Ha Youn Lee, PhD

Assistant Professor of Biostatistics and Computational Biology
Ph.D. (2000) Seoul National University, Korea
 

Contact Information:

University of Rochester
Dept of Biostatistics and Computational Biology
601 Elmwood Avenue Box 630
Rochester, New York 14642
 
Office: Saunders Research Building 4169
Phone: (585) 275-0041
Fax: (585) 273-1031
E-mail: hayoun_lee@urmc.rochester.edu
 

Research Interests

My research focuses on developing mathematical modeling and physical reasoning to inform future of the biological and medical sciences. I have been developing mathematical equations and computer simulations which can integrate different experimental and clinical measures. My theories have been applied to i) quantitatively portrait sequence evolution and viral replication during very early stage of HIV infection; ii) unite previous conflicting observations of the relationships between the rate of HIV evolution and disease progression; iii) quantify cell proliferation and death kinetics based on different types of immune cell labeling data; iv) assess the roles of different immune components for viral containment during primary influenza infection My research is supported by a newly (2009) funded NIH R01 award that studies on sequence evolution and viral replication during early HIV infection, and on defining vaccine-inducible host immune functions that can be expected to lead to containment of infection and long-term protection from disease.

Selected Publications

B.N. Bimber, P. Chugh, E.E. Giorgi, B. Kim, A.L. Almudevar, S. Dewhurst, D.H. O'Connor, H.Y. Lee.  Nef gene evolution from a single transmitted strain in acute SIV infection.  Retrovirology 6:57 (2009).

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. (in press).

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:(2009).

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).

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).

B. Keele, E. Giorgi, J. Salazar-Gonzalez, J. Decker, K. Pham, M. Salazar, C. Sun, T. Grayson, S. Wang, H. Li, X. Wei, C. Jiang, J. Kirchherr, F. Gao, J. Anderson, L. Ping, R. Swanstrom, 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, and 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).

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).

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 pathogenesis.  J. Virology 82: 3725-3735 (2008).

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).

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).

A. Lee, H.Y. Lee and M. Kardar.  Symmetry Breaking Motility.  Phys. Rev. Lett. 95:138101 (2005).

H.Y. Lee, M. Yahyanejad, and M. Kardar.  Symmetry considerations and development of pinwheels in visual maps.  Proc. Natl. Acad. Sci. 100: 16036 (2003).

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).

H.Y. Lee and M. Kardar.  Macroscopic equations for pattern formation in mixtures of microtubules and motors.  Phys. Rev. E 64: 056113 (2001).

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).

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).

 

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