I received my PhD in 2003 from the department of Microbiology and Immunology at UNC Chapel Hill in the lab of Ron Swanstrom. The lab is generally interested in HIV evolution. My research has focused on identifying correlations between entry phenotype and sequence changes in the envelope protein (gp120) and (more recently) covariation between sites in Protease. Here is the abstract from my thesis.

My background is mostly in molecular biology, but in the last several years I've been drawn to questions that can be addressed by the use of computers for the analysis of sequence information. HIV-1 is one of the most sequenced organisms on earth, and (in my opinion) is the premier model organism for the study of molecular evolution. I've had the opportuity to consider co-variability among sites and regions in HIV, viral phylogeny, evidence for selective pressure, and the relationship between phenotype and sequence among large numbers of sequences.

In the course of carrying out my research, I've written some software for manipulating and analyzing DNA and protein sequences, mostly in Python and Matlab.

Much of my work has relied on HIV sequences that are publicly available at the Los Alamos HIV Sequence Database and the database of HIV Protease sequences maintained at Stanford.

Brumme, Z.L., Dong, W.W., Yip, B., Wynhoven, B., Hoffman, N.G., Swanstrom, R., Jensen, M.A., Mullins, J.I., Hogg, R.S., Montaner, J.S., Harrigan, P.R. 2004. Clinical and immunological impact of HIV envelope V3 sequence variation after starting initial triple antiretroviral therapy. AIDS. 18:F1-9.

Henderson, G. J., Hoffman, N. G., Fiscus, S. A., Hoffman, I., Kitrinos, K.M., Banda, T., Martinson, F., Kazembe, P., Chilongozi, D., Cohen, M.S., and Swanstrom, R. 2004. HIV-1 populations in blood and breast milk are similar. Virology (accepted for publication).

Ritola, K., Pilcher, C. D., Fiscus, S. A., Hoffman, N. G., Nelson, J. A., Kitrinos, K. M., Hicks, C. B., Eron, J. J., and Swanstrom, R. 2004. Multiple V1/V2 env variants are frequently present during primary infection with human immunodeficiency virus type 1 (HIV-1). Journal of Virology. 78:11208-11218.

Hoffman, N.G., Schiffer, C.A., Swanstrom, R. 2003. Covariation of amino acid positions in HIV-1 protease. Virology. 314:536-548.

Kitrinos, K. M., Hoffman, N. G., Nelson, J. A. E., and Swanstrom, R. 2003. Turnover of env Variable Region 1 and 2 Genotypes in Subjects with Late-Stage Human Immunodeficiency Virus Type 1 Infection. J. Virol. 77:6811-6822.

Hoffman, N. G., F. Seillier-Moiseiwitsch, J. Ahn, J. M. Walker, and R. Swanstrom. 2002. Variability in the human immunodeficiency virus type 1 gp120 Env protein linked to phenotype-associated changes in the V3 loop. J Virol. 76:3852-3864. (pdf version)

McGrath, K. M., N. G. Hoffman, W. Resch, J. A. Nelson, and R. Swanstrom. 2001. Using HIV-1 sequence variability to explore virus biology. Virus Res. 76:137-160.

Resch, W., N. Hoffman, and R. Swanstrom. 2001. Improved success of phenotype prediction of the human immunodeficiency virus type 1 from envelope variable loop 3 sequence using neural networks. Virology. 288:51-62.(pdf version)

Before graduate school I worked in the lab of Dr. Brian Kay (then at UNC) where we used peptide ligands generated using phage-displayed random peptide libraries to identify interesting proteins.

Kurakin, A., N. G. Hoffman, and B. K. Kay. 1998. Molecular recognition properties of the C-terminal Sh3 domain of the Cbl associated protein, Cap. Journal of Peptide Research. 52:331-337.

Ribon, V., J. A. Printen, N. G. Hoffman, B. K. Kay, and A. R. Saltiel. 1998. A novel, multifuntional c-Cbl binding protein in insulin receptor signaling in 3T3-L1 adipocytes. Molecular & Cellular Biology. 18:872-879.

Yamabhai, M., N. G. Hoffman, N. L. Hardison, P. S. McPherson, L. Castagnoli, G. Cesareni, and B. K. Kay. 1998. Intersectin, a novel adaptor protein with two Eps15 homology and five Src homology 3 domains. Journal of Biological Chemistry. 273:31401-31407.

Ward, J. G., P. Blomberg, N. G. Hoffman, and M. C. Yao. 1997. The intranuclear organization of normal, hemizygous and excision-deficient rRNA genes during developmental amplification in Tetrahymena thermophila. Chromosoma. 106:233-242.

Hoffman, N. G., A. B. Sparks, J. M. Carter, and B. K. Kay. 1996. Binding properties of SH3 peptide ligands identified from phage-displayed random peptide libraries. Molecular Diversity. 2:5-12.

Sparks, A. B., N. G. Hoffman, S. J. McConnell, D. M. Fowlkes, and B. K. Kay. 1996. Cloning of ligand targets: systematic isolation of SH3 domain-containing proteins. Nature Biotechnology. 14:741-744.

Sparks, A. B., J. E. Rider, N. G. Hoffman, D. M. Fowlkes, L. A. Quillam, and B. K. Kay. 1996. Distinct ligand preferences of Src homology 3 domains from Src, Yes, Abl, Cortactin, p53bp2, PLCgamma, Crk, and Grb2. Proceedings of the National Academy of Sciences of the United States of America. 93:1540-1544.