Publications
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, Promising 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 4(10):e0003878 (2024). Read Here
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 62:e01558-23 (2024). Read Here
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 171:105639 (2024). Read Here
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 11:e02285-23 (2023). Read Here
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 13:12093 (2023). Read Here
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 164: 105491 (2023). Read Here
44. S. Y. Park, G. Faraci, S. Nanda, S. Ter-Saakyan, T.M.T. Love, W. J. Mack, M. Dube and H. Y. Lee: Gut microbiome in people living with HIV is associated with impaired thiamine and folate syntheses. Microbial Pathogenesis 160: 105209 (2021). Read Here
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 11:13669 (2021). Read Here
42. S. Y. Park, G. Faraci, G. Murphy, C. Pilcher, M. P. Busch, and H. Y. Lee: Microdrop HIV sequencing for incidence and drug resistance surveillance. Journal of Infectious Diseases 224:1048-1059 (2021). Read Here
41. J.‑M. Kim*, S. Y. Park*, D. Lee, J.‑S. Kim, Y. Park, J. Gwack, M. Kim, D. H. Song, S. Jeong, Y.‑S. Chung, C. K. Yoo, H. Y. Lee , and M.‑G . Han: Genomic investigation of the coronavirus disease-2019 outbreak in the Republic of Korea. Scientific Reports 11:6009 (2021). Read Here
40. S. Y. Park, S. Nanda, G. Faraci, Y. Park, and H. Y. Lee: CCMP: Software-as-a-service approach for fully-automated microbiome profiling.
Journal of Biomedical Informatics: X 2:100040, 2019. Read Here
39. M.P. Dube, S. Y. Park, H. Ross, T. M.T. Love, S.R. Morris, and H. Y. Lee: Daily HIV pre-exposure prophylaxis (PrEP) with tenofovir disoproxil fumarate-emtricitabine reduced Streptococcus and increased Erysipelotrichaceae in rectal microbiota.
Scientific Reports 8:15212, 2018. Read Here
38. S. Y. Park, T. M.T. Love, S. Kapoor, and H. Y. Lee: HIITE: HIV-1 Incidence and Infection Time Estimator. Bioinformatics 34: 2046-2052, 2018. Read Here
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 H. Y. Lee: The HIV Genomic Incidence Assay Meets False Recency Rate and Mean Duration of Recency Infection Performance Standards. Scientific Reports 7: 7480, 2017. Read Here
36. H. Y. Lee, C. Ren, and S. Y. Park. Characterizing DNA corona rigidity in DNA-directed gold nanoparticle crystalline structures. J. Phys. Chem. C 120: 18307-18315, 2016. Read Here
35. S. Y. Park, W. J. Mack and H. Y. Lee. Enhancement of viral escape in HIV-1 Nef by STEP vaccination. AIDS 30:2449-2458, 2016. Read Here
34. S. Y. Park, T. M. Love, A. S. Perelson, W. J. Mack and H. Y. Lee. Molecular clock of HIV-1 envelope genes under early immune selection. Retrovirology 13:38, 2016. Read Here
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. 32:1308-1315, 2016. Read Here
32. S. Y. Park, N. Goeken, H. J. Lee, R. Bolan, M. P. Dube and H. Y. Lee: Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform. Journal of Virology 88:2977, 2014. Read Here
31. M.-S. Park, S. Y. Park, K. R. Miller, E. J. Collins, and H. Y. Lee: Accurate Structure Prediction of Peptide-MHC complexes for Identifying Highly Immunogenic Antigens. Molecular Immunology 56:81-90, 2013. Read Here
30. S. Y. Park, T. M. T. Love, J. Nelson, S. Thurston, A. S. Perelson, and H. Y. Lee: Designing a Genome-Based HIV-1 Incidence Assay with High Sensitivity and Specificity. AIDS 25:F13-F19, 2011. Read Here
29. H. Y. Lee and M. Kardar: The statistics of lines in natural images and implications for visual detection. Physica A 389:2975, 2010. Read Here
28. T. M. Love, S. W. Thurston, M. C. Keefer, S. Dewhurst, and 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. J. Virol. 84:5802, 2010. Read Here
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. 71:1649, 2009. Read Here
26. B. N. Bimber, P. Chugh, E. E. Giorgi, B. Kim, A. L. Almudevar, S. Dewhurst, D. H. O’Connor, and H. Y. Lee: Nef gene evolution from a single transmitted strain in acute SIV infection, Retrovirology 6:57, 2009. Read Here
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, J. Virology 83:7151, 2009. Read Here
24. 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). Read Here
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, 4(12):e100240, 2008. Read Here
22. C. Beargie, T. Liu, M. Corriveau, H. Y. Lee,J. Gott, and R. Bundshuh: Genome annotation in the presence of insertional RNA editing, Bioinformatics 24:2571-2578, 2008. Read Here
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, H. 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, Proc. Natl. Acad. Sci. 105:7552-7557, 2008. Read Here
20. J. M. Kilby, H. Y. Lee, J. D. Hazelwood, A. Bansal, R. P. Bucy, M. S. Saag, G. M. Shaw, E. P. Acosta, V. A. Johnson, A. S. Perelson, and P. A. Goepfert: Treatment Response in Acute/Early Infection Versus Advanced AIDS: Equivalent First and Second Phases of HIV RNA Decline, AIDS 22:957-962, 2008. Read Here
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, H. 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, J. Virology 82: 3725-3735, 2008. Read Here
18. H. Y. Lee and A. S. Perelson: Modeling T cell Proliferation and Death In Vitro Based on Labeling Data: Generalization of the Smith-Martin Cell Cycle Model, Bull. Math. Biol. 70: 21-44, 2008. Read Here
17. I. Maljkovic Berry, R. Ribeiro, M. Kothari, G. Athreya, M. Daniels, H. 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, J. Virology 81: 10625-10635, 2007. Read Here
16. H. Y. Lee and M. Kardar: Patterns and Symmetries in the Visual Cortex and in Natural Images. J. Stat. Phys. 125: 1247, 2006. Read Here
15. A. Lee, H. Y. Lee and M. Kardar: Symmetry Breaking Motility, Phys. Rev. Lett. 95: 138101, 2005. Read Here
14. H. Y. Lee, M. Yahyanejad, and M. Kardar, Symmetry considerations and development of pinwheels in visual maps: Proc. Natl. Acad. Sci. 100: 16036, 2003. Read Here
13. M. W. Deem and H. Y. Lee, Sequence space localization in the immune system response to vaccination and disease: Phys. Rev. Lett. 91: 068101, 2003. Read Here
12. J. Kim, Y. Park, B. Kahng, and H. Y. Lee: Self-organized patterns in mixtures of microtubules and motor proteins, J. Korean Phys. Soc. 42: 162, 2003.
11. H. Y. Lee and M. Kardar: Macroscopic equations for pattern formation in mixtures of microtubules and motors, Phys. Rev. E, 64: 056113, 2001. Read Here
10. H. Y. Lee, H.-W. Lee, and D. Kim: Phase diagram of congested traffic flow: an empirical study, Phys. Rev. E 62: 4737, 2000. Read Here
9. H. Y. Lee, H.-W. Lee, and D. Kim: Traffic states of a model highway with on-ramp, Physica A 281: 78, 2000. Read Here
8. L. Neubert, H. Y. Lee, and M. Schreckenberg: Density waves and jamming transition in cellular automaton models for traffic flow, J. Phys. A 32: 6517, 1999. Read Here
7. H. Y. Lee, H.-W. Lee, and D. Kim: Dynamic states of a continuum traffic equation with on-ramp, Phys. Rev. E 59: 5101, 1999. Read Here
6. H. Y. Lee, H.-W. Lee, and D. Kim: Recurring hump state near on-ramp on highways, New Physics 38, S123, 1998.
5. H.-W. Lee, H. Y. Lee, and D. Kim: Traffic flow theory, Physics and High Technology 8: 33, 1998.
4. H. Y. Lee, H.-W. Lee, and D. Kim: Origin of synchronized traffic flow on highways and its dynamic phase transition, Phys. Rev. Lett. 81: 1130, 1998. Read Here
3.H. Y. Lee, D. Kim, and M.Y. Choi: Genetic polymorphism in evolving population, Phys. Rev. E 57: 4842, 1998. Read Here
2. M. Y. Choi, H. Y. Lee, D. Kim, and S. H. Park: Entropic Sampling and Natural Selection in Biological Evolution, J. Phys. A 30: L749, 1997. Read Here
1. M.Y. Choi and H. Y. Lee: Traffic flow and 1/f fluctuations, Phys. Rev. E 52: 5979, 1995. Read Here