Research Topics
| ROBERT WILLIAM SHAFERSummaryAffiliation: Stanford University Country: USA Publications
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Publications
A multifaceted analysis of HIV-1 protease multidrug resistance phenotypesKathleen 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...- 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.... - 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%... - World Antimalarial Resistance Network (WARN) III: molecular markers for drug resistant malariaChristopher V Plowe
Center for Vaccine Development, University of Maryland School of Medicine, 685 West Baltimore Street, HSF1 480, Baltimore, Maryland 21201, USA
Malar J 6:121. 2007.... - 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... - Rationale and uses of a public HIV drug-resistance databaseRobert W Shafer
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
J Infect Dis 194:S51-8. 2006..Such genotype-treatment, genotype-phenotype, and genotype-outcome correlations are contained in the Stanford HIV RT and Protease Sequence Database and have specific usefulness... 
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...- Drug resistance and antiretroviral drug developmentRobert W Shafer
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
J Antimicrob Chemother 55:817-20. 2005..Clinical studies are required, however, to delineate the full spectrum of mutations responsible for resistance to a new drug and to identify the settings in which a new drug is likely to be most useful for salvage therapy... - HIV-1 drug resistance mutations: an updated framework for the second decade of HAARTRobert W Shafer
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA, USA
AIDS Rev 10:67-84. 2008..CCR5 inhibitor resistance results from mutations that promote gp120 binding to an inhibitor-bound CCR5 receptor or CXCR4 tropism; however, the genotypic correlates of these processes are not yet well characterized... - 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... - Comparison of four-drug regimens and pairs of sequential three-drug regimens as initial therapy for HIV-1 infectionRobert W Shafer
Stanford University Medical Center, Stanford, Calif, USA
N Engl J Med 349:2304-15. 2003..It is unclear whether therapy for human immunodeficiency virus type 1 (HIV-1) should be initiated with a four-drug or two sequential three-drug regimens... - 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... - Human immunodeficiency virus type 1 isolates with the reverse transcriptase (RT) mutation Q145M retain nucleoside and nonnucleoside RT inhibitor susceptibilityVici Varghese
Department of Medicine, Stanford University School of Medicine, Stanford, California, USA
Antimicrob Agents Chemother 53:2196-8. 2009..We report that Q145M and other Q145 mutations do not emerge with RT inhibitors nor decrease RT inhibitor susceptibility. Q145M should not, therefore, be considered an RT inhibitor resistance mutation... - Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutationsYumi Mitsuya
Department of Medicine, Division of Infectious Diseases, Stanford University Medical Center, Stanford, California 94305, USA
J Virol 82:10747-55. 2008.... - 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... - Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patientsSeverine Margeridon-Thermet
Department of Medicine, Stanford University, Stanford, CA, USA
J Infect Dis 199:1275-85. 2009..UDPS detected low-prevalence HBV variants with NRTI-resistance mutations, G-to-A hypermutation, and low-level dual genotype infection with a sensitivity not previously possible... - Case files from Stanford University Medical Center: Drug resistance testing in previously untreated patients with HIV--knowing what to look for and choosing appropriate therapyRobert W Shafer
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
MedGenMed 8:32. 2006 - Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistanceChunlin Wang
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, CA 94305, USA
Genome Res 17:1195-201. 2007..With appropriate analysis, ultra-deep pyrosequencing is a promising method for characterizing genetic diversity and detecting minor yet clinically relevant variants in biological samples with complex genetic populations... - HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithmsJaideep Ravela
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California 94301, USA
J Acquir Immune Defic Syndr 33:8-14. 2003..Determining the clinical significance of these mutation patterns responsible for interalgorithm discordances will improve interalgorithm concordance and the accuracy of genotypic resistance interpretation... - 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... - Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencingMatthew J Gonzales
Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
J Acquir Immune Defic Syndr 34:398-402. 2003.... - Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaborationRami Kantor
Division of Infectious Disease and Center for AIDS Research, Stanford University, Stanford, California, USA
PLoS Med 2:e112. 2005..The genetic differences among HIV-1 subtypes may be critical to clinical management and drug resistance surveillance as antiretroviral treatment is expanded to regions of the world where diverse non-subtype-B viruses predominate... - 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... - 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... - 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... - Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatmentsThomas D Wu
Department of Biochemistry, Stanford University, Stanford, California 94305, USA
J Virol 77:4836-47. 2003..The presence of mutational clusters provides insight into the complex mutational patterns required for HIV-1 protease inhibitor resistance... - Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group studyTodd Hulgan
Division of Infectious Diseases, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
AIDS 19:1341-9. 2005..The objective of this study was to determine if NRTI-associated peripheral neuropathy is associated with European mitochondrial haplogroups... - 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... - 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... - 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... 
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.... - Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutationVici Varghese
Department of Medicine, Stanford University School of Medicine, Stanford, California, United States of America
PLoS ONE 5:e10992. 2010..Several lines of evidence suggest that K65R is more common in HIV-1 subtype C than subtype B viruses... - 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.... - Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vectorElizabeth C Reuman
Department of Medicine, Stanford University School of Medicine, Division of Infectious Diseases, 300 Pasteur Drive, Grant Building, Room S 146, Stanford, CA 94305, USA
Antimicrob Agents Chemother 54:934-6. 2010..Investigational integrase inhibitors with activity against these clones are likely to retain activity against the most clinically relevant raltegravir-resistant variants... - 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... - 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... - 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... - 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... - Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapyRami Kantor
Division of Infectious Diseases and AIDS Research, Stanford University, Stanford, California 94301, USA
Antimicrob Agents Chemother 46:1086-92. 2002..The persistence of L90M, V82A/F/T, G48V, and I84V during salvage therapy suggests that these mutations play a role in clinical resistance to multiple PIs... - Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assaysNancy S Shulman
Center for AIDS Research, Division of Infectious Diseases, Stanford University, Stanford, CA 97305, USA
J Acquir Immune Defic Syndr 39:78-81. 2005..In fact, there was a report that a commercial multicycle assay did not readily detect hypersusceptibility... - 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... - 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... - Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapyRami Kantor
Division of Infectious Diseases, Center for AIDS Research, Stanford University, Stanford, California, USA
AIDS 18:1503-11. 2004..The frequency with which new drug-resistance mutations (DRM) developed and their potential consequences in patients continuing unchanged treatment despite persistent viremia were assessed... - Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitorsMatthew J Gonzales
Division of Infectious Diseases, Department of Medicine, Stanford University, CA, USA
AIDS 17:791-9. 2003..Most NRTI mutations group into one of three clusters, although several (e.g., M184V) occur in multiple mutational contexts... - HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapyRami Kantor
Division of Infectious Diseases and AIDS Research, Stanford University, California 94305, USA
AIDS Res Hum Retroviruses 18:1407-13. 2002..Comparison of subtype C RT and protease sequences with a large database of subtype B sequences identified subtype C-specific polymorphisms and candidate drug resistance mutations... - Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patientsNancy S Shulman
Stanford University School of Medicine, California 94305, USA
J Acquir Immune Defic Syndr 31:121-7. 2002..d4T susceptibility greater than 1.4-fold change was associated with failure to achieve significant viral load reduction after 8 weeks of d4T monotherapy... - Genotypic testing for human immunodeficiency virus type 1 drug resistanceRobert W Shafer
Division of Infectious Diseases and Geographic Medicine, Stanford University, Stanford, California 94305, USA
Clin Microbiol Rev 15:247-77. 2002..This review describes the genetic mechanisms of HIV-1 drug resistance and summarizes published data linking individual RT and protease mutations to in vitro and in vivo resistance to the currently available HIV drugs... - Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: an international comparison (The GUESS Study)Andrew R Zolopa
Stanford University School of Medicine, Stanford, CA 94305 5107, USA
Clin Infect Dis 41:92-9. 2005..We sought to determine how much agreement exists within a group of experts in the interpretation of complex genotypes... - The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B dataRami Kantor
Division of Infectious Diseases, Brown University, Providence, Rhode Island, USA
MedGenMed 7:71. 2005 - 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... - Case files from Stanford University Medical Center: ten years of HAART: a long wait for full HIV suppressionNancy Shulman
Division of Infectious Diseases, Department of Medicine, Stanford University, Stanford, California, USA
MedGenMed 9:10. 2007 - 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... - Web resources for HIV type 1 genotypic-resistance test interpretationTommy F Liu
Division of Infectious Diseases, Stanford University, Stanford, California 94301, USA
Clin Infect Dis 42:1608-18. 2006..We describe the scientific principles of HIV-1 genotypic-resistance test interpretation and the most commonly used Web-based resources for clinicians ordering genotypic drug-resistance tests... - Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosidesMichael P Dube
Division of Infectious Diseases, Indiana University, Indianapolis, Indiana, USA
AIDS 19:1807-18. 2005..To determine if particular components of antiretroviral drug regimens are associated with greater insulin resistance, dyslipidemia, and peripheral lipoatrophy... - 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.... - Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapyAsha R Kallianpur
Department of Medicine, Divisions of General Internal Medicine and Public Health, Nashville, TN, USA
AIDS 20:1503-13. 2006..Since iron deficiency is associated with some types of PN, and iron is essential for mitochondrial function, we tested the hypothesis that hemochromatosis (HFE) gene mutations influence susceptibility to NRTI-induced PN... - 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... - Butting heads with resistanceRobert W Shafer
Stanford University School of Medicine, Stanford, California, USA
IAPAC Mon 12:180-9. 2006 - 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... - Case files from Stanford University Medical Center: the initial presentation of HIV-1 infection--where public and personal health meetMinghsun Liu
Division of Infectious Diseases, Stanford University Medical Center, Stanford, California, USA
MedGenMed 8:24. 2006 - Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN)Matthew J Gonzales
Division of Infectious Diseases, Stanford University Medical Center, 300 Pasteur Drive, Room S-156, CA 94305, USA
Bioinformatics 18:886-7. 2002..AVAILABILITY: Syn-SCAN is implemented on the web and can be downloaded from http://hivdb.stanford.edu... - A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolutionRobert J Gifford
Division of Infectious Diseases, Stanford University, Stanford, CA 94305, USA
Proc Natl Acad Sci U S A 105:20362-7. 2008..The discovery of pSIVgml illustrates the utility of endogenous sequences for the study of contemporary retroviruses and indicates that primate lentiviruses may be considerably older and more broadly distributed than previously thought... - Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotypeMaurizio Zazzi
Department of Molecular Biology, University of Siena, Siena, Italy
J Antimicrob Chemother 53:356-60. 2004..To compare three methods for using HIV-1 genotype to predict antiretroviral drug susceptibility... - 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... - Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and DSusan H Eshleman
Department of Pathology, Johns Hopkins Medical Institutions, Ross Building 646, 720 Rutland Avenue, Baltimore, MD 21205, USA
AIDS Res Hum Retroviruses 18:507-11. 2002..The large number of different types of pol recombinants identified suggests that recombination occurs readily in the pol region. Perinatal transmission of the recombinant viruses demonstrates their evolutionary stability... - 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... - Educational attainment and response to HAART during initial therapy for HIV-1 infectionLinda G Marc
Cornell HIV Clinical Trials Unit, New York, NY, USA
J Psychosom Res 63:207-16. 2007.... - Reverse transcriptase and protease sequence evolution in two HIV-1-infected couplesSarah Palmer
HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702 1201, USA
J Acquir Immune Defic Syndr 31:285-90. 2002.... - Pharmacokinetics of nelfinavir and efavirenz in antiretroviral-naive, human immunodeficiency virus-infected subjects when administered alone or in combination with nucleoside analog reverse transcriptase inhibitorsPatrick F Smith
Adult ACTG Pharmacology Support Laboratory, Laboratory for Antiviral Research, Department of Pharmacy Practice, School of Pharmacy and Pharmaceutical Sciences, University at Buffalo, Buffalo, NY 12460, USA
Antimicrob Agents Chemother 49:3558-61. 2005..There were no significant differences in efavirenz pharmacokinetics... - Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group studyAlison A Motsinger
Vanderbilt University School of Medicine, Nashville, Tennessee 37203, USA
Pharmacogenet Genomics 16:837-45. 2006..We examined whether long-term responses to efavirenz, and/or plasma efavirenz exposure, are better predicted by multilocus genetic interactions than by individual polymorphisms... - Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependentJoke Snoeck
Rega Institute for Medical Research, Minderbroedersstraat 10, 3000 Leuven, Belgium
Antimicrob Agents Chemother 50:694-701. 2006..It is not yet known whether therapy response is subtype dependent, but the advice given to clinicians based on a genotypic interpretation algorithm differs according to the subtype... - Drug resistance mutations in HIV-1Jonathan M Schapiro
Vanderbilt University Medical Center, Nashville, TN, USA
Top HIV Med 11:92-6. 2003 - Pharmacogenetics of long-term responses to antiretroviral regimens containing Efavirenz and/or Nelfinavir: an Adult Aids Clinical Trials Group StudyDavid W Haas
Vanderbilt University School of Medicine, Nashville, TN 37203, USA
J Infect Dis 192:1931-42. 2005..Nelfinavir is a substrate for P-glycoprotein, which is encoded by MDR1. The present study examined associations between genetic variants and long-term responses to treatment... - HIV sequence databasesCarla Kuiken
Los Alamos National Laboratory, Los Alamos, NM 87545, USA
AIDS Rev 5:52-61. 2003..The types of data and services these two databases offer, the tools they provide, and the way they are set up and operated are described in detail... - Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapineDenise Lecossier
INSERM U552, , Paris, France
J Acquir Immune Defic Syndr 38:37-42. 2005..These findings support the idea that minority viral populations with distinct resistance genotypes, although undetectable by standard genotyping, can contribute to the failure of salvage regimens... - Comparison of sequential three-drug regimens as initial therapy for HIV-1 infectionGregory K Robbins
Harvard Medical School, Boston, USA
N Engl J Med 349:2293-303. 2003..The optimal sequencing of antiretroviral regimens for the treatment of infection with human immunodeficiency virus type 1 (HIV-1) is unknown. We compared several different antiretroviral treatment strategies... - Algorithm specification interface for human immunodeficiency virus type 1 genotypic interpretationBradley J Betts
J Clin Microbiol 41:2792-4. 2003 - Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: results from ACTG 384Rajesh T Gandhi
Massachusetts General Hospital, Boston, MA, USA
J Acquir Immune Defic Syndr 42:426-34. 2006..To assess the effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy (ART)...
Research Grants
- Public HIV Drug Resistance DatabaseRobert Shafer; Fiscal Year: 2009..UCL is on the forefront of research into the problem of transmitted drug resistance and Oxford University is on the forefront of research on virus evolution and population genetics. ..
- Public HIV Drug Resistance DatabaseRobert Shafer; Fiscal Year: 2007..UCL is on the forefront of research into the problem of transmitted drug resistance and Oxford University is on the forefront of research on virus evolution and population genetics. ..
- Identification of Mulit-Drug Resistant HIV-1 IsolatesRobert Shafer; Fiscal Year: 2007....
- IDENTIFICATION OF MULTIDRUG RESISTANT HIV1 ISOLATESRobert Shafer; Fiscal Year: 2001..A set of well-characterized multidrug-resistance HIV-1 isolates will also be of the utmost value to researchers in the areas of antiretroviral drug development and drug resistance. ..
- Public HIV Drug Resistance DatabaseROBERT WILLIAM SHAFER; Fiscal Year: 2010..UCL is on the forefront of research into the problem of transmitted drug resistance and Oxford University is on the forefront of research on virus evolution and population genetics. ..