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Items: 1 to 20 of 83

1.

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.

2.

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.

3.

Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1.

Edwards CT, Holmes EC, Wilson DJ, Viscidi RP, Abrams EJ, Phillips RE, Drummond AJ.

BMC Evol Biol. 2006 Mar 23;6:28.

4.

A framework including recombination for analyzing the dynamics of within-host HIV genetic diversity.

Sargsyan O.

PLoS One. 2014 Feb 7;9(2):e87655. doi: 10.1371/journal.pone.0087655. eCollection 2014.

5.

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.

6.

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.

7.

Recombination elevates the effective evolutionary rate and facilitates the establishment of HIV-1 infection in infants after mother-to-child transmission.

Sanborn KB, Somasundaran M, Luzuriaga K, Leitner T.

Retrovirology. 2015 Nov 16;12:96. doi: 10.1186/s12977-015-0222-0.

8.

Diversity of the human immunodeficiency virus type 1 (HIV-1) env sequence after vertical transmission in mother-child pairs infected with HIV-1 subtype A.

Verhofstede C, Demecheleer E, De Cabooter N, Gaillard P, Mwanyumba F, Claeys P, Chohan V, Mandaliya K, Temmerman M, Plum J.

J Virol. 2003 Mar;77(5):3050-7.

9.

Characterization of HIV-1 envelope gp41 genetic diversity and functional domains following perinatal transmission.

Ramakrishnan R, Mehta R, Sundaravaradan V, Davis T, Ahmad N.

Retrovirology. 2006 Jul 4;3:42.

10.

Short communication: phylodynamics analysis of the human immunodeficiency virus type 1 envelope gene in mother and child pairs.

Santos LA, Gray RR, Monteiro-Cunha JP, Strazza E, Kashima S, Santos Ede S, Araújo TH, Gonçalves Mde S, Salemi M, Alcantara LC.

AIDS Res Hum Retroviruses. 2015 Sep;31(9):913-20. doi: 10.1089/AID.2014.0352. Epub 2015 Jul 23.

PMID:
26123053
11.

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.

12.

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.

13.

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.

14.

Modeling sequence evolution in HIV-1 infection with recombination.

Giorgi EE, Korber BT, Perelson AS, Bhattacharya T.

J Theor Biol. 2013 Jul 21;329:82-93. doi: 10.1016/j.jtbi.2013.03.026. Epub 2013 Apr 6.

15.

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.

16.

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.

17.

Previously transmitted HIV-1 strains are preferentially selected during subsequent sexual transmissions.

Redd AD, Collinson-Streng AN, Chatziandreou N, Mullis CE, Laeyendecker O, Martens C, Ricklefs S, Kiwanuka N, Nyein PH, Lutalo T, Grabowski MK, Kong X, Manucci J, Sewankambo N, Wawer MJ, Gray RH, Porcella SF, Fauci AS, Sagar M, Serwadda D, Quinn TC.

J Infect Dis. 2012 Nov;206(9):1433-42. doi: 10.1093/infdis/jis503. Epub 2012 Sep 19. Erratum in: J Infect Dis. 2013 Feb 1;207(3):546.

18.

Maintenance of Nef-mediated modulation of major histocompatibility complex class I and CD4 after sexual transmission of human immunodeficiency virus type 1.

Noviello CM, Pond SL, Lewis MJ, Richman DD, Pillai SK, Yang OO, Little SJ, Smith DM, Guatelli JC.

J Virol. 2007 May;81(9):4776-86. Epub 2007 Feb 28.

19.

SPMM: estimating infection duration of multivariant HIV-1 infections.

Love TM, Park SY, Giorgi EE, Mack WJ, Perelson AS, Lee HY.

Bioinformatics. 2016 May 1;32(9):1308-15. doi: 10.1093/bioinformatics/btv749. Epub 2015 Dec 31.

20.

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