Department of Computer Science

PhD Candidate and Graduate Research Assistant

Nam-Phuong Duc Nugyen, MS

I am a sixth year PhD student studying Computer Science under the supervision of Dr. Tandy WarnowMy research interest is in the area of computational phylogenetics, with an emphasis on developing methods for analyzing ultra-large datasets.  My current projects include ultra-large alignment and tree estimation techniques and taxonomic profiling of metagenomic datasets.  In my spare time, you can catch me playing guitar under the UT Tower.


Nam Nguyen, MS


Office Phone: (512)  232-0801

Office Location: GSC 4.424C


1. Nguyen, N., Mirarab, S., Guo, S., Wang, L., Kim, J., & Warnow, T.  Ultra-large alignments using families of Hidden Markov Models.  In preparation for Science.

2. Mirarab, S., Nguyen, N., & Warnow, T.  PASTA: ultra-large multiple sequence alignment.  Accepted to RECOMB 2014.

3. Wickett, N., Mirarab, S., Nguyen, N., Warnow, T., Carpenter, E., Matasci, N.,…, & Leebens-Mack, J.  A phylotranscriptomics analysis of the origin and early diversification of land plants.  In submission to PNAS

4. Nguyen, N., Mirarab, S., Liu, B., Pop, M., & Warnow, T.   TIPP: Taxonomic Identification and Phylogenetic Profiling.  In submission to Proceedings of the IEEE Bioinformatics of DNA.

5. Mirarab, S., Nguyen, N., & Warnow, T. (2012). SEPP: SATé-Enabled Phylogenetic Placement. Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing, 247–58.

6. Nguyen, N., Mirarab, S., & Warnow, T. (2012). MRL and SuperFine+MRL: new supertree methods. Algorithms for molecular biology : AMB, 7(1), 3. doi:10.1186/1748-7188-7-3

7. Nguyen, N., Myers, C., Kuwahara, H., Winstead, C., & Keener, J. (2010). Design and analysis of a robust genetic Muller C-element. Journal of theoretical biology, 264(2), 174–87. doi:10.1016/j.jtbi.2009.10.026

8. Myers, C. J., Barker, N., Jones, K., Kuwahara, H., Madsen, C., & Nguyen, N. (2009). iBioSim: a tool for the analysis and design of genetic circuits. Bioinformatics (Oxford, England), 25(21), 2848–9.

9. Nguyen, N. (2009). Design and analysis of genetic circuits. University of Utah. Masters Thesis.

10. Nguyen, N., Barker, N., Kuwahara, H., Madsen, C., & Myers, C. J. (2008). Synthesis of Genetic Circuits from Graphical Specifications. 2008 Int. Workshop on Logic Synthesis.

11. Nguyen, N., Kuwahara, H., Myers, C. J., & Keener, J. P. (2007). The Design of a Genetic Muller C-Element. The Thirteenth International Symposium on Asynchronous Circuits and Systems. (Best Paper Award)