​PUBLICATIONS
Peer Reviewed

1. H. Y. Lee, C. Ren, and S. Y. Park. Characterizing DNA corona rigidity in DNA-directed gold nanoparticle crystalline structures. Journal of Physical Chemistry C (in press).

2. 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

3. 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

4. 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

5. 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

6. 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

7. 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

8. 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

9. 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

10. 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

11. 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

12. 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

13. 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

14. 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

15. 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

16. 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

17. 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

18. 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

19. 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

20. 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

21. 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

22. A. Lee, H. Y. Lee and M. Kardar: Symmetry Breaking Motility, Phys. Rev. Lett. 95: 138101, 2005. Read Here

23. 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

24. 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

25. 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.

26. 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

27. 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

28. 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

29. 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

30. 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

31. H. Y. Lee, H.-W. Lee, and D. Kim: Recurring hump state near on-ramp on highways, New Physics 38, S123, 1998.

32. H.-W. Lee, H. Y. Lee, and D. Kim: Traffic flow theory, Physics and High Technology  8: 33, 1998.

33. 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

34. H. Y. Lee, D. Kim, and M.Y. Choi: Genetic polymorphism in evolving population, Phys. Rev. E 57: 4842, 1998. Read Here

35. 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

36. M.Y. Choi and H. Y. Lee: Traffic flow and 1/f  fluctuations, Phys. Rev. E 52: 5979, 1995. Read Here