Research Topics
| Soo Yon RheeSummaryAffiliation: Stanford University Country: USA Publications
| Collaborators
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Detail Information
Publications
Multiple independent origins of a protease inhibitor resistance mutation in salvage therapy patientsAmit Kapoor
Blood Systems Research Institute, San Francisco, CA 94118, USA
Retrovirology 5:7. 2008....- Estimating the individualized HIV-1 genetic barrier to resistance using a nelfinavir fitness landscapeKristof 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... - Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitorsSoo 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%... - Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discoverySoo 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/... - HIV-1 protease mutations and protease inhibitor cross-resistanceSoo Yon Rhee
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
Antimicrob Agents Chemother 54:4253-61. 2010.... - HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypesSoo 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... - Predictive value of HIV-1 genotypic resistance test interpretation algorithmsSoo 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... - HIV-1 protease and reverse transcriptase mutations for drug resistance surveillanceRobert 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... - Consensus drug resistance mutations for epidemiological surveillance: basic principles and potential controversiesRobert 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... - Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutationsRajin 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... - Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistanceRobert 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... - The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistanceRobert 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... - Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutationsElizabeth 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.... - Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatmentYumi 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... - Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infectionOliver 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... - HIV-1 subtype B protease and reverse transcriptase amino acid covariationSoo 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... - HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravirVici 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... - Human immunodeficiency virus reverse transcriptase and protease sequence databaseSoo-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... - Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testingSoo-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... - Sequencing-based detection of low-frequency human immunodeficiency virus type 1 drug-resistant mutants by an RNA/DNA heteroduplex generator-tracking assayAmit 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... - HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillanceSoo-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... - HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mLYumi 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... - Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observationMatthew 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... - Minority variants associated with transmitted and acquired HIV-1 nonnucleoside reverse transcriptase inhibitor resistance: implications for the use of second-generation nonnucleoside reverse transcriptase inhibitorsVici 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... - Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutationsElizabeth 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... - Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistanceElizabeth 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... - Genotypic predictors of human immunodeficiency virus type 1 drug resistanceSoo-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... - N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failureYumi Mitsuya
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94305, USA
AIDS Res Hum Retroviruses 22:1300-5. 2006.... - Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assaysJie Zhang
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
J Acquir Immune Defic Syndr 38:439-44. 2005..CONCLUSION: The PhenoSense assay is more precise than the Antivirogram assay and superior at detecting resistance to abacavir, didanosine, and stavudine... - 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 regionsMatthew 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... - Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistanceAndre 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... - Super learning: an application to the prediction of HIV-1 drug resistanceSandra 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... - Virologic efficacy of boosted double versus boosted single protease inhibitor therapyMaya 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... - Viral population estimation using pyrosequencingNicholas 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...