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Optimized SMRT-UMI protocol produces highly accurate sequence datasets from diverse populations - application to HIV-1 quasispecies.
Westfall DH, Deng W, Pankow A, Murrell H, Chen L, Zhao H, Williamson C, Rolland M, Murrell B, Mullins JI. Westfall DH, et al. Among authors: zhao h. bioRxiv [Preprint]. 2023 Feb 24:2023.02.23.529831. doi: 10.1101/2023.02.23.529831. bioRxiv. 2023. Update in: Virus Evol. 2024 Mar 02;10(1):veae019. doi: 10.1093/ve/veae019 PMID: 36865215 Free PMC article. Updated. Preprint.
Prevention efficacy of the broadly neutralizing antibody VRC01 depends on HIV-1 envelope sequence features.
Juraska M, Bai H, deCamp AC, Magaret CA, Li L, Gillespie K, Carpp LN, Giorgi EE, Ludwig J, Molitor C, Hudson A, Williamson BD, Espy N, Simpkins B, Rudnicki E, Shao D, Rossenkhan R, Edlefsen PT, Westfall DH, Deng W, Chen L, Zhao H, Bhattacharya T, Pankow A, Murrell B, Yssel A, Matten D, York T, Beaume N, Gwashu-Nyangiwe A, Ndabambi N, Thebus R, Karuna ST, Morris L, Montefiori DC, Hural JA, Cohen MS, Corey L, Rolland M, Gilbert PB, Williamson C, Mullins JI. Juraska M, et al. Among authors: zhao h. Proc Natl Acad Sci U S A. 2024 Jan 23;121(4):e2308942121. doi: 10.1073/pnas.2308942121. Epub 2024 Jan 19. Proc Natl Acad Sci U S A. 2024. PMID: 38241441 Free PMC article.
Improved detection of rare HIV-1 variants using 454 pyrosequencing.
Larsen BB, Chen L, Maust BS, Kim M, Zhao H, Deng W, Westfall D, Beck I, Frenkel LM, Mullins JI. Larsen BB, et al. Among authors: zhao h. PLoS One. 2013 Oct 2;8(10):e76502. doi: 10.1371/journal.pone.0076502. eCollection 2013. PLoS One. 2013. PMID: 24098517 Free PMC article.
RV144 vaccine imprinting constrained HIV-1 evolution following breakthrough infection.
Lewitus E, Sanders-Buell E, Bose M, O'Sullivan AM, Poltavee K, Li Y, Bai H, Mdluli T, Donofrio G, Slike B, Zhao H, Wong K, Chen L, Miller S, Lee J, Ahani B, Lepore S, Muhammad S, Grande R, Tran U, Dussupt V, Mendez-Rivera L, Nitayaphan S, Kaewkungwal J, Pitisuttithum P, Rerks-Ngarm S, O'Connell RJ, Janes H, Gilbert PB, Gramzinski R, Vasan S, Robb ML, Michael NL, Krebs SJ, Herbeck JT, Edlefsen PT, Mullins JI, Kim JH, Tovanabutra S, Rolland M. Lewitus E, et al. Among authors: zhao h. Virus Evol. 2021 Jul 9;7(2):veab057. doi: 10.1093/ve/veab057. eCollection 2021. Virus Evol. 2021. PMID: 34532060 Free PMC article.
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. Herbeck JT, et al. Among authors: zhao h. J Virol. 2011 Aug;85(15):7523-34. doi: 10.1128/JVI.02697-10. Epub 2011 May 18. J Virol. 2011. PMID: 21593162 Free PMC article.
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