​PUBLICATIONS

41. 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. J. Infectious Diseases (in press). 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, H. Y. Lee: Developing High-Throughput HIV Incidence Assay with Pyrosequencing Platform. J. Virol. 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. E. Giorgi, B. F. Keeke, B. Gaschen, G. S. Athreya, J. F. Salazar-Gonzalez, K. T. Pham, P. A. Geopfert, J. M. Kilby, M. S. Saag, E. L. Delwart, M. P. Busch, B. H. Hahn, G. M. Shaw, B. T. Korber, T. Bhattacharya, A. S. Perelson: Modeling Sequence Evolution in Acute HIV-1 Infection J. Theor. Biol 261:341, 2009. Read Here

26. 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

25. 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

24. 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

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