email: herbeck [the at sign] uw [the dot sign] edu

Acting Assistant Professor

Department of Global Health, University of Washington, Seattle, WA

My primary research interests are in epidemiology, genomics, phylogenetics, and population genetics, and in the application of these fields to the understanding of HIV and AIDS.

I started the HIV Virulence Trends Working Group, a collaboration with multiple international HIV cohorts from North America, Europe and Africa, with the goal of better understanding how HIV evolves in human populations. We are funded by the National Evolutionary Synthesis Center (www.nescent.org). This collaboration has the potential to change how we understand the last 50 years of HIV evolution in humans, how cohorts around the world collect and record clinical and virological data, and how scientists model future trends in HIV epidemiology and evolution.

Education

Postdoctoral fellow, HIV genetics and virology, University of Washington School of Medicine, 2004 to 2009

Postdoctoral scientist, Bacterial genomics, Marine Biological Laboratory, 2003

Ph.D., Environmental Science, Policy and Management, University of California, Berkeley, 2002

B.S., Biology, Tufts University, 1995

Additional courses

University of Washington Network Modeling for Epidemics Summer Course, 2013

University of Washington Annual Principles of STD/HIV Research Course, 2005

Teaching

I have recently taught several guest lectures in "BIO 354, Foundations in Evolution and Systematics" and "MICROM 101, Microbes and Society" at the University of Washington.

I am also a lecturer in the ongoing workshop series, "Bioinformatics in the Tropics: HIV Sequence Analysis" that are sponsored by the Wellcome Trust and the CDC. These workshops have taken place at the: University of KwaZulu-Natal, Durban, South Africa (September, 2013), Uganda Virus Research Institute, Entebbe, Uganda, (April, 2014), and the Centro de Pesquisa Gonçalo Muniz/Fiocruz, Bahia, Brazil (May, 2014). The teaching includes lectures and practical sessions on methods of HIV phylogenetics and molecular epidemiology.

Publications (grouped by subject matter)

Evolution of HIV virulence

2014. Herbeck, J.T., Mittler, J., Gottlieb, G.S., and J.I. Mullins. An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load. PLoS Computational Biology.

2012. Herbeck, J.T., Mueller V., Maust B.S., Ledergerber B., Torti C., Di Giambenedetto S., Gras L., Guenthard H.F., Jacobson L.P., Mullins J.I., Gottlieb G.S. Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission. AIDS, 26: 193-205.

2011. Mueller V., Fraser C., Herbeck, J.T.. A strong case for viral genetic factors in HIV virulence. Viruses, 3: 204-16.

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. 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

HIV evolution after infection

2011. Herbeck, J.T., Rolland M., Liu Y., McLaughlin S., McNevin J., Zhao H., Wong K., Stoddard J.N., Raugi D., Sorensen S., Genowati I., Birditt B., McKay A., Diem K., Maust B.S., Deng W., Collier A.C., Stekler J.D., McElrath M.J., Mullins J.I. Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes. J Virol, 85: 7523-34.

2010. Boutwell, C., Rolland, M., Herbeck, J.T., Mullins, J.I. and T.A. Allen. Viral evolution and escape during acute HIV-1 infection. Journal of Infectious Diseases, 202 Suppl 2: S309-14.

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.

HIV molecular epidemiology

2014. Co-first authors: Dennis, A.M., Herbeck, J.T., Leigh Brown, A., Kellam, P., de Oliveira, T., Pillay, D., Fraser, C., and M.S. Cohen. Phylogenetic studies of transmission dynamics in generalized HIV epidemics: An essential tool where the burden is greatest? Journal of AIDS, in press.

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

Host factors associated with HIV acquisition and progression

2013. McLaren PJ, Coulonges C, Ripke S, van den Berg L, Buchbinder S, ... Herbeck, J.T. ..., et al. Association study of common genetic variants and HIV-1 acquisition in 6,300 infected cases and 7,200 controls. PLoS Pathogens, 9(7): e1003515.

2011. Nikolova M., Carriere M., Jenabian M.A., Limou S., Younas M., Kok A., Hue S., Seddiki N., Hulin A., Delaneau O., Schuitemaker H., Herbeck, J.T., Mullins J.I., Muhtarova M., Bensussan A., Zagury J.F., Lelievre J.D., Levy Y. CD39/adenosine pathway is involved in AIDS progression. PLoS Pathogens, 7:e1002110.

2011. Bol S.M., Moerland P.D., Limou S., van Remmerden Y., Coulonges C., van Manen D., Herbeck, J.T., Fellay J., Sieberer M., Sietzema J.G., van 't Slot R., Martinson J., Zagury J.F., Schuitemaker H., van 't Wout A.B. Genome-wide association study identifies single nucleotide polymorphism in DYRK1A associated with replication of HIV-1 in monocyte-derived macrophages. PLoS One, 6: e17190.

2010. Le Clerc, S., Coulonges, C., Delaneau, O., van Manen, D., Herbeck, J.T., Limou, S., et al. Screening low frequency SNPs from genome wide association study reveals a new risk allele for progression to AIDS. Journal of AIDS, 56: 279-84.

2010. Limou, S., Coulonges, C., Herbeck, J.T., van Manen, D., An, P., Le Clerc, et al. Multiple-cohort genetic association study reveals CXCR6 as a new chemokine receptor risk involved in AIDS long-term non-progression. Journal of Infectious Diseases, 202: 908-15.

2010. Herbeck, J.T., Gottlieb, G., Maust, B., Wong, K.G., Detels, R., Phair, J., Martinson, J., Winkler, C.A., O'Brien, S.J., Jacobson, L., Margolick, J., Kaslow, R.A. and J.I. Mullins. Multistage genome-wide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS. Journal of Infectious Diseases, 201: 618-626.

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

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

Bacterial genomics

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

Evolution of codon usage bias

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