CARRIE A DYKES

Summary

Affiliation: University of Rochester
Country: USA

Publications

  1. pmc vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments
    Jingming Ma
    Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
    BMC Bioinformatics 11:261. 2010
  2. ncbi request reprint Analysis of env sequence evolution in human immunodeficiency virus-infected patients receiving therapy with nonnucleoside reverse-transcriptase inhibitors
    C Dykes
    Infectious Diseases Unit, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Infect Dis 182:316-20. 2000
  3. pmc Human immunodeficiency virus type 1 protease inhibitor drug-resistant mutants give discordant results when compared in single-cycle and multiple-cycle fitness assays
    Carrie Dykes
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Clin Microbiol 48:4035-43. 2010
  4. pmc Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, New York 14642, USA
    J Virol 80:2380-9. 2006
  5. pmc A randomized trial of therapeutic drug monitoring of protease inhibitors in antiretroviral-experienced, HIV-1-infected patients
    Lisa M Demeter
    University of Rochester School of Medicine and Dentistry, New York, USA
    AIDS 23:357-68. 2009
  6. pmc Sequences in the U3 region of human immunodeficiency virus 1 improve efficiency of minus strand transfer in infected cells
    Dorota Piekna-Przybylska
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Box 712, Rochester, NY 14642, USA
    Virology 410:368-74. 2011
  7. pmc Clinical significance of human immunodeficiency virus type 1 replication fitness
    Carrie Dykes
    Infectious Diseases Division, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Clin Microbiol Rev 20:550-78. 2007
  8. ncbi request reprint Relative replication fitness of efavirenz-resistant mutants of HIV-1: correlation with frequency during clinical therapy and evidence of compensation for the reduced fitness of K103N + L100I by the nucleoside resistance mutation L74V
    Christine E Koval
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Virology 353:184-92. 2006
  9. ncbi request reprint Detection of drug-resistant minority variants of HIV-1 during virologic failure of indinavir, lamivudine, and zidovudine
    Carrie Dykes
    University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Infect Dis 189:1091-6. 2004
  10. doi request reprint Modeling and estimation of kinetic parameters and replicative fitness of HIV-1 from flow-cytometry-based growth competition experiments
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY, 14642, USA
    Bull Math Biol 70:1749-71. 2008

Research Grants

Collaborators

Detail Information

Publications15

  1. pmc vFitness: a web-based computing tool for improving estimation of in vitro HIV-1 fitness experiments
    Jingming Ma
    Department of Biostatistics and Computational Biology, School of Medicine and Dentistry, University of Rochester, Rochester, NY 14642, USA
    BMC Bioinformatics 11:261. 2010
    ..The accurate estimation of viral fitness relies on complicated computations based on statistical methods. This calls for tools that are easy to access and intuitive to use for various experiments of viral fitness...
  2. ncbi request reprint Analysis of env sequence evolution in human immunodeficiency virus-infected patients receiving therapy with nonnucleoside reverse-transcriptase inhibitors
    C Dykes
    Infectious Diseases Unit, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Infect Dis 182:316-20. 2000
    ..Thus, we found no significant correlation of NNRTI therapy with changes in env HTA patterns, suggesting that these treatments had little short-term impact on HIV-1 quasi-species diversity...
  3. pmc Human immunodeficiency virus type 1 protease inhibitor drug-resistant mutants give discordant results when compared in single-cycle and multiple-cycle fitness assays
    Carrie Dykes
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Clin Microbiol 48:4035-43. 2010
    ..We propose that discordant results in the MCA and SCA are due to alterations in late events in the virus life cycle that are not captured in an SCA, such as burst size, cell-to-cell transmission, or infected-cell life span...
  4. pmc Modeling and estimation of replication fitness of human immunodeficiency virus type 1 in vitro experiments by using a growth competition assay
    Hulin Wu
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, New York 14642, USA
    J Virol 80:2380-9. 2006
    ..A user-friendly computational tool also has been developed and is publicly available on the World Wide Web at http://www.urmc.rochester.edu/bstools/vfitness/virusfitness.htm...
  5. pmc A randomized trial of therapeutic drug monitoring of protease inhibitors in antiretroviral-experienced, HIV-1-infected patients
    Lisa M Demeter
    University of Rochester School of Medicine and Dentistry, New York, USA
    AIDS 23:357-68. 2009
    ..NIQs < or = 1 may predict poor outcome and identify patients who could benefit from dose escalation...
  6. pmc Sequences in the U3 region of human immunodeficiency virus 1 improve efficiency of minus strand transfer in infected cells
    Dorota Piekna-Przybylska
    Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Box 712, Rochester, NY 14642, USA
    Virology 410:368-74. 2011
    ..Alteration of segment 1 had the greatest effect. Alteration of motif 9 or both sequences also caused a reduction, but smaller than alteration of segment 1 alone...
  7. pmc Clinical significance of human immunodeficiency virus type 1 replication fitness
    Carrie Dykes
    Infectious Diseases Division, Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Clin Microbiol Rev 20:550-78. 2007
    ..In addition, the strength of the correlations between fitness and clinical outcomes is modest, suggesting that, at present, it would be difficult to utilize these assays for clinical management...
  8. ncbi request reprint Relative replication fitness of efavirenz-resistant mutants of HIV-1: correlation with frequency during clinical therapy and evidence of compensation for the reduced fitness of K103N + L100I by the nucleoside resistance mutation L74V
    Christine E Koval
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    Virology 353:184-92. 2006
    ..These studies have important implications for the design of more durable NNRTI-nucleoside combination regimens...
  9. ncbi request reprint Detection of drug-resistant minority variants of HIV-1 during virologic failure of indinavir, lamivudine, and zidovudine
    Carrie Dykes
    University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
    J Infect Dis 189:1091-6. 2004
    ..Selection for indinavir-resistant variants on treatment with indinavir, lamivudine, and zidovudine may occur slowly, depending on the genetic context in which they arise...
  10. doi request reprint Modeling and estimation of kinetic parameters and replicative fitness of HIV-1 from flow-cytometry-based growth competition experiments
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, NY, 14642, USA
    Bull Math Biol 70:1749-71. 2008
    ..Practical identifiability was investigated via Monte Carlo simulations...
  11. ncbi request reprint Identification of a preferred region for recombination and mutation in HIV-1 gag
    Carrie Dykes
    Department of Medicine, University of Rochester School of Medicine and Dentistry, NY, USA
    Virology 326:262-79. 2004
    ....
  12. pmc Evaluation of a multiple-cycle, recombinant virus, growth competition assay that uses flow cytometry to measure replication efficiency of human immunodeficiency virus type 1 in cell culture
    Carrie Dykes
    Department of Medicine, University of Rochester School of Medicine and Dentistry, Rochester, NY 14642, USA
    J Clin Microbiol 44:1930-43. 2006
    ..This flow cytometry-based growth competition assay offers advantages over current assays for HIV replication efficiency and should prove useful for the evaluation of patient samples in clinical trials...
  13. pmc Reduced fitness in cell culture of HIV-1 with nonnucleoside reverse transcriptase inhibitor-resistant mutations correlates with relative levels of reverse transcriptase content and RNase H activity in virions
    Jiong Wang
    Department of Medicine, School of Medicine and Dentistry, University of Rochester, Rochester, New York, USA
    J Virol 84:9377-89. 2010
    ..For the other NNRTI mutants, reductions in RT content decreased both polymerization and RNase H activity in virions. RNase H reduction was compounded by intrinsic RNase H defects in the mutant RTs...
  14. pmc Nonnucleoside reverse transcriptase inhibitor-resistant HIV is stimulated by efavirenz during early stages of infection
    Jiong Wang
    Department of Medicine, University of Rochester School of Medicine and Dentistry, 601 Elmwood Ave, Rochester, NY 14642, USA
    J Virol 85:10861-73. 2011
    ..Our results indicate that stimulation most likely occurs through a mechanism whereby NNRTIs stimulate priming or elongation of the tRNA...
  15. pmc Differential equation modeling of HIV viral fitness experiments: model identification, model selection, and multimodel inference
    Hongyu Miao
    Department of Biostatistics and Computational Biology, University of Rochester School of Medicine and Dentistry, 601 Elmwood Avenue, Box 630, Rochester, New York 14642, USA
    Biometrics 65:292-300. 2009
    ..We expect that the proposed modeling and inference approaches for the DE models can be widely used for a variety of biomedical studies...

Research Grants2

  1. Impact of NNRTI-resistance on RNase H & HIV replication
    CARRIE A DYKES; Fiscal Year: 2010
    ....