Publications
2018
Fong Y**, Shen X**, Ashley VC, Deal A, Seaton KE, Yu C, Grant SP, Ferrari G, deCamp A*, Bailer RT, Koup RA, Montefiori D, Haynes BF, Sarzotti-Kelsoe M, Graham BS, Carpp LN, Hammer SM, Sobieszczyk M, Karuna S, Swann E, DeJesus E, Mulligan M, Frank I, Buchbinder S, Novak RM, McElrath MJ, Kalams S, Keefer M, Frahm NA, Janes HE, Gilbert PB**, Tomaras GD**. "Vaccine-induced antibody responses modify the association between T-cell immune responses and HIV-1 infection risk in HVTN 505." J Infect Dis. 2018 Jan 8. doi: 10.1093/infdis/jiy008. [Epub ahead of print] **Contributed equally.
De Montigny S, Adamson B, Masse B, Garrison LP, Kublin JG, Gilbert PB, Dimitriv D. "Projected effectiveness and added value of HIV vaccination campaigns in South Africa: A modeling study." Scientific Reports), 8(1). https://doi.org/10.1038/s41598-018-24268-4
Lee U, Sun Y, Scheike T, Gilbert PB. "Analysis of generalized semiparametric regression models for cumulative incidence functions with missing covariate." Computational Statistics & Data Analysis, 122, 59-79.
Janes H,Corey L,Ramjee G,Carpp LN,Lombard C,Cohen MS, Gilbert PB, Gray GE. "Weighing the evidence of efficacy of oral PrEP for HIV prevention in women in southern Africa." AIDS Res Hum Retroviruses. 2018 May 6. doi: 10.1089/AID.2018.0031. [Epub ahead of print]
2017
Aiyegbo M, Shmelkov E, Dominguez L, Goger M, Battacharya S, deCamp A, Gilbert PB, Berman P, Cardozo T. "Peptide Targeted by Human Antibodies Associated With HIV Vaccine-Associated Protection Assumes a Dynamic α-Helical Structure." PLoS One. 2017;12(1). PMCID: PMC5249078.
Fu R, Gilbert PB. "Joint modeling of longitudinal and survival data with the Cox model and two-phase sampling." Lifetime Data Analysis. 2017;23(1):136-159. PMCID: PMC5035179.
Huang Y, Zhang L, Janes H, Frahm N, Isaac A, Kim J, Montefiori D, McElrath MJ, Tomaras GD, Gilbert PB. "Predictors of durable immune responses six months after the last vaccinations in preventative HIV vaccine trials." Vaccine. 2017;35(8):1184-93. PMID: 28131393.
Huang Y, Zhang L, Ledgerwood J, Gruneberg N, Bailer R, Isaacs A, Seaton K, Mayer KH, Capparelli E, Corey L, Gilbert PB. "Population pharmacokinetics analysis of VRC01, a broadly neutralizing HIV-1 monoclonal antibody, in healthy adults." mAbs. 2017 Apr3;1-9. PMID: 28368743
Gilbert PB, Excler JL, Tomaras GD, Carpp LN, Haynes BF, Liao HX, Montefiori DC, Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Tovanabutra S, Francis DP, Lee C, Sinangil F, Berman PW, Premsri N, Kunasol P, O’Connell RJ, Michael NL, Robb ML. "Antibody to HSV gD peptide induced by vaccination does not protect against HSV-2 infection in HSV-2 seronegative women." PLoS One. 2017 May 11;12(5). PMID: 28493891 PMCID: PMC5426618
Benkeser D, Carone M, Gilbert PB. "Improved estimation of the cumulative incidence of rare outcomes." Stat Med. 2017 Jul 2. Epub ahead of print.
Perez LG, Martinez DR, deCamp AC, Pinter A, Berman PW, Francis D, Sinangil F, Lee C, Greene K, Gao H, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, O’Connell RJ, Robb ML, Michael NL, Kim JH, Gibert PB, Montefiori DC. "V1V2-Specific Complement Activating Serum IgG as a Correlate of Reduced HIV-1 Infection Risk in RV144." PLoS One. 2017 Jul 5;12(7). PMID: 28678869.
Fiore-Gartland A, Kullman N, deCamp AC, Clenaghan G, Yang W, Magaret CA, Edlefsen PT, Gilbert PB. "SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials." Bioinformatics. 2017 Apr 4:btx168.
Janes, HE, Cohen KW, Frahm N, [et al including Gilbert PB]. "Higher T cell responses induced by DNA/rAd5 HIV-1 preventive vaccine are associated with lower HIV-1 infection risk in an efficacy trial." Journal of Infectious Diseases 2017 May (JID 2017:215)
deCamp A, Rolland M, Edlefsen P, [et al including Gilbert PB] . "Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120." PLoS One.
Moodie Z,Juraska M,Huang Y,Zhuang Y,Fong Y,Carpp LN,Self SG,Chambonneau L,Small R,Jackson N,Noriega F, Gilbert PB. "Neutralizing Antibody Correlates Analysis of Tetravalent Dengue Vaccine Efficacy Trials in Asia and Latin America." Journal of Infectious Diseases 2017 December ( jix609)
2016
Boeckh M, Gilbert PB. "Search continues for a CMV vaccine for transplant recipients." The Lancet Haematology. 2016;3(2):e58-9. PMID: 26853642.
Churchyard G, Mlisana K, Karuna S, Williamson AL, Williamson C, Morris L, Tomaras G, De Rosa SE, Gilbert PB, Gu N, Mkhize N, Hermanus T, Allen M, Pensiero M, Barnett S, Gray G, Bekker LG, Montefiori DC, Kublin J, Corey L and the NIAID-funded HIV Vaccine Trials Network. "Sequential immunization with gp140 boosts immune responses primed by Modified Vaccinia Ankara or DNA in HIV-uninfected South African participants." PLoS One. 2016;11(9):e0161753. PMCID: PMC5008759.
Fiore-Gartland A, Manso BA, Friedrich DP, Gabriel EE, Finak G, Moodie Z, Hertz T, De Rosa SC, Frahm N, Gilbert PB, McElrath MJ. "Pooled-peptide epitope mapping strategies are efficient and highly sensitive: an evaluation of methods for identifying human T cell epitope specificities in large-scale HIV vaccine efficacy trials." PLoS One. 2016;11(2):e0147812. PMCID: PMC4749288.
Fong Y, Di C, Huang Y, Gilbert PB. "Model-robust inference for continuous change point models." Biometrics. 2016. PMID: 27858965. Epublished ahead of print.
Gilbert PB, Huang Y. "Predicting overall vaccine efficacy in a new setting by re-calibrating baseline covariate and intermediate response endpoint effect modifiers of Type-Specific vaccine efficacy." Epidemiological Methods. 2016;5(1).
Gilbert PB, Huang Y, Janes HE. "Modeling HIV vaccine trials of the future." Current Opinion in HIV&AIDS. 2016; 11(6):620-627. PMCID: PMC5077275.
Gilbert PB, Janes HE, Huang Y. "Power/sample size calculations for assessing correlates of risk in clinical efficacy trials." Statistics in Medicine. 2016;35(21):45-59. PMCID: PMC4965346.
Hanscom B, Janes H, Guarino P, Huang Y, Brown E, Chen YQ, Hammer S, Gilbert PB, Donnell D. "Preventing HIV-1 infection in women using oral Pre-Exposure Prophylaxis: A Meta-analysis of current evidence." Journal of Acquired Immune Deficiency Syndromes. 2016;83(5):606-608. PMCID: PMC5175411.
Hertz T, Logan MG, Rolland M, Magaret CA, Rademeyer C, Fiore-Gartland A, Edlefsen PT, DeCamp A, Ahmed H, Ngandu N, Larsen BB, Frahm N, Marais J, Thebus R, Geraghty D, Hural J, Corey L, Kublin J, Gray G, McElrath MJ, Mullin JI, Gilbert PB, Williamson C. "A study of vaccine-induced immune pressure on breakthrough infections in the Phambili Phase 2b HIV-1 vaccine efficacy trial." Vaccine. 2016;34(47):5792-5801. PMID: 27756485.
Huang Y, DiazGranados C, Janes H, Huang Y, deCamp A, Metch B, Grant S, Sanchez B, Phogat S, Koutsoukos M, Kanesa-Thasan N, Bourguignon P, Collard A, Buchbinder S, Tomaras GD, McElrath MJ, Kublin J, Corey L, Gilbert PB. "Selection of HIV vaccine candidates for concurrent testing in an efficacy trial." Current Opinion in Virology. 2016;17:57-65. PMCID: PMC4902743.
Huang Y, Gilbert PB, Fu R, Janes HE. "Statistical methods for down-selection of treatment regimens based on multiple endpoints, with application to HIV vaccine trials." Biostatistics. 2016. PMID: 27649715. Epublished ahead of print.
Juraska M, Gilbert PB. "Mark-specific hazard ratio model with missing multivariate marks." Lifetime Data Analysis. 2016;22(4):606-25. PMCID: PMC4848257.
Peng X, Li SS, Gilbert PB, Geraghty DE, Katze MG. "FCGR2C polymorphisms associated with HIV-1 vaccine protection are linked to altered expression of Fc-γ receptors in human B cells." PLoS One. 2016;11(3):e0152425. PMCID: PMC4807760.
Qi L, Sun Y, Gilbert PB. "Generalized semiparametric varying-coefficient model for longitudinal data with applications to adaptive treatment randomization." Biometrics. 2016. PMID: 27918612. Epublished ahead of print.
Sun Y, Li M, Gilbert PB. "Goodness-of-fit test of the stratified mark-specific proportional hazards model with continuous mark." Computational Statistics and Data Analysis. 2016;93:348-358. PMCID: PMC4598956.
Sun Y, Qian X, Shou Q, Gilbert PB. "Analysis of two-phase sampling data with semiparametric additive hazards models." Lifetime Data Analysis. 2016. PMID: 26995733. Epublished ahead of print.
Yang G, Sun Y, Gilbert PB. "Estimation of stratified mark-specific proportional hazards models under two-phase sampling with application to HIV vaccine efficacy trials." Statistics in Biosciences. 2016. Epublished ahead of print.
2015
Corey L, Gilbert PB, Tomaras G, Haynes BF, Pantaleo G, Fauci AS. "Immune correlates of vaccine protection against HIV-1 acquisition." Science Translational Medicine. 2015;21;7(310):310rv7. PMID: 26491081.
Edlefsen PT, Rolland M, Hertz T, Tovanabutra S, Gartland AJ, deCamp AC, Magaret CA, Ahmed H, Gottardo R, Juraska M, McCoy C, Larsen BB, Sanders-Buell E, Carrico C, Menis S, Bose M, Team RVS, Arroyo MA, O'Connell RJ, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Robb ML, Kirys T, Georgiev IS, Kwong PD, Scheffler K, Pond SL, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB. "Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial." PLoS Computational Biology. 2015;11(2):e1003973. PMCID: PMC4315437.
Fong Y, Gilbert PB. "Calibration weighted estimation of semiparametric transformation models for two-phase sampling." Statistics in Medicine. 2015;34(10):1695-707. PMCID: PMC4390487.
Fuchs JD, Bart PA, Frahm N, Morgan C, Gilbert PB, Kochar N, DeRosa S, Tomaras G, Wagner T, Baden L, Koblin B, Rouphael N, Kalams S, Keefer M, Goepfert P, Sobieszczyk M, Mayer K, Swann E, Liao H-X, Haynes B, Graham B, McElrath MJ for the NIAID HIV Vaccine Trials Network. "Safety and immunogenicity of a recombinant adenovirus serotype 35-vectored HIV-1 vaccine in adenovirus serotype 5 seronegative and seropositive individuals." Journal of AIDS and Clinical Research. 2015;6(5). PMCID: PMC4648371.
Gabriel EE, Sachs MC, Gilbert PB. "Comparing and combining biomarkers as principle surrogates for time-to-event clinical endpoints." Statistics in Medicine. 2015;34(3):381-95. PMID: 25352131.
Gilbert PB, Gabriel EE, Huang Y, Chan ISF. "Surrogate endpoint evaluation: Principal surrogate criteria and the prentice definition." Journal of Causal Inference. 2015;3(2):157-175.
Gilbert PB, Sun Y. "Inferences on relative failure rates in stratified mark-specific proportional hazards models with missing marks, with application to human immunodeficiency virus vaccine efficacy trials." Journal of the Royal Statistical Society: Series C (Applied Statistics). 2015;64(1):49-73. PMCID: PMC4310507.
Huang Y, Follmann D, Nason M, Zhang L, Huang Y, Mehrotra D, Moodie Z, Metch B, Janes HE, Keefer M, Churchyard G, Robb M, Fast PE, Duerr A, McElrath MJ, Corey L, Mascola JR, Graham BS, Sobieszczyk M, Kublin J, Robertson M, Hammer SM, Gray GE, Buchbinder S, Gilbert PB. "Effect of rAd5-vector HIV-1 preventive vaccines on HIV-1 acquisition: a participant-level meta-analysis of randomized trials." PLoS One. 2015; 10(9):e0136626. PMCID: PMC4558095.
Huang Y, Karuna ST, Janes H, Frahm N, Nason M, Edlefsen PT, Kublin JG, Corey L, McElrath MJ, Gilbert PB. "Use of placebos in Phase 1 preventive HIV vaccine clinical trials." Vaccine. 2015;33(6):749-52. PMCID: PMC4554766.
Janes H, Herbeck JT, Tovanabutra S, Thomas R, Frahm N, Duerr A, Hural J, Corey L, Self SG, Buchbinder S, McElrath MJ, O'Connell RJ, Paris RM, Rerks-Ngarm S, Nitayaphan S, Pitisuttihum P, Kaewkungwal J, Robb ML, Michael NL, Mullins JI, Kim JH, Gilbert PB, Rolland M. "HIV-1 infections with multiple founders are associated with higher viral loads than infections with single founders." Nature Medicine. 2015;21(10):1139-41. PMCID: PMC4598284.
Juraska M, Gilbert PB. "Mark-specific hazard ratio model with missing multivariate marks." Lifetime Data Analysis. PMID: 26511033. Epublished ahead of print.
Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart P-A, Pantaleo G, Tomaras GD, Rerks-Ngarm S, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Michael NL, Kim JH, Robb ML, O'Connell RJ, Karasavvas N, Gilbert PB, DeRosa S, McElrath MJ, Gottardo R. "COMPASS identifies T-cell subsets correlated with clinical outcomes." Nature Biotechnology. 2015;33(6):610-16. PMCID: PMC4569006.
Moodie Z, Metch B, Bekker LG, Churchyard G, Nchabeleng M, Mlisana K, Laher F ,Roux S, Mngadi K, Innes C, Mathebula M, Allen M, Bentley C, Gilbert PB, Robertson M,Kublin J, Corey L, Gray G. "Continued follow-up of Phambili Phase 2b randomized HIV-1 vaccine trial participants supports increased HIV-1 acquisition among vaccinated men." PLoS One. 2015;10(9):e0137666. PMCID: PMC4569275.
Neafsey DE, Juraska M, Bedford T, Benkeser D, Valim C, Griggs A, Lievens M, Abdulla S, Adjei S, Agbenyega T, Agnandji ST, Aide P, Anderson S, Anson D, Aponte JJ, Asante KP, Ejon P, Birkett AJ, Bruls M, Connolly KM, D’Alessandro U, Dobao C, Gesase S, Greenwood B, Grimsby J, Tinto H, Hamel MJ, Hoffman I, Kamthunzi S, Kremsner PG, Leach A, Lell B, Lennon NJ, Lusingu J, Marsh K, Martinson F, Molel JT, Moss EL, Njuguna P, Ockenhouse CF, Ragama Oqutu B, Otieno W, Otieno L, Otieno K, Owusu-AgyeiS, Park DJ, Pellé K, Robbins D, Russ C, Ryan EM, Sacarial J, Sogoloff B, SorghoH, Tanner M, Theander T, Valea I, Volkman SK, Yu Q, Lapierre D, Birren BW, Gilbert PB, Wirth DF. "Genetic diversity and protective efficacy of the RTS,S/AS01 Malaria vaccine." New England Journal of Medicine. 2015;373(21):2025-2037. PMID: 26488565.
Permar SR, Fong Y, Vandergrift N, Fouda GG, Gilbert PB, Parks R, Jaeger FH, Pollara J, Martelli A, Liebl BE, Lloyd K, Yates NL, Overman RG, Shen X, Whitaker K, Chen H, Pritchett J, Solomon E, Friberg E, Marshall DJ, Whitesides JF, Gurley TC, Von Holle T, Martinez DR, Cai F, Kumar A, Xia SM, Lu X, Louzao R, Wilkes S, Datta S, Sarzotti-Kelsoe M, Liao HX, Ferrari G, Alam SM, Montefiori DC, Denny TN, Moody MA, Tomaras GD, Gao F, Haynes BF. "Maternal HIV-1 envelope-specific antibody responses and reduced risk of perinatal transmission." The Journal of Clinical Investigation. 2015;125(7):2702-6. PMID: 26053661.
Prentice HA, Tomaras GD, Geraghty DE, Apps R, Fong Y, Ehrenberg PK, Rolland M, Kijak GH, Krebs SJ, Nelson W, DeCamp A, Shen X, Yates NL, Zolla-Pazner S, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Ferrari G, McElrath MJ, Montefiori DC, Bailer RT, Koup RA, O'Connell RJ, Robb ML, Michael NL, Gilbert PB, Kim JH, Thomas R. "HLA class II genes modulate vaccine-induced antibody responses to affect HIV-1 acquisition." Science Translational Medicine. 2015;7(296):296ra112. PMID: 26180102.
Sun Y, Li M, Gilbert PB. "Goodness-of-fit test of the stratified mark-specific proportional hazards model with continuous mark." Computational Statistics and Data Analysis. 2015. PMCID: PMC4598956. Epublished ahead of print.
Vasan S, Rerks-Ngarm S, Gilbert PB, Haynes B, Nitayapan S, Pitisuttihum P, Kaewkungwal J, Excler JL, Robb M, Michael N, Kim J, O'Connell R. "Letter to the Editor on: The RV144 vaccine regimen was not associated with enhancement of infection." Human Vaccines & Immunotherapeutics. 2015;11(4):1036-7. PMID: 25746053.
Williams WB, Liao HX, Moody MA, Kepler TB, Alam SM, Gao F, Wiehe K, Trama AM, Jones K, Zhang R, Song H, Marshall DJ, Whitesides JF, Sawatzki K, Hua A, Liu P, Tay MZ, Seaton KE, Shen X, Foulger A, Lloyd KE, Parks R, Pollara J, Ferrari G, Yu JS, Vandergrift N, Montefiori DC, Sobieszczyk ME, Hammer S, Karuna S, Gilbert PB, Grove D, Grunenberg N, McElrath MJ, Mascola JR, Koup RA, Corey L, Nabel GJ, Morgan C, Churchyard G, Maenza J, Keefer M, Graham BS, Baden LR, Tomaras GD, Haynes BF. "HIV-1 VACCINES. Diversion of HIV-1 vaccine-induced immunity by gp41-microbiota cross-reactive antibodies." Science. 2015;349(6249):aab1253. PMCID: PMC4562404.
2014
Bart P, Huang Y, Karuna ST, Chappuis S, Gaillard J, Kochar N, Shen X, Allen MA, Ding S, Hural J, Liao HX, Haynes BF, Graham BS, Gilbert PB, McElrath MJ, Montefiori DC, Tomaras GD, Pantaleo G, Frahm N. "HIV-specific humoral responses benefit from stronger prime in phase 1b clinical trial." Journal of Clinical Investigation. 2014;124(11):4843-56. PMCID: PMC4347219.
Dai JY, Li SS, Gilbert PB. "Case-only method for cause-specific hazards models with application to assessing differential vaccine efficacy by viral and host genetics." Biostatistics. 2014;15(1):196-203. PMCID: PMC3862206.
Frey S, Peiperl L, McElrath MJ, Goepfert P, Keefer M, Baden L, Lally M, Blattner B, Harro C, Hammer S, Gorse G, Mayer K, Hural J, Tomaras G, Levy Y, Gilbert PB, deCamp A, Russell N, Elizaga M, Allen M, Corey L. "Phase I/II randomized trial of safety and immunogenicity of LIPO-5 alone, ALVAC-HIV (vCP1452) alone, and ALVAC-HIV (vCP1452) prime/LIPO-5 boost in healthy, HIV-1 uninfected adult participants." Clinical and Vaccine Immunology. 2014;21(11):1589-99. PMCID: PMC4248765.
Gabriel EE, Gilbert PB. "Evaluating principal surrogate endpoints with time-to-event data accounting for time-varying treatment efficacy." Biostatistics. 2014;15(2):251-65. PMCID: PMC3944974.
Gartland A, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty D, Kijak GH, Edlefsen PT, Frahm N, Larsen BB, Tovanabutra S, Sanders-Buell E, deCamp AC, Magaret CA, Ahmed H, Goodridge JP, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O’Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O’Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, Sidney J, Sette A, Zolla-Pazner S, Montefiori D, McElrath MJ, Mullins JI, Kim JH, Gilbert PB, Hertz T. "Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial." Journal of Virology. 2014;88(15):8242-55. PMCID: PMC4135964.
Gilbert PB*, Gabriel EE*, Miao X, Li X, Su SC, Parrino J, Chan IS. "Fold rise in antibody titers by measured by glycoprotein-based enzyme-linked immunosorbent assay is an excellent correlate of protection for a herpes zoster vaccine, demonstrated via the vaccine efficacy curve." Journal of Infectious Diseases. 2014;210(10):1573-81. PMCID: PMC4215071. *Contributed equally.
Gilbert PB, Yu X, Rotnitzky A. "Optimal auxiliary-covariate-based two-phase sampling design for semiparametric efficient estimation of a mean or mean difference, with application to clinical trials." Statistics in Medicine. 2014;33(6):901-17. PMCID: PMC4021041.
Gray GE, Moodie Z, Metch B, Gilbert PB, Bekker LG, Churchyard G, Nchabeleng M, Mlisana K, Laher F, Roux S, Mngadi K, Innes C, Mathebula M, Allen M, McElrath MJ, Robertson M, Kublin J, Corey L, on behalf of the HVTN 503/Phambili study team. "Recombinant adenovirus type 5 HIV gag/pol/nef vaccine in South Africa: unblinded, long-term follow-up of the phase 2b HVTN 503/Phambili study." The Lancet Infectious Diseases. 2014;14(5):388-96. PMCID: PMC4174314.
Huang Y, Duerr A, Frahm N, Zhang L, Moodie Z, De Rosa S, McElrath MJ, Gilbert PB. "Immune-correlates analysis of an HIV-1 vaccine efficacy trial reveals an association of nonspecific interferon-gamma secretion with increased HIV-1 infection risk: A cohort-based modeling study." PLoS One. 2014;9(11):e108631. PMCID: PMC4219669.
Li SS*, Gilbert PB*, Tomaras GD, Kijak G, Ferrari G, Thomas R, Pyo CW, Zolla-Pazner S, Montefiori D, Liao HX, Nabel G, Pinter A, Evans DT, Gottardo R, Dai JY, Janes H, Morris D, Fong Y, Edlefsen PT, Li F, Frahm N, Alpert MD, Prentice H, Rerks-Ngarm S, Pitisuttithum P, Kaewkungwal J, Nitayaphan S, Robb ML, O'Connell RJ, Haynes BF, Michael NL, Kim JH, McElrath MJ, Geraghty DE. "FCGR2C polymorphisms associate with HIV-1 vaccine protection in RV144 trial." Journal of Clinical Investigation. 2014;124(9):3879-90. PMCID: PMC4151214. *Contributed equally.
Richardson A, Hudgens MG, Gilbert PB, Fine JP. "Nonparametric bounds and sensitivity analysis of treatment effects." Statistical Science. 2014;29(4):596-618. PMCID: PMC4317325.
Scott J, deCamp A, Juraska M, Fay MP, Gilbert PB. "Finite-sample corrected generalized estimating equation of population average treatment effects in stepped wedge cluster randomized trials." Statistical Methods in Medical Research. 2014;0962280214552092. PMCID: PMC4411204.
Talley AK, Healy SA, Finney OC, Murphy SC, Kublin J, Salas CJ, Lundebjerg S, Gilbert PB, Van Voorhis WC, Whisler J, Wang R, Ockenhouse CF, Heppner DG, Kappe SH, Duffy PE. "Safety and comparability of controlled human Plasmodium falciparum infection by mosquito bite in malaria-naive subjects at a new facility for sporozoite challenge." PLoS One. 2014;9(11):e109654. PMCID: PMC4236046.
Yates NL, Liao HX, Fong Y, deCamp A, Vandergrift NA, Williams WT, Alam SM, Ferrari G, Yang ZY, Seaton KE, Berman PW, Alpert MD, Evans DT, O'Connell RJ, Francis D, Sinangil F, Lee C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Pinter A, Zolla-Pazner S, Gilbert PB, Nabel GJ, Michael NL, Kim JH, Montefiori DC, Haynes BF, Tomaras GD. "Vaccine-induced env V1-V2 IgG3 correlates with lower HIV-1 infection risk and declines soon after vaccination." Science Translational Medicine. 2014;6(228):228ra39. PMCID: PMC4116665.
Zolla-Pazner S, deCamp A, Gilbert PB, Williams C, Yates NL, Williams WT, Howington R, Fong Y, Morris DE, Soderberg KA, Irene C, Reichman C, Pinter A, Parks R, Pitisuttithum P, Kaewkungwal J, Rerks-Ngarm S, Nitayaphan S, Andrews C, O'Connell RJ, Yang ZY, Nabel GJ, Kim JH, Michael NL, Montefiori DC, Liao HX, Haynes BF, Tomaras GD. "Vaccine-induced IgG antibodies to V1V2 regions of multiple HIV-1 subtypes correlate with decreased risk of HIV-1 infection." PLoS One. 2014;9(2):e87572. PMCID: PMC3913641.
Zolla-Pazner S, Edlefsen PT, Rolland M, Kong XP, deCamp A, Gottardo R, Williams C, Tovanabutra S, Sharpe-Cohen S, Mullins JI, deSouza MS, Karasavvas N, Nitayaphan S, Rerks-Ngarm S, Pitisuttihum P, Kaewkungwal J, O'Connell RJ, Robb ML, Michael NL, Kim JH, Gilbert PB. "Vaccine-induced human antibodies specific for the third variable region of HIV-1 gp120 impose immune pressure on infecting viruses." EBioMedicine. 2014;1(1):37-45. PMCID: PMC4293639.
2013
Dai JY, Gilbert PB, Hughes JP, Brown ER. "Estimating the efficacy of preexposure prophylaxis for HIV prevention among participants with a threshold level of drug concentration." American Journal of Epidemiology. 2013;177(3):256-63. PMCID: PMC3577049.
Duerr A, Huang Y, Buchbinder S, Coombs RW, Sanchez J, del Rio C, Casapia M, Santiago S, Huang Y, Gilbert PB, Corey L, Robertson MN. "Reply to Richie and Villasante." Journal of Infectious Diseases. 2013;207(4):690-2. PMCID: PMC4200031.
Edlefsen PT, Gilbert PB, Rolland M. "Sieve analysis in HIV-1 vaccine efficacy trials." Current Opinion in HIV and AIDS. 2013;8(5):432-6. PMCID: PMC3863593.
Fong Y, Sebestyen K, Yu X, Gilbert PB, Self SG. "nCal: an R package for non-linear calibration." Bioinformatics. 2013;29(20):2653-4. PMCID: PMC3789552.
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(503):789-800. PMCID: PMC3811958.
Gottardo R, Bailer RT, Korber BT, Gnanakaran S, Phillips J, Shen X, Tomaras GD, Turk E, Imholte G, Eckler L, Wenschuh H, Zerweck J, Greene K, Gao H, Berman PW, Francis D, Sinangil F, Lee C, Nitayaphan S, Rerks-Ngarm S, Kaewkungwal J, Pitisuttithum P, Tartaglia J, Robb ML, Michael NL, Kim JH, Zolla-Pazner S, Haynes BF, Mascola JR, Self S, Gilbert PB, Montefiori DC. "Plasma IgG to linear epitopes in the V2 and V3 regions of HIV-1 gp120 correlate with a reduced risk of infection in the RV144 vaccine efficacy trial." PLoS One. 2013;8(9):e75665. PMCID: PMC3784573.
Hammer SM, Sobieszczyk ME, Janes H, Karuna ST, Mulligan MJ, Grove D, Koblin BA, Buchbinder SP, Keefer MC, Tomaras GD, Frahm N, Hural J, Anude C, Graham BS, Enama ME, Adams E, DeJesus E, Novak RM, Frank I, Bentley C, Ramirez S, Fu R, Koup RA, Mascola J, Nabel GJ, Montefiori DC, Kublin J, McElrath MJ, Corey L, Gilbert PB, on behalf of the HIV Vaccine Trials Network 505 Study Team. "Efficacy trial of a DNA/rAd5 HIV-1 preventive vaccine." New England Journal of Medicine. 2013;369(22):2083-2092. PMCID: PMC4030634.
Hertz T, Ahmed H, Friedrich DP, Casimiro DR, Self SG, Corey L, McElrath MJ, Buchbinder S, Horton H, Frahm N, Robertson MN, Graham BS, Gilbert PB. "HIV-1 Vaccine-induced T-Cell reponse cluster in epitope hotspots that differ from those induced in natural infection with HIV-1." PLoS Pathogens. 2013;9(6):e1003404. PMCID: PMC3688560.
Huang Y, Gilbert PB, Wolfson J. "Design and estimation for evaluating principal surrogate markers in vaccine trials." Biometrics. 2013;69(2):301-9. PMCID: PMC3713795.
Janes H, Friedrich DP, Krambrink A, Smith RJ, Kallas EG, Horton H, Casimiro DR, Carrington M, Geraghty DE, Gilbert PB, McElrath MJ, Frahm N. "Vaccine-induced gag-specific T cells are associated with reduced viremia after HIV-1 infection." Journal of Infectious Diseases. 2013;208(8):1231-9. PMCID: PMC3778967.
Janes H, Gilbert PB, Buchbinder S, Kublin J, Sobieszczyk ME, Hammer SM. "In pursuit of an HIV vaccine: designing efficacy trials in the context of partially effective nonvaccine prevention modalities." AIDS Research and Human Retroviruses. 2013;29(11):1513-23. PMCID: PMC3809388.
Juraska M, Gilbert PB. "Mark-specific hazard ratio model with multivariate continuous marks: an application to vaccine efficacy." Biometrics. 2013;69(2):328-37. PMCID: PMC3940058.
Liu P, Yates NL, Shen X, Bonsignori M, Moody MA, Liao HX, Fong Y, Alam SM, Overman RG, Denny T, Ferrari G, Ochsenbauer C, Kappes JC, Polonis VR, Pitisuttithum P, Kaewkungwal J, Nitayaphan S, Rerks-Ngarm S, Montefiori DC, Gilbert PB, Michael NL, Kim JH, Haynes BF, Tomaras GD. "Infectious virion capture by HIV-1 gp120-specific IgG from RV144 vaccinees." Journal of Virology. 2013;87(14):7828-36. PMCID: PMC3700223.
Rerks-Ngarm S, Paris RM, Chunsutthiwat S, Premsri N, Namwat C, Bowonwatanuwong C, Li SS, Kaewkungkal J, Trichavaroj R, Churikanont N, de Souza MS, Andrews C, Francis D, Adams E, Flores J, Gurunathan S, Tartaglia J, O'Connell RJ, Eamsila C, Nitayaphan S, Ngauy V, Thongcharoen P, Kunasol P, Michael NL, Robb ML, Gilbert PB, Kim JH. "Extended evaluation of the virologic, immunologic, and clinical course of volunteers who acquired HIV-1 infection in a phase III vaccine trial of ALVAC-HIV and AIDSVAX B/E." Journal of Infectious Diseases. 2013;207(8):1195-205. PMID: 22837492.
Rolland M, Manocheewa S, Swain JV, Lanxon-Cookson EC, Kim M, Westfall DH, Larsen BB, Gilbert PB, Mullins JI. "HIV-1 conserved-element vaccines: relationship between sequence conservation and replicative capacity. Journal of Virology." 2013;87(10):5461-7. PMCID: PMC3648173.
Sun Y, Li M, Gilbert PB. "Mark-specific proportional hazards model with multivariate continuous marks and its application to HIV vaccine efficacy trials." Biostatistics. 2013;14(1):60-74. PMCID: PMC3520499.
Tomaras GD, Ferrari G, Shen X, Alam SM, Liao HX, Pollara J, Bonsignori M, Moody MA, Fong Y, Chen X, Poling B, Nicholson CO, Zhang R, Lu X, Parks R, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Gilbert PB, Kim JH, Michael NL, Montefiori DC, Haynes BF. "Vaccine-induced plasma IgA specific for the C1 region of the HIV-1 envelope blocks binding and effector function of IgG." Proceedings of the National Academy of Sciences of the United States of America. 2013;110(22):9019-24. PMCID: PMC3670311.
Zolla-Pazner S, deCamp AC, Cardozo T, Karasavvas N, Gottardo R, Williams C, Morris DE, Tomaras G, Rao M, Billings E, Berman P, Shen X, Andrews C, O'Connell RJ, Ngauy V, Nitayaphan S, de Souza M, Korber B, Koup R, Bailer RT, Mascola JR, Pinter A, Montefiori D, Haynes BF, Robb ML, Rerks-Ngarm S, Michael NL, Gilbert PB, Kim JH. "Analysis of V2 antibody responses induced in vaccinees in the ALVAC/AIDSVAX HIV-1 vaccine efficacy trial." PLoS One. 2013;8(1):e53629. PMCID: PMD3547933.
2012
Bonsignori M, Pollara J, Moody MA, Alpert MD, Chen X, Hwang KK, Gilbert PB, Huang Y, Gurley TC, Kozink DM, Marshall DJ, Whitesides JF, Tsao CY, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Kim JH, Michael NL, Tomaras GD, Montefiori DC, Lewis GK, DeVico A, Evans DT, Ferrari G, Liao HX, Haynes BF. "Antibody-dependent cellular cytotoxicity-mediating antibodies from an HIV-1 vaccine efficacy trial target multiple epitopes and preferentially use the VH1 gene family." Journal of Virology. 2012;86(21):11521-32. PMCID: PMC3486290.
Dai JY, Gilbert PB, Masse BR. "Partially hidden Markov model for time-varying principal stratification in HIV prevention trials. Journal of the American Statistical Association." 2012;107(497):52-65. PMCID: PMC3649016.
Duerr A, Huang Y, Buchbinder S, Coombs RW, Sanchez J, del Rio C, Casapia M, Santiago S, Gilbert PB, Corey L, Robertson MN, Step HST. "Extended follow-up confirms early vaccine-enhanced risk of HIV acquisition and demonstrates waning effect over time among participants in a randomized trial of recombinant adenovirus HIV vaccine (Step Study)." Journal of Infectious Diseases. 2012;206(2):258-66. PMCID: PMC3490694.
Fuchs JD, Morgan C, Bart P, Kochar N, Frahm N, Swann E, Gilbert PB, DeRosa S, Graham B, Nabel G, Liao H, Haynes B, Tomaras G. "DNA and recombinant adenovirus serotype 35 and 5 preventive HIV-1 vaccines with Env A inserts elicit cross-clade binding and V1V2 antibodies." Retrovirology. 2012;9(Suppl 2): P136. PMID: PMC3442017.
Haynes BF, Gilbert PB, McElrath MJ, Zolla-Pazner S, Tomaras GD, Alam SM, Evans DT, Montefiori DC, Karnasuta C, Sutthent R, Liao HX, DeVico AL, Lewis GK, Williams C, Pinter A, Fong Y, Janes H, deCamp A, Huang Y, Rao M, Billings E, Karasavvas N, Robb ML, Ngauy V, de Souza MS, Paris R, Ferrari G, Bailer RT, Soderberg KA, Andrews C, Berman PW, Frahm N, De Rosa SC, Alpert MD, Yates NL, Shen X, Koup RA, Pitisuttithum P, Kaewkungwal J, Nitayaphan S, Rerks-Ngarm S, Michael NL, Kim JH. "Immune-correlates analysis of an HIV-1 vaccine efficacy trial." New England Journal of Medicine. 2012;366(14):1275-86. PMCID: PMC3371689.
Huang Y, Gilbert PB, Janes H. "Assessing treatment-selection markers using a potential outcomes framework." Biometrics. 2012;68(3):687-96. PMCID: PMC3417090.
Janes H, Frahm N, deCamp A, Rolland M, Gabriel E, Wolfson J, Hertz T, Kallas E, Goepfert P, Friedrich DP, Corey L, Mullins JI, McElrath MJ, Gilbert PB. "MRKAd5 HIV-1 Gag/Pol/Nef vaccine-induced T-cell responses inadequately predict distance of breakthrough HIV-1 sequences to the vaccine or viral load." PLoS One. 2012;7(8):e43396. PMCID: PMC3428369.
Karasavvas N, Billings E, Rao M, Williams C, Zolla-Pazner S, Bailer RT, Koup RA, Madnote S, Arworn D, Shen X, Tomaras GD, Currier JR, Jiang M, Magaret C, Andrews C, Gottardo R, Gilbert PB, Cardozo TJ, Rerks-Ngarm S, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Paris R, Greene K, Gao H, Gurunathan S, Tartaglia J, Sinangil F, Korber BT, Montefiori DC, Mascola JR, Robb ML, Haynes BF, Ngauy V, Michael NL, Kim JH, de Souza MS, for the MOPH TAVEG Collaboration. "The Thai phase III HIV type 1 vaccine trial (RV144) regimen induces antibodies that target conserved regions within the V2 loop of gp120. AIDS Research and Human Retroviruses." 2012;28(11):1444-57. PMCID: PMC3484815.
Kublin JG, Morgan CA, Day TA, Gilbert PB, Self SG, McElrath MJ, Corey L. "HIV Vaccine Trials Network: activities and achievements of the first decade and beyond." Clinical Investigation. 2012;2(3):245-54. PMCID: PMC3521567.
Montefiori DC, Karnasuta C, Huang Y, Ahmed H, Gilbert PB, de Souza MS, McLinden R, Tovanabutra S, Laurence-Chenine A, Sanders-Buell E, Moody MA, Bonsignori M, Ochsenbauer C, Kappes J, Tang H, Greene K, Gao H, LaBranche CC, Andrews C, Polonis VR, Rerks-Ngarm S, Pitisuttithum P, Nitayaphan S, Kaewkungwal J, Self SG, Berman PW, Francis D, Sinangil F, Lee C, Tartaglia J, Robb ML, Haynes BF, Michael NL, Kim JH. "Magnitude and breadth of the neutralizing antibody response in the RV144 and Vax003 HIV-1 vaccine efficacy trials." Journal of Infectious Diseases. 2012;206(3):431-41. PMCID: PMC3392187.
Plotkin SA, Gilbert PB. "Nomenclature for immune correlates of protection after vaccination." Clinical Infectious Diseases. 2012;54(11):1615-7. PMCID: PMC3348952.
Qureshi H, Ma ZM, Huang Y, Hodge G, Thomas MA, DiPasquale J, DeSilva V, Fritts L, Bett AJ, Casimiro DR, Shiver JW, Robert-Guroff M, Robertson MN, McChesney MB, Gilbert PB, Miller CJ. "Low-dose penile SIVmac251 exposure of rhesus macaques infected with adenovirus type 5 (Ad5) and then immunized with a replication-defective Ad5-based SIV gag/pol/nef vaccine recapitulates the results of the phase IIb step trial of a similar HIV-1 vaccine." Journal of Virology. 2012;86(4):2239-50. PMCID: PMC3302390.
Robb ML, Rerks-Ngarm S, Nitayaphan S, Pitisuttithum P, Kaewkungwal J, Kunasol P, Khamboonruang C, Thongcharoen P, Morgan P, Benenson M, Paris RM, Chiu J, Adams E, Francis D, Gurunathan S, Tartaglia J, Gilbert PB, Stablein D, Michael NL, Kim JH. "Risk behaviour and time as covariates for efficacy of the HIV vaccine regimen ALVAC-HIV (vCP1521) and AIDSVAX B/E: a post-hoc analysis of the Thai phase 3 efficacy trial RV 144." Lancet Infectious Diseases. 2012;12(7):531-7. PMCID: PMC3530398.
Rolland M*, Edlefsen PT*, Larsen BB, Tovanabutra S, Sanders-Buell E, Hertz T, deCamp AC, Carrico C, Menis S, Magaret CA, Ahmed H, Juraska M, Chen L, Konopa P, Nariya S, Stoddard JN, Wong K, Zhao H, Deng W, Maust BS, Bose M, Howell S, Bates A, Lazzaro M, O'Sullivan A, Lei E, Bradfield A, Ibitamuno G, Assawadarachai V, O'Connell RJ, deSouza MS, Nitayaphan S, Rerks-Ngarm S, Robb ML, McLellan JS, Georgiev I, Kwong PD, Carlson JM, Michael NL, Schief WR, Gilbert PB*, Mullins JI*, Kim JH*. "Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2." Nature. 2012;490(7420):417-20. PMCID: PMC3551291. *Contributed equally.
Rolland M, Gilbert PB. "Evaluating immune correlates in HIV type 1 vaccine efficacy trials: what RV144 may provide." AIDS Research and Human Retroviruses. 2012;28(4):400-4. PMCID: PMC3316118.
Sindhi R, Ashokkumar C, Higgs BW, Gilbert PB, Sun Q, Ranganathan S, Jaffe R, Snyder S, Ningappa M, Soltys KA, Bond GJ, Mazariegos GV, Abu-Elmagd K, Zeevi A. "Allospecific CD154 + T-cytotoxic memory cells as potential surrogate for rejection risk in pediatric intestine transplantation." Pediatric Transplantation. 2012;16(1):83-91. PMID: 22122074.
Sun Y, Gilbert PB. "Estimation of stratified mark-specific proportional hazards models with missing marks." Scandinavian Journal of Statistics, Theory and Applications. 2012;39(1):34-52. PMCID: PMC3601495.
Sun Y, Wang HJ, Gilbert PB. "Quantile regression for competing risks data with missing cause of failure." Statistica Sinica. 2012;22(2):703-28. PMCID: PMC3742132.
Todd CA, Greene KM, Yu X, Ozaki DA, Gao H, Huang Y, Wang M, Li G, Brown R, Wood B, D'Souza MP, Gilbert PB, Montefiori DC, Sarzotti-Kelsoe M. "Development and implementation of an international proficiency testing program for a neutralizing antibody assay for HIV-1 in TZM-bl cells." Journal of Immunological Methods. 2012;375(1-2):57-67. PMCID: PMC3332116.
Wecker M, Gilbert PB, Russell N, Hural J, Allen M, Pensiero M, Chulay J, Chiu YL, Abdool Karim SS, Burke DS, and the HIV Vaccine Trials Network. "Phase I safety and immunogenicity evaluations of an alphavirus replicon HIV-1 subtype C gag vaccine in healthy HIV-1-uninfected adults." Clinical and Vaccine Immunology. 2012;19(10):1651-60. PMCID: PMC3485893.
Yu XS, Gilbert PB, Hioe CE, Zolla-Pazner S, Self SG. "Statistical approaches to analyzing HIV-1 neutralizing antibody assay data." Statistics in Biopharmaceutical Research. 2012;4(1):1-13. PMCID: PMC3959164.
2011
Billings EA, Karasavvas N, de Souza MS, Currier J, Pitisuttithum P, Kaewkunwal J, Nitayaphan S, Gilbert PB, Tomaras GD, Zolla-Pazner SB, Haynes BF, Michael NL, Rerks-Ngarm S, Kim JH, Rao M. "Surface plasmon resonance analysis of anti-gp120 V2-specific IgG antibodies generated in the RV144 Thai Trial." AIDS Research and Human Retroviruses. 2011;27(10):A21-A2.
Corey L, Nabel GJ, Dieffenbach C, Gilbert PB, Haynes BF, Johnston M, Kublin J, Lane HC, Pantaleo G, Picker LJ, Fauci AS. "HIV-1 vaccines and adaptive trial designs. Science Translational Medicine." 2011;3(79):79ps13. PMCID: PMC3616511.
Fitzgerald DW, Janes H, Robertson M, Coombs R, Frank I, Gilbert PB, Loufty M, Mehrotra D, Duerr A, Step Study Protocol Team. "An Ad5-vectored HIV-1 vaccine elicits cell-mediated immunity but does not affect disease progression in HIV-1-infected male subjects: results from a randomized placebo-controlled trial (the Step study)." Journal of Infectious Diseases. 2011;203(6):765-72. PMCID: PMC3119328.
Gilbert PB, Berger JO, Stablein D, Becker S, Essex M, Hammer SM, Kim JH, Degruttola VG. "Statistical interpretation of the RV144 HIV vaccine efficacy trial in Thailand: A case study for statistical issues in efficacy trials." Journal of Infectious Diseases. 2011;203(7):969-75. PMCID: PMC3068028.
Gilbert PB, Grove D, Gabriel E, Huang Y, Gray G, Hammer SM, Buchbinder SP, Kublin J, Corey L, Self SG. "A sequential Phase 2b trial design for evaluating vaccine efficacy and immune correlates for multiple HIV vaccine regimens." Statistical Communications in Infectious Diseases. 2010;2(1): 1. PMCID: PMC3502884.
Gilbert PB, Hudgens MG, Wolfson J. Commentary on "Principal stratification - a goal or a tool?" by Judea Pearl. International Journal of Biostatistics. 2011;7(1):Article 36. PMCID: PMC3204668.
Gnanakaran S, Bhattacharya T, Daniels M, Keele BF, Hraber PT, Lapedes AS, Shen T, Gaschen B, Krishnamoorthy M, Li H, Decker JM, Salazar-Gonzalez JF, Wang S, Jiang C, Gao F, Swanstrom R, Anderson JA, Ping LH, Cohen MS, Markowitz M, Goepfert PA, Saag MS, Eron JJ, Hicks CB, Blattner WA, Tomaras GD, Asmal M, Letvin NL, Gilbert PB, deCamp AC, Magaret CA, Schief WR, Ban YE, Zhang M, Soderberg KA, Sodroski JG, Haynes BF, Shaw GM, Hahn BH, Korber B. "Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections." PLoS Pathogens. 2011;7(9):e1002209. PMCID: PMC3182927.
Huang Y, Gilbert PB. "Comparing biomarkers as principal surrogate endpoints." Biometrics. 2011;67(4):1442-51. PMCID: PMC3163011.
Letvin NL, Rao SS, Montefiori DC, Seaman MS, Sun Y, Lim SY, Yeh WW, Asmal M, Gelman RS, Shen L, Whitney JB, Seoighe C, Lacerda M, Keating S, Norris PJ, Hudgens MG, Gilbert PB, Buzby AP, Mach LV, Zhang J, Balachandran H, Shaw GM, Schmidt SD, Todd JP, Dodson A, Mascola JR, Nabel GJ. Immune and genetic correlates of vaccine protection against mucosal infection by SIV in monkeys. Science Translational Medicine. 2011;3(81):81ra36. PMCID: PMC3718279.
Rolland M, Tovanabutra S, deCamp AC, Frahm N, Gilbert PB, Sanders-Buell E, Heath L, Magaret CA, Bose M, Bradfield A, O'Sullivan A, Crossler J, Jones T, Nau M, Wong K, Zhao H, Raugi DN, Sorensen S, Stoddard JN, Maust BS, Deng W, Hural J, Dubey S, Michael NL, Shiver J, Corey L, Li F, Self SG, Kim J, Buchbinder S, Casimiro DR, Robertson MN, Duerr A, McElrath MJ, McCutchan FE, Mullins JI. "Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial." Nature Medicine. 2011;17(3):366-71. PMCID: PMC3053571.
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(3):1100-10. PMCID: PMC3116075.
2010
Gilbert PB. "Some design issues in phase 2B vs phase 3 prevention trials for testing efficacy of products or concepts." Statistics in Medicine. 2010;29(10):1061-71. PMCID: PMC2929839.
Gilbert PB, Jin Y. "Semiparametric estimation of the average causal effect of treatment on an outcome measured after a postrandomization event, with missing outcome data." Biostatistics. 2010;11(1):34-47. PMCID: PMC2800161.
Gilbert PB, Wang M, Wrin T, Petropoulos C, Gurwith M, Sinangil F, D'Souza P, Rodriguez-Chavez IR, deCamp A, Giganti M, Berman PW, Self SG, Montefiori DC. "Magnitude and breadth of a nonprotective neutralizing antibody response in an efficacy trial of a candidate HIV-1 gp120 vaccine." Journal of Infectious Diseases. 2010;202(4):595-605. PMCID: PMC2946208.
Novitsky V, Wang R, Bussmann H, Lockman S, Baum M, Shapiro R, Thior I, Wester C, Wester CW, Ogwu A, Asmelash A, Musonda R, Campa A, Moyo S, van Widenfelt E, Mine M, Moffat C, Mmalane M, Makhema J, Marlink R, Gilbert PB, Seage GR, 3rd, DeGruttola V, Essex M. "HIV-1 subtype C-infected individuals maintaining high viral load as potential targets for the "test-and-treat" approach to reduce HIV transmission." PLoS One. 2010;5(4):e10148. PMCID: PMC2853582.
Seaman MS, Janes H, Hawkins N, Grandpre LE, Devoy C, Giri A, Coffey RT, Harris L, Wood B, Daniels MG, Bhattacharya T, Lapedes A, Polonis VR, McCutchan FE, Gilbert PB, Self SG, Korber BT, Montefiori DC, Mascola JR. "Tiered categorization of a diverse panel of HIV-1 Env pseudoviruses for assessment of neutralizing antibodies." Journal of Virology. 2010;84(3):1439-52. PMCID: PMC2812321.
Wolfson J, Gilbert PB. "Statistical identifiability and the surrogate endpoint problem, with application to vaccine trials." Biometrics. 2010;66(4):1153-61. PMCID: PMC3597127.
Zhang M, Gilbert PB. "Increasing the efficiency of prevention trials by incorporating baseline covariates." Statistical Communications in Infectious Diseases. 2010;2(1). PMCID: PMC2997740.
2009
Gilbert PB, Qin L, Self SG. Response to Andrew Dunning's comment on "Evaluating a surrogate endpoint at three levels, with application to vaccine development". Statistics in Medicine. 2009;28(4):716-9. PMCID: PMC2646675.
Gilbert PB, Sato A, Sun X, Mehrotra DV. "Efficient and robust method for comparing the immunogenicity of candidate vaccines in randomized clinical trials." Vaccine. 2009;27(3):396-401. PMCID: PMC2653280.
Gray ES, Taylor N, Wycuff D, Moore PL, Tomaras GD, Wibmer CK, Puren A, deCamp A, Gilbert PB, Wood B, Montefiori DC, Binley JM, Shaw GM, Haynes BF, Mascola JR, Morris L. "Antibody specificities associated with neutralization breadth in plasma from human immunodeficiency virus type 1 subtype C-infected blood donors." Journal of Virology. 2009;83(17):8925-37. PMCID: PMC2738176.
Huang Y, Gilbert PB, Montefiori DC, Self SG. "Simultaneous evaluation of the magnitude and breadth of a left and right censored multivariate response, with application to HIV vaccine development." Statistics in Biopharmaceutical Research. 2009;1(1):81-91. PMCID: PMC2805400.
Hudgens MG, Gilbert PB. "Assessing vaccine effects in repeated low-dose challenge experiments." Biometrics. 2009;65(4):1223-32. PMCID: PMC2794923.
Hudgens MG, Gilbert PB, Mascola JR, Wu CD, Barouch DH, Self SG. "Power to detect the effects of HIV vaccination in repeated low-dose challenge experiments." Journal of Infectious Diseases. 2009;200(4):609-13. PMCID: PMC2754821.
Jones NG, deCamp A, Gilbert PB, Peterson ML, Gurwith M, Cao H. "AIDSVAX immunization induces HIV-specific CD8+ T-cell responses in high-risk, HIV-negative volunteers who subsequently acquire HIV infection." Vaccine. 2009;27(7):1136-40. PMCID: PMC2676722.
Kittikraisak W, van Griensven F, Martin M, McNicholl J, Gilbert PB, Chuachoowong R, Vanichseni S, Sutthent R, Tappero JW, Mastro TD, Hu DJ, Gurwith M, Kitayaporn D, Sangkum U, Choopanya K. "Blood and seminal plasma HIV-1 RNA levels among HIV-1-infected injecting drug users participating in the AIDSVAX B/E efficacy trial in Bangkok, Thailand." Journal of Acquired Immune Deficiency Syndromes. 2009;51(5):601-8. PMCID: PMC2764047.
Sun Y, Gilbert PB, McKeague IW. "Proportional hazards models with continuous marks." Annals of Statistics. 2009;37(1):394-426. PMCID: PMC2762218.
Wick WD, Gilbert PB, Yang OO. "Predicting the impact of blocking human immunodeficiency virus type 1 Nef in vivo." Journal of Virology. 2009;83(5):2349-56. PMCID: PMC2643708.
2008
Buchbinder SP, Mehrotra DV, Duerr A, Fitzgerald DW, Mogg R, Li D, Gilbert PB, Lama JR, Marmor M, Del Rio C, McElrath MJ, Casimiro DR, Gottesdiener KM, Chodakewitz JA, Corey L, Robertson MN. "Efficacy assessment of a cell-mediated immunity HIV-1 vaccine (the Step Study): a double-blind, randomised, placebo-controlled, test-of-concept trial." Lancet. 2008;372(9653):1881-93. PMCID: PMC2721012.
Gilbert PB, Hudgens MG. "Evaluating candidate principal surrogate endpoints." Biometrics. 2008;64(4):1146-54. PMCID: PMC2726718.
Gilbert PB, McKeague IW, Sun Y. "The 2-sample problem for failure rates depending on a continuous mark: an application to vaccine efficacy." Biostatistics. 2008;9(2):263-76. PMID: 17704528.
Gilbert PB, Qin L, Self SG. "Evaluating a surrogate endpoint at three levels, with application to vaccine development." Statistics in Medicine. 2008;27(23):4758-78. PMCID: PMC2646675.
Gilbert PB, Qin L, Self SG. "Comment on "Evaluating a surrogate endpoint at three levels, with application to vaccine development". Statistics in Medicine. 2008;27(29):6268-70. PMCID: PMC4510047.
Gilbert PB, Wu C, Jobes DV. "Genome scanning tests for comparing amino acid sequences between groups." Biometrics. 2008;64(1):198-207. PMID: 17608781.
Li Z, Gilbert PB, Nan B. "Weighted likelihood method for grouped survival data in case-cohort studies with application to HIV vaccine trials." Biometrics. 2008;64(4):1247-55. PMID: 17032178.
Qin L, Gilbert PB, Follmann D, Li D. "Assessing surrogate endpoints in vaccine trials with case-cohort sampling and the Cox model." Annals of Applied Statistics. 2008;2(1):386-407. PMCID: PMC2601643.
Sun Y, Hyun S, Gilbert PB. "Testing and estimation of time-varying cause-specific hazard ratios with covariate adjustment." Biometrics. 2008;64(4):1070-9. PMID: 18355384.
Yang Y, Gilbert PB, Longini IM, Halloran ME. "A Bayesian framework for estimating vaccine efficacy per infectious contact." Annals of Applied Statistics. 2008;2(4):1409-31. PMCID: PMC2630256.
2007
Follmann D, Duerr A, Tabet S, Gilbert PB, Moodie Z, Fast P, Cardinali M, Self SG. "Endpoints and regulatory issues in HIV vaccine clinical trials: lessons from a workshop." Journal of Acquired Immune Deficiency Syndromes. 2007;44(1):49-60. PMCID: PMC2682948.
Forthal DN, Gilbert PB, Landucci G, Phan T. "Recombinant gp120 vaccine-induced antibodies inhibit clinical strains of HIV-1 in the presence of Fc receptor-bearing effector cells and correlate inversely with HIV infection rate." Journal of Immunology. 2007;178(10):6596-603. PMID: 17475891.
Hudgens MG, Maathuis MH, Gilbert PB. "Nonparametric estimation of the joint distribution of a survival time subject to interval censoring and a continuous mark variable." Biometrics. 2007;63(2):372-80. PMID: 17688489.
Jemiai Y, Rotnitzky A, Shepherd BE, Gilbert PB. "Semiparametric estimation of treatment effects given base-line covariates on an outcome measured after a post-randomization event occurs." Journal of the Royal Statistical Society, Series B-Statistical Methodology. 2007;69:879-901.
Li F, Gilbert PB, Self SG. "Identification of cross-neutralization determinants by GAP analysis: a mutational behavior approach." Current HIV Research. 2007;5(1):87-96. PMCID: PMC2837843.
Li F, Horton H, Gilbert PB, McElrath MJ, Corey L, Self SG. "HIV-1 CTL-based vaccine immunogen selection: antigen diversity and cellular response features." Current HIV Research. 2007;5(1):97-107. PMID: 17266561.
Nickle DC, Heath L, Jensen MA, Gilbert PB, Mullins JI, Kosakovsky Pond SL. "HIV-specific probabilistic models of protein evolution." PLoS One. 2007;2(6):e503. PMCID: PMC1876811.
Qin L, Gilbert PB, Corey L, McElrath MJ, Self SG. "A framework for assessing immunological correlates of protection in vaccine trials." Journal of Infectious Diseases. 2007;196(9):1304-12. PMID: 17922394.
Shepherd BE, Gilbert PB, Lumley T. "Sensitivity analyses comparing time-to-event outcomes existing only in a subset selected postrandomization." Journal of the American Statistical Association. 2007;102(478):573-82. PMCID: PMC2613336.
Shepherd BE, Gilbert PB, Mehrotra DV. "Eliciting a counterfactual sensitivity parameter." American Statistician. 2007;61(1):56-63.
2006
Cai T, Gilbert PB, Self SG. "Joint inferences on vaccine efficacy against infection and disease with application to the first HIV vaccine efficacy trial." Journal of Biopharmaceutical Statistics. 2006;16(4):517-38. PMID: 16892911.
Li F, Malhotra U, Gilbert PB, Hawkins NR, Duerr AC, McElrath MJ, Corey L, Self SG. "Peptide selection for human immunodeficiency virus type 1 CTL-based vaccine evaluation." Vaccine. 2006;24(47-48):6893-904. PMID: 16890329.
Mehrotra DV, Li X, Gilbert PB. "A comparison of eight methods for the dual-endpoint evaluation of efficacy in a proof-of-concept HIV vaccine trial." Biometrics. 2006;62(3):893-900. PMID: 16984333.
Moodie Z, Rossini AJ, Hudgens MG, Gilbert PB, Self SG, Russell ND. "Statistical evaluation of HIV vaccines in early clinical trials." Contemporary Clinical Trials. 2006;27(2):147-60. PMID: 16426900.
Ndung'u T, Sepako E, McLane MF, Chand F, Bedi K, Gaseitsiwe S, Doualla-Bell F, Peter T, Thior I, Moyo SM, Gilbert PB, Novitsky VA, Essex M. "HIV-1 subtype C in vitro growth and coreceptor utilization." Virology. 2006;347(2):247-60. PMID: 16406460.
Novitsky VA, Gilbert PB, Shea K, McLane MF, Rybak N, Klein I, Thior I, Ndung'u T, Lee TH, Essex ME. "Interactive association of proviral load and IFN-gamma-secreting T cell responses in HIV-1C infection." Virology. 2006;349(1):142-55. PMID: 16519915.
Pitisuttithum P, Gilbert PB, Gurwith M, Heyward W, Martin M, van Griensven F, Hu D, Tappero JW, Choopanya K. "Randomized, double-blind, placebo-controlled efficacy trial of a bivalent recombinant glycoprotein 120 HIV-1 vaccine among injection drug users in Bangkok, Thailand." Journal of Infectious Diseases. 2006;194(12):1661-71. PMID: 17109337.
Shapiro RL, Thior I, Gilbert PB, Lockman S, Wester C, Smeaton LM, Stevens L, Heymann SJ, Ndung'u T, Gaseitsiwe S, Novitsky V, Makhema J, Lagakos S, Essex M. "Maternal single-dose nevirapine versus placebo as part of an antiretroviral strategy to prevent mother-to-child HIV transmission in Botswana." AIDS. 2006;20(9):1281-88. PMID: 16816557.
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(2):332-42. PMID: 16918897.
Thior I, Lockman S, Smeaton LM, Shapiro RL, Wester C, Heymann SJ, Gilbert PB, Stevens L, Peter T, Kim S, van Widenfelt E, Moffat C, Ndase P, Arimi P, Kebaabetswe P, Mazonde P, Makhema J, McIntosh K, Novitsky V, Lee TH, Marlink R, Lagakos S, Essex M. "Breastfeeding plus infant zidovudine prophylaxis for 6 months vs formula feeding plus infant zidovudine for 1 month to reduce mother-to-child HIV transmission in Botswana: a randomized trial: the Mashi Study." JAMA: The Journal of the American Medical Association. 2006;296(7):794-805. PMID: 16905785.
Wick WD, Gilbert PB, Self SG. "On modeling HIV and T cells in vivo: assessing causal estimators in vaccine trials." PLoS Computational Biology. 2006;2(6):e64. PMCID: 1479086.
2005
Flynn MN, Forthal DN, Harro CD, Judson FN, Mayer KH, Para MF, Gilbert PB, Hudgens MG, Metch BJ, Self SG, Berman PW, Francis DP, Gurwith M, Heyward WL, Jobes DV, Peterson ML, Popovic V, Sinangil FM, Adamczyk A, Baker RL, Brand D, Brown SJ, Buchbinder S, Buggy BP, Cade J, Caldwell MC, Celum C, Creticos C, Coutinho RA, Lindenburg K, Daly P, DeJesus E, Di-Carlo R, Fenstersheib M, Gripshover B, Gorse GJ, Belshe R, Grossman H, Henry K, Hewitt RG, Hogg R, Jacobson JM, Jemsek J, Judson F, Kahn JO, Keefer MC, Kessler H, Koblin B, Kostman J, Lally M, Logue K, Marmor M, Mayer K, McKinsey D, Miskin BM, Morales JO, Mulligan MJ, Myers RA, Novak R, Para M, Piliero P, Poblete R, Rhame F, Riddler S, Richter RW, Sampson JH, Sands M, Santiago S, Shikuma C, Somero MS, Thomas E, Thompson M, Tyring SK, Vincelette J, Vrooman PS, Yangco BG, rgp120 HIV Vaccine Study Group. "Placebo-controlled phase 3 trial of a recombinant glycoprotein 120 vaccine to prevent HIV-1 infection." Journal of Infectious Diseases. 2005;191(5):654-65. PMID: 15688278.
Gilbert PB. "A modified false discovery rate multiple-comparisons procedure for discrete data, applied to human immunodeficiency virus genetics." Journal of the Royal Statistical Society, Series C-Applied Statistics. 2005;54:143-58.
Gilbert PB, Ackers ML, Berman PW, Francis DP, Popovic V, Hu DJ, Heyward WL, Sinangil F, Shepherd BE, Gurwith M. "HIV-1 virologic and immunologic progression and initiation of antiretroviral therapy among HIV-1-infected subjects in a trial of the efficacy of recombinant glycoprotein 120 vaccine." Journal of Infectious Diseases. 2005;192(6):974-83. PMID: 16107949.
Gilbert PB, Novitsky V, Essex M. "Covariability of selected amino acid positions for HIV type 1 subtypes C and B." AIDS Research and Human Retroviruses. 2005;21(12):1016-30. PMID: 16379605.
Gilbert PB, Peterson ML, Follmann D, Hudgens MG, Francis DP, Gurwith M, Heyward WL, Jobes DV, Popovic V, Self SG, Sinangil F, Burke D, Berman PW. "Correlation between immunologic responses to a recombinant glycoprotein 120 vaccine and incidence of HIV-1 infection in a phase 3 HIV-1 preventive vaccine trial." Journal of Infectious Diseases. 2005;191(5):666-77. PMID: 15688279.
Gilbert PB, Rossini AJ, Shankarappa R. "Two-sample tests for comparing intra-individual genetic sequence diversity between populations." Biometrics. 2005;61(1):106-17. PMID: 15797083.
Gilbert PB, Sun Y. "Failure time analysis of HIV vaccine effects on viral load and antiretroviral therapy initiation." Biostatistics. 2005;6(3):374-94. PMID: 15831584.
Li M, Gao F, Mascola JR, Stamatatos L, Polonis VR, Koutsoukos M, Voss G, Goepfert P, Gilbert PB, Greene KM, Bilska M, Kothe DL, Salazar-Gonzalez JF, Wei X, Decker JM, Hahn BH, Montefiori DC. "Human immunodeficiency virus type 1 env clones from acute and early subtype B infections for standardized assessments of vaccine-elicited neutralizing antibodies." Journal of Virology. 2005;79(16):10108-25. PMCID: PMC1182643.
Mascola JR, D'Souza P, Gilbert PB, Hahn BH, Haigwood NL, Morris L, Petropoulos CJ, Polonis VR, Sarzotti M, Montefiori DC. "Recommendations for the design and use of standard virus panels to assess neutralizing antibody responses elicited by candidate human immunodeficiency virus type 1 vaccines." Journal of Virology. 2005;79(16):10103-7. PMCID: PMC1182642.
Meier AS, Gilbert PB. "Accuracy and precision of estimating intervention efficacy when the timing of observed events differ by treatment arm." Contemporary Clinical Trials. 2005;26(5):598-610. PMID: 16112914.
2004
Evans TG, Frey S, Israel H, Chiu J, El-Habib R, Gilbert PB, Gaitan A, Montefiori DC. "Long-term memory B-cell responses in recipients of candidate human immunodeficiency virus type 1 vaccines." Vaccine. 2004;22(20):2626-30. PMID: 15193388.
Gilbert PB. "Goodness-of-fit tests for semiparametric biased sampling models." Journal of Statistical Planning and Inference. 2004;118(1-2):51-81.
Gilbert PB, McKeague IW, Sun Y. "Tests for comparing mark-specific hazards and cumulative incidence functions." Lifetime Data Analysis. 2004;10(1):5-28. PMID: 15130048.
Huang CC, Barreda P, Mendoza V, Guzman L, Gilbert PB. "A comparative analysis of abandoned street children and formerly abandoned street children in La Paz, Bolivia." Archives of Disease in Childhood. 2004;89(9):821-26. PMCID: PMC1763218.
Hudgens MG, Gilbert PB, Self SG. "Endpoints in vaccine trials." Statistical Methods in Medical Research. 2004;13(2):89-114. PMID: 15068256.
Lee D, Graham BS, Chiu YL, Gilbert PB, McElrath MJ, Belshe RB, Buchbinder SP, Sheppard HW, Koblin BA, Mayer KH, Keefer MC, Mulligan MJ, Celum CL. "Breakthrough infections during phase 1 and 2 prime-boost HIV-1 vaccine trials with canarypox vectors (ALVAC) and booster dose of recombinant gp120 or gp160." Journal of Infectious Diseases. 2004;190(5):903-7. PMID: 15295694.
Renjifo B, Gilbert PB, Chaplin B, Msamanga G, Mwakagile D, Fawzi W, Essex M. "Preferential in-utero transmission of HIV-1 subtype C as compared to HIV-1 subtype A or D." AIDS. 2004;18(12):1629-36. PMID: 15280773.
2003
Gilbert PB, Bosch RJ, Hudgens MG. "Sensitivity analysis for the assessment of causal vaccine effects on viral load in HIV vaccine trials." Biometrics. 2003;59(3):531-41. PMID: 14601754.
Gilbert PB, Chiu YL, Allen M, Lawrence DN, Chapdu C, Israel H, Holman D, Keefer MC, Wolff M, Frey SE. "Long-term safety analysis of preventive HIV-1 vaccines evaluated in AIDS vaccine evaluation group NIAID-sponsored Phase I and II clinical trials." Vaccine. 2003;21(21-22):2933-47. PMID: 12798637.
Gilbert PB, DeGruttola VG, Hudgens MG, Self SG, Hammer SM, Corey L. "What constitutes efficacy for a human immunodeficiency virus vaccine that ameliorates viremia: Issues involving surrogate end points in phase 3 trials." Journal of Infectious Diseases. 2003;188(2):179-93. PMID: 12854072.
Gilbert PB, McKeague IW, Eisen G, Mullins C, Gueye NA, Mboup S, Kanki PJ. "Comparison of HIV-1 and HIV-2 infectivity from a prospective cohort study in Senegal." Statistics in Medicine. 2003;22(4):573-93. PMID: 12590415.
Montano M, Russell M, Gilbert PB, Thior I, Lockman S, Shapiro R, Chang SY, Lee Tun-Hou, Essex M. "Comparative prediction of perinatal human immunodeficiency virus type 1 transmission, using multiple virus load markers." Journal of Infectious Diseases. 2003;188(3):406-13. PMID: 12870122.
Novitsky V, Gilbert PB, Peter T, McLane MF, Gaolekwe S, Rybak N, Thior I, Ndung'u T, Marlink R, Lee TH, Essex M. "Association between virus-specific T-cell responses and plasma viral load in human immunodeficiency virus type 1 subtype C infection." Journal of Virology. 2003;77(2):882-90. PMCID: PMC140844.
Renjifo B, Chung M, Gilbert PB, Mwakagile D, Msamanga G, Fawzi W, Essex M. "In-utero transmission of quasispecies among human immunodeficiency virus type 1 genotypes." Virology. 2003;307(2):278-82. PMID: 12667797.
Weiser S, Wolfe W, Bangsberg D, Thior I, Gilbert PB, Makhema J, Kebaabetswe P, Dickenson D, Mompati K, Essex M, Marlink R. "Barriers to antiretroviral adherence for patients living with HIV infection and AIDS in Botswana." Journal of Acquired Immune Deficiency Syndromes. 2003;34(3):281-88. PMID: 14600572.
2002
Gilbert PB, Wei LJ, Kosorok MR, Clemens JD. "Simultaneous inferences on the contrast of two hazard functions with censored observations." Biometrics. 2002;58(4):773-80. PMID: 12495131.
Mani I, Gilbert PB, Sankale JL, Eisen G, Mboup S, Kanki PJ. "Intrapatient diversity and its correlation with viral setpoint in human immunodeficiency virus type 1 CRF02_A/G-IbNG infection." Journal of Virology. 2002;76(21):10745-55. PMCID: PMC136616.
Novitsky V, Cao H, Rybak N, Gilbert PB, McLane MF, Gaolekwe S, Peter T, Thior I, Ndung'u T, Marlink R, Lee TH, Essex M. "Magnitude and frequency of cytotoxic T-lymphocyte responses: identification of immunodominant regions of human immunodeficiency virus type 1 subtype C." Journal of Virology. 2002;76(20):10155-68. PMCID: PMC136554.
Novitsky V, Smith UR, Gilbert PB, McLane MF, Chigwedere P, Williamson C, Ndung'u T, Klein I, Chang SY, Peter T, Thior I, Foley BT, Gaolekwe S, Rybak N, Gaseitsiwe S, Vannberg F, Marlink R, Lee TH, Essex M. "Human immunodeficiency virus type 1 subtype C molecular phylogeny: consensus sequence for an AIDS vaccine design?" Journal of Virology. 2002;76(11):5435-51. PMCID: 137027.
Wu L, Gilbert PB. "Flexible weighted log-rank tests optimal for detecting early and/or late survival differences." Biometrics. 2002;58(4):997-1004. PMID: 12495155.
2001
Gilbert PB. "Interpretability and robustness of sieve analysis models for assessing HIV strain variations in vaccine efficacy." Statistics in Medicine. 2001;20(2):263-79. PMID: 11169601.
Gilbert PB, DeGruttola V, Hammer SM, Kuritzkes DR. "Virologic and regimen termination surrogate end points in AIDS clinical trials." JAMA: The Journal of the American Medical Association. 2001;285(6):777-84. PMID: 11176916.
Gilbert PB, Novitsky VA, Montano MA, Essex M. "An efficient test for comparing sequence diversity between two populations." Journal of Computational Biology. 2001;8(2):123-39. PMID: 1145431.
Gilbert PB, Self SG, Rao M, Naficy A, Clemens J. "Sieve analysis: Methods for assessing from vaccine trial data how vaccine efficacy varies with genotypic and phenotypic pathogen variation." Journal of Clinical Epidemiology. 2001;54(1):68-85. PMID: 11165470.
Havlir DV, Bassett R, Levitan D, Gilbert PB, Tebas P, Collier AC, Hirsch MS, Ignacio C, Condra J, Gunthard HF, Richman DD, Wong JK. "Prevalence and predictive value of intermittent viremia with combination HIV therapy." JAMA: The Journal of the American Medical Association. 2001;286(2):171-79. PMID: 11448280.
Havlir DV, Gilbert PB, Bennett K, Collier AC, Hirsch MS, Tebas P, Adams EM, Wheat LJ, Goodwin D, Schnittman S, Holohan MK, Richman DD. "Effects of treatment intensification with hydroxyurea in HIV-infected patients with virologic suppression." AIDS. 2001;15(11):1379-88. PMID: 11504959.
McKeague IW, Gilbert PB, Kanki PJ. "Omnibus tests for comparison of competing risks with adjustment for covariate effects." Biometrics. 2001;57(3):818-28. PMID: 11550933.
Novitsky V, Rybak N, McLane MF, Gilbert PB, Chigwedere P, Klein I, Gaolekwe S, Chang SY, Peter T, Thior I, Ndung'u T, Vannberg F, Foley BT, Marlink R, Lee TH, Essex M. "Identification of human immunodeficiency virus type 1 subtype C Gag-, Tat-, Rev-, and Nef-specific elispot-based cytotoxic T-lymphocyte responses for AIDS vaccine design." Journal of Virology. 2001;75(19):9210-28. PMCID: 114489. PMID: 11533184.
Rivera-Morales LG, Novitsky VA, Trujillo JR, Lavalle-Montalvo C, Cano-Dominguez C, Ramos-Jimenez J, Jimenez-Rios E, Flores-Flores L, Lopez-Guillen P, Gilbert PB, Vannberg F, Tamez-Guerra R, Rodriguez-Padilla C, Essex M. "The molecular epidemiology of HIV type 1 of men in Mexico." AIDS Research and Human Retroviruses. 2001;17(1):87-92. PMID: 11177387.
2000
Gilbert PB. "Comparison of competing risks failure time methods and time-independent methods for assessing strain variations in vaccine protection." Statistics in Medicine. 2000;19(22):3065-86. PMID: 11113943.
Gilbert PB. "Some statistical issues in the design of HIV-1 vaccine and treatment trials." Statistical Methods in Medical Research. 2000;9(3):207-29. PMID: 11084705.
Gilbert PB. "Large sample theory of maximum likelihood estimates in semiparametric biased sampling models." Annals of Statistics. 2000;28(1):151-94.
Gilbert PB. "Developing an AIDS vaccine by sieving." Chance. 2000; 13:16-21.
Gilbert PB, Hanna GJ, De Gruttola V, Martinez-Picado J, Kuritzkes DR, Johnson VA, Richman DD, D'Aquila RT. "Comparative analysis of HIV type 1 genotypic resistance across antiretroviral trial treatment regimens." AIDS Research and Human Retroviruses. 2000;16(14):1325-36. PMID: 11018852.
Gilbert PB, Ribaudo HJ, Greenberg L, Yu G, Bosch RJ, Tierney C, Kuritzkes DR. "Considerations in choosing a primary endpoint that measures durability of virological suppression in an antiretroviral trial." AIDS. 2000;14(13):1961-72. PMID: 10997401.
Segal S, Su M, Gilbert PB. "The effect of a rapid change in availability of epidural analgesia on the cesarean delivery rate: a meta-analysis." American Journal of Obstetrics and Gynecology. 2000;183(4):974-78. PMID: 11035349.
1999
Christie PD, Edelberg JM, Picard MH, Foulkes AS, Mamuya W, Weiler-Guettler H, Rubin RH, Gilbert PB, Rosenberg RD. "A murine model of myocardial microvascular thrombosis." Journal of Clinical Investigation. 1999;104(5):533-39. PMID: 10497767.
Gilbert PB, Lele SR, Vardi Y. "Maximum likelihood estimation in semiparametric selection bias models with application to AIDS vaccine trials." Biometrika. 1999;86(1):27-43.
Renjifo B, Gilbert PB, Chaplin B, Vannberg F, Mwakagile D, Msamanga G, Hunter D, Fawzi W, Essex M. "Emerging recombinant human immunodeficiency viruses: Uneven representation of the envelope V3 region." AIDS. 1999;13(13):1613-21. PMID: 10509561.
1998
DeGruttola V, Hughes M, Gilbert PB, Phillips A. "Trial design in the era of highly effective antiviral drug combinations for HIV infection." AIDS. 1998;12 Suppl A:S149-56. PMID: 9632997.
Gilbert PB, DeGruttola V, Hammer S. "Efficient trial designs for studying combination antiretroviral treatments in patients with various resistance profiles." Journal of Infectious Diseases. 1998;178(2):340-8. PMID: 9697713.
Gilbert PB, Self SG, Ashby MA. "Statistical methods for assessing differential vaccine protection against human immunodeficiency virus types." Biometrics. 1998;54(3):799-814. PMID: 9750238.
Scharfstein DO, Tsiatis AA, Gilbert PB. "Semiparametric efficient estimation in the generalized odds-rate class of regression models for right-censored time-to-event data." Lifetime Data Analysis. 1998;4(4):355-91. PMID: 9880995.
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