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Items: 22

1.

Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment.

Rossenkhan R, Rolland M, Labuschagne JPL, Ferreira RC, Magaret CA, Carpp LN, Matsen Iv FA, Huang Y, Rudnicki EE, Zhang Y, Ndabambi N, Logan M, Holzman T, Abrahams MR, Anthony C, Tovanabutra S, Warth C, Botha G, Matten D, Nitayaphan S, Kibuuka H, Sawe FK, Chopera D, Eller LA, Travers S, Robb ML, Williamson C, Gilbert PB, Edlefsen PT.

Viruses. 2019 Jul 3;11(7). pii: E607. doi: 10.3390/v11070607.

2.

Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features.

Magaret CA, Benkeser DC, Williamson BD, Borate BR, Carpp LN, Georgiev IS, Setliff I, Dingens AS, Simon N, Carone M, Simpkins C, Montefiori D, Alter G, Yu WH, Juraska M, Edlefsen PT, Karuna S, Mgodi NM, Edugupanti S, Gilbert PB.

PLoS Comput Biol. 2019 Apr 1;15(4):e1006952. doi: 10.1371/journal.pcbi.1006952. eCollection 2019 Apr.

3.

A clinical, proteomics, and artificial intelligence-driven model to predict acute kidney injury in patients undergoing coronary angiography.

Ibrahim NE, McCarthy CP, Shrestha S, Gaggin HK, Mukai R, Magaret CA, Rhyne RF, Januzzi JL Jr.

Clin Cardiol. 2019 Feb;42(2):292-298. doi: 10.1002/clc.23143. Epub 2019 Jan 8.

4.

Viral genetic diversity and protective efficacy of a tetravalent dengue vaccine in two phase 3 trials.

Juraska M, Magaret CA, Shao J, Carpp LN, Fiore-Gartland AJ, Benkeser D, Girerd-Chambaz Y, Langevin E, Frago C, Guy B, Jackson N, Duong Thi Hue K, Simmons CP, Edlefsen PT, Gilbert PB.

Proc Natl Acad Sci U S A. 2018 Sep 4;115(36):E8378-E8387. doi: 10.1073/pnas.1714250115. Epub 2018 Aug 20.

5.

A clinical and proteomics approach to predict the presence of obstructive peripheral arterial disease: From the Catheter Sampled Blood Archive in Cardiovascular Diseases (CASABLANCA) Study.

McCarthy CP, Ibrahim NE, van Kimmenade RRJ, Gaggin HK, Simon ML, Gandhi P, Kelly N, Motiwala SR, Mukai R, Magaret CA, Barnes G, Rhyne RF, Garasic JM, Januzzi JL Jr.

Clin Cardiol. 2018 Jul;41(7):903-909. doi: 10.1002/clc.22939. Epub 2018 Jun 14.

6.

Basis and Statistical Design of the Passive HIV-1 Antibody Mediated Prevention (AMP) Test-of-Concept Efficacy Trials.

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 J, Ledgerwood J, Graham BS, Mascola JR, Cohen M, Corey L.

Stat Commun Infect Dis. 2017 Jan;9(1). pii: 20160001. doi: 10.1515/scid-2016-0001. Epub 2017 Jun 6.

7.

Sieve analysis of breakthrough HIV-1 sequences in HVTN 505 identifies vaccine pressure targeting the CD4 binding site of Env-gp120.

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.

PLoS One. 2017 Nov 17;12(11):e0185959. doi: 10.1371/journal.pone.0185959. eCollection 2017.

8.

Usefulness of Multiple Biomarkers for Predicting Incident Major Adverse Cardiac Events in Patients Who Underwent Diagnostic Coronary Angiography (from the Catheter Sampled Blood Archive in Cardiovascular Diseases [CASABLANCA] Study).

McCarthy CP, van Kimmenade RRJ, Gaggin HK, Simon ML, Ibrahim NE, Gandhi P, Kelly N, Motiwala SR, Belcher AM, Harisiades J, Magaret CA, Rhyne RF, Januzzi JL Jr.

Am J Cardiol. 2017 Jul 1;120(1):25-32. doi: 10.1016/j.amjcard.2017.03.265. Epub 2017 Apr 12.

PMID:
28487034
9.

SieveSifter: a web-based tool for visualizing the sieve analyses of HIV-1 vaccine efficacy trials.

Fiore-Gartland A, Kullman N, deCamp AC, Clenaghan G, Yang W, Magaret CA, Edlefsen PT, Gilbert PB.

Bioinformatics. 2017 Aug 1;33(15):2386-2388. doi: 10.1093/bioinformatics/btx168.

10.

A Clinical and Biomarker Scoring System to Predict the Presence of Obstructive Coronary Artery Disease.

Ibrahim NE, Januzzi JL Jr, Magaret CA, Gaggin HK, Rhyne RF, Gandhi PU, Kelly N, Simon ML, Motiwala SR, Belcher AM, van Kimmenade RRJ.

J Am Coll Cardiol. 2017 Mar 7;69(9):1147-1156. doi: 10.1016/j.jacc.2016.12.021.

11.

Higher T-Cell Responses Induced by DNA/rAd5 HIV-1 Preventive Vaccine Are Associated With Lower HIV-1 Infection Risk in an Efficacy Trial.

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.

J Infect Dis. 2017 May 1;215(9):1376-1385. doi: 10.1093/infdis/jix086.

12.

A study of vaccine-induced immune pressure on breakthrough infections in the Phambili phase 2b HIV-1 vaccine efficacy trial.

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.

Vaccine. 2016 Nov 11;34(47):5792-5801. doi: 10.1016/j.vaccine.2016.09.054. Epub 2016 Oct 15.

13.

Transmitted/Founder HIV-1 Subtype C Viruses Show Distinctive Signature Patterns in Vif, Vpr, and Vpu That Are Under Subsequent Immune Pressure During Early Infection.

Rossenkhan R, MacLeod IJ, Brumme ZL, Magaret CA, Sebunya TK, Musonda R, Gashe BA, Edlefsen PT, Novitsky V, Essex M.

AIDS Res Hum Retroviruses. 2016 Oct/Nov;32(10-11):1031-1045. Epub 2016 Jul 26.

14.

No Evidence of Pritelivir Resistance Among Herpes Simplex Virus Type 2 Isolates After 4 Weeks of Daily Therapy.

Edlefsen PT, Birkmann A, Huang ML, Magaret CA, Kee JJ, Diem K, Goldner T, Timmler B, Stoelben S, Ruebsamen-Schaeff H, Zimmermann H, Warren T, Wald A, Corey L.

J Infect Dis. 2016 Jul 15;214(2):258-64. doi: 10.1093/infdis/jiw129. Epub 2016 Apr 7.

15.

Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial.

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, Kijak GH, Bose M; RV144 Sequencing Team, 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.

PLoS Comput Biol. 2015 Feb 3;11(2):e1003973. doi: 10.1371/journal.pcbi.1003973. eCollection 2015 Feb. Erratum in: PLoS Comput Biol. 2016 Jan;12(1):e1004733.

16.

Analysis of HLA A*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial.

Gartland AJ, Li S, McNevin J, Tomaras GD, Gottardo R, Janes H, Fong Y, Morris D, Geraghty DE, 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.

J Virol. 2014 Aug;88(15):8242-55. doi: 10.1128/JVI.01164-14. Epub 2014 May 14.

17.

Analysis of HIV using a high resolution melting (HRM) diversity assay: automation of HRM data analysis enhances the utility of the assay for analysis of HIV incidence.

Cousins MM, Swan D, Magaret CA, Hoover DR, Eshleman SH.

PLoS One. 2012;7(12):e51359. doi: 10.1371/journal.pone.0051359. Epub 2012 Dec 11.

18.

Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2.

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.

Nature. 2012 Oct 18;490(7420):417-20. doi: 10.1038/nature11519. Epub 2012 Sep 10.

19.

Comparison of a high-resolution melting assay to next-generation sequencing for analysis of HIV diversity.

Cousins MM, Ou SS, Wawer MJ, Munshaw S, Swan D, Magaret CA, Mullis CE, Serwadda D, Porcella SF, Gray RH, Quinn TC, Donnell D, Eshleman SH, Redd AD.

J Clin Microbiol. 2012 Sep;50(9):3054-9. doi: 10.1128/JCM.01460-12. Epub 2012 Jul 11.

20.

Machine learning competition in immunology - Prediction of HLA class I binding peptides.

Zhang GL, Ansari HR, Bradley P, Cawley GC, Hertz T, Hu X, Jojic N, Kim Y, Kohlbacher O, Lund O, Lundegaard C, Magaret CA, Nielsen M, Papadopoulos H, Raghava GP, Tal VS, Xue LC, Yanover C, Zhu S, Rock MT, Crowe JE, Panayiotou C, Polycarpou MM, Duch W, Brusic V.

J Immunol Methods. 2011 Nov 30;374(1-2):1-4. doi: 10.1016/j.jim.2011.09.010. Epub 2011 Sep 29. No abstract available.

PMID:
21986107
21.

Recurrent signature patterns in HIV-1 B clade envelope glycoproteins associated with either early or chronic infections.

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.

PLoS Pathog. 2011 Sep;7(9):e1002209. doi: 10.1371/journal.ppat.1002209. Epub 2011 Sep 29.

22.

Genetic impact of vaccination on breakthrough HIV-1 sequences from the STEP trial.

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.

Nat Med. 2011 Mar;17(3):366-71. doi: 10.1038/nm.2316. Epub 2011 Feb 27.

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