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Volumn 25, Issue 8, 2009, Pages 1040-1047

Stochastic modelling of genotypic drug-resistance for human immunodeficiency virus towards long-term combination therapy optimization

Author keywords

[No Author keywords available]

Indexed keywords

ABACAVIR; DIDANOSINE; EFAVIRENZ; LAMIVUDINE; LOPINAVIR; STAVUDINE; ZIDOVUDINE;

EID: 64549129092     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn568     Document Type: Article
Times cited : (11)

References (37)
  • 1
    • 0034995757 scopus 로고    scopus 로고
    • Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region
    • Anderson,J.P. et al. (2001) Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region. J. Mol. Evol., 53, 55-62.
    • (2001) J. Mol. Evol , vol.53 , pp. 55-62
    • Anderson, J.P.1
  • 2
    • 0002035566 scopus 로고
    • Reducing bias and inefficiency in the selection algorithm
    • Grefenstette, J.J, ed, Hillsdale, New Jersey, USA, Lawrence Erlbaum Associates, pp
    • Baker,J.E. (1987) Reducing bias and inefficiency in the selection algorithm. In Grefenstette, J.J. (ed.), Proceedings of the Second International Conference on Genetic Algorithms and their Application, Hillsdale, New Jersey, USA, Lawrence Erlbaum Associates, pp. 14-21.
    • (1987) Proceedings of the Second International Conference on Genetic Algorithms and their Application , pp. 14-21
    • Baker, J.E.1
  • 3
    • 0043092351 scopus 로고    scopus 로고
    • Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes
    • Beerenwinkel,N. et al. (2003) Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res., 31 3850-3855.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3850-3855
    • Beerenwinkel, N.1
  • 4
    • 33845394419 scopus 로고    scopus 로고
    • A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data
    • Beerenwinkel,N. and Drton,M. (2007) A mutagenetic tree hidden Markov model for longitudinal clonal HIV sequence data. Biostatistics, 8, 53-71.
    • (2007) Biostatistics , vol.8 , pp. 53-71
    • Beerenwinkel, N.1    Drton, M.2
  • 5
    • 11244257420 scopus 로고    scopus 로고
    • Mutation, fitness, viral diversity and predictive markers of disease progression in a computational model of HIV-1 infection
    • Castiglione,F. et al. (2004) Mutation, fitness, viral diversity and predictive markers of disease progression in a computational model of HIV-1 infection. AIDS Res. Hum. Retrov., 20, 1316-1325.
    • (2004) AIDS Res. Hum. Retrov , vol.20 , pp. 1316-1325
    • Castiglione, F.1
  • 7
    • 36949005400 scopus 로고    scopus 로고
    • Optimization of HAART with genetic algorithms and agent-based models of HIV infection
    • Castiglione,F. et al. (2007) Optimization of HAART with genetic algorithms and agent-based models of HIV infection. Bioinformatics 23, 3350-3355.
    • (2007) Bioinformatics , vol.23 , pp. 3350-3355
    • Castiglione, F.1
  • 8
    • 84954964873 scopus 로고
    • LOWESS: A program for smoothing scatterplots by robust locally weighted regression
    • Cleveland,W.S. (1981) LOWESS: A program for smoothing scatterplots by robust locally weighted regression. Am. Stat., 35, 54.
    • (1981) Am. Stat , vol.35 , pp. 54
    • Cleveland, W.S.1
  • 9
    • 37549044257 scopus 로고    scopus 로고
    • Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment
    • Deforche,K. et al. (2007) Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. Bioinformatics, 24, 34-41.
    • (2007) Bioinformatics , vol.24 , pp. 34-41
    • Deforche, K.1
  • 10
    • 27744561912 scopus 로고    scopus 로고
    • The prognostic value to predict virological outcomes of 14 distinct systems used to interpret the results of genotypic HIV-1 drug resistance testing in untreated patients starting their first HAART
    • De Luca,A. et al. (2003) The prognostic value to predict virological outcomes of 14 distinct systems used to interpret the results of genotypic HIV-1 drug resistance testing in untreated patients starting their first HAART. HIV Med., 4, 20.
    • (2003) HIV Med , vol.4 , pp. 20
    • De Luca, A.1
  • 11
    • 0032967837 scopus 로고    scopus 로고
    • Population HIV-1 dynamics in vivo: Applicable models and inferential tools for virological data from AIDS clinical trials
    • Ding,A.A. and Wu,H. (1999) Population HIV-1 dynamics in vivo: Applicable models and inferential tools for virological data from AIDS clinical trials. Biometrics, 55, 410-418.
    • (1999) Biometrics , vol.55 , pp. 410-418
    • Ding, A.A.1    Wu, H.2
  • 12
    • 0034019536 scopus 로고    scopus 로고
    • A comparison study on models and fitting procedures for biphasic viral dynamics in HIV-1 infected patients treated with antiviral therapies
    • Ding,A.A. and Wu,H. (2000) A comparison study on models and fitting procedures for biphasic viral dynamics in HIV-1 infected patients treated with antiviral therapies. Biometrics, 56, 293-300.
    • (2000) Biometrics , vol.56 , pp. 293-300
    • Ding, A.A.1    Wu, H.2
  • 13
    • 33846596702 scopus 로고    scopus 로고
    • Randomized open-label trial of two simplified, class-sparing regimens following a first suppressive three or four-drug regimen
    • Fischl,M.A. et al. (2007) Randomized open-label trial of two simplified, class-sparing regimens following a first suppressive three or four-drug regimen. AIDS, 21, 325-333.
    • (2007) AIDS , vol.21 , pp. 325-333
    • Fischl, M.A.1
  • 14
    • 0037696057 scopus 로고    scopus 로고
    • Modeling HIV dynamics and antiviral response with consideration of time-varying drug exposures, adherence and phenotypic sensitivity
    • Huang,Y. et al. (2003) Modeling HIV dynamics and antiviral response with consideration of time-varying drug exposures, adherence and phenotypic sensitivity. Math. Biosci., 184, 165-186.
    • (2003) Math. Biosci , vol.184 , pp. 165-186
    • Huang, Y.1
  • 15
    • 0001855041 scopus 로고
    • On some stochastic models in genetics
    • Gurland,J, ed, University of Wisconsin Press, Madison, WI, pp
    • Karlin,S. and McGregor,J. (1964) On some stochastic models in genetics. In Gurland,J. (ed.) Stochastic Problems in Medicine and Biology. University of Wisconsin Press, Madison, WI, pp. 245-271.
    • (1964) Stochastic Problems in Medicine and Biology , pp. 245-271
    • Karlin, S.1    McGregor, J.2
  • 16
    • 33750451933 scopus 로고    scopus 로고
    • Viral and latent reservoir persistence in HIV-1 infected patients on therapy
    • Kim,H. and Perelson,A.S. (2006) Viral and latent reservoir persistence in HIV-1 infected patients on therapy. PLoS Comput. Biol., 2 e135.
    • (2006) PLoS Comput. Biol , vol.2
    • Kim, H.1    Perelson, A.S.2
  • 18
    • 37849009397 scopus 로고    scopus 로고
    • Modelling and control of HIV dynamics
    • Landi,A. et al. (2008) Modelling and control of HIV dynamics. Comput. Methods Prog. Biomed., 89, 162-168.
    • (2008) Comput. Methods Prog. Biomed , vol.89 , pp. 162-168
    • Landi, A.1
  • 19
    • 0031010764 scopus 로고    scopus 로고
    • Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history
    • Leitner,T. et al. (1997) Tempo and mode of nucleotide substitutions in gag and env gene fragments in human immunodeficiency virus type 1 populations with a known transmission history. J. Virol., 71, 4761-4770.
    • (1997) J. Virol , vol.71 , pp. 4761-4770
    • Leitner, T.1
  • 20
    • 0029075130 scopus 로고
    • Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase
    • Mansky,L.M. and Temin,H.M. (1995) Lower in vivo mutation rate of human immunodeficiency virus type 1 than that predicted from the fidelity of purified reverse transcriptase. J. Virol., 69, 5087-5094.
    • (1995) J. Virol , vol.69 , pp. 5087-5094
    • Mansky, L.M.1    Temin, H.M.2
  • 21
    • 0003540748 scopus 로고
    • Genetic algorithms + data structures = evolution programs
    • Springer-Verlag, NY
    • Michalewicz,Z. (1994) Genetic algorithms + data structures = evolution programs. AI series, Springer-Verlag, NY.
    • (1994) AI series
    • Michalewicz, Z.1
  • 22
    • 0032576426 scopus 로고    scopus 로고
    • Changing patterns of mortality across Europe in patients infected with HIV-1
    • Mocroft,A. et al. (1998) Changing patterns of mortality across Europe in patients infected with HIV-1. Lancet, 352, 1725-1730.
    • (1998) Lancet , vol.352 , pp. 1725-1730
    • Mocroft, A.1
  • 23
    • 0034005931 scopus 로고    scopus 로고
    • A model of HIV-1 pathogenesis that includes an intracellular delay
    • Nelson,P.W. et al. (2000) A model of HIV-1 pathogenesis that includes an intracellular delay. Math. Biosci., 163, 201-215.
    • (2000) Math. Biosci , vol.163 , pp. 201-215
    • Nelson, P.W.1
  • 25
    • 0001918317 scopus 로고    scopus 로고
    • Mathematical analysis of HIV-1 dynamics in vivo
    • Perelson,A.S. and Nelson,P.W. (1999) Mathematical analysis of HIV-1 dynamics in vivo. SIAM Rev., 41, 3-44.
    • (1999) SIAM Rev , vol.41 , pp. 3-44
    • Perelson, A.S.1    Nelson, P.W.2
  • 26
    • 0035941395 scopus 로고    scopus 로고
    • Use of a stochastic model to develop understanding of the impact of different patterns of antiretroviral drug use on resistance development
    • Phillips,A.N. et al. (2001) Use of a stochastic model to develop understanding of the impact of different patterns of antiretroviral drug use on resistance development. AIDS, 15, 2211-2220.
    • (2001) AIDS , vol.15 , pp. 2211-2220
    • Phillips, A.N.1
  • 28
    • 0032968677 scopus 로고    scopus 로고
    • A stochastic model for primary HIV infection: Optimal timing of therapy
    • Ribeiro,R.M. and Bonhoeffer,S. (1999) A stochastic model for primary HIV infection: Optimal timing of therapy. AIDS, 13, 351-357.
    • (1999) AIDS , vol.13 , pp. 351-357
    • Ribeiro, R.M.1    Bonhoeffer, S.2
  • 29
    • 0034608864 scopus 로고    scopus 로고
    • Production of resistant HIV mutants during antiretroviral therapy
    • Ribeiro,R.M. and Bonhoeffer,S. (2000) Production of resistant HIV mutants during antiretroviral therapy. Proc. Natl Acad. Sci. USA, 97, 7681-7686.
    • (2000) Proc. Natl Acad. Sci. USA , vol.97 , pp. 7681-7686
    • Ribeiro, R.M.1    Bonhoeffer, S.2
  • 30
    • 43549094732 scopus 로고    scopus 로고
    • Class-sparing regimens for initial treatment of HIV-1 infection
    • Riddler,S.A. et al. (2008) Class-sparing regimens for initial treatment of HIV-1 infection. N. Engl. J. Med., 358, 2095-2106.
    • (2008) N. Engl. J. Med , vol.358 , pp. 2095-2106
    • Riddler, S.A.1
  • 31
    • 0029007143 scopus 로고
    • Drug resistance and heterogeneous long-term virologic responses of human immunodeficiency virus type 1-infected subjects to zidovudine and didanosine combination therapy. The AIDS Clinical Trials Group 143 Virology Team
    • Shafer,R.W. et al. (1995) Drug resistance and heterogeneous long-term virologic responses of human immunodeficiency virus type 1-infected subjects to zidovudine and didanosine combination therapy. The AIDS Clinical Trials Group 143 Virology Team. J. Infect. Dis., 172, 70-78.
    • (1995) J. Infect. Dis , vol.172 , pp. 70-78
    • Shafer, R.W.1
  • 32
    • 58149210039 scopus 로고
    • A stochastic model for drug resistance in AIDS chemotherapy and the HIV incubation distribution
    • Tan,W.Y. (1995) A stochastic model for drug resistance in AIDS chemotherapy and the HIV incubation distribution. Stat. Probab. Lett. 25, 289-299.
    • (1995) Stat. Probab. Lett , vol.25 , pp. 289-299
    • Tan, W.Y.1
  • 34
    • 0002124649 scopus 로고
    • Variations and fluctuations of the number of individuals in animal species living together
    • McGraw-Hill, New York, USA
    • Volterra,V. (1931) Variations and fluctuations of the number of individuals in animal species living together. In Animal Ecology. McGraw-Hill, New York, USA.
    • (1931) Animal Ecology
    • Volterra, V.1
  • 35
    • 0011419832 scopus 로고    scopus 로고
    • Characterization of viral dynamics in human immunodeficiency virus type 1-infected patients treated with combination antiretroviral therapy: Relationships to host factors, cellular restoration and virological endpoints
    • Wu,H. et al. (1999) Characterization of viral dynamics in human immunodeficiency virus type 1-infected patients treated with combination antiretroviral therapy: Relationships to host factors, cellular restoration and virological endpoints. J. Infect. Dis., 179, 799-807.
    • (1999) J. Infect. Dis , vol.179 , pp. 799-807
    • Wu, H.1
  • 36
    • 0035065394 scopus 로고    scopus 로고
    • Estimating mutation rate and generation time from longitudinal samples of DNA sequences
    • Fu,Y.-X. (2001) Estimating mutation rate and generation time from longitudinal samples of DNA sequences. Mol. Biol. Evol., 18, 620-626.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 620-626
    • Fu, Y.-X.1
  • 37
    • 21844462147 scopus 로고    scopus 로고
    • Multiple drug class-wide resistance associated with poorer survival after treatment failure in a cohort of hiv-infected patients
    • Zaccarelli,M. et al. (2005) Multiple drug class-wide resistance associated with poorer survival after treatment failure in a cohort of hiv-infected patients. AIDS, 19, 1081-1089.
    • (2005) AIDS , vol.19 , pp. 1081-1089
    • Zaccarelli, M.1


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