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Dean NE, Halloran ME. Protecting the herd with vaccination. Science. In press. (link to come)


Davis JT, Chinazzi M, Perra N, Mu K, Pastore Y Piontti A, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Longini IM Jr, Halloran ME, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave. Nature. 2021 Dec;600(7887):127-132. doi: 10.1038/s41586-021-04130-w. Epub 2021 Oct 25. PMCID: PMC8636257.

Katzelnick LC, Zambrana JV, Elizondo D, Collado D, Garcia N, Arguello S, Mercado JC, Miranda T, Ampie O, Mercado BL, Narvaez C, Gresh L, Binder RA, Ojeda S, Sanchez N, Plazaola M, Latta K, Schiller A, Coloma J, Carrillo FB, Narvaez F, Halloran ME, Gordon A, Kuan G, Balmaseda A, Harris E. Dengue and Zika virus infections in children elicit cross-reactive protective and enhancing antibodies that persist long term. Sci Transl Med. 2021 Oct 6;13(614):eabg9478. doi: 10.1126/scitranslmed.abg9478. Epub 2021 Oct 6. PMCID: PMC8693842.

Madewell ZJ, Pastore Y Piontti A, Zhang Q, Burton N, Yang Y, Longini IM, Halloran ME, Vespignani A, Dean NE. Using simulated infectious disease outbreaks to inform site selection and sample size for individually randomized vaccine trials during an ongoing epidemic. Clin Trials. 2021 Oct;18(5):630-638. doi: 10.1177/17407745211028898. Epub 2021 Jul 3. PMCID: PMC8478719

Rustom Antia R, Halloran ME. Transition to endemicity: Understanding COVID-19. Immunity. 2021 Oct 12;54(10):2172-2176. Epub 2021 Sep24. PMCID: PMC8461290

Rane M, Rohani P, Halloran ME. Durability of protection after 5 does of acellular pertussis vaccine among 5-9 year old children in King County, Washington, Vaccine. 2021 Oct 1;39(41):6144-6150. doi: 10.1016/j.vaccine.2021.08.070. Epub 2021 Sep 4. PubMed PMID: 34493409. PMCID in progress

Halloran ME. Discussion on "Estimating vaccine efficacy over time after a randomized study is unblinded" by Anastasios A. Tsiatis and Marie Davidian. Biometrics. 2021 Aug 22;. doi: 10.1111/biom.13540. [Epub ahead of print] PubMed PMID: 34420223, PMCID in progress

Rane MS, Rohani P, Halloran ME. Association of Diphtheria-Tetanus-Acellular Pertussis Vaccine Timeliness and Number of Doses With Age-Specific Pertussis Risk in Infants and Young Children. JAMA Netw Open. 2021 Aug 2;4(8):e2119118. doi: 10.1001/jamanetworkopen.2021.19118. PMCID: PMC8356064

Potter GE, Carnegie NB, Sugimoto JD, Diallo A, Victor JC, Neuzil KM, Halloran ME. Using social contact data to improve the overall effect estimate of a cluster-randomized influenza vaccination program in Senegal. J Roy Stat Soc, Series C, DOI: 10.1111/rssc.12522. Aug 2, 2021;00:1-21. On-line ahead of print, PMID and PMCID in process.

Madewell ZJ, Yang Y, Longini, Jr. I, Halloran ME, Dean, NE. Factors associated with household transmission of SARS-CoV-2: an updated systematic review and meta-analysis. JAMA Netw Open. 2021 Aug; 4(8): e2122240, published Aug 27 DOI: /jamanetworkopen.2021.22240, PMCID: PMC8397928

Feldstein LR, Ferdinands J, Self WH, Randolph AG, Aboodi M, Baughman AH, Brown SM, Exline MC, Files DC, Gibbs K, Ginde AA, Gong MN, Grijalva CG, Halasa N, Khan A, Lindsell CJ, Margaret Newhams M, Peltan ID, Prekker ME, Rice TW, Shapiro NI, Steingrub J, Talbot HK, Halloran ME, Patel M. Modeling the impacts of clinical influenza testing on influenza vaccine effectiveness estimates, J Infect Dis. 2021 Dec 15;224(12):2035-2042. doi: 10.1093/infdis/jiab273. [Epub ahead of print] PMC in process, PubMed PMID: 34013330

Rane M, Halloran ME. Estimating population level effects of DTaP vaccine using routinely collected immunization data. Clin Infect Dis. 2021 Apr 21;ciab333. doi: 10.1093/cid/ciab333. Online ahead of print. PubMed PMID: 33881527, PMCID in process.

Rane MS, Page LC, McVeigh E, Miller K, Baure D, Halloran ME, Duchin JS. Improving adolescent human papillomavirus (HPV) immunization uptake in school-based health centers through awareness campaigns. Vaccine. 2021 Mar 19;39(12):1765-1772. doi: 10.1016/j.vaccine.2021.02.006. Epub 2021 Feb 25; PubMed Central PMCID: PMC8021275

Chakladar S, Rosin S, Hudgens MG, Halloran ME, Clemens JD, Ali M, Emch ME. Inverse probability weighted estimators of vaccine effects accommodating partial interference and censoring. Biometrics. 2021 Mar 25;. doi: 10.1111/biom.13459. [Epub ahead of print] PMCID: PMC8463630

Li F, Li Y-Y, Liu M-J, Fang L-Q, Dean NE, Wong GWK, Yang X-B, Longini IM, Halloran ME, Wang H-J, Liu P-L, Pang Y-H, Yan Y-Q, Liu S, Xia W, Lu X-X, Liu Q, Yang Y, Xu S-Q. Household transmission of SARS-CoV-2 and risk factors for susceptibility and infectivity in Wuhan: a retrospective observational study. Lancet Infect Dis. 2021 May; 21(5): 617–628. Online ahead of print 2021 Jan 18. doi:10.1016/S1473-3099(20)30981-6 PMCID: PMC7833912

Mistry D, Litvinova M, Piontti A P-Y, Chinazzi M, Fumanelli L, Gomes MFC, Haque SA, Liu Q-F, Mu K, Xiong X, Halloran ME, Longini IM, Merler S, Ajellit M and Vespignani A. Inferring high resolution human mixing patterns for disease modeling. Inferring high resolution human mixing patterns for disease modeling. Nat Comm 2021; 12:323, PMCID: PMC7803761

Buchanan AL, Bessey S, Goedel WC, King M, Murray EJ, Friedman S, Halloran ME, Marshall BDL. Disseminated Effects in Agent Based Models: A Potential Outcomes Framework and Application to Inform Pre-Exposure Prophylaxis Coverage Levels for HIV Prevention. Am J Epidemiol. 2021 May 4; 190(5):935-948. doi: 10.1093/aje/kwaa239. [Epub ahead of print], PMCID: PMC8096482

Feldstein LR, Self WH, Ferdinands JM, Randolph AG, Aboodi M, Baughman AH, Brown SM, Exline MC, Files DC, Gibbs K, Ginde AA, Gong MN, Grijalva CG, Halasa N, Khan A, Lindsell CJ, Newhams M, Peltan ID, Prekker ME, Rice TW, Shapiro NI, Steingrub J, Talbot HK, Halloran ME, Patel M. Incorporating real-time influenza detection into the test-negative design for estimating influenza vaccine effectiveness: The real-time test-negative design (rtTND). Clin Infect Dis. 2021 May 4;72(9):1669-1675. Doi:10.1093/cid/ci1453. [Epub ahead of print] PMCID PMC8096266

Davis JT, Chinazzi M, Perra N, Mu K, Piontti APY, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Halloran ME, Longini IM Jr, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave in Europe and the United States. medRxiv. 2021 Mar 26;. doi: 10.1101/2021.03.24.21254199. PubMed PMID: 33791745; PubMed Central PMCID: PMC8010777

Niang MN, Sugimoto JD, Diallo A, Diarra B, Ortiz JR, Lewis KDC, Lafond KE, Halloran ME, Widdowson M-A, Neuzil KM, and Victor JC. Estimates of Inactivated Influenza Vaccine Effectiveness Among Children in Senegal: Results From 2 Consecutive Cluster-Randomized Controlled Trials in 2010 and 2011, Clin Infect Dis 2021 Jun 15;72(12):e959-e969 doi:10.1093/cid/ciaa1689, Online ahead of print, PMCID: PMC8204774


Dean NE, Piontti A P-Y, Madewell ZJ, Cummings DAT, Hitchings MDT, Joshi K, Kahn R, Vespignani A, Halloran ME, Longini IM. Ensemble forecast modeling for the design of COVID-19 vaccine efficacy trials, Vacc, 2020 Oct 27; 38(46), 7213-7216. PMCID: PMC7492005

Manrique-Saide P, Dean NE, Halloran ME, Longini IM, Collins MH, Waller LA, Gomez-Dantes H, Lenhart A, Hladish TJ, Che-Mendoza1 A, Kirstein OD, Romer Y, Correa-Morales F, Palacio-Vargas J, Mendez-Vales R, Granja Pérez P, Pavia-Ruz N, Ayora-Talavera G and Vazquez-Prokopec GM. The TIRS trial: protocol for a cluster randomized controlled trial assessing the efficacy of preventive targeted indoor residual spraying to reduce Aedes-borne viral illnesses in Merida, Mexico. Trials, 2020 Oct 8;21(1):839. doi: 10.1186/s13063-020-04780-7. PMCID: PMC7542575

WHO Ad Hoc Expert Group on the Next Steps for Covid-19 Vaccine Evaluation, Krause PR, Fleming TR, Longini IM, Peto R, Beral V, Bhargava B, Cravioto A, Cramer J, Ellenberg SS, Figueroa JP, Halloran ME, Henao-Restrepo AM, Ryan MJ, Levine MM, Nason M, Nohynek HM, Plotkin S, Rees H, Singh JA, Swaminathan S. Placebo-Controlled Trials of Covid-19 Vaccines - Why We Still Need Them. N Engl J Med. 2020 Dec 2. doi: 10.1056/NEJMp2033538. Epub ahead of print. PMID: 33264543

Wenzel NS, Atkins KE, van Leeuwen E, Halloran ME, Baguelin M. Cost-effectiveness of live-attenuated influenza vaccination among school-age children. Vaccine. 2021 Jan 8;39(2):447-456. doi: 10.1016/j.vaccine.2020.10.007. Epub 2020 Dec 4. PubMed PMID: 33280855

Magaret AS, Jacob ST, Halloran ME, Guthrie KA, Magaret CA, Johnston C, Simon NR, Wald A. Multigroup, Adaptively Randomized Trials Are Advantageous for Comparing Coronavirus Disease 2019 (COVID-19) Interventions. Ann Intern Med. 2020 Jun 11;M20-2933. Epub 2020/06/12. doi: 10.7326/M20-2933. PMCID: PMC7322770

Ogburn EL, Bierer BE, Brookmeyer R, Choirat C, Dean NE, De Gruttola V, Ellenberg SS, Halloran ME, Hanley DF, Jr., Lee JK, Wang R, Scharfstein DO. Aggregating data from COVID-19 trials. Science (New York, NY). 2020 Jun 12;368(6496):1198-9. Epub 2020/06/13. doi: 10.1126/science.abc8993. PMID: 32527823

Katzelnick LC, Narvaez C, Arguello S, Lopez Mercado B, Collado D, Ampie O, Elizondo D, Miranda T, Bustos Carillo F, Mercado JC, Latta K, Schiller A, Segovia-Chumbez B, Ojeda S, Sanchez N, Plazaola M, Coloma J, Halloran ME, Premkumar L, Gordon A, Narvaez F, de Silva AM, Kuan G, Balmaseda A, Harris E. Zika virus infection enhances future risk of severe dengue disease. Science. 2020 Aug 28;369(6507):1123-1128. doi: 10.1126/science.abb6143. PMCID: PMC8274975

Zhang J, Litvinova M, Wang W, Wang Y, Deng X, Chen X, Li M, Zheng W, Yi L, Chen X, Wu Q, Liang Y, Wang X, Yang J, Sun K, Longini IM, Jr., Halloran ME, Wu P, Cowling BJ, Merler S, Viboud C, Vespignani A, Ajelli M, Yu H. Evolving epidemiology and transmission dynamics of coronavirus disease 2019 outside Hubei province, China: a descriptive and modelling study. The Lancet Infect Dis. 2020 Jul;20(7):793-802. Epub 2020/04/02. doi: 10.1016/S1473-3099(20)30230-9. PMCID: PMC7269887

Madewell ZJ, Yang Y, Longini IM, Halloran ME, Dean NE. Household transmission of SARS-CoV-2: a systematic review and meta-analysis. JAMA Netw Open. 2020 Dec 1;3(12):e2031756, DOI: 10.1001/jamanetworkopen.2020.31756 Dec 14. PMCID: PMC7737089

Davis JT, Chinazzi M, Perra N, Mu K, Pastore YPA, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Halloran ME, Longini IM, Viboud C, Vespignani A. Estimating the establishment of local transmission and the cryptic phase of the COVID-19 pandemic in the USA. medRxiv: the Preprint Server for Health Sciences. 2020. Epub 2020/07/18, this article is a pre-print. doi: 10.1101/2020.07.06.20140285. PMCID: PMC7359534

Dean NE, Halloran, ME, Longini IM. Temporal Confounding in the Test Negative Design, Am J Epidemiol. 2020 May 16. doi: 10.1093/aje/kwaa084, online ahead of print. PMCID: PMC7604521

Ulrich A, McKearnan SB, Lammert S, Julian Wolfson J, Jonathan Pletcher J, Halloran ME, Basta, NE. Validity of university students' self-reported meningococcal B vaccination status during and after an outbreak, J Am Coll Health. 2020 Jul16;1-6. doi: 10.1080/07448481.2020.1772270, online ahead of print. PMCID: PMC7881838

Kilpatrick KW, Hudgens MG, Halloran ME. Estimands and inference in cluster-randomized vaccine trials. Pharm Stat. 2020 Sep;19(5):710-719. doi: 10.1002/pst.2026. Epub 2020 May 5. PMCID: PMC8273646

Aleta A, Mart´ın-Corral D, Pastore y Piontti A, Ajelli M, Litvinova M, Chinazzi M, Dean NE, Halloran ME, Longini IM, Merler S, Pentland A, Vespignani A, Moro E, Moreno Y. Modeling the impact of testing, contact tracing and household quarantine on second-waves of the COVID-19, Nat Hum Behav. 2020 Sep;4(9):967-971. doi: 10.1038/s41562-020-0931-9. Epub 2020 Aug 5. PMCID: PMC7641501

Lee EC, Chao DL, Lemaitre J, Matrajt L, Pasetto D, Perez-Saez J, Finger F, Rinaldo A, Sugimoto JD, Halloran ME, Longini IM, Ternier T, Vissieres K, Azman AS, Lessler J and Ivers LC. Achieving coordinated national immunity and cholera elimination in Haiti through vaccination: a modeling study, Lancet Glob Health. 2020 Aug; 8(8):e1081-1089 , PMCID: PMC7738665

Hladish TJ, Pearson CAB, Toh KB, Rojas DP, Pablo Manrique-Said P, Vazquez-Prokopec GM, Halloran ME, Ira M. Longini IM. Designing effective control of dengue with combined interventions, PNAS USA. 2020 Feb 11;117(6):3319-3325. doi: 10.1073/pnas.1903496117. Epub 2020Jan23. PMCID: PMC7022216

Buckee CO, Balsari S, Chan J, Crosas M, Dominici F, Gasser U, Grad YH, Grenfell B, Halloran ME, Kraemer MUG, Lipsitch M, Metcalf CJE, Meyers LA, Perkins TA, Santillana M, Scarpino SV, Viboud C, Wesolowski A, Schroeder A. Aggregated mobility data could help fight COVID-19. Science (New York, NY). 2020, Apr 10;368(6487):145-146. Epub 2020 Mar 23. doi: 10.1126/science.abb8021. PMC in process, PMID: 32205458

Chinazzi M, Davis JT, Ajelli M, Gioannini C, Litvinova M, Merler S, Pastore YPA, Mu K, Rossi L, Sun K, Viboud C, Xiong X, Yu H, Halloran ME, Longini IM, Jr., Vespignani A. The effect of travel restrictions on the spread of the 2019 novel coronavirus (COVID-19) outbreak. Science (New York, NY). 2020. Epub 2020/03/08. doi: 10.1126/science.aba9757. PMCID: PMC7164386. FUNDING: Halloran MIDAS U5

Ajelli M, Litvinova M, Merler S, Muyembe-Tamfum J-J, Mulangu S, Touré A, Diallo A, Bagayoko A, Bah A, Bah I, Barry A, Barry F, Chérif, M, Condé D, Diallo, A, Diallo, AA, Diallo F, Diakité M, Doré, K, Mapan KA, Koundouno T, Onivogui PK, Lamah F, Maneno H, Nomou A, Sekouba K, Sani I, Soumah A, Sy, M-M, Gsell,P-S, Halloran ME, Henao-Restrepo AM, Fall I-S, Ryan MJ, Salama P, Vespignani A, Longini Jr. IM, Vaccination Strategies for Ebola in the Democratic Republic of Congo, in press, N Engl J Med. 2020

Halloran ME, Longini IM, Gilbert PB. Designing a Study of Correlates of Risk for Ebola Vaccination, Am J Epidemiol. 2020 Aug 1;189(8):747-754. doi: 10.1093/aje/kwaa001 201. PMCID: PMC7407270

Dean NE, Gsell PS, Brookmeyer R, Crawford FW, Donnelly CA, Ellenberg SS, Fleming TR, Halloran ME, Horby P, Jaki T, Krause PR, Longini IM, Mulangu S, Muyembe-Tamfum JJ, Nason MC, Smith PG, Wang R, Henao-Restrepo AM, De Gruttola V. Creating a Framework for Conducting Randomized Clinical Trials during Disease Outbreaks. N Engl J Med. 2020 Apr 2;382(14):1366-1369. doi: 10.1056/NEJMsb1905390. PubMed Central PMCID: PMC7490833

Matrajt L, Halloran ME, Antia R. Successes and Failures of the Live-attenuated Influenza Vaccine: Can We Do Better?. Clin Infect Dis. 2020 Mar 3;70(6):1029-1037. doi: 10.1093/cid/ciz358. PubMed PMID: 31056675; PubMed Central PMCID: PMC731905


Black, A, Moncla L, Laiton-Donato K, Potter B, Pardo L, Rico A, Tovar C, Rojas DP, Longini IM, Halloran ME, Pelaez-Carvajal D, Ramirez JD, Mercado-Reyes M, Bedford T. Genomic epidemiology supports multiple introductions and cryptic transmission of Zika virus in Colombia, under revision. 2019 BMC Infect Dis. 2019, Nov 12;19(1):963. doi: 10.1186/s12879-019-4566-2. PMCID: PMC6852897.

Feldstein LR, Ellis EM, Rowhani-Rahbar A, Hennessey MJ, Staples JE, Halloran ME, Weaver MR. Estimating the cost of illness and burden of diseases associated with the 2014-2015 chikungunya outbreak in the U. S. Virgin Islands. PLoS Negl Trop Dis 2019 Jul 19:13(7):e0007563. doi:10.1371/journalpntd.0007563 PMCID: PMC6668848

Potter GE, Wong J, Sugimoto J, Diallo A, Victor JC, Neuzil K, Halloran ME. Networks of face-to-face social contacts in Niakhar, Senegal. PLoS One. 2019 Aug 6;14(8):e0220443. doi: 10.1371/journal.pone.0220443. eCollection 2019. PMCID: PMC6684077

Tsang TK, Ghebremariam SL, Gresh L, Gordon A, Halloran ME, Katzelnick LC, Rojas DP, Kuan G, Balmaseda A, Sugimoto JD, Harris E, Longini IM, Yang Y. Effects of infection history on dengue virus infection and pathogenicity. Nat Commun. 2019 Mar doi: 10.1038/s41467-019-09193-y. 18;10(1):1246. PMCID: PMC6423047

Basta NE and Halloran ME. Evaluating the effectiveness of vaccines using a regression discontinuity design. Am J Epidemiol. 2019 Feb 13. doi:10.1093/aje/kwz04. 188(6):987-990. PMCID: PMC6580688

Schwartz LM, Zaman K, Yunus M, Basunia AH, Faruque ASG, Ahmed T, Rahman M, Sugimoto JD, Halloran ME, Rowhani-Rahbar A, Neuzil KM, Victor JC. Impact of rotavirus vaccine introduction in children less than 2 years of age presenting for medical care with diarrhea in rural Matlab, Bangladesh. Clin Infect Dis. 2019 Dec 15; 69(12): 2059–2070. DOI: 10.1093/cid/ciz133. PMCID: PMC6880338

Ortiz JR, Sugimoto JD, Neuzil KM, Halloran ME, Victor JC. Reply to Skowronki and De Serres. Clin Infect Dis. 2019 Nov 27;69(12):2231-2232. doi: 10.1093/cid/ciz352 May 6 pii:ciz352. PMID 31056688.

Diallo A, Diop O, Diop D, Niang MN, Sugimoto JD, Ortiz JR, Faye A, Diarra B, Goudiaby D, Lewis KDC, Emery SL, Zangenah SZ, Lafond KE, Sokhna C, Halloran ME, Widdowson M-A, Neuzil KM, Victor JC. Effectiveness of seasonal influenza vaccination of children in Senegal during a year of vaccine mismatch: a cluster-randomized trial. Clin Infect Dis. 2019, Oct 30;69(10):1780-1788. doi: 10.1093/cid/ciz066. PMCID: PMC6821165

Dean NE, Gsell, P-S, Brookmeyer R, De Gruttola V, Donnelly CA, Halloran ME, Jasseh M, Nason M, Riveros X, Watson C, Henao-Restrepo AM, Longini IM. Design of vaccine efficacy trials during public health emergencies. Sci Transl Med. 2019; Jul 3;11(499) doi: 10.1126/scitranslmed.aat0360. PMCID PMC6613811


Tsang TK, Chen TM, Longini IM Jr, Halloran ME, Wu Y, Yang Y. Transmissibility of Norovirus in Urban Versus Rural Households in a Large Community Outbreak in China. Epidemiology. 2018 Sep;29(5):675-683. doi: 10.1097/EDE.0000000000000855. PubMed PMID: 29847497; PubMed Central PMCID: PMC6066449.

Lee JM, Huddleston J, Doud MB, Hooper KA, Wu NC, Bedford T, Bloom JD. Deep mutational scanning of hemagglutinin helps predict evolutionary fates of human H3N2 influenza variants. Proc Natl Acad Sci U S A. 2018 Aug 28;115(35):E8276-E8285. doi: 10.1073/pnas.1806133115. Epub 2018 Aug 13. PubMed PMID: 30104379; PubMed Central PMCID: PMC6126756.

Zarnitsyna VI, Bulusheva I, Handel A, Longini IM, Halloran ME, Antia R. Intermediate levels of vaccination coverage may minimize seasonal influenza outbreaks. PLoS One. 2018 Jun 26;13(6):e0199674. doi: 10.1371/journal.pone.0199674. eCollection 2018. PubMed PMID: 29944709; PubMed Central PMCID: PMC6019388.

Hladish TJ, Pearson CAB, Patricia Rojas D, Gomez-Dantes H, Halloran ME, Vazquez-Prokopec GM, Longini IM. Forecasting the effectiveness of indoor residual spraying for reducing dengue burden. PLoS Negl Trop Dis. 2018 Jun 25;12(6):e0006570. doi: 10.1371/journal.pntd.0006570. eCollection 2018 Jun. PubMed PMID: 29939983; PubMed Central PMCID: PMC6042783.

Pavía-Ruz N, Diana Patricia Rojas, Salha Villanueva, Granja P, Balam-May A, Longini IM, Halloran ME, Manrique-Saide P, Gómez- Dantés H. Seroprevalence of Dengue Antibodies in Three Urban Settings in Yucatan, Mexico. Am J Trop Med Hyg. 2018 Apr;98(4):1202-1208. doi: 10.4269/ajtmh.17-0382. Epub 2018 Feb 15. PubMed PMID: 29460714; PubMed Central PMCID: PMC5928812.

Bisanzio D, Dzul-Manzanilla F, Gomez-Dantés H, Pavia-Ruz N, Hladish TJ, Lenhart A, Palacio-Vargas J, González Roldan JF, Correa-Morales F, Sánchez-Tejeda G, Kuri Morales P, Manrique- Saide P, Longini IM, Halloran ME, Vazquez-Prokopec GM. Spatiotemporal coherence of dengue, chikungunya and Zika outbreaks in Merida, Mexico. PLoS Negl Trop Dis. 2018 Mar 15;12(3):e0006298. doi: 10.1371/journal.pntd.0006298. eCollection 2018 Mar. PubMed PMID: 29543910; PubMed Central PMCID: PMC5870998.

Dean NE, Halloran ME, Longini IM. Design of vaccine trials during outbreaks with and without a delayed vaccination comparator. Ann Appl Stat. 2018 Mar;12(1):330-347. doi: 10.1214/17-AOAS1095. Epub 2018 Mar 9. PubMed PMID: 29606991; PubMed Central PMCID: PMC5878056.

Feldstein LR, Rowhani-Rahbar A, Staples JE, Halloran ME, Ellis EM. An Assessment of Household and Individual-Level Mosquito Prevention Methods during the Chikungunya Virus Outbreak in the United States Virgin Islands, 2014-2015. Am J Trop Med Hyg. 2018 Mar;98(3):845-848. doi: 10.4269/ajtmh.17-0799. Epub 2018 Feb 1. PubMed PMID: 29405105; PubMed Central PMCID: PMC5930869.

Fong Y, Halloran ME, Park JK, Marks F, Clemens JD, Chao DL. Efficacy of a bivalent killed whole-cell cholera vaccine over five years: a re-analysis of a cluster-randomized trial. BMC Infect Dis. 2018 Feb 20;18(1):84. doi: 10.1186/s12879-018-2981-4. PubMed PMID: 29463233; PubMed Central PMCID: PMC5819652.

Yang Y, Meng Y, Halloran ME, Longini IM Jr. Reply to Aguiar and Stollenwerk. Clin Infect Dis. 2018 Feb 1;66(4):642. doi: 10.1093/cid/cix883. PubMed PMID: 29088434; PubMed Central PMCID: PMC5848237.

Basta NE, Berthe A, Keita M, Onwuchekwa U, Tamboura B, Traore A, Hassan-King M, Manigart O, Nascimento M, Stuart JM, Trotter C, Blake J, Carr AD, Gray SJ, Newbold LS, Deng Y, Wolfson J, Halloran ME, Greenwood B, Borrow R, Sow SO. Meningococcal carriage within households in the African meningitis belt: A longitudinal pilot study. J Infect. 2018 Feb;76(2):140-148. doi: 10.1016/j.jinf.2017.11.006. Epub 2017 Nov 29. PubMed PMID: 29197599; PubMed Central PMCID: PMC5790055.

Halloran ME, Hudgens MG. Estimating population effects of vaccination using large, routinely collected data. Stat Med. 2018 Jan 30;37(2):294-301. doi: 10.1002/sim.7392. Epub 2017 Jul 19. PubMed PMID: 28722190; PubMed Central PMCID: PMC5735016.

Yang Y, Meng Y, Halloran ME, Longini IM Jr. Dependency of Vaccine Efficacy on Preexposure and Age: A Closer Look at a Tetravalent Dengue Vaccine. Clin Infect Dis. 2018 Jan 6;66(2):178- 184. doi: 10.1093/cid/cix766. PubMed PMID: 29020332; PubMed Central PMCID: PMC5850009.

Rojas, DP, Abigail Barrera-Fuentes, GA, Pavia-Ruz, N, Salgado-Rodriguez, M, Che-Mendoza, A, Manrique-Saide, P, Vazquez-Prokopec, GM, Halloran, ME, Longini, IM, Gomez-Dantés H. Epidemiology of dengue and other arboviruses in a cohort of school children and their families in Yucatan, Mexico: Baseline and first year follow-up. PLoS Negl Trop Dis. 2018; Nov; 12(11). PMCID: PMC6248893

Sun K, Zhang Q, Pastore-Piontti A, Chinazzi M, Mistry D, Dean NE, Rojas DP, Merler S, Poletti P, Rossi L, Halloran ME, Longini IM Jr, Vespignani A. Quantifying the risk of local Zika virus transmission in the contiguous US during the 2015-2016 ZIKV epidemic. BMC Med. 2018 Oct 18;16(1):195. doi:10.1186/s12916-018-1185-5. PMCID: PMC6194624


Halloran ME, Auranen K, Baird S, Basta NE, Bellan SE, Brookmeyer R, Cooper BS, DeGruttola V, Hughes JP, Lessler J, Lofgren ET, Longini IM, Onnela JP, Özler B, Seage GR, Smith TA, Vespignani A, Vynnycky E, Lipsitch M. Simulations for designing and interpreting intervention trials in infectious diseases. BMC Med. 2017 Dec 29;15(1):223. doi: 10.1186/s12916-017-0985-3. PubMed PMID: 29287587; PubMed Central PMCID: PMC5747936.

Katzelnick LC, Gresh L, Halloran ME, Mercado JC, Kuan G, Gordon A, Balmaseda A, Harris E. Antibody-dependent enhancement of severe dengue disease in humans. Science. 2017 Nov 17;358(6365):929-932. doi: 10.1126/science.aan6836. Epub 2017 Nov 2. PubMed PMID: 29097492; PubMed Central PMCID: PMC5858873.

Metsky HC, Matranga CB, Wohl S, Schaffner SF, Freije CA, Winnicki SM, West K, Qu J, Baniecki ML, Gladden-Young A, Lin AE, Tomkins-Tinch CH, Ye SH, Park DJ, Luo CY, Barnes KG, Shah RR, Chak B, Barbosa-Lima G, Delatorre E, Vieira YR, Paul LM, Tan AL, Barcellona CM, Porcelli MC, Vasquez C, Cannons AC, Cone MR, Hogan KN, Kopp EW, Anzinger JJ, Garcia KF, Parham LA, Ramírez RMG, Montoya MCM, Rojas DP, Brown CM, Hennigan S, Sabina B, Scotland S, Gangavarapu K, Grubaugh ND, Oliveira G, Robles-Sikisaka R, Rambaut A, Gehrke L, Smole S, Halloran ME, Villar L, Mattar S, Lorenzana I, Cerbino-Neto J, Valim C, Degrave W, Bozza PT, Gnirke A, Andersen KG, Isern S, Michael SF, Bozza FA, Souza TML, Bosch I, Yozwiak NL, MacInnis BL, Sabeti PC. Zika virus evolution and spread in the Americas. Nature. 2017 Jun 15;546(7658):411-415. doi: 10.1038/nature22402. Epub 2017 May 24. PubMed PMID: 28538734; PubMed Central PMCID: PMC5563848.

Zhang Q, Sun K, Chinazzi M, Pastore Y Piontti A, Dean NE, Rojas DP, Merler S, Mistry D, Poletti P, Rossi L, Bray M, Halloran ME, Longini IM Jr, Vespignani A. Spread of Zika virus in the Americas. Proc Natl Acad Sci U S A. 2017 May 30;114(22):E4334-E4343. doi: 10.1073/pnas.1620161114. Epub 2017 Apr 25. PubMed PMID: 28442561; PubMed Central PMCID: PMC5465916.

Zaman K, Sack DA, Neuzil KM, Yunus M, Moulton LH, Sugimoto JD, Fleming JA, Hossain I, Arifeen SE, Azim T, Rahman M, Lewis KDC, Feller AJ, Qadri F, Halloran ME, Cravioto A, Victor JC. Effectiveness of a live oral human rotavirus vaccine after programmatic introduction in Bangladesh: A cluster-randomized trial. PLoS Med. 2017 Apr 18;14(4):e1002282. doi: 10.1371/journal.pmed.1002282. eCollection 2017 Apr. PubMed PMID: 28419095; PubMed Central PMCID: PMC5395158.

Feldstein LR, Rowhani-Rahbar A, Staples JE, Weaver MR, Halloran ME, Ellis EM. Persistent Arthralgia Associated with Chikungunya Virus Outbreak, US Virgin Islands, December 2014-February 2016. Emerg Infect Dis. 2017 Apr;23(4):673-676. doi: 10.3201/eid2304.161562. PubMed PMID: 28322703; PubMed Central PMCID: PMC5367425.

Schwartz LM, Halloran ME, Rowhani-Rahbar A, Neuzil KM, Victor JC. Rotavirus vaccine effectiveness in low-income settings: An evaluation of the test-negative design. Vaccine. 2017 Jan 3;35(1):184-190. doi: 10.1016/j.vaccine.2016.10.077. Epub 2016 Nov 18. PubMed PMID: 27876198; PubMed Central PMCID: PMC5154240.


Halloran ME, Hudgens MG. Dependent Happenings: A Recent Methodological Review. Curr Epidemiol Rep. 2016 Dec;3(4):297- 305. doi: 10.1007/s40471-016-0086-4. Epub 2016 Jul 28. PubMed PMID: 28133589; PubMed Central PMCID: PMC5267358.

Gabriel EE, Daniels MJ, Halloran ME. Comparing biomarkers as trial level general surrogates. Biometrics. 2016 Dec;72(4):1046- 1054. doi: 10.1111/biom.12513. Epub 2016 Apr 1. PubMed PMID: 27038302; PubMed Central PMCID: PMC5045774.

Merler S, Ajelli M, Fumanelli L, Parlamento S, Pastore Y Piontti A, Dean NE, Putoto G, Carraro D, Longini IM Jr, Halloran ME, Vespignani A. Containing Ebola at the Source with Ring Vaccination. PLoS Negl Trop Dis. 2016 Nov 2;10(11):e0005093. doi: 10.1371/journal.pntd.0005093. eCollection 2016 Nov. PubMed PMID: 27806049; PubMed Central PMCID: PMC5091901.

Complete Feldstein LR, Ellis EM, Rowhani-Rahbar A, Halloran ME, Ellis BR. The First Reported Outbreak of Chikungunya in the U.S. Virgin Islands, 2014-2015. Am J Trop Med Hyg. 2016 Oct 5;95(4):885- 889. Epub 2016 Jul 11. PubMed PMID: 27402523; PubMed Central PMCID: PMC5062794.

Ajelli M, Merler S, Fumanelli L, Pastore Y Piontti A, Dean NE, Longini IM Jr, Halloran ME, Vespignani A. Spatiotemporal dynamics of the Ebola epidemic in Guinea and implications for vaccination and disease elimination: a computational modeling analysis. BMC Med. 2016 Sep 7;14(1):130. doi: 10.1186/s12916-016-0678-3. PubMed PMID: 27600737; PubMed Central PMCID: PMC5013652.

Koepke AA, Longini IM Jr, Halloran ME, Wakefield J, Minin VN. Predictive modeling of cholera outbreaks in Bangladesh. Ann Appl Stat. 2016 Jun;10(2):575-595. Epub 2016 Jul 22. PubMed PMID: 27746850; PubMed Central PMCID: PMC5061460.

Feldstein LR, Matrajt L, Elizabeth Halloran M, Keitel WA, Longini IM Jr; H5N1 Vaccine Working Group. Extrapolating theoretical efficacy of inactivated influenza A/H5N1 virus vaccine from human immunogenicity studies. Vaccine. 2016 Jul 19;34(33):3796-802. doi: 10.1016/j.vaccine.2016.05.067. Epub 2016 Jun 20. PubMed PMID: 27268778; PubMed Central PMCID: PMC5168719.

Rojas DP, Dean NE, Yang Y, Kenah E, Quintero J, Tomasi S, Ramirez EL, Kelly Y, Castro C, Carrasquilla G, Halloran ME, Longini IM. The epidemiology and transmissibility of Zika virus in Girardot and San Andres island, Colombia, September 2015 to January 2016. Euro Surveill. 2016 Jul 14;21(28). doi: 10.2807/1560- 7917.ES.2016.21.28.30283. PubMed PMID: 27452806; PubMed Central PMCID: PMC5124348.

Hladish TJ, Pearson CA, Chao DL, Rojas DP, Recchia GL, Gómez- Dantés H, Halloran ME, Pulliam JR, Longini IM. Projected Impact of Dengue Vaccination in Yucatán, Mexico. PLoS Negl Trop Dis. 2016 May 26;10(5):e0004661. doi: 10.1371/journal.pntd.0004661. eCollection 2016 May. PubMed PMID: 27227883; PubMed Central PMCID: PMC4882069.

Dean NE, Halloran ME, Yang Y, Longini IM. Transmissibility and Pathogenicity of Ebola Virus: A Systematic Review and Metaanalysis of Household Secondary Attack Rate and Asymptomatic Infection. Clin Infect Dis. 2016 May 15;62(10):1277-1286. doi: 10.1093/cid/ciw114. Epub 2016 Feb 29. Review. PubMed PMID: 26932131; PubMed Central PMCID: PMC4845791.

Fang LQ, Yang Y, Jiang JF, Yao HW, Kargbo D, Li XL, Jiang BG, Kargbo B, Tong YG, Wang YW, Liu K, Kamara A, Dafae F, Kanu A, Jiang RR, Sun Y, Sun RX, Chen WJ, Ma MJ, Dean NE, Thomas H, Longini IM Jr, Halloran ME, Cao WC. Transmission dynamics of Ebola virus disease and intervention effectiveness in Sierra Leone. Proc Natl Acad Sci U S A. 2016 Apr 19;113(16):4488-93. doi: 10.1073/pnas.1518587113. Epub 2016 Mar 28. PubMed PMID: 27035948; PubMed Central PMCID: PMC4843458.

Complete Kenah E, Britton T, Halloran ME, Longini IM Jr. Molecular Infectious Disease Epidemiology: Survival Analysis and Algorithms Linking Phylogenies to Transmission Trees. PLoS Comput Biol. 2016 Apr 12;12(4):e1004869. doi: 10.1371/journal.pcbi.1004869. eCollection 2016 Apr. PubMed PMID: 27070316; PubMed Central PMCID: PMC4829193.

Zhou J, Chu H, Hudgens MG, Halloran ME. A Bayesian approach to estimating causal vaccine effects on binary post-infection outcomes. Stat Med. 2016 Jan 15;35(1):53-64. doi: 10.1002/sim.6573. Epub 2015 Jul 20. PubMed PMID: 26194767; PubMed Central PMCID: PMC4715486.


Chao DL, Park JK, Marks F, Ochiai RL, Longini IM, Halloran ME. The contribution of neighbours to an individual's risk of typhoid outcome. Epidemiol Infect. 2015 Dec;143(16):3520-7. doi: 10.1017/S0950268815000692. Epub 2015 May 4. PubMed PMID: 25936682; PubMed Central PMCID: PMC4619120.

Matrajt L, Britton T, Halloran ME, Longini IM Jr. One versus two doses: What is the best use of vaccine in an influenza pandemic? Epidemics. 2015 Dec;13:17-27. doi: 10.1016/j.epidem.2015.06.001. Epub 2015 Jun 22. PubMed PMID: 26616038; PubMed Central PMCID: PMC4664891.

Schwartz LM, Halloran ME, Durbin AP, Longini IM Jr. The dengue vaccine pipeline: Implications for the future of dengue control. Vaccine. 2015 Jun 26;33(29):3293-8. doi: 10.1016/j.vaccine.2015.05.010. Epub 2015 May 16. Review. PubMed PMID: 25989449; PubMed Central PMCID: PMC4470297.

Gessner BD, Halloran ME, Khan I. The case for a typhoid vaccine probe study and overview of design elements. Vaccine. 2015 Jun 19;33 Suppl 3:C30-5. doi: 10.1016/j.vaccine.2015.03.085. Epub 2015 Apr 23. Review. PubMed PMID: 25912286; PubMed Central PMCID: PMC4633310.

Lipsitch M, Eyal N, Halloran ME, Hernán MA, Longini IM, Perencevich EN, Grais RF. Vaccine testing. Ebola and beyond. Science. 2015 Apr 3;348(6230):46-8. doi: 10.1126/science.aaa3178. PubMed PMID: 25838371; PubMed Central PMCID: PMC4408019.

Yang Y, Zhang Y, Fang L, Halloran ME, Ma M, Liang S, Kenah E, Britton T, Chen E, Hu J, Tang F, Cao W, Feng Z, Longini IM Jr. Household transmissibility of avian influenza A (H7N9) virus, China, February to May 2013 and October 2013 to March 2014. Euro Surveill. 2015 Mar 12;20(10):21056. PubMed PMID: 25788253; PubMed Central PMCID: PMC4404303.

Lessler J, Edmunds WJ, Halloran ME, Hollingsworth TD, Lloyd AL. Seven challenges for model-driven data collection in experimental and observational studies. Epidemics. 2015 Mar;10:78-82. doi: 10.1016/j.epidem.2014.12.002. Epub 2014 Dec 16. PubMed PMID: 25843389; PubMed Central PMCID: PMC4387311.

Merler S, Ajelli M, Fumanelli L, Gomes MF, Piontti AP, Rossi L, Chao DL, Longini IM Jr, Halloran ME, Vespignani A. Spatiotemporal spread of the 2014 outbreak of Ebola virus disease in Liberia and the effectiveness of non-pharmaceutical interventions: a computational modelling analysis. Lancet Infect Dis. 2015 Feb;15(2):204-11. doi: 10.1016/S1473-3099(14)71074-6. Epub 2015 Jan 7. PubMed PMID: 25575618; PubMed Central PMCID: PMC4409131.


Lofgren ET, Halloran ME, Rivers CM, Drake JM, Porco TC, Lewis B, Yang W, Vespignani A, Shaman J, Eisenberg JN, Eisenberg C, Marathe M, Scarpino SV, Alexander KA, Meza R, Ferrari MJ, Hyman JM, Meyers LA, Eubank S. Opinion: Mathematical models: a key tool for outbreak response. Proc Natl Acad Sci U S A. 2014 Dec 23;111(51):18095-6. doi: 10.1073/pnas.1421551111. Epub 2014 Dec 10. PubMed PMID: 25502594; PubMed Central PMCID: PMC4280577.

Tran CH, Sugimoto JD, Pulliam JR, Ryan KA, Myers PD, Castleman JB, Doty R, Johnson J, Stringfellow J, Kovacevich N, Brew J, Cheung LL, Caron B, Lipori G, Harle CA, Alexander C, Yang Y, Longini IM Jr, Halloran ME, Morris JG Jr, Small PA Jr. Schoollocated influenza vaccination reduces community risk for influenza and influenza-like illness emergency care visits. PLoS One. 2014 Dec 9;9(12):e114479. doi: 10.1371/journal.pone.0114479. eCollection 2014. PubMed PMID: 25489850; PubMed Central PMCID: PMC4260868.

Dimitrov DT, Troeger C, Halloran ME, Longini IM, Chao DL. Comparative effectiveness of different strategies of oral cholera vaccination in Bangladesh: a modeling study. PLoS Negl Trop Dis. 2014 Dec 4;8(12):e3343. doi: 10.1371/journal.pntd.0003343. eCollection 2014 Dec. PubMed PMID: 25473851; PubMed Central PMCID: PMC4256212.

VanderWeele TJ, Tchetgen Tchetgen EJ, Halloran ME. Interference and Sensitivity Analysis. Stat Sci. 2014 Nov;29(4):687-706. PubMed PMID: 25620841; PubMed Central PMCID: PMC4300555.

Halloran ME, Vespignani A, Bharti N, Feldstein LR, Alexander KA, Ferrari M, Shaman J, Drake JM, Porco T, Eisenberg JN, Del Valle SY, Lofgren E, Scarpino SV, Eisenberg MC, Gao D, Hyman JM, Eubank S, Longini IM Jr. Ebola: mobility data. Science. 2014 Oct 24;346(6208):433. doi: 10.1126/science.346.6208.433-a. PubMed PMID: 25342792; PubMed Central PMCID: PMC4408607.

Poletto C, Gomes MF, Pastore y Piontti A, Rossi L, Bioglio L, Chao DL, Longini IM, Halloran ME, Colizza V, Vespignani A. Assessing the impact of travel restrictions on international spread of the 2014 West African Ebola epidemic. Euro Surveill. 2014 Oct 23;19(42). pii: 20936. PubMed PMID: 25358040; PubMed Central PMCID: PMC4415609.

Halloran ME, Longini IM Jr. Emerging, evolving, and established infectious diseases and interventions. Science. 2014 Sep 12;345(6202):1292-4. doi: 10.1126/science.1254166. PubMed PMID: 25214617; PubMed Central PMCID: PMC4408765.

Perez-Heydrich C, Hudgens MG, Halloran ME, Clemens JD, Ali M, Emch ME. Assessing effects of cholera vaccination in the presence of interference. Biometrics. 2014 Sep;70(3):731-44. doi: 10.1111/biom.12184. Epub 2014 May 20. PubMed PMID: 24845800; PubMed Central PMCID: PMC4239215.

Yang Y, Halloran ME, Chen Y, Kenah E. A pathway EM-algorithm for estimating vaccine efficacy with a non-monotone validation set. Biometrics. 2014 Sep;70(3):568-78. doi: 10.1111/biom.12173. Epub 2014 Apr 25. PubMed PMID: 24766139; PubMed Central PMCID: PMC4209209.


Basta NE, Stuart JM, Nascimento MC, Manigart O, Trotter C, Hassan-King M, Chandramohan D, Sow SO, Berthe A, Bedru A, Tekletsion YK, Collard JM, Jusot JF, Diallo A, Basséne H, Daugla DM, Gamougam K, Hodgson A, Forgor AA, Omotara BA, Gadzama GB, Watkins ER, Rebbetts LS, Diallo K, Weiss NS, Halloran ME, Maiden MC, Greenwood B. Methods for identifying Neisseria meningitidis carriers: a multi-center study in the African meningitis belt. PLoS One. 2013 Oct 23;8(10):e78336. doi: 10.1371/journal.pone.0078336. eCollection 2013. PubMed PMID: 24194921; PubMed Central PMCID: PMC3806823.

Hertz T, Oshansky CM, Roddam PL, DeVincenzo JP, Caniza MA, Jojic N, Mallal S, Phillips E, James I, Halloran ME, Thomas PG, Corey L. HLA targeting efficiency correlates with human T-cell response magnitude and with mortality from influenza A infection. Proc Natl Acad Sci U S A. 2013 Aug 13;110(33):13492-7. doi: 10.1073/pnas.1221555110. Epub 2013 Jul 22. PubMed PMID: 23878211; PubMed Central PMCID: PMC3746844.

MenAfriCar Consortium. Meningococcal carriage in the African meningitis belt. Trop Med Int Health. 2013 Aug;18(8):968-78. doi: 10.1111/tmi.12125. Epub 2013 May 18. PubMed PMID: 23682910; PubMed Central PMCID: PMC3950817.

Complete Auranen K, Rinta-Kokko H, Halloran ME. Estimating strain-specific and overall efficacy of polyvalent vaccines against recurrent pathogens from a cross-sectional study. Biometrics. 2013 Mar;69(1):235-44. doi: 10.1111/j.1541-0420.2012.01826.x. Epub 2013 Feb 4. PubMed PMID: 23379663; PubMed Central PMCID: PMC3622115.

Small DS, Cheng J, Halloran ME, Rosenbaum PR. Case Definition and Design Sensitivity. J Am Stat Assoc. 2013 Jan 1;108(504):1457-1468. PubMed PMID: 24482549; PubMed Central PMCID: PMC3904399.


Yang Y, Longini IM Jr, Halloran ME, Obenchain V. A hybrid EM and Monte Carlo EM algorithm and its application to analysis of transmission of infectious diseases. Biometrics. 2012 Dec;68(4):1238-49. doi: 10.1111/j.1541-0420.2012.01757.x. Epub 2012 Apr 16. PubMed PMID: 22506893; PubMed Central PMCID: PMC3402623.

Halloran ME, Hudgens MG. Comparing bounds for vaccine effects on infectiousness. Epidemiology. 2012 Nov;23(6):931-2. doi: 10.1097/EDE.0b013e31826d0741. PubMed PMID: 23038122; PubMed Central PMCID: PMC3482261.

Chao DL, Halstead SB, Halloran ME, Longini IM Jr. Controlling dengue with vaccines in Thailand. PLoS Negl Trop Dis. 2012;6(10):e1876. doi: 10.1371/journal.pntd.0001876. Epub 2012 Oct 25. PubMed PMID: 23145197; PubMed Central PMCID: PMC3493390.

Vanderweele TJ, Tchetgen Tchetgen EJ, Halloran ME. Components of the indirect effect in vaccine trials: identification of contagion and infectiousness effects. Epidemiology. 2012 Sep;23(5):751-61. doi: 10.1097/EDE.0b013e31825fb7a0. Erratum in: Epidemiology. 2012 Nov;23(6):940. PubMed PMID: 22828661; PubMed Central PMCID: PMC3415570.

Halloran ME. The Minicommunity Design to Assess Indirect Effects of Vaccination. Epidemiol Methods. 2012 Aug 1;1(1):83-105.PubMed PMID: 23599908; PubMed Central PMCID: PMC3627501.

Matrajt L, Longini IM Jr. Critical immune and vaccination thresholds for determining multiple influenza epidemic waves. Epidemics. 2012 Mar;4(1):22-32. doi: 10.1016/j.epidem.2011.11.003. Epub 2011 Dec 7. PubMed PMID: 22325011; PubMed Central PMCID: PMC3703471.

Halloran ME, Hudgens MG. Causal inference for vaccine effects on infectiousness. Int J Biostat. 2012 Jan 6;8(2). pii: /j/ijb.2012.8.issue- 2/1557-4679.1354/1557-4679.1354.xml. doi: 10.2202/1557- 4679.1354. PubMed PMID: 22499732; PubMed Central PMCID: PMC3348179.


Kenah E, Chao DL, Matrajt L, Halloran ME, Longini IM Jr. The global transmission and control of influenza. PLoS One. 2011 May 6;6(5):e19515. doi: 10.1371/journal.pone.0019515. PubMed PMID: 21573121; PubMed Central PMCID: PMC3089626.

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. doi: 10.1097/EDE.0b013e3182060ca5. PubMed PMID: 21233714; PubMed Central PMCID: PMC3755879.


Yang Y, Halloran ME, Daniels MJ, Longini IM Jr, Burke DS, Cummings DA. Modeling Competing Infectious Pathogens from a Bayesian Perspective: Application to Influenza Studies with Incomplete Laboratory Results. J Am Stat Assoc. 2010 Dec;105(492):1310-1322. PubMed PMID: 21472041; PubMed Central PMCID: PMC3070363.

Complete Chao DL, Halloran ME, Longini IM Jr. School opening dates predict pandemic influenza A(H1N1) outbreaks in the United States. J Infect Dis. 2010 Sep 15;202(6):877-80. doi: 10.1086/655810. PubMed PMID: 20704486; PubMed Central PMCID: PMC2939723.

Chao DL, Halloran ME, Obenchain VJ, Longini IM Jr. FluTE, a publicly available stochastic influenza epidemic simulation model. PLoS Comput Biol. 2010 Jan 29;6(1):e1000656. doi: 10.1371/journal.pcbi.1000656. PubMed PMID: 20126529; PubMed Central PMCID: PMC2813259.


Halloran ME. On influenza and school closings: time for prospective studies. Epidemiology. 2009 Nov;20(6):793-5. doi: 10.1097/EDE.0b013e3181ba43c9. PubMed PMID: 19770772; PubMed Central PMCID: PMC2903453.

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 Oct 30;326(5953):729-33. doi: 10.1126/science.1177373. Epub 2009 Sep 10. PubMed PMID: 19745114; PubMed Central PMCID: PMC2880578.

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 Sep 15;170(6):679-86. doi: 10.1093/aje/kwp237. Epub 2009 Aug 13. PubMed PMID: 19679750; PubMed Central PMCID: PMC2737588.

Abu-Raddad LJ, Sabatelli L, Achterberg JT, Sugimoto JD, Longini IM Jr, Dye C, Halloran ME. Epidemiological benefits of moreeffective tuberculosis vaccines, drugs, and diagnostics. Proc Natl Acad Sci U S A. 2009 Aug 18;106(33):13980-5. doi: 10.1073/pnas.0901720106. Epub 2009 Aug 3. PubMed PMID: 19666590; PubMed Central PMCID: PMC2720405.

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. doi: 10.1093/biostatistics/kxn045. Epub 2009 Feb 6. PubMed PMID: 19202152; PubMed Central PMCID: PMC2733175.


Hudgens MG, Halloran ME. Toward Causal Inference With Interference. J Am Stat Assoc. 2008 Jun;103(482):832-842. PubMed PMID: 19081744; PubMed Central PMCID: PMC2600548.

Halloran ME, Ferguson NM, Eubank S, Longini IM Jr, Cummings DA, Lewis B, Xu S, Fraser C, Vullikanti A, Germann TC, Wagener D, Beckman R, Kadau K, Barrett C, Macken CA, Burke DS, Cooley P. Modeling targeted layered containment of an influenza pandemic in the United States. Proc Natl Acad Sci U S A. 2008 Mar 25;105(12):4639-44. doi: 10.1073/pnas.0706849105. Epub 2008 Mar 10. PubMed PMID: 18332436; PubMed Central PMCID: PMC2290797.

Yang Y, Gilbert P, Longini IM, Halloran ME. A Bayesian Framework for Estimating Vaccine Efficacy per Infectious Contact. Ann Appl Stat. 2008;2(4):1409-1431. PubMed PMID: 19169384; PubMed Central PMCID: PMC2630256.


Yang Y, Longini IM, Halloran ME. A Data-Augmentation Method for Infectious Disease Incidence Data from Close Contact Groups. Comput Stat Data Anal. 2007 Aug 15;51(12):6582-6595. PubMed PMID: 18704156; PubMed Central PMCID: PMC2131714.

Yang Y, Longini IM, Halloran ME. A Resampling-Based Test to Detect Person-To-Person Transmission of Infectious Disease. Ann Appl Stat. 2007 Jun 1;1(1):211-228. PubMed PMID: 19436773; PubMed Central PMCID: PMC2680309.

Halloran ME, Piedra PA, Longini IM Jr, Gaglani MJ, Schmotzer B, Fewlass C, Herschler GB, Glezen WP. Efficacy of trivalent, coldadapted, influenza virus vaccine against influenza A (Fujian), a drift variant, during 2003-2004. Vaccine. 2007 May 16;25(20):4038-45. Epub 2007 Mar 12. PubMed PMID: 17395338; PubMed Central PMCID: PMC2883284.


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. Epub 2006 Mar 23. PubMed PMID: 16556610; PubMed Central PMCID: PMC2766283.

Yang Y, Longini IM Jr, Halloran ME. Design and Evaluation of Prophylactic Interventions Using Infectious Disease Incidence Data from Close Contact Groups. J R Stat Soc Ser C Appl Stat. 2006 May;55(3):317-330. PubMed PMID: 22457545; PubMed Central PMCID: PMC3312606.

Hudgens MG, Halloran ME. Causal Vaccine Effects on Binary Postinfection Outcomes. J Am Stat Assoc. 2006 Mar;101(473):51- 64. PubMed PMID: 19096723; PubMed Central PMCID: PMC2603579.

Davis JT, Chinazzi M, Perra N, Mu K, Pastore Y Piontti A, Ajelli M, Dean NE, Gioannini C, Litvinova M, Merler S, Rossi L, Sun K, Xiong X, Longini IM Jr, Halloran ME, Viboud C, Vespignani A. Cryptic transmission of SARS-CoV-2 and the first COVID-19 wave. Nature. 2021 Dec;600(7887):127-132. doi: 10.1038/s41586-021-04130-w. Epub 2021 Oct 25. PMCID: PMC8636257.