Art F Y Poon

Summary

Affiliation: British Columbia
Country: Canada

Publications

  1. pmc Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses
    Art F Y Poon
    British Columbia Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 8:e78122. 2013
  2. pmc Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data
    Art F Y Poon
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    PLoS Comput Biol 8:e1002753. 2012
  3. pmc Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1
    Art F Y Poon
    British Columbia Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    Mol Biol Evol 27:819-32. 2010
  4. doi request reprint Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data
    Art F Y Poon
    BC Centre for Excellence in HIV AIDS, Vancouver, Canada
    AIDS 25:2019-26. 2011
  5. pmc Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes
    Guinevere Q Lee
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    AIDS Res Hum Retroviruses 29:979-84. 2013
  6. pmc Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing
    David J H F Knapp
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    J Clin Microbiol 51:444-51. 2013
  7. pmc Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing
    Richard H Liang
    BC Centre for Excellence in HIV AIDS, Vancouver, BC, V6Z 1Y6, Canada
    Nucleic Acids Res 42:e98. 2014
  8. doi request reprint Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint
    Rachel A McGovern
    British Columbia Centre for Excellence in HIV AIDS, Vancouver, Canada V6Z 1Y6
    J Antimicrob Chemother 68:2007-14. 2013
  9. pmc An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data
    Rosemary M McCloskey
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    J Virol 88:6181-94. 2014
  10. pmc "Deep" Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1
    David J H F Knapp
    BC Centre for Excellence in HIV AIDS, Vancouver, BC, Canada
    PLoS ONE 9:e99508. 2014

Collaborators

Detail Information

Publications17

  1. pmc Mapping the shapes of phylogenetic trees from human and zoonotic RNA viruses
    Art F Y Poon
    British Columbia Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
    PLoS ONE 8:e78122. 2013
    ..The kernel approach presented here potentially represents an important new tool for characterizing the evolution and epidemiology of RNA viruses. ..
  2. pmc Reconstructing the dynamics of HIV evolution within hosts from serial deep sequence data
    Art F Y Poon
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    PLoS Comput Biol 8:e1002753. 2012
    ..We observed highly patient-specific distributions and time-scales of mutation accumulation, implying that the role of a fitness valley is contingent on the genotype of the transmitted variant...
  3. pmc Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1
    Art F Y Poon
    British Columbia Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    Mol Biol Evol 27:819-32. 2010
    ..Phylogenetic reconstruction from these data revealed correlated substitutions at Y120/Q125 or N157/S169 repeated across multiple lineages in every host, indicating convergent within-host evolution shaped by epistatic interactions...
  4. doi request reprint Dates of HIV infection can be estimated for seroprevalent patients by coalescent analysis of serial next-generation sequencing data
    Art F Y Poon
    BC Centre for Excellence in HIV AIDS, Vancouver, Canada
    AIDS 25:2019-26. 2011
    ..To reconstruct dates of HIV infection by the coalescent analysis of longitudinal next-generation sequencing (NGS) data...
  5. pmc Comparison of population and 454 "deep" sequence analysis for HIV type 1 tropism versus the original trofile assay in non-B subtypes
    Guinevere Q Lee
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    AIDS Res Hum Retroviruses 29:979-84. 2013
    ..Collective analysis of non-B subtypes revealed a performance similar to subtype B, whereas a subtype-specific analysis revealed overestimation (subtype D) or underestimation (subtype A)...
  6. pmc Factors influencing the sensitivity and specificity of conventional sequencing in human immunodeficiency virus type 1 tropism testing
    David J H F Knapp
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    J Clin Microbiol 51:444-51. 2013
    ..75; P << 0.001); however, concordance in tropism inference was only 83%. Input copy number and PCR replication are important factors in minority species detection in samples with significant heterogeneity...
  7. pmc Theoretical and experimental assessment of degenerate primer tagging in ultra-deep applications of next-generation sequencing
    Richard H Liang
    BC Centre for Excellence in HIV AIDS, Vancouver, BC, V6Z 1Y6, Canada
    Nucleic Acids Res 42:e98. 2014
    ..Thirdly, the use of pIDs could influence amplification and sequencing. We examined the effects of several intrinsic and extrinsic factors on sequencing reads at both the individual and ensemble level. ..
  8. doi request reprint Maraviroc treatment in non-R5-HIV-1-infected patients results in the selection of extreme CXCR4-using variants with limited effect on the total viral setpoint
    Rachel A McGovern
    British Columbia Centre for Excellence in HIV AIDS, Vancouver, Canada V6Z 1Y6
    J Antimicrob Chemother 68:2007-14. 2013
    ..Using deep sequencing methods, we intensively investigated the selective pressure of maraviroc on the viral population in four patients with dual/mixed HIV-1 experiencing treatment failure...
  9. pmc An evaluation of phylogenetic methods for reconstructing transmitted HIV variants using longitudinal clonal HIV sequence data
    Rosemary M McCloskey
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    J Virol 88:6181-94. 2014
    ....
  10. pmc "Deep" Sequencing Accuracy and Reproducibility Using Roche/454 Technology for Inferring Co-Receptor Usage in HIV-1
    David J H F Knapp
    BC Centre for Excellence in HIV AIDS, Vancouver, BC, Canada
    PLoS ONE 9:e99508. 2014
    ....
  11. doi request reprint Use of cellular HIV DNA to predict virologic response to maraviroc: performance of population-based and deep sequencing
    Luke C Swenson
    BC Centre for Excellence in HIV AIDS, Vancouver, Canada
    Clin Infect Dis 56:1659-66. 2013
    ..Here we assess genotypic testing of cellular human immunodeficiency virus (HIV) DNA from peripheral blood mononuclear cells (PBMCs) to predict virologic responses in treatment-experienced patients beginning maraviroc-containing regimens...
  12. pmc Replication fitness of multiple nonnucleoside reverse transcriptase-resistant HIV-1 variants in the presence of etravirine measured by 454 deep sequencing
    Chanson J Brumme
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    J Virol 87:8805-7. 2013
    ..Using this method, we show that the Y181V mutation in the HIV-1 reverse transcriptase in particular confers a clear selective advantage to the virus over 14 other NNRTI resistance mutations in the presence of etravirine in vitro. ..
  13. pmc In vitro selection of clinically relevant bevirimat resistance mutations revealed by "deep" sequencing of serially passaged, quasispecies-containing recombinant HIV-1
    David J H F Knapp
    BC Centre for Excellence in HIV AIDS, 603 1081 Burrard St, Vancouver, BC, Canada
    J Clin Microbiol 49:201-8. 2011
    ....
  14. pmc Prolonged and substantial discordance in prevalence of raltegravir-resistant HIV-1 in plasma versus PBMC samples revealed by 454 "deep" sequencing
    Guinevere Q Lee
    BC Centre for Excellence in HIV AIDS, Vancouver, BC, Canada
    PLoS ONE 7:e46181. 2012
    ..Overall, our observations suggested that plasma and PBMC hosted drastically different HIV-1 populations even after a prolonged exposure to raltegravir selection pressure...
  15. pmc Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load
    Art F Y Poon
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    PLoS ONE 6:e21189. 2011
    ....
  16. doi request reprint Silent mutations are selected in HIV-1 reverse transcriptase and affect enzymatic efficiency
    P Richard Harrigan
    BC Centre for Excellence in HIV AIDS, Vancouver, British Columbia, Canada
    AIDS 22:2501-8. 2008
    ..Missense mutations in HIV-1 reverse transcriptase are frequently selected in response to therapy; we examined whether silent mutations were also selected for by HIV therapy...
  17. pmc Compensatory mutations are repeatable and clustered within proteins
    Brad H Davis
    Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
    Proc Biol Sci 276:1823-7. 2009
    ..These results suggest that compensatory evolution at the protein level is partially predictable and may be convergent...