Publications

Statistical Center for HIV/AIDS Research and Prevention (SCHARP)

Publications

We are the Statistical and Data Management Center (SDMC) for multiple HIV research networks, including HIV Prevention Trials Network, HIV Vaccine Trials Network, Microbicides Trial Network, Collaboration for AIDS Vaccine Discovery, and Vaccine Immunology Statistical Center. Here are a few selected publications related to SCHARP’s work.  

Microbicide Trials Network

Dai JY, Hendrix CW, Richardson BA, Kelly C, Marzinke M, Chirenje ZM, Marrazzo JM, Brown ER. Pharmacological Measures of Treatment Adherence and Risk of HIV Infection in the VOICE Study. J Infect Dis. 2015, Epub ahead of print. PubMed PMID: 26123563.

Dimitrov D, Donnell D, Brown ER. High Incidence Is Not High Exposure: What Proportion of Prevention Trial Participants Are Exposed to HIV? PLoS One. 2015;10(1):e0115528. PMCID: PMC4287619.

Balkus JE, Nair G, Montgomery ET, Mishra A, Palanee-Phillips T, Ramjee G, Panchia R, Selepe P, Richardson BA, Chirenje ZM, Marrazzo JM. Age-Disparate Partnerships and Risk of HIV-1 Acquisition among South African Women Participating in the VOICE Trial. J Acquir Immune Defic Syndr. 2015; 70(2): 212-7. PMCID: PMC4573287.

Noguchi LM, Richardson BA, Baeten JM, Hillier SL, Balkus JE, Chirenje ZM, Bunge K, Ramjee G, Nair G, Palanee-Phillips T, Selepe P, van der Straten A, Parikh UM, Gomez K, Piper JM, Watts DH, Marrazzo JM. Risk of HIV-1 acquisition among women who use different types of injectable progestin contraception in South Africa: a prospective cohort study. Lancet HIV. 2015;2(7):e279-e87. PMCID: PMC4491329.

Marrazzo JM, Ramjee G, Richardson BA, Gomez K, Mgodi N, Nair G, Palanee T, Nakabiito C, van der Straten A, Noguchi L, Hendrix CW, Dai JY, Ganesh S, Mkhize B, Taljaard M, Parikh UM, Piper J, Masse B, Grossman C, Rooney J, Schwartz JL, Watts H, Marzinke MA, Hillier SL, McGowan IM, Chirenje ZM. Tenofovir-based preexposure prophylaxis for HIV infection among African women. N Engl J Med. 2015;372(6):509-18. PMCID: PMC4341965.

Marrazzo, Ramjee, Richardson, et al. (2015 New England Journal Medicine)

Click for high-res version

HIV Vaccine Trials Network

Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart PA, 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 P, C De Rosa S, McElrath MJ, Gottardo R COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat Biotechnol. 2015 Jun;33(6):610-6. doi: 10.1038/nbt.3187. Epub 2015 May 25. PubMed PMID: 26006008; PubMed Central PMCID: PMC4569006.

Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart PA, 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 P, C De Rosa S, McElrath MJ, Gottardo R. COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat Biotechnol. 2015 Jun;33(6):610-6. doi: 10.1038/nbt.3187. Epub 2015 May 25. PubMed PMID: 26006008; PubMed Central PMCID: PMC4569006.

Jin X, Morgan C, Yu X, DeRosa S, Tomaras GD, Montefiori DC, Kublin J, Corey L, Keefer MC; NIAID HIV Vaccine Trials Network. Multiple factors affect immunogenicity of DNA plasmid HIV vaccines in human clinical trials. Vaccine. 2015 May 11;33(20):2347-53. doi: 10.1016/j.vaccine.2015.03.036. Epub 2015 Mar 25. PubMed PMID: 25820067; PubMed Central PMCID: PMC4433533.

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 JR, Nabel GJ, Montefiori DC, Kublin J, McElrath MJ, Corey L, Gilbert PB; HVTN 505 Study Team. Efficacy trial of a DNA/rAd5 HIV-1 preventive vaccine. N Engl J Med. 2013 Nov 28;369(22):2083-92. doi: 10.1056/NEJMoa1310566. Epub 2013 Oct 7. PubMed PMID: 24099601; PubMed Central PMCID: PMC4030634. Free full text

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. Nat Med. 2011 Mar;17(3):366-71. doi: 10.1038/nm.2316. Epub 2011 Feb 27. PubMed PMID: 21358627; PubMed Central PMCID: PMC3053571. Free full text

HIV Prevention Trials Network

Donnell D, Hughes JP, Wang L, Chen YQ, Fleming TR. Study design considerations for evaluating efficacy of systemic preexposure prophylaxis interventions. J Acquir Immune Defic Syndr. 2013 Jul;63 Suppl 2:S130-4. PubMed PMID: 23764624; PubMed Central PMCID: PMC3725298.

Chen YQ, Masse B, Wang L, Ou SS, Li X, Donnell D, McCauley M, Gamble T, RibauldoHJ, Cohen MS, Fleming TR. Statistical considerations for the HPTN 052 Study to evaluate the effectiveness of early versus delayed antiretroviral strategies to prevent the sexual transmission of HIV-1 in serodiscordant couples. Contemp Clin Trials. 2012 Nov;33(6):1280-6. PubMed PMID: 22813645; PubMed Central PMCID: PMC3468650.

Dimitrov D, Donnell D, Brown ER. High incidence is not high exposure: what proportion of prevention trial participants are exposed to HIV?. PLoS One. 2015;10(1):e0115528. PubMed PMID: 25569838; PubMed Central PMCID: PMC4287619.

Metzger DS, Donnell D, Celentano DD, Jackson JB, Shao Y, Aramrattana A, Wei L, Fu L, Ma J, Lucas GM, Chawarski M, Ruan Y, Richardson P, Shin K, Chen RY, Sugarman J, Dye BJ, Rose SM, Beauchamp G, Burns DN, HPTN 058 Protocol Team. Expanding substance use treatment options for HIV prevention with buprenorphine-naloxone: HIV Prevention Trials Network 058. J Acquir Immune Defic Syndr. 2015 Apr 15;68(5):554-61.PubMed PMID: 25564105; PubMed Central PMCID: PMC4382671.

Hughes JP, Haley DF, Frew PM, Golin CE, Adimora AA, Kuo I, Justman J, Soto-Torres L, Wang J, Hodder S. Regression to the mean and changes in risk behavior following study enrollment in a cohort of US women at risk for HIV. Ann Epidemiol. 2015 Jun;25(6):439-44. PubMed PMID: 25883065; PubMed Central PMCID: PMC4433583.

Vaccine Immunology Statistical Center

Finak G, McDavid A, Chattopadhyay P, Dominguez M, De Rosa S, Roederer M, Gottardo R. Mixture models for single-cell assays with applications to vaccine studies. Biostatistics. 2014 Jan;15(1):87-101. doi: 10.1093/biostatistics/kxt024. PMID: 23887981; PMCID: PMC3862207.

Finak G, Frelinger J, Jiang W, Newell EW, Ramey J, Davis MM, Kalams SA, De Rosa SC, Gottardo R. OpenCyto: an open source infrastructure for scalable, robust, reproducible, and automated, end-to-end flow cytometry data analysis. PLoS Comput Biol. 2014 Aug 28;10(8):e1003806. doi: 10.1371/journal.pcbi.1003806. eCollection 2014 Aug. PMID: 25167361.

Lin L, Finak G, Ushey K, Seshadri C, Hawn TR, Frahm N, Scriba TJ, Mahomed H, Hanekom W, Bart PA, 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 P, C De Rosa S,McElrath MJ, Gottardo R. COMPASS identifies T-cell subsets correlated with clinical outcomes. Nat Biotechnol. 2015 Jun;33(6):610-6. doi: 10.1038/nbt.3187. PMID: 26006008; PMCID: PMC4569006.

García-Arriaza J, Perdiguero B, Heeney J, Seaman M, Montefiori DC, Labranche C, Yates NL, Shen X, Tomaras GD, Ferrari G, Foulds KE, McDermott A, Kao SF, Roederer M, Hawkins N, Self S, Yao J, Farrell P, Phogat S, Tartaglia J, Barnett SW, Burke B, Cristillo A, Weiss D, Lee C, Kibler K, Jacobs B, Asbach B, Wagner R, Ding S, Pantaleo G, Esteban M. Head-to-Head Comparison of Poxvirus NYVAC and ALVAC Vectors Expressing Identical HIV-1 Clade C Immunogens in Prime-Boost Combination with Env Protein in Nonhuman Primates. J Virol. 2015 Aug;89(16):8525-39. doi: 10.1128/JVI.01265-15. PMID: 26041302.

O'Ryan M, Bandyopadhyay AS, Villena R, Espinoza M, Novoa J, Weldon WC, Oberste MS, Self S, Borate BR, Asturias EJ, Clemens R, Orenstein W, Jimeno J, Rüttimann R, Costa Clemens SA; Chilean IPV/bOPV study group. Inactivated poliovirus vaccine given alone or in a sequential schedule with bivalent oral poliovirus vaccine in Chilean infants: a randomised, controlled, open-label, phase 4, non-inferiority study. Lancet Infect Dis. 2015 Nov;15(11):1273-82. doi: 10.1016/S1473-3099(15)00219-4. PMID: 26318714.