FRED Publications


How to cite FRED

If you use FRED in your research, please use the following citation:

Grefenstette JJ, Brown ST, Rosenfeld R, Depasse J, Stone NT, Cooley PC, Wheaton WD, Fyshe A, Galloway DD, Sriram A, Guclu H, Abraham T, Burke DS. FRED (A Framework for Reconstructing Epidemic Dynamics): An open-source software system for modeling infectious diseases and control strategies using census-based populations. BMC Public Health, 2013 Oct;13(1), 940. doi: 10.1186/1471-2458-13-940. PubMed PMID: 24103508. Publication data.


Other publications using FRED

2025
Increasing child vaccination coverage can reduce influenza cases across age groups: An agent-based modeling study. Williams KV, Krauland MG, Nowalk MP, Harrison LH, Williams JV, Roberts MS, Zimmerman RK 2025 Mar;90(3):106443. doi: 10.1016/j.jinf.2025.106443. Epub 2025 Feb 12. PMID: 39952478.

2024
Influenza Vaccination, Household Composition, and Race-Based Differences in Influenza Incidence: An Agent-Based Modeling Study. Williams KV, Krauland MG, Harrison LH, Williams JV, Roberts MS, Zimmerman RK. PMID: 39541556 PMCID: PMC11715590 (available on 2026-02-01) DOI: 10.2105/AJPH.2024.307878 Am J Public Health. 2025 Feb;115(2):209-216. doi: 10.2105/AJPH.2024.307878. Epub 2024 Nov 14. PMID: 39541556.

Modeling the Impact of COVID-19 Mitigation Strategies in Pennsylvania, USA. Krauland MG, Roberts MS MDM Policy Pract. 2024 20;9(1):23814683241260744. doi: 10.1177/23814683241260744. eCollection 2024 Jan-Jun. PMID: 38911124.

2023
The Impact of the Good Behavior Game on Risk for Drug Use Disorder in an Agent-Based Model of Southern Sweden. Lönn SL, Krauland MG, Fagan AA, Sundquist K, Roberts MS, Kendler KS J Stud Alcohol Drugs . 2023 Nov;84(6):863-873. doi: 10.15288/jsad.22-00413. Epub 2023 Aug 30. PMID: 37650838 PMCID: PMC10765974 DOI: 10.15288/jsad.22-00413 PMID: 37650838.

2022
Agent-based model of the impact of higher influenza vaccine efficacy on seasonal influenza burden. Krauland MG, Zimmerman RK, Williams KV, Raviotta JM, Harrison LH, Williams JV, Roberts MS 2023 Apr:13:100249. doi: 10.1016/j.jvacx.2022.100249. Epub 2022 Dec 15. PMID: 36536801 PMCID: PMC9753457 DOI: 10.1016/j.jvacx.2022.100249 PMID: 36536801.

Can a Two-Dose Influenza Vaccine Regimen Better Protect Older Adults? An Agent-Based Modeling Study. Williams KV, Krauland MG, Harrison LH, Williams JV, Roberts MS, Zimmerman RK PMID: 36366307 PMCID: PMC9697266 DOI: 10.3390/vaccines10111799 2022 Oct 26;10(11):1799. doi: 10.3390/vaccines10111799. PMID: 36366307.

Impact of Low Rates of Influenza on Next-Season Influenza Infections. Krauland MG, Galloway DD, Raviotta JM, Zimmerman RK, Roberts MS PMID: 35305778 PMCID: PMC8866158 DOI: 10.1016/j.amepre.2021.11.007 2022 Apr;62(4):503-510. doi: 10.1016/j.amepre.2021.11.007. Epub 2022 Feb 24. PMID: 35305778.

2021
Estimating the Impact of Low Influenza Activity in 2020 on Population Immunity and Future Influenza Seasons in the United States. Lee K, Jalal H, Raviotta JM, Krauland MG, Zimmerman RK, Burke DS, Roberts MS PMID: 35024374 PMCID: PMC8743127 DOI: 10.1093/ofid/ofab607 2021 Dec 23;9(1):ofab607. doi: 10.1093/ofid/ofab607. eCollection 2022 Jan. PMID: 35024374.

2020
Development of a Synthetic Population Model for Assessing Excess Risk for Cardiovascular Disease Death. Krauland MG, Frankeny RJ, Lewis J, Brink L, Hulsey EG, Roberts MS, Hacker KA PMID: 32870312 PMCID: PMC7489828 DOI: 10.1001/jamanetworkopen.2020.15047 2020 Sep 1;3(9):e2015047. doi: 10.1001/jamanetworkopen.2020.15047. PMID: 32870312.

Detecting critical slowing down in high-dimensional epidemiological systems. Brett T, Ajelli M, Liu QH, Krauland MG, Grefenstette JJ, van Panhuis WG, Vespignani A, Drake JM, Rohani P PMID: 32150536 PMCID: PMC7082051 DOI: 10.1371/journal.pcbi.1007679 2020 Mar 9;16(3):e1007679. doi: 10.1371/journal.pcbi.1007679. eCollection 2020 Mar. PMID: 32150536.

Integrating Social Dynamics Into Modeling Cigarette and E-Cigarette Use. Chu KH, Shensa A, Colditz JB, Sidani JE, Hoffman BL, Sinclair D, Krauland MG, Primack BA PMID: 32090652 PMCID: PMC7256966 DOI: 10.1177/1090198119876242 2020 Apr;47(2):191-201. doi: 10.1177/1090198119876242. Epub 2020 Feb 24. PMID: 32090652.

2019
Sinclair D, Grefenstette JJ, Krauland MG, Galloway DD, Frankeny RJ, Travis C, Burke DS, and Roberts, MS. Forecasted Size of Measles Outbreaks Associated With Vaccination Exemptions for Schoolchildren, JAMA Netw Open. 2019;2(8):e199768. doi:10.1001/jamanetworkopen.2019.9768. PubMed PMID: 31433482.

Exploring the potential public health benefits of universal influenza vaccine. DePasse JV, Nowalk MP, Smith KJ, Raviotta JM, Shim E, Zimmerman RK, Brown ST. Hum Vaccin Immunother. 2019;15(12):2919-2926. doi: 10.1080/21645515.2019.1619406. Epub 2019 Jun 18. PMID: 31091166.

2017
Does cost-effectiveness of influenza vaccine choice vary across the U.S.? An agent-based modeling study. DePasse JV, Nowalk MP, Smith KJ, Raviotta JM, Shim E, Zimmerman RK, Brown ST. Vaccine. 2017 Jul 13;35(32):3974-3981. doi: 10.1016/j.vaccine.2017.05.093. Epub 2017 Jun 9. PMID: 28606814.

Does Choice of Influenza Vaccine Type Change Disease Burden and Cost-Effectiveness in the United States? An Agent-Based Modeling Study. DePasse JV, Smith KJ, Raviotta JM, Shim E, Nowalk MP, Zimmerman RK, Brown ST. Am J Epidemiol. 2017 May 1;185(9):822-831. doi: 10.1093/aje/kww229. PMID: 28402385.

2016
Guclu H, Kumar S, Galloway D, Krauland M, Sood R, Bocour A, Hershey TB, van Nostrand E, Potter M. An Agent-Based Model for Addressing the Impact of a Disaster on Access to Primary Care Services, Disaster Med Public Health Prep. 2016 Jun;10(3):386-93. doi: 10.1017/dmp.2016.44. Epub 2016 Apr 14. PubMed PMID: 27075561.

Cost Effectiveness of Influenza Vaccine Choices in Children Aged 2-8 Years in the U.S. Smith KJ, Raviotta JM, DePasse JV, Brown ST, Shim E, Patricia Nowalk M, Zimmerman RK. Am J Prev Med. 2016 May;50(5):600-608. doi: 10.1016/j.amepre.2015.12.010. Epub 2016 Feb 8. PMID: 26868283.

2015
Kumar S, Piper K, Galloway DD, Hadler JL, and Grefenstette JJ. Is population structure sufficient to generate area-level inequalities in influenza rates? An examination using agent-based models BMC Public Health, 2015 Sep 23;15(1):947. doi:10.1186/s12889-015-2284-2. PubMed PMID: 26400564. Publication data.

Liu F, Enanoria WT, Zipprich J, Blumberg S, Harriman K, Ackley SF, Wheaton WD, Allpress JL, Porco TC. The role of vaccination coverage, individual behaviors, and the public health response in the control of measles epidemics: an agent-based simulation for California. BMC Public Health. 2015 May 1;15(1):447. [Epub ahead of print] PubMed PMID: 25928152.

2014
Lukens S, DePasse J, Rosenfeld R, Ghedin E, Mochan E, Brown ST, Grefenstette J, Burke DS, Swigon D, Clermont G. A large-scale immuno-epidemiological simulation of influenza A epidemics. BMC Public Health. 2014 Sep 29;14:1019. doi: 10.1186/1471-2458-14-1019. PubMed PMID: 25266818; PubMed Central PMCID: PMC4194421.

2013
Kumar S, Grefenstette JJ, Galloway DD, Albert SM, and Burke DS. Policies to reduce influenza in the workplace: Impact assessments using an agent-based model. Am J Public Health, 2013 Aug;103(8):1406-11. doi: 10.2105/AJPH.2013.301269. Epub 2013 Jun 13. PubMed PMID: 23763426. Publication data.

2012
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 (e-Science 2012), pp.1-5, 8-12 Oct. 2012 doi: 10.1109/eScience.2012.6404444.

2011
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. BMC Public Health. 2011 May 20;11:353. doi: 10.1186/1471-2458-11-353. PubMed PMID: 21599920; PubMed Central PMCID: PMC3119163

Cooley P, Brown S, Cajka J, Chasteen B, Ganapathi L, Grefenstette J, Hollingsworth CR, Lee BY, Levine B, Wheaton WD, Wagener DK. The role of subway travel in an influenza epidemic: A New York City simulation. J Urban Health. 2011 Oct;88(5):982-95. PubMed PMID: 21826584; PubMed Central PMCID: PMC3191213.

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. PubMed PMID: 21653968; PubMed Central PMCID: PMC3385997

2010
Lee BY, Brown ST, Cooley PC, Zimmerman RK, Wheaton WD, Zimmer SM, Grefenstette JJ, Assi TM, Furphy TJ, Wagener DK, Burke DS. A computer simulation of employee vaccination to mitigate an influenza epidemic. Am J Prev Med. 2010 Mar;38(3):247-57. Epub 2009 Dec 30. PubMed PMID: 20042311; PubMed Central PMCID: PMC2833347.

Lee BY, Brown ST, Cooley P, Potter MA, Wheaton WD, Voorhees RE, Stebbins S, Grefenstette JJ, Zimmer SM, Zimmerman RK, Assi TM, Bailey RR, Wagener DK, Burke DS. Simulating school closure strategies to mitigate an influenza epidemic. J Public Health Manag Pract. 2010 May-Jun;16(3):252-61. PubMed PMID: 20035236; PubMed Central PMCID: PMC2901099.

Lee BY, Brown ST, Korch G, Cooley PC, Zimmerman RK, Wheaton WD, Zimmer SM, Grefenstette JJ, Bailey RR, Assi TM, Burke DS. A computer simulation of vaccine prioritization, allocation, and rationing during the 2009 H1N1 influenza pandemic. Vaccine. 2010 Jul 12;28(31):4875-9. doi: 10.1016/j.vaccine.2010.05.002. Epub 2010 May 16. PubMed PMID: 20483192; PubMed Central PMCID:PMC2906666

Lee BY, Brown ST, Cooley P, Grefenstette JJ, Zimmerman RK, Zimmer SM, Potter MA, Rosenfeld R, Wheaton WD, Wiringa AE, Bacon KM, Burke DS. Vaccination deep into a pandemic wave potential mechanisms for a "third wave" and the impact of vaccination. Am J Prev Med. 2010 Nov;39(5):e21-9. PubMed PMID: 20965375; PubMed Central PMCID: PMC2975455.