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Results: 8

1.

A multiple-alignment based primer design algorithm for genetically highly variable DNA targets.

Brodin J, Krishnamoorthy M, Athreya G, Fischer W, Hraber P, Gleasner C, Green L, Korber B, Leitner T.

BMC Bioinformatics. 2013 Aug 21;14:255. doi: 10.1186/1471-2105-14-255.

PMID:
23965160
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
20973976
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
21352769
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
19660475
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Quantitating the multiplicity of infection with human immunodeficiency virus type 1 subtype C reveals a non-poisson distribution of transmitted variants.

Abrahams MR, Anderson JA, Giorgi EE, Seoighe C, Mlisana K, Ping LH, Athreya GS, Treurnicht FK, Keele BF, Wood N, Salazar-Gonzalez JF, Bhattacharya T, Chu H, Hoffman I, Galvin S, Mapanje C, Kazembe P, Thebus R, Fiscus S, Hide W, Cohen MS, Karim SA, Haynes BF, Shaw GM, Hahn BH, Korber BT, Swanstrom R, Williamson C; CAPRISA Acute Infection Study Team; Center for HIV-AIDS Vaccine Immunology Consortium.

J Virol. 2009 Apr;83(8):3556-67. doi: 10.1128/JVI.02132-08. Epub 2009 Feb 4. Erratum in: J Virol. 2009 Jul;83(13):6974.

PMID:
19193811
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
18490657
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
18256145
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Unequal evolutionary rates in the human immunodeficiency virus type 1 (HIV-1) pandemic: the evolutionary rate of HIV-1 slows down when the epidemic rate increases.

Maljkovic Berry I, Ribeiro R, Kothari M, Athreya G, Daniels M, Lee HY, Bruno W, Leitner T.

J Virol. 2007 Oct;81(19):10625-35. Epub 2007 Jul 18.

PMID:
17634235
[PubMed - indexed for MEDLINE]
Free PMC Article

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