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The evolutionary rate dynamically tracks changes in HIV-1 epidemics: application of a simple method for optimizing the evolutionary rate in phylogenetic trees with longitudinal data.

Maljkovic Berry I, Athreya G, Kothari M, Daniels M, Bruno WJ, Korber B, Kuiken C, Ribeiro RM, Leitner T.

Epidemics. 2009 Dec;1(4):230-9. doi: 10.1016/j.epidem.2009.10.003. Epub 2009 Nov 12.


HIV-1 Populations in Semen Arise through Multiple Mechanisms.

Anderson JA, Ping LH, Dibben O, Jabara CB, Arney L, Kincer L, Tang Y, Hobbs M, Hoffman I, Kazembe P, Jones CD, Borrow P, Fiscus S, Cohen MS, Swanstrom R; Center for HIV/AIDS Vaccine Immunology.

PLoS Pathog. 2010 Aug 19;6(8):e1001053. doi: 10.1371/journal.ppat.1001053.


Genetic analyses of HIV-1 env sequences demonstrate limited compartmentalization in breast milk and suggest viral replication within the breast that increases with mastitis.

Gantt S, Carlsson J, Heath L, Bull ME, Shetty AK, Mutsvangwa J, Musingwini G, Woelk G, Zijenah LS, Katzenstein DA, Mullins JI, Frenkel LM.

J Virol. 2010 Oct;84(20):10812-9. doi: 10.1128/JVI.00543-10. Epub 2010 Jul 21.


Genetic composition of replication competent clonal HIV-1 variants isolated from peripheral blood mononuclear cells (PBMC), HIV-1 proviral DNA from PBMC and HIV-1 RNA in serum in the course of HIV-1 infection.

Edo-Matas D, van Gils MJ, Bowles EJ, Navis M, Rachinger A, Boeser-Nunnink B, Stewart-Jones GB, Kootstra NA, van 't Wout AB, Schuitemaker H.

Virology. 2010 Sep 30;405(2):492-504. doi: 10.1016/j.virol.2010.06.029. Epub 2010 Jul 17.


Recombination rate and selection strength in HIV intra-patient evolution.

Neher RA, Leitner T.

PLoS Comput Biol. 2010 Jan 29;6(1):e1000660. doi: 10.1371/journal.pcbi.1000660.


Compartmentalization and clonal amplification of HIV-1 variants in the cerebrospinal fluid during primary infection.

Schnell G, Price RW, Swanstrom R, Spudich S.

J Virol. 2010 Mar;84(5):2395-407. doi: 10.1128/JVI.01863-09. Epub 2009 Dec 16.


Evidence for limited genetic compartmentalization of HIV-1 between lung and blood.

Heath L, Fox A, McClure J, Diem K, van 't Wout AB, Zhao H, Park DR, Schouten JT, Twigg HL, Corey L, Mullins JI, Mittler JE.

PLoS One. 2009 Sep 14;4(9):e6949. doi: 10.1371/journal.pone.0006949.


Lack of in vivo compartmentalization among HIV-1 infected naïve and memory CD4+ T cell subsets.

Heeregrave EJ, Geels MJ, Brenchley JM, Baan E, Ambrozak DR, van der Sluis RM, Bennemeer R, Douek DC, Goudsmit J, Pollakis G, Koup RA, Paxton WA.

Virology. 2009 Oct 10;393(1):24-32. doi: 10.1016/j.virol.2009.07.011. Epub 2009 Aug 20.


Cross-sectional characterization of HIV-1 env compartmentalization in cerebrospinal fluid over the full disease course.

Harrington PR, Schnell G, Letendre SL, Ritola K, Robertson K, Hall C, Burch CL, Jabara CB, Moore DT, Ellis RJ, Price RW, Swanstrom R.

AIDS. 2009 May 15;23(8):907-15. doi: 10.1097/QAD.0b013e3283299129.


Variable fitness impact of HIV-1 escape mutations to cytotoxic T lymphocyte (CTL) response.

Troyer RM, McNevin J, Liu Y, Zhang SC, Krizan RW, Abraha A, Tebit DM, Zhao H, Avila S, Lobritz MA, McElrath MJ, Le Gall S, Mullins JI, Arts EJ.

PLoS Pathog. 2009 Apr;5(4):e1000365. doi: 10.1371/journal.ppat.1000365. Epub 2009 Apr 3.


Genetic drift of HIV populations in culture.

Voronin Y, Holte S, Overbaugh J, Emerman M.

PLoS Genet. 2009 Mar;5(3):e1000431. doi: 10.1371/journal.pgen.1000431. Epub 2009 Mar 20.


Major coexisting human immunodeficiency virus type 1 env gene subpopulations in the peripheral blood are produced by cells with similar turnover rates and show little evidence of genetic compartmentalization.

Ince WL, Harrington PR, Schnell GL, Patel-Chhabra M, Burch CL, Menezes P, Price RW, Eron JJ Jr, Swanstrom RI.

J Virol. 2009 May;83(9):4068-80. doi: 10.1128/JVI.02486-08. Epub 2009 Feb 11.


Dynamic correlation between intrahost HIV-1 quasispecies evolution and disease progression.

Lee HY, Perelson AS, Park SC, Leitner T.

PLoS Comput Biol. 2008 Dec;4(12):e1000240. doi: 10.1371/journal.pcbi.1000240. Epub 2008 Dec 12.


An exploratory algorithm to identify intra-host recombinant viral sequences.

Salemi M, Gray RR, Goodenow MM.

Mol Phylogenet Evol. 2008 Nov;49(2):618-28. doi: 10.1016/j.ympev.2008.08.017. Epub 2008 Aug 31.


The generation and maintenance of genetic variation by frequency-dependent selection: constructing polymorphisms under the pairwise interaction model.

Trotter MV, Spencer HG.

Genetics. 2008 Nov;180(3):1547-57. doi: 10.1534/genetics.108.088880. Epub 2008 Sep 14.


Autologous neutralizing humoral immunity and evolution of the viral envelope in the course of subtype B human immunodeficiency virus type 1 infection.

Bunnik EM, Pisas L, van Nuenen AC, Schuitemaker H.

J Virol. 2008 Aug;82(16):7932-41. doi: 10.1128/JVI.00757-08. Epub 2008 Jun 4.


Genetic drift of norovirus genotype GII-4 in seven consecutive epidemic seasons in Hungary.

Reuter G, Pankovics P, Szucs G.

J Clin Virol. 2008 Jun;42(2):135-40. doi: 10.1016/j.jcv.2008.02.014. Epub 2008 Apr 16.


Deciphering human immunodeficiency virus type 1 transmission and early envelope diversification by single-genome amplification and sequencing.

Salazar-Gonzalez JF, Bailes E, Pham KT, Salazar MG, Guffey MB, Keele BF, Derdeyn CA, Farmer P, Hunter E, Allen S, Manigart O, Mulenga J, Anderson JA, Swanstrom R, Haynes BF, Athreya GS, Korber BT, Sharp PM, Shaw GM, Hahn BH.

J Virol. 2008 Apr;82(8):3952-70. doi: 10.1128/JVI.02660-07. Epub 2008 Feb 6.


BEAST: Bayesian evolutionary analysis by sampling trees.

Drummond AJ, Rambaut A.

BMC Evol Biol. 2007 Nov 8;7:214.


Frequency-Dependent Selection in a Periodic Environment.

Forster R, Wilke CO.

Physica A. 2007 Jul 15;381:255-264.

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