Pei L, Hughes MD. A statistical framework for quantile equivalence clinical trials with application to pharmacokinetic studies which bridge from HIV-infected adults to children. Biometrics. 2008 Dec; 64(4):1117-25.

Wruck LC, Yiannoutsis CT, Hughes MD. A sequential design to estimate sensitivity and specificity of a diagnostic test. Statistics in Medicine. 2006;25(20):3458-3473.

O’Quigley J, Hughes M, Fenton T. Dose-finding designs for HIV studies. Biometrics. 2001;57:1018-1029.

Hughes MD. Analysis and design issues for studies using censored biomarker measurements, with an example of viral load measurements in HIV clinical trials. Statistics in Medicine, 2000.

Hughes MD. Power considerations for clinical trials using multivariate time-to-event data. Statistics in Medicine, 1997; 16:865-882.

Daniels MJ and Hughes MD. Meta-analysis for the evaluation of potential surrogate markers. Statistics in Medicine, 1997; 16:1965-1982.

Gulick RM, Su Z, Flexner C, Hughes MD, Skolnik PR, Wilkin TJ, Gross R, Krambrink A, Coakley E, Greaves WL, Zolopa A, Reichman R, Godfrey C, Hirsch M, Kuritzkes DR. Phase II study of the safety and efficacy of vicriviroc, a CCR5 inhibitor, in HIV-1-infected, treatment-experienced patients. ACTG 5211. Journal of Infectious Diseases. 2007;196:304-312.

Soh C-H, Oleske JM, Brady MT, Spector SA, Borkowsky W, Burchett SK, Foca MD, Handelsman E, Jiménez E, Dankner WM, Hughes MD. Long-term effects of protease- inhibitor-based combination therapy on CD4 T-cell recovery in HIV-1 infected children and adolescents. Lancet. 2003;362:2045-51.

Gortmaker SL, Hughes M, Cervia J, Brady M, Johnson GM, Seage GR, Song LY, Dankner WM, Oleske JM, for the Pediatric AIDS Clinical Trials Group Protocol 219 Team. Effect of combination therapy including protease inhibitors on mortality among children and adolescents infected with HIV-1. New England Journal of Medicine. 2001;345:1522-1528.

HIV Surrogate Marker Collaborative Group. Human immunodeficiency virus type 1 (HIV-1) RNA level and CD4 count as prognostic markers and surrogate endpoints: a meta-analysis. AIDS Research and Human Retroviruses. 2000;16:1123-1133.

Hughes MD, Johnson VA, Hirsch MS, et al. Monitoring HIV-1 RNA levels in plasma in addition to CD4+ lymphocyte count improves assessment of antiretroviral therapeutic response. Annals of Internal Medicine, 1997; 126:929-938.

Hammer SM, Squires KE, Hughes MD, et al. A controlled trial of two nucleoside analogues plus indinavir in persons with human immunodeficiency virus and CD4 cell counts of 200 per cubic millimeter or less. New England Journal of Medicine, 1997; 337:725-733.