Publications

Peer Reviewed Publications (2003 to 2021)

Walter KS, Martinez L, Arakaki-Sanchez D, Sequera VG, Sanabria GE, Cohen T, Ko AI, García-Basteiro AL, Rueda ZV, Olarte RL, Espinal M, Croda J, Andrews JR. The escalating tuberculosis crisis in Central and South American prisons. The Lancet. Accepted for publication.

Cords O, Martinez L, Warren J, O’Marr JM, Walter KS, Cohen T, Zheng J, Ko A, Croda J, Andrews JR. Incidence and Prevalence of Tuberculosis in Incarcerated Populations: A Systematic Review and Meta-analysis of 157 Studies from 56 Countries. Lancet Public Health. Accepted for publication.

Gunasekera KS, Walters E, van der Zalm MM, Palmer M, Warren JL, Hesseling AC, Cohen T, Seddon JA.Development of a treatment algorithm for HIV-uninfected children evaluated for pulmonary tuberculosis.Clin Infect Dis. 2021 Jan 15:ciab018. doi: 10.1093/cid/ciab018. Online ahead of print. PMID: 33449999 

Havumaki J,  Cohen T,  Zhai C,  Miller JC,  Guikema SD,  Eisenberg MC,  Zelner J. Protective impacts of household-based tuberculosis contact tracing are robust across endemic incidence levels and community contact patterns. PLoS Computational Biology.  Accepted for publication.

Chitwood MH, Pelissari DM, Marques da Silva GD, Bartholomay P, Rocha MS, Arakaki-Sanchez D, Sanchez M, Cohen T,  Castro MC, Menzies NA. Trends in Untreated Tuberculosis in Large Brazilian Municipalities, 2008-2017. Emerging Infectious Diseases. 2021. https://wwwnc.cdc.gov/eid/article/27/3/20-4094_article.

Pitzer VE, Chitwood M, Havumaki J, Menzies NA, Perniciaro S, Warren JL, Weinberger DM, Cohen T. The impact of changes in diagnostic testing practices on estimates of COVID-19 transmission in the United States. American Journal of Epidemiology. 2020. doi: 10.1101/2020.04.20.20073338. PubMed PMID: 32511624; PMCID: 7276051. pdf_pitzer2020_medRxIV

Yaesoubi R, Havumaki J, Chitwood M, Menzies NA, Gonsalves G, Salomon JA, Paltiel AD, Cohen T. Adaptive policies for use of physical distancing interventions during the COVID-19 pandemic. Medical Decision Making.  2020. doi: 10.1101/2020.05.29.20065714. PubMed PMID: 32577698; PMCID: 7302307. pdf_yaesoubi2020_medRxIV

Hill AN, Cohen T, Salomon JA , Menzies NA. High-resolution estimates of tuberculosis incidence among non-U.S.-born persons residing in the United States, 2000-2016. Epidemics. 2020 Dec;33:100419. doi: 10.1016/j.epidem.2020.100419. Epub 2020 Nov 10. PMID: 33242759. pdf_hill2020_epidemics

Cudahy PGT, Wilson DW, Cohen T. Risk factors for recurrent tuberculosis after successful treatment in a high burden setting: a cohort study. BMC Infect Dis 2020 Oct 23;20(1):789.  doi: 10.1186/s12879-020-05515-4. PMID: 33097000;PMCID: PMC7585300. pdf_cudahy2020_BMCid

Walter KS, Colijn C, Cohen T, Mathema B, Liu Q, Bowers J, Engelthaler DM, Narechania A, Lemmer D, Croda J, Andrews JR. Genomic variant-identification methods may alter Mycobacterium tuberculosis transmission inferences. Microb Genom. 2020 Aug;6(8). doi: 10.1099/mgen.0.000418. Epub 2020 Jul 31.PMID: 32735210; PMCID: PMC7641424. pdf_Walters2020_microgenome

Marx FM, Cohen T, Menzies NA, Salomon JA, Theron G, Yaesoubi R.  Cost-effectiveness of post-treatment follow-up examinations and secondary prevention of tuberculosis in a high-incidence setting: a model-based analysis. Lancet Glob Health. 2020 Sep;8(9):e1223-e1233. doi: 10.1016/S2214-109X(20)30227-8.  PMID: 32827484; PMCID 7549318. pdf_marx2020_lancetGH

Leuba SI, Yaesoubi R, Antillon M, Cohen T, Zimmer C.  Tracking and predicting U.S. influenza activity with a real-time surveillance network. 2020 Nov 2;16(11)e1008180. doin:10.1371/journal.pcbi.1008180. PLoS Comput Biol. PMID: 33137088; PMCID: PMC7707518. pdf_leuba2020_plosCompBio

Cates LL, Crudu V, Codreanu A, Ciobanu N, Fosburgh H, Cohen T, Menzies NA. The Laboratory Costs of Diagnosing Tuberculosis and Tuberculosis Drug Resistance in Moldova.  Accepted for Publication. The International Journal of Tuberculosis and Lung Disease. 

Hsieh YL, Andreas J, Menzies NA, Yaesoubi R, Salomon, SA,  Girma B, Gunde L, Eaton J, Auld A, Odo M, Kiyiika CN, Kalua T, Chiwandira B, Corbett E, Hosseinipour MC, CohenT*, Kunkel A.* An evaluation of 6-month versus continuous isoniazid preventive therapy for M. tuberculosis in adults living with HIV/AIDS in Malawi.  Journal of Acquired Immune Deficiency Syndromes. 2020 Dec15:85(5):643 Doi: 10.1097/QAI.0000000000002497.

Gunasekera KS, Zelner J, Becerra MC, Contreras C, Franke MF, Lecca L, Murray MB, Warren JL, Cohen T.  Children as sentinels of tuberculosis transmission: disease mapping of programmatic data.  BMC Med. 2020 Sep 2;18(1):234. doi: 10.1186/s12916-020-01702-x.PMID: 32873309. pdf_gunasekera2020_BMCmed

Yaesoubi R, Cohen T, Hsu K, Gift TL, Chesson H, Salomon JA, Grad YH. Adaptive guidelines for the treatment of gonorrhea to increase the effective life span of antibiotics among men who have sex with men in the United States: A mathematical modeling study. PLoS Med. 2020;17(4):e1003077. doi: 10.1371/journal.pmed.1003077. PubMed PMID: 32243443; PMCID: 7122693. pdf_yaesoubi2020_plosMED

Weinberger DM, Chen J, Cohen T, Crawford FW, Mostashari F, Olson D, Pitzer VE, Reich NG, Russi M, Simonsen L, Watkins A, Viboud C. Estimation of Excess Deaths Associated With the COVID-19 Pandemic in the United States, March to May 2020. JAMA Intern Med. 2020. doi: 10.1001/jamainternmed.2020.3391. PubMed PMID: 32609310; PMCID: 7330834. 

Santos ADS, Oliveira RD, Lemos EF, Lima F, Cohen T, Cords O, Martinez L, Goncalves C, Ko A, Andrews JR, Croda J. Yield, Efficiency and Costs of Mass Screening Algorithms for Tuberculosis in Brazilian Prisons. Clin Infect Dis. 2020. doi: 10.1093/cid/ciaa135. PubMed PMID: 32064514.

Quaife M, Houben R, Allwood B, Cohen T, Coussens AK, Harries AD, van Kampen S, Marx FM, Sweeney S, Wallis RS, Menzies NA. Post-tuberculosis mortality and morbidity: valuing the hidden epidemic. Lancet Respir Med. 2020;8(4):332-3. doi: 10.1016/S2213-2600(20)30039-4. PubMed PMID: 32057300. pdf_quaife2020_lancetRM

Morozova O, Crawford FW, Cohen T, Paltiel AD, Altice FL. Cost-effectiveness of expanding the capacity of opioid agonist treatment in Ukraine: dynamic modeling analysis. Addiction. 2020;115(3):437-50. doi: 10.1111/add.14797. PubMed PMID: 31478285; PMCID: 7015766.

Menzies NA, Parriott A, Shrestha S, Dowdy DW, Cohen T, Salomon JA, Marks SM, Hill AN, Winston CA, Asay GR, Barry P, Readhead A, Flood J, Kahn JG, Shete PB. Comparative Modeling of Tuberculosis Epidemiology and Policy Outcomes in California. Am J Respir Crit Care Med. 2020;201(3):356-65. doi: 10.1164/rccm.201907-1289OC. PubMed PMID: 31626560. 

Menzies NA, Bellerose M, Testa C, Swartwood N, Malyuta Y, Cohen T, Marks SM, Hill AN, Date AA, Maloney SA, Bowden SE, Grills AW, Salomon JA. Impact of Effective Global Tuberculosis Control on Health and Economic Outcomes in the United States. Am J Respir Crit Care Med. 2020. doi: 10.1164/rccm.202003-0526OC. PubMed PMID: 32645277

Martinez L, Cords O, Horsburgh CR, Andrews JR, Pediatric TBCSC. The risk of tuberculosis in children after close exposure: a systematic review and individual-participant meta-analysis. Lancet. 2020;395(10228):973-84. Epub 2020/03/23. doi: 10.1016/S0140-6736(20)30166-5. PubMed PMID: 32199484; PMCID: 7289654 pdf_martinez2020_lancet

Gunasekera K, Cohen T, Gao W, Ayles H, Godfrey-Faussett P, Claassens M. Smoking and HIV associated with subclinical tuberculosis: analysis of a population-based prevalence survey. Int J Tuberc Lung Dis. 2020;24(3):340-6. doi: 10.5588/ijtld.19.0387. PubMed PMID: 32228765

Crawford FW, Marx FM, Zelner J, Cohen T. Transmission Modeling with Regression Adjustment for Analyzing Household-based Studies of Infectious Disease: Application to Tuberculosis. Epidemiology. 2020;31(2):238-47. doi: 10.1097/EDE.0000000000001143. PubMed PMID: 31764276

Zimmer C, Leuba SI, Cohen T, Yaesoubi R. Accurate quantification of uncertainty in epidemic parameter estimates and predictions using stochastic compartmental models. Stat Methods Med Res. 2019;28(12):3591-608. doi: 10.1177/0962280218805780. PubMed PMID: 30428780; PMCID: 6517086

Thain N, Le C, Crossa A, Ahuja SD, Meissner JS, Mathema B, Kreiswirth B, Kurepina N, Cohen T, Chindelevitch L. Towards better prediction of Mycobacterium tuberculosis lineages from MIRU-VNTR data. Infect Genet Evol. 2019;72:59-66. doi: 10.1016/j.meegid.2018.06.029. PubMed PMID: 29960078; PMCID: 6708508

Stimson J, Gardy J, Mathema B, Crudu V, Cohen T, Colijn C. Beyond the SNP Threshold: Identifying Outbreak Clusters Using Inferred Transmissions. Mol Biol Evol. 2019;36(3):587-603. doi: 10.1093/molbev/msy242. PubMed PMID: 30690464; PMCID: 6389316

Marx FM, Cohen T, Lombard C, Hesseling AC, Dlamini SS, Beyers N, Naidoo P. Notification of relapse and other previously treated tuberculosis in the 52 health districts of South Africa. Int J Tuberc Lung Dis. 2019;23(8):891-9. doi: 10.5588/ijtld.18.0609. PubMed PMID: 31533878

MacPherson P, Khundi M, Nliwasa M, Choko AT, Phiri VK, Webb EL, Dodd PJ, Cohen T, Harris R, Corbett EL. Disparities in access to diagnosis and care in Blantyre, Malawi, identified through enhanced tuberculosis surveillance and spatial analysis. BMC Med. 2019;17(1):21. doi: 10.1186/s12916-019-1260-6. PubMed PMID: 30691470; PMCID: 6350280

Mabud TS, de Lourdes Delgado Alves M, Ko AI, Basu S, Walter KS, Cohen T, Mathema B, Colijn C, Lemos E, Croda J, Andrews JR. Evaluating strategies for control of tuberculosis in prisons and prevention of spillover into communities: An observational and modeling study from Brazil. PLoS Med. 2019;16(1):e1002737. doi: 10.1371/journal.pmed.1002737. PubMed PMID: 30677013; PMCID: 6345418 following competing interests: SB receives a stipend as a specialty consulting editor for PLOS Medicine and serves on the journal’s editorial board. pdf_mabud2019_plosMED

Cudahy PGT, Andrews JR, Bilinski A, Dowdy DW, Mathema B, Menzies NA, Salomon JA, Shrestha S, Cohen T. Spatially targeted screening to reduce tuberculosis transmission in high-incidence settings. Lancet Infect Dis. 2019;19(3):e89-e95. Epub 12/13. doi: 10.1016/S1473-3099(18)30443-2. PubMed PMID: 30554997; PMCID: 6401264. pdf_cudahy2019_lancetID

Becerra MC, Huang CC, Lecca L, Bayona J, Contreras C, Calderon R, Yataco R, Galea J, Zhang Z, Atwood S, Cohen T, Mitnick CD, Farmer P, Murray M. Transmissibility and potential for disease progression of drug resistant Mycobacterium tuberculosis: prospective cohort study. BMJ. 2019;367:l5894. doi: 10.1136/bmj.l5894. PubMed PMID: 31649017; PMCID: 6812583. pdf_becerra201_BMJ

Arifin SMN, Zimmer C, Trotter C, Colombini A, Sidikou F, LaForce FM, Cohen T, Yaesoubi R. Cost-Effectiveness of Alternative Uses of Polyvalent Meningococcal Vaccines in Niger: An Agent-Based Transmission Modeling Study. Med Decis Making. 2019;39(5):553-67. doi: 10.1177/0272989X19859899. PubMed PMID: 31268405; PMCID: 6786941

Zimmer C, Leuba SI, Yaesoubi R, Cohen T. Use of daily Internet search query data improves real-time projections of influenza epidemics. J R Soc Interface. 2018;15(147). doi: 10.1098/rsif.2018.0220. PubMed PMID: 30305417; PMCID: 6228485. pdf_Zimmer2018_JRSI

Zelner J, Murray M, Becerra M, Galea J, Lecca L, Calderon R, Yataco R, Zhang Z, Cohen T. Protective effects of household-based TB interventions are robust to neighbourhood-level variation in exposure risk in Lima, Peru: a model-based analysis. Int J Epidemiol. 2018;47(1):185-92. doi: 10.1093/ije/dyx171. PubMed PMID: 29025111

Yang C, Lu L, Warren JL, Wu J, Jiang Q, Zuo T, Gan M, Liu M, Liu Q, DeRiemer K, Hong J, Shen X, Colijn C, Guo X, Gao Q, Cohen T. Internal migration and transmission dynamics of tuberculosis in Shanghai, China: an epidemiological, spatial, genomic analysis. Lancet Infect Dis. 2018;18(7):788-95. doi: 10.1016/S1473-3099(18)30218-4. PubMed PMID: 29681517; PMCID: 60350  pdf_yang2018_lancetID

Yaesoubi R, Trotter C, Colijn C, Yaesoubi M, Colombini A, Resch S, Kristiansen PA, LaForce FM, Cohen T. The cost-effectiveness of alternative vaccination strategies for polyvalent meningococcal vaccines in Burkina Faso: A transmission dynamic modeling study. PLoS Med. 2018;15(1):e1002495. doi: 10.1371/journal.pmed.1002495. PubMed PMID: 29364884; PMCID: 5783340 pdf_yaesoubi2018_plosMED

Wilson D, Moosa MS, Cohen T, Cudahy P, Aldous C, Maartens G. Evaluation of Tuberculosis Treatment Response With Serial C-Reactive Protein Measurements. Open Forum Infect Dis. 2018;5(11):ofy253. doi: 10.1093/ofid/ofy253. PubMed PMID: 30474046; PMCID: 6240901

Warren JL, Grandjean L, Moore DAJ, Lithgow A, Coronel J, Sheen P, Zelner JL, Andrews JR, Cohen T. Investigating spillover of multidrug-resistant tuberculosis from a prison: a spatial and molecular epidemiological analysis. BMC Med. 2018;16(1):122. doi: 10.1186/s12916-018-1111-x. PubMed PMID: 30071850; PMCID: 6091024 pdf_warren2018_BMCmed

Wallis RS, Cohen T, Menzies NA, Churchyard G. Pan-tuberculosis regimens: an argument for. Lancet Respir Med. 2018;6(4):239-40. Epub 2018/03/30. doi: 10.1016/S2213-2600(18)30096-1. PubMed PMID: 29595501 pdf_wallis2018_lancetID

Morozova O, Cohen T, Crawford FW. Risk ratios for contagious outcomes. J R Soc Interface. 2018;15(138). doi: 10.1098/rsif.2017.0696. PubMed PMID: 29343627; PMCID: 5805970

Menzies NA, Wolf E, Connors D, Bellerose M, Sbarra AN, Cohen T, Hill AN, Yaesoubi R, Galer K, White PJ, Abubakar I, Salomon JA. Progression from latent infection to active disease in dynamic tuberculosis transmission models: a systematic review of the validity of modelling assumptions. Lancet Infect Dis. 2018;18(8):e228-e38. doi: 10.1016/S1473-3099(18)30134-8. PubMed PMID: 29653698; PMCID: 6070419. pdf_menzies2018_lancetID

Menzies NA, Hill AN, Cohen T, Salomon JA. The impact of migration on tuberculosis in the United States. Int J Tuberc Lung Dis. 2018;22(12):1392-403. doi: 10.5588/ijtld.17.0185. PubMed PMID: 30606311; PMCID: 6353558

Menzies NA, Cohen T, Hill AN, Yaesoubi R, Galer K, Wolf E, Marks SM, Salomon JA. Prospects for Tuberculosis Elimination in the United States: Results of a Transmission Dynamic Model. Am J Epidemiol. 2018;187(9):2011-20. doi: 10.1093/aje/kwy094. PubMed PMID: 29762657; PMCID: 6119121

Marx FM, Yaesoubi R, Menzies NA, Salomon JA, Bilinski A, Beyers N, Cohen T. Tuberculosis control interventions targeted to previously treated people in a high-incidence setting: a modelling study. Lancet Glob Health. 2018;6(4):e426-e35. doi: 10.1016/S2214-109X(18)30022-6. PubMed PMID: 29472018; PMCID: 5849574. pdf_marx2018_lancetGH

Cudahy PGT, Warren JL, Cohen T, Wilson D. Trends in C-Reactive Protein, D-Dimer, and Fibrinogen during Therapy for HIV-Associated Multidrug-Resistant Tuberculosis. Am J Trop Med Hyg. 2018;99(5):1336-41. doi: 10.4269/ajtmh.18-0322. PubMed PMID: 30226135; PMCID: 6221241

Auld SC, Shah NS, Cohen T, Martinson NA, Gandhi NR. Where is tuberculosis transmission happening? Insights from the literature, new tools to study transmission and implications for the elimination of tuberculosis. Respirology. 2018. doi: 10.1111/resp.13333. PubMed PMID: 29869818; PMCID: 6281783

Zimmer C, Yaesoubi R, Cohen T. A Likelihood Approach for Real-Time Calibration of Stochastic Compartmental Epidemic Models. PLoS Comput Biol. 2017;13(1):e1005257. doi: 10.1371/journal.pcbi.1005257. PubMed PMID: 28095403; PMCID: 5240920 pdf_zimmer2017_plosCompBio

Verguet S, Riumallo-Herl C, Gomez GB, Menzies NA, Houben R, Sumner T, Lalli M, White RG, Salomon JA, Cohen T, Foster N, Chatterjee S, Sweeney S, Baena IG, Lonnroth K, Weil DE, Vassall A. Catastrophic costs potentially averted by tuberculosis control in India and South Africa: a modelling study. Lancet Glob Health. 2017;5(11):e1123-e32. doi: 10.1016/S2214-109X(17)30341-8. PubMed PMID: 29025634; PMCID: 5640802. pdf_verguet2017_lancetGH

Nathavitharana RR, Shi CX, Chindelevitch L, Calderon R, Zhang Z, Galea JT, Contreras C, Yataco R, Lecca L, Becerra MC, Murray MB, Cohen T. Polyclonal Pulmonary Tuberculosis Infections and Risk for Multidrug Resistance, Lima, Peru. Emerg Infect Dis. 2017;23(11):1887-90. doi: 10.3201/eid2311.170077. PubMed PMID: 29048297; PMCID: 5652442

Mathema B, Andrews JR, Cohen T, Borgdorff MW, Behr M, Glynn JR, Rustomjee R, Silk BJ, Wood R. Drivers of Tuberculosis Transmission. J Infect Dis. 2017;216(suppl_6):S644-S53. doi: 10.1093/infdis/jix354. PubMed PMID: 29112745; PMCID: 5853844. pdf_mathema2017_JID

Manson AL, Cohen KA, Abeel T, Desjardins CA, Armstrong DT, Barry CE, 3rd, Brand J, Consortium TBGG, Chapman SB, Cho SN, Gabrielian A, Gomez J, Jodals AM, Joloba M, Jureen P, Lee JS, Malinga L, Maiga M, Nordenberg D, Noroc E, Romancenco E, Salazar A, Ssengooba W, Velayati AA, Winglee K, Zalutskaya A, Via LE, Cassell GH, Dorman SE, Ellner J, Farnia P, Galagan JE, Rosenthal A, Crudu V, Homorodean D, Hsueh PR, Narayanan S, Pym AS, Skrahina A, Swaminathan S, Van der Walt M, Alland D, Bishai WR, Cohen T, Hoffner S, Birren BW, Earl AM. Genomic analysis of globally diverse Mycobacterium tuberculosis strains provides insights into the emergence and spread of multidrug resistance. Nat Genet. 2017;49(3):395-402. doi: 10.1038/ng.3767. PubMed PMID: 28092681; PMCID: 5402762

Kunkel A, Lewnard JA, Pitzer VE, Cohen T. Antimicrobial Resistance Risks of Cholera Prophylaxis for United Nations Peacekeepers. Antimicrob Agents Chemother. 2017;61(8). doi: 10.1128/AAC.00026-17. PubMed PMID: 28533237; PMCID: 5527623. 

Kunkel A, Furin J, Cohen T. Population implications of the use of bedaquiline in people with extensively drug-resistant tuberculosis: are fears of resistance justified? Lancet Infect Dis. 2017;17(12):e429-e33. doi: 10.1016/S1473-3099(17)30299-2. PubMed PMID: 28533094. pdf_kunkel2017_lancetID

Kendall EA, Shrestha S, Cohen T, Nuermberger E, Dooley KE, Gonzalez-Angulo L, Churchyard GJ, Nahid P, Rich ML, Bansbach C, Forissier T, Lienhardt C, Dowdy DW.  Priority-Setting for Novel Drug Regimens to Treat Tuberculosis: An Epidemiologic Model. PLoS Med. 2017;14(1):e1002202. doi: 10.1371/journal.pmed.1002202. PubMed PMID: 28045934; PMCID: 5207633.   pdf_kendall2017_plos

Kendall EA, Cohen T, Mitnick CD, Dowdy DW. Second line drug susceptibility testing to inform the treatment of rifampin-resistant tuberculosis: a quantitative perspective. Int J Infect Dis. 2017;56:185-9. doi: 10.1016/j.ijid.2016.12.010. PubMed PMID: 28007660; PMCID: 5576040. pdf_kendall2017_IJID

Fofana MO, Shrestha S, Knight GM, Cohen T, White RG, Cobelens F, Dowdy DW. A Multistrain Mathematical Model To Investigate the Role of Pyrazinamide in the Emergence of Extensively Drug-Resistant Tuberculosis. Antimicrob Agents Chemother. 2017;61(3). doi: 10.1128/AAC.00498-16. PubMed PMID: 27956422; PMCID: 5328532

Abel Zur Wiesch P, Clarelli F, Cohen T. Using Chemical Reaction Kinetics to Predict Optimal Antibiotic Treatment Strategies. PLoS Comput Biol. 2017;13(1):e1005321. doi: 10.1371/journal.pcbi.1005321. PubMed PMID: 28060813; PMCID: 5257006. pdf_abel2017_plosCompBio

Zhang Z, Manjourides J, Cohen T, Hu Y, Jiang Q. Spatial measurement errors in the field of spatial epidemiology. Int J Health Geogr. 2016;15(1):21. doi: 10.1186/s12942-016-0049-5. PubMed PMID: 27368370; PMCID: 4930612. pdf_zhang2016_IJHG

Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Manjourides J, Grenfell BT, Cohen T. Identifying Hotspots of Multidrug-Resistant Tuberculosis Transmission Using Spatial and Molecular Genetic Data. J Infect Dis. 2016;213(2):287-94. doi: 10.1093/infdis/jiv387. PubMed PMID: 26175455; PMCID: 4690150. 

Yates TA, Khan PY, Knight GM, Taylor JG, McHugh TD, Lipman M, White RG, Cohen T, Cobelens FG, Wood R, Moore DA, Abubakar I. The transmission of Mycobacterium tuberculosis in high burden settings. Lancet Infect Dis. 2016;16(2):227-38. doi: 10.1016/S1473-3099(15)00499-5. PubMed PMID: 26867464. pdf_yates2016_lancetID

Yaesoubi R, Cohen T. Identifying cost-effective dynamic policies to control epidemics. Stat Med. 2016;35(28):5189-209. Epub 07/24. doi: 10.1002/sim.7047. PubMed PMID: 27449759; PMCID: 5096998. pdf_yaesoubi2011_plos2016_statmed

Salvatore PP, Becerra MC, Abel zur Wiesch P, Hinkley T, Kaur D, Sloutsky A, Cohen T. Fitness Costs of Drug Resistance Mutations in Multidrug-Resistant Mycobacterium tuberculosis: A Household-Based Case-Control Study. J Infect Dis. 2016;213(1):149-55. doi: 10.1093/infdis/jiv347. PubMed PMID: 26092854; PMCID: 4676541

Mitnick CD, White RA, Lu C, Rodriguez CA, Bayona J, Becerra MC, Burgos M, Centis R, Cohen T, Cox H, D’Ambrosio L, Danilovitz M, Falzon D, Gelmanova IY, Gler MT, Grinsdale JA, Holtz TH, Keshavjee S, Leimane V, Menzies D, Migliori GB, Milstein MB, Mishustin SP, Pagano M, Quelapio MI, Shean K, Shin SS, Tolman AW, van der Walt ML, Van Deun A, Viiklepp P.  Collaborative Group for Analysis of Bacteriology Data in MDRTBT. Multidrug-resistant tuberculosis treatment failure detection depends on monitoring interval and microbiological method. Eur Respir J. 2016;48(4):1160-70. doi: 10.1183/13993003.00462-2016. PubMed PMID: 27587552; PMCID: 5045442

Menzies NA, Gomez GB, Bozzani F, Chatterjee S, Foster N, Baena IG, Laurence YV, Qiang S, Siroka A, Sweeney S, Verguet S, Arinaminpathy N, Azman AS, Bendavid E, Chang ST, Cohen T, Denholm JT, Dowdy DW, Eckhoff PA, Goldhaber-Fiebert JD, Handel A, Huynh GH, Lalli M, Lin HH, Mandal S, McBryde ES, Pandey S, Salomon JA, Suen SC, Sumner T, Trauer JM, Wagner BG, Whalen CC, Wu CY, Boccia D, Chadha VK, Charalambous S, Chin DP, Churchyard G, Daniels C, Dewan P, Ditiu L, Eaton JW, Grant AD, Hippner P, Hosseini M, Mametja D, Pretorius C, Pillay Y, Rade K, Sahu S, Wang L, Houben R, Kimerling ME, White RG, Vassall A. Cost-effectiveness and resource implications of aggressive action on tuberculosis in China, India, and South Africa: a combined analysis of nine models. Lancet Glob Health. 2016;4(11):e816-e26. doi: 10.1016/S2214-109X(16)30265-0. PubMed PMID: 27720689; PMCID: 5527122. pdf_menzies2016_lancetGH

Mears J, Vynnycky E, Lord J, Borgdorff MW, Cohen T, Crisp D, Innes JA, Lilley M, Maguire H, McHugh TD, Woltmann G, Abubakar I, Sonnenberg P.  Thorax. 2016;71(8):734-41. doi: 10.1136/thoraxjnl-2014-206480. PubMed PMID: 25882538. pdf_mears2016_thorax

Marx FM, Floyd S, Ayles H, Godfrey-Faussett P, Beyers N, Cohen T.  High burden of prevalent tuberculosis among previously treated people in Southern Africa suggests potential for targeted control interventions. Eur Respir J. 2016;48(4):1227-30. doi: 10.1183/13993003.00716-2016. PubMed PMID: 27390274; PMCID: 5512114

Lieberman TD, Wilson D, Misra R, Xiong LL, Moodley P, Cohen T, Kishony R. Genomic diversity in autopsy samples reveals within-host dissemination of HIV-associated Mycobacterium tuberculosis. Nat Med. 2016;22(12):1470-4. doi: 10.1038/nm.4205. PubMed PMID: 27798613; PMCID: 5508070. pdf_lieberman2016_natmed

Kunkel A, Crawford FW, Shepherd J, Cohen T. Benefits of continuous isoniazid preventive therapy may outweigh resistance risks in a declining tuberculosis/HIV coepidemic. AIDS. 2016;30(17):2715-23. doi: 10.1097/QAD.0000000000001235. PubMed PMID: 27782966; PMCID: 5089846

Kunkel A, Cobelens FG, Cohen T. Tradeoffs in Introduction Policies for the Anti-Tuberculosis Drug Bedaquiline: A Model-Based Analysis. PLoS Med. 2016;13(10):e1002142. doi: 10.1371/journal.pmed.1002142. PubMed PMID: 27727274; PMCID: 5058480. pdf_kunkel2015_plosMED

Kunkel A, Abel Zur Wiesch P, Nathavitharana RR, Marx FM, Jenkins HE, Cohen T. Smear positivity in paediatric and adult tuberculosis: systematic review and meta-analysis. BMC Infect Dis. 2016;16:282. doi: 10.1186/s12879-016-1617-9. PubMed PMID: 27296716; PMCID: 4906576. pdf_kunkel2016_bmcID

Jezmir J, Cohen T, Zignol M, Nyakan E, Hedt-Gauthier BL, Gardner A, Kamle L, Injera W, Carter EJ. Use of Lot Quality Assurance Sampling to Ascertain Levels of Drug Resistant Tuberculosis in Western Kenya. PLoS One. 2016;11(5):e0154142. doi: 10.1371/journal.pone.0154142. PubMed PMID: 27167381; PMCID: 4864281. pdf_jezmir2016_plos

Houben R, Menzies NA, Sumner T, Huynh GH, Arinaminpathy N, Goldhaber-Fiebert JD, Lin HH, Wu CY, Mandal S, Pandey S, Suen SC, Bendavid E, Azman AS, Dowdy DW, Bacaer N, Rhines AS, Feldman MW, Handel A, Whalen CC, Chang ST, Wagner BG, Eckhoff PA, Trauer JM, Denholm JT, McBryde ES, Cohen T, Salomon JA, Pretorius C, Lalli M, Eaton JW, Boccia D, Hosseini M, Gomez GB, Sahu S, Daniels C, Ditiu L, Chin DP, Wang L, Chadha VK, Rade K, Dewan P, Hippner P, Charalambous S, Grant AD, Churchyard G, Pillay Y, Mametja LD, Kimerling ME, Vassall A, White RG. Feasibility of achieving the 2025 WHO global tuberculosis targets in South Africa, China, and India: a combined analysis of 11 mathematical models. Lancet Glob Health. 2016;4(11):e806-e15. doi: 10.1016/S2214-109X(16)30199-1. PubMed PMID: 27720688; PMCID: 6375908. pdf_houben2016_lancetGH

Heidebrecht CL, Podewils LJ, Pym AS, Cohen T, Mthiyane T, Wilson D. Assessing the utility of Xpert((R)) MTB/RIF as a screening tool for patients admitted to medical wards in South Africa. Sci Rep. 2016;6:19391. Epub 2016/01/21. doi: 10.1038/srep19391. PubMed PMID: 26786396; PMCID: 4726405. pdf_heidebrecht2016_SciRep

Heidebrecht CL, Podewils LJ, Pym A, Mthiyane T, Cohen T. Assessing Local Risk of Rifampicin-Resistant Tuberculosis in KwaZulu-Natal, South Africa Using Lot Quality Assurance Sampling. PLoS One. 2016;11(4):e0153143. doi: 10.1371/journal.pone.0153143. PubMed PMID: 27050561; PMCID: 4822784. pdf_heidebrecht2016_plos

Colman RE, Anderson J, Lemmer D, Lehmkuhl E, Georghiou SB, Heaton H, Wiggins K, Gillece JD, Schupp JM, Catanzaro DG, Crudu V, Cohen T, Rodwell TC, Engelthaler DM. Rapid Drug Susceptibility Testing of Drug-Resistant Mycobacterium tuberculosis Isolates Directly from Clinical Samples by Use of Amplicon Sequencing: a Proof-of-Concept Study. J Clin Microbiol. 2016;54(8):2058-67. doi: 10.1128/JCM.00535-16. PubMed PMID: 27225403; PMCID: 4963505

Colijn C, Cohen T. Whole-genome sequencing of Mycobacterium tuberculosis for rapid diagnostics and beyond. Lancet Respir Med. 2016;4(1):6-8. Epub 2015/12/17. doi: 10.1016/S2213-2600(15)00510-X. PubMed PMID: 26669892. pdf_colijn2016_lancetRM

Cohen T, Chindelevitch L, Misra R, Kempner ME, Galea J, Moodley P, Wilson D. Within-Host Heterogeneity of Mycobacterium tuberculosis Infection Is Associated With Poor Early Treatment Response: A Prospective Cohort Study. J Infect Dis. 2016;213(11):1796-9. doi: 10.1093/infdis/jiw014. PubMed PMID: 26768249; PMCID: 4857469

Chindelevitch L, Colijn C, Moodley P, Wilson D, Cohen T. ClassTR: Classifying Within-Host Heterogeneity Based on Tandem Repeats with Application to Mycobacterium tuberculosis Infections. PLoS Comput Biol. 2016;12(2):e1004475. doi: 10.1371/journal.pcbi.1004475. PubMed PMID: 26829497; PMCID: 4734664 pdf_Chindelevitch2016_ploscompbio

Andre E, Isaacs C, Affolabi D, Alagna R, Brockmann D, de Jong BC, Cambau E, Churchyard G, Cohen T, Delmee M, Delvenne JC, Farhat M, Habib A, Holme P, Keshavjee S, Khan A, Lightfoot P, Moore D, Moreno Y, Mundade Y, Pai M, Patel S, Nyaruhirira AU, Rocha LE, Takle J, Trebucq A, Creswell J, Boehme C. Connectivity of diagnostic technologies: improving surveillance and accelerating tuberculosis elimination. Int J Tuberc Lung Dis. 2016;20(8):999-1003. doi: 10.5588/ijtld.16.0015. PubMed PMID: 27393530; PMCID: 4937753

Theron G, Jenkins HE, Cobelens F, Abubakar I, Khan AJ, Cohen T, Dowdy DW. Data for action: collection and use of local data to end tuberculosis. Lancet. 2015;386(10010):2324-33. doi: 10.1016/S0140-6736(15)00321-9. PubMed PMID: 26515676; PMCID: 4708262 pdf_theron2015_lancet

Seddon JA, Jenkins HE, Liu L, Cohen T, Black RE, Vos T, Becerra MC, Graham SM, Sismanidis C, Dodd PJ. Counting children with tuberculosis: why numbers matter. Int J Tuberc Lung Dis. 2015;19 Suppl 1:9-16. doi: 10.5588/ijtld.15.0471. PubMed PMID: 26564535; PMCID: 4708268. 

Plazzotta G, Cohen T, Colijn C. Magnitude and sources of bias in the detection of mixed strain M. tuberculosis infection. J Theor Biol. 2015;368:67-73. doi: 10.1016/j.jtbi.2014.12.009. PubMed PMID: 25553967; PMCID: 7011203. pdf_plazzotta2015_JTB

Mears J, Abubakar I, Cohen T, McHugh TD, Sonnenberg P. Effect of study design and setting on tuberculosis clustering estimates using Mycobacterial Interspersed Repetitive Units-Variable Number Tandem Repeats (MIRU-VNTR): a systematic review. BMJ Open. 2015;5(1):e005636. doi: 10.1136/bmjopen-2014-005636. PubMed PMID: 25609667; PMCID: 4305070. pdf_mears2015_BMJopen

Kunkel A, Colijn C, Lipsitch M, Cohen T. How could preventive therapy affect the prevalence of drug resistance? Causes and consequences. Philos Trans R Soc Lond B Biol Sci. 2015;370(1670):20140306. doi: 10.1098/rstb.2014.0306. PubMed PMID: 25918446; PMCID: 4424438

Knight GM, Colijn C, Shrestha S, Fofana M, Cobelens F, White RG, Dowdy DW, Cohen T. The Distribution of Fitness Costs of Resistance-Conferring Mutations Is a Key Determinant for the Future Burden of Drug-Resistant Tuberculosis: A Model-Based Analysis. Clin Infect Dis. 2015;61Suppl 3:S147-54. doi: 10.1093/cid/civ579. PubMed PMID: 26409276; PMCID: 4583567

Jia Z, Huang X, Wu H, Zhang T, Li N, Ding P, Sun Y, Liu Z, Wei F, Zhang H, Jiao Y, Ji Y, Zhang Y, Guo C, Li W, Mou D, Xia W, Li Z, Chen D, Yan H, Chen X, Zhao J, Meyers K, Cohen T, Mayer K, Salomon JA, Lu Z, Dye C. HIV burden in men who have sex with men: a prospective cohort study 2007-2012. Sci Rep. 2015;5:11205. doi: 10.1038/srep11205. PubMed PMID: 26135810; PMCID: 5393284. pdf_jia2015_scirep

Colijn C, Cohen T. How competition governs whether moderate or aggressive treatment minimizes antibiotic resistance. Elife. 2015;4:e10559. doi: 10.7554/eLife.10559. PubMed PMID: 26393685; PMCID: 4641510

Chindelevitch L, Menzies NA, Pretorius C, Stover J, Salomon JA, Cohen T. Evaluating the potential impact of enhancing HIV treatment and tuberculosis control programmes on the burden of tuberculosis. J R Soc Interface. 2015;12(106). doi: 10.1098/rsif.2015.0146. PubMed PMID: 25878131; PMCID: 4424692

Chang HH, Cohen T, Grad YH, Hanage WP, O’Brien TF, Lipsitch M. Origin and proliferation of multiple-drug resistance in bacterial pathogens. Microbiol Mol Biol Rev. 2015;79(1):101-16. Epub 2015/02/06. doi: 10.1128/MMBR.00039-14. PubMed PMID: 25652543; PMCID: 4402963

Birger RB, Kouyos RD, Cohen T, Griffiths EC, Huijben S, Mina MJ, Volkova V, Grenfell B, Metcalf CJE. The potential impact of coinfection on antimicrobial chemotherapy and drug resistance. Trends Microbiol. 2015;23(9):537-44. Epub 2015/06/02. doi: 10.1016/j.tim.2015.05.002. PubMed PMID: 26028590; PMCID: 4835347

Abel Zur Wiesch P, Abel S, Gkotzis S, Ocampo P, Engelstadter J, Hinkley T, Magnus C, Waldor MK, Udekwu K, Cohen T. Classic reaction kinetics can explain complex patterns of antibiotic action. Sci Transl Med. 2015;7(287):287ra73. doi: 10.1126/scitranslmed.aaa8760. PubMed PMID: 25972005; PMCID: 4554720

Zwerling A, White RG, Vassall A, Cohen T, Dowdy DW, Houben RM. Modeling of novel diagnostic strategies for active tuberculosis – a systematic review: current practices and recommendations. PLoS One. 2014;9(10):e110558. doi: 10.1371/journal.pone.0110558. PubMed PMID: 25340701; PMCID: 4207742. pdf_zwerling2014_plos

Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Grenfell BT, Cohen T. Bacillus Calmette-Guerin and isoniazid preventive therapy protect contacts of patients with tuberculosis. Am J Respir Crit Care Med. 2014;189(7):853-9. doi: 10.1164/rccm.201310-1896OC. PubMed PMID: 24592878; PMCID: 4225829

Zelner JL, Murray MB, Becerra MC, Galea J, Lecca L, Calderon R, Yataco R, Contreras C, Zhang Z, Grenfell BT, Cohen T. Age-specific risks of tuberculosis infection from household and community exposures and opportunities for interventions in a high-burden setting. Am J Epidemiol. 2014;180(8):853-61. doi: 10.1093/aje/kwu192. PubMed PMID: 25190676; PMCID: 4188339. 

Stagg HR, Cohen T, Becerra MC, Anderson LF, Abubakar I. A tale of two settings: the role of the Beijing genotype in the epidemiology of multidrug-resistant tuberculosis. Eur Respir J. 2014;43(2):632-5. doi: 10.1183/09031936.00140513. PubMed PMID: 24036242

Shrestha S, Knight GM, Fofana M, Cohen T, White RG, Cobelens F, Dowdy DW. Drivers and trajectories of resistance to new first-line drug regimens for tuberculosis. Open Forum Infect Dis. 2014;1(2):ofu073. doi: 10.1093/ofid/ofu073. PubMed PMID: 25734143; PMCID: 4281792. 

Pretorius C, Menzies NA, Chindelevitch L, Cohen T, Cori A, Eaton JW, Fraser C, Gopalappa C, Hallett TB, Salomon JA, Stover J, White RG, Dodd PJ. The potential effects of changing HIV treatment policy on tuberculosis outcomes in South Africa: results from three tuberculosis-HIV transmission models. AIDS. 2014;28 Suppl 1:S25-34. doi: 10.1097/QAD.0000000000000085. PubMed PMID: 24468944. pdf_pretorious2014_AIDS

Odone A, Amadasi S, White RG, Cohen T, Grant AD, Houben RM. The impact of antiretroviral therapy on mortality in HIV positive people during tuberculosis treatment: a systematic review and meta-analysis. PLoS One. 2014;9(11):e112017. doi: 10.1371/journal.pone.0112017. PubMed PMID: 25391135; PMCID: 4229142. pdf_odone2014_plos

Mears J, Abubakar I, Crisp D, Maguire H, Innes JA, Lilley M, Lord J, Cohen T, Borgdorff MW, Vynnycky E, McHugh TD, Sonnenberg P. Prospective evaluation of a complex public health intervention: lessons from an initial and follow-up cross-sectional survey of the tuberculosis strain typing service in England. BMC Public Health. 2014;14:1023. doi: 10.1186/1471-2458-14-1023. PubMed PMID: 25273511; PMCID: 4194411. pdf_mears2014_BMCph

Langley I, Lin HH, Egwaga S, Doulla B, Ku CC, Murray M, Cohen T, Squire SB. Assessment of the patient, health system, and population effects of Xpert MTB/RIF and alternative diagnostics for tuberculosis in Tanzania: an integrated modelling approach. Lancet Glob Health. 2014;2(10):e581-91. doi: 10.1016/S2214-109X(14)70291-8. PubMed PMID: 25304634. pdf_langley2014_lancetGH

Kouyos RD, Metcalf CJ, Birger R, Klein EY, Abel zur Wiesch P, Ankomah P, Arinaminpathy N, Bogich TL, Bonhoeffer S, Brower C, Chi-Johnston G, Cohen T, Day T, Greenhouse B, Huijben S, Metlay J, Mideo N, Pollitt LC, Read AF, Smith DL, Standley C, Wale N, Grenfell B. The path of least resistance: aggressive or moderate treatment? Proc Biol Sci. 2014;281(1794):20140566. Epub 2014/09/26. doi: 10.1098/rspb.2014.0566. PubMed PMID: 25253451; PMCID: 4211439

Jenkins HE, Tolman AW, Yuen CM, Parr JB, Keshavjee S, Perez-Velez CM, Pagano M, Becerra MC, Cohen T. Incidence of multidrug-resistant tuberculosis disease in children: systematic review and global estimates. Lancet. 2014;383(9928):1572-9. doi: 10.1016/S0140-6736(14)60195-1. PubMed PMID: 24671080; PMCID: 4094366. pdf_jenkins2014_lancet

Jenkins HE, Gegia M, Furin J, Kalandadze I, Nanava U, Chakhaia T, Cohen T. Geographical heterogeneity of multidrug-resistant tuberculosis in Georgia, January 2009 to June 2011. Euro Surveill. 2014;19(11). doi: 10.2807/1560-7917.es2014.19.11.20743. PubMed PMID: 24679722; PMCID: 4090679. 

Jenkins HE, Crudu V, Soltan V, Ciobanu A, Domente L, Cohen T. High risk and rapid appearance of multidrug resistance during tuberculosis treatment in Moldova. Eur Respir J. 2014;43(4):1132-41. doi: 10.1183/09031936.00203613. PubMed PMID: 24558181; PMCID: 4005038 

Huang CC, Tchetgen ET, Becerra MC, Cohen T, Hughes KC, Zhang Z, Calderon R, Yataco R, Contreras C, Galea J, Lecca L, Murray M. The effect of HIV-related immunosuppression on the risk of tuberculosis transmission to household contacts. Clin Infect Dis. 2014;58(6):765-74. doi: 10.1093/cid/cit948. PubMed PMID: 24368620; PMCID: 3935504

Huang CC, Tchetgen ET, Becerra MC, Cohen T, Galea J, Calderon R, Yataco R, Contreras C, Zhang ZB, Lecca L, Murray M. Cigarette smoking among tuberculosis patients increases risk of transmission to child contacts. Int J Tuberc Lung Dis. 2014;18(11):1285-91. doi: 10.5588/ijtld.14.0309. PubMed PMID: 25299859. 

Hu Y, Xiong C, Zhang Z, Luo C, Cohen T, Gao J, Zhang L, Jiang Q. Changing patterns of spatial clustering of schistosomiasis in Southwest China between 1999-2001 and 2007-2008: assessing progress toward eradication after the World Bank Loan Project. Int J Environ Res Public Health. 2014;11(1):701-12. Epub 2014/01/08. doi: 10.3390/ijerph110100701. PubMed PMID: 24394217; PMCID: 3924469

Houben RM, Dowdy DW, Vassall A, Cohen T, Nicol MP, Granich RM, Shea JE, Eckhoff P, Dye C, Kimerling ME, White RG, TB MAC TB-HIV meeting participants. How can mathematical models advance tuberculosis control in high HIV prevalence settings? Int J Tuberc Lung Dis. 2014;18(5):509-14. doi: 10.5588/ijtld.13.0773. PubMed PMID: 24903784; PMCID: 4436821.

Field N, Cohen T, Struelens MJ, Palm D, Cookson B, Glynn JR, Gallo V, Ramsay M, Sonnenberg P, Maccannell D, Charlett A, Egger M, Green J, Vineis P, Abubakar I. Strengthening the Reporting of Molecular Epidemiology for Infectious Diseases (STROME-ID): an extension of the STROBE statement. Lancet Infect Dis. 2014;14(4):341-52. Epub 2014/03/19. doi: 10.1016/S1473-3099(13)70324-4. PubMed PMID: 24631223. pdf_field2014_lancetID

Eaton JW, Menzies NA, Stover J, Cambiano V, Chindelevitch L, Cori A, Hontelez JA, Humair S, Kerr CC, Klein DJ, Mishra S, Mitchell KM, Nichols BE, Vickerman P, Bakker R, Barnighausen T, Bershteyn A, Bloom DE, Boily MC, Chang ST, Cohen T, Dodd PJ, Fraser C, Gopalappa C, Lundgren J, Martin NK, Mikkelsen E, Mountain E, Pham QD, Pickles M, Phillips A, Platt L, Pretorius C, Prudden HJ, Salomon JA, van de Vijver DA, de Vlas SJ, Wagner BG, White RG, Wilson DP, Zhang L, Blandford J, Meyer-Rath G, Remme M, Revill P, Sangrujee N, Terris-Prestholt F, Doherty M, Shaffer N, Easterbrook PJ, Hirnschall G, Hallett TB. Health benefits, costs, and cost-effectiveness of earlier eligibility for adult antiretroviral therapy and expanded treatment coverage: a combined analysis of 12 mathematical models. Lancet Glob Health. 2014;2(1):e23-34. doi: 10.1016/S2214-109X(13)70172-4. PubMed PMID: 25104632. pdf_eaton2014_lancetGH

Dowdy DW, Houben R, Cohen T, Pai M, Cobelens F, Vassall A, Menzies NA, Gomez GB, Langley I, Squire SB, White R, TB MAC meeting participants. Impact and cost-effectiveness of current and future tuberculosis diagnostics: the contribution of modelling. Int J Tuberc Lung Dis. 2014;18(9):1012-8. doi: 10.5588/ijtld.13.0851. PubMed PMID: 25189546; PMCID: 4436823. 

Cohen T, Jenkins HE, Lu C, McLaughlin M, Floyd K, Zignol M. On the spread and control of MDR-TB epidemics: an examination of trends in anti-tuberculosis drug resistance surveillance data. Drug Resist Updat. 2014;17(4-6):105-23. doi: 10.1016/j.drup.2014.10.001. PubMed PMID: 25458783; PMCID: 4358299

Bantubani N, Kabera G, Connolly C, Rustomjee R, Reddy T, Cohen T, Pym AS. High rates of potentially infectious tuberculosis and multidrug-resistant tuberculosis (MDR-TB) among hospital inpatients in KwaZulu Natal, South Africa indicate risk of nosocomial transmission. PLoS One. 2014;9(3):e90868. doi: 10.1371/journal.pone.0090868. PubMed PMID: 24625669; PMCID: 3953209 pdf_bantubani2014_plos

Yuen CM, Tolman AW, Cohen T, Parr JB, Keshavjee S, Becerra MC. Isoniazid-resistant tuberculosis in children: a systematic review. Pediatr Infect Dis J. 2013;32(5):e217-26. doi: 10.1097/INF.0b013e3182865409. PubMed PMID: 23348808; PMCID: 3709006

Yaesoubi R, Cohen T. Identifying dynamic tuberculosis case-finding policies for HIV/TB coepidemics. Proc Natl Acad Sci U S A. 2013;110(23):9457-62. doi: 10.1073/pnas.1218770110. PubMed PMID: 23690585; PMCID: 3677479

Mills HL, Cohen T, Colijn C. Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis. Sci Transl Med. 2013;5(180):180ra49. doi: 10.1126/scitranslmed.3005260. PubMed PMID: 23576815; PMCID: 3714172. 

Mills HL, Cohen T, Colijn C. Response to comment on “Community-wide isoniazid preventive therapy drives drug-resistant tuberculosis: a model-based analysis”. Sci Transl Med. 2013;5(204):204lr4. doi: 10.1126/scitranslmed.3007442. PubMed PMID: 24068734. 

Jenkins HE, Plesca V, Ciobanu A, Crudu V, Galusca I, Soltan V, Serbulenco A, Zignol M, Dadu A, Dara M, Cohen T. Assessing spatial heterogeneity of multidrug-resistant tuberculosis in a high-burden country. Eur Respir J. 2013;42(5):1291-301. doi: 10.1183/09031936.00111812. PubMed PMID: 23100496; PMCID: 3800490

Jenkins HE, Ciobanu A, Plesca V, Crudu V, Galusca I, Soltan V, Cohen T. Risk factors and timing of default from treatment for non-multidrug-resistant tuberculosis in Moldova. Int J Tuberc Lung Dis. 2013;17(3):373-80. doi: 10.5588/ijtld.12.0464. PubMed PMID: 23407226; PMCID: 3710709. 

Izu A, Cohen T, Degruttola V.  Bayesian estimation of mixture models with prespecified elements to compare drug resistance in treatment-naive and experienced tuberculosis cases. PLoS Comput Biol. 2013;9(3):e1002973. doi: 10.1371/journal.pcbi.1002973. PubMed PMID: 23555210; PMCID: 3605089. pdf_izu2013_ploscompbio

Ford CB, Shah RR, Maeda MK, Gagneux S, Murray MB, Cohen T, Johnston JC, Gardy J, Lipsitch M, Fortune SM. Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis. Nat Genet. 2013;45(7):784-90. doi: 10.1038/ng.2656. PubMed PMID: 23749189; PMCID: 3777616

Dowdy DW, Dye C, Cohen T. Data needs for evidence-based decisions: a tuberculosis modeler’s ‘wish list‘. Int J Tuberc Lung Dis. 2013;17(7):866-77. doi: 10.5588/ijtld.12.0573. PubMed PMID: 23743307; PMCID: 4041555. 

Anderson LF, Tamne S, Watson JP, Cohen T, Mitnick C, Brown T, Drobniewski F, Abubakar I. Treatment outcome of multi-drug resistant tuberculosis in the United Kingdom: retrospective-prospective cohort study from 2004 to 2007. Euro Surveill. 2013;18(40). doi: 10.2807/1560-7917.es2013.18.40.20601. PubMed PMID: 24128699. 

Sergeev R, Colijn C, Murray M, Cohen T. Modeling the dynamic relationship between HIV and the risk of drug-resistant tuberculosis. Sci Transl Med. 2012;4(135):135ra67. doi: 10.1126/scitranslmed.3003815. PubMed PMID: 22623743; PMCID: 3387814. 

Robinson K, Cohen T, Colijn C. The dynamics of sexual contact networks: effects on disease spread and control. Theor Popul Biol. 2012;81(2):89-96. doi: 10.1016/j.tpb.2011.12.009. PubMed PMID: 22248701; PMCID: 3328800. 

Menzies NA, Cohen T, Lin HH, Murray M, Salomon JA. Population health impact and cost-effectiveness of tuberculosis diagnosis with Xpert MTB/RIF: a dynamic simulation and economic evaluation. PLoS Med. 2012;9(11):e1001347. doi: 10.1371/journal.pmed.1001347. PubMed PMID: 23185139; PMCID: 3502465. pdf_menzies2012_plos

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;92(3):273-9. doi: 10.1016/j.tube.2012.02.003. PubMed PMID: 22401962; PMCID: 3323731. 

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;18(5):811-3. doi: 10.3201/eid1805.111467. PubMed PMID: 22516236; PMCID: 3358052

Lin HH, Dowdy D, Dye C, Murray M, Cohen T. The impact of new tuberculosis diagnostics on transmission: why context matters. Bull World Health Organ. 2012;90(10):739-47A. doi: 10.2471/BLT.11.101436. PubMed PMID: 23109741; PMCID: 3471051.

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;23(2):293-300. doi: 10.1097/EDE.0b013e3182459455. PubMed PMID: 22249242; PMCID: 3276714. 

Gegia M, Cohen T, Kalandadze I, Vashakidze L, Furin J. Outcomes among tuberculosis patients with isoniazid resistance in Georgia, 2007-2009. Int J Tuberc Lung Dis. 2012;16(6):812-6. doi: 10.5588/ijtld.11.0637. PubMed PMID: 22507372; PMCID: 3786434. 

Cohen T, van Helden PD, Wilson D, Colijn C, McLaughlin MM, Abubakar I, Warren RM. Mixed-strain mycobacterium tuberculosis infections and the implications for tuberculosis treatment and control. Clin Microbiol Rev. 2012;25(4):708-19. doi: 10.1128/CMR.00021-12. PubMed PMID: 23034327; PMCID: 3485752. 

Cohen T, Manjourides J, Hedt-Gauthier B. Linking surveillance with action against drug-resistant tuberculosis. Am J Respir Crit Care Med. 2012;186(5):399-401. doi: 10.1164/rccm.201203-0394PP. PubMed PMID: 22592806; PMCID: 3443807. 

Abubakar I, Stagg HR, Cohen T, Mangtani P, Rodrigues LC, Pimpin L, Watson JM, Squire SB, Zumla A. Controversies and unresolved issues in tuberculosis prevention and control: a low-burden-country perspective. J Infect Dis. 2012;205 Suppl 2:S293-300. doi: 10.1093/infdis/jir886. PubMed PMID: 22448025. 

Yaesoubi R, Cohen T. Dynamic health policies for controlling the spread of emerging infections: influenza as an example. PLoS One. 2011;6(9):e24043. doi: 10.1371/journal.pone.0024043. PubMed PMID: 21915279; PMCID: 3167826. pdf_yaesoubi2011_plos

Yaesoubi R, Cohen T. Generalized Markov Models of Infectious Disease Spread: A Novel Framework for Developing Dynamic Health Policies. Eur J Oper Res. 2011;215(3):679-87. doi: 10.1016/j.ejor.2011.07.016. PubMed PMID: 21966083; PMCID: 3182455.

Sergeev R, Colijn C, Cohen T. Models to understand the population-level impact of mixed strain M. tuberculosis infections. J Theor Biol. 2011;280(1):88-100. doi: 10.1016/j.jtbi.2011.04.011. PubMed PMID: 21514304; PMCID: 3111980. pdf_yaesoubi2011_JTBio

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;8(63):1510-20. doi: 10.1098/rsif.2011.0160. PubMed PMID: 21508012; PMCID: 3163428. 

Lin HH, Langley I, Mwenda R, Doulla B, Egwaga S, Millington KA, Mann GH, Murray M, Squire SB, Cohen T. A modeling framework to support the selection and implementation of new tuberculosis diagnostic tools. Int J Tuberc Lung Dis. 2011;15(8):996-1004. doi: 10.5588/ijtld.11.0062. PubMed PMID: 21740663.

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;139(11):1784-93. doi: 10.1017/S0950268810002797. PubMed PMID: 21205434; PMCID: 3153578

Jenkins HE, Zignol M, Cohen T. Quantifying the burden and trends of isoniazid resistant tuberculosis, 1994-2009. PLoS One. 2011;6(7):e22927. doi: 10.1371/journal.pone.0022927. PubMed PMID: 21829557; PMCID: 3146514. pdf_jenkins2011_plos

Izu A, Cohen T, Mitnick C, Murray M, De Gruttola V. Bayesian methods for fitting mixture models that characterize branching tree processes: An application to development of resistant TB strains. Stat Med. 2011;30(22):2708-20. doi: 10.1002/sim.4287. PubMed PMID: 21717491; PMCID: 3219798. pdf_izu2011_StatMed

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;84(2):192-9. doi: 10.4269/ajtmh.2011.10-0363. PubMed PMID: 21292884; PMCID: 3029167. 

Goldhaber-Fiebert JD, Jeon CY, Cohen T, Murray MB. Diabetes mellitus and tuberculosis in countries with high tuberculosis burdens: individual risks and social determinants. Int J Epidemiol. 2011;40(2):417-28. doi: 10.1093/ije/dyq238. PubMed PMID: 21252210; PMCID: 3621385.

Gardner A, Cohen T, Carter EJ. Tuberculosis among participants in an academic global health medical exchange program. J Gen Intern Med. 2011;26(8):841-5. doi: 10.1007/s11606-011-1669-x. PubMed PMID: 21359579; PMCID: 3138970. 

Colijn C, Cohen T, Ganesh A, Murray M. Spontaneous emergence of multiple drug resistance in tuberculosis before and during therapy. PLoS One. 2011;6(3):e18327. doi: 10.1371/journal.pone.0018327. PubMed PMID: 21479171; PMCID: 3068161. pdf_colijn2011_plos

Cohen T, Wilson D, Wallengren K, Samuel EY, Murray M. Mixed-strain Mycobacterium tuberculosis infections among patients dying in a hospital in KwaZulu-Natal, South Africa. J Clin Microbiol. 2011;49(1):385-8. doi: 10.1128/JCM.01378-10. PubMed PMID: 20980576; PMCID: 3020455. 

Cohen T, Murray M, Abubakar I, Zhang Z, Sloutsky A, Arteaga F, Chalco K, Franke MF, Becerra MC. Multiple introductions of multidrug-resistant tuberculosis into households, Lima, Peru. Emerg Infect Dis. 2011;17(6):969-75. doi: 10.3201/eid/1706.101471. PubMed PMID: 21749756; PMCID: 3358204.

Brooks-Pollock E, Becerra MC, Goldstein E, Cohen T, Murray MB. Epidemiologic inference from the distribution of tuberculosis cases in households in Lima, Peru. J Infect Dis. 2011;203(11):1582-9. doi: 10.1093/infdis/jir162. PubMed PMID: 21592987; PMCID: 3096792. 

Shin SS, Keshavjee S, Gelmanova IY, Atwood S, Franke MF, Mishustin SP, Strelis AK, Andreev YG, Pasechnikov AD, Barnashov A, Tonkel TP, Cohen T. Development of extensively drug-resistant tuberculosis during multidrug-resistant tuberculosis treatment. Am J Respir Crit Care Med. 2010;182(3):426-32. doi: 10.1164/rccm.200911-1768OC. PubMed PMID: 20413630; PMCID: 2921603. 

Lipsitch M, Tchetgen Tchetgen E, Cohen T. Negative controls: a tool for detecting confounding and bias in observational studies. Epidemiology. 2010;21(3):383-8. doi: 10.1097/EDE.0b013e3181d61eeb. PubMed PMID: 20335814; PMCID: 3053408.  

Colijn C, Cohen T, Fraser C, Hanage W, Goldstein E, Givon-Lavi N, Dagan R, Lipsitch M. What is the mechanism for persistent coexistence of drug-susceptible and drug-resistant strains of Streptococcus pneumoniae? J R Soc Interface. 2010;7(47):905-19. doi: 10.1098/rsif.2009.0400. PubMed PMID: 19940002; PMCID: 2871802. 

Cohen T, Murray M, Wallengren K, Alvarez GG, Samuel EY, Wilson D. The prevalence and drug sensitivity of tuberculosis among patients dying in hospital in KwaZulu-Natal, South Africa: a postmortem study. PLoS Med. 2010;7(6):e1000296. doi: 10.1371/journal.pmed.1000296. PubMed PMID: 20582324; PMCID: 2889914. pdf_cohen2010_plos

Cohen T, Hedt BL, Pagano M. Estimating the magnitude and direction of bias in tuberculosis drug resistance surveys conducted only in the public sector: a simulation study. BMC Public Health. 2010;10:355. doi: 10.1186/1471-2458-10-355. PubMed PMID: 20565947; PMCID: 2898828. 

Brooks-Pollock E, Cohen T, Murray M. The impact of realistic age structure in simple models of tuberculosis transmission. PLoS One. 2010;5(1):e8479. doi: 10.1371/journal.pone.0008479. PubMed PMID: 20062531; PMCID: 2797602. pdf_brookspol2010_plos

Lipsitch M, Lajous M, O’Hagan JJ, Cohen T, Miller JC, Goldstein E, Danon L, Wallinga J, Riley S, Dowell SF, Reed C, McCarron M. Use of cumulative incidence of novel influenza A/H1N1 in foreign travelers to estimate lower bounds on cumulative incidence in Mexico. PLoS One. 2009;4(9):e6895. doi: 10.1371/journal.pone.0006895. PubMed PMID: 19742302; PMCID: 2731883. pdf_lipsitch2009_plos

Lipsitch M, Colijn C, Cohen T, Hanage WP, Fraser C. No coexistence for free: neutral null models for multistrain pathogens. Epidemics. 2009;1(1):2-13. doi: 10.1016/j.epidem.2008.07.001. PubMed PMID: 21352747; PMCID: 3099423. pdf_lipsitch2009_epidemics

Colijn C, Cohen T, Murray M. Latent coinfection and the maintenance of strain diversity. Bull Math Biol. 2009;71(1):247-63. doi: 10.1007/s11538-008-9361-y. PubMed PMID: 19082663; PMCID: 2652765. 

Cohen T, Dye C, Colijn C, Williams B, Murray M. Mathematical models of the epidemiology and control of drug-resistant TB. Expert Rev Respir Med. 2009;3(1):67-79. doi: 10.1586/17476348.3.1.67. PubMed PMID: 20477283. pdf_cohen2009_ERRM

Blaya JA, Cohen T, Rodriguez P, Kim J, Fraser HS. Personal digital assistants to collect tuberculosis bacteriology data in Peru reduce delays, errors, and workload, and are acceptable to users: cluster randomized controlled trial. Int J Infect Dis. 2009;13(3):410-8. doi: 10.1016/j.ijid.2008.09.015. PubMed PMID: 19097925; PMCID: 2673336.pdf_blaya2009_IJID

Lin HH, Murray M, Cohen T, Colijn C, Ezzati M. Effects of smoking and solid-fuel use on COPD, lung cancer, and tuberculosis in China: a time-based, multiple risk factor, modelling study. Lancet. 2008;372(9648):1473-83. doi: 10.1016/S0140-6736(08)61345-8. PubMed PMID: 18835640; PMCID: 2652750. pdf_lin2008_lancet

Dagan R, Barkai G, Givon-Lavi N, Sharf AZ, Vardy D, Cohen T, Lipsitch M, Greenberg D. Seasonality of antibiotic-resistant streptococcus pneumoniae that causes acute otitis media: a clue for an antibiotic-restriction policy? J Infect Dis. 2008;197(8):1094-102. doi: 10.1086/528995. PubMed PMID: 18419528; PMCID: 2652754. 

Cohen T, Colijn C, Wright A, Zignol M, Pym A, Murray M. Challenges in estimating the total burden of drug-resistant tuberculosis. Am J Respir Crit Care Med. 2008;177(12):1302-6. doi: 10.1164/rccm.200801-175PP. PubMed PMID: 18369201; PMCID: 2720088. 

Cohen T, Colijn C, Murray M. Modeling the effects of strain diversity and mechanisms of strain competition on the potential performance of new tuberculosis vaccines. Proc Natl Acad Sci U S A. 2008;105(42):16302-7. doi: 10.1073/pnas.0808746105. PubMed PMID: 18849476; PMCID: 2570977. 

Cohen T, Colijn C, Finklea B, Wright A, Zignol M, Pym A, Murray M. Are survey-based estimates of the burden of drug resistant TB too low? Insight from a simulation study. PLoS One. 2008;3(6):e2363. doi: 10.1371/journal.pone.0002363. PubMed PMID: 18523659; PMCID: 2408555. pdf_cohen2008_plos

Lipsitch M, Cohen T, Murray M, Levin BR. Antiviral resistance and the control of pandemic influenza. PLoS Med. 2007;4(1):e15. doi: 10.1371/journal.pmed.0040015. PubMed PMID: 17253900; PMCID: 1779817. pdf_lipsitch2007_plos

Colijn C, Cohen T, Murray M. Emergent heterogeneity in declining tuberculosis epidemics. J Theor Biol. 2007;247(4):765-74. doi: 10.1016/j.jtbi.2007.04.015. PubMed PMID: 17540410; PMCID: 2652758. pdf_colijn2007_jtbio

Cohen T, Colijn C, Finklea B, Murray M. Exogenous re-infection and the dynamics of tuberculosis epidemics: local effects in a network model of transmission. J R Soc Interface. 2007;4(14):523-31. doi: 10.1098/rsif.2006.0193. PubMed PMID: 17251134; PMCID: 2373405

Cohen T, Lipsitch M, Walensky RP, Murray M. Beneficial and perverse effects of isoniazid preventive therapy for latent tuberculosis infection in HIV-tuberculosis coinfected populations. Proc Natl Acad Sci U S A. 2006;103(18):7042-7. doi: 10.1073/pnas.0600349103. PubMed PMID: 16632605; PMCID: 1459015. 

Cohen T, Murray M. Incident tuberculosis among recent US immigrants and exogenous reinfection. Emerg Infect Dis. 2005;11(5):725-8. doi: 10.3201/eid1105.041107. PubMed PMID: 15890129; PMCID: 3320369. 

Cohen T, Murray M. Modeling epidemics of multidrug-resistant M. tuberculosis of heterogeneous fitness. Nat Med. 2004;10(10):1117-21. doi: 10.1038/nm1110. PubMed PMID: 15378056; PMCID: 2652755

Cohen T, Becerra MC, Murray MB. Isoniazid resistance and the future of drug-resistant tuberculosis. Microb Drug Resist. 2004;10(4):280-5. doi: 10.1089/mdr.2004.10.280. PubMed PMID: 15650371; PMCID: 2652757.

Lipsitch M, Cohen T, Cooper B, Robins JM, Ma S, James L, Gopalakrishna G, Chew SK, Tan CC, Samore MH, Fisman D, Murray M. Transmission dynamics and control of severe acute respiratory syndrome. Science. 2003;300(5627):1966-70. doi: 10.1126/science.1086616. PubMed PMID: 12766207; PMCID: 2760158.

Cohen T, Sommers B, Murray M. The effect of drug resistance on the fitness of Mycobacterium tuberculosis. Lancet Infect Dis. 2003;3(1):13-21. doi: 10.1016/s1473-3099(03)00483-3. PubMed PMID: 12505028. pdf_cohen2003_lancetID