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Items: 1 to 20 of 112


An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1.

Kosakovsky Pond SL, Posada D, Stawiski E, Chappey C, Poon AF, Hughes G, Fearnhill E, Gravenor MB, Leigh Brown AJ, Frost SD.

PLoS Comput Biol. 2009 Nov;5(11):e1000581. doi: 10.1371/journal.pcbi.1000581. Epub 2009 Nov 26.


Automated subtyping of HIV-1 genetic sequences for clinical and surveillance purposes: performance evaluation of the new REGA version 3 and seven other tools.

Pineda-Peña AC, Faria NR, Imbrechts S, Libin P, Abecasis AB, Deforche K, Gómez-López A, Camacho RJ, de Oliveira T, Vandamme AM.

Infect Genet Evol. 2013 Oct;19:337-48. doi: 10.1016/j.meegid.2013.04.032. Epub 2013 May 7.


Novel HIV-1 recombinants spreading across multiple risk groups in the United Kingdom: the identification and phylogeography of Circulating Recombinant Form (CRF) 50_A1D.

Foster GM, Ambrose JC, Hué S, Delpech VC, Fearnhill E, Abecasis AB, Leigh Brown AJ, Geretti AM; UK HIV Drug Resistance Database.

PLoS One. 2014 Jan 15;9(1):e83337. doi: 10.1371/journal.pone.0083337. eCollection 2014.


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.


Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form.

Abecasis AB, Lemey P, Vidal N, de Oliveira T, Peeters M, Camacho R, Shapiro B, Rambaut A, Vandamme AM.

J Virol. 2007 Aug;81(16):8543-51. Epub 2007 Jun 6.


COMET: adaptive context-based modeling for ultrafast HIV-1 subtype identification.

Struck D, Lawyer G, Ternes AM, Schmit JC, Bercoff DP.

Nucleic Acids Res. 2014 Oct;42(18):e144. doi: 10.1093/nar/gku739. Epub 2014 Aug 12.


Identification of new, emerging HIV-1 unique recombinant forms and drug resistant viruses circulating in Cameroon.

Ragupathy V, Zhao J, Wood O, Tang S, Lee S, Nyambi P, Hewlett I.

Virol J. 2011 Apr 23;8:185. doi: 10.1186/1743-422X-8-185.


Development of a novel human immunodeficiency virus type 1 subtyping tool, Subtype Analyzer (STAR): analysis of subtype distribution in London.

Gale CV, Myers R, Tedder RS, Williams IG, Kellam P.

AIDS Res Hum Retroviruses. 2004 May;20(5):457-64.


Detection of viral sequence fragments of HIV-1 subfamilies yet unknown.

Unterthiner T, Schultz AK, Bulla J, Morgenstern B, Stanke M, Bulla I.

BMC Bioinformatics. 2011 Apr 11;12:93. doi: 10.1186/1471-2105-12-93.


Forty-one near full-length HIV-1 sequences from Kenya reveal an epidemic of subtype A and A-containing recombinants.

Dowling WE, Kim B, Mason CJ, Wasunna KM, Alam U, Elson L, Birx DL, Robb ML, McCutchan FE, Carr JK.

AIDS. 2002 Sep 6;16(13):1809-20. Erratum in: AIDS 2002 Oct 18;16(15):2104.


Using genomic signatures for HIV-1 sub-typing.

Pandit A, Sinha S.

BMC Bioinformatics. 2010 Jan 18;11 Suppl 1:S26. doi: 10.1186/1471-2105-11-S1-S26.


Extensive intrasubtype recombination in South African human immunodeficiency virus type 1 subtype C infections.

Rousseau CM, Learn GH, Bhattacharya T, Nickle DC, Heckerman D, Chetty S, Brander C, Goulder PJ, Walker BD, Kiepiela P, Korber BT, Mullins JI.

J Virol. 2007 May;81(9):4492-500. Epub 2007 Feb 21.


Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E.

Anderson JP, Rodrigo AG, Learn GH, Madan A, Delahunty C, Coon M, Girard M, Osmanov S, Hood L, Mullins JI.

J Virol. 2000 Nov;74(22):10752-65.


A genetic analysis of HIV-1 from Punjab, India reveals the presence of multiple variants.

Jameel S, Zafrullah M, Ahmad M, Kapoor GS, Sehgal S.

AIDS. 1995 Jul;9(7):685-90.


jpHMM at GOBICS: a web server to detect genomic recombinations in HIV-1.

Zhang M, Schultz AK, Calef C, Kuiken C, Leitner T, Korber B, Morgenstern B, Stanke M.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W463-5.


HIV type 1 group M subtype G in Cameroon: five genome sequences.

Yamaguchi J, Ndembi N, Ngansop C, Mbanya D, Kaptué L, Gürtler LG, Devare SG, Brennan CA.

AIDS Res Hum Retroviruses. 2009 Apr;25(4):469-73. doi: 10.1089/aid.2008.0296.


New subtypes and genetic recombination in HIV type 1-infecting patients with highly active antiretroviral therapy in Peru (2008-2010).

Yabar CA, Acuña M, Gazzo C, Salinas G, Cárdenas F, Valverde A, Romero S.

AIDS Res Hum Retroviruses. 2012 Dec;28(12):1712-22. doi: 10.1089/AID.2012.0040. Epub 2012 Jun 25.


An isolate of human immunodeficiency virus type 1 originally classified as subtype I represents a complex mosaic comprising three different group M subtypes (A, G, and I).

Gao F, Robertson DL, Carruthers CD, Li Y, Bailes E, Kostrikis LG, Salminen MO, Bibollet-Ruche F, Peeters M, Ho DD, Shaw GM, Sharp PM, Hahn BH.

J Virol. 1998 Dec;72(12):10234-41.

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