Soo Yon Rhee

Summary

Affiliation: Stanford University
Country: USA

Publications

  1. pmc Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes
    Soo Yon Rhee
    Department of Medicine, Stanford University, Stanford, CA, USA
    AIDS Res Ther 9:13. 2012
  2. pmc A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes
    Kathleen M Doherty
    Department of Chemistry, Wellesley College, MA 02481, USA
    BMC Bioinformatics 12:477. 2011
  3. pmc Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
    Amit Kapoor
    Blood Systems Research Institute, San Francisco, CA 94118, USA
    Retrovirology 5:7. 2008
  4. pmc Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape
    Kristof Theys
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    BMC Bioinformatics 11:409. 2010
  5. pmc HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes
    Soo Yon Rhee
    Division of Infectious Disease, Stanford University, Stanford, California, USA
    AIDS 20:643-51. 2006
  6. pmc Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
    Retrovirology 5:74. 2008
  7. ncbi request reprint Predictive value of HIV-1 genotypic resistance test interpretation algorithms
    Soo Yon Rhee
    Division of Infectious Diseases, Dept of Medicine, Stanford University, Stanford, CA 94305, USA
    J Infect Dis 200:453-63. 2009
  8. pmc HIV-1 protease mutations and protease inhibitor cross-resistance
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Antimicrob Agents Chemother 54:4253-61. 2010
  9. doi request reprint Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
    Soo Yon Rhee
    Department of Medicine, Stanford University, CA, United States
    Antiviral Res 88:269-75. 2010
  10. pmc HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, CA 94301, USA
    J Infect Dis 192:456-65. 2005

Detail Information

Publications39

  1. pmc Standardized representation, visualization and searchable repository of antiretroviral treatment-change episodes
    Soo Yon Rhee
    Department of Medicine, Stanford University, Stanford, CA, USA
    AIDS Res Ther 9:13. 2012
    ..abstract:..
  2. pmc A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes
    Kathleen M Doherty
    Department of Chemistry, Wellesley College, MA 02481, USA
    BMC Bioinformatics 12:477. 2011
    ..Understanding the phenotypic and genotypic patterns responsible for multi-PI resistance is necessary for developing PIs that are active against clinically-relevant PI-resistant HIV-1 variants...
  3. pmc Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patients
    Amit Kapoor
    Blood Systems Research Institute, San Francisco, CA 94118, USA
    Retrovirology 5:7. 2008
    ....
  4. pmc Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscape
    Kristof Theys
    Rega Institute for Medical Research, Katholieke Universiteit Leuven, Leuven, Belgium
    BMC Bioinformatics 11:409. 2010
    ..By simulation of evolution over this landscape, the individualized genetic barrier to NFV resistance may be estimated for an isolate...
  5. pmc HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes
    Soo Yon Rhee
    Division of Infectious Disease, Stanford University, Stanford, California, USA
    AIDS 20:643-51. 2006
    ..As additional non-B sequences from persons with well-characterized antiretroviral treatment histories have become available, the program has been extended to subtypes A, C, D, F, G, CRF01, and CRF02...
  6. pmc Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
    Retrovirology 5:74. 2008
    ..1% of sequences--were nonpolymorphic. Several accessory INI-resistance mutations including L74M, T97A, V151I, G163R, and S230N were also polymorphic with polymorphism rates ranging between 0.5% to 2.0%...
  7. ncbi request reprint Predictive value of HIV-1 genotypic resistance test interpretation algorithms
    Soo Yon Rhee
    Division of Infectious Diseases, Dept of Medicine, Stanford University, Stanford, CA 94305, USA
    J Infect Dis 200:453-63. 2009
    ..Multiple drug-resistance interpretation algorithms have been developed, but their predictive value has rarely been evaluated using contemporary clinical data sets...
  8. pmc HIV-1 protease mutations and protease inhibitor cross-resistance
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Antimicrob Agents Chemother 54:4253-61. 2010
    ....
  9. doi request reprint Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery
    Soo Yon Rhee
    Department of Medicine, Stanford University, CA, United States
    Antiviral Res 88:269-75. 2010
    ..HBVrtDB and HBVseq are available at http://hivdb.stanford.edu/HBV/releaseNotes/...
  10. pmc HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, CA 94301, USA
    J Infect Dis 192:456-65. 2005
    ..In contrast, nonpolymorphic treatment-associated mutations may be more sensitive and specific markers of transmitted HIV-1 drug resistance...
  11. pmc N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure
    Yumi Mitsuya
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    AIDS Res Hum Retroviruses 22:1300-5. 2006
    ....
  12. pmc Human immunodeficiency virus reverse transcriptase and protease sequence database
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Nucleic Acids Res 31:298-303. 2003
    ..Sequence data on two new molecular targets of HIV drug therapy--gp41 (cell fusion) and integrase--will be added to the database in 2003...
  13. pmc HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance
    Robert W Shafer
    Division of Infectious Diseases, Stanford University, Stanford, California, USA
    AIDS 21:215-23. 2007
    ..However, such programs will not produce comparable estimates unless a standardized list of drug-resistance mutations is used to define transmitted resistance...
  14. pmc Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation
    Matthew J Gonzales
    Department of Medicine Division of Infectious Diseases, Stanford University, Stanford, USA
    J Infect Dis 188:397-405. 2003
    ..Although HIV-1 PR and RT genes from treated persons may become highly divergent, these changes usually are the result of sequence evolution, rather than superinfection...
  15. pmc Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility
    George L Melikian
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
    Antimicrob Agents Chemother 56:2305-13. 2012
    ....
  16. pmc Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations
    Rajin Shahriar
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Antimicrob Agents Chemother 53:4869-78. 2009
    ..The spectrum of treatment-selected mutations is changing as data for more individuals are collected, treatment exposures change, and the number of available sequences from non-subtype B viruses increases...
  17. pmc Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations
    Elizabeth Johnston
    Division of Infectious Diseases, Stanford University, Stanford, CA, USA
    AIDS 19:731-3. 2005
    ..Testing the activity of new antiretroviral compounds against this panel of drug-resistant clones will determine their relative activity against many clinically relevant NRTI-resistant viruses...
  18. ncbi request reprint Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversies
    Robert W Shafer
    Division of Infectious Diseases, Stanford University, Stanford, CA, USA
    Antivir Ther 13:59-68. 2008
    ..The process used to create a previously published list of drug resistance mutations for HIV-1 surveillance is reviewed and alternative approaches to this process are discussed...
  19. pmc Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance
    Elizabeth Johnston
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    Antimicrob Agents Chemother 48:4864-8. 2004
    ..In combination with other drug resistance mutations, L23I was associated with multidrug resistance and a compensatory increase in replication capacity...
  20. pmc Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance
    Robert J Gifford
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
    AIDS 22:717-25. 2008
    ..The potential impact of undetected lethal editing on genotypic estimation of transmitted drug resistance was assessed...
  21. pmc HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL
    Yumi Mitsuya
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford 94305, and Kaiser Permanente Medical Care Program Northern California, Oakland, CA, USA
    J Acquir Immune Defic Syndr 43:56-9. 2006
    ..Genotype validity was confirmed in 49 of 50 patients with a previous or follow-up genotype. The belief that genotypic resistance testing is unreliable in samples with low-level viremia should be reassessed...
  22. pmc Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
    Antimicrob Agents Chemother 48:3122-6. 2004
    ..Characterization of the phenotypic and clinical significance of these common patterns may lead to improved treatment recommendations for a large proportion of patients for whom antiretroviral therapy is failing...
  23. pmc Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations
    Elizabeth C Reuman
    Division of Infectious Diseases, Department of Medicine, Stanford University, 300 Pasteur Drive, Grant S 146, Stanford, CA 94305, USA
    J Antimicrob Chemother 65:1477-85. 2010
    ....
  24. pmc The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance
    Robert J Gifford
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
    Bioinformatics 25:1197-8. 2009
    ..Availability: http://cpr.stanford.edu/cpr/index.html...
  25. ncbi request reprint Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection
    Oliver Bembom
    Division of Biostatistics, University of California, Berkeley, CA, USA
    Stat Med 28:152-72. 2009
    ..This finding suggests that targeted estimation of variable importance represents a promising approach to biomarker discovery...
  26. pmc Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assay
    Amit Kapoor
    Department of Medicine, University of California, San Francisco, 94118, USA
    J Virol 78:7112-23. 2004
    ..The enhanced detection of minority drug resistance variants using a sequencing-based assay may improve the efficacy of genotype-assisted salvage therapies...
  27. pmc Genotypic predictors of human immunodeficiency virus type 1 drug resistance
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    Proc Natl Acad Sci U S A 103:17355-60. 2006
    ..Mutation regression coefficients showed that, within a drug class, cross-resistance patterns differ for different mutation subsets and that cross-resistance has been underestimated...
  28. pmc Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays
    Jie Zhang
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    J Acquir Immune Defic Syndr 38:439-44. 2005
    ..Although 2 widely used susceptibility assays have been developed, their precision and sensitivity have not been assessed...
  29. pmc Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment
    Yumi Mitsuya
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
    J Infect Dis 196:1177-9. 2007
    ..Most PI-treated patients should respond favorably to DRV-based salvage therapy...
  30. pmc Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine
    Michele W Tang
    Division Infectious Diseases, Department of Medicine, Stanford University, California 94305, USA
    J Infect Dis 207:S70-7. 2013
    ..However, because resistance testing is rarely available in resource-limited settings, it is critical to identify the cross-resistance patterns associated with first-line stavudine failure...
  31. pmc HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir
    Vici Varghese
    Department of Medicine, Stanford University School of Medicine, Stanford, California 94305, USA
    AIDS Res Hum Retroviruses 26:1323-6. 2010
    ..However, none of the major INI-resistance mutations was found to be polymorphic in either study and there were no significant changes in the prevalence of any of the minor INI-resistance mutations...
  32. pmc Protease and reverse transcriptase mutation patterns in HIV type 1 isolates from heavily treated persons: comparison of isolates from Northern California with isolates from other regions
    Matthew J Gonzales
    Division of Infestious Diseases, Department of Medicine, Stanford University Medical Center, Stanford, CA 94305, USA
    AIDS Res Hum Retroviruses 19:909-15. 2003
    ..The majority of clusters contained Northern California and literature sequences in similar proportions...
  33. pmc HIV-1 subtype B protease and reverse transcriptase amino acid covariation
    Soo Yon Rhee
    Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, United States of America
    PLoS Comput Biol 3:e87. 2007
    ..Whereas accessory nucleoside RT inhibitor-resistance mutations nearly always follow primary nucleoside RT inhibitor-resistance mutations, accessory PI-resistance mutations often preceded primary PI-resistance mutations...
  34. pmc Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing
    George L Melikian
    Department of Medicine, Stanford University, Stanford, CA, USA
    J Antimicrob Chemother 69:12-20. 2014
    ....
  35. pmc Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitors
    Vici Varghese
    Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
    J Acquir Immune Defic Syndr 52:309-15. 2009
    ..Therefore, we sought to determine how often NNRTI-resistant mutations other than K103N occur as minority variants in plasma samples for which standard genotypic resistance testing detects K103N alone...
  36. pmc Virologic efficacy of boosted double versus boosted single protease inhibitor therapy
    Maya L Petersen
    Division of Biostatistics, School of Public Health, University of California, Berkeley, CA 94720, USA
    AIDS 21:1547-54. 2007
    ..We compared the probability of attaining an undetectable HIV RNA level after using either boosted double or boosted single PI regimens...
  37. ncbi request reprint Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance
    Andre Altmann
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Antivir Ther 12:169-78. 2007
    ..The virus's evolutionary potential for escaping from drug pressure is explored as an additional predictor...
  38. pmc Super learning: an application to the prediction of HIV-1 drug resistance
    Sandra E Sinisi
    University of California, Berkeley, USA
    Stat Appl Genet Mol Biol 6:Article7. 2007
    ..Specifically, we apply the super learner to predict susceptibility to a specific protease inhibitor, nelfinavir, using a set of database-derived non-polymorphic treatment-selected mutations...
  39. pmc Viral population estimation using pyrosequencing
    Nicholas Eriksson
    Department of Statistics, University of Chicago, Chicago, Illinois, United States of America
    PLoS Comput Biol 4:e1000074. 2008
    ..Thus, pyrosequencing can be used for cost-effective estimation of the structure of virus populations, promising new insights into viral evolutionary dynamics and disease control strategies...