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Impact of HLA-driven HIV adaptation on virulence in populations of high HIV seroprevalence.
Proc Natl Acad Sci U S A. 2014 Dec 16;111(50):E5393-400. doi: 10.1073/pnas.1413339111. Epub 2014 Dec 1.
2
Reply to Jefferys: Declining HIV virulence.
Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2119. doi: 10.1073/pnas.1503591112. Epub 2015 Mar 24.
3
Impact of HLA selection pressure on HIV fitness at a population level in Mexico and Barbados.
J Virol. 2014 Sep;88(18):10392-8. doi: 10.1128/JVI.01162-14. Epub 2014 Jul 9.
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Evidence for HIV weakening over time.
Proc Natl Acad Sci U S A. 2015 Apr 28;112(17):E2118. doi: 10.1073/pnas.1502380112. Epub 2015 Mar 24.
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Pol-Driven Replicative Capacity Impacts Disease Progression in HIV-1 Subtype C Infection.
J Virol. 2018 Sep 12;92(19). doi: 10.1128/JVI.00811-18. Print 2018 Oct 1.
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Population-Level Immune-Mediated Adaptation in HIV-1 Polymerase during the North American Epidemic.
J Virol. 2015 Nov 11;90(3):1244-58. doi: 10.1128/JVI.02353-15. Print 2016 Feb 1.
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Extensive host immune adaptation in a concentrated North American HIV epidemic.
AIDS. 2018 Sep 10;32(14):1927-1938. doi: 10.1097/QAD.0000000000001912.

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Predicting pathogen evolution and immune evasion in the age of artificial intelligence.
Comput Struct Biotechnol J. 2025 Mar 28;27:1370-1382. doi: 10.1016/j.csbj.2025.03.044. eCollection 2025.
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HIV-1 adapts to HLA class II-associated selection pressure exerted by CD4 and CD8 T cells.
Sci Adv. 2025 Feb 14;11(7):eadr4238. doi: 10.1126/sciadv.adr4238.
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Sustained aviremia despite anti-retroviral therapy non-adherence in male children after in utero HIV transmission.
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Accelerating Bayesian inference of dependency between mixed-type biological traits.
PLoS Comput Biol. 2023 Aug 28;19(8):e1011419. doi: 10.1371/journal.pcbi.1011419. eCollection 2023 Aug.
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Adaptation to HLA-associated immune pressure over the course of HIV infection and in circulating HIV-1 strains.
PLoS Pathog. 2022 Dec 16;18(12):e1010965. doi: 10.1371/journal.ppat.1010965. eCollection 2022 Dec.

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1
Progress towards the 2020 targets for HIV diagnosis and antiretroviral treatment in South Africa.
South Afr J HIV Med. 2017 Jul 27;18(1):694. doi: 10.4102/sajhivmed.v18i1.694. eCollection 2017.
2
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic.
PLoS Genet. 2014 Apr 24;10(4):e1004295. doi: 10.1371/journal.pgen.1004295. eCollection 2014 Apr.
4
Role of transmitted Gag CTL polymorphisms in defining replicative capacity and early HIV-1 pathogenesis.
PLoS Pathog. 2012;8(11):e1003041. doi: 10.1371/journal.ppat.1003041. Epub 2012 Nov 29.
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HIV and HLA class I: an evolving relationship.
Immunity. 2012 Sep 21;37(3):426-40. doi: 10.1016/j.immuni.2012.09.005.
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Widespread impact of HLA restriction on immune control and escape pathways of HIV-1.
J Virol. 2012 May;86(9):5230-43. doi: 10.1128/JVI.06728-11. Epub 2012 Feb 29.
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Role of acute infection in HIV transmission.
Lancet. 2011 Dec 3;378(9807):1913; author reply 1914-5. doi: 10.1016/S0140-6736(11)61832-1.
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Prevention of HIV-1 infection with early antiretroviral therapy.
N Engl J Med. 2011 Aug 11;365(6):493-505. doi: 10.1056/NEJMoa1105243. Epub 2011 Jul 18.

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