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BIT Core Supported Publications

If work performed for you at the CFAR BIT core results in publication, please acknowledge us with the following statement so that we may continue to bring you excellent service:

This work was performed with the support of the Bioinformatics and Information Technologies (BIT) core at the UC San Diego Center for AIDS Research (P30 AI036214).


Gianella S, Strain MC, Rought SE, Vargas MV, Little SJ, Richman DD, Spina CA, Smith DM. Associations between virologic and immunologic dynamics in blood and in the male genital tract. J Virol. 2012 Feb;86(3):1307-15. Epub 2011 Nov 23. PubMed PMID: 22114342; PubMed Central PMCID: PMC3264378.

Pacold ME, Pond SL, Wagner GA, Delport W, Bourque DL, Richman DD, Little SJ, Smith DM. Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS. 2012 Jan 14;26(2):157-65. PubMed PMID: 22045341.


Wertheim JO, Kosakovsky Pond SL. Purifying selection can obscure the ancient age of viral lineages. Mol Biol Evol. 2011 Dec;28(12):3355-65. Epub 2011 Jun 24. PubMed PMID: 21705379; PubMed Central PMCID: PMC3247791.

Farrer RA, Weinert LA, Bielby J, Garner TW, Balloux F, Clare F, Bosch J, Cunningham AA, Weldon C, du Preez LH, Anderson L, Pond SL, Shahar-Golan R, Henk DA, Fisher MC. Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A. 2011 Nov 15;108(46):18732-6. Epub 2011 Nov 7. PubMed PMID: 22065772; PubMed Central PMCID: PMC3219125.

Gianella S, Delport W, Pacold ME, Young JA, Choi JY, Little SJ, Richman DD, Kosakovsky Pond SL, Smith DM. Detection of minority resistance during early HIV-1 infection: natural variation and spurious detection rather than transmission and evolution of multiple viral variants. J Virol. 2011 Aug;85(16):8359-67. Epub 2011 Jun 1. PubMed PMID: 21632754; PubMed Central PMCID: PMC3147985.

Mehta SR, Wertheim JO, Delport W, Ene L, Tardei G, Duiculescu D, Pond SL, Smith DM. Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infect Genet Evol. 2011 Jul;11(5):975-9. Epub 2011 Mar 23. PubMed PMID: 21439403; PubMed Central PMCID: PMC3104099.

Poon AF, Aldous JL, Mathews WC, Kitahata M, Kahn JS, Saag MS, Rodríguez B, Boswell SL, Frost SD, Haubrich RH. Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on
pre-therapy CD4 and viral load. PLoS One. 2011;6(6):e21189. Epub 2011 Jun 20. PubMed PMID: 21701595; PubMed Central PMCID: PMC3118815.


Mehta SR, Delport W, Brouwer KC, Espitia S, Patterson T, Pond SK, Strathdee SA, Smith DM. The relatedness of HIV epidemics in the United States-Mexico border region. AIDS Res Hum Retroviruses. 2010 Dec;26(12):1273-7. Epub 2010 Oct 26. PubMed PMID: 20977301; PubMed Central PMCID: PMC3011998.

Pacold M, Smith D, Little S, Cheng PM, Jordan P, Ignacio C, Richman D, Pond SK. Comparison of methods to detect HIV dual infection. AIDS Res Hum Retroviruses. 2010 Dec;26(12):1291-8. Epub 2010 Oct 18. PubMed PMID: 20954840; PubMed Central PMCID: PMC3011997.

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