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• Review: Influence of ART on HIV genetics.

  Simonetti FR, Kearney MF. Simonetti FR, et al. Curr Opin HIV AIDS. 2015 Jan;10(1):49-54. doi: 10.1097/COH.0000000000000120. Curr Opin HIV AIDS. 2015. PMID: 25389802 Free PMC article. Review.
• 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. Gnanakaran S, et al. PLoS Pathog. 2011 Sep;7(9):e1002209. doi: 10.1371/journal.ppat.1002209. Epub 2011 Sep 29. PLoS Pathog. 2011. PMID: 21980282 Free PMC article. Clinical Trial.
• 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. Herbeck JT, et al. J Virol. 2011 Aug;85(15):7523-34. doi: 10.1128/JVI.02697-10. Epub 2011 May 18. J Virol. 2011. PMID: 21593162 Free PMC article.
• Human immunodeficiency virus type 1 population genetics and adaptation in newly infected individuals.

  Kearney M, Maldarelli F, Shao W, Margolick JB, Daar ES, Mellors JW, Rao V, Coffin JM, Palmer S. Kearney M, et al. J Virol. 2009 Mar;83(6):2715-27. doi: 10.1128/JVI.01960-08. Epub 2008 Dec 30. J Virol. 2009. PMID: 19116249 Free PMC article.
• Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1.

  Ritola K, Pilcher CD, Fiscus SA, Hoffman NG, Nelson JA, Kitrinos KM, Hicks CB, Eron JJ Jr, Swanstrom R. Ritola K, et al. J Virol. 2004 Oct;78(20):11208-18. doi: 10.1128/JVI.78.20.11208-11218.2004. J Virol. 2004. PMID: 15452240 Free PMC article.