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Items: 36

1.

HIV-1 Neutralizing Antibody Signatures and Application to Epitope-Targeted Vaccine Design.

Bricault CA, Yusim K, Seaman MS, Yoon H, Theiler J, Giorgi EE, Wagh K, Theiler M, Hraber P, Macke JP, Kreider EF, Learn GH, Hahn BH, Scheid JF, Kovacs JM, Shields JL, Lavine CL, Ghantous F, Rist M, Bayne MG, Neubauer GH, McMahan K, Peng H, Chéneau C, Jones JJ, Zeng J, Ochsenbauer C, Nkolola JP, Stephenson KE, Chen B, Gnanakaran S, Bonsignori M, Williams LD, Haynes BF, Doria-Rose N, Mascola JR, Montefiori DC, Barouch DH, Korber B.

Cell Host Microbe. 2019 Jan 9;25(1):59-72.e8. doi: 10.1016/j.chom.2018.12.001.

2.

Systematic Analysis of Monoclonal Antibodies against Ebola Virus GP Defines Features that Contribute to Protection.

Saphire EO, Schendel SL, Fusco ML, Gangavarapu K, Gunn BM, Wec AZ, Halfmann PJ, Brannan JM, Herbert AS, Qiu X, Wagh K, He S, Giorgi EE, Theiler J, Pommert KBJ, Krause TB, Turner HL, Murin CD, Pallesen J, Davidson E, Ahmed R, Aman MJ, Bukreyev A, Burton DR, Crowe JE Jr, Davis CW, Georgiou G, Krammer F, Kyratsous CA, Lai JR, Nykiforuk C, Pauly MH, Rijal P, Takada A, Townsend AR, Volchkov V, Walker LM, Wang CI, Zeitlin L, Doranz BJ, Ward AB, Korber B, Kobinger GP, Andersen KG, Kawaoka Y, Alter G, Chandran K, Dye JM; Viral Hemorrhagic Fever Immunotherapeutic Consortium.

Cell. 2018 Aug 9;174(4):938-952.e13. doi: 10.1016/j.cell.2018.07.033.

3.

Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence.

Ke R, Li H, Wang S, Ding W, Ribeiro RM, Giorgi EE, Bhattacharya T, Barnard RJO, Hahn BH, Shaw GM, Perelson AS.

Proc Natl Acad Sci U S A. 2018 Jul 24;115(30):E7139-E7148. doi: 10.1073/pnas.1805267115. Epub 2018 Jul 9.

4.

Tracking HIV-1 recombination to resolve its contribution to HIV-1 evolution in natural infection.

Song H, Giorgi EE, Ganusov VV, Cai F, Athreya G, Yoon H, Carja O, Hora B, Hraber P, Romero-Severson E, Jiang C, Li X, Wang S, Li H, Salazar-Gonzalez JF, Salazar MG, Goonetilleke N, Keele BF, Montefiori DC, Cohen MS, Shaw GM, Hahn BH, McMichael AJ, Haynes BF, Korber B, Bhattacharya T, Gao F.

Nat Commun. 2018 May 15;9(1):1928. doi: 10.1038/s41467-018-04217-5.

5.

Infant transmitted/founder HIV-1 viruses from peripartum transmission are neutralization resistant to paired maternal plasma.

Kumar A, Smith CEP, Giorgi EE, Eudailey J, Martinez DR, Yusim K, Douglas AO, Stamper L, McGuire E, LaBranche CC, Montefiori DC, Fouda GG, Gao F, Permar SR.

PLoS Pathog. 2018 Apr 19;14(4):e1006944. doi: 10.1371/journal.ppat.1006944. eCollection 2018 Apr.

6.

Development of broad neutralization activity in simian/human immunodeficiency virus-infected rhesus macaques after long-term infection.

Gao N, Wang W, Wang C, Gu T, Guo R, Yu B, Kong W, Qin C, Giorgi EE, Chen Z, Townsley S, Hu SL, Yu X, Gao F.

AIDS. 2018 Mar 13;32(5):555-563. doi: 10.1097/QAD.0000000000001724.

PMID:
29239895
7.

Correction: Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization.

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, Karim SA, Karim QA, Kim JH, Hahn BH, Gao F, Swanstrom R, Morris L, Montefiori DC, Williamson C.

PLoS Pathog. 2017 Sep 25;13(9):e1006641. doi: 10.1371/journal.ppat.1006641. eCollection 2017 Sep.

8.

Transmission of Multiple HIV-1 Subtype C Transmitted/founder Viruses into the Same Recipients Was not Determined by Modest Phenotypic Differences.

Song H, Hora B, Giorgi EE, Kumar A, Cai F, Bhattacharya T, Perelson AS, Gao F.

Sci Rep. 2016 Dec 2;6:38130. doi: 10.1038/srep38130.

9.

Features of Recently Transmitted HIV-1 Clade C Viruses that Impact Antibody Recognition: Implications for Active and Passive Immunization.

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.

PLoS Pathog. 2016 Jul 19;12(7):e1005742. doi: 10.1371/journal.ppat.1005742. eCollection 2016 Jul. Erratum in: PLoS Pathog. 2017 Sep 25;13(9):e1006641.

10.

No Association between the Mitochondrial Genome and Prostate Cancer Risk: The Multiethnic Cohort.

Giorgi EE, Li Y, Caberto CP, Beckman KB, Lum-Jones A, Haiman CA, Le Marchand L, Stram DO, Saxena R, Cheng I.

Cancer Epidemiol Biomarkers Prev. 2016 Jun;25(6):1001-3. doi: 10.1158/1055-9965.EPI-16-0111. Epub 2016 Mar 28.

11.

SPMM: estimating infection duration of multivariant HIV-1 infections.

Love TM, Park SY, Giorgi EE, Mack WJ, Perelson AS, Lee HY.

Bioinformatics. 2016 May 1;32(9):1308-15. doi: 10.1093/bioinformatics/btv749. Epub 2015 Dec 31.

12.

Longitudinal Antigenic Sequences and Sites from Intra-Host Evolution (LASSIE) Identifies Immune-Selected HIV Variants.

Hraber P, Korber B, Wagh K, Giorgi EE, Bhattacharya T, Gnanakaran S, Lapedes AS, Learn GH, Kreider EF, Li Y, Shaw GM, Hahn BH, Montefiori DC, Alam SM, Bonsignori M, Moody MA, Liao HX, Gao F, Haynes BF.

Viruses. 2015 Oct 21;7(10):5443-75. doi: 10.3390/v7102881.

13.

Single-Genome Sequencing of Hepatitis C Virus in Donor-Recipient Pairs Distinguishes Modes and Models of Virus Transmission and Early Diversification.

Li H, Stoddard MB, Wang S, Giorgi EE, Blair LM, Learn GH, Hahn BH, Alter HJ, Busch MP, Fierer DS, Ribeiro RM, Perelson AS, Bhattacharya T, Shaw GM.

J Virol. 2015 Oct 14;90(1):152-66. doi: 10.1128/JVI.02156-15. Print 2016 Jan 1.

14.

Human Non-neutralizing HIV-1 Envelope Monoclonal Antibodies Limit the Number of Founder Viruses during SHIV Mucosal Infection in Rhesus Macaques.

Santra S, Tomaras GD, Warrier R, Nicely NI, Liao HX, Pollara J, Liu P, Alam SM, Zhang R, Cocklin SL, Shen X, Duffy R, Xia SM, Schutte RJ, Pemble Iv CW, Dennison SM, Li H, Chao A, Vidnovic K, Evans A, Klein K, Kumar A, Robinson J, Landucci G, Forthal DN, Montefiori DC, Kaewkungwal J, Nitayaphan S, Pitisuttithum P, Rerks-Ngarm S, Robb ML, Michael NL, Kim JH, Soderberg KA, Giorgi EE, Blair L, Korber BT, Moog C, Shattock RJ, Letvin NL, Schmitz JE, Moody MA, Gao F, Ferrari G, Shaw GM, Haynes BF.

PLoS Pathog. 2015 Aug 3;11(8):e1005042. doi: 10.1371/journal.ppat.1005042. eCollection 2015 Aug.

15.

Comparison of Immunogenicity in Rhesus Macaques of Transmitted-Founder, HIV-1 Group M Consensus, and Trivalent Mosaic Envelope Vaccines Formulated as a DNA Prime, NYVAC, and Envelope Protein Boost.

Hulot SL, Korber B, Giorgi EE, Vandergrift N, Saunders KO, Balachandran H, Mach LV, Lifton MA, Pantaleo G, Tartaglia J, Phogat S, Jacobs B, Kibler K, Perdiguero B, Gomez CE, Esteban M, Rosati M, Felber BK, Pavlakis GN, Parks R, Lloyd K, Sutherland L, Scearce R, Letvin NL, Seaman MS, Alam SM, Montefiori D, Liao HX, Haynes BF, Santra S.

J Virol. 2015 Jun;89(12):6462-80. doi: 10.1128/JVI.00383-15. Epub 2015 Apr 8.

16.

A multivalent clade C HIV-1 Env trimer cocktail elicits a higher magnitude of neutralizing antibodies than any individual component.

Bricault CA, Kovacs JM, Nkolola JP, Yusim K, Giorgi EE, Shields JL, Perry J, Lavine CL, Cheung A, Ellingson-Strouss K, Rademeyer C, Gray GE, Williamson C, Stamatatos L, Seaman MS, Korber BT, Chen B, Barouch DH.

J Virol. 2015 Mar;89(5):2507-19. doi: 10.1128/JVI.03331-14. Epub 2014 Dec 24.

17.

Fine-mapping IGF1 and prostate cancer risk in African Americans: the multiethnic cohort study.

Giorgi EE, Stram DO, Taverna D, Turner SD, Schumacher F, Haiman CA, Lum-Jones A, Tirikainen M, Caberto C, Duggan D, Henderson BE, Le Marchand L, Cheng I.

Cancer Epidemiol Biomarkers Prev. 2014 Sep;23(9):1928-32. doi: 10.1158/1055-9965.EPI-14-0333. Epub 2014 Jun 5.

18.

Cross-reactive potential of human T-lymphocyte responses in HIV-1 infection.

Giorgi EE, Balachandran H, Muldoon M, Letvin NL, Haynes BF, Korber BT, Santra S.

Vaccine. 2014 Jun 30;32(31):3995-4000. doi: 10.1016/j.vaccine.2014.04.040. Epub 2014 May 14.

19.

Protective efficacy of a global HIV-1 mosaic vaccine against heterologous SHIV challenges in rhesus monkeys.

Barouch DH, Stephenson KE, Borducchi EN, Smith K, Stanley K, McNally AG, Liu J, Abbink P, Maxfield LF, Seaman MS, Dugast AS, Alter G, Ferguson M, Li W, Earl PL, Moss B, Giorgi EE, Szinger JJ, Eller LA, Billings EA, Rao M, Tovanabutra S, Sanders-Buell E, Weijtens M, Pau MG, Schuitemaker H, Robb ML, Kim JH, Korber BT, Michael NL.

Cell. 2013 Oct 24;155(3):531-9. doi: 10.1016/j.cell.2013.09.061. Epub 2013 Oct 24.

20.

Modeling sequence evolution in HIV-1 infection with recombination.

Giorgi EE, Korber BT, Perelson AS, Bhattacharya T.

J Theor Biol. 2013 Jul 21;329:82-93. doi: 10.1016/j.jtbi.2013.03.026. Epub 2013 Apr 6.

21.

Phenotypic properties of transmitted founder HIV-1.

Parrish NF, Gao F, Li H, Giorgi EE, Barbian HJ, Parrish EH, Zajic L, Iyer SS, Decker JM, Kumar A, Hora B, Berg A, Cai F, Hopper J, Denny TN, Ding H, Ochsenbauer C, Kappes JC, Galimidi RP, West AP Jr, Bjorkman PJ, Wilen CB, Doms RW, O'Brien M, Bhardwaj N, Borrow P, Haynes BF, Muldoon M, Theiler JP, Korber B, Shaw GM, Hahn BH.

Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):6626-33. doi: 10.1073/pnas.1304288110. Epub 2013 Mar 29.

22.

A note on two-sample tests for comparing intra-individual genetic sequence diversity between populations.

Giorgi EE, Bhattacharya T.

Biometrics. 2012 Dec;68(4):1323-6; author reply 1326. doi: 10.1111/j.1541-0420.2012.01775.x. Epub 2012 Sep 24.

23.

Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing.

Li H, Stoddard MB, Wang S, Blair LM, Giorgi EE, Parrish EH, Learn GH, Hraber P, Goepfert PA, Saag MS, Denny TN, Haynes BF, Hahn BH, Ribeiro RM, Perelson AS, Korber BT, Bhattacharya T, Shaw GM.

PLoS Pathog. 2012;8(8):e1002880. doi: 10.1371/journal.ppat.1002880. Epub 2012 Aug 23.

24.

Role of donor genital tract HIV-1 diversity in the transmission bottleneck.

Boeras DI, Hraber PT, Hurlston M, Evans-Strickfaden T, Bhattacharya T, Giorgi EE, Mulenga J, Karita E, Korber BT, Allen S, Hart CE, Derdeyn CA, Hunter E.

Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):E1156-63. doi: 10.1073/pnas.1103764108. Epub 2011 Nov 7.

25.

Genital tract sequestration of SIV following acute infection.

Whitney JB, Hraber PT, Luedemann C, Giorgi EE, Daniels MG, Bhattacharya T, Rao SS, Mascola JR, Nabel GJ, Korber BT, Letvin NL.

PLoS Pathog. 2011 Feb;7(2):e1001293. doi: 10.1371/journal.ppat.1001293. Epub 2011 Feb 17.

26.

Epitope-specific CD8+ T lymphocytes cross-recognize mutant simian immunodeficiency virus (SIV) sequences but fail to contain very early evolution and eventual fixation of epitope escape mutations during SIV infection.

Cale EM, Hraber P, Giorgi EE, Fischer W, Bhattacharya T, Leitner T, Yeh WW, Gleasner C, Green LD, Han CS, Korber B, Letvin NL.

J Virol. 2011 Apr;85(8):3746-57. doi: 10.1128/JVI.02420-10. Epub 2011 Feb 9.

27.

Estimating time since infection in early homogeneous HIV-1 samples using a poisson model.

Giorgi EE, Funkhouser B, Athreya G, Perelson AS, Korber BT, Bhattacharya T.

BMC Bioinformatics. 2010 Oct 25;11:532. doi: 10.1186/1471-2105-11-532.

28.

Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing.

Fischer W, Ganusov VV, Giorgi EE, Hraber PT, Keele BF, Leitner T, Han CS, Gleasner CD, Green L, Lo CC, Nag A, Wallstrom TC, Wang S, McMichael AJ, Haynes BF, Hahn BH, Perelson AS, Borrow P, Shaw GM, Bhattacharya T, Korber BT.

PLoS One. 2010 Aug 20;5(8):e12303. doi: 10.1371/journal.pone.0012303.

29.

High Multiplicity Infection by HIV-1 in Men Who Have Sex with Men.

Li H, Bar KJ, Wang S, Decker JM, Chen Y, Sun C, Salazar-Gonzalez JF, Salazar MG, Learn GH, Morgan CJ, Schumacher JE, Hraber P, Giorgi EE, Bhattacharya T, Korber BT, Perelson AS, Eron JJ, Cohen MS, Hicks CB, Haynes BF, Markowitz M, Keele BF, Hahn BH, Shaw GM.

PLoS Pathog. 2010 May 13;6(5):e1000890. doi: 10.1371/journal.ppat.1000890.

30.

Modeling sequence evolution in acute HIV-1 infection.

Lee HY, Giorgi EE, Keele BF, Gaschen B, Athreya GS, Salazar-Gonzalez JF, Pham KT, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Hahn BH, Shaw GM, Korber BT, Bhattacharya T, Perelson AS.

J Theor Biol. 2009 Nov 21;261(2):341-60. doi: 10.1016/j.jtbi.2009.07.038. Epub 2009 Aug 4. Review. Erratum in: J Theor Biol. 2012 Mar 21;297:187.

31.

Nef gene evolution from a single transmitted strain in acute SIV infection.

Bimber BN, Chugh P, Giorgi EE, Kim B, Almudevar AL, Dewhurst S, O'Connor DH, Lee HY.

Retrovirology. 2009 Jun 8;6:57. doi: 10.1186/1742-4690-6-57.

32.

Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection.

Salazar-Gonzalez JF, Salazar MG, Keele BF, Learn GH, Giorgi EE, Li H, Decker JM, Wang S, Baalwa J, Kraus MH, Parrish NF, Shaw KS, Guffey MB, Bar KJ, Davis KL, Ochsenbauer-Jambor C, Kappes JC, Saag MS, Cohen MS, Mulenga J, Derdeyn CA, Allen S, Hunter E, Markowitz M, Hraber P, Perelson AS, Bhattacharya T, Haynes BF, Korber BT, Hahn BH, Shaw GM.

J Exp Med. 2009 Jun 8;206(6):1273-89. doi: 10.1084/jem.20090378. Epub 2009 Jun 1.

33.

Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1.

Keele BF, Li H, Learn GH, Hraber P, Giorgi EE, Grayson T, Sun C, Chen Y, Yeh WW, Letvin NL, Mascola JR, Nabel GJ, Haynes BF, Bhattacharya T, Perelson AS, Korber BT, Hahn BH, Shaw GM.

J Exp Med. 2009 May 11;206(5):1117-34. doi: 10.1084/jem.20082831. Epub 2009 May 4.

34.

Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants.

Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium.

J Virol. 2009 Apr;83(8):3556-67. doi: 10.1128/JVI.02132-08. Epub 2009 Feb 4. Erratum in: J Virol. 2009 Jul;83(13):6974.

35.

Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection.

Keele BF, Giorgi EE, Salazar-Gonzalez JF, Decker JM, Pham KT, Salazar MG, Sun C, Grayson T, Wang S, Li H, Wei X, Jiang C, Kirchherr JL, Gao F, Anderson JA, Ping LH, Swanstrom R, Tomaras GD, Blattner WA, Goepfert PA, Kilby JM, Saag MS, Delwart EL, Busch MP, Cohen MS, Montefiori DC, Haynes BF, Gaschen B, Athreya GS, Lee HY, Wood N, Seoighe C, Perelson AS, Bhattacharya T, Korber BT, Hahn BH, Shaw GM.

Proc Natl Acad Sci U S A. 2008 May 27;105(21):7552-7. doi: 10.1073/pnas.0802203105. Epub 2008 May 19.

36.

Common genetic variation at PTEN and risk of sporadic breast and prostate cancer.

Haiman CA, Stram DO, Cheng I, Giorgi EE, Pooler L, Penney K, Le Marchand L, Henderson BE, Freedman ML.

Cancer Epidemiol Biomarkers Prev. 2006 May;15(5):1021-5.

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