CRISPR based editing of SIV proviral DNA in ART treated non-human primates.
Mancuso P, Chen C, Kaminski R, Gordon J, Liao S, Robinson JA, Smith MD, Liu H, Sariyer IK, Sariyer R, Peterson TA, Donadoni M, Williams JB, Siddiqui S, Bunnell BA, Ling B, MacLean AG, Burdo TH, Khalili K. Nat Commun. 2020 Nov 27;11(1):6065. doi: 10.1038/s41467-020-19821-7. PMID: 33247091 PMCID: PMC7695718 

Sequential LASER ART and CRISPR Treatments Eliminate HIV-1 in a Subset of Infected Humanized Mice.
Dash PK, Kaminski R, Bella R, Su H, Mathews S, Ahooyi TM, Chen C, Mancuso P, Sariyer R, Ferrante P, Donadoni M, Robinson JA, Sillman B, Lin Z, Hilaire JR, Banoub M, Elango M, Gautam N, Mosley RL, Poluektova LY, McMillan J, Bade AN, Gorantla S, Sariyer IK, Burdo TH, Young WB, Amini S, Gordon J, Jacobson JM, Edagwa B, Khalili K, Gendelman HE. Nat Commun. 2019 Jul 2;10(1):2753. doi: 10.1038/s41467-019-10366-y. PMID: 31266936 PMCID: PMC6606613 

CRISPR editing of CCR5 and HIV-1 facilitates viral elimination in antiretroviral drug-suppressed virus-infected humanized mice.
Dash PK, Chen C, Kaminski R, Su H, Mancuso P, Sillman B, Zhang C, Liao S, Sravanam S, Liu H, Waight E, Guo L, Mathews S, Sariyer R, Mosley RL, Poluektova LY, Caocci M, Amini S, Gorantla S, Burdo TH, Edagwa B, Gendelman HE, Khalili K. Proc Natl Acad Sci U S A. 2023 May 9;120(19):e2217887120. doi: 10.1073/pnas.2217887120. Epub 2023 May 1. PMID: 37126704 PMCID: PMC10175831 

Strategic self-limiting production of infectious HIV particles by CRISPR in permissive cells.
Liu H, Chen C, Liao S, Sohaii DK, Cruz CRY, Burdo TH, Cradick TJ, Mehta A, Barrero C, Florez M, Gordon J, Grauzam S, Dressman J, Amini S, Bollard CM, Kaminski R, Khalili K. Mol Ther Nucleic Acids. 2023 May 19;32:1010-1025. doi: 10.1016/j.omtn.2023.04.027. eCollection 2023 Jun 13. PMID: 37346975 PMCID: PMC10280355 

Modeling HIV-1 infection and NeuroHIV in hiPSCs-derived cerebral organoid cultures.
Donadoni M, Cakir S, Bellizzi A, Swingler M, Sariyer IK. J Neurovirol. 2024 Aug;30(4):362-379. doi: 10.1007/s13365-024-01204-z. Epub 2024 Apr 10. PMID: 38600307 PMCID: PMC1146438 

Suppression of HSV-1 infection and viral reactivation by CRISPR-Cas9 gene editing in 2D and 3D culture models.
Bellizzi A, Çakır S, Donadoni M, Sariyer R, Liao S, Liu H, Ruan GX, Gordon J, Khalili K, Sariyer IK. Mol Ther Nucleic Acids. 2024 Jul 19;35(3):102282. doi: 10.1016/j.omtn.2024.102282. eCollection 2024 Sep 10. PMID: 39176174 PMCID: PMC11339036 

CRISPR-Cas9-mediated genome editing delivered by a single AAV9 vector inhibits HSV-1 reactivation in a latent rabbit keratitis model.
Amrani N, Luk K, Singh P, Shipley M, Isik M, Donadoni M, Bellizzi A, Khalili K, Sariyer IK, Neumann D, Gordon J, Ruan GX. Mol Ther Methods Clin Dev. 2024 Aug 14;32(3):101303. doi: 10.1016/j.omtm.2024.101303. eCollection 2024 Sep 12. PMID: 39610766 PMCID: PMC11602521 

Gender dependent modulation of opioid dependance genes and signaling pathways in HIV-1 Transgenic rats at morphine tolerance.
Bishir M, Huang W, Sariyer IK, Chang SL. J Neurovirol. 2025 May 7. doi: 10.1007/s13365-025-01257-8. Online ahead of print. PMID: 40332726 PMCID: In progress 

iPSC-derived three-dimensional brain organoid models and neurotropic viral infections.
Swingler M, Donadoni M, Bellizzi A, Cakir S, Sariyer IK. J Neurovirol. 2023 Apr;29(2):121-134. doi: 10.1007/s13365-023-01133-3. Epub 2023 Apr 25. PMID: 37097597 PMCID: PMC10127962 

Recent advances in discovery and functional analysis of the small proteins and microRNA expressed by polyomaviruses.
Saribas AS, Jensen LE, Safak M. Virology. 2025 Jan;602:110310. doi:10.1016/j.virol.2024.110310. Epub 2024 Nov 22. PMID: 39612622 PMCID: in progress 

JC virus small tumor antigen promotes S phase entry and cell cycle progression.
Biffi R, Benoit SW, Sariyer IK, Safak M. Tumour Virus Res. 2024 Dec;18:200298. doi: 10.1016/j.tvr.2024.200298. Epub 2024 Nov 23. PMID: 39586476 PMCID: PMC11647237 

Human neurotropic polyomavirus, JC virus, late coding region encodes a novel nuclear protein, ORF4, which targets the promyelocytic leukemia nuclear bodies (PML-NBs) and modulates their reorganization.
Saribas AS, Bellizzi A, Wollebo HS, Beer T, Tang HY, Safak M. Virology. 2023 Oct;587:109866. doi: 10.1016/j.virol.2023.109866. Epub 2023 Aug 19. PMID: 37741199 PMCID: PMC10602023 

A Comprehensive Proteomics Analysis of the JC Virus (JCV) Large and Small Tumor Antigen Interacting Proteins: Large T Primarily Targets the Host Protein Complexes with V-ATPase and Ubiquitin Ligase Activities While Small t Mostly Associates with Those Having Phosphatase and Chromatin-Remodeling Functions.
Saribas S, Safak M. Viruses. 2020 Oct 20;12(10):1192. doi: 10.3390/v12101192. PMID: 33092197 PMCID: PMC7594058 

A comprehensive proteomics analysis of JC virus Agnoprotein-interacting proteins: Agnoprotein primarily targets the host proteins with coiled-coil motifs.
Saribas AS, Datta PK, Safak M. Virology. 2020 Jan 15;540:104-118. doi: 10.1016/j.virol.2019.10.005. Epub 2019 Oct 20. PMID: 31765920 PMCID: PMC6957716 

Neural tube defects induce abnormal astrocyte development by activation and epigenetic permissiveness of STAT3.
Janik K, Jin LQ, Kyzy KZ, Kaminski R, Smith GM, Krynska B. Exp Neurol. 2025 Jul;389:115231. doi: 10.1016/j.expneurol.2025.115231. Epub 2025 Mar 30. PMID: 40169106 PMCID: in progress 

Lipid nanocarrier targeting activated macrophages for antiretroviral therapy of HIV reservoir. Wu D, Si M, Xue HY, Tran NT, Khalili K, Kaminski R, Wong HL. Nanomedicine (Lond). 2023 Aug;18(20):1343-1360. doi: 10.2217/nnm-2023-0120. Epub 2023 Oct 10. PMID: 37815117 PMCID: PMC10652294 

Preclinical safety and biodistribution of CRISPR targeting SIV in non-human primates. Burdo TH, Chen C, Kaminski R, Sariyer IK, Mancuso P, Donadoni M, Smith MD, Sariyer R, Caocci M, Liao S, Liu H, Huo W, Zhao H, Misamore J, Lewis MG, Simonyan V, Thompson EE, Xu EY, Cradick TJ, Gordon J, Khalili K. Gene Ther. 2024 May;31(5-6):224-233. doi: 10.1038/s41434-023-00410-4. Epub 2023 Aug 17. PMID: 37587230 PMCID: PMC11090835 

IFNα and β Mediated JCPyV Suppression through C/EBPβ-LIP Isoform.
May D, Bellizzi A, Kassa W, Cipriaso JM, Caocci M, Wollebo HS. Viruses. 2021 Sep 26;13(10):1937. doi: 10.3390/v13101937. PMID: 34696366 PMCID: PMC8537971 

Elevated Asparagine Biosynthesis Drives Brain Tumor Stem Cell Metabolic Plasticity and Resistance to Oxidative Stress.
Thomas TM, Miyaguchi K, Edwards LA, Wang H, Wollebo H, Aiguo L, Murali R, Wang Y, Braas D, Michael JS, Andres AM, Zhang M, Khalili K, Gottlieb RA, Perez JM, Yu JS. Mol Cancer Res. 2021 Aug;19(8):1375-1388. doi: 10.1158/1541-7786.MCR-20-0086. Epub 2021 Apr 16. PMID: 33863814 PMCID: PMC8349847

Neurotropic Viruses as Acute and Insidious Drivers of Aging.
Rocchi A, Wollebo HS, Khalili K. Biomolecules. 2025 Apr 1;15(4):514. doi: 10.3390/biom15040514. PMID: 40305226 PMCID: PMC12025245