Publications
2024
Juraska M, Bai H, deCamp AC, Magaret CA, Li L, Gillespie K, Carpp LN, Giorgi EE, Ludwig J, Molitor C, Hudson A, Williamson BD, Espy N, Simpkins B, Rudnicki E, Shao D~, Rossenkhan R~, Edlefsen PT, Westfall DH, Deng W, Chen L, Zhao H, Bhattacharya T, Murrell B, Yssel A, Matten D, York T, Beaume N, Gwashu-Nyangiwe A, Ndabambi N, Thebus R, Karuna ST, Morris L, Montefiori DC, Hural JA, Cohen MS, Corey L, Rolland M, Gilbert PB, Williamson C, Mullins JI. Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features. PNAS. 2024 Jan 23;121(4):e2308942121. PMID: 38241441 DOI: 10.1073/pnas.2308942121.
Miner MD, deCamp A, Grunenberg N, De Rosa SC, Fiore-Gartland A, Bar K, Spearman P, Allen M, Yu P, Manso B, Frahm N, Kalams S, Baden L, Keefer MC, Scott HM, Novak R, Tieu HV, Tomaras GD, Kublin JG, McElrath MJ, Corey L, Frank I on behalf of the HVTN 085 Study Team (*Edlefsen PT is a member of The HVTN 085 Study Team) Polytopic fractional delivery of an HIV vaccine alters cellular responses and results in increased epitope breadth in a phase 1 randomized trial. February 2024 EBioMedicine 100(14):104987 DOI: 10.1016/j.ebiom.2024.104987
Peters MQ, Domenjo-Vila E, Carlson M,Edlefsen PT, Gasper M, Dabee S, Armistead B, Whidbey C, JaspanHB, Prlic M, Harrington WE. A non-invasive method to sample immune cells in the lower female genital tractusing menstrual discs.ImmunoHorizons.(2024) 8 (2): 182–192.PMCID: PMC10871271PMID: 38370684DOI:10.4049/immunohorizons.230010565.
Joy J, Gervassi A, Chen L, Kirshenbaum B, Styrchak S, Ko D, McLaughlin S,Shao D~,Kosmider E~,EdlefsenPT, Maenza J, Collier AC, Mullins JI, Horton H, Frenkel LM. Antigen specificities and proviral integrationsites differ in HIV-infected cells by timing of antiretroviral-treatment initiation.J Clin Invest.2024 Jun4:e159569.PMID: 38833307DOI: 10.1172/JCI159569.
~Student or Postdoc of PT Edlefsen.
Kosmider E, Wallner J, Gervassi A, Bender Ignacio RA,Pinto-Santini D, Gornalusse G, Pandey U, Hladik F, Edlefsen PT, Lama JR, Duerr AC, Frenkel LM. Observational study of effects of HIV acquisition and antiretroviral treatment on biomarkers of systemic immune activation. PLoS One. 2024 Jul 8;19(7):e0288895.doi: 10.1371/journal.pone.0288895. PMID: 38976697; PMCID: PMC11230552.67.
Varco-Merth B, Chaunzwa M, Duell DM, Marenco A, Goodwin W, Dannay R, Nekorchuk M, Shao D, Busman-Sahay K, Fennessey CM, Silipino L, Hull M, Bosche WJ, Fast R, Oswald K, Shoemaker R, Bochart R, MacAllister R, Labriola CS, Smedley JV, Axthelm MK, Davenport MP, Edlefsen PT, Estes JD, Keele BF, Lifson JD, Lewin SR, Picker LJ, Okoye AA. Impact of alemtuzumab-mediated lymphocyte depletion on SIV reservoir establishment and persistence. PLoS Pathog. 2024 Aug 22;20(8):e1012496. doi:10.1371/journal.ppat.1012496. PMID: 39173097; PMCID: PMC11373844.68.
Tisoncik-Go J, Lewis TB, Whitmore LS, Voss K, Niemeyer S, Dai J, Kim P, Hubbell K, Iwayama N, AhrensC, Wangari S, Murnane R, Edlefsen PT, Guerriero KA, Gale M Jr, Fuller DH, O'Connor MA. Chronic innateimmune impairment and ZIKV persistence in the gastrointestinal tract during SIV infection in pigtail macaques
Dubois MM, Jao J, Sun S, Legbedze J, Schenkel S, Mmasa N, Kgole SW, Masasa G, Happel AU, Iwase SC,Haghighat R, Moyo S, Sharma TS, Edlefsen PT, Shao D, Jaspan H, Powis KM. Infectious Morbidity and All-cause Mortality of Infants HIV-exposed Uninfected Compared to Infants HIV-unexposed Uninfected in Botswana. Pediatr Infect Dis J. 2024 Oct 31. doi: 10.1097/INF.0000000000004603. Epub ahead of print. PMID:39486012
2023
Hawman DW, Meade-White K, Leventhal S, Song W~, Randall S, Archer J, Lewis TB, Brown B, Iwayama N, Ahrens C, Garrison W, Wangari S, Guerriero KA, Hanley P, Lovaglio J, Saturday G, Edlefsen PT, Khandhar A, Feldmann H, Fuller DH, Erasmus JH. A replicon RNA vaccine can induce durable protective immunity from SARS-CoV-2 in nonhuman primates after neutralizing antibodies have waned. PLOS Plathogens. 2023 Apr 19;19(4):e1011298. PMCID: PMC10150980.
Harwood OE, Balgeman AJ, Weaver AJ, Ellis-Connell AL, Weiler AM, Erickson KN, Matschke LM, Golfinos AE, Vezys V, Skinner PJ, Safrit JT, Edlefsen PT, Reynolds MR, Friedrich TC, O'Connor SL. Transient T Cell Expansion, Activation, and Proliferation in Therapeutically Vaccinated Simian Immunodeficiency Virus-Positive Macaques Treated with N-803. J Virol. 2022 Dec 14;96(23):e0142422. DOI: 10.1128/jvi.01424-22. Epub 2022 Nov 15. PMID: 36377872; PMCID: PMC9749465. 2023
O’Connor MA, Hawman DW, Meade-White K, Leventhal S, Song W~, Randall S, Archer J, Lewis TB, Brown B, Fredericks MN, Sprouse KR,Tunggal H, Maughan M, Iwayama N, Ahrens C, Garrison W, Wangari S, Guerriero KA, Hanley P, Lovaglio J , Saturday G, Veesler D, Edlefsen PT, Khandhar AP, Feldmann H, Fuller DH, Erasmus JH. A replicon RNA vaccine can induce durable protective immunity from SARS-CoV-2 in nonhuman primates after neutralizing antibodies have waned. PLOS Pathogens. 2023;19(4):p.e1011298. PMCID: PMC10150980.
Seaton KE, Huang Y, Karuna S, Heptinstall JR, Brackett C, Chiong K, Zhang L, Yates NL, Sampson M, Rudnicki E, Juraska M, deCamp A, Edlefsen PT, Mullins JI, Williamson C, Rossenkhan R~. Pharmacokinetic serum concentrations of VRC01 correlate with prevention of HIV-1 acquisition. EBioMedicine. 2023;93. PMCID: PMC10363420.
Tisoncik-Go J, Voss KM, Lewis TB, Muruato AE, Kuller L, Finn EE, Betancourt D, Wangari S, Ahrens J, Iwayama N, Grant RF, Murnane RD, Edlefsen PT, Fuller DH, Barber GN, Gale Jr M, O’Connor MA. Evaluation of the immunogenicity and efficacy of an rVSV vaccine against Zika virus infection in macaca nemestrina. Frontiers in Virology. 2023;3:1108420. PMCID: PMC10306241.
Vigdorovich V, Patel H, Watson A, Raappana A, Reynolds L, Selman W, Beeman S, Edlefsen PT, Kappe SH, Sather DN. Coimmunization with Preerythrocytic Antigens alongside Circumsporozoite Protein Can Enhance Sterile Protection against Plasmodium Sporozoite Infection. Microbiology Spectrum. 2023;11(2):e03791-22. PMCID: PMC10100930.
Iwase SC, Edlefsen PT, Bhebhe L, Motsumi K, Moyo S, Happel AU, Shao D~, Mmasa N, Schenkel S, Gasper MA, Dubois M, Files MA, Seshadri C, Duffy F, Aitchison J, Netea MG, Jao J, Cameron DW, Gray CM, Jaspan HB, Powis KM. T-SPOT.TB Reactivity in Southern African Children With and Without in Utero Human Immunodeficiency Virus Exposure. Clin Infect Dis. 2023 Oct 13;77(8):1133-1136. DOI: 10.1093/cid/ciad356. PMID: 37293702; PMCID: PMC10573724.
Plumlee CR, Barrett HW, Shao D~, Lien KA, Cross LM, Cohen SB, Edlefsen PT, Urdahl KB. Assessing vaccine-mediated protection in an ultra-low dose Mycobacterium tuberculosis murine model. PLOS Pathogens. 2023 Nov 27. DOI: 10.1371/journal.ppat.1011825.
Reeves D, Mayer B, deCamp A, Huang Y, Zhang B, Carpp L, Magaret C, Gilbert P, Montefiori D, Bar K, Morris L, Mkhize N, Williamson C, Mullins J, Seaton K, Tomaras G, Andrew P, Mgodi N, Ledgerwood J, Cohen M, Corey L, Naidoo L, Orrell C, Goepfert P, Casapia M, Sobieszczyk M, Karuna S, Edupuganti S, Juraska M, Schiffer J, Cardozo-Ojeda E, Rossenkhan R~, Edlefsen PT. High monoclonal neutralization titers reduced breakthrough HIV-1 viral loads in the Antibody Mediated Prevention trials. Nature Communications 14, 8299 (2023). DOI: 10.1038/s41467-023-43384-y
Domenjo-Vila E, Carlson M, Edlefsen PT, Gasper M, Dabee S, Armistead B, Whidbey C, Jaspan HB, Prlic M, Harrington WE. A non-invasive method to sample immune cells in the lower female genital tract using menstrual discs. ImmunoHorizons. DOI: 10.1101/2023.11.16.567469
~ Student or Postdoc of PT Edlefsen
2022
Verweij MC, Hansen SG, Iyer R, John N, Malouli D, Morrow D, Scholz I, Womack J, Abdulhaqq S, Gilbride RM, Hughes CM, Ventura AB, Ford JC, Selseth AN, Oswald K, Shoemaker R, Berkemeier B, Bosche WJ, Hull M, Shao D~, Sacha JB, Axthelm MK, Edlefsen PT, Lifson JD, Picker LJ, Fruh K. Modulation of MHC-E transport by viral decoy ligands is required for RhCMV/SIV vaccine efficacy. Science. 2021;372(6541). PMCID: PMC8354429.
Gilbert PB, Huang Y, deCamp AC, Karuna S, Zhang Y, Magaret CA, Giorgi EE, Korber B, Edlefsen PT, Rossenkhan R~, Juraska M, Rudnicki E, Kochar N, Huang Y, Carpp LN, Barouch DH, Mkhize NN, Hermanus T, Kgagudi P, Bekker V, Kaldine H, Mapengo RE, Eaton A, Domin E, West C, Feng W, Tang H, Seaton KE, Heptinstall J, Brackett C, Chiong K, Tomaras GD, Andrew P, Mayer BT, Reeves DB, Sobieszczyk ME, Garrett N, Sanchez J, Gay C, Makhema J, Williamson C, Mullins JI, Hural J, Cohen MS, Corey L, Montefiori DC, Morris L. Neutralization titer biomarker for antibody-mediated prevention of HIV-1 acquisition. Nature Medicine. 2022;28(9):1924-32. PMCID: PMC9499869.
Hansen SG, Hancock MH, Malouli D, Marshall EE, Hughes CM, Randall KT, Morrow D, Ford JC, Gilbride RM, Selseth AN, Trethewy RE, Bishop LM, Oswald K, Shoemaker R, Berkemeier B, Bosche WJ, Hull M, Silipino L, Nekorchuk M, Busman-Sahay K, Estes JD, Axthelm MK, Smedley J, Shao D~, Edlefsen PT, Lifson JD, Fruh K, Nelson JA, Picker LJ. Myeloid cell tropism enables MHC-E-restricted CD8(+) T cell priming and vaccine efficacy by the RhCMV/SIV vaccine. Science Immunology. 2022;7(72):eabn9301. PMCID: PMC9387538.
Varco-Merth BD, Brantley W, Marenco A, Duell DD, Fachko DN, Richardson B, Busman-Sahay K, Shao D~, Flores W, Engelman K, Fukazawa Y, Wong SW, Skalsky RL, Smedley J, Axthelm MK, Lifson JD, Estes JD, Edlefsen PT, Picker LJ, Cameron CM, Henrich TJ, Okoye AA. Rapamycin limits CD4+ T cell proliferation in simian immunodeficiency virus-infected rhesus macaques on antiretroviral therapy. The Journal of Clinical Investigation. 2022;132(10). PMCID: PMC9106346.
2021
Barrenas F, Hansen SG, Law L, Driscoll C, Green RR, Smith E, Chang J, Golez I, Urion T, Peng X, Whitmore L, Newhouse D, Hughes CM, Morrow D, Randall KT, Selseth AN, Ford JC, Gilbride RM, Randall BE, Ainslie E, Oswald K, Shoemaker R, Fast R, Bosche WJ, Axthelm MK, Fukazawa Y, Pavlakis GN, Felber BK, Fourati S, Sekaly RP, Lifson JD, Komorowski J, Kosmider E~, Shao D~, Song W~, Edlefsen PT, Picker LJ, Gale M, Jr. Interleukin-15 response signature predicts RhCMV/SIV vaccine efficacy. PLoS Pathogens. 2021;17(7):e1009278. PMCID: PMC8284654.
Ford ES, Sholukh AM, Boytz R, Carmack SS, Klock A, Phasouk K, Shao D~, Rossenkhan R~, Edlefsen PT, Peng T, Johnston C, Wald A, Zhu J, Corey L. B cells, antibody-secreting cells, and virus-specific antibodies respond to herpes simplex virus 2 reactivation in skin. The Journal of Clinical Investigation. 2021;131(9). PMCID: PMC8087200.
Jacob PE, Gong R, Edlefsen PT, Dempster AP. A Gibbs sampler for a class of random convex polytopes. Journal of the American Statistical Association. 2021;116(535):1181-92. PMCID: PMC8945543.
Jacob PE, Gong R, Edlefsen PT, Dempster AP. Rejoinder - A Gibbs sampler for a class of random convex polytopes. Journal of the American Statistical Association. 2021;116(535):1211-14. doi: 10.1080/01621459.2021.1945458.
Ford ES, Sholukh AM, Boytz RM, Carmack SS, Klock A, Phasouk K, Shao J~, Rossenkhan R~, Edlefsen PT, Peng T, Johnston C, Wald A, Zhu J, Corey L. B cells and HSV-specific antibodies respond to HSV-2 reactivation in skin. Clin Invest. 2021 May 3;131(9):e142088. doi:10.1172/JCI142088.
Kidzeru E, Gasper MA, Shao D~, Edlefsen PT, Lejarcegui N, Havyarimana E, Urdahl K, Gantt S, Horton H, Jaspan H, Gervassi A. Myeloid-derived suppressor cells and their association with vaccine immunogenicity in South African infants. Journal of Leukocyte Biology. 2021;110(5):939-50. PMCID: PMC8292449.
Lewitus E, Sanders-Buell E, Bose M, O'Sullivan AM, Poltavee K, Li Y, Bai H, Mdluli T, Donofrio G, Slike B, Zhao H, Wong K, Chen L, Miller S, Lee J, Ahani B, Lepore S, Muhammad S, Grande R, Tran U, Dussupt V, Mendez-Rivera L, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Rerks-Ngarm S, O'Connell RJ, Janes H, Gilbert PB, Gramzinski R, Vasan S, Robb ML, Michael NL, Krebs SJ, Herbeck JT, Edlefsen PT, Mullins JI, Kim JH, Tovanabutra S, Rolland M. RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection. Virus Evolution. 2021;7(2):veab057. PMCID: PMC8438874.
Malouli D, Hansen SG, Hancock MH, Hughes CM, Ford JC, Gilbride RM, Ventura AB, Morrow D, Randall KT, Taher H, Uebelhoer LS, McArdle MR, Papen CR, Espinosa Trethewy R, Oswald K, Shoemaker R, Berkemeier B, Bosche WJ, Hull M, Greene JM, Axthelm MK, Shao D~, Edlefsen PT, Grey F, Nelson JA, Lifson JD, Streblow D, Sacha JB, Fruh K, Picker LJ. Cytomegaloviral determinants of CD8(+) T cell programming and RhCMV/SIV vaccine efficacy. Science Immunology. 2021;6(57). PMCID: PMC8244349.
Mdluli T, Jian N, Slike B, Paquin-Proulx D, Donofrio G, Alrubayyi A, Gift S, Grande R, Bryson M, Lee A, Dussupt V, Mendez-Rivera L, Sanders-Buell E, Chenine AL, Tran U, Li Y, Brown E, Edlefsen PT, O'Connell R, Gilbert P, Nitayaphan S, Pitisuttihum P, Rerks-Ngarm S, Robb ML, Gramzinski R, Alter G, Tovanabutra S, Georgiev IS, Ackerman ME, Polonis VR, Vasan S, Michael NL, Kim JH, Eller MA, Krebs SJ, Rolland M. Correction: RV144 HIV-1 vaccination impacts post-infection antibody responses. PLoS Pathogens. 2021;17(3):e1009386. PMCID: PMC7924741.
10. Okoye AA, Duell DD, Fukazawa Y, Varco-Merth B, Marenco A, Behrens H, Chaunzwa M, Selseth AN, Gilbride RM, Shao D~, Edlefsen PT, Geleziunas R, Pinkevych M, Davenport MP, Busman-Sahay K, Nekorchuk M, Park H, Smedley J, Axthelm MK, Estes JD, Hansen SG, Keele BF, Lifson JD, Picker LJ. CD8+ T cells fail to limit SIV reactivation following ART withdrawal until after viral amplification. The Journal of Clinical Investigation. 2021;131(8). PMCID: PMC8262469.
2020
Taher H, Mahyari E, Kreklywich C, Uebelhoer LS, McArdle MR, Mostrom MJ, Bhusari A, Nekorchuk M, E X, Whitmer T, Scheef EA, Sprehe LM, Roberts DL, Hughes CM, Jackson KA, Selseth AN, Ventura AB, Cleveland-Rubeor HC, Yue Y, Schmidt KA, Shao J, Edlefsen PT, Smedley J, Kowalik TF, Stanton RJ, Axthelm MK, Estes JD, Hansen SG, Kaur A, Barry PA, Bimber BN, Picker LJ, Streblow DN, Fruh K, Malouli D. In vitro and in vivo characterization of a recombinant rhesus cytomegalovirus containing a complete genome. PLoS Pathogens. 2020;16(11):e1008666. PMCID: PMC7723282.
Rolland M, Tovanabutra S, Dearlove B, Li Y, Owen CL, Lewitus E, Sanders-Buell E, Bose M, O'Sullivan A, Rossenkhan R, Labuschagne JPL, Edlefsen PT, Reeves DB, Kijak G, Miller S, Poltavee K, Lee J, Bonar L, Harbolick E, Ahani B, Pham P, Kibuuka H, Maganga L, Nitayaphan S, Sawe FK, Eller LA, Gramzinski R, Kim JH, Michael NL, Robb ML, RV217 Study Team. Molecular dating and viral load growth rates suggested that the eclipse phase lasted about a week in HIV-1 infected adults in East Africa and Thailand. PLoS Pathogens. 2020;16(2):e1008179. PMCID: PMC7004303.
Mdluli T, Jian N, Slike B, Paquin-Proulx D, Donofrio G, Alrubayyi A, Gift S, Grande R, Bryson M, Lee A, Dussupt V, Mendez-Riveria L, Sanders-Buell E, Chenine AL, Tran U, Li Y, Brown E, Edlefsen PT, O'Connell R, Gilbert P, Nitayaphan S, Pitisuttihum P, Rerks-Ngarm S, Robb ML, Gramzinski R, Alter G, Tovanabutra S, Georgiev IS, Ackerman ME, Polonis VR, Vasan S, Michael NL, Kim JH, Eller MA, Krebs SJ, Rolland M. RV144 HIV-1 vaccination impacts post-infection antibody responses. PLoS Pathogens. 2020;16(12):e1009101. PMCID: PMC7748270.
Curlin ME, Shao J, Diaz G, Edlefsen PT, Novak RM, Mayer KH, Allen M, Morgan C, Maenza J, Buchbinder S, Keefer MC, Rosa SC, Corey L, Duerr A, NIAID HIV Vaccine Trials Network (HVTN). Long-term mucosal T cell activation and homing phenotypes in recipients of an Ad5-vectored HIV vaccine. Vaccine. 2020;38(36):5814-21. PMID: 32680773.
2019
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. Combining Viral Genetics and Statistical Modeling to Improve HIV-1 Time-of-infection Estimation towards Enhanced Vaccine Efficacy Assessment. Viruses. 2019;11(7). PMCID: PMC6669737.
Marshall EE, Malouli D, Hansen SG, Gilbride RM, Hughes CM, Ventura AB, Ainslie E, Selseth AN, Ford JC, Burke D, Kreklywich CN, Womack J, Legasse AW, Axthelm MK, Kahl C, Streblow D, Edlefsen PT, Picker LJ, Fruh K. Enhancing safety of cytomegalovirus-based vaccine vectors by engaging host intrinsic immunity. Science Translational Medicine. 2019;11(501). PMCID: PMC6830438.
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. Prediction of VRC01 neutralization sensitivity by HIV-1 gp160 sequence features. PLoS Computational Biology. 2019;15(4):e1006952. PMCID: PMC6459550.
Hansen SG, Womack J, Scholz I, Renner A, Edgel KA, Xu G, Ford JC, Grey M, St Laurent B, Turner JM, Planer S, Legasse AW, Richie TL, Aguiar JC, Axthelm MK, Villasante ED, Weiss W, Edlefsen PT, Picker LJ, Fruh K. Cytomegalovirus vectors expressing Plasmodium knowlesi antigens induce immune responses that delay parasitemia upon sporozoite challenge. PLoS One. 2019;14(1):e0210252. PMCID: PMC6343944.
Hansen SG, Marshall EE, Malouli D, Ventura AB, Hughes CM, Ainslie E, Ford JC, Morrow D, Gilbride RM, Bae JY, Legasse AW, Oswald K, Shoemaker R, Berkemeier B, Bosche WJ, Hull M, Womack J, Shao J~, Edlefsen PT, Reed JS, Burwitz BJ, Sacha JB, Axthelm MK, Fruh K, Lifson JD, Picker LJ. A live-attenuated RhCMV/SIV vaccine shows long-term efficacy against heterologous SIV challenge. Science Translational Medicine. 2019;11(501). PMCID: PMC6788755.
2018
Wood LF, Brown B, Lennard K, Karaoz U, Havyarimana E, Passmore JS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie E, Sodora DL, Jaspan HB. Feeding-related gut microbial composition associates with peripheral T cell activation and mucosal gene expression in African infants. Clinical Infectious Diseases. 2018;67(8):1237-46. PMCID: PMC6455922.
Okoye AA, Hansen SG, Vaidya M, Fukazawa Y, Park H, Duell DM, Lum R, Hughes CM, Ventura AB, Ainslie E, Ford JC, Morrow D, Gilbride RM, Legasse AW, Hesselgesser J, Geleziunas R, Li Y, Oswald K, Shoemaker R, Fast R, Bosche WJ, Borate BR, Edlefsen PT, Axthelm MK, Picker LJ, Lifson JD. Early antiretroviral therapy limits SIV reservoir establishment to delay or prevent post-treatment viral rebound. Nature Medicine. 2018;24(9):1430-40. PMCID: PMC6389357
O'Connor M, Tisoncik-Go J, Lewis T, Miller C, Bratt D, Moats C, Edlefsen PT, Smedley J, Klatt N, Gale M, Fuller D. Early cellular innate immune responses drive Zika viral persistence and tissue tropism in pigtail macaques. Nature Communications. 2018;9(1):3371. PMCID: PMC6105614.
Juraska M, Magaret CA, Shao J, Carpp LN, Fiore-Gartland AJ, Benkeser D, Edlefsen PT*, Gilbert PB* [* co-senior author]. Viral Genetic Diversity and Protective Efficacy of a Tetravalent Dengue Vaccine in two Phase 3 Trials. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(36):E8378-E87. PMCID: PMC6130398.
Herbeck JT, Peebles K, Edlefsen PT, Rolland M, Murphy JT, Gottlieb GS, Abernethy N, Mullins JI, Mittler JE, Goodreau SM. HIV population-level adaptation can rapidly diminish the impact of a partially effective vaccine. Vaccine. 2018;36(4):514-20. doi: 10.1016/j.vaccine.2017.12.004. PMCID: PMC6701864.
Hansen SG, Xu G, Ford JC, Marshall EE, Malouli D, Gilbride RM, Hughes CM, Ventura AB, Ainslie E, Randall KT, Selseth AN, Rundstrom P, Herlache L, Lewis MS, Planer SL, Turner JM, Fischer M, Armstrong C, Zweig RC, Sylwester AW, Legasse AW, Laddy DJ, Stone M, Bonavia A, Evans TG, Messerle M, Jarvis MA, Früh K, Axthelm MK, Edlefsen PT, Picker LJ. Prevention of tuberculosis in rhesus macaques by a cytomegalovirus-based vaccine. Nature Medicine. 2018;24(2):130-43. PMCID: PMC5909823.
2017
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;33(15):2386-8. PMCID: PMC5860116.
deCamp AC, Rolland M, Edlefsen PT, Sanders-Buell E, Hall B, Magaret CA, Gartland AJ, 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, 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, Geraght DE, Frahm N, Tomaras GD, McElrath MJ, Frenkel L, Strychak 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;12(11): e0185959. PMCID: PMC5693417.
2016
Rossenkhan R, MacLeod IJ, Brumme ZL, Magaret CA, Sebunya TK, Musonda R, Gashe BA, Edlefsen PT, Novitsky V, Essex M. 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. AIDS Research and Human Retroviruses. 2016;32(10-11):1031-45. PMCID: PMC5067802.
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;34(47):5792-801. PMCID: PMC5309337.
Edlefsen PT*#, Birkmann A*, Huang M-L, Magaret CA, Kee JJ~, Diem K, Golder T, Timmler B, Stoelben S, Ruebsamen-Schaeff H, Zimmermann H, Warren T, Wald A, Corey L [* co-first author # corresponding author]. No evidence of resistance of HSV-2 to pritelivir following four weeks of daily therapy. Journal of Infectious Diseases. 2016;214(2):258-64. PMCID: PMC4918824.
2015
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.
Fukazawa Y, Lum R, Okoye AA, Park H, Matsuda K, Young Bae J, Hagen SI, Shoemaker R, Swanson T, Legasse AW, Axthelm MK, Hesselgesser J, Geleziunas R, Hirsch VM, Edlefsen PT, Piatak M, Lifson JD, Picker LJ. A B cell follicle sanctuary permits persistent productive SIV infection in elite controllers. Nature Medicine. 2015;21(2)132-9. PMCID: PMC4320022.
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, Kosakovsky Pond SL, Carlson JM, Michael NL, Schief WR, Mullins JI, Kim JH, Gilbert PB [* co-first author]. Comprehensive sieve analysis of breakthrough HIV-1 sequences in the RV144 vaccine efficacy trial. PLoS Computational Biology. 2015;11(2):e1003973. PMCID: PMC4315437.
2014
Zolla-Pazner S, Edlefsen PT, Rolland M, Kong XP, deCamp A, Gottardo R, Williams C, Tovanabutra S, Mullins J, deSouza M, Karasavvas N, Nitayaphan S, Rerks-Ngarm S, Pitisuttihum P, Kaewkungwal J, O'Connell R, Robb M, Michael N, Kim J, Gilbert P. 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.
Wagner TA, McLaughlin S, Garg K, Cheung CYK, Larsen BB, Styrchak S, Huang H, Edlefsen PT, Mullins JI, Frenkel LM. HIV latency. Proliferation of cells with HIV integrated into cancer genes contributes to persistent infection. Science. 2014;345(6196):570-3. PMCID: PMC4230336.
Sterrett S, Learn GH, Edlefsen PT, Haynes BF, Hahn BH, Shaw GH, Bar KJ. Low multiplicity of HIV-1 infection and no vaccine enhancement in VAX003 injection drug users. Open Forum Infectious Diseases. 2014;1(2):ofu056. PMCID: PMC4281816.
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.
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 J, Mullins JI, Kim JH, Gilbert PB, Hertz T. Analysis of HLAA*02 association with vaccine efficacy in the RV144 HIV-1 vaccine trial. Journal of Virology. 2014;88(15):8242-55. PMCID: PMC4135964.
Edlefsen PT. Leaky vaccines protect highly-exposed recipients at a lower rate: implications for vaccine efficacy estimation and sieve analysis. Computational and Mathematical Methods in Medicine. 2014;2014:813789. PMCID: PMC4033482.
Dommaraju K, Kijak G, Carlson JM, Larsen BB, Tovanabutra S, Geraghty DE, Deng W, Maust BS, Edlefsen PT, Sanders-Buell E, Ratto-Kimk S, deSouza MS, Rerks-Ngarm S, Nitayaphan S, Pitisuttihum P, Kaewkungwal J, O'Connell RJ, Robb ML, Michael NL, Mullins JI, Kim JH, Rolland, M. CD8 and CD4 epitope predictions in RV144: no strong evidence of a T-cell driven sieve effect in HIV-1 breakthrough sequences from trial participants. PLoS One. 2014;9(10):e111334. PMCID: PMC4211711.
deCamp A, Hraber P, Bailer R, Seaman M, Ochsenbauer C, Kappes J, Gottardo R, Edlefsen PT, Self S, Tang H, Greene K, Gao H, Daniel X, Sarzotti-Kelsoe M, LaBranche C, Mascola J, Korber B, Montefiori D. Global Panel of HIV-1 Env Reference Strains for Standardized Assessments of Vaccine-Elicited Neutralizing Antibodies. Journal of Virology. 2014;88(5):2489-507. PMCID: PMC3958090.
2013
Hansen SG, Piatak Jr M, Ventura AB, Hughes CM, Gilbride RM, Ford JC, Oswald K, Shoemaker R, Yuan L, Lewis MS, Gilliam AN, Xu G, Whizin N, Burwitz BJ, Planer SL, Turner JM, Legasse AW, Axthelm MK, Nelson JA, Früh K, Sacha JB, Estes JD, Edlefsen PT, Lifson JD, Picker LJ. Immune clearance of highly pathogenic SIV infection. Nature. 2013;502(7469):100-4. PMCID: PMC3849456.
Hansen SG, Sacha JB, Hughes CM, Ford JC, Burwitz BJ, Scholz I, Gilbride RM, Lewis MS, Gilliam AN, Ventura AB, Malouli D, Xu G, Richards R, Whizin N, Reed JS, Hammond KB, Fischer M, Turner JM, Legasse AW, Axthelm MK, Edlefsen PT, Nelson JA, Lifson JD, Früh K, Picker LJ. Cytomegalovirus Vectors Violate CD8+ T Cell Epitope Recognition Paradigms. Science. 2013;340(6135):1237874. PMCID: PMC3816976.
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.
2012
Rolland M*, Edlefsen PT*, Brendan B. Larsen BB, Tovanabutra S, Sanders-Buell E, Hertz T, deCamp AC, Carrico C, Menis S, Magaret CA, Ahmed H, JuraskaM, 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, Haynes BF, Michael NL, Schief W, Gilbert PB, Mullins JI, Kim JH [* co-first author]. Increased HIV-1 vaccine efficacy against viruses with genetic signatures in Env V2. Nature. 2012;490(7420):417-20. PMCID: PMC3551291.
Fukazawa Y, Park H, Cameron MJ, Lefebvre F, Lum R, Coombes N, Mahyari E, Hagen S, Bae JY, Reyes III MD, Swanson T, Legasse AW, Sylwester A, Hansen SG, Smith AT, Shoemaker R, Li Y, Oswald K, Axthelm MK, McDermott A, Ferrari G, Montefiori DC, Edlefsen PT, Piatak, Jr. M, Lifson JD, Sékaly RP, Picker LJ. Lymph node T cell responses predict the efficacy of live attenuated SIV vaccines. Nature Medicine. 2012;18(11):1673-81. PMCID: PMC3493820.
2010
Edlefsen PT, Liu JS. Transposon identification using profile HMMs. BMC Genomics. 2010 Feb 10; 11(Suppl 1):S10 1471-2164. PMCID: PMC2822524.
2009
Edlefsen PT, Liu C, Dempster AP. Estimating limits from Poisson counting data using Dempster-Shafer analysis. Annals of Applied Statistics. 2009;3(2):764-790. WOS: 000271979600012.
2005
Kolker E, Picone AF, Galperin MY, Romine MF, Higdon R, Makarova KS, Kolker N, Anderson GA, Qiu X, Auberry KJ, Babnigg G,Beliaev AS, Edlefsen P, Elias DA, Gorby YA, Holzman T, Klappenbach JA, Konstantinidis KT, Land ML, Lipton MS, McCue LA, Monroe M, Pasa-Tolic L, Pinchuk G, Purvine S, Serres MH, Tsapin S, Zakrajsek BA, Zhu W, Zhou J, Larimer FW, Lawrence CE, Riley M, Collart FR, Yates JR 3rd, Smith RD, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations. Proceedings of the National Academy of Sciences in the United States of America. 2005;102(6):2099-104. PMCID: PMC548307.
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