Burke DS, Halstead SB. The wages of original antigenic sin. Emerg Infect Dis. 2010 Jun;16(6):1023–4. URL.

Ross T, Zimmer S, Burke D, Crevar C, Carter D, Stark J, et al. Seroprevalence Following the Second Wave of Pandemic 2009 H1N1 Influenza. PLoS Curr. 2010 Jan;2:RRN1148. URL.

Shi P, Keskinocak P, Swann JL, Lee BY. Modelling seasonality and viral mutation to predict the course of an influenza pandemic. Epidemiol Infect. 2010 Oct;138(10):1472–81. URL.

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 Jan;10:778. URL.

Yang Y, Halloran ME, Daniels MJ, Longini IM Jr, Burke DS, Cummings DAT. Modeling Competing Infectious Pathogens from a Bayesian Perspective: Application to Influenza Studies with Incomplete Laboratory Results. J Am Stat Assoc. 2010 Dec;105(492):1310–22. URL.

Zhang Y, Lee BY, Donohue JM. Ambulatory antibiotic use and prescription drug coverage in older adults. Arch Intern Med. 2010 Aug 9;170(15):1308–14. URL.

Zimmer SM, Crevar CJ, Carter DM, Stark JH, Giles BM, Zimmerman RK, et al. Seroprevalence following the second wave of Pandemic 2009 H1N1 influenza in Pittsburgh, PA, USA. PLoS One. 2010 Jan;5(7):e11601. URL.

Zimmerman RK, Lauderdale DS, Tan SM, Wagener DK. Prevalence of high-risk indications for influenza vaccine varies by age, race, and income. Vaccine. 2010 Sep 7;28(39):6470–7. URL.

2009

Beigi RH, Bunge K, Song Y, Lee BY. Epidemiologic and economic effect of methicillin-resistant Staphylococcus aureus in obstetrics. Obstet Gynecol. 2009 May;113(5):983–91.

Beigi RH, Wiringa AE, Bailey RR, Assi TM, Lee BY. Economic value of seasonal and pandemic influenza vaccination during pregnancy. Clin Infect Dis. 2009 Dec;49(12):1784–92.

Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, et al. Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States. N Engl J Med. 2009 Dec;361(27):2619–27.

Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, et al. Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States. N Engl J Med. 2009 Dec 31;361(27):2619–27. URL.

Cauchemez S, Donnelly CA, Reed C, Ghani AC, Fraser C, Kent CK, et al. Household transmission of 2009 pandemic influenza A (H1N1) virus in the United States. N Engl J Med. 2009 Dec 31;361(27):2619–27. URL.

Cauchemez S, Ferguson NM, Wachtel C, Tegnell A, Saour G, Duncan B, et al. Closure of schools during an influenza pandemic. Lancet Infect Dis. 2009 Aug;9(8):473–81. URL.

Cummings DA, Iamsirithaworn S, Lessler JT, McDermott A, Prasanthong R, Nisalak A, et al. The impact of the demographic transition on dengue in Thailand: insights from a statistical analysis and mathematical modeling. PLoS Med. 2009 Sep;6(9):e1000139.

Dreisigmeyer DW, Rosenfeld R, DePasse J V., Ghedin E, Price I, Clermont G. A multi-reservoir model of influenza evolution. J Crit Care. 2009 Sep;24(3):e33–4. URL.

Epstein JM. Modelling to contain pandemics. Nature. 2009 Aug;460(7256):687.

Evans D, Cauchemez S, Hayden FG. “Prepandemic” immunization for novel influenza viruses, “swine flu” vaccine, Guillain-Barré syndrome, and the detection of rare severe adverse events. J Infect Dis. 2009 Aug 1;200(3):321–8. URL.

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Kerkhove MD Van, Hollingsworth TD, et al. Pandemic potential of a strain of influenza A (H1N1): early findings. Science. 2009 Jun 19;324(5934):1557–61. URL.

Garske T, Legrand J, Donnelly CA, Ward H, Cauchemez S, Fraser C, et al. Assessing the severity of the novel influenza A/H1N1 pandemic. BMJ. 2009 Jan;339:b2840. URL.

Ghani A, Baguelin M, Griffin J, Flasche S, van Hoek AJ, Cauchemez S, et al. The Early Transmission Dynamics of H1N1pdm Influenza in the United Kingdom. PLoS Curr. 2009 Nov;1:RRN1130. URL.

Johansson MA, Cummings DA, Glass GE. Multiyear climate variability and dengue--El Nino southern oscillation, weather, and dengue incidence in Puerto Rico, Mexico, and Thailand: a longitudinal data analysis. PLoS Med. 2009 Nov;6(11):e1000168.

Lee BY, Bailey RR, Wiringa AE, Assi TM, Beigi RH. Antiviral medications for pregnant women for pandemic and seasonal influenza: an economic computer model. Obstet Gynecol. 2009 Nov;114(5):971–80.

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

Lee BY, Mehrotra A, Burns RM, Harris KM. Alternative vaccination locations: who uses them and can they increase flu vaccination rates? Vaccine. 2009 Jul;27(32):4252–6.

Lee BY, Tai JH, Bailey RR, Smith KJ. The timing of influenza vaccination for older adults (65 years and older). Vaccine. 2009 Nov;27(50):7110–5.

Lee BY, Tsui BY, Bailey RR, Smith KJ, Muder RR, Lewis GJ, et al. Should vascular surgery patients be screened preoperatively for methicillin-resistant Staphylococcus aureus? Infect Control Hosp Epidemiol. 2009 Dec;30(12):1158–65.

Legrand J, Egan JR, Hall IM, Cauchemez S, Leach S, Ferguson NM. Estimating the location and spatial extent of a covert anthrax release. PLoS Comput Biol. 2009 Jan;5(1):e1000356. URL.

Lempel H, Epstein JM, Hammond RA. Economic cost and health care workforce effects of school closures in the U.S. PLoS Curr. 2009 Oct;1:RRN1051.

Lessler J, Reich NG, Cummings DA, of Health NYCD, Team MHSII, Nair HP, et al. Outbreak of 2009 pandemic influenza A (H1N1) at a New York City school. N Engl J Med. 2009 Dec;361(27):2628–36.

Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM. Managing and reducing uncertainty in an emerging influenza pandemic. N Engl J Med. 2009 Jul 9;361(2):112–5. URL.

MacIntyre CR, Cauchemez S, Dwyer DE, Seale H, Cheung P, Browne G, et al. Face mask use and control of respiratory virus transmission in households. Emerg Infect Dis. 2009 Feb;15(2):233–41. URL.

Shim E, Galvani AP. Impact of transmission dynamics on the cost-effectiveness of rotavirus vaccination. Vaccine. 2009 Jun 19;27(30):4025–30. URL.

Shim E, Galvani AP. Evolutionary repercussions of avian culling on host resistance and influenza virulence. PLoS One. 2009 Jan;4(5):e5503. URL.

Shim E, Hampson K, Cleaveland S, Galvani AP. Evaluating the cost-effectiveness of rabies post-exposure prophylaxis: a case study in Tanzania. Vaccine. 2009 Nov 27;27(51):7167–72. URL.

Shim E, Kochin B, Galvani A. Insights from epidemiological game theory into gender-specific vaccination against rubella. Math Biosci Eng. 2009 Oct;6(4):839–54. URL.

Truscott J, Fraser C, Hinsley W, Cauchemez S, Donnelly C, Ghani A, et al. Quantifying the transmissibility of human influenza and its seasonal variation in temperate regions. PLoS Curr. 2009 Jan;1:RRN1125. URL.

Fraser C, Donnelly CA, Cauchemez S, Hanage WP, Van Kerkhove MD, Hollingsworth TD, et al. Pandemic potential of a strain of influenza A (H1N1): early findings. Science. 2009 Jun 19;324(5934):1557–61. URL.

Reich NG, Lessler J, Cummings DAT, Brookmeyer R. Estimating incubation period distributions with coarse data. Stat Med. 2009 Sep 30;28(22):2769–84. URL.

2008

Carrat F, Vergu E, Ferguson NM, Lemaitre M, Cauchemez S, Leach S, et al. Time lines of infection and disease in human influenza: a review of volunteer challenge studies. Am J Epidemiol. 2008 Apr 1;167(7):775–85. URL.

Cauchemez S, Ferguson NM. Likelihood-based estimation of continuous-time epidemic models from time-series data: application to measles transmission in London. J R Soc Interface. 2008 Aug 6;5(25):885–97. URL.

Cauchemez S, Valleron A-J, Boëlle P-Y, Flahault A, Ferguson NM. Estimating the impact of school closure on influenza transmission from Sentinel data. Nature. 2008 Apr 10;452(7188):750–4. URL.

Epstein JM, Parker J, Cummings D, Hammond RA. Coupled contagion dynamics of fear and disease: mathematical and computational explorations. PLoS One. 2008;3(12):e3955.

Halloran ME, Ferguson NM, Eubank S, Longini IM Jr, Cummings DA, Lewis B, et al. Modeling targeted layered containment of an influenza pandemic in the United States. Proc Natl Acad Sci U S A. 2008 Mar;105(12):4639–44.

Parrish CR, Holmes EC, Morens DM, Park E-C, Burke DS, Calisher CH, et al. Cross-species virus transmission and the emergence of new epidemic diseases. Microbiol Mol Biol Rev. 2008 Sep;72(3):457–70. URL.

2007

Epstein JM, Goedecke DM, Yu F, Morris RJ, Wagener DK, Bobashev G V. Controlling pandemic flu: the value of international air travel restrictions. PLoS One. 2007 May;2(5):e401.

Lessler J, Cummings DA, Fishman S, Vora A, Burke DS. Transmissibility of swine flu at Fort Dix, 1976. J R Soc Interface. 2007 Aug;4(15):755–62.

Longini IM Jr, Halloran ME, Nizam A, Yang Y, Xu S, Burke DS, et al. Containing a large bioterrorist smallpox attack: a computer simulation approach. Int J Infect Dis. 2007 Mar;11(2):98–108.

2006

Burke DS, Epstein JM, Cummings DA, Parker JI, Cline KC, Singa RM, et al. Individual-based computational modeling of smallpox epidemic control strategies. Acad Emerg Med. 2006 Nov;13(11):1142–9.

Cauchemez S, Boelle P-Y, Donnelly CA, Ferguson NM, Thomas G, Leung GM, et al. Real-time estimates in early detection of SARS. Emerg Infect Dis. 2006 Jan;12(1):110–3. URL.

Cauchemez S, Boëlle P-Y, Thomas G, Valleron A-J. Estimating in real time the efficacy of measures to control emerging communicable diseases. Am J Epidemiol. 2006 Sep 15;164(6):591–7. URL.

Cauchemez S, Temime L, Valleron A-J, Varon E, Thomas G, Guillemot D, et al. S. pneumoniae transmission according to inclusion in conjugate vaccines: Bayesian analysis of a longitudinal follow-up in schools. BMC Infect Dis. 2006 Jan;6:14. URL.

Ferguson NM, Cummings DA, Fraser C, Cajka JC, Cooley PC, Burke DS. Strategies for mitigating an influenza pandemic. Nature. 2006 Jul;442(7101):448–52.

Shim E. A note on epidemic models with infective immigrants and vaccination. Math Biosci Eng. 2006 Jul;3(3):557–66. URL.

2005

Cummings DA, Schwartz IB, Billings L, Shaw LB, Burke DS. Dynamic effects of antibody-dependent enhancement on the fitness of viruses. Proc Natl Acad Sci U S A. 2005 Oct;102(42):15259–64.

Ferguson NM, Cummings DAT, Cauchemez S, Fraser C, Riley S, Meeyai A, et al. Strategies for containing an emerging influenza pandemic in Southeast Asia. Nature. 2005 Sep 8;437(7056):209–14. URL.

Longini IM Jr, Nizam A, Xu S, Ungchusak K, Hanshaoworakul W, Cummings DA, et al. Containing pandemic influenza at the source. Science. 2005 Aug;309(5737):1083–7.

Schwartz IB, Shaw LB, Cummings DA, Billings L, McCrary M, Burke DS. Chaotic desynchronization of multistrain diseases. Phys Rev Stat nonlinear, soft matter Phys. 2005 Dec;72(6 Pt 2):66201.

2004

Cauchemez B, Extramiana F, Cauchemez S, Cosson S, Zouzou H, Meddane M, et al. High-flow perfusion of sheaths for prevention of thromboembolic complications during complex catheter ablation in the left atrium. J Cardiovasc Electrophysiol. 2004 Mar;15(3):276–83. URL.

Viboud C, Boëlle P-Y, Cauchemez S, Lavenu A, Valleron A-J, Flahault A, et al. Risk factors of influenza transmission in households. Br J Gen Pract. 2004 Sep;54(506):684–9. URL.

 

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