Joshua T Herbeck

Summary

Affiliation: University of Washington
Country: USA

Publications

  1. pmc Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
    J Infect Dis 201:618-26. 2010
  2. ncbi request reprint Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria)
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
    Mol Biol Evol 22:520-32. 2005
  3. ncbi request reprint Converging on a general model of protein evolution
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98103, USA
    Trends Biotechnol 23:485-7. 2005
  4. pmc Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies
    Joshua T Herbeck
    University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS ONE 4:e6915. 2009
  5. pmc Lack of evidence for changing virulence of HIV-1 in North America
    Joshua T Herbeck
    University of Washington School of Medicine, Seattle, Washington, USA
    PLoS ONE 3:e1525. 2008
  6. pmc Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
    AIDS 26:193-205. 2012
  7. pmc A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
    Genetics 165:1651-60. 2003
  8. ncbi request reprint Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
    AIDS Res Hum Retroviruses 23:755-60. 2007
  9. pmc Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host
    Joshua T Herbeck
    Department of Microbiology, SC 42, University of Washington, Seattle, WA 98195, USA
    J Virol 80:1637-44. 2006
  10. pmc An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load
    Joshua T Herbeck
    Department of Microbiology, University of Washington, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003673. 2014

Detail Information

Publications14

  1. pmc Multistage genomewide association study identifies a locus at 1q41 associated with rate of HIV-1 disease progression to clinical AIDS
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
    J Infect Dis 201:618-26. 2010
    ..To investigate host genetic determinants of the rate of progression to clinical AIDS, we performed a multistage genomewide association study...
  2. ncbi request reprint Nonhomogeneous model of sequence evolution indicates independent origins of primary endosymbionts within the enterobacteriales (gamma-Proteobacteria)
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
    Mol Biol Evol 22:520-32. 2005
    ..This application of a nonhomogeneous model offers a computationally feasible way to test specific phylogenetic hypotheses for taxa with heterogeneous and nonstationary base composition...
  3. ncbi request reprint Converging on a general model of protein evolution
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98103, USA
    Trends Biotechnol 23:485-7. 2005
    ..These results indicate that a general model of protein evolution will emerge as more functional genomic data from a diversity of organisms accumulate...
  4. pmc Fidelity of SNP array genotyping using Epstein Barr virus-transformed B-lymphocyte cell lines: implications for genome-wide association studies
    Joshua T Herbeck
    University of Washington School of Medicine, Seattle, Washington, United States of America
    PLoS ONE 4:e6915. 2009
    ..LCL are created in a transformation process that entails in vitro infection of human B-lymphocytes with the Epstein-Barr Virus (EBV)...
  5. pmc Lack of evidence for changing virulence of HIV-1 in North America
    Joshua T Herbeck
    University of Washington School of Medicine, Seattle, Washington, USA
    PLoS ONE 3:e1525. 2008
    ....
  6. pmc Is the virulence of HIV changing? A meta-analysis of trends in prognostic markers of HIV disease progression and transmission
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
    AIDS 26:193-205. 2012
    ..Published data to date have provided conflicting results...
  7. pmc A conservative test of genetic drift in the endosymbiotic bacterium Buchnera: slightly deleterious mutations in the chaperonin groEL
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, Woods Hole, Massachusetts 02543, USA
    Genetics 165:1651-60. 2003
    ..Rather, they further support the hypothesis that drift is an important force driving accelerated protein evolution in this obligate mutualist...
  8. ncbi request reprint Prevalence and genetic diversity of HIV type 1 subtypes A and D in women attending antenatal clinics in Uganda
    Joshua T Herbeck
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
    AIDS Res Hum Retroviruses 23:755-60. 2007
    ..This report suggests that among pregnant women in Uganda A and D subtypes are transmitted without geographic constraints, and are not associated with significantly different transmission rates...
  9. pmc Human immunodeficiency virus type 1 env evolves toward ancestral states upon transmission to a new host
    Joshua T Herbeck
    Department of Microbiology, SC 42, University of Washington, Seattle, WA 98195, USA
    J Virol 80:1637-44. 2006
    ..These results have important implications for the study of HIV population genetics and rational vaccine design, including favoring the inclusion of viral gene sequences taken early in infection...
  10. pmc An HIV Epidemic Model Based on Viral Load Dynamics: Value in Assessing Empirical Trends in HIV Virulence and Community Viral Load
    Joshua T Herbeck
    Department of Microbiology, University of Washington, Seattle, Washington, United States of America
    PLoS Comput Biol 10:e1003673. 2014
    ..We find that community viral load evolves in association with SPVL, in the absence of prevention programs such as antiretroviral therapy, and that the mean community viral load is not necessarily a strong predictor of HIV incidence. ..
  11. pmc Demographic processes affect HIV-1 evolution in primary infection before the onset of selective processes
    Joshua T Herbeck
    Department of Microbiology, SC 42, University of Washington School of Medicine, Seattle, WA 98195 8070, USA
    J Virol 85:7523-34. 2011
    ..Furthermore, the diversity of HIV strains coupled with complex and individual-specific patterns of CTL escape did not reveal shared sequence characteristics of acute infection that could be harnessed for vaccine design...
  12. ncbi request reprint Gene expression level influences amino acid usage, but not codon usage, in the tsetse fly endosymbiont Wigglesworthia
    Joshua T Herbeck
    Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, Marine Biological Laboratory, 7 MBL Street, Woods Hole, MA 02543, USA
    Microbiology 149:2585-96. 2003
    ..However, these impacts of mutation and drift are apparently attenuated by selection on amino acid composition at high-expression genes...
  13. ncbi request reprint HIV-1 over time: fitness loss or robustness gain?
    Morgane Rolland
    Nat Rev Microbiol 5:C1. 2007
  14. ncbi request reprint Evolutionary patterns of codon usage in the chloroplast gene rbcL
    Dennis P Wall
    Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
    J Mol Evol 56:673-88; discussion 689-90. 2003
    ..This suggests that codon usage bias may be constrained by particular amino acids and, thus, may serve as a good predictor of what residues are most important for protein fitness...