Here are some of my earlier methods papers dealing with causal inference methods. Most of the principal stratification research was with my PhD advisor, Peter Gilbert.
Principal Stratification Sensitivity Analyses
Shepherd BE, Gilbert PB, Jemiai Y, Rotnitzky A. Sensitivity analyses comparing outcomes only existing in a subset selected post-randomization, conditional on covariates, with application to HIV vaccine trials. Biometrics 2006; 62: 332-342. link
Shepherd BE, Gilbert PB, Mehrotra DV. Eliciting a counterfactual sensitivity parameter. The American Statistician 2007; 61: 56-63. link
Shepherd BE, Gilbert PB, Lumley T. Sensitivity analyses comparing time-to-event outcomes only existing in a subset selected post-randomization. Journal of the American Statistical Association 2007; 102: 573-582. link
Jemiai Y, Rotnitzky A, Shepherd BE, Gilbert PB. Semiparametric estimation of treatment effects given baseline covariates on an outcome measured after a post-randomization event occurs. Journal of the Royal Statistical Society, Series B 2007; 69: 879-901. link
Shepherd BE, Redman MW, Ankerst DP. Does finasteride affect the severity of prostate cancer? A causal sensitivity analysis. Journal of the American Statistical Association 2008; 103: 1392-1404. link
Shepherd BE, Gilbert PB, Dupont CT. Sensitivity analyses comparing time-to-event outcomes only existing in a subset selected postrandomization and relaxing monotonicity. Biometrics 2011; 67: 1100-1110. link
Lu X, Mehrotra DV, Shepherd BE. Rank-based principal stratum sensitivity analyses. Statistics in Medicine 2013; 32: 4526-4539. link
Gilbert PB, Shepherd BE, Hudgens MG. Sensitivity analysis of per-protocol time-to-event treatment efficacy in randomized clinical trials. Journal of the American Statistical Association 2013; 108: 789-800. link
Gilbert PB, Blette BS, Shepherd BE, Hudgens MG. Post-randomization biomarker effect modification analysis in an HIV vaccine clinical trial. Journal of Causal Inference 2020; 8: 54-69. link
Time-Dependent Confounding
Shepherd BE, Jenkins CA, Rebeiro PF, Stinnette SE, Bebawy SS, McGowan CC, Hulgan T, Sterling TR. Estimating the optimal CD4 count for HIV-infected patients to start antiretroviral therapy. Epidemiology 2010; 21:698-705. link
Ray WA, Liu Q, Shepherd BE. Performance of time-dependent propensity scores: a pharmacoepidemiology case study. Pharmacoepidemiology and Drug Safety 2015; 24: 98-106. link
Shepherd BE, Liu Q, Mercaldo N, Jenkins CA, Lau B, Cole SR, Saag MS, Sterling TR. Comparing results from multiple imputation and dynamic marginal structural models for estimating when to start antiretroviral therapy. Statistics in Medicine 2016; 35: 4335-4351. link