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URMC / Labs / Brent Johnson Lab / Publications




  • Brust CMJ, Shah S, Mlisana K, Moodley P, Allana S, Campbell A, Johnson BA, Master I, Mthiyane T, Lachman S, Larkan L-M, Ning Y, Malik A, Smith JP, Gandhi NR (2018) Improved survival and cure rates with concurrent treatment for MDR-TB/HIV co-infection in KwaZulu-Natal, South Africa. Clinical Infectious Disease (In press)
  • Rice J, Johnson BA, Strawderman RL (2018) Modeling the rate of HIV testing from repeated binary data among potential never-testers. Biostatistics (In press)
  • Rice J, Strawderman RL, Johnson BA (2018) Regularity of a renewal process estimated from binary data. Biometrics (In press)
  • McIntyre J, Johnson BA, Rappaport SM (2018) Monte Carlo methods for nonparametric regression with heteroscedastic measurement error. Biometrics (In press)


  • Siedner MJ, Bwana MB, Moosa Y, Paul M, Pillay S, Aturinda I, Ard K, Muyindike W, Moodley P, Brijkumar J, Rautenberg T, George G, Johnson BA, Gandhi RT, Sunpath H, Marconi VC (2017) The REVAMP trial to evaluate HIV resistance testing in Sub-Saharan Africa: a case study in clinical in resource limited settings to optimize effectiveness and cost effectiveness estimates. HIV Clinical Trials 18(4): 149-155.
  • Freeland R, Sullivan SP, Riley E, Johnson BA, Mitchell J, McFarland D, Sullivan PS, Stephenson R (2017) Project NEXUS: protocol to provide home-based HIV testing and counseling for male couples. JMIR Research Protocols 6(1):e101
  • Mustanksi B, Madkins K, Greene GJ, Parsons JT, Johnson BA, Sullivan P, Bass M, Abel R (2016) Internet-based HIV prevention with at-home sexually transmitted infection testing for young men having sex with men: study protocol of a randomized control trial of Keep It Up! 2.0. JMIR Research Protocols 6(1), e1.
  • Sherazi S, Kutyifa V, McNitt S, Papernov A, Hallinan W, Chen L, Storozynsky E, Johnson BA, Strawderman RL, Massey T, Zareba W, Alexis JD (2016) Gender differences in the risk of neurological events and subsequent outcomes in left ventricular assist device patients. J Cardiac Failure (Accepted)
  • Johnson BA, McKenney J, Ricca AV, Rosenberg ES, Liu C, Sharma A, Sullivan PS (2016) Risk factors associated with repeated HIV testing among Internet-using men who have sex with men. AIDS Education and Prevention. (Accepted)
  • Mishra-Kalyani PS, Johnson BA, Glass JD, Long Q. (2016) Estimating the palliative effect of percutaneous endoscopic gastrostomy in an observational registry using principal stratification and generalized propensity scores. Scientific Reports. 6:33431.
  • Wall K, Kilembe W, Vwalika B, Htee Khu N, Brill I, Chomba E, Johnson BA, Haddad L, Tichacek A, Allen S. (2016) Hormonal contraceptive use among HIV-positive women does not increase transmission risk to male partners, Zambia, 1994--2012. Journal of Infectious Diseases 214(7):1063-1071.
  • Johnson BA. (2016) Nonparametric 2-sample tests of the marginal mark distribution with censored marks. Scandinavian Journal of Statistics (In press)
  • Lu X, Johnson BA. (2016) Direct estimation for adaptive treatment length policies: methods and application to evaluating the effect of delayed PEG insertion. Biometrics 73(3):981-989.
  • Braverman JM, Hamilton MB, Johnson BA. (2016) Patterns of substitution rate variation at many nuclear loci in two species trios in the Brassicaceae partitioned with ANOVA. Journal of Molecular Evolution. 83(3):97-109.
  • Zhao Y, Chung M, Johnson BA, Moreno CS, Long Q. (2016) Hierarchical feature selection incorporating known and novel biological information: identifying genomic features related to prostate cancer recurrence. Journal of the American Statistical Association 111:1427-1439.
  • Feinstein B, Johnson BA, Parsons J, Mustanski BM. (2016) Reactions to testing HIV negative: measurement and associations with sexual risk behavior among young MSM who recently tested HIV negative. AIDS and Behavior. 21(5):1467-1477.
  • Johnson BA, Long Q, Huang Y, Chansky K, and Redman, M. (2016) Model selection and inference for censored lifetime medical expenditures. Biometrics. 72:731-741.


  • Long Q, Johnson BA. (2015) Variable selection in the presence of missing data: resampling and imputation. Biostatistics. 16, 596-610.
  • Sharma A, Johnson BA, Sullivan PS. (2015) Evaluating interventions to promote routine preventive screenings: a comparison of analytical outcomes. Contemporary Clinical Trials. 41,152-159.
  • Wall K, Kilembe W, Vwalika B, Htee Khu N, Brill I, Chomba E, Johnson BA, Haddad L, Tichacek A, Allen S. (2015) Hormonal contraception does not increase women's HIV acquisition risk in Zambian discordant couples, 1994-2012. Contraception. 91, 480-487.
  • Johnson BA. (2015) On Huberized calibration regression for censored medical cost data. Statistics in Biosciences. 7, 367-378.
  • Jain S, Frank G, McCormick K, Wu B, Johnson BA. (2015) Impact of physician scorecards on emergency department resource use, quality, and efficiency. Pediatrics. 136, e670-e679.
  • Lu X, Johnson BA. (2015) Direct estimation of the mean outcome on treatment when treatment assignment and discontinuation compete. Biometrika. 102(4), 797-807.
  • Colasanti J, McDaniel D, Johnson B, Del Rio C, Sunpath H, and Marconi VC. (2015) Novel predictors of poor retention following a down-referral from a hospital-based ART program in South Africa. AIDS Research and Human Retroviruses. (In Press)
  • Berg C, Nehl E, Wang X, Ding Y, He N, Johnson BA, Wong FY (2014) A comparison of HIV-positive and negative MSM smokers in Chengdu, China: Quit attempts and healthcare provider intervention on smoking. AIDS Care. 26(9), 1201-1207
  • Hare AQ, Ordonez CE, Johnson BA, Del Rio C, Kearns RA, Wu B, Hampton J, Wu P, Sunpath H, Marconi VC. (2014) Gender-specific risk factors for virologic failure in KwaZulu-Natal: Automobile ownership and financial insecurity. AIDS and Behavior. 2014 Jul 19 [Epub ahead of print].
  • Kim Y-M, Zhou Y, Gao Y, Fu JS, Johnson BA, Huang C, Liu Y. (2014) Spatially-resolved estimation of ozone-related mortality in the United States under two representative concentration pathways (RCPs) and their uncertainty. Climatic Change. 128, 71-84.
  • Carnathan D, Wetzel KS, Yu J, Lee ST, Johnson BA, Paiardini M, Yan J, Morrow M, Sardesai NY, Weiner DB, Ertl HCJ, Silvestri G. (2014) Activated CD4+CCR5+ T-cells in the rectum predict increased SIV acquisition and higher viremia in SIVGag/Tat vaccinated macaques. Proceedings of the National Academy of Sciences. 112(2), 518-523.


  • Wu J, Zhou Y, Gao Y, Fu JS, Johnson BA, Huang C, Kim Y-M, Liu Y (2013) Estimation and uncertainty analysis of impacts of future heat waves on mortality in the Eastern United States. Environmental Health Perspectives doi:10.1289/ehp.1306670.
  • Wu P, Johnson BA, Nachega J, Wu B, Ordonez C, Hare A, Kearns R, Murphy R, Sunpath H, Marconi V. (2013) The combination of pill count and self-reported adherence is a strong predictor of first-line ART failure for adults in South Africa. Current HIV Research. 12(5), 366-375.
  • Raysoni AU, Stock TH, Sarnat JA, Montoya-Sosa T, Sarnat SE, Holguin F, Greenwald R, Johnson B, Li W-W (2013) Characterization of traffic-related air pollutant metrics at four schools in El Paso, Texas, USA: Implications for exposure assessment and siting schools in urban areas. Atmospheric Environment. 80, 140-151.
  • Marconi VC, Johnson BA, Wu B, Quinn-Hare A, Ordonez C, Kuritzkes DR (2013) Individual-level Early Warning Indicators for first-line virologic failure independent of adherence measures in a South African urban clinic AIDS Patient Care and STDs. 27, 657-668.
  • Khosropour CM, Johnson BA, Ricca AV, Sullivan PS (2013) A randomized trial of text messaging to enhance retention in an internet-based cohort study of men who have sex with men (MSM) J Med Internet Res. 25(8):e194. doi:10.2196/jmlr.2756.
  • Rappaport SM, Johnson BA, Bois FY, Kupper LL, Kim S, Thomas R. (2013) Ignoring and adding errors do not improve the science. Carcinogenesis. 34, 1689-1691.
  • Greenwald R, Johnson BA, Hoskins A, Dworski R. (2013) Exhaled breath condensate formate after inhaled allergen provocation in atopic asthmatics in vivo. J Asthma. 50, 619-622.
  • Johnson BA, Ribaudo H, Gulick RM, Eron JJ. (2013) Modeling clinical endpoints as a function of time of switch to second-line ART with incomplete data on switching times. Biometrics. 69, 732-740.
  • Traxinger K, Kelly C, Johnson BA, Lyles RH, Glass JD. (2013) Prognosis and epidemiology of amyotrophic lateral sclerosis: analysis of a clinic population from 1997 - 2011. Neurology: Clinical Practice. 3, 313-320.
  • Chung M, Long Q, and Johnson BA. (2013) A tutorial on rank-based coefficient estimation for censored data in small- and large-scale problems. Statistics and Computing. 23, 601-614.
  • Rappaport SM, Kim S, Thomas R, Johnson BA, Bois F, and Kupper LL. (2012) Low-dose Metabolism of Benzene in Humans: Science and Obfuscation. Carcinogenesis. 34, 2-9.
  • Zora J, Sarnat SE, Raysoni AU, Greenwald R, Johnson BA, Stock TH, Holguin F, Li WW, Sarnat JA. (2012) Associations between urban air pollution and pediatric asthma control in El Paso, Texas. Science of the Total Environment. 448, 56-65.
  • Garber D, O'Mara L, Gangadhara S, McQuoid M, Zhang X, Zheng R, Gill K, Verma M, Yu T, Johnson BA, Li B, Derdeyn C, Ibegbu C, Altman J, Hunter E, Feinberg M. (2012) Deletion of specific immune modulatory genes from modified vaccine ankara-based HIV vaccines engenders immunogenicity in Rhesus macaques. Journal of Virology. 86(23):12605-12615.
  • Long Q, Zhang X, Zhao Y, Johnson BA, Bostick RM. (2012) Modeling clinical outcome using multiple correlated functional biomarkers: A Bayesian approach. Statistical Methods in Medical Research. doi: 10.1177/0962280212460444
  • Greenwald R, Sarnat JA, Li WW, Raysoni AU, Johnson BA, Sarnat SE, Stock TH, Holguin F, Montoya-Sosa T. (2012) Associations between source-indicative pollution metrics and increases in pulmonary inflammation and reduced lung function in a panel of asthmatic children. Air Quality, Atmosphere, and Health. doi: 10.1007/s11869-012-0186-3.
  • Li L, Eron J, Ribaudo H, Gulick RM, Johnson BA. (2012) Evaluating the effect of early versus late ARV regimen change after failure on the initial regimen: results from the AIDS Clinical Trials Group Study A5095. Journal of the American Statistical Association. 107, 542-554.
  • Sunpath H, Wu B, Hampton J, Johnson BA, Moosa Y, Ordonez C, Kuritzkes DR, Marconi VC. (2012) High rate of K65R for ART naive patients with subtype C HIV infection failing a TDF-containing first-line regimen in South Africa. AIDS. 26, 1679-84.
  • Sarnat S, Raysoni AU, Li W, Holguin F, Johnson BA, Flores-Luevano S, Garcia J, and Sarnat JA. (2012) Air pollution and acute respiratory response in a panel of asthmatic children along the U.S.-Mexico border. Environmental Health Perspectives, 160, 437-444.


  • Long Q, Chung M, Moreno C, Johnson BA. (2011) Risk prediction for cancer recurrence through regularized estimation with simultaneous adjustment for nonlinear clinical effects. Annals of Applied Statistics. 5, 2003-2023.
  • Johnson BA, Long Q, Chung M. (2011) On path restoration for censored outcomes. Biometrics. 67, 1379-1388.
  • Johnson BA, Long Q. (2011) Survival ensembles by the sum of pairwise differences. Annals of Applied Statistics. 5, 1081-1101.
  • Long Q, Zhang X, and Johnson BA. (2011) Robust estimation of area under the ROC curve using auxiliary variables in the presence of missing biomarker values. Biometrics. 67, 559-567.
  • Long Q, Johnson BA, Osunkoya A, Lai Y-H, et al. (2010) Protein-coding and microRNA biomarkers of recurrence of prostate cancer following radical prostatectomy. The American Journal of Pathology. 197, 46-54.
  • Jain S, Elon L, DeGuzman M, Johnson BA, Frank G. (2010) Physician practice variation in the pediatric emergency department and its impact on resource utilization and quality of care. Pediatric Emergency Care. 26, 902-908.
  • Cooper LAD, Gutman DA, Long Q, Johnson BA, Choletti SR et al. (2010) The Proneural Molecular Signature Is Enriched in Oligodendrogliomas and Predicts Improved Survival among Diffuse Gliomas. PLoS ONE. 5, e12548. doi:10.1371/journal.pone.0012548.




  • Rebeiz AG, Dery J-P, Tsiatis AA, O'Shea JC, Johnson BA, Hellkamp AS, Pieper KS, Gilchrist IC, Slater J, Muhlestein B, Joseph D, Kitt MM, and Tcheng JE. (2004). Optimal duration of Eptifibatide infusion in percutaneous coronary intervention (an ESPRIT substudy). Am J Cardiol. 94, 926-92