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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.


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.


HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC.

Wood N, Bhattacharya T, Keele BF, Giorgi E, Liu M, Gaschen B, Daniels M, Ferrari G, Haynes BF, McMichael A, Shaw GM, Hahn BH, Korber B, Seoighe C.

PLoS Pathog. 2009 May;5(5):e1000414. doi: 10.1371/journal.ppat.1000414. Epub 2009 May 8.


An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data.

McCloskey RM, Liang RH, Harrigan PR, Brumme ZL, Poon AF.

J Virol. 2014 Jun;88(11):6181-94. doi: 10.1128/JVI.00483-14. Epub 2014 Mar 19.


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.


A new algorithm for analysis of within-host HIV-1 evolution.

Ren F, Ogishima S, Tanaka H.

Pac Symp Biocomput. 2001:595-605.


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.


Human immunodeficiency virus type 1 genetic evolution in children with different rates of development of disease.

Ganeshan S, Dickover RE, Korber BT, Bryson YJ, Wolinsky SM.

J Virol. 1997 Jan;71(1):663-77.


Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1.

Poss M, Rodrigo AG, Gosink JJ, Learn GH, de Vange Panteleeff D, Martin HL Jr, Bwayo J, Kreiss JK, Overbaugh J.

J Virol. 1998 Oct;72(10):8240-51.


Impact of CCR5delta32 host genetic background and disease progression on HIV-1 intrahost evolutionary processes: efficient hypothesis testing through hierarchical phylogenetic models.

Edo-Matas D, Lemey P, Tom JA, Serna-Bolea C, van den Blink AE, van 't Wout AB, Schuitemaker H, Suchard MA.

Mol Biol Evol. 2011 May;28(5):1605-16. doi: 10.1093/molbev/msq326. Epub 2010 Dec 6.


Intra-host evolutionary rates in HIV-1C env and gag during primary infection.

Novitsky V, Wang R, Rossenkhan R, Moyo S, Essex M.

Infect Genet Evol. 2013 Oct;19:361-8. doi: 10.1016/j.meegid.2013.02.023. Epub 2013 Mar 20.


Transmission of single and multiple viral variants in primary HIV-1 subtype C infection.

Novitsky V, Wang R, Margolin L, Baca J, Rossenkhan R, Moyo S, van Widenfelt E, Essex M.

PLoS One. 2011 Feb 9;6(2):e16714. doi: 10.1371/journal.pone.0016714.


Predicting demographic group structures based on DNA sequence data.

Anderson JP, Learn GH, Rodrigo AG, He X, Wang Y, Weinstock H, Kalish ML, Robbins KE, Hood L, Mullins JI.

Mol Biol Evol. 2003 Jul;20(7):1168-80. Epub 2003 May 30.


Restricted genetic diversity of HIV-1 subtype C envelope glycoprotein from perinatally infected Zambian infants.

Zhang H, Tully DC, Hoffmann FG, He J, Kankasa C, Wood C.

PLoS One. 2010 Feb 18;5(2):e9294. doi: 10.1371/journal.pone.0009294. Erratum in: PLoS One. 2010;5(3). doi: 10.1371/annotation/c2dd3548-93b7-480e-991a-93a728bca5fe. PLoS One. 2010;5(3). doi: 10.1371/annotation/eadee58d-56c0-4399-b007-d80cc71e3f8a.


Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner.

Frange P, Meyer L, Jung M, Goujard C, Zucman D, Abel S, Hochedez P, Gousset M, Gascuel O, Rouzioux C, Chaix ML; ANRS PRIMO Cohort Study Group.

PLoS One. 2013 Jul 9;8(7):e69144. doi: 10.1371/journal.pone.0069144. Print 2013.


Virus population homogenization following acute human immunodeficiency virus type 1 infection.

Learn GH, Muthui D, Brodie SJ, Zhu T, Diem K, Mullins JI, Corey L.

J Virol. 2002 Dec;76(23):11953-9.


Relaxation of adaptive evolution during the HIV-1 infection owing to reduction of CD4+ T cell counts.

Leal É, Casseb J, Hendry M, Busch MP, Diaz RS.

PLoS One. 2012;7(6):e39776. doi: 10.1371/journal.pone.0039776. Epub 2012 Jun 29.


The heterosexual human immunodeficiency virus type 1 epidemic in Thailand is caused by an intersubtype (A/E) recombinant of African origin.

Gao F, Robertson DL, Morrison SG, Hui H, Craig S, Decker J, Fultz PN, Girard M, Shaw GM, Hahn BH, Sharp PM.

J Virol. 1996 Oct;70(10):7013-29.

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