Publications

• Western diet reduces small intestinal intraepithelial lymphocytes via FXR-Interferon pathway.Hung CT, Ma C, Panda SK, Trsan T, Hodel M, Frein J, Foster A, Sun S, Wu HT, Kern J, Mishra R, Jain U, Ho YC, Colonna M, Stappenbeck TS, Liu TC. Mucosal Immunol. 2024 Oct; 2024 Jul 9. PMID: 38992433.
• The single-cell opioid responses in the context of HIV (SCORCH) consortium.Ament SA, Campbell RR, Lobo MK, Receveur JP, Agrawal K, Borjabad A, Byrareddy SN, Chang L, Clarke D, Emani P, Gabuzda D, Gaulton KJ, Giglio M, Giorgi FM, Gok B, Guda C, Hadas E, Herb BR, Hu W, Huttner A, Ishmam MR, Jacobs MM, Kelschenbach J, Kim DW, Lee C, Liu S, Liu X, Madras BK, Mahurkar AA, Mash DC, Mukamel EA, Niu M, O'Connor RM, Pagan CM, Pang APS, Pillai P, Repunte-Canonigo V, Ruzicka WB, Stanley J, Tickle T, Tsai SA, Wang A, Wills L, Wilson AM, Wright SN, Xu S, Yang J, Zand M, Zhang L, Zhang J, Akbarian S, Buch S, Cheng CS, Corley MJ, Fox HS, Gerstein M, Gummuluru S, Heiman M, Ho YC, Kellis M, Kenny PJ, Kluger Y, Milner TA, Moore DJ, Morgello S, Ndhlovu LC, Rana TM, Sanna PP, Satterlee JS, Sestan N, Spector SA, Spudich S, Tilgner HU, Volsky DJ, White OR, Williams DW, Zeng H. Mol Psychiatry. 2024 Jun 15; 2024 Jun 15. PMID: 38879719.
• Pioneering Data Processing for Convolutional Neural Networks to Enhance the Diagnostic Accuracy of Traditional Chinese Medicine Pulse Diagnosis for Diabetes.Yeh WC, Kuo CY, Chen JM, Ku TH, Yao DJ, Ho YC, Lin RY. Bioengineering (Basel). 2024 Jun 2; 2024 Jun 2. PMID: 38927797.
• Exploring novel HIV-1 reverse transcriptase inhibitors with drug-resistant mutants: A double mutant surprise.Hollander K, Chan AH, Frey KM, Hunker O, Ippolito JA, Spasov KA, Yeh YJ, Jorgensen WL, Ho YC, Anderson KS. Protein Sci. 2023 Dec. PMID: 37861472.
• Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence.Wei Y, Davenport TC, Collora JA, Ma HK, Pinto-Santini D, Lama J, Alfaro R, Duerr A, Ho YC. Immunity. 2023 Nov 14; 2023 Nov 2. PMID: 37922905.
• Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels.Wong M, Wei Y, Ho YC. Curr Opin HIV AIDS. 2023 Sep 1; 2023 Jul 17. PMID: 37535039.
• Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation.Collora JA, Ho YC. Genome Res. 2023 Jun; 2023 Jun 9. PMID: 37295842.
• Interferon opens up: HIV-induced inflammation reconfigures 3D chromatin conformation and affects where HIV integrates.Wei Y, Ho YC. Mol Cell. 2022 Dec 15. PMID: 36525953.
• Inhibition of a Chromatin and Transcription Modulator, SLTM, Increases HIV-1 Reactivation Identified by a CRISPR Inhibition Screen.Pedersen SF, Collora JA, Kim RN, Yang K, Razmi A, Catalano AA, Yeh YJ, Mounzer K, Tebas P, Montaner LJ, Ho YC. J Virol. 2022 Jul 13; 2022 Jun 22. PMID: 35730977.
• Single-cell multiomics reveals persistence of HIV-1 in expanded cytotoxic T cell clones.Collora JA, Liu R, Pinto-Santini D, Ravindra N, Ganoza C, Lama JR, Alfaro R, Chiarella J, Spudich S, Mounzer K, Tebas P, Montaner LJ, van Dijk D, Duerr A, Ho YC. Immunity. 2022 Jun 14; 2022 Mar 22. PMID: 35320704.
• TCR-mimic bispecific antibodies to target the HIV-1 reservoir.Sengupta S, Board NL, Wu F, Moskovljevic M, Douglass J, Zhang J, Reinhold BR, Duke-Cohan J, Yu J, Reed MC, Tabdili Y, Azurmendi A, Fray EJ, Zhang H, Hsiue EH, Jenike K, Ho YC, Gabelli SB, Kinzler KW, Vogelstein B, Zhou S, Siliciano JD, Sadegh-Nasseri S, Reinherz EL, Siliciano RF. Proc Natl Acad Sci U S A. 2022 Apr 12; 2022 Apr 8. PMID: 35394875.
• The loud minority: Transcriptionally active HIV-1-infected cells survive, proliferate, and persist.Collora JA, Ho YC. Cell. 2022 Jan 20. PMID: 35063069.
• A multidimensional HIV-1 persistence model for clonal expansion and viral rebound in vitro.Eshetu A, Ho YC. Cell Rep Methods. 2021 Dec 20; 2021 Dec 20. PMID: 35475216.
• Design and implementation of a cohort study of persons living with HIV infection who are initiating medication treatment for opioid use disorder to evaluate HIV-1 persistence.Schultheis A, Sanchez M, Pedersen S, Kyriakides T, Ho YC, Kluger Y, Springer SA. Contemp Clin Trials Commun. 2021 Dec; 2021 Nov 11. PMID: 34825103.
• The Clonal Expansion Dynamics of the HIV-1 Reservoir: Mechanisms of Integration Site-Dependent Proliferation and HIV-1 Persistence.Yeh YJ, Yang K, Razmi A, Ho YC. Viruses. 2021 Sep 17; 2021 Sep 17. PMID: 34578439.
• Restriction of SARS-CoV-2 replication by targeting programmed -1 ribosomal frameshifting.Sun Y, Abriola L, Niederer RO, Pedersen SF, Alfajaro MM, Silva Monteiro V, Wilen CB, Ho YC, Gilbert WV, Surovtseva YV, Lindenbach BD, Guo JU. Proc Natl Acad Sci U S A. 2021 Jun 29. PMID: 34185680.
• Measuring the size and decay dynamics of the HIV-1 latent reservoir.Liu R, Catalano AA, Ho YC. Cell Rep Med. 2021 Apr 20; 2021 Apr 20. PMID: 33948579.
• Shock-and-kill versus block-and-lock: Targeting the fluctuating and heterogeneous HIV-1 gene expression.Yeh YJ, Ho YC. Proc Natl Acad Sci U S A. 2021 Apr 20. PMID: 33758027.
• The XPB Subunit of the TFIIH Complex Plays a Critical Role in HIV-1 Transcription and XPB Inhibition by Spironolactone Prevents HIV-1 Reactivation from Latency.Mori L, Jenike K, Yeh YJ, Lacombe B, Li C, Getzler A, Mediouni S, Cameron M, Pipkin M, Ho YC, Ramirez BC, Valente S. J Virol. 2021 Feb 15; 2020 Nov 25. PMID: 33239456.
• The single-cell landscape of immunological responses of CD4+ T cells in HIV versus severe acute respiratory syndrome coronavirus 2.Collora JA, Liu R, Albrecht K, Ho YC. Curr Opin HIV AIDS. 2021 Jan. PMID: 33165008.
• Recommendations for measuring HIV reservoir size in cure-directed clinical trials.Abdel-Mohsen M, Richman D, Siliciano RF, Nussenzweig MC, Howell BJ, Martinez-Picado J, Chomont N, Bar KJ, Yu XG, Lichterfeld M, Alcami J, Hazuda D, Bushman F, Siliciano JD, Betts MR, Spivak AM, Planelles V, Hahn BH, Smith DM, Ho YC, Buzon MJ, Gaebler C, Paiardini M, Li Q, Estes JD, Hope TJ, Kostman J, Mounzer K, Caskey M, Fox L, Frank I, Riley JL, Tebas P, Montaner LJ. Nat Med. 2020 Sep; 2020 Sep 7. PMID: 32895573.
• Filgotinib suppresses HIV-1-driven gene transcription by inhibiting HIV-1 splicing and T cell activation.Yeh YJ, Jenike KM, Calvi RM, Chiarella J, Hoh R, Deeks SG, Ho YC. J Clin Invest. 2020 Sep 1. PMID: 32573496.
• Longitudinal study reveals HIV-1-infected CD4+ T cell dynamics during long-term antiretroviral therapy.Antar AA, Jenike KM, Jang S, Rigau DN, Reeves DB, Hoh R, Krone MR, Keruly JC, Moore RD, Schiffer JT, Nonyane BA, Hecht FM, Deeks SG, Siliciano JD, Ho YC, Siliciano RF. J Clin Invest. 2020 Jul 1. PMID: 32191639.
• Single-cell transcriptional landscapes reveal HIV-1-driven aberrant host gene transcription as a potential therapeutic target.Liu R, Yeh YJ, Varabyou A, Collora JA, Sherrill-Mix S, Talbot CC Jr, Mehta S, Albrecht K, Hao H, Zhang H, Pollack RA, Beg SA, Calvi RM, Hu J, Durand CM, Ambinder RF, Hoh R, Deeks SG, Chiarella J, Spudich S, Douek DC, Bushman FD, Pertea M, Ho YC. Sci Transl Med. 2020 May 13. PMID: 32404504.
• SARS-CoV-2: a storm is raging.Pedersen SF, Ho YC. J Clin Invest. 2020 May 1. PMID: 32217834.
• The forces driving clonal expansion of the HIV-1 latent reservoir.Liu R, Simonetti FR, Ho YC. Virol J. 2020 Jan 7; 2020 Jan 7. PMID: 31910871.
• The Landscape of Persistent Viral Genomes in ART-Treated SIV, SHIV, and HIV-2 Infections.Bender AM, Simonetti FR, Kumar MR, Fray EJ, Bruner KM, Timmons AE, Tai KY, Jenike KM, Antar AAR, Liu PT, Ho YC, Raugi DN, Seydi M, Gottlieb GS, Okoye AA, Del Prete GQ, Picker LJ, Mankowski JL, Lifson JD, Siliciano JD, Laird GM, Barouch DH, Clements JE, Siliciano RF. Cell Host Microbe. 2019 Jul 10. PMID: 31295427.
• Apobec3A maintains HIV-1 latency through recruitment of epigenetic silencing machinery to the long terminal repeat.Taura M, Song E, Ho YC, Iwasaki A. Proc Natl Acad Sci U S A. 2019 Feb 5; 2019 Jan 22. PMID: 30670656.
• A quantitative approach for measuring the reservoir of latent HIV-1 proviruses.Bruner KM, Wang Z, Simonetti FR, Bender AM, Kwon KJ, Sengupta S, Fray EJ, Beg SA, Antar AAR, Jenike KM, Bertagnolli LN, Capoferri AA, Kufera JT, Timmons A, Nobles C, Gregg J, Wada N, Ho YC, Zhang H, Margolick JB, Blankson JN, Deeks SG, Bushman FD, Siliciano JD, Laird GM, Siliciano RF. Nature. 2019 Feb; 2019 Jan 30. PMID: 30700913.
• Expanded cellular clones carrying replication-competent HIV-1 persist, wax, and wane.Wang Z, Gurule EE, Brennan TP, Gerold JM, Kwon KJ, Hosmane NN, Kumar MR, Beg SA, Capoferri AA, Ray SC, Ho YC, Hill AL, Siliciano JD, Siliciano RF. Proc Natl Acad Sci U S A. 2018 Mar 13; 2018 Feb 26. PMID: 29483265.
• Latent HIV reservoirs exhibit inherent resistance to elimination by CD8+ T cells.Huang SH, Ren Y, Thomas AS, Chan D, Mueller S, Ward AR, Patel S, Bollard CM, Cruz CR, Karandish S, Truong R, Macedo AB, Bosque A, Kovacs C, Benko E, Piechocka-Trocha A, Wong H, Jeng E, Nixon DF, Ho YC, Siliciano RF, Walker BD, Jones RB. J Clin Invest. 2018 Feb 1; 2018 Jan 22. PMID: 29355843.
• Defective HIV-1 Proviruses Are Expressed and Can Be Recognized by Cytotoxic T Lymphocytes, which Shape the Proviral Landscape.Pollack RA, Jones RB, Pertea M, Bruner KM, Martin AR, Thomas AS, Capoferri AA, Beg SA, Huang SH, Karandish S, Hao H, Halper-Stromberg E, Yong PC, Kovacs C, Benko E, Siliciano RF, Ho YC. Cell Host Microbe. 2017 Apr 12. PMID: 28407485.
• Proliferation of latently infected CD4(+) T cells carrying replication-competent HIV-1: Potential role in latent reservoir dynamics.Hosmane NN, Kwon KJ, Bruner KM, Capoferri AA, Beg S, Rosenbloom DI, Keele BF, Ho YC, Siliciano JD, Siliciano RF. J Exp Med. 2017 Apr 3; 2017 Mar 24. PMID: 28341641.
• Paucity of Intact Non-Induced Provirus with Early, Long-Term Antiretroviral Therapy of Perinatal HIV Infection.Rainwater-Lovett K, Ziemniak C, Watson D, Luzuriaga K, Siberry G, Petru A, Chen Y, Uprety P, McManus M, Ho YC, Lamers SL, Persaud D. PLoS One. 2017; 2017 Feb 8. PMID: 28178277.
• Defective proviruses rapidly accumulate during acute HIV-1 infection.Bruner KM, Murray AJ, Pollack RA, Soliman MG, Laskey SB, Capoferri AA, Lai J, Strain MC, Lada SM, Hoh R, Ho YC, Richman DD, Deeks SG, Siliciano JD, Siliciano RF. Nat Med. 2016 Sep; 2016 Aug 8. PMID: 27500724.
• Efforts to eliminate the latent reservoir in resting CD4+ T cells: strategies for curing HIV-1 infection.Ho YC, Siliciano JD. J Virus Erad. 2015 Oct 1; 2015 Oct 1. PMID: 27482420.
• Investigation of the Anti-Melanogenic and Antioxidant Characteristics of Eucalyptus camaldulensis Flower Essential Oil and Determination of Its Chemical Composition.Huang HC, Ho YC, Lim JM, Chang TY, Ho CL, Chang TM. Int J Mol Sci. 2015 May 7; 2015 May 7. PMID: 25961954.
• Measuring reversal of HIV-1 latency ex vivo using cells from infected individuals.Ho YC, Laird GM, Siliciano RF. Proc Natl Acad Sci U S A. 2014 May 13; 2014 May 5. PMID: 24799684.
• Sprouty-2 regulates HIV-specific T cell polyfunctionality.Chiu YL, Shan L, Huang H, Haupt C, Bessell C, Canaday DH, Zhang H, Ho YC, Powell JD, Oelke M, Margolick JB, Blankson JN, Griffin DE, Schneck JP. J Clin Invest. 2014 Jan. PMID: 24292711.
• Replication-competent noninduced proviruses in the latent reservoir increase barrier to HIV-1 cure.Ho YC, Shan L, Hosmane NN, Wang J, Laskey SB, Rosenbloom DI, Lai J, Blankson JN, Siliciano JD, Siliciano RF. Cell. 2013 Oct 24; 2013 Oct 24. PMID: 24243014.
• Challenges in detecting HIV persistence during potentially curative interventions: a study of the Berlin patient.Yukl SA, Boritz E, Busch M, Bentsen C, Chun TW, Douek D, Eisele E, Haase A, Ho YC, Hütter G, Justement JS, Keating S, Lee TH, Li P, Murray D, Palmer S, Pilcher C, Pillai S, Price RW, Rothenberger M, Schacker T, Siliciano J, Siliciano R, Sinclair E, Strain M, Wong J, Richman D, Deeks SG. PLoS Pathog. 2013; 2013 May 9. PMID: 23671416.
• Factors associated with development of complications among adults with influenza: a 3-year prospective analysis.Wu UI, Wang JT, Ho YC, Pan SC, Chen YC, Chang SC. J Formos Med Assoc. 2012 Jul; 2012 Jun 12. PMID: 22817813.
• Mycobacterium tuberculosis complex enhances susceptibility of CD4 T cells to HIV through a TLR2-mediated pathway.Thayil SM, Ho YC, Bollinger RC, Blankson JN, Siliciano RF, Karakousis PC, Page KR. PLoS One. 2012; 2012 Jul 23. PMID: 22844428.
• Seroprevalence of hepatitis A virus infection in persons with HIV infection in Taiwan: implications for hepatitis A vaccination.Sun HY, Kung HC, Ho YC, Chien YF, Chen MY, Sheng WH, Hsieh SM, Wu CH, Liu WC, Hung CC, Chang SC. Int J Infect Dis. 2009 Sep; 2009 Feb 8. PMID: 19208490.
• Prognostic factors for fatal adult influenza pneumonia.Ho YC, Wang JL, Wang JT, Wu UI, Chang CW, Wu HS, Chen CH, Chuang YM, Chang SC. J Infect. 2009 Jun; 2009 Mar 25. PMID: 19386366.
• High levels of mecA DNA detected by a quantitative real-time PCR assay are associated with mortality in patients with methicillin-resistant Staphylococcus aureus bacteremia.Ho YC, Chang SC, Lin SR, Wang WK. J Clin Microbiol. 2009 May; 2009 Mar 11. PMID: 19279177.
• Clinical presentation and outcome of toxoplasmic encephalitis in patients with human immunodeficiency virus type 1 infection.Ho YC, Sun HY, Chen MY, Hsieh SM, Sheng WH, Chang SC. J Microbiol Immunol Infect. 2008 Oct. PMID: 19122919.
• Osteonecrosis in patients with human immunodeficiency virus type 1 infection in Taiwan.Ho YC, Shih TT, Lin YH, Hsiao CF, Chen MY, Hsieh SM, Sheng WH, Sun HY, Hung CC, Chang SC. Jpn J Infect Dis. 2007 Nov. PMID: 18032839.
• Emergence of cefotaxime resistance in Citrobacter freundii causing necrotizing fasciitis and osteomyelitis.Chuang YM, Tseng SP, Teng LJ, Ho YC, Hsueh PR. J Infect. 2006 Sep; 2006 Jan 10. PMID: 16375973.