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Items: 1 to 20 of 185


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.


Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data.

Poon AF, Swenson LC, Bunnik EM, Edo-Matas D, Schuitemaker H, van 't Wout AB, Harrigan PR.

PLoS Comput Biol. 2012;8(11):e1002753. doi: 10.1371/journal.pcbi.1002753. Epub 2012 Nov 1.


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.


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.


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.


A single early introduction of HIV-1 subtype B into Central America accounts for most current cases.

Murillo W, Veras N, Prosperi M, de Rivera IL, Paz-Bailey G, Morales-Miranda S, Juarez SI, Yang C, DeVos J, Marín JP, Mild M, Albert J, Salemi M.

J Virol. 2013 Jul;87(13):7463-70. doi: 10.1128/JVI.01602-12. Epub 2013 Apr 24.


Activities of transmitted/founder and chronic clade B HIV-1 Vpu and a C-terminal polymorphism specifically affecting virion release.

Jafari M, Guatelli J, Lewinski MK.

J Virol. 2014 May;88(9):5062-78. doi: 10.1128/JVI.03472-13. Epub 2014 Feb 26.


Transmitted/founder simian immunodeficiency virus envelope sequences in vesicular stomatitis and Semliki forest virus vector immunized rhesus macaques.

Gambhira R, Keele BF, Schell JB, Hunter MJ, Dufour JP, Montefiori DC, Tang H, Rose JK, Rose N, Marx PA.

PLoS One. 2014 Oct 31;9(10):e109678. doi: 10.1371/journal.pone.0109678. eCollection 2014.


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.


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.


Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host.

Herbeck JT, Nickle DC, Learn GH, Gottlieb GS, Curlin ME, Heath L, Mullins JI.

J Virol. 2006 Feb;80(4):1637-44.


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.


Characterization of human immunodeficiency virus type 1 (HIV-1) diversity and tropism in 145 patients with primary HIV-1 infection.

Rieder P, Joos B, Scherrer AU, Kuster H, Braun D, Grube C, Niederöst B, Leemann C, Gianella S, Metzner KJ, Böni J, Weber R, Günthard HF.

Clin Infect Dis. 2011 Dec;53(12):1271-9. doi: 10.1093/cid/cir725. Epub 2011 Oct 12.


Evaluation of cervical mucosa in transmission bottleneck during acute HIV-1 infection using a cervical tissue-based organ culture.

Shen C, Ding M, Ratner D, Montelaro RC, Chen Y, Gupta P.

PLoS One. 2012;7(3):e32539. doi: 10.1371/journal.pone.0032539. Epub 2012 Mar 7.


Syncytium-inducing (SI) phenotype suppression at seroconversion after intramuscular inoculation of a non-syncytium-inducing/SI phenotypically mixed human immunodeficiency virus population.

Cornelissen M, Mulder-Kampinga G, Veenstra J, Zorgdrager F, Kuiken C, Hartman S, Dekker J, van der Hoek L, Sol C, Coutinho R, et al.

J Virol. 1995 Mar;69(3):1810-8.


Incorporating indels as phylogenetic characters: impact for interfamilial relationships within Arctoidea (Mammalia: Carnivora).

Luan PT, Ryder OA, Davis H, Zhang YP, Yu L.

Mol Phylogenet Evol. 2013 Mar;66(3):748-56. doi: 10.1016/j.ympev.2012.10.023. Epub 2012 Nov 10.


Untangling the influences of unmodeled evolutionary processes on phylogenetic signal in a forensically important HIV-1 transmission cluster.

Doyle VP, Andersen JJ, Nelson BJ, Metzker ML, Brown JM.

Mol Phylogenet Evol. 2014 Jun;75:126-37. doi: 10.1016/j.ympev.2014.02.022. Epub 2014 Feb 28.


Bayesian coestimation of phylogeny and sequence alignment.

Lunter G, Miklós I, Drummond A, Jensen JL, Hein J.

BMC Bioinformatics. 2005 Apr 1;6:83.

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