Publications

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Reed C, Angulo FJ, Swerdlow DL, Lipsitch M, Meltzer MI, Jernigan D, Finelli L.
Estimates of the prevalence of pandemic (H1N1) 2009, United States, April–July 2009.
Emerg Infect Dis. 2009 Dec; [Epub ahead of print]

Goldstein E, Apolloni A, Lewis B, Miller JC, Macauley M, Eubank S, Lipsitch M, Wallinga J.
Distribution of vaccine/antivirals and the 'least spread line' in a stratified population.
J R Soc Interface. 2009 Oct 14; [Epub ahead of print]

Lipsitch M, Hayden FG, Cowling BJ, Leung GM.
How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count.
Lancet. 2009 Oct 3;374(9696):1209-11.

Stelling J, Yih WK, Galas M, Kulldorff M, Pichel M, Terragno R, Tuduri E, Espetxe S, Binsztein N, O'Brien TF, Platt R.
Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes.
Epidemiol Infect. 2009 Oct 2:1-11.

Bansal S, Pourbohloul B, Grenfell B, Meyers LA.
The shifting demographic landscape of influenza.
PLoS Currents: Influenza. 2009 Oct 2; RRN1047.

Lempel H, Epstein JM, Hammond RA.
Economic cost and health care workforce effects of school closures in the U.S.
PLoS Currents: Influenza. 2009 Oct 1; RRN1048.

White LF, Wallinga J, Finelli L, Reed C, Riley S, Lipsitch M, Pagano M.
Estimation of the reproductive number and the serial interval in early phase of the 2009 influenza A/H1N1 pandemic in the USA.
Influenza Other Respi Viruses. 2009 Sep 28 [Epub ahead of print]

Handel A, Longini IM Jr, Antia R.
Intervention strategies for an influenza pandemic taking into account secondary bacterial infections.
Epidemics, 2009 Sep;1(3):185-195.

Presanis AM, Lipsitch M, De Angelis D, et al.
The severity of pandemic H1N1 influenza in the United States, April – July 2009.
PLoS Currents: Influenza. 2009 Sep 25; RRN1042.

Yang Y, Sugimoto JD, Halloran ME, Basta NE, Chao DL, Matrajt L, Potter G, Kenah E, Longini IM Jr.
The transmissibility and control of pandemic influenza A (H1N1) virus.
Science. 2009 Sep 10. [Epub ahead of print]

Pourbohloul B, Ahued A, Davoudi B, Meza R, Meyers LA, Skowronski DM, et al.
Initial human transmission dynamics of the pandemic (H1N1) 2009 virus in North America.
Influenza Other Respi Viruses. 2009 Sept;3(5):215-22.

Bisset K and Marathe M.
A CYBER environment to PANDEMIC.
SciDAC Review, Number 13, Summer 2009, 36-47.

Basta NE, Chao DL, Halloran ME, Matrajt L, Longini IM Jr.
Strategies for pandemic and seasonal influenza vaccination of schoolchildren in the United States.
Am J Epidemiol. 2009 Aug 13; [Epub ahead of print]

Epstein JM.
Modelling to contain pandemics.
Nature. 2009 Aug 6;460(7256):687.

Zimmer SM, Burke DS.
Historical perspective - Emergence of Influenza A (H1N1) Viruses.
N Engl J Med. 2009 Jul 16;361(3):279-285.

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.

Handel A, Longini IM Jr, Antia R.
Towards a quantitative understanding of the within-host dynamics of influenza A infections.
J R Soc Interface. 2009 May 27. [Epub ahead of print]

Wu JT, Leung GM, Lipsitch M, Cooper BS, Riley S.
Hedging against antiviral resistance during the next influenza pandemic using small stockpiles of an alternative chemotherapy.
PLoS Med. 2009 May 19;6(5):e1000085.

Wheaton WD, Cajka JC, Chasteen BM, Wagener DK, Cooley PC, Ganapathi L, & et al.
Synthesized population databases: A US geospatial database for agent-based models.
RTI Press Publication No. MR-0010-0905. 2009 May.

Yang Y, Halloran ME, Longini IM Jr.
A Bayesian model for evaluating influenza antiviral efficacy in household studies with asymptomatic infections.
Biostatistics. 2009 Apr; 10(2):390-403.

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.

Johansson MA, Dominici F, Glass GE.
Local and global effects of climate on dengue transmission in Puerto Rico.
PLoS Negl Trop Dis. 2009;3(2):e382.

Basta NE, Halloran ME, Matrajt L, Longini IM Jr.
Estimating influenza vaccine efficacy from challenge and community-based study data.
Am J Epidemiol. 2008 Dec 15;168(12):1343-52.

Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C.
No coexistence for free: neutral null models for multistrain pathogens.
Epidemics, 2008 Nov 4; [Epub ahead of print]

Kenah E, Lipsitch M, Robins JM.
Generation interval contraction and epidemic data analysis.
Math Biosci. 2008 May;213(1):71-9.

Takahashi K, Kulldorff M, Tango T, Yih K.
A flexibly shaped space-time scan statistic for disease outbreak detection and monitoring.
Int J Health Geogr. 2008 Apr 11;7:14.

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

Halloran ME, Ferguson NM, Eubank S, Longini IM Jr, Cummings DAT, Lewis B, Xu S, Fraser C, Vullikanti A, Germann TC, Wagener D, Beckman R, Kadau K, Barrett C, Macken CA, Burke DS, Cooley P.
Modeling targeted layered containment of an influenza pandemic in the United States.
Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4639-44.

Rosvall M, Bergstrom CT.
Maps of random walks on complex networks reveal community structure.
Proc Natl Acad Sci U S A. 2008 Jan 29;105(4):1118-23.

Kenah E, Robins JM.
Network-based analysis of stochastic SIR epidemic models with random and proportionate mixing.
J Theor Biol. 2007 Dec 21;249(4):706-22.

Longini IM Jr, Nizam A, Ali M, Yunus M, Shenvi N, Clemens JD.
Controlling endemic cholera with oral vaccines.
PLoS Med. 2007 Nov 27;4(11):e336.

Schmid-Hempel P, Frank SA.
Pathogenesis, virulence, and infective dose.
PLoS Pathog. 2007 Oct;3(10):e147.

Kenah E, Robins JM.
Second look at the spread of epidemics on networks.
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 Sep;76(3 Pt 2):036113.

Yang Y, Halloran ME, Sugimoto JD, Longini IM.
Detecting human-to-human transmission of avian influenza A (H5N1).
Emerg Infect Dis. 2007 Sep;13(9):1348-53.

Pitzer VE, Olsen SJ, Bergstrom CT, Dowell SF, Lipsitch M.
Little evidence for genetic susceptibility to influenza A (H5N1) from family clustering data.
Emerg Infect Dis. 2007 Jul;13(7):1074-6.

Halloran ME, Piedra PA, Longini IM Jr, Gaglani MJ, Schmotzer B, Fewlass C, Herschler GB, Glezen WP.
Efficacy of trivalent, cold-adapted, influenza virus vaccine against influenza A (Fujian), a drift variant, during 2003-2004.
Vaccine. 2007 May 16;25(20):4038-45.

Pitzer VE, Leung GM, Lipsitch M.
Estimating variability in the transmission of severe acute respiratory syndrome to household contacts in Hong Kong, China.
Am J Epidemiol. 2007 May 10; [Epub ahead of print]

Billings L, Schwartz IB, Shaw LB, McCrary M, Burke DS, Cummings DAT.
Instabilities in multiserotype disease models with antibody-dependent enhancement.
J Theor Biol. 2007 May 7;246(1):18-27.

Epstein JM, Goedecke DM, Yu F, Morris RJ, Wagener DK, Bobashev GV.
Controlling pandemic flu: the value of international air travel restrictions.
PLoS ONE. 2007 May 2; 2:e401.

Bootsma MC, Ferguson NM.
The effect of public health measures on the 1918 influenza pandemic in US cities.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7588-93.

Hatchett RJ, Mecher CE, Lipsitch M.
Public health interventions and epidemic intensity during the 1918 influenza pandemic.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7582-7.

Rosvall M, Bergstrom CT.
An information-theoretic framework for resolving community structure in complex networks.
Proc Natl Acad Sci U S A. 2007 May 1;104(18):7327-31.

Lipsitch M, O’hagan JJ.
Patterns of antigenic diversity and the mechanisms that maintain them.
J R Soc Interface. 2007 Apr 10; [Epub ahead of print]

Lessler J, Cummings DA, Fishman S, Vora A, Burke DS.
Transmissibility of swine flu at Fort Dix, 1976.
J R Soc Interface. 2007 Apr 3; [Epub ahead of print]

Handel A, Longini IM Jr., Antia R.
What is the best control strategy for multiple infectious disease outbreaks?
P Roy Soc B-Biol Sci. 2007 Mar 22;274(1611):833-7.

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

Wallinga J, Lipsitch M.
How generation intervals shape the relationship between growth rates and reproductive numbers.
Proc Biol Sci. 2007 Feb 22;274(1609):599-604.

Lipsitch M, Cohen T, Murray M, Levin BR.
Antiviral resistance and the control of pandemic influenza.
PLoS Med. 2007 Jan 23;4(1):e15.

Halloran ME, Hayden FG, Yang Y, Longini IM Jr, Monto AS.
Antiviral effects on influenza viral transmission and pathogenicity: observations from household-based trials.
Am J Epidemiol. 2007 Jan 15;165(2):212-21.

Yates A, Antia R, Regoes RR.
How do pathogen evolution and host heterogeneity interact in disease emergence?
Proc Biol Sci. 2006 Dec 22;273(1605):3075-83.

Barbour AG, Dai Q, Restrepo BI, Stoenner HG, Frank SA.
Pathogen escape from host immunity by a genome program for antigenic variation.
Proc Natl Acad Sci U S A. 2006 Nov 28;103(48):18290-5.

Halloran ME.
Invited commentary: challenges of using contact data to understand acute respiratory disease transmission.
Am J Epidemiol. 2006 Nov 15;164(10):945-6.

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

Scharfstein DO, Halloran ME, Chu H, Daniels MJ.
On estimation of vaccine efficacy using validation samples with selection bias.
Biostatistics. 2006 Oct;7(4):615-29.

Handel A, Regoes RR, Antia R.
The role of compensatory mutations in the emergence of drug resistance.
PLoS Comput Biol. 2006 Oct;2(10):e137.

Holmberg SD, Layton CM, Ghneim GS, Wagener DK.
State plans for containment of pandemic influenza.
Emerg Infect Dis. 2006 Sep;12(9):1414-17.

Ferguson NM, Cummings DA, Fraser C, Cajka JC, Cooley PC, Burke DS.
Strategies for mitigating an influenza pandemic.
Nature. 2006 Jul 27;442(7101):448-52.

Mills CE, Robins JM, Bergstrom CT, Lipsitch M.
Pandemic influenza: risk of multiple introductions and the need to prepare for them.
PLoS Med. 2006 Jun;3(6):e135.

Lipsitch M, Robins JM, Mills CE, Bergstrom CT.
Multiple outbreaks and flu containment plans
Science. 2006 May 12;312(5775):845.

Yang Y, Longini IM Jr, Halloran ME.
Design and evaluation of prophylactic interventions using infectious disease incidence data from close contact groups.
Applied Statistics. 2006 May;55(3):317-30.

Germann TC, Kadau K, Longini IM Jr, Macken CA.
Mitigation strategies for pandemic influenza in the United States.
Proc Natl Acad Sci U S A. 2006 Apr 11;103(15):5935-40.

Dibble C.
Computational laboratories for spatial agent-based models.
In: Tesfatsion L, Judd KL, eds. Handbook of computational economics, vol 2: Agent-based computational economics. North-Holland: 2006.

Halloran ME, Longini IM Jr.
Public health. Community studies for vaccinating schoolchildren against influenza.
Science. 2006 Feb 3;311(5761):615-6.

Eubank S.
Network based models of infectious disease spread.
Jpn J Infect Dis. 2005 Dec;58(6):S9-13.

Schwartz IB, Shaw LB, Cummings DA, Billings L, McCrary M, Burke DS.
Chaotic desynchronization of multistrain diseases.
Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Dec 1;72(6 Pt 2):066201.

Cummings DA, Schwartz IB, Billings L, Shaw LB, Burke DS.
Dynamic effects of antibody-dependent enhancement on the fitness of viruses.
PNAS. 2005 Oct 18;102(42):15259-64.

Ferguson NM, Cummings DA, Cauchemez S, Fraser C, Riley S, Meeyai A, Iamsirithaworn S, Burke DS.
Strategies for containing an emerging influenza pandemic in Southeast Asia.
Nature. 2005 Sep 8;437(7056):209-14.

Longini IM Jr., Nizam A, Xu S, Ungchusak K, Hanshaoworakul W, Cummings DA, Halloran ME.
Containing pandemic influenza at the source.
Science. 2005 Aug 12;309(5737):1083-7.

Ganusov VV, Antia R.
Pathology during acute infections: contributions of intracellular pathogens and the CTL response.
Biol Lett. 2005 Jun 22;1(2):239-42.

Barrett CL, Eubank SG, Smith JP.
If smallpox strikes Portland....
Sci Am. 2005 Mar;292(3):42-9.

Longini IM Jr., Halloran ME.
Strategy for distribution of influenza vaccine to high-risk groups and children.
Am J Epidemiol. 2005 Feb 15;161(4):303-6.

Ferguson NM, Fraser C, Donnelly CA, Ghani AC, Anderson RM.
Public health. Public health risks from the avian H5N1 influenza epidemic.
Science. 2004 May 14;304(5673):968-9.