Department of Computer Science

Post Doctoral Researcher

Nam-Phuong Duc Nguyen, PhD

I am a second year postdoctoral researcher at the Institute of Genomic Biology at UIUC studying computational metagenomics under the supervision of Dr. Rebecca StumpfMy research interest is in the area of computational phylogenetics, with an emphasis on developing methods for analyzing ultra-large datasets.  My current projects include taxonomic identification and profiling of metagenomic datasets, improved algorithms for multiple sequence alignment and remote homology detection, and phylogenetic and phylogenomic studies.


Nam Nguyen, PhD

Office Location: IGB 3437


12. Nguyen, N., Mirarab, S., Kumar, K., and Warnow, T. (2015) Ultra-large alignments using Phylogeny-aware Profiles. Genome Biology, 16:124--136; also published in the Proceedings of RECOMB 2015.

11. Wickett, N., Mirarab, S. (co-first author), Nguyen, N., Warnow, T., Carpenter, E., Matasci, N., Ayyampalayam, S., Barker, M., Burleigh, J., Gitzendanner, M., Ruhfel, B., Wafula, E., Der, J., Graham, S., Mathews, S., Melkonian, M., Soltis, D., Soltis, P., Miles, N., Rothfels, C., Pokorny, L., Shaw, A., DeGironimo, L., Stevenson, D., Surek, B., Villarreal, J., Roure, B., Philippe, H., DePamphilis, C., Chen, T., Deyholos, M., Baucom, R., Kutchan, T., Augustin, M., Wang, J., Zhang, Y., Tian, Z., Yan, Z., Wu, X., Sun, X., Wong, G., and Leebens-Mack, J. (2014) A phylotranscriptomic analysis of the origin and early diversification of land plants, Proceedings of the National Academy of Sciences, 111(45):E4859--68.

10. Nguyen, N., Mirarab, S., Liu, B., Pop, M., and Warnow, T. (2014) TIPP: Taxonomic identification and
phylogenetic profiling. Bioinformatics, doi:10.1093/bioinformatics/btu721.

9. Mirarab, S., Nguyen, N., Guo, S., Wang, L.S., Kim, J., and Warnow, T. (2014)  PASTA: Ultra-Large Multiple Sequence Alignment of nucleotide and amino-acid sequences. Journal of Computational Biology, 22(5):377-86. doi: 10.1089/cmb.2014.0156.

8. Mirarab, S., Nguyen, N., and Warnow, T. (2014) PASTA: ultra-large multiple sequence alignment. In
proceedings of RECOMB 2014, 177{191}.

7. 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

5. 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

4. 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.

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

2. 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.

1. 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)