{"id":46,"date":"2023-03-30T03:13:55","date_gmt":"2023-03-30T03:13:55","guid":{"rendered":"http:\/\/eucalyptus.usc.edu\/?page_id=46"},"modified":"2026-01-11T15:03:10","modified_gmt":"2026-01-11T15:03:10","slug":"publications","status":"publish","type":"page","link":"https:\/\/eucalyptus.usc.edu\/?page_id=46","title":{"rendered":""},"content":{"rendered":"

Publications<\/h4>\n

51. S. Y. Park, C. Takayama, J. Ryu, M. Sattah, Z. Badii, J. W. Kim, R.W. Shafer, P. M. Gorbach, H. Y. Lee, Design and evaluation of next-generation HIV genotyping for detection of resistance mutations to 28 antiretroviral drugs across five major classes including lenacapavir. Clinical Infectious Diseases <\/em>81<\/strong>:e360-e369 (2025). Read Here<\/strong><\/a><\/span><\/p>\n

50. R. Schaefer, L. Donalds, M. Leus, C. E. Osakwe, B. Chimukangara, S. Dalal, A. Duerr, F. Gao, D. V. Glidden, B. Grinsztejn, J. Justman, G. Kumwenda, O. Laeyendecker, H. Y. Lee, F. Maldarelli, K. H. Mayer, J. Murray, B. S. Parekh, B. Rice, M. N. Robertson, S. Saito, V. Vannappagari, M. Warren, D. Zeballos, J. Zinserling, V. Miller,\u00a0Promising results of HIV prevention trials highlight the benefits of collaboration in global health: The perspective of the Forum HIV Recency Assay Working Group. PLoS Global Public Health<\/em> 4<\/strong>(10):e0003878 (2024). Read Here<\/strong><\/a><\/span><\/p>\n

49. S. Y. Park, G. Faraci, P. Ward, H. Y. Lee: Utilizing cost-effective portable equipment to enhance COVID-19 variant tracking both on-site and at a large-scale. Journal of Clinical Microbiology <\/em>62<\/strong>:<\/em>e01558-23 (2024). Read Here<\/strong><\/a><\/span><\/p>\n

48. S. Y. Park, G. Faraci, K. Ganesh, M. P. Dube, and H. Y. Lee: Portable Nanopore sequencing solution for next-generation HIV drug resistance testing. Journal of Clinical Virology<\/em> 171<\/strong>:105639 (2024). Read Here<\/strong><\/span><\/a><\/p>\n

47. G. Faraci, S. Y. Park, T. M. T. Love, M. P. Dube, and H.Y. Lee: Precision detection of recent HIV infections using high-throughput genomic incidence assay. Microbiology Spectrum<\/em> 11<\/strong>:e02285-23 (2023). Read Here<\/strong><\/a><\/span><\/p>\n

46. S. Y. Park, S. Ter-Saakyan, G. Faraci and H. Y. Lee: Immune cell identifier and classifier (ImmunIC) for single cell transcriptomic readouts. Scientific Reports <\/em>13<\/strong>:12093 (2023). Read Here<\/strong><\/a><\/span><\/p>\n

45. G. Faraci, S. Y. Park, M. Dube and H. Y. Lee: Full-spectrum HIV drug resistance mutation detection by high-resolution complete pol gene sequencing. Journal of Clinical Virology<\/em> 164<\/strong>: 105491 (2023). Read Here<\/strong><\/a><\/span><\/p>\n

44. S. Y. Park, G. Faraci, S. Nanda, S. Ter-Saakyan, T.M.T. Love, W. J. Mack, M. Dube and H. Y. Lee: <\/span>Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses. Microbial Pathogenesis\u00a0<\/em>160<\/strong>: 105209 (2021).\u00a0\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

43. S. Y. Park, G. Faraci, P. Ward, J. F. Emerson and H. Y. Lee: High-precision and cost-efficient sequencing for real-time COVID-19 surveillance. Scientific Reports\u00a0<\/em>11<\/strong>:13669 (2021).\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

42. S. Y. Park, G. Faraci, G. Murphy, C. Pilcher, M. P. Busch, and\u00a0H. Y. Lee: Microdrop HIV sequencing for incidence and drug resistance surveillance. Journal of Infectious Diseases <\/em>224<\/strong>:1048-1059 (2021).\u00a0Read Here<\/strong><\/a><\/p>\n

41.\u00a0J.\u2011M. Kim*, S. Y. Park*, D. Lee, J.\u2011S. Kim, Y. Park, J. Gwack, M. Kim, D. H. Song, S. Jeong, Y.\u2011S. Chung, C. K. Yoo,\u00a0H. Y. Lee\u00a0, and M.\u2011G . Han:\u00a0Genomic investigation of the coronavirus disease-2019 outbreak in the Republic of Korea. Scientific Reports <\/em>11<\/strong>:6009 (2021).\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

40. S. Y. Park, S. Nanda, G. Faraci, Y. Park, and\u00a0<\/span>H. Y. Lee: CCMP: Software-as-a-service approach for fully-automated microbiome profiling.<\/span>
\n\u00a0Journal of Biomedical Informatics: X<\/em>\u00a02<\/strong>:100040, 2019.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

39. M.P. Dube,\u00a0\u00a0S. Y. Park, H. Ross, T. M.T. Love, S.R. Morris, and\u00a0H. Y. Lee: Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus<\/em> and increased Erysipelotrichaceae<\/em> in rectal microbiota.<\/span>
\n\u00a0Scientific Reports<\/em>\u00a08<\/strong>:15212, 2018.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

\u200b38. S. Y. Park, T. M.T. Love, S. Kapoor, and H. Y. Lee: HIITE: HIV-1 Incidence and Infection Time Estimator. Bioinformatics<\/em>\u00a034<\/strong>: 2046-2052, 2018.\u00a0Read Here<\/strong><\/a><\/p>\n

37. S. Y. Park, T. M. T. Love, L. Reynell, C. Yu, T. M. Kang, K. Anastos, J. DeHovitz, C. Liu, K. M. Kober, M. Cohen, W. J. Mack, and\u00a0H. Y. Lee: The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards.\u00a0Scientific Reports<\/em> 7<\/strong>: 7480, 2017.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

36.\u00a0<\/span>H. Y. Lee, C. Ren, and S. Y. Park.\u00a0Characterizing DNA corona rigidity in DNA-directed gold nanoparticle crystalline structures. J. Phys. Chem. C <\/em>120<\/strong>: 18307-18315, 2016.\u00a0Read Here<\/a><\/strong><\/span><\/p>\n

35. S. Y. Park, W. J. Mack and H. Y. Lee. Enhancement of viral escape in HIV-1 Nef by STEP vaccination. AIDS\u00a0<\/em>30<\/strong>:2449-2458, 2016.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

34. S. Y. Park, T. M. Love, A. S. Perelson, W. J. Mack and\u00a0H. Y. Lee.\u00a0Molecular clock of HIV-1 envelope genes under early immune selection. Retrovirology<\/em>\u00a013<\/strong>:38, 2016.\u00a0R<\/strong><\/span>ead Here<\/strong><\/span><\/a><\/p>\n

33. T. M. Love, S. Y. Park, E. E. Giorgi, W. J. Mack, A. S. Perelson and H. Y. Lee: SPMM: Estimating Infection Duration of Multivariant HIV-1 Infections. Bioinformatics<\/em>. 32<\/strong>:1308-1315, 2016<\/span>.\u00a0<\/span>R<\/strong><\/span>ead Here<\/strong><\/span><\/a><\/p>\n

32. S. Y. Park, N. Goeken, H. J. Lee, R. Bolan, M. P. Dube and H. Y. Lee<\/span>: Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform.\u00a0Journal of Virology<\/em>\u00a088<\/strong>:2977, 2014.<\/span>\u00a0<\/span>Read Here<\/span><\/a><\/strong><\/p>\n

31. M.-S. Park, S. Y. Park, K. R. Miller, E. J. Collins, and\u00a0H. Y. Lee: Accurate Structure Prediction of Peptide-MHC complexes for Identifying Highly Immunogenic Antigens.\u00a0Molecular Immunology<\/em>\u00a056<\/strong>:81-90, 2013.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

30. S. Y. Park, T. M. T. Love, J. Nelson, S. Thurston, A. S. Perelson, and\u00a0H. Y. Lee: Designing a Genome-Based HIV-1 Incidence Assay with High Sensitivity and Specificity.\u00a0AIDS<\/em>\u00a025<\/strong>:F13-F19, 2011.\u00a0Read Here<\/strong><\/a><\/p>\n

29. H. Y. Lee and M. Kardar: The statistics of lines in natural images and implications for visual detection. Physica A 389<\/strong>:2975, 2010. Read Here<\/a><\/strong><\/p>\n

28. T. M. Love, S. W. Thurston, M. C. Keefer, S. Dewhurst, and\u00a0<\/span>H. Y. Lee: Mathematical modeling of ultradeep sequencing data reveals that acute CD8+ T lymphocyte responses exert strong selective pressure in simian immunodeficiency virus-infected macaques but still fail to clear founder epitope sequences.\u00a0<\/span>J. Virol.<\/em>\u00a0<\/span>84<\/strong>:5802, 2010.\u00a0<\/span>Read Here<\/span><\/strong><\/a><\/p>\n

27. H. Y. Lee, E. Hawkins, M. S. Zand, T. Mosmann, H. Wu, P. D. Hodgkin, and A. S. Perelson: Interpreting CFSE Obtained Division Histories of B cells In Vitro with Smith-Martin and Cyton Type Models, Bull. Math. Biol.\u00a0\u00a0<\/em>71<\/strong>:1649, 2009.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

26. B. N. Bimber, P. Chugh, E. E. Giorgi, B. Kim, A. L. Almudevar, S. Dewhurst, D. H. O\u2019Connor, and\u00a0H. Y. Lee: Nef gene evolution from a single transmitted strain in acute SIV infection,\u00a0Retrovirology<\/em>\u00a0\u00a06<\/strong>:57, 2009.\u00a0Read Here<\/strong><\/a><\/p>\n

25. H. Y. Lee, D. J. Topham, S. Y. Park, J. Treanor, T. Mosmann, X. Jin, B. Ward, H. Miao, A. S. Perelson, M. Zand, and H. Wu: Simulation and Prediction of the Adaptive Immune Response to Influenza A Infection,\u00a0J. Virology<\/em>\u00a0\u00a083<\/strong>:7151, 2009.\u00a0Read Here<\/a><\/strong><\/p>\n

24.\u00a0<\/strong>H. Y. Lee, E. E.Giorgi, B.F. Keeke, B. Gaschen, G. S. Athreya, J. F. Salazar-Gonzalez, K. T. Pham, P. A. Goepfert, J. M. Kilby, M. S. Saag, E. L. Delwart, M. P. Busch, B. H. Hahn, G. M. Shaw, B. T. Korber, T. Bhattacharya, and A. S. Perelson, Journal of Theoretical Biology, 261:341-360 (2009).\u00a0Read Here<\/a><\/strong><\/p>\n

23. H. Y. Lee,A. S. Perelson, S. C. Park, and T. Leitner: Dynamic Correlation Between Intrahost HIV-1 Quasispecies Evolution and Disease Progression. PLoS Comp. Biology,<\/em>\u00a04<\/strong>(12):e100240, 2008.\u00a0Read Here<\/strong><\/a><\/span><\/p>\n

22. C. Beargie, T. Liu,\u00a0<\/strong>M. Corriveau,<\/strong> H. Y. Lee,J. Gott,\u00a0<\/strong>and R. Bundshuh: Genome annotation in the presence of insertional RNA editing,\u00a0Bioinformatics<\/em>\u00a024<\/strong>:2571-2578, 2008.\u00a0Read Here<\/strong><\/a><\/p>\n

21. B. Keele, E. Giorgi, J. Salazar-Gonzalez, J. Decker, K. Pham, M. Salazar, Sun C, T. Grayson, S. Wang, H. Li, X. Wei, Jiang C, J. Kirchherr, F. Gao, J. Anderson, L. Ping, Swanstrom R, G. Tomaras, B. Blattner, P. Goepfert, E. Delwart, M. Busch, M. Cohen, D. Montefiori, B. Haynes, B. Gashen, G. Athreya,\u00a0H. Y. Lee, N. Wood, C. Seoighe, A. Perelson, T. Bhattacharya, B. Korber, B. Hahn, G. Shaw: Identification and Characterization of Transmitted and Early Founder Virus Envelopes in Primary HIV-1 Infection,\u00a0Proc. Natl. Acad. Sci.\u00a0<\/em>105<\/strong>:7552-7557, 2008.\u00a0Read Here<\/a><\/strong><\/p>\n

20. J. M. Kilby,\u00a0H. Y. Lee, J. D. Hazelwood, \u00a0A. Bansal, R. P. Bucy, M. S. Saag, G. M. Shaw,\u00a0 E. P. Acosta, V. A. Johnson, A. S. Perelson, and\u00a0P. A. Goepfert:\u00a0Treatment Response in Acute\/Early Infection Versus Advanced AIDS: Equivalent First and Second Phases of HIV RNA Decline<\/em>, AIDS<\/em>\u00a022<\/strong>:957-962, 2008.\u00a0Read Here<\/strong><\/a><\/p>\n

19. S. N. Gordon, R. M. Dunham, J. C. Engram, J. Estes, Z. Wang, N. R. Klatt, M. Paiardini, I. V. Pandrea, C. Apetrei, D. L. Sodora,\u00a0H. Y. Lee, A. T. Haase, M. D. Miller, A. Kaur, S. I. Staprans, A. S. Perelson, M. B. Feinberg, and G. Silvestri: Short-lived infected cells support virus replication in naturally SIV-infected sooty mangabeys: implications for AIDS pathegenesis,<\/em>\u00a0J. Virology<\/em>\u00a082<\/strong>: 3725-3735, 2008.\u00a0Read Here<\/strong><\/a><\/p>\n

18. H. Y. Lee\u00a0and A. S. Perelson: Modeling T cell Proliferation and Death In Vitro Based on Labeling Data: Generalization of the Smith-Martin Cell Cycle Model,\u00a0Bull. Math. Biol<\/em>.\u00a070<\/strong>: 21-44, 2008.\u00a0Read Here<\/strong><\/a><\/p>\n

17. I. Maljkovic Berry, R. Ribeiro, M. Kothari, G. Athreya, M. Daniels,\u00a0H. Y. Lee, W. Bruno, and T. Leitner: Unequal evolutionary rates in the HIV-1 pandemic: The evolutionary rate of HIV-1 slows down when the epidemic rate increases,\u00a0J. Virology<\/em>\u00a081<\/strong>: 10625-10635, 2007.\u00a0Read Here<\/strong><\/a><\/p>\n

16. H. Y. Lee\u00a0and M. Kardar: Patterns and Symmetries in the Visual Cortex and in Natural Images.\u00a0J. Stat. Phys.<\/em>\u00a0125<\/strong>: 1247, 2006. Read Here<\/a><\/strong><\/p>\n

15. A. Lee,\u00a0H. Y. Lee\u00a0and M. Kardar: Symmetry Breaking Motility,\u00a0Phys. Rev. Lett<\/em>. 95<\/strong>: 138101, 2005. Read Here<\/a><\/strong><\/p>\n

14. H. Y. Lee, M. Yahyanejad, and M. Kardar, Symmetry considerations and development of pinwheels in visual maps:\u00a0Proc. Natl. Acad. Sci.<\/em>\u00a0100<\/strong>: 16036, 2003.\u00a0Read Here<\/strong><\/a><\/p>\n

13. M. W. Deem and\u00a0H. Y. Lee, Sequence space localization in the immune system response to vaccination and disease:\u00a0Phys. Rev. Lett.\u00a0<\/em>91<\/strong>: 068101, 2003.\u00a0Read Here<\/strong><\/a><\/p>\n

12. J. Kim, Y. Park, B. Kahng, and\u00a0H. Y. Lee: Self-organized patterns in mixtures of microtubules and motor proteins, J. Korean Phys. Soc.\u00a0<\/em>42<\/strong>: 162, 2003.<\/p>\n

11. H. Y. Lee\u00a0and M. Kardar: Macroscopic equations for pattern formation in mixtures of microtubules and motors,\u00a0Phys. Rev. E<\/em>,\u00a064<\/strong>: 056113, 2001.\u00a0Read Here<\/strong><\/a><\/p>\n

10. H. Y. Lee, H.-W. Lee, and D. Kim: Phase diagram of congested traffic flow: an empirical study,\u00a0Phys. Rev. E<\/em>\u00a0\u00a062<\/strong>: 4737, 2000.\u00a0Read Here<\/strong><\/a><\/p>\n

9. H. Y. Lee, H.-W. Lee, and D. Kim: Traffic states of a model highway with on-ramp,\u00a0Physica A<\/em>\u00a0\u00a0281<\/strong>: 78, 2000. Read Here<\/a><\/strong><\/p>\n

8. L. Neubert,\u00a0H. Y. Lee, and M. Schreckenberg: Density waves and jamming transition in cellular automaton models for traffic flow,\u00a0J. Phys. A<\/em>\u00a0\u00a032<\/strong>: 6517, 1999. Read Here<\/a><\/strong><\/p>\n

7. H. Y. Lee, H.-W. Lee, and D. Kim: Dynamic states of a continuum traffic equation with on-ramp, Phys. Rev. E<\/em>\u00a059<\/strong>: 5101, 1999.\u00a0Read Here<\/strong><\/a><\/p>\n

6. H. Y. Lee, H.-W. Lee, and D. Kim: Recurring hump state near on-ramp on highways, New Physics<\/em> 38<\/strong>, S123, 1998.<\/p>\n

5. H.-W. Lee,\u00a0H. Y. Lee, and D. Kim: Traffic flow theory,\u00a0Physics and High Technology<\/em>\u00a0\u00a08<\/strong>: 33, 1998.<\/p>\n

4. H. Y. Lee, H.-W. Lee, and D. Kim: Origin of synchronized traffic flow on highways and its dynamic phase transition,\u00a0Phys. Rev. Lett<\/em>.\u00a081<\/strong>: 1130, 1998. Read Here<\/a><\/strong><\/p>\n

3.H. Y. Lee, D. Kim, and M.Y. Choi: Genetic polymorphism in evolving population,\u00a0Phys. Rev. E<\/em>\u00a057<\/strong>: 4842, 1998. Read Here<\/a><\/strong><\/p>\n

2. M. Y. Choi,\u00a0\u00a0H. Y. Lee, D. Kim, and S. H. Park: Entropic Sampling and Natural Selection in Biological Evolution,\u00a0J. Phys. A<\/em>\u00a0\u00a030<\/strong>: L749, 1997.\u00a0Read Here<\/a><\/strong><\/p>\n

1. M.Y. Choi and\u00a0H. Y. Lee: Traffic flow and\u00a01\/f<\/em>\u00a0 fluctuations,\u00a0Phys. Rev. E<\/em>\u00a052<\/strong>: 5979, 1995.\u00a0Read Here<\/a><\/strong><\/p>\n","protected":false},"excerpt":{"rendered":"

Publications 51. S. Y. Park, C. Takayama, J. Ryu, M. Sattah, Z. Badii, J. W. Kim, R.W. Shafer, P. M. Gorbach, H. Y. Lee, Design and evaluation of next-generation HIV genotyping for detection of resistance mutations to 28 antiretroviral drugs across five major classes including lenacapavir. Clinical Infectious Diseases 81:e360-e369 (2025). Read Here 50. R. … Continue reading <\/span><\/a><\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-46","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=\/wp\/v2\/pages\/46","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=46"}],"version-history":[{"count":21,"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=\/wp\/v2\/pages\/46\/revisions"}],"predecessor-version":[{"id":382,"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=\/wp\/v2\/pages\/46\/revisions\/382"}],"wp:attachment":[{"href":"https:\/\/eucalyptus.usc.edu\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=46"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}