Manuscripts

2017

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

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. Statistical Communications in Infectious Diseases. 2017. 9(1).

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.

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

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.

Benkeser D, Carone M, Gilbert PB. Improved estimation of the cumulative incidence of rare outcomes. Stat Med. 2017 Jul 2. [Epub ahead of print]

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

 

2016

Hanscom B, Janes HE, Guarino PD, Huang Y, Brown ER, Chen YQ, Hammer SM, Gilbert PB, Donnell DJ. Preventing HIV-1 Infection in Women using Oral Pre-Exposure Prophylaxis: A Meta-analysis of Current Evidence. J Acquir Immune Defic Syndr. 2016 Dec 15;73(5):606-608

Imholte G, Gottardo R. Bayesian hierarchical modeling for subject-level response classification in peptide microarray immunoassays. Biometrics. 2016 Dec;72(4):1206-1215

Astronomo RD, Santra S, Ballweber-Fleming L, Westerberg KG, Mach L, Hensley-McBain T, Sutherland L, Mildenberg B, Morton G, Yates NL, Mize GJ, Pollara J, Hladik F, Ochsenbauer C, Denny TN, Warrier R, Rerks-Ngarm S, Pitisuttithum P, Nitayapan S, Kaewkungwal J, Ferrari G, Shaw GM, Xia SM, Liao HX, Montefiori DC, Tomaras GD, Haynes BF, McElrath MJ. Neutralization Takes Precedence Over IgG or IgA Isotype-related Functions in Mucosal HIV-1 Antibody-mediated Protection. EBioMedicine. 2016 Dec;14:97-111

Moodley N, Gray G, Bertram M. The Price of Prevention: Cost Effectiveness of Biomedical HIV Prevention Strategies in South Africa. Clin Res HIV/AIDS. 2016; 3(1): 1031.

Ramachandran S, Mishra S, Condie N, Pickles M. How do HIV-negative individuals in sub-Saharan Africa change their sexual risk behaviour upon learning their serostatus? A systematic review. Sex Transm Infect. 2016 Dec;92(8):571-578.

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, Mullins 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 Nov 11;34(47):5792-5801

Nemes E, Burgers WA, Riou C, Andersen-Nissen E, Ferrari G, Gray CM, Scriba T. Teaching advanced flow cytometry in Africa: 10 years of lessons learned. Cytometry A. 2016 Nov;89(11):971-974.

Gilbert PB, Huang Y, Janes HE. Modeling HIV vaccine trials of the future. Curr Opin HIV AIDS. 2016 Nov;11(6):620-627.

Keefer M, Zheng B, Rosenberg AF, Kobie JJ. Increased steady-state memory B cell subsets among high-risk participants in an HIV vaccine trial. AIDS Res Hum Retroviruses. 2016 Oct/Nov;32(10-11):1143-1148

Safrit JT, Tomaras GD, Hanke T, deCamp AC, Voronin Y. The Landscape of Targeted Immune Responses in the HIV-1 Vaccine Field. AIDS Res Hum Retroviruses. 2016 Oct/Nov;32(10-11):944-946

Fong Y, Yin S and Huang Y. Combining biomarkers linearly and nonlinearly for classification using the area under the ROC curve. Stat Med. 2016 Sep 20;35(21):3792-809.

Gilbert PB, Janes H and Huang Y. Power/sample size calculations for assessing correlates of risk in clinical efficacy trials. Stat Med. 2016 Sep 20;35(21):3745-59

Churchyard G, Mlisana K, Karuna S, Williamson AL, Williamson C, Morris L, Tomaras GD, De Rosa SC, Gilbert PB, Gu N, Yu C, Mkhize NN, Hermanus T, Allen M, Pensiero M, Barnett SW, Gray G, Bekker LG, Montefiori DC, Kublin J, Corey L. Sequential Immunization with gp140 Boosts Immune Responses Primed by Modified Vaccinia Ankara or DNA in HIV-Uninfected South African Participants. PLoS One. 2016 Sep 1;11(9):e0161753

Lama JR, Karuna ST, Grant SP, Swann EM, Ganoza C, Segura P, Montano SM, Lacherre M, De Rosa SC, Buchbinder S, Sanchez J, McElrath MJ, Lemos MP, for the HVTN 914 Study Team. Transient Peripheral Immune Activation follows Elective Sigmoidoscopy or Circumcision in a Cohort Study of MSM at Risk of HIV Infection. PLoS One. 2016 Aug 18;11(8):e0160487

Siskind RL, Andrasik M, Karuna ST, Broder GB, Collins C, Liu A, Lucas JP, Harper GW, Renzullo PO. Engaging Transgender People in NIH-Funded HIV/AIDS Clinical Trials Research. J Acquir Immune Defic Syndr. 2016 Aug 15;72 Suppl 3:S243-7.

Leitman EM, Hurst J, Mori M, Kublin J, Ndung'u T, Walker BD, Carlson J, Gray GE, Matthews PC, Frahm N, Goulder PJR. Lower Viral Loads and Slower CD4 Decline in MRKAd5 HIV-1 Vaccinees Expressing Disease-Susceptible HLA-B*58:02. J Infect Dis. 2016 Aug 1;214(3):379-89

Rademeyer C, Korber B, Seaman MS, Giorgi EE, Thebus R, Robles A, Sheward DJ, Wagh K, Garrity J, Carey BR, Gao H, Greene KM, Tang H, Bandawe GP, Marais JC, Diphoko TE, Hraber P, Tumba N, Moore PL, Gray GE, Kublin J, McElrath MJ, Vermeulen M, Middelkoop K, Bekker LG, Hoelscher M, Maboko L, Makhema J, Robb ML, Abdool Karim S, Abdool Karim Q, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C. Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization. PLoS Pathog. 2016 Jul 19;12(7):e1005742.

Hayes PJ, Cox JH, Coleman AR, Fernandez N, Bergin PJ, Kopycinski JT, Nitayaphan S, Pitisuttihum P, de Souza M, Duerr A, Morgan C, Gilmour JW. Adenovirus based HIV-1 vaccine candidates tested in efficacy trials elicit CD8 T-cells with limited breadth of HIV-1 inhibition. AIDS. 2016 Jul 17;30(11):1703-12.

Gray GE, Mayer KH, Elizaga ML, Bekker LG, Allen M, Morris L, Montefiori D, De Rosa SC, Sato A, Gu N, Tomaras GD, Tucker T, Barnett SW, Mkhize NN, Shen X, Downing K, Williamson C, Pensiero M, Corey L, Williamson AL; NIAID-funded HIV Vaccine Trials Network. Subtype C gp140 vaccine boosts immune responses primed by SAAVI DNA-C2 and MVA-C HIV vaccine after more than a two year gap (HVTN 073E/SAAVI 102). Clin Vaccine Immunol. 2016 Jun 6;23(6):496-506

McDavid A, Finak G, Gottardo R. The contribution of cell cycle to heterogeneity in single-cell RNA-seq data. Nat Biotechnol. 2016 Jun 9;34(6):591-3.

Carlson JM, Du VY, Pfeifer N, Bansal A, Tan VY, Power K, Brumme CJ, Kreimer A, DeZiel CE, Fusi N, Schaefer M, Brockman MA, Gilmour J, Price MA, Kilembe W, Haubrich R, John M, Mallal S, Shapiro R, Frater J, Harrigan PR, Ndung'u T, Allen S, Heckerman D, Sidney J, Allen TM, Goulder PJ, Brumme ZL, Hunter E, Goepfert PA. Impact of pre-adapted HIV transmission. Nat Med. 2016 Jun;22(6):606-13.

Hughes SM, Shu Z, Levy CN, Ferre AL, Hartig H, Fang C, Lentz G, Fialkow M, Kirby AC, Adams Waldorf KM, Veazey RS, Germann A, von Briesen H, McElrath MJ, Dezzutti CS, Sinclair E, Baker CA, Shacklett BL, Gao D, Hladik F. Cryopreservation of Human Mucosal Leukocytes. PLoS One. 2016 May 27;11(5):e0156293. eCollection 2016.

Lemos MP, Karuna ST, Mize GJ, Fong Y, Montano SM, Ganoza C, Lama JR, Sanchez J, McElrath MJ. In Men at Risk of HIV Infection, IgM, IgG1, IgG3 and IgA Reach the Human Foreskin Epidermis. Mucosal Immunol. 2016 May;9(3):798-808

Lhomme E, Richert L, Moodie Z, Pasin C, Kalams SA, Morgan C, Self S, De Rosa SC, Thiébaut R. Early CD4+ T Cell Responses Are Associated with Subsequent CD8+ T Cell Responses to an rAd5-Based Prophylactic Prime-Boost HIV Vaccine Strategy. PLoS One. 2016 Apr 28;11(4):e0152952.

Mkhize NN, Durgiah R, Ashley V, Archary D, Garrett NJ, Karim QA, Karim SS, Moore PL, Yates N, Passmore JS, Tomaras GD, Morris L. Broadly neutralizing antibody specificities detected in the genital tract of HIV-1 infected women. AIDS. 2016 Apr 24;30(7):1005-14.

Moodley N, Gray G, Bertram M. Projected economic evaluation of the national implementation of a hypothetical HIV vaccination program among adolescents in South Africa, 2012. BMC Public Health. 2016 Apr 14;16(1):330.

Kriek JM, Jaumdally SZ, Masson L, Little F, Mbulawa Z, Gumbi PP, Barnabas SL, Moodley J, Denny L, Coetzee D, Williamson AL, Passmore JS. Female genital tract inflammation, HIV co-infection and persistent mucosal Human Papillomavirus (HPV) infections. Virology. 2016 Apr 8;493:247-254.

Fu R, Gilbert PB. Joint modeling of longitudinal and survival data with the Cox model and two-phase sampling. Lifetime Data Anal. 2016 Mar 23. [Epub ahead of print]

Gray GE, Laher F, Lazarus E, Ensoli B, Corey L. Approaches to preventative and therapeutic HIV vaccines. Curr Opin Virol. 2016 Mar 14;17:104-109.

Havenar-Daughton C, Lindqvist M, Heit A, Wu JE, Reiss SM, Kendric K, Bélanger S, Kasturi SP, Landais E, Akondy RS, McGuire HM, Bothwell M, Vagefi PA, Scully E; IAVI Protocol C Principal Investigators, Tomaras GD, Davis MM, Poignard P, Ahmed R, Walker BD, Pulendran B, McElrath MJ, Kaufmann DE, Crotty S. CXCL13 is a plasma biomarker of germinal center activity. Proc Natl Acad Sci U S A. 2016 Mar 8;113(10):2702-7

Gray GE, Laher F, Doherty T, Abdool Karim S, Hammer S, Mascola J, Beyrer C and Corey L. Which New Health Technologies Do We Need to Achieve an End to HIV/AIDS? PLoS Biol. 2016 Mar 2;14(3):e1002372

Baden LR, Karita E, Mutua G, Bekker LG, Gray G, Page-Shipp L, Walsh SR, Nyombayire J, Anzala O, Roux S, Laher F, Innes C, Seaman MS, Cohen YZ, Peter L, Frahm N, McElrath MJ, Hayes P, Swann E, Grunenberg N, Grazia-Pau M, Weijtens M, Sadoff J, Dally L, Lombardo A, Gilmour J, Cox J, Dolin R, Fast P, Barouch DH, Laufer DS; B003-IPCAVD004-HVTN091 Study Group. Assessment of the Safety and Immunogenicity of 2 Novel Vaccine Platforms for HIV-1 Prevention: A Randomized Trial. Ann Intern Med. 2016 Mar 1;164(5):313-22.

Nicholas KJ, Greenplate AR, Flaherty DK, Matlock BK, Juan JS, Smith RM, Irish JM, Kalams SA. Multiparameter analysis of stimulated human peripheral blood mononuclear cells: A comparison of mass and fluorescence cytometry. Cytometry A. 2016 Mar;89(3):271-80

Walsh SR, Moodie Z, Fiore-Gartland AJ, Morgan C, Wilck MB, Hammer SM, Buchbinder SP, Kalams SA, Goepfert PA, Mulligan MJ, Keefer MC, Baden LR, Swann EM, Grant S, Ahmed H, Hertz T, Self SG, Friedrich D, Frahm N, Liao H-X, Montefiori DC, Tomaras GD, McElrath MJ, Hural J, Graham BS, Jin X, the HVTN 083 Study Group, and the NIAID HIV Vaccine Trials Network. Vaccination with heterologous HIV envelope sequences and heterologous adenovirus vectors increases T cell responses to conserved regions (HVTN 083). J Infect Dis. 2016 Feb 15;213(4):541-50.

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 Feb 10;11(2):e0147812

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 J, Gray G, Kublin J, Corey L, Gilbert PB. Selection of HIV vaccine candidates for concurrent testing in an efficacy trial. Curr Opin Virol. 2016 Jan 28;17:57-65.

Gilbert PB and 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. Epidemiologic Methods. 2016 Jan 23. [Epub ahead of print]

Deschamps MM, Metch B, Morgan C, Zorilla CD, Donastorg Y, Swann E, Taina D, Patrice J, Pape JW on behalf of the HVTN 907 Study Team. Feasibility of Identifying a Female Sex Worker Cohort at High Risk of HIV Infection in the Caribbean for HIV Vaccine Efficacy Trials: Longitudinal Results of HVTN 907. J Acquir Immune Defic Syndr. 2016 Jan 1;71(1):70-7.

Sajadi MM, Farshidpour M, Brown EP, Ouyang X, Seaman MS, Pazgier M, Ackerman ME, Robinson H, Tomaras G, Parsons MS, Charurat M, DeVico AL, Redfield RR, Lewis GK. Lambda light chain bias associated with enhanced binding and function of anti-HIV Env glycoprotein antibodies.  J Infect Dis. 2016 Jan 1;213(1):156-64.

Moodley N, Gray G, Bertram M. The Case for Adolescent HIV Vaccination in South Africa: A Cost-Effectiveness Analysis. Medicine. 2016 Jan;95(4):e2528.

Sun Y, Li M, Gilbert PB. Goodness-of-fit test of the stratified mark-specific proportional hazards model with continuous mark. Comput Stat Data Anal. 2016 Jan 1;93:348-358.

Imholte G, Sauteraud R, Gottardo R. Analyzing Peptide Microarray Data with the R pepStat Package. Methods Mol Biol. 2016;1352:127-42

Finak G, Gottardo R. Promises and Pitfalls of High-Throughput Biological Assays. Methods Mol Biol. 2016;1415:225-43.