1. Stephens AJ, Tchetgen Tchetgen EJ, DeGruttola V. “Augmented generalized estimating equations for improving efficiency and validity of estimation in cluster randomized trials by leveraging cluster-level and individual-level covariates.” Statistics in Medicine. 2012 May 10;31(10):915-930. PMCID: PMC3495191
  2. Goyal R, Wang R, DeGruttola V. “Editorial commentary: network epidemic models: assumptions and interpretations.” Clin Infect Dis. 2012 Jul;55(2):276-8. PMCID: PMC3403840
  3. 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 Comp Bio. 2013;9(3):e1002973. PMCID: PMC3605089
  4. Wang R, Weng J, Moyo S, Pain D, Barr CD, Maruapula D, Mongwato D, Makhema J, Novitsky V, Essex M. “Short communication: effect of short-course antenatal zidovudine and single-dose nevirapine on the BED capture enzyme immunoassay levels in HIV type 1 subtype C infection.” AIDS Research and Human Retroviruses. 2013;29(6):901-906. PMCID: PMC3653368
  5. Stock S, DeGruttola V. “Recursive Partitioning for Monotone Missing at Random Longitudinal Markers”. Statistics in Medicine. 2013 Mar 15;32(6):978-94. PMCID: PMC3754451
  6. Stephens A, Tchetgen Tchetgen EJ, De Gruttola V. “Flexible covariate-adjusted exact tests of randomized treatment effects with application to a trial of HIV education.” Annals of Applied Statistics. 2013 Dec 23;7(4):2106-2137. PMCID: PMC3935423
  7. Novitsky V, Bussmann H, Logan A, Moyo S, Widenfelt E, Okui L, Mmalane M, Baca J, Buck L, Phillips E, Tim D, McLane MF, Lei Q, Wang R, Makhema J, Lockman S, DeGruttola V, Essex M. “Phylogenetic Relatedness of Circulating HIV-1C Variants in Mochudi, Botswana.” PLoS One. 2013 Dec 11;8(12):e80589. PMCID: PMC3859477
  8. Burns DN, DeGruttola V, Pilcher CD, Kretzschmar M, Gordon CM, Flanagan EH, Duncombe C, Cohen MS. “Toward an endgame: finding and engaging people unaware of their HIV-1 infection in treatment and prevention.” AIDS Res Hum Retroviruses. 2014 Mar;30(3):217-24. PMCID: PMC3938938
  9. Wang R, Goyal R, Lei Q, Essex M, De Gruttola V. “Sample size considerations in the design of cluster randomized trials of combination HIV prevention”. Clin Trials. 2014 Mar 20;11(3):309-318.  NIHMS558805    ACCEPTED MANUSCRIPT    EXAMPLE CODE    EXAMPLE CODE 2
  10. Stephens A, Tchetgen Tchetgen E, De Gruttola V. “Locally efficient estimation of marginal treatment effects when outcomes are correlated: is the prize worth the chase?” Int J Biostat. 2014 May 1;10(1):59-75. doi: 10.1515/ijb-2013-0031. PMC Journal – In Process
  11. Wirth K, Tchetgen Tchetgen EJ. “Accounting for selection bias in association studies with complex survey data.” Epidemiology. 2014;25(3):444-453. PMCID: PMC3981932
  12. Carnegie NB, Wang R, Novitsky V, De Gruttola V. “Linkage of viral sequences among HIV-infected village residents in Botswana: estimation of linkage rates in the presence of missing data.” PLoS Comput Biol. 2014 Jan;10(1):e1003430. PMCID: PMC3886896    EXAMPLE CODE
  13. Goyal R, Blitzstein J, DeGruttola V. “Sampling Networks from Their Posterior Predictive Distribution.” Network Science. 2014 April;2(1):107-131. NIHMS599825     SOFTWARE
  14. Lynch M, DeGruttola V. “Predicting time to threshold for initiating antiretroviral treatment to evaluate cost of treatment as HIV prevention”. JRSSC. In Press. PMC Journal – In Process
  15. Gleeson J, Cellai D, Onnela JP, Porter MA, Reed-Tsochas F. “A Simple Generative Model of Collective Online Behaviour.” PNAS. published ahead of print July 7, 2014, doi:10.1073/pnas.1313895111. PMC Journal – In Process
    SIMULATION CODE (In order to run, 2 additional data files are needed – interested parties should contact Jukka-Pekka Onnela)
  16. Carnegie NB, Krivitsky PN, Hunter DR, Goodreau SM. “An approximation method for improving dynamic network model fitting.” Journal of Computational and Graphical Statistics. doi: 10.1080/10618600.2014.903087. NIHMS589216    SOFTWARE
  17. Goodreau SM, Carnegie NB, Vittinghoff E, Lama JR, Sanchez J, Fuchs J and Buchbinder SP. “Can male circumcision have an impact on the HIV epidemic in men who have sex with men?” PLoS ONE, accepted
  18. Le Grand R., Bosquet N., Dispinseri S., Hopewell N., Gosse L., Desjardins D., Shen X., Tomaras G., Saidi H., Prague M., Barnett S., Thiebaut R., Cope A., Scarlatti G., Shattock R.J. Superior efficacy of a microbicide and vaccine combination over single prevention approaches against vaginal SHIV challenge in cynomolgus monkeys. Journal of Virology   2016 May 12;90(11):5315-28. doi: 10.1128/JVI.00230-16. Print 2016 Jun 1. PubMed PMID: 27009957; PubMed Central PMCID: PMC4934744.
  19. Prague M. Dynamical modeling for Optimization of treatment in HIV infected patients. Statistical French Society journal in press. PMC5269533.
  20. – Prague M., Gran JM., Thiébaut R., Aalen A., Commenges D. Dynamic versus marginal structural models for estimating the effect of HAART on CD4 in observational studies : application to the Aquitaine Cohort study and the Swiss HIV Cohort Study. Biometrics, in press.
  21. Abuelezam N, McCormick A, Fussel T, Afriyie A, Wood R. DeGruttola V, Freedburg, M. Lipsitch M, Seage G. Can the heterosexual HIV epidemic be eliminated in South Africa using combination prevention? A modeling analysis” Am J Epidemiol (2016) 184 (3): 239-248. PMC4967594.
  22. Tendani Gaolathe, Kathleen E. Wirth, Molly Pretorius Holme, Joseph Makhema, Sikhulile Moyo,                                         Unoda Chakalisa, Etienne Kadima Yankinda, Quanhong Lei, Mompati Mmalane, Vlad Novitsky, Lillian Okui, Erik van Widenfelt, Kathleen M. Powis, Nealia Khan, Kara Bennett, Hermann Bussmann, Scott Dryden-Peterson, Refeletswe Lebelonyane, Shenaaz el-Halabi, Lisa A. Mills, Tafireyi Marukutira, Rui Wang, Eric J. Tchetgen Tchetgen, Victor DeGruttola, M. Essex, Shahin Lockman. Botswana’s Progress Toward Achieving the 2020 UNAIDS 90–90–90 Antiretroviral 1 Treatment and Virologic Suppression Goals: Results of a Population-Based Survey, Lancet HIV 2016 3(5) , e221–e230. PMC5146754.
  23. Prague M, Wang R, Stephens, A, Tchetgen Tchetgen E, DeGruttola V. Accounting for interactions and complex inter-subject dependency in estimating treatment effect in cluster randomized trials with missing outcomes, Biometrics, 2016, 72 (4) 1066–1077. SOFTWARE
  24. Oldenburg CE, Bärnighausen T, Tanser F, Iwuji CC, DeGruttola V, Seage GR, Mimiaga MJ, Mayer K, Pillay D, Harling G. Antiretroviral therapy to prevent HIV acquisition in serodiscordant couples in a hyperendemic community in rural South Africa.  Clin Infect Dis.  2016 Aug 15;63(4):548-54. doi: 10.1093/cid/ciw335. Epub 2016 May 20. PubMed PMID: 27208044; PubMed Central PMCID: PMC4967606.
  25. Carnegie, N, Wang R, DeGruttola V. Estimation of the overall treatment effect in the presence of interference in cluster-randomized trials of infectious disease prevention, Epidemiology Methods, 2016. (1) 57-68 DOI: 10.1515/em-2015-0016.
  26. Balzer L, Staples P, Onnela JP, DeGruttola V. Using network-based simulations and targeted maximum likelihood estimation to evaluate the effect of adding pre-exposure prophylaxis to an ongoing test-and-treat trial. Clinical Trials 2017 epub ahead of print. PMC5377920.
  27. Harling G, Prague M, Onnela JP, DeGruttola V. Leveraging contact network structure in the design of cluster randomized trials. Clinical Trials, 2017 14(1) 37-47. PMC5300908.
  28. Wang R and DeGruttola V. The use of permutation tests for the analysis of parallel and stepped-wedge cluster-randomized trials. Statistics in Medicine. 2017 Aug 15;36(18):2831-2843. doi: 10.1002/sim.7329. Epub 2017 May 2. PubMed PMID: 28464567; PubMed Central PMCID: PMC5507602.
  29. Goyal R and DeGruttola V, Inference on Network Statistics by Restricting the Network Space: Applications to Sexual History Data. Statistics in Medicine, to appear. Nihms885662
  30. Zhao R, Catalano P, DeGruttola V, and Michor F. Estimating Mono- and Bi-phasic Regression Parameters using a Mixture Piecewise Linear Bayesian Hierarchical Model. PLoS One, to appear.
  31. Prague M, Wang R, DeGruttola V. CRTgeeDR: an R package for Doubly Robust Generalized Estimating Equations Estimations in Cluster Randomized Trials with Missing Data. R journal to appear.
  32. Carnegie, Effects of contact network structure on epidemic transmission trees: implications for data required to estimate network structure. SIM Epub NIHMS 851386
  33. Balzer LJ, All generalizations are dangerous, even this one. Epidemiology 2017 PMC5488351.]
  34. Yang and Lok. A goodness-of-fit test for structureal nested mean models. Biometrika 2016, : PMC5152627.
  36. Novitsky V, Moyo S, Wang R, Gaseitsiwe S, Essex M. Deciphering multiplicity of HIV-1C infection: transmission of closely related multiple viral lineages. PLOS one, 11(11):e0166746. PMCID: PMC5125632.
  37. Moyo S, Wilkinson E, Vandormael A, Wang R, Weng J, Kotokwe KP, Gaseitsiwe S, Musonda R, Makhema J, Essex M, Engelbrecht S, de Oliveira T, Novitsky V. Pairwise diversity and tMRCA as potential markers for HIV infection recency. Medicine, 2017 Feb; 96(6):e6041. PMCID: PMC5313003