Selected Publications

  1. Wang Y, Gornalusse GG, Siegel DA, Barbehenn A, Hoh R, Martin J, Hecht F, Pilcher C, Semenova L, Murdoch DM, Margolis DM, Levy CN, Jerome KR, Rudin CD, Hladik F, Deeks SG, Lee SA, Browne EP. NF-κB dependent gene expression and plasma IL-1β, TNFα and GCSF drive transcriptomic diversity and CD4:CD8 ratio in people with HIV on ART. bioRxiv [Preprint]. 2025 Feb 14:2025.02.14.638232. doi: 10.1101/2025.02.14.638232.

  2. Janssens J, Wedrychowski A, Kim SJ, Isbell C, Hoh R, Pillai SK, Henrich TJ, Deeks SG, Roan NR, Lee SA, Yukl SA. Longitudinal changes in the transcriptionally active and intact HIV reservoir after starting ART during acute infection. J Virol. 2025 Mar 18;99(3):e0143124.

  3. Frouard J, Telwatte S, Luo X, Elphick N, Thomas R, Arneson D, Roychoudhury P, Butte AJ, Wong JK, Hoh R, Deeks SG, Lee SA, Roan NR, Yukl S. HIV-SEQ REVEALS GLOBAL HOST GENE EXPRESSION DIFFERENCES BETWEEN HIV-TRANSCRIBING CELLS FROM VIREMIC AND SUPPRESSED PEOPLE WITH HIV. bioRxiv [Preprint]. 2024 Dec 20:2024.12.17.629023. doi: 10.1101/2024.12.17.629023.

  4. Barbehenn A, Shi L, Shao J, Hoh R, Hartig HM, Pae V, Sarvadhavabhatla S, Donaire S, Sheikhzadeh C, Milush J, Laird GM, Mathias M, Ritter K, Peluso MJ, Martin J, Hecht F, Pilcher C, Cohen SE, Buchbinder S, Havlir D, Gandhi M, Henrich TJ, Hatano H, Wang J, Deeks SG, Lee SA. Rapid biphasic decay of intact and defective HIV DNA reservoir during acute treated HIV disease. Nat Commun. 2024 Nov 18;15(1):9966.

  5. Babcock BR, Kosters A, Eddins DJ, Donaire MSB, Sarvadhavabhatla S, Pae V, Beltran F, Murray VW, Gill G, Xie G, Dobosh BS, Giacalone VD, Tirouvanziam RM, Ramonell RP, Jenks SA, Sanz I, Lee FE, Roan NR, Lee SA, Ghosn EEB. Transient anti-interferon autoantibodies in the airways are associated with recovery from COVID-19. Sci Transl Med. 2024 Nov 6;16(772):eadq1789.

  6. Whitehill GD, Joy J, Marino FE, Krause R, Mallick S, Courtney H, Park K, Carey J, Hoh R, Hartig H, Pae V, Sarvadhavabhatla S, Donaire S, Deeks SG, Lynch RM, Lee SA, Bar KJ. Autologous neutralizing antibody responses after antiretroviral therapy in acute and early HIV-1. J Clin Invest. 2024 Apr 23;134(11):e176673.

  7. Dwivedi AK, Gornalusse GG, Siegel DA, Barbehenn A, Thanh C, Hoh R, Hobbs KS, Pan T, Gibson EA, Martin J, Hecht F, Pilcher C, Milush J, Busch MP, Stone M, Huang ML, Reppetti J, Vo PM, Levy CN, Roychoudhury P, Jerome KR, Hladik F, Henrich TJ, Deeks SG, Lee SA. A cohort-based study of host gene expression: tumor suppressor and innate immune/inflammatory pathways associated with the HIV reservoir size. PLoS Pathog. 2023 Nov 29;19(11):e1011114.
  8. Augusto DG, Murdolo LD, Chatzileontiadou DSM, Sabatino JJ Jr, Yusufali T, Peyser ND, Butcher X, Kizer K, Guthrie K, Murray VW, Pae V, Sarvadhavabhatla S, Beltran F, Gill GS, Lynch KL, Yun C, Maguire CT, Peluso MJ, Hoh R, Henrich TJ, Deeks SG, Davidson M, Lu S, Goldberg SA, Kelly JD, Martin JN, Vierra-Green CA, Spellman SR, Langton DJ, Dewar-Oldis MJ, Smith C, Barnard PJ, Lee S, Marcus GM, Olgin JE, Pletcher MJ, Maiers M, Gras S, Hollenbach JA. A common allele of HLA is associated with asymptomatic SARS-CoV-2 infection. Nature. 2023 Aug;620(7972):128-136.
  9. Siegel DA, Thanh C, Wan E, Hoh R, Hobbs K, Pan T, Gibson EA, Kroetz DL, Martin J, Hecht F, Pilcher C, Martin M, Carrington M, Pillai S, Busch MP, Stone M, Levy CN, Huang ML, Roychoudhury P, Hladik F, Jerome KR, Kiem HP, Henrich TJ, Deeks SG, Lee SA. Host variation in type I interferon signaling genes (MX1), C-C chemokine receptor type 5 gene, and major histocompatibility complex class I alleles in treated HIV+ noncontrollers predict viral reservoir size. AIDS. 2023 Mar 1;37(3):477-488.
  10. Neidleman J, Luo X, McGregor M, Xie G, Murray V, Greene WC, Lee SA, Roan NR. mRNA vaccine-induced T cells respond identically to SARS-CoV-2 variants of concern but differ in longevity and homing properties depending on prior infection status. Elife. 2021 Oct 12;10:e72619.
  11. Ma T, Ryu H, McGregor M, Babcock B, Neidleman J, Xie G, George AF, Frouard J, Murray V, Gill G, Ghosn E, Newell EW, Lee SA, Roan NR. Protracted yet Coordinated Differentiation of Long-Lived SARS-CoV-2-Specific CD8+ T Cells during Convalescence. J Immunol. 2021 Sep 1;207(5):1344-1356.
  12. Neidleman J, Luo X, George AF, McGregor M, Yang J, Yun C, Murray V, Gill G, Greene WC, Vasquez J, Lee SA, Ghosn E, Lynch KL, Roan NR. Distinctive features of SARS-CoV-2-specific T cells predict recovery from severe COVID-19. Cell Rep. 2021 Jul 20;36(3):109414.
  13. Johnson KA, Chen MJ, Kohn R, Sachdev D, Bacon O, Lee S, Cohen SE. Acute HIV at the Time of Initiation of Pre-exposure or Post-exposure Prophylaxis: Impact on Drug Resistance and Clinical Outcomes. J Acquir Immune Defic Syndr. 2021 Jun 1;87(2):818-825.
  14. Telwatte S, Martin HA, Marczak R, Fozouni P, Vallejo-Gracia A, Kumar GR, Murray V, Lee S, Ott M, Wong JK, Yukl SA. Novel RT-ddPCR assays for measuring the levels of subgenomic and genomic SARS-CoV-2 transcripts. Methods. 2021 Apr 18:S1046-2023(21)00103-1.
  15. Neidleman J, Luo X, Frouard J, Xie G, Gill G, Stein ES, McGregor M, Ma T, George AF, Kosters A, Greene WC, Vasquez J, Ghosn E, Lee S, and Roan NR. SARS-CoV-2-Specific T Cells Exhibit Phenotypic Features of Helper Function, Lack of Terminal Differentiation, and High Proliferation Potential. Cell Rep Med. 2020 Sep 22;1(6):100081.
  16. Lee SA, Telwatte S, Hatano H, Kashuba ADM, Cottrell ML, Hoh R, Liegler TJ, Stephenson S, Somsouk M, Hunt PW, Deeks SG, Yukl S, Savic RM. Antiretroviral therapy concentrations differ in gut vs. lymph node tissues and are associated with HIV viral transcription by a novel RT-ddPCR assay. J Acquir Immune Defic Syndr. 2020 Apr 15;83(5):530-537.
  17. McGinnis CS, Siegel DA, Xie G, Gartner ZJ, Roan NR, Lee SA. No detectable alloreactive transcriptional responses during donor-multiplexed single-cell RNA sequencing of peripheral blood mononuclear cells. BMC Biol. 2021 In Press.
  18. Telwatte S and Lee SA, Somsouk M, Hatano H, Baker C, Kaiser P, Kim P, Chen TH, Milush J, Hunt PW, Deeks SG, Wong JK, Yukl SA. Gut and blood differ in constitutive blocks to HIV transcription, suggesting tissue-specific differences in the mechanisms that govern HIV latency. PLoS Pathog. 2018 Nov 15;14(11):e1007357.
  19. Coffey S, Bacchetti P, Sachdev D, Bacon O, Jones D, Ospina-Norvell C, Torres S, Lynch E, Camp C, Mercer-Slomoff R, Lee S, Christopoulos K, Pilcher C, Hsu L, Jin C, Scheer S, Havlir D, Gandhi M. RAPID antiretroviral therapy: high virologic suppression rates with immediate antiretroviral therapy initiation in a vulnerable urban clinic population. AIDS. 2019 Apr 1;33(5):825-832.
  20. Cohen SE, Sachdev D, Lee SA, Scheer S, Bacon O, Chen MJ, Okochi H, Anderson PL, Kearney MF, Coffey S, Scott H, Grant RM, Havlir D, Gandhi M. Acquisition of tenofovir-susceptible, emtricitabine-resistant HIV despite high adherence to daily pre-exposure prophylaxis: a case report. Lancet HIV. 2018 Nov 29.
  21. Lee SA, Elliott JH, McMahon J, Hartogenesis W, Bumpus NN, Lifson JD, Gorelick RJ, Bacchetti P, Deeks SG, Lewin SR, Savic RM. Population Pharmacokinetics and Pharmacodynamics of Disulfiram on Inducing Latent HIV-1 Transcription in a Phase 2b Trial. Clin Pharmacol Ther. 2018 Aug 23.
  22. Lee SA, Byakwaga H, Boum Y, Burdo TH, Williams KC, Lederman MM, Huang Y, Tracy RP, Cao H, Haberer JE, Kembabazi A, Bangsberg DR, Martin JN, and Hunt PW. Immunologic Pathways that Predict Mortality in HIV-Infected Ugandans Initiating Antiretroviral Therapy. J Infect Dis. 2017 Apr 15;215(8):1270-1274.
  23. Lee SA, Deeks SG. The Benefits of Early Antiretroviral Therapy for HIV Infection: How Early is Early Enough? EBioMedicine. 2016 Aug 5.
  24. Lee SA, Bacchetti P, Chomont N, Fromentin R, Lewin SR, O'Doherty U, Palmer S, Richman DD, Siliciano JD, Yukl SA, Deeks SG, Burbelo PD. Anti-HIV Antibody Responses and the HIV Reservoir Size during Antiretroviral Therapy. PLoS One. 2016 Aug 2.
  25. Lee SA, Mefford JA, Huang Y, Witte JS, Martin JN, Haas DW, Mclaren PJ, Mushiroda T, Kubo M, Byakwaga H, Hunt PW, Kroetz DL. Host Genetic Predictors of the Kynurenine Pathway of Tryptophan Catabolism Among Treated HIV-Infected Ugandans. AIDS. 2016 Apr 14.
  26. Elliott JH, McMahon JH, Chang CC, Lee SA, Hartogensis W, Bumpus N, Savic R, Roney J, Hoh R, Solomon A, Piatak M, Gorelick RJ, Lifson J, Bacchetti P, Deeks SG, Lewin SR. Short-term administration of disulfiram for reversal of latent HIV infection: a phase 2 dose-escalation study. Lancet HIV. 2015 Dec;2(12):e520-9.
  27. Lee SA, Plett SK, Luetkemeyer AF, Borgo GM, Ohliger MA, Conrad MB, Cookson BT, Sengupta DJ, Koehler JE. Bartonella quintana Aortitis in a Man with AIDS, Diagnosed by Needle Biopsy and 16S rRNA Gene Amplification. J Clin Microbiol. 2015 Aug;53(8):2773-6.
  28. Ramirez CM, Sinclair E, Epling L, Lee SA, Jain V, Hsue PY, Hatano H, Conn D, Hecht FM, Martin JN, Mccune JM, Deeks SG, Hunt PW. Immunologic profiles distinguish aviremic HIV-infected adults. AIDS. 2016 Feb 5.
  29. Freeman ML, Mudd JC, Shive CL, Younes SA, Panigrahi S, Sieg SF, Lee SA, Hunt PW, Calabrese LH, Gianella S, Rodriguez B, Lederman MM. CD8 T-Cell Expansion and Inflammation Linked to CMV Coinfection in ART-treated HIV Infection. Clin Infect Dis. 2016 Feb 1;62(3):392-6.
  30. Serrano-Villar S, Sainz T, Lee SA, Hunt PW, Sinclair E, Shacklett BL, Ferre AL, Hayes TL, Somsouk M, Hsue PY, Van Natta ML, Meinert CL, Lederman MM, Hatano H, Jain V, Huang Y, Hecht FM, Martin JN, McCune JM, Moreno S, Deeks SG. HIV-infected individuals with low CD4/CD8 ratio despite effective antiretroviral therapy exhibit altered T cell subsets, heightened CD8+ T cell activation, and increased risk of non-AIDS morbidity and mortality. PLoS Pathog. 2014 May 15;10(5):e1004078.
  31. Lee SA, Sinclair E, Hatano H, Hsue P, Epling L, Hecht F, Bangsberg DR, Martin JN, McCune JM, Deeks SG, Hunt PW. Impact of HIV on CD8+ T Cell CD57 Expression is Distinct from that of CMV and Aging. PLoS One. 2014 Feb 27;9(2).
  32. Lee SA, Haiman CA, Burtt NP, Pooler LC, Cheng I, Kolonel LN, Pike MC, Altshuler D, Hirschhorn JN, Henderson BE, Stram DO. A comprehensive analysis of common genetic variation in prolactin (PRL) and PRL receptor (PRLR) genes in relation to plasma prolactin levels and breast cancer risk: the multiethnic cohort. BMC Med Genet. 2007; 8:72.
  33. Lee SA, Yeka A, Nsobya SL, Dokomajilar C, Rosenthal PJ, Talisuna A, Dorsey G. Complexity of Plasmodium falciparum infections and antimalarial drug efficacy at 7 sites in Uganda. J Infect Dis. 2006 Apr 15; 193(8):1160-3.
  34. Lee S, Kolonel L, Wilkens L, Wan P, Henderson B, Pike M. Postmenopausal hormone therapy and breast cancer risk: the Multiethnic Cohort. Int J Cancer. 2006 Mar 1; 118(5):1285-91.
  35. Lee SA, Ross RK, Pike MC. An overview of menopausal oestrogen-progestin hormone therapy and breast cancer risk. Br J Cancer. 2005 Jun 6; 92(11):2049-58.