email: herbeck [at] u [dot] washington [dot] edu
phone: (206)-732-6149
Center for AIDS Research and Department of Microbiology, University of Washington, Seattle, WA
Education
B.S., Biology, Tufts University, 1995
Ph.D., Population Genetics / Phylogenetics, University of California, Berkeley, 2002
Postdoc, Marine Biological Laboratory, 2003
Research
My primary research interests are in population genetics and phylogenetics, and in the application of these fields to the understanding of HIV and AIDS. I am currently a senior postdoctoral fellow in the group of Jim Mullins at the University of Washington. I often work with scientists from the Laboratory of Genomic Diversity at the NCI, and with scientists involved with the Multicenter AIDS Cohort Study (MACS).
Publications
2009. Herbeck, J.T., Gottlieb, G.S., Winkler, C.A., Nelson, G.W., An, P., Maust, B.S., Wong, K.G, Troyer, J.L., Goedert, J.J., Kessing, B.D., Detels, R., Wolinsky, S.M., Martinson, J., Buchbinder, S., Kirk, G.D., Jacobson, L.J., Margolick, J.B., Kaslow, R.A., O'Brien, S.J., and J.I. Mullins. Two-stage genome-wide association study identifies a locus at 1q41 associated with delayed HIV-1 disease progression to clinical AIDS. Journal of Infectious Diseases, in press.
2009. Herbeck, J.T., Gottlieb, G.S., Wong, K.G, and J.I. Mullins. Fidelity of SNP array genotyping using Epstein-Barr Virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies. PLoS ONE, 4: e6915. .pdf
2008. Herbeck, J.T., Gottlieb, G.S., Hu, Z., Jacobson, L., Margolick, J., Detels, R., Phair, J., Rinaldo, C., and J.I. Mullins. Lack of evidence for changing virulence of HIV-1 in North America: an analysis of greater than 20 years of observation in the MACS cohort. PLoS ONE, 3: e1525. .pdf 2007. Rolland, M., Brander, C., Nickle, D.C., Herbeck, J.T., Gottlieb, G.S., Campbell, M.S., Maust, B.M., and J.I. Mullins. HIV-1 over time: fitness loss or robustness gain? Nature Reviews Microbiology, 5: 1-2. .pdf 2007. Herbeck, J.T., Lyagoba, F., Moore, S.W., Shindo, N., Biryahwaho, B., Kaleebu, P., and J.I. Mullins. Prevalence and genetic diversity of HIV-1 subtypes A and D in women attending antenatal clinics in Uganda. AIDS Research and Human Retroviruses, 23: 755-760. .pdf 2007. Bhattacharya, T., Daniels, M., Heckerman, D., Foley, B., Frahm, N., Kadie, C., Carlson, J., Yusim, K., McMahon, B., Gaschen, B., Mallal, S., Mullins, J.I., Nickle, D.C., Herbeck, J., Rousseau, C., Learn, G.H., Miura, T., Brander, C., Walker, B., and B. Korber. Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science, 315: 1583-1586. .pdf 2007. Gottlieb G.S., Hawes S.E., Nickle D.C., Herbeck, J.T., Kiviat N.B., Mullins J.I., Sow P.S. Presenting plasma HIV RNA level and rate of CD4 T-cell decline. JAMA, 297: 805. .pdf 2006. Herbeck, J.T., Nickle, D.C., Learn, G.H., Gottlieb, G.S., Curlin, M.E., Heath, L., and J.I. Mullins. HIV-1 env evolves toward ancestral states upon transmission to a new host. Journal of Virology, 80: 1637-1644. .pdf ***Article of significant interest selected from this issue by the Editors. 2005. Herbeck, J.T. and D.P. Wall. Converging on a general model of protein evolution. Trends in Biotechnology, 23: 485-487. .pdf 2004. Herbeck, J.T., Degnan, P.H., and J.J. Wernegreen. Non-homogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria). Molecular Biology and Evolution, 22: 520-532. .pdf 2003. Herbeck, J.T., Funk, D.J., Degnan, P.H., and J.J. Wernegreen. A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL. Genetics, 165: 1651-1660. .pdf 2003. Herbeck, J.T., Wall, D.P., and J.J. Wernegreen. Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont wigglesworthia. Microbiology, 149: 2585-2596. .pdf 2003. Herbeck, J.T. and J. Novembre. Codon usage patterns in COI across multiple insect orders. Journal of Molecular Evolution, 56: 691-701. .pdf 2003. Wall, D.P. and J.T. Herbeck. Evolutionary patterns of codon usage in the Chloroplast Gene rbcL. Journal of Molecular Evolution, 56: 673-688. .pdf 1996. Bloch Qazi, M.C., Herbeck, J.T., and S. Lewis. Mechanisms of sperm transfer and storage in the red flour beetle (Coleoptera: Tenebrionidae). Annals of the Entomological Society of America, 89: 892-897.