Publications

Selected Publications

• Park Y, He J, Eleya S, Wu Z, Fiches GN, Zhou D, Watters EG, He ZM, Shanaka KA, Lepcha TT, Liu Y, Santoso NG, Zhu J. NAT10 Suppresses RNA Sensing Induced IFN-β Transactivation to Promote Viral Infection via Interfering with IRF3 Activities. bioRxiv. 2025 Sep 1;. doi: 10.1101/2025.09.01.673489. PubMed PMID: 40949982; PubMed Central PMCID: PMC12424707.

• Wu Z, Lepcha TT, Zhou D, He Z, Fiches GN, Park Y, He J, Chen J, Shanaka KASN, Oghumu S, Zhao W, Ma A, Ma Q, Zhu J, Santoso NG.Analysis of head and neck cancer scRNA-seq data identified PRDM6 promotes tumor progression by modulating immune gene expression. Front Immunol. 2025;16:1596916. doi: 10.3389/fimmu.2025.1596916. eCollection 2025. PubMed PMID: 40936897; PubMed Central PMCID: PMC12420620.

• Fnu T, Shi P, Zhang W, Fang Y, Mitani Y, Zhang Y, Gabre J, Ei-Rifai W, Zaika A, Chen Q, Zhu J, Wang TC, Jiang M, Que J. The SOX4-Semaphorin3C axis promotes Esophageal Adenocarcinoma progression. Cancer Lett. 2025 Aug 26:218005. doi: 10.1016/j.canlet.2025.218005. Online ahead of print.

• Wu Z, Zhou D, He Z, Fiches GN, Park Y, He J, Chen J, Shanaka KASN, Lepcha TT, Desai P, Zhu J, Santoso NG. m5C RNA Methylation Is Dysregulated by Oncogenic Herpesviruses via c-Myc Signaling to Counteract Host Antiviral Factors. bioRxiv. 2025 May 8;. doi: 10.1101/2025.05.07.652742. PubMed PMID: 40654933; PubMed Central PMCID: PMC12248048.

• Sarkar P, Wang X, Hu W, Zhu J, Ho WZ. Human Microglia Models for NeuroHIV. Viruses. 2025 Apr 29;17(5). doi: 10.3390/v17050641. PubMed PMID: 40431653.

• Wu Z, Lepcha TT, Zhou D, He Z, Fiches GN, Park Y, He J, Shanaka KASN, Oghumu S, Zhao W, Ma A, Ma Q, Zhu J, Santoso NG. Analysis of Head and Neck Cancer scRNA-seq Data Identified PRDM6 Promotes Tumor Progression by Modulating Immune Gene Expression. bioRxiv. 2025 Mar 7;. doi: 10.1101/2025.03.04.641548. PubMed PMID: 40093183; PubMed Central PMCID: PMC11908237.

• Li TW, Park Y, Watters EG, Wang X, Zhou D, Fiches GN, Wu Z, Badley AD, Sacha JB, Ho WZ, Santoso NG, Qi J, Zhu J. KDM5A/B contribute to HIV-1 latent infection and survival of HIV-1 infected cells. Antiviral Res. 2024 Aug;228:105947. doi: 10.1016/j.antiviral.2024.105947. Epub 2024 Jun 24. PubMed PMID: 38925368. 

• Wang P, Liu JB, Wang X, Meng FZ, Xiao QH, Liu L, Zhu J, Hu WH, Ho WZ. Activation of Toll-like receptor 3 inhibits HIV infection of human iPSC-derived microglia. J Med Virol. 2023 Nov;95(11):e29217. doi: 10.1002/jmv.29217. PubMed PMID: 37933090; PubMed Central PMCID: PMC10655899. 

• Huang H, Fang Y, Jiang M, Zhang Y, Biermann J, Melms JC, Danielsson JA, Yang Y, Qiang L, Liu J, Zhou Y, Wang M, Hu Z, Wang TC, Saqi A, Sun J, Matsumoto I, Cardoso WV, Emala CW, Zhu J, Izar B, Mou H, Que J. Contribution of Trp63(CreERT2)-labeled cells to alveolar regeneration is independent of tuft cells. Elife. 2022 Sep 21;11. doi: 10.7554/eLife.78217. PubMed PMID: 36129169; PubMed Central PMCID: PMC9553211. 

• Li TW, Kenney AD, Park JG, Fiches GN, Liu H, Zhou D, Biswas A, Zhao W, Que J, Santoso N, Martinez-Sobrido L, Yount JS, Zhu J. SARS-CoV-2 Nsp14 protein associates with IMPDH2 and activates NF-κB signaling. Front Immunol. 2022;13:1007089. doi: 10.3389/fimmu.2022.1007089. eCollection 2022. PubMed PMID: 36177032; PubMed Central PMCID: PMC9513374. 

• Zhou D, Wu Z, Park JG, Fiches GN, Li TW, Ma Q, Huang H, Biswas A, Martinez-Sobrido L, Santoso NG, Zhu J. FACT subunit SUPT16H associates with BRD4 and contributes to silencing of interferon signaling. Nucleic Acids Res. 2022 Aug 26;50(15):8700-8718. doi: 10.1093/nar/gkac645. PubMed PMID: 35904816; PubMed Central PMCID: PMC9410884. 

• Miller J, Dakic A, Spurgeon M, Saenz F, Kallakury B, Zhao B, Zhang J, Zhu J, Ma Q, Xu Y, Lambert P, Schlegel R, Riegel AT, Liu X. AIB1 is a novel target of the high-risk HPV E6 protein and a biomarker of cervical cancer progression. J Med Virol. 2022 Aug;94(8):3962-3977. doi: 10.1002/jmv.27795. Epub 2022 Apr 27. PubMed PMID: 35437795; PubMed Central PMCID: PMC9199254. 

• Fu X, Cheng D, Luo Z, Wagner A, Fitting S, Cong X, Xu W, Maas K, Wan Z, Zhu J, Zhou Z, Stoops WW, McRae-Clark A, Jiang W. Oral Enrichment of Streptococcus and its Role in Systemic Inflammation Related to Monocyte Activation in Humans with Cocaine Use Disorder. J Neuroimmune Pharmacol. 2022 Jun;17(1-2):305-317. doi: 10.1007/s11481-021-10007-6. Epub 2021 Aug 26. PubMed PMID: 34448131; PubMed Central PMCID: PMC8881519. 

• Eltobgy MM, Zani A, Kenney AD, Estfanous S, Kim E, Badr A, Carafice C, Daily K, Whitham O, Pietrzak M, Webb A, Kawahara J, Eddy AC, Denz P, Lu M, Kc M, Peeples ME, Li J, Zhu J, Que J, Robinson R, Rosas Mejia O, Rayner RE, Hall-Stoodley L, Seveau S, Gavrilin MA, Zhang X, Thomas J, Kohlmeier JE, Suthar MS, Oltz E, Tedeschi A, Robledo-Avila FH, Partida-Sanchez S, Hemann EA, Abdelrazik E, Forero A, Nimjee SM, Boyaka PN, Cormet-Boyaka E, Yount JS, Amer AO. Caspase-4/11 exacerbates disease severity in SARS-CoV-2 infection by promoting inflammation and immunothrombosis. Proc Natl Acad Sci U S A. 2022 May 24;119(21):e2202012119. doi: 10.1073/pnas.2202012119. Epub 2022 May 19. PubMed PMID: 35588457; PubMed Central PMCID: PMC9173818. 

• Fiches GN, Wu Z, Zhou D, Biswas A, Li TW, Kong W, Jean M, Santoso NG, Zhu J. Polyamine biosynthesis and eIF5A hypusination are modulated by the DNA tumor virus KSHV and promote KSHV viral infection. PLoS Pathog. 2022 Apr;18(4):e1010503. doi: 10.1371/journal.ppat.1010503. eCollection 2022 Apr. PubMed PMID: 35486659; PubMed Central PMCID: PMC9094511. 

• Luo Z, Li M, Li TW, Lv Z, Ye Z, Cisneros WJ, Zhang J, Yuan L, Hultquist JF, Migueles SA, Huang L, Zhu J, Jiang W. Differential Expression of CREM/ICER Isoforms Is Associated with the Spontaneous Control of HIV Infection. mBio. 2022 Feb 22;13(1):e0197921. doi: 10.1128/mbio.01979-21. Epub 2022 Jan 4. PubMed PMID: 35041523; PubMed Central PMCID: PMC8725591. 

• Biswas A, Zhou D, Fiches GN, Wu Z, Liu X, Ma Q, Zhao W, Zhu J, Santoso NG. Inhibition of polo-like kinase 1 (PLK1) facilitates reactivation of gamma-herpesviruses and their elimination. PLoS Pathog. 2021 Jul;17(7):e1009764. doi: 10.1371/journal.ppat.1009764. eCollection 2021 Jul. PubMed PMID: 34297745; PubMed Central PMCID: PMC8336821. 

• Wu Z, Lawrence PJ, Ma A, Zhu J, Xu D, Ma Q. Single-Cell Techniques and Deep Learning in Predicting Drug Response. Trends Pharmacol Sci. 2020 Dec;41(12):1050-1065. doi: 10.1016/j.tips.2020.10.004. Epub 2020 Nov 2. Review. PubMed PMID: 33153777; PubMed Central PMCID: PMC7669610. 

• Fiches GN, Zhou D, Kong W, Biswas A, Ahmed EH, Baiocchi RA, Zhu J, Santoso N. Profiling of immune related genes silenced in EBV-positive gastric carcinoma identified novel restriction factors of human gammaherpesviruses. PLoS Pathog. 2020 Aug;16(8):e1008778. doi: 10.1371/journal.ppat.1008778. eCollection 2020 Aug. PubMed PMID: 32841292; PubMed Central PMCID: PMC7473590. 

• Zhou D, Hayashi T, Jean M, Kong W, Fiches G, Biswas A, Liu S, Yosief HO, Zhang X, Bradner J, Qi J, Zhang W, Santoso N, Zhu J. Inhibition of Polo-like kinase 1 (PLK1) facilitates the elimination of HIV-1 viral reservoirs in CD4(+) T cells ex vivo. Sci Adv. 2020 Jul;6(29):eaba1941. doi: 10.1126/sciadv.aba1941. eCollection 2020 Jul. PubMed PMID: 32832623; PubMed Central PMCID: PMC7439358. 

• Kong W, Biswas A, Zhou D, Fiches G, Fujinaga K, Santoso N, Zhu J. Nucleolar protein NOP2/NSUN1 suppresses HIV-1 transcription and promotes viral latency by competing with Tat for TAR binding and methylation. PLoS Pathog. 2020 Mar;16(3):e1008430. doi: 10.1371/journal.ppat.1008430. eCollection 2020 Mar. PubMed PMID: 32176734; PubMed Central PMCID: PMC7098636. 

• Kong W, Rivera-Serrano EE, Neidleman JA, Zhu J. HIV-1 Replication Benefits from the RNA Epitranscriptomic Code. J Mol Biol. 2019 Dec 6;431(24):5032-5038. doi: 10.1016/j.jmb.2019.09.021. Epub 2019 Oct 15. Review. PubMed PMID: 31626810; PubMed Central PMCID: PMC6953616. 

• Kong W, Hayashi T, Fiches G, Xu Q, Li MZ, Que J, Liu S, Zhang W, Qi J, Santoso N, Elledge SJ, Zhu J. Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions. Genomics Proteomics Bioinformatics. 2019 Jun;17(3):319-331. doi: 10.1016/j.gpb.2018.12.010. Epub 2019 Sep 5. PubMed PMID: 31494268; PubMed Central PMCID: PMC6818353. 

• Huang H, Kong W, Jean M, Fiches G, Zhou D, Hayashi T, Que J, Santoso N, Zhu J. A CRISPR/Cas9 screen identifies the histone demethylase MINA53 as a novel HIV-1 latency-promoting gene (LPG). Nucleic Acids Res. 2019 Aug 22;47(14):7333-7347. doi: 10.1093/nar/gkz493. PubMed PMID: 31165872; PubMed Central PMCID: PMC6698651. 

• Jean MJ, Zhou D, Fiches G, Kong W, Huang H, Purmal A, Gurova K, Santoso NG, Zhu J. Curaxin CBL0137 has the potential to reverse HIV-1 latency. J Med Virol. 2019 Aug;91(8):1571-1576. doi: 10.1002/jmv.25487. Epub 2019 May 1. PubMed PMID: 30989696; PubMed Central PMCID: PMC6599568. 

• Jean MJ, Fiches G, Hayashi T, Zhu J. Current Strategies for Elimination of HIV-1 Latent Reservoirs Using Chemical Compounds Targeting Host and Viral Factors. AIDS Res Hum Retroviruses. 2019 Jan;35(1):1-24. doi: 10.1089/AID.2018.0153. Epub 2018 Dec 12. Review. PubMed PMID: 30351168; PubMed Central PMCID: PMC6343200. 

• Simpson S, Fiches G, Jean MJ, Dieringer M, McGuinness J, John SP, Shamay M, Desai P, Zhu J, Santoso NG. Inhibition of Tip60 Reduces Lytic and Latent Gene Expression of Kaposi's Sarcoma-Associated Herpes Virus (KSHV) and Proliferation of KSHV-Infected Tumor Cells. Front Microbiol. 2018;9:788. doi: 10.3389/fmicb.2018.00788. eCollection 2018. PubMed PMID: 29740418; PubMed Central PMCID: PMC5928232. 

• Kong W, Li H, Zhu J. Zika virus: The transboundary pathogen from mosquito and updates. Microb Pathog. 2018 Jan;114:476-482. doi: 10.1016/j.micpath.2017.12.031. Epub 2017 Dec 11. Review. PubMed PMID: 29241768. 

• Jiang M, Li H, Zhang Y, Yang Y, Lu R, Liu K, Lin S, Lan X, Wang H, Wu H, Zhu J, Zhou Z, Xu J, Lee DK, Zhang L, Lee YC, Yuan J, Abrams JA, Wang TC, Sepulveda AR, Wu Q, Chen H, Sun X, She J, Chen X, Que J. Transitional basal cells at the squamous-columnar junction generate Barrett's oesophagus. Nature. 2017 Oct 26;550(7677):529-533. doi: 10.1038/nature24269. Epub 2017 Oct 12. PubMed PMID: 29019984; PubMed Central PMCID: PMC5831195. 

• Jean MJ, Hayashi T, Huang H, Brennan J, Simpson S, Purmal A, Gurova K, Keefer MC, Kobie JJ, Santoso NG, Zhu J. Curaxin CBL0100 Blocks HIV-1 Replication and Reactivation through Inhibition of Viral Transcriptional Elongation. Front Microbiol. 2017;8:2007. doi: 10.3389/fmicb.2017.02007. eCollection 2017. PubMed PMID: 29089933; PubMed Central PMCID: PMC5651003. 

• Hayashi T, Jean M, Huang H, Simpson S, Santoso NG, Zhu J. Screening of an FDA-approved compound library identifies levosimendan as a novel anti-HIV-1 agent that inhibits viral transcription. Antiviral Res. 2017 Oct;146:76-85. doi: 10.1016/j.antiviral.2017.08.013. Epub 2017 Aug 24. PubMed PMID: 28842263; PubMed Central PMCID: PMC5654649. 

• Huang H, Liu S, Jean M, Simpson S, Huang H, Merkley M, Hayashi T, Kong W, Rodríguez-Sánchez I, Zhang X, Yosief HO, Miao H, Que J, Kobie JJ, Bradner J, Santoso NG, Zhang W, Zhu J. A Novel Bromodomain Inhibitor Reverses HIV-1 Latency through Specific Binding with BRD4 to Promote Tat and P-TEFb Association. Front Microbiol. 2017;8:1035. doi: 10.3389/fmicb.2017.01035. eCollection 2017. PubMed PMID: 28638377; PubMed Central PMCID: PMC5461361. 

• Jean MJ, Power D, Kong W, Huang H, Santoso N, Zhu J. Identification of HIV-1 Tat-Associated Proteins Contributing to HIV-1 Transcription and Latency. Viruses. 2017 Apr 1;9(4). doi: 10.3390/v9040067. PubMed PMID: 28368303; PubMed Central PMCID: PMC5408673. 

• Liu K, Xie F, Gao A, Zhang R, Zhang L, Xiao Z, Hu Q, Huang W, Huang Q, Lin B, Zhu J, Wang H, Que J, Lan X. SOX2 regulates multiple malignant processes of breast cancer development through the SOX2/miR-181a-5p, miR-30e-5p/TUSC3 axis. Mol Cancer. 2017 Mar 14;16(1):62. doi: 10.1186/s12943-017-0632-9. PubMed PMID: 28288641; PubMed Central PMCID: PMC5348847. 

• Huang H, Santoso N, Power D, Simpson S, Dieringer M, Miao H, Gurova K, Giam CZ, Elledge SJ, Zhu J. FACT Proteins, SUPT16H and SSRP1, Are Transcriptional Suppressors of HIV-1 and HTLV-1 That Facilitate Viral Latency. J Biol Chem. 2015 Nov 6;290(45):27297-27310. doi: 10.1074/jbc.M115.652339. Epub 2015 Sep 16. PubMed PMID: 26378236; PubMed Central PMCID: PMC4646377. 

• Power D, Santoso N, Dieringer M, Yu J, Huang H, Simpson S, Seth I, Miao H, Zhu J. IFI44 suppresses HIV-1 LTR promoter activity and facilitates its latency. Virology. 2015 Jul;481:142-50. doi: 10.1016/j.virol.2015.02.046. Epub 2015 Mar 14. PubMed PMID: 25776761; PubMed Central PMCID: PMC4437885. 

• Liu ZP, Wu H, Zhu J, Miao H. Systematic identification of transcriptional and post-transcriptional regulations in human respiratory epithelial cells during influenza A virus infection. BMC Bioinformatics. 2014 Oct 4;15(1):336. doi: 10.1186/1471-2105-15-336. PubMed PMID: 25281301; PubMed Central PMCID: PMC4287445. 

• Bera A, Perkins EM, Zhu J, Zhu H, Desai P. DNA binding and condensation properties of the herpes simplex virus type 1 triplex protein VP19C. PLoS One. 2014;9(8):e104640. doi: 10.1371/journal.pone.0104640. eCollection 2014. PubMed PMID: 25121591; PubMed Central PMCID: PMC4133253. 

• Larman HB, Liang AC, Elledge SJ, Zhu J. Discovery of protein interactions using parallel analysis of translated ORFs (PLATO). Nat Protoc. 2014 Jan;9(1):90-103. doi: 10.1038/nprot.2013.167. Epub 2013 Dec 12. PubMed PMID: 24336473; PubMed Central PMCID: PMC4129458. 

• Zhu J, Davoli T, Perriera JM, Chin CR, Gaiha GD, John SP, Sigiollot FD, Gao G, Xu Q, Qu H, Pertel T, Sims JS, Smith JA, Baker RE, Maranda L, Ng A, Elledge SJ, Brass AL. Comprehensive identification of host modulators of HIV-1 replication using multiple orthologous RNAi reagents. Cell Rep. 2014 Oct 23;9(2):752-66. doi: 10.1016/j.celrep.2014.09.031. Epub 2014 Oct 16. PubMed PMID: 25373910; PubMed Central PMCID: PMC4926641. 

• Zhu J, Larman HB, Gao G, Somwar R, Zhang Z, Laserson U, Ciccia A, Pavlova N, Church G, Zhang W, Kesari S, Elledge SJ. Protein interaction discovery using parallel analysis of translated ORFs (PLATO). Nat Biotechnol. 2013 Apr;31(4):331-334. doi: 10.1038/nbt.2539. Epub 2013 Mar 17. PubMed PMID: 23503679; PubMed Central PMCID: PMC4110636. 

• Zhu J, Gaiha GD, John SP, Pertel T, Chin CR, Gao G, Qu H, Walker BD, Elledge SJ, Brass AL. Reactivation of latent HIV-1 by inhibition of BRD4. Cell Rep. 2012 Oct 25;2(4):807-16. doi: 10.1016/j.celrep.2012.09.008. Epub 2012 Oct 4. PubMed PMID: 23041316; PubMed Central PMCID: PMC3523124. 

• Woodard C, Shamay M, Liao G, Zhu J, Ng AN, Li R, Newman R, Rho HS, Hu J, Wan J, Qian J, Zhu H, Hayward SD. Phosphorylation of the chromatin binding domain of KSHV LANA. PLoS Pathog. 2012;8(10):e1002972. doi: 10.1371/journal.ppat.1002972. Epub 2012 Oct 18. PubMed PMID: 23093938; PubMed Central PMCID: PMC3475679. 

• Shamay M, Liu J, Li R, Liao G, Shen L, Greenway M, Hu S, Zhu J, Xie Z, Ambinder RF, Qian J, Zhu H, Hayward SD. A protein array screen for Kaposi's sarcoma-associated herpesvirus LANA interactors links LANA to TIP60, PP2A activity, and telomere shortening. J Virol. 2012 May;86(9):5179-91. doi: 10.1128/JVI.00169-12. Epub 2012 Feb 29. PubMed PMID: 22379092; PubMed Central PMCID: PMC3347335. 

• Zheng D, Wan J, Cho YG, Wang L, Chiou CJ, Pai S, Woodard C, Zhu J, Liao G, Martinez-Maza O, Qian J, Zhu H, Hayward GS, Ambinder RF, Hayward SD. Comparison of humoral immune responses to Epstein-Barr virus and Kaposi's sarcoma-associated herpesvirus using a viral proteome microarray. J Infect Dis. 2011 Dec 1;204(11):1683-91. doi: 10.1093/infdis/jir645. Epub 2011 Oct 11. PubMed PMID: 21990424; PubMed Central PMCID: PMC3203236. 

• Zhu J*, Li R*, Xie Z, Liao G, Liu J, Chen MR, Hu S, Woodard C, Lin J, Taverna SD, Desai P, Ambinder RF, Hayward GS, Qian J, Zhu H, Hayward SD. Conserved herpesvirus kinases target the DNA damage response pathway and TIP60 histone acetyltransferase to promote virus replication. Cell Host Microbe. 2011 Oct 20;10(4):390-400. doi: 10.1016/j.chom.2011.08.013. PubMed PMID: 22018239; PubMed Central PMCID: PMC3253558. * Equal contributions.

• Zhu J, Liao G, Shan L, Zhang J, Chen MR, Hayward GS, Hayward SD, Desai P, Zhu H. Protein array identification of substrates of the Epstein-Barr virus protein kinase BGLF4. J Virol. 2009 May;83(10):5219-31. doi: 10.1128/JVI.02378-08. Epub 2009 Feb 25. PubMed PMID: 19244323; PubMed Central PMCID: PMC2682057. 

• Zhu J, Gopinath K, Murali A, Yi G, Hayward SD, Zhu H, Kao C. RNA-binding proteins that inhibit RNA virus infection. Proc Natl Acad Sci U S A. 2007 Feb 27;104(9):3129-34. doi: 10.1073/pnas.0611617104. Epub 2007 Feb 20. PubMed PMID: 17360619; PubMed Central PMCID: PMC1805585. 

• Lu JY, Lin YY, Qian J, Tao SC, Zhu J, Pickart C, Zhu H. Functional dissection of a HECT ubiquitin E3 ligase. Mol Cell Proteomics. 2008 Jan;7(1):35-45. doi: 10.1074/mcp.M700353-MCP200. Epub 2007 Oct 19. PubMed PMID: 17951556; PubMed Central PMCID: PMC2861892. 

• Chen CS, Korobkova E, Chen H, Zhu J, Jian X, Tao SC, He C, Zhu H. A proteome chip approach reveals new DNA damage recognition activities in Escherichia coli. Nat Methods. 2008 Jan;5(1):69-74. doi: 10.1038/nmeth1148. Epub 2007 Dec 16. PubMed PMID: 18084297; PubMed Central PMCID: PMC2576280. 

• Fujimuro M, Liu J, Zhu J, Yokosawa H, Hayward SD. Regulation of the interaction between glycogen synthase kinase 3 and the Kaposi's sarcoma-associated herpesvirus latency-associated nuclear antigen. J Virol. 2005 Aug;79(16):10429-41. doi: 10.1128/JVI.79.16.10429-10441.2005. PubMed PMID: 16051835; PubMed Central PMCID: PMC1182668.

• Yang Z, Zhu J, Sriadibhatla S, Gebhart C, Alakhov V, Kabanov A. Promoter- and strain-selective enhancement of gene expression in a mouse skeletal muscle by a polymer excipient Pluronic P85. J Control Release. 2005 Nov 28;108(2-3):496-512. doi: 10.1016/j.jconrel.2005.08.015. Epub 2005 Sep 9. PubMed PMID: 16154658.