Publications

Research Articles

• Stacia Phillips, Alice Baek, Sanggu Kim, Shuliang Chen, and Li Wu, “Protocol for the generation of HIV-1 genomic RNA with altered levels of N6-methyladenosine (m6A)” STAR*Protocols (Cell press), 2022 Aug 10;3(3):101616. doi: 10.1016/j.xpro.2022.101616. eCollection 2022 Sep 16.
• Shihyoung Kim, Alice Baek, Rajni Kant Shukla, Sophie G Cressman, Hannah Yu, Sarah Golconda, Hye Won Choi, John C Reneau, Zhirui Wang, Christene A. Huang, Namal P. M. Liyanage and Sanggu Kim*, “CD3e immunotoxin spares CD62Llo effector Tregs and reshapes organ-specific tissue-resident T-cell composition via preferential depletion of CD3ehi T cells.” ⁺Frontiers in Immunology, 2022 Oct 26;13:1011190. doi: 10.3389/fimmu.2022.1011190. eCollection 2022.
• Shihyoung Kim, Rajni Kant Shukla, Eunsoo Kim,Sophie G. Cressman, Hannah Yu, Alice Baek, Hyewon Choi, Alan Kim, Amit Sharma, Zhirui Wang, Christene A. Huang, John C. Reneau, Prosper N. Boyaka, Namal P. M. Liyanage, and Sanggu Kim* “Comparison of CD3e Antibody and CD3e-sZAP Immunotoxin Treatment in Mice Identifies sZAP as the Main Driver of Vascular Leakage” Biomedicines 2022, 10, 1221. https://doi.org/10.3390/biomedicines10061221 
• Chi-Ling Chiang; Eileen Hu; Lingqian Chang; Kevan Zapolnik; Xiaokui Mo; Jadwiga Labanowska; Junfeng Shi; Tzyy-Jye doong; Arletta Lozanski; Pearlly Yan; Ralf bundschuh; Logan A. Walker; Daniel Gallegoperez; Wu lu; Meixiao long; Sanggu Kim; Nyla heerema; Gerard lozanski; Jennifer Woyach; John C. Byrd; L. James Lee; Natarajan Muthusamy, “Leukemia Initiating HSCs in Chronic Lymphocytic Leukemia Reveal Clonal leukemogenesis and Differential Drug Sensitivity” Cell Reports (Cell press), 2022, 40 (3) 19; https://doi.org/10.1016/j.celrep.2022.111115. 
• Dong-Hwan Kim, Young Min Choi, Joonbum Lee, Sangsu Shin, Sanggu Kim, Yeunsu Suh and Kichoon Lee. “Differential Expression of MSTN Isoforms in Muscle between Broiler and Layer Chickens.” Animals 2022, 12(5), 539; https://doi.org/10.3390/ani12050539. 
• Gajendra W Suryawanshi, Hubert Arokium, Sanggu Kim, Wannisa Khamaikawin, Samantha Lin, Saki Shimizu, Koollawat Chupradit, YooJin Lee, Yiming Xie, Xin Guan, Vasantika Suryawanshi, Angela P Presson, Dong Sung An, Irvin S Y Chen. “Longitudinal clonal tracking in humanized mice reveals sustained polyclonal repopulation of gene-modified human-HSPC despite vector integration bias.” Stem Cell Res Ther. 2021 Oct 7;12(1):528. doi: 10.1186/s13287-021-02601-5. PubMed PMID: 34620229; PubMed Central PMCID: PMC8499514. 
• Dong-Hwan Kim, Joonbum Lee, Sanggu Kim, Hyun S Lillehoj, Kichoon Lee, “Hypertrophy of Adipose Tissues in Quail Embryos by in ovo Injection of All- Trans Retinoic Acid”, Frontiers in Physiology. 2021 May 21;12:681562. PMID: 34093239 PMCID: PMC8176229 DOI: 10.3389/fphys.2021.681562
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• Gajendra W. Suryawanshi; Wannisa Khamaikawin; Jing Wen; Saki Shimizu; Hubert Arokium; Yiming Xie; Eugene Wang; Shihyoung Kim; Hyewon Choi; Chong Zhang; Angela P. Presson; Namshin Kim; Dong-Sung An; Irvin S. Y. Chen; Sanggu Kim*, “The clonal repopulation of HSPC gene-modified with anti-HIV-1 RNAi is not impacted by pre-existing HIV-1 infection”, Science Advances, 2020, DOI: 10.1126/sciadv.aay9206 
• Song Xu, Sanggu Kim, Irvin SY Chen and Tom Chou, “Modeling large fluctuations of thousands of clones during hematopoiesis: The role of stem cell self-renewal and bursty progenitor dynamics in rhesus macaque.” PLoS Computational Biology, 2018, Oct 18; 14(10);e1006489. PMID:30335762; PMCID: PMC6218102; DOI:10.1371/journal.pcbi.1006489
• Khamaikawin W, Shimizu S, Kamata M, Cortado R, Jung Y, Lam J, Wen J, Kim P, Xie Y, Kim S, Arokium H, Presson AP, Chen ISY, An DS. Modeling Anti-HIV-1 HSPC-Based Gene Therapy in Humanized Mice Previously Infected with HIV-1. Molecular therapy. Methods & clinical development. 2018; 9:23-32. PubMed [journal] PMID: 29322065, PMCID: PMC5751878
• Suryawanshi GW, Xu S, Xie Y, Chou T, Kim N, Chen ISY, Kim S. Bidirectional Retroviral Integration Site PCR Methodology and Quantitative Data Analysis Workflow. Journal of visualized experiments : JoVE. 2017; (124). PubMed [journal] PMID: 28654067, PMCID: PMC5608418
• Goyal S*, Kim S*, Chen IS, Chou T. Mechanisms of blood homeostasis: lineage tracking and a neutral model of cell populations in rhesus macaques. BMC Biol. 2015 Oct 20;13:85. doi: 10.1186/s12915-015-0191-8. PubMed PMID: 26486451; PubMed Central PMCID: PMC4615871.  

• Kim S, Kim N, Presson AP, Metzger ME, Bonifacino AC, Sehl M, Chow SA, Crooks GM, Dunbar CE, An DS, Donahue RE, Chen IS. Dynamics of HSPC repopulation in nonhuman primates revealed by a decade-long clonal-tracking study. Cell Stem Cell. 2014 Apr 3;14(4):473-85. doi: 10.1016/j.stem.2013.12.012. PubMed PMID: 24702996; PubMed Central PMCID: PMC4009343.   

• Arokium H, Kamata M*, Kim S*, Kim N, Liang M, Presson AP, Chen IS. Deep sequencing reveals low incidence of endogenous LINE-1 retrotransposition in human induced pluripotent stem cells. PLoS One. 2014 Oct 7;9(10):e108682. doi: 10.1371/journal.pone.0108682. eCollection 2014. PubMed PMID: 25289675; PubMed Central PMCID: PMC4188539.   

• Kim S, Kim YC, Qi H, Su K, Morrison SL, Chow SA. Efficient identification of human immunodeficiency virus type 1 mutants resistant to a protease inhibitor by using a random mutant library. Antimicrob Agents Chemother. 2011 Nov;55(11):5090-8. doi: 10.1128/AAC.00687-11. Epub 2011 Aug 29. PubMed PMID: 21876045; PubMed Central PMCID: PMC3195011.  

• Presson AP, Kim N, Xiaofei Y, Chen IS, Kim S. Methodology and software to detect viral integration site hot-spots. BMC Bioinformatics. 2011 Sep 14;12:367. doi: 10.1186/1471-2105-12-367. PubMed PMID: 21914224; PubMed Central PMCID: PMC3203353.   

• Kim S, Kim N, Presson AP, An DS, Mao SH, Bonifacino AC, Donahue RE, Chow SA, Chen IS. High-throughput, sensitive quantification of repopulating hematopoietic stem cell clones. J Virol. 2010 Nov;84(22):11771-80. doi: 10.1128/JVI.01355-10. Epub 2010 Sep 15. PubMed PMID: 20844053; PubMed Central PMCID: PMC2977897.   

• Kim S, Rusmevichientong A, Dong B, Remenyi R, Silverman RH, Chow SA. Fidelity of target site duplication and sequence preference during integration of xenotropic murine leukemia virus-related virus. PLoS One. 2010 Apr 20;5(4):e10255. doi: 10.1371/journal.pone.0010255. PubMed PMID: 20421928; PubMed Central PMCID: PMC2857682.   

• Shimizu S, Kamata M, Kittipongdaja P, Chen KN, Kim S, Pang S, Boyer J, Qin FX, An DS, Chen IS. Characterization of a potent non-cytotoxic shRNA directed to the HIV-1 co-receptor CCR5. Genet Vaccines Ther. 2009 Jun 10;7:8. doi: 10.1186/1479-0556-7-8. PubMed PMID: 19515239; PubMed Central PMCID: PMC2701936.   

• Kim S*, Vatakis DN*, Kim N, Chow SA, Zack JA. Human immunodeficiency virus integration efficiency and site selection in quiescent CD4+ T cells. J Virol. 2009 Jun;83(12):6222-33. doi: 10.1128/JVI.00356-09. Epub 2009 Apr 15. PubMed PMID: 19369341; PubMed Central PMCID: PMC2687367.   

• Kim S, Kim N, Dong B, Boren D, Lee SA, Das Gupta J, Gaughan C, Klein EA, Lee C, Silverman RH, Chow SA. Integration site preference of xenotropic murine leukemia virus-related virus, a new human retrovirus associated with prostate cancer. J Virol. 2008 Oct;82(20):9964-77. doi: 10.1128/JVI.01299-08. Epub 2008 Aug 6. PubMed PMID: 18684813; PubMed Central PMCID: PMC2566297. 

• Dong B, Kim S, Hong S, Das Gupta J, Malathi K, Klein EA, Ganem D, Derisi JL, Chow SA, Silverman RH. An infectious retrovirus susceptible to an IFN antiviral pathway from human prostate tumors. Proc Natl Acad Sci U S A. 2007 Jan 30;104(5):1655-60. Epub 2007 Jan 18. PubMed PMID: 17234809; PubMed Central PMCID: PMC1776164. 

• Kim S, Kim Y, Liang T, Sinsheimer JS, Chow SA. A high-throughput method for cloning and sequencing human immunodeficiency virus type 1 integration sites. J Virol. 2006 Nov;80(22):11313-21. Epub 2006 Sep 13. PubMed PMID: 16971446; PubMed Central PMCID: PMC1642152. 

• Kim Y, Kim S, Earnest TN, Hol WG. Precursor structure of cephalosporin acylase. Insights into autoproteolytic activation in a new N-terminal hydrolase family. J Biol Chem. 2002 Jan 25;277(4):2823-9. Epub 2001 Nov 8. PubMed PMID: 11706000. 

• Kim S, Kim Y. Active site residues of cephalosporin acylase are critical not only for enzymatic catalysis but also for post-translational modification. J Biol Chem. 2001 Dec 21;276(51):48376-81. Epub 2001 Oct 16. PubMed PMID: 11604409.