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Lewis B, Eubank S, Abrams AM, Kleinman K.
In silico surveillance: evaluating outbreak detection with simulation models.
BMC Med Inform Decis Mak. 2013 Jan 23;13(1):12. [Epub ahead of print]

Chitnis N, Hyman JM, Manore CA.
Modelling vertical transmission in vector-borne diseases with applications to Rift Valley fever.
J Biol Dyn. 2013;7:11-40.

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.

Shaman J, Karspeck A.
Forecasting seasonal outbreaks of influenza.
Proc Natl Acad Sci U S A. 2012 Dec 11;109(50):20425-30. Epub 2012 Nov 26.

Macal CM, North MJ, Collier N, Dukic VM, Lauderdale DS, David MZ, Daum RS, Shumm P, Evans JA, Wilder JR, Wegner DT.
Modeling the Spread of Community-Associated MRSA.
In: Laroque C, Himmelspach J, Pasupathy R, Rose O, Uhrmacher AM, eds. Proceedings of the 2012 Winter Simulation Conference.
Berlin, Germany: December 9-12, 2012.

Porco TC, Oh P, Flood JM.
Anti-tuberculosis drug resistance acquired during treatment: an analysis of cases reported in California, 1994-2006.
Clin Infect Dis. 2012 Dec 7. [Epub ahead of print]

Connor TR, Corander J, Hanage WP.
Population subdivision and the detection of recombination in non-typable Haemophilus influenzae.
Microbiology. 2012 Dec;158(Pt 12):2958-64. Epub 2012 Oct 4.

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

Goldstein E, Viboud C, Charu V, Lipsitch M.
Improving the estimation of influenza-related mortality over a seasonal baseline.
Epidemiology. 2012 Nov;23(6):829-38.

Goldstein E, Wallinga J, Lipsitch M.
Vaccine allocation in a declining epidemic.
J R Soc Interface. 2012 Nov 7;9(76):2798-803.

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.

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.

Cowling BJ, Nishiura H.
Virus interference and estimates of influenza vaccine effectiveness from test-negative studies.
Epidemiology. 2012 Nov;23(6):930-1.

Lipsitch M, Bloom BR.
Rethinking biosafety in research on potential pandemic pathogens.
MBio. 2012 Oct 9;3(5). pii: e00360-12.

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 Oct 8. [Epub ahead of print]

Chao DL, Halstead SB, Halloran ME, Longini IM. Link to external Web site
Controlling dengue with vaccines in Thailand.
PLoS Negl Trop Dis 6(10): e1876.

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.

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 Oct;31(10):2295-303.

Miller JC.
A note on the derivation of epidemic final sizes.
Bull Math Biol. 2012 Sep;74(9):2125-41.

Miller JC, Volz EM.
Model hierarchies in edge-based compartmental modeling for infectious disease spread.
J Math Biol. 2012 Aug 22. [Epub ahead of print]

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 Aug 15;206(4):543-51.

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. Epub 2012 Apr 25.

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 Aug;18(8):1290-7.

Willems RJ, Top J, van Schaik W, Leavis H, Bonten M, Sirén J, Hanage WP, Corander J.
Restricted gene flow among hospital subpopulations of Enterococcus faecium.
MBio. 2012 Jul 17;3(4):e00151-12.

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 Jul 1;206(1):73-80.

Grad YH, Miller JC, Lipsitch M.
Cholera modeling: challenges to quantitative analysis and predicting the impact of interventions.
Epidemiology. 2012 Jul;23(4):523-30

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 Jul;23(4):531-42.

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 Jun 22;30(30):4517-23.

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 Jul 22;279(1739):2736-2743. Epub 2012 Mar 7.

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 Jun 22;336(6088):1506; author reply 1506.

Lipsitch M, Plotkin JB, Simonsen L, Bloom B
Evolution, safety, and highly pathogenic influenza viruses.
Science. 2012 Jun 22;336(6088):1529-31.

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 Jun 7;9(71):1208-15.

Cowling BJ.
Airborne Transmission of Influenza: Implications for Control in Healthcare and Community Settings.
Clin Infect Dis. 2012 Jun;54(12):1778-83. Epub 2012 Mar 15.

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 Jun;54(12):1778-83. Epub 2012 Mar 15

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 Jun;158(Pt 6):1560-9.

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.

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. 2012 May 21. [Epub ahead of print]

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 May 21;30(24):3675-82.

Cohen T, Manjourides J, Hedt-Gauthier B.
Linking Surveillance with Action against Drug-resistant Tuberculosis.
MAm J Respir Crit Care Med. 2012 May 16. [Epub ahead of print]

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 May 15;26(8):987-95.

Miller JC, Slim AC, Volz EM.
Edge-based compartmental modelling for infectious disease spread.
J R Soc Interface. 2012 May 7;9(70):890-906. Epub 2011 Oct 5.

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?
CJ Public Health Manag Pract. 2012 May;18(3):233-40.

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 May;92(3):273-9. Epub 2012 Mar 6.

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. 2012 May;6(3):167-75.

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 May;18(5):811-3.

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 Apr 24;109(17):6763-8. Epub 2012 Mar 19.

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):620-9. Epub 2012 Apr 23.

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 Apr 16. [Epub ahead of print]

Klick B, Nishiura H, Cowling BJ.
Optimal design of intervention studies to prevent influenza in healthy cohorts.
PLoS One. 2012;7(4):e35166. Epub 2012 Apr 13.

Shapiro BJ, Friedman J, Cordero OX, Preheim SP, Timberlake SC, Szabó G, Polz MF, Alm EJ.
Population genomics of early events in the ecological differentiation of bacteria.
Science. 2012 Apr 6;336(6077):48-51

Buckee CO, Recker M.
Evolution of the Multi-Domain Structures of Virulence Genes in the Human Malaria Parasite, Plasmodium falciparum.
PLoS Comput Biol. 2012 Apr;8(4):e1002451. Epub 2012 Apr 12.

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 Mar;54(6):784-91. Epub 2012 Jan 19.

Cobey S, Lipsitch M.
Niche and neutral effects of acquired immunity permit coexistence of pneumococcal serotypes.
Science. 2012 Mar 16;335(6074):1376-80. Epub 2012 Mar 1.

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;86(3):417-25.

Potter GE, Handcock MS, Longini IM Jr, Halloran ME.
Estimating within-school contact networks to understand influenza transmission.
Ann Appl Stat. 2012 Mar;6(1):1-26.

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 Mar;23(2):293-300.

Matrajt L, Longini IM Jr. Link to external Web site
Critical immune and vaccination thresholds for determining multiple influenza epidemic waves.
Epidemics. 2012 Mar;4(1):22-32.

Longini IM Jr.
A theoretic framework to consider the effect of immunizing schoolchildren against influenza: implications for research.
Pediatrics. 2012 Mar;129 Suppl 2:S63-7.

Robinson K, Cohen T, Colijn C.
The dynamics of sexual contact networks: Effects on disease spread and control.
Theor Popul Biol. 2012 Mar;81(2):89-96. Epub 2012 Jan 8.

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-Møller 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 Feb 21;109(8):3065-70. Epub 2012 Feb 6. 2012 Mar;81(2):89-96. Epub 2012 Jan 8.

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 Feb 7;294:48-55.

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 Feb;205(4):631-4. Epub 2011 Dec 23.

Shaman J, Lipsitch M.
The El Nino-Southern Oscillation (ENSO)-pandemic Influenza connection: Coincident or causal?
Proc Natl Acad Sci U S A. 2012 Jan 17. [Epub ahead of print]

O'Hagan JJ, Hernán 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 Jan 14;26(2):123-6.

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 Jan 1;175(1):54-9.

Klick B, Leung GM, Cowling BJ.
Optimal design of studies of influenza transmission in households. I: Case-ascertained studies.
Epidemiol Infect. 2012 Jan;140(1):106-14.

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 Jan;40(1):e6. Epub 2011 Nov 7.

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. Epub 2011 Dec 27.

Gluckman PD, Bergstrom CT.
Evolutionary biology within medicine: a perspective of growing value.
BMJ. 2011 Dec 19;343:d7671.

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 Dec 16;334(6062):1518-24.

Yaesoubi R, Cohen T.
Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies.
Eur J Oper Res. 2011 Dec 16;215(3):679-687. PubMed PMID: 21966083; PubMed Central PMCID: PMC3182455.

Hernán MA, Lipsitch M. Link to external Web site
Reply to cochrane neuraminidase inhibitors review team.
Clin Infect Dis. 2011 Dec;53(12):1303-4.

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 Nov;22(6):793-6.

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 Nov 11;8(1):44.

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 Nov;139(11):1784-93. Epub 2010 Dec 23.

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 Oct 14;13(4):e85.

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 during 2008-2009.
Epidemiology 2011 Nov;22(6):781-92

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 Oct 7;8(63):1510-20. Epub 2011 Apr 20. PubMed PMID: 21508012; PubMed Central PMCID: PMC3163428.

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. Epub 2010 Dec 1.

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 Oct;8(10):e1001103. Epub 2011 Oct 4. PubMed PMID: 21990967; PubMed Central PMCID: PMC3186812.

Mostofsky E, Lipsitch M, Regev-Yochay G.
Is methicillin-resistant Staphylococcus aureus replacing methicillin-susceptible S. aureus?
J Antimicrob Chemother. 2011 Oct;66(10):2199-214. Epub 2011 Jul 7. PubMed PMID: 21737459; PubMed Central PMCID: PMC3172038.

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 Oct;17(10):693-700.

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 Oct;52(2):146-50. Epub 2011 Jul 29. PubMed PMID: 21802983; PubMed Central PMCID: PMC3175291.

Cooley PC, Brown ST, 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 Oct;88(5):982-95.

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. Epub 2011 Sep 13.

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 Sep 30;30(22):2708-20. doi: 10.1002/sim.4287. Epub 2011 Jun 30. PubMed PMID: 21717491.

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. 2011 Sep 22. [Epub ahead of print]

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 Sep 21.

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. Epub 2011 Sep 13.

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 Sep 8;343:d5408. doi: 10.1136/bmj.d5408. PubMed PMID: 21903689; PubMed Central PMCID: PMC3168935.

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. Epub 2011 Sep 29.

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 Sep;35(5):872-900. doi: 10.1111/j.1574-6976.2011.00284.x. Epub 2011 Jul 4. PubMed PMID: 21658083.

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 Sep;7(9):e1002225. Epub 2011 Sep 1.

Chao DL, Bloom JD, Kochin BF, Antia R, Longini IM Jr.
The global spread of drug-resistant influenza.
J R Soc Interface. 2011 Aug 24. [Epub ahead of print]

Cauchemez S, Ferguson NM.
Methods to infer transmission risk factors in complex outbreak data.
J R Soc Interface. 2011 Aug 10.

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 Aug 1;53(3):280-3. PubMed PMID: 21765076; PubMed Central PMCID: PMC3202320.

Wu JT, Cowling BJ.
The use of mathematical models to inform influenza pandemic preparedness and response.
Exp Biol Med (Maywood). 2011 Aug 1;236(8):955-61. Epub 2011 Jul 4.

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 Aug;6(8):e23380. Epub 2011 Aug 24. PubMed PMID: 21887246; PubMed Central PMCID: PMC3160845.

Hernán 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 Aug;53(3):277-9. Epub 2011 Jun 15.

Althouse BM, Ng YY, Cummings DA.
Prediction of dengue incidence using search query surveillance.
PLoS Negl Trop Dis.2011 Aug;5(8):e1258. Epub 2011 Aug 2.

Smith J, Lipsitch M, Almond JW.
Vaccine production, distribution, access, and uptake.
Lancet. 2011 Jul 30;378(9789):428-38. Epub 2011 Jun 12.

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 Jul 26;29(33):5512-8.

Amaro RE, Swift RV, Votapka L, Li WW, Walker RC, Bush RM.
Mechanism of 150-cavity formation in influenza neuraminidase.
Nat Commun. 2011 Jul 12;2:388.

Sergeev R, Colijn C, Cohen T.
Models to understand the population-level impact of mixed strain M. tuberculosis infections.
J Theor Biol. 2011 Jul 7;280(1):88-100. Epub 2011 Apr 16. PubMed PMID: 21514304; PubMed Central PMCID: PMC3111980.

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. 2011 Jul 7.

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 Jul;8(7): e1001051.

Kelly H, Cowling B.
Insights from Europe related to pandemic influenza A(H1N1)2009 have international relevance.
Euro Surveill. 2011 Jun 30;16(26). pii: 19899. PubMed PMID: 21745446.

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 Jun 2;11(1):425.

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 Jun; 203(12):1710-8.

Volz EM, Miller JC, Galvani A, Ancel Meyers L.
Effects of heterogeneous and clustered contact patterns on infectious disease dynamics.
PLoS Comput Biol. 2011 Jun;7(6):e1002042. Epub 2011 Jun2.

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 Jun;8(6):e1000442. Epub 2011 Jun 21.

Smith G, Dunipace S. Link to external Web site
How backyard poultry flocks influence the effort required to curtail avian influenza epidemics in commercial poultry flocks.
Epidemics. 2011 Jun;3(2):71-75.

Lipsitch M, Finelli L, Heffernan RT, Leung GM, Redd SC; for the 2009 H1N1 Surveillance Group.
Improving the evidence base for decision making during a pandemic: The example of 2009 influenza A/H1N1.
Biosecur Bioterror. 2011 Jun;9(2):89-115.

Dukic VM, David MZ, Lauderdale DS. Link to external Web site
Internet queries and methicillin-resistant Staphylococcus aureus surveillance.
Emerg Infect Dis. 2011 Jun;17(6).

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 Jun;32(6):562-72.

Rorres C, Pelletier STK, Smith G. Link to external Web site
Stochastic modeling of animal epidemics using data collected over three different spatial scales.
Epidemics. 2011 Jun;3(2):61-70.

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 Jun;30(6):1141-50.

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 Jun;18(2):93-104.

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 May 27. [Epub ahead of print]

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 May 20;11:353.

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 May 15;173(10):1121-30. Epub 2011 Mar 22.

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 May 12;29(21):3811-7. Epub 2011 Mar 23.

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 May 7. doi: 10.1111/j.1469-0691.2011.03571.x. [Epub ahead of print]

Kenah E, Chao DL, Halloran ME, Matrajt L, Longini IM.
The global transmission and control of influenza.
PLoS One. 2011 May 6;6(5):e19515.

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 May;57(5):724-32. Epub 2011 Mar 10.

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 May;84(5):764-72.

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 May;32(5):465-71.

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 May;5 Suppl 1:226-9. PubMed PMID: 21761590.

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 May;43(5):482-6. Epub 2011 Apr 24.

Reich NG, Perl TM, Cummings DA, Lessler J.
Visualizing clinical evidence: citation networks for the incubation periods of respiratory viral infections.
PLoS One. 2011 Apr 29;6(4):e19496.

Chao DL, Halloran ME, Longini IM.
Vaccination strategies for epidemic cholera in Haiti with implications for the developing world.
Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7081-5.

Andrews JR, Basu S.
Transmission dynamics and control of cholera in Haiti: an epidemic model.
Lancet. 2011 Apr 9;377(9773):1248-55. Epub 2011 Mar 15.

Rosvall M, Bergstrom CT.
Multilevel compression of random walks on networks reveals hierarchical organization in large integrated systems.
PLoS One. 2011 Apr 8;6(4):e18209.

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 Apr 4. doi: 10.1111/j.1469-0691.2011.03525.x. [Epub ahead of print]

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 Apr;17(4):640-6. doi: 10.1111/j.1469-0691.2010.03345.x. Epub 2010 Oct 26.

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 Apr;101(4):707-13. Epub 2011 Feb 17.

Wells CR, Tchuenche JM, Meyers LA, Galvani AP, Bauch CT.
Impact of Imitation Processes on the Effectiveness of Ring Vaccination.
Bull Math Biol. 2011 Mar 16.

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 Mar 11;6(3):e17713.

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 3;29(11):2149-58. Epub 2011 Jan 6.

Barrett C, Bisset K, Leidig J, Marathe A, Marathe M.
Economic and social impact of influenza mitigation strategies by demographic class.
Epidemics. 2011 Mar;3(1):19-31.

Rorres  C, Pelletier STK, Bruhn MC, Smith G. Link to external Web site
Ongoing estimation of the epidemic parameters of a stochastic, spatial, discrete-time model for a 1983-84 avian influenza epidemic.
Avian Diseases. 2011 Mar;55(1):35-42.

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.

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 Mar;22(2):180-7.

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 Feb 28;30(5):549-59. doi: 10.1002/sim.3883.

Shim E, Meyers LA, Galvani AP.
Optimal H1N1 vaccination strategies based on self-interest versus group interest.
BMC Public Health. 2011 Feb 25;11 Suppl 1:S4.

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 Feb 15. doi: 10.1111/j.1469-0691.2011.03491.x. [Epub ahead of print]

Cauchemez S, Bhattarai A, Marchbanks TL, Fagan RP, Ostroff S, Ferguson NM, Swerdlow D; 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 Feb 15;108(7):2825-30. Epub 2011 Jan 31.

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 Feb 1;20(1102):1-26.

Lee BY, Bacon KM, Bailey R, Wiringa AE, Smith KJ.
The potential economic value of a hookworm vaccine.
Vaccine. 2011 Feb 1;29(6):1201-10. Epub 2010 Dec 16.

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 Feb;84(2):192-9. Review.

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.

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 27;7(1):e1001062.

Shaman J, Goldstein E, Lipsitch M.
Absolute humidity and pandemic versus epidemic influenza.
Am J Epidemiol. 2011 Jan 15;173(2):127-35.

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 Jan 4;5(1):e935.

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 Jan 1;52 Suppl 1:S154-60.

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 Jan 1;52 Suppl 1:S123-30.

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 1;7(1):115-9. Epub 2011 Jan 1.

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 Jan;17(1):e1-9.

Shim E.
Prioritization of delayed vaccination for pandemic influenza.
Math Biosci Eng. 2011 Jan;8(1):95-112. doi: 10.3934/mbe.2011.8.95.

Potter GE, Handcock MS, Longini IM Jr, Halloran ME.
Estimating within-household contact networks from ego-centric data.
Ann Appl Stat. 2011;5(3):1816-1838.

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;6(5):e20139. Epub 2011 May 31.

Epstein JM, Pankajakshan R, Hammond RA.
Combining computational fluid dynamics and agent-based modeling: A new approach to evacuation planning.
PLoS One. 2011;2011:194507. Epub 2010 Dec 23.

Yaesoubi R, Cohen T.
Dynamic health policies for controlling the spread of emerging infections: influenza as an example.
PLoS One. 2011;6(9):e24043. Epub 2011 Sep 6. PubMed PMID: 21915279; PubMed Central PMCID: PMC3167826.

Kenah E, Miller JC.
Epidemic percolation networks, epidemic outcomes, and interventions.
Interdiscip Perspect Infect Dis. 2011;2011:543520. Epub 2011 Feb 21.

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.

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. Epub 2011 Dec 27.

Jenkins HE, Zignol M, Cohen T.
Quantifying the burden and trends of isoniazid resistant tuberculosis, 1994-2009.
PLoS One. 2011;6(7):e22927. Epub 2011 Jul 29. PubMed PMID: 21829557; PubMed Central PMCID: PMC3146514.

Shaman J, Jeon CY, Giovannucci E, Lipsitch M.
Shortcomings of vitamin D-based model simulations of seasonal influenza.
PLoS One 2011;6(6):e20743. Epub 2011 Jun 3.

Lipsitch M, Mills C, Robins J. Link to external Web site
Estimates of the basic reproductive number for 1918 pandemic influenza in the United States: implications for policy. Submitted.



Other articles include:

Riley S.
Large-scale spatial-transmission models of infectious disease.
Science. 2007 Jun 1;316(5829):1298-1301.

Burke DS. Link to external Web site
Curing disparity: epidemiology in silicon.
eJournal USA: Global Issues. 2006 Oct;11(3):13-14.

Eubank S, Guclu H, Kumar VS, Marathe MV, Srinivasan A, Toroczkai Z, Wang N.
Modelling disease outbreaks in realistic urban social networks.
Nature. 2004 May 13;429(6988):180-4.

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