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Items: 13

1.

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.

Dommaraju K, Kijak G, Carlson JM, Larsen BB, Tovanabutra S, Geraghty DE, Deng W, Maust BS, Edlefsen PT, Sanders-Buell E, Ratto-Kim 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.

PLoS One. 2014 Oct 28;9(10):e111334. doi: 10.1371/journal.pone.0111334. eCollection 2014.

2.

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.

3.

Improved detection of rare HIV-1 variants using 454 pyrosequencing.

Larsen BB, Chen L, Maust BS, Kim M, Zhao H, Deng W, Westfall D, Beck I, Frenkel LM, Mullins JI.

PLoS One. 2013 Oct 2;8(10):e76502. doi: 10.1371/journal.pone.0076502. eCollection 2013.

4.

Indel and Carryforward Correction (ICC): a new analysis approach for processing 454 pyrosequencing data.

Deng W, Maust BS, Westfall DH, Chen L, Zhao H, Larsen BB, Iyer S, Liu Y, Mullins JI.

Bioinformatics. 2013 Oct 1;29(19):2402-9. doi: 10.1093/bioinformatics/btt434. Epub 2013 Jul 29.

5.

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.

6.

Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission.

Herbeck JT, Müller V, Maust BS, Ledergerber B, Torti C, Di Giambenedetto S, Gras L, Günthard HF, Jacobson LP, Mullins JI, Gottlieb GS.

AIDS. 2012 Jan 14;26(2):193-205. doi: 10.1097/QAD.0b013e32834db418.

7.

Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes.

Herbeck JT, Rolland M, Liu Y, McLaughlin S, McNevin J, Zhao H, Wong K, Stoddard JN, Raugi D, Sorensen S, Genowati I, Birditt B, McKay A, Diem K, Maust BS, Deng W, Collier AC, Stekler JD, McElrath MJ, Mullins JI.

J Virol. 2011 Aug;85(15):7523-34. doi: 10.1128/JVI.02697-10. Epub 2011 May 18.

8.

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.

9.

Amino-acid co-variation in HIV-1 Gag subtype C: HLA-mediated selection pressure and compensatory dynamics.

Rolland M, Carlson JM, Manocheewa S, Swain JV, Lanxon-Cookson E, Deng W, Rousseau CM, Raugi DN, Learn GH, Maust BS, Coovadia H, Ndung'u T, Goulder PJ, Walker BD, Brander C, Heckerman DE, Mullins JI.

PLoS One. 2010 Sep 1;5(9). pii: e12463. doi: 10.1371/journal.pone.0012463.

10.

DIVEIN: a web server to analyze phylogenies, sequence divergence, diversity, and informative sites.

Deng W, Maust BS, Nickle DC, Learn GH, Liu Y, Heath L, Kosakovsky Pond SL, Mullins JI.

Biotechniques. 2010 May;48(5):405-8. doi: 10.2144/000113370.

11.

Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS.

Herbeck JT, Gottlieb GS, Winkler CA, Nelson GW, An P, Maust BS, Wong KG, Troyer JL, Goedert JJ, Kessing BD, Detels R, Wolinsky SM, Martinson J, Buchbinder S, Kirk GD, Jacobson LP, Margolick JB, Kaslow RA, O'Brien SJ, Mullins JI.

J Infect Dis. 2010 Feb 15;201(4):618-26. doi: 10.1086/649842.

12.

HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load.

Rousseau CM, Daniels MG, Carlson JM, Kadie C, Crawford H, Prendergast A, Matthews P, Payne R, Rolland M, Raugi DN, Maust BS, Learn GH, Nickle DC, Coovadia H, Ndung'u T, Frahm N, Brander C, Walker BD, Goulder PJ, Bhattacharya T, Heckerman DE, Korber BT, Mullins JI.

J Virol. 2008 Jul;82(13):6434-46. doi: 10.1128/JVI.02455-07. Epub 2008 Apr 23.

13.

HIV-1 over time: fitness loss or robustness gain?

Rolland M, Brander C, Nickle DC, Herbeck JT, Gottlieb GS, Campbell MS, Maust BS, Mullins JI.

Nat Rev Microbiol. 2007 Sep;5(9):C1. No abstract available.

PMID:
17703224

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