Manuscripts

2018

Bekker LG, Moodie Z, Grunenberg N, Laher F, Tomaras GD, Cohen KW, Allen M, Malahleha M, Mngadi K, Daniels B, Innes C, Bentley C, Frahm N, Morris DE, Morris L, Mkhize NN, Montefiori DC, Sarzotti-Kelsoe M, Grant S, Yu C, Mehra VL, Pensiero MN, Phogat S, DiazGranados CA, Barnett SW, Kanesa-thasan N, Koutsoukos M, Michael NL, Robb ML, Kublin JG, Gilbert PB, Corey L, Gray GE, McElrath MJ on behalf of the HVTN 100 Protocol Team. A phase 1/2 HIV-1 vaccine trial of a Subtype C ALVAC-HIV and Bivalent Subtype C gp120/MF59 vaccine regimen in low risk HIV uninfected South African adults. Lancet HIV. 2018 Jul;5(7):e366-e378

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 Aug;34(8):645-656

Dietrich JJ, Lazarus E, Andrasik M, Hornschuh S, Otwombe K, Morgan C, Isaacs AJ, Huang Y, Laher F, Kublin JG, Gray GE. Mobile Phone Questionnaires for Sexual Risk Data Collection Among Young Women in Soweto, South Africa. AIDS Behav. 2018 Jul;22(7):2312-2321.

Yu T, Wu L, Gilbert P. New approaches for censored longitudinal data in joint modelling of longitudinal and survival data, with application to HIV vaccine studies. Lifetime Data Anal. 2018 Jun 8. [Epub ahead of print]

Huang Y, Karuna S, Carpp LN, Reeves D, Pegu A, Seaton K, Mayer K, Schiffer J, Mascola J, Gilbert PB. Modeling Cumulative Overall Prevention Efficacy for the VRC01 Phase 2b Efficacy Trials. Hum Vaccin Immunother. 2018 Apr 23:1-35. [Epub ahead of print].

de Montigny S, Adamson BJS, Mâsse BR, Garrison LP Jr, Kublin JG, Gilbert PB, Dimitrov DT. Projected effectiveness and added value of HIV vaccination campaigns in South Africa: A modeling study. Sci Rep. 2018 Apr 17;8(1):6066.

Yates NL, deCamp AC, Korber BT, Liao HX, Irene C, Pinter A, Peacock J, Harris LJ, Sawant S, Hraber P, Shen X, Rerks-Ngarm S, Pitisuttithum P, Nitayapan S, Berman PW, Robb ML, Pantaleo G, Zolla-Pazner S, Haynes BF, Alam SM, Montefiori DC, Tomaras GD. HIV-1 Envelope Glycoproteins from Diverse Clades Differentiate Antibody Responses and Durability among Vaccinees. J Virol. 2018 Mar 28;92(8).

Fong Y, Shen X, Ashley VC, Deal A, Seaton KE, Yu C, Grant SP, Ferrari G, deCamp AC, 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. Modification of the Association Between T-Cell Immune Responses and Human Immunodeficiency Virus Type 1 Infection Risk by Vaccine-Induced Antibody Responses in the HVTN 505 Trial. J Infect Dis. 2018 Mar 28;217(8):1280-1288.

Wills S, Hwang KK, Liu P, Dennison SM, Tay MZ, Shen X, Pollara J, Lucas JT, Parks R, Rerks-Ngarm S, Pitisuttithum P, Nitayapan S, Kaewkungwal J, Thomas R, Kim JH, Michael NL, Robb ML, McRaven M, Montefiori DC, Hope TJ, Liao HX, Moody MA, Ferrari G, Haynes BF, Alam SM, Bonsignori M, Tomaras GD. HIV-1-Specific IgA Monoclonal Antibodies from an HIV-1 Vaccinee Mediate Galactosylceramide Blocking and Phagocytosis. J Virol. 2018 Mar 14;92(7).

Auclair S, Liu F, Niu Q, Hou W, Churchyard G, Morgan C, Frahm N, Nitayaphan S, Pitisuthithum P, Rerks-Ngarm S, Kimata JT, Soong L, Franchini G, Robb M, Kim J, Michael N, Hu H. Distinct susceptibility of HIV vaccine vector-induced CD4 T cells to HIV infection. PLoS Pathog. 2018 Feb 23;14(2):e1006888

Thiam-Diouf A, Metch B, Sharpec C, Mulugetad R and Andrasik MP. Substance use patterns of HVTN phase I clinical trial participants: Enrollment, risk reduction counseling and retention. Vaccine. 2018 Feb 21;36(9):1235-1242.

Benkeser D, Carone M, Gilbert PB. Improved estimation of the cumulative incidence of rare outcomes. Stat Med. 2018 Jan 30;37(2):280-293.

2017

Mayer KH, Seaton KE, Huang Y, Grunenberg N, Isaacs A, Allen M, Ledgerwood JE, Frank I, Sobieszczyk ME, Baden LR, Rodriguez B, Van Tieu H, Tomaras GD, Deal A, Goodman D, Bailer RT, Ferrari G, Jensen R, Hural J, Graham BS, Mascola JR, Corey L, Montefiori DC; HVTN 104 Protocol Team; and the NIAID HIV Vaccine Trials Network. Safety, pharmacokinetics, and immunological activities of multiple intravenous or subcutaneous doses of an anti-HIV monoclonal antibody, VRC01, administered to HIV-uninfected adults: Results of a phase 1 randomized trial. PLoS Med. 2017 Nov 14;14(11):e1002435

Li SS, Kochar NK, Elizaga M, Hay CM, Wilson GJ, Cohen KW, De Rosa SC, Xu R, Ota-Setlik A, Morris D, Finak G, Allen M, Tieu HV, Frank I, Sobieszczyk ME, Hannaman D, Gottardo R, Gilbert PB, Tomaras GD, Corey L, Clarke DK, Egan MA, Eldridge JH, McElrath MJ, Frahm N; NIAID HIV Vaccine Trials Network. DNA priming increases frequency of T-cell responses to a VSV HIV vaccine with specific enhancement of CD8+ T-cell responses by IL-12 pDNA. Clin Vaccine Immunol. 2017 Nov 6;24(11)

Buchbinder SP, Grunenberg NA, Sanchez BJ, Seaton KE, Ferrari G, Moody MA, Frahm N, Montefiori DC, Hay CM, Goepfert PA, Baden LR, Robinson HL, Yu X, Gilbert PB, McElrath MJ, Huang Y, Tomaras GD, on behalf of the HVTN 094 Study Group. Immunogenicity of a novel Clade B HIV-1 vaccine combination: Results of phase 1 randomized placebo controlled trial of an HIV-1 GM-CSF-expressing DNA prime with a modified vaccinia Ankara vaccine boost in healthy HIV-1 uninfected adults. PLoS One. 2017 Jul 20;12(7):e0179597

Akondy RS, Fitch M, Edupuganti S, Yang S, Kissick HT, Li KW, Youngblood BA, Abdelsamed HA, McGuire DJ, Cohen KW, Alexe G, Nagar S, McCausland MM, Gupta S, Tata P, Haining WN, McElrath MJ, Zhang D, Hu B, Greenleaf WJ, Goronzy JJ, Mulligan MJ, Hellerstein M, Ahmed R. Origin and differentiation of human memory CD8 T cells after vaccination. Nature. 2017 Dec 21;552(7685):362-367.

Lennard K, Dabee S, Barnabas SL, Havyarimana E, Blakney A, Jaumdally SZ, Botha G, Mkhize NN, Bekker LG, Lewis DA, Gray G, Mulder N, Passmore JS, Jaspan HB. Microbial composition predicts genital tract inflammation and persistent bacterial vaginosis in adolescent South African women. Infect Immun. 2017 Dec 19;86(1).

McGuire EP, Fong Y, Toote C, Cunningham CK, McFarland EJ, Borkowsky W, Barnett S, Itell HL, Kumar A, Gray G, McElrath MJ, Tomaras GD, Permar SR, Fouda GG. HIV-Exposed Infants Vaccinated with an MF59/Recombinant gp120 Vaccine Have Higher-Magnitude Anti-V1V2 IgG Responses than Adults Immunized with the Same Vaccine. J Virol. 2017 Dec 14;92(1).

Sneller MC, Justement JS, Gittens KR, Petrone ME, Clarridge KE, Proschan MA, Kwan R, Shi V, Blazkova J, Refsland EW, Morris DE, Cohen KW, McElrath MJ, Xu R, Egan MA, Eldridge JH, Benko E, Kovacs C, Moir S, Chun TW, Fauci AS. A randomized controlled safety/efficacy trial of therapeutic vaccination in HIV-infected individuals who initiated antiretroviral therapy early in infection. Sci Transl Med. 2017 Dec 6;9(419).

deCamp AC, Rolland M, Edlefsen PT, Sanders-Buell E, Hall B, Magaret CA, Fiore-Gartland AJ, Juraska M, Carpp LN, Karuna ST, Bose M, LePore S, Miller S, O'Sullivan A, Poltavee K, Bai H, Dommaraju K, Zhao H, Wong K, Chen L, Ahmed H, Goodman D, Tay MZ, Gottardo R, Koup RA, Bailer R, Mascola JR, Graham BS, Roederer M, O'Connell RJ, Michael NL, Robb ML, Adams E, D'Souza P, Kublin J, Corey L, Geraghty DE, Frahm N, Tomaras GD, McElrath MJ, Frenkel L, Styrchak S, Tovanabutra S, Sobieszczyk ME, Hammer SM, Kim JH, Mullins JI, 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. 2017 Nov 17;12(11):e0185959

Morris L and Mkhize NN. Prospects for passive immunity to prevent HIV infection. PLoS Med. 2017 Nov 14;14(11):e1002436

Fiore-Gartland A, Panoskaltsis-Mortari A, Agan AA, Mistry AJ, Thomas PG, Matthay MA; PALISI PICFlu Investigators, Hertz T, Randolph AG. Cytokine Profiles of Severe Influenza Virus-Related Complications in Children. Front Immunol. 2017 Nov 6;8:1423.

Fong Y, Huang Y, Gilbert PB, Permar SR. chngpt: threshold regression model estimation and inference. BMC Bioinformatics. 2017 Oct 16;18(1):454

Cohen MS, Corey L. Broadly neutralizing antibodies to prevent HIV-1. Science. 2017 Oct 6;358(6359):46-47

Yu T, Wu L, Gilbert PB. A joint model for mixed and truncated longitudinal data and survival data, with application to HIV vaccine studies. Biostatistics. 2017 Sep 23. [Epub ahead of print]

Rakshit S, Adiga V, Nayak S, Sahoo PN, Sharma PK, van Meijgaarden KE, Uk J AJ, Dhar C, Souza GD, Finak G, De Rosa SC, Ottenhoff THM, Vyakarnam A. Circulating Mycobacterium tuberculosis DosR latency antigen-specific, polyfunctional, regulatory IL10+ Th17 CD4 T-cells differentiate latent from active tuberculosis. Sci Rep. 2017 Sep 20;7(1):11948

Hensel MT, Peng T, Cheng A, De Rosa SC, Wald A, Laing KJ, Jing L, Dong L, Magaret AS, Koelle DM. Selective expression of CCR10 and CXCR3 by circulating human HSV-specific CD8 T-cells. J Virol. 2017 Sep 12;91(19).

Fong Y, Huang Y, Lemos MP, McElrath MJ. Rank-based two-sample tests for paired data with missing values. Biostatistics. 2017 Aug 24. [Epub ahead of print]

Moncunill G, De Rosa SC, Ayestaran A, Nhabomba AJ, Mpina M, Cohen KW, Jairoce C, Rutishauser T, Campo JJ, Harezlak J, Sanz H, Díez-Padrisa N, Williams NA, Morris D, Aponte JJ, Valim C, Daubenberger C, Dobaño C, McElrath MJ. RTS,S/AS01E Malaria Vaccine Induces Memory and Polyfunctional T Cell Responses in a Pediatric African Phase III Trial. Front Immunol. 2017 Aug 23;8:1008. eCollection 2017.

Richardson S, Seekaew P, Koblin B, Vazquez T, Nandi V and Tieu HV. Barriers and facilitators of HIV vaccine and prevention study participation among Young Black MSM and transwomen in New York City. PLoS One. 2017 Jul 19;12(7):e0181702

Andriesen J, Bull S, Dietrich J, Haberer J, van der Pol B, Voronin Y, Wall K, Whalen C, Priddy F. Using Digital Technologies in Clinical HIV Research: Real-World Applications and Considerations for Future Work. J Med Internet Res 2017;19(7):e274

Fiore-Gartland A, Kullman N, DeCamp AC, Clenaghan G, Yang W, Magaret C, Edlefsen PT and Gilbert PB. SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials. Bioinformatics. 2017 Aug 1;33(15):2386-2388.

Huang Y, Zhang L, Ledgerwood J, Grunenberg N, Bailer R, Isaacs A, Seaton K, Mayer KH, Capparelli E, Corey L, Gilbert PB. Population pharmacokinetics analysis of VRC01, an HIV-1 broadly neutralizing monoclonal antibody, in healthy adults. 2017 Jul;9(5):792-800

Heit A, Schmitz F, Gerdts S, Flach B, Moore MS, Perkins JA, Robins HS, Aderem A, Spearman P, Tomaras GD, De Rosa SC, McElrath MJ. Vaccination establishes clonal relatives of germinal center T cells in the blood of humans. J Exp Med. 2017 Jul 3;214(7):2139-2152.

Painter JE, DiClemente RJ, Jimenez L, Stuart T, Sales JM, Mulligan MJ. Exploring evidence for behavioral risk compensation among participants in an HIV vaccine clinical trial. Vaccine. 2017 Jun 16;35(28):3558-3563.

Buckingham L, Becher J, Voytek CD, Fiore D, Dunbar D, Davis-Vogel A, Metzger DS, Frank I. Going social: Success in online recruitment of men who have sex with men for prevention HIV vaccine research. Vaccine. 2017 Jun 14;35(27):3498-3505.

Fong Y, Di C, Huang Y, Gilbert PB. Model-robust inference for continuous threshold regression models. Biometrics. Biometrics. 2017 Jun;73(2):452-462

Wang, L, Richardson T S and Zhou XH. Causal analysis of ordinal treatments and binary outcomes under truncation by death. J R Stat Soc Series B Stat Methodol. 2017 Jun;79(3):719-735

Adamson BJS, Carlson JJ, Kublin JG, Garrison LP. The Potential Cost-Effectiveness of Pre-Exposure Prophylaxis Combined with HIV Vaccines in the United States. Vaccines (Basel). 2017 May 24;5(2).

McElrath MJ. Adjuvants: tailoring humoral immune responses. Curr Opin HIV AIDS. 2017 May;12(3):278-284

Janes HE, Cohen KW, Frahm N, De Rosa SC, Sanchez B, Hural J, Magaret CA, Karuna S, Bentley C, Gottardo R, Finak G, Grove D, Shen M, Graham BS, Koup RA, Mulligan MJ, Koblin B, Buchbinder SP, Keefer MC, Adams E, Anude C, Corey L, Sobieszczyk M, Hammer SM, Gilbert PB, McElrath MJ. Higher T cell responses induced by DNA/rAd5 HIV-1 preventive vaccine are associated with lower HIV-1 infection risk in an efficacy trial. J Infect Dis. 2017 May 1;215(9):1376-1385

Corey L and Gray GE. Preventing acquisition of HIV is the only path to an AIDS-free generation. Proc Natl Acad Sci U S A. 2017 Apr 11;114(15):3798-3800

Huang Y, Gilbert P, Fu R, Janes H. Statistical methods for down-selection of treatment regimens based on multiple endpoints, with application to HIV vaccine trials. Biostatistics. 2017 Apr 1;18(2):230-243

Cohen KW and Frahm N. Current views on the potential for development of a HIV vaccine. Expert Opin Biol Ther. 2017 Mar;17(3):295-303.

Bekker LG and Gray GE. Hope for HIV control in southern Africa: The continued quest for a vaccine. PLoS Med. 2017 Feb 28;14(2):e1002241

Huang Y, Zhang L, Janes H, Frahm N, Isaacs A, Kim JH, Montefiori D, McElrath MJ, Tomaras GD, Gilbert PB. Predictors of durable immune responses six months after the last vaccination in preventive HIV vaccine trials. Vaccine. 2017 Feb 22;35(8):1184-1193.

Jaworski JP, Bryk P, Brower Z, Zheng B, Hessell AJ, Rosenberg AF, Wu TT, Sanz I, Keefer MC, Haigwood NL, Kobie JJ. Pre-existing neutralizing antibody mitigates B cell dysregulation and enhances the Env-specific antibody response in SHIV-infected rhesus macaques. PLoS One. 2017 Feb 21;12(2):e0172524.

Tomaras GD and Plotkin SA. Complex immune correlates of protection in HIV-1 vaccine efficacy trials. Immunol Rev. 2017 Jan;275(1):245-261

Fu R, Gilbert PB. Joint modeling of longitudinal and survival data with the Cox model and two-phase sampling. Lifetime Data Anal. 2017 Jan;23(1):136-159

Gilbert PB, Juraska M, deCamp AC, Karuna S, Edupuganti S, Mgodi N, Donnell DJ, Bentley C, Sista N, Andrew P, Isaacs A, Huang Y, Zhang L, Capparelli E, Kochar N, Wang J, Eshleman SH, Mayer KH, Magaret CA, Hural J, Kublin JG, Gray G, Montefiori DC, Gomez MM, Burns DN, McElrath MJ, Ledgerwood J, Graham BS, Mascola JR, Cohen M, Corey L. (2017). Basis and Statistical Design of the Passive HIV-1 Antibody Mediated Prevention (AMP) Test-of-Concept Efficacy Trials. Stat Commun Infect Dis. 2017 Jan;9(1).