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Hiv-1 subtype b protease and reverse transcriptase amino acid covariation,” PLoS computational biology
, 2007
"... Despite the high degree of HIV-1 protease and reverse transcriptase (RT) mutation in the setting of antiretroviral therapy, the spectrum of possible virus variants appears to be limited by patterns of amino acid covariation. We analyzed patterns of amino acid covariation in protease and RT sequences ..."
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Cited by 10 (0 self)
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Despite the high degree of HIV-1 protease and reverse transcriptase (RT) mutation in the setting of antiretroviral therapy, the spectrum of possible virus variants appears to be limited by patterns of amino acid covariation. We analyzed patterns of amino acid covariation in protease and RT
transcriptase
"... Identification of a rare mutation at reverse transcriptase Lys65 (K65E) in HIV-1-infected patients failing on nucleos(t)ide reverse ..."
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Identification of a rare mutation at reverse transcriptase Lys65 (K65E) in HIV-1-infected patients failing on nucleos(t)ide reverse
Distinguishing Functional Amino Acid Covariation from Background Linkage Disequilibrium in HIV Protease and Reverse Transcriptase
"... Correlated amino acid mutation analysis has been widely used to infer functional interactions between different sites in a protein. However, this analysis can be confounded by important phylogenetic effects broadly classifiable as background linkage disequilibrium (BLD). We have systematically separ ..."
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Cited by 6 (0 self)
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or (S,S) pairs cannot. Our analysis of the pol gene — including the protease and the reverse transcriptase genes — in HIV reveals that (A,A) covariation levels are enormously higher than for either (A,S) or (S,S), and thus cannot be attributed to phylogenetic effects. The magnitude of these effects
transcriptase and
, 2003
"... protease inhibitors and is active against several drug-resistant HIV-1 strains in vitro ..."
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protease inhibitors and is active against several drug-resistant HIV-1 strains in vitro
Polymorphism in HIV-1 non-subtype B protease and reverse transcriptase and its potential impact on drug susceptibility and drug resistance evolution
- AIDS Reviews
"... HIV-1 non-subtype B viruses are predominant worldwide. At least 9 different HIV-1 group M subtypes and 14 circulating recombinant forms differ from one another by 10-15 % in their pol gene, which includes the coding regions for the viral protease and reverse transcriptase (RT), the current targets o ..."
Abstract
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Cited by 21 (0 self)
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HIV-1 non-subtype B viruses are predominant worldwide. At least 9 different HIV-1 group M subtypes and 14 circulating recombinant forms differ from one another by 10-15 % in their pol gene, which includes the coding regions for the viral protease and reverse transcriptase (RT), the current targets
Substitutions in the Reverse Transcriptase and Protease Genes of HIV-1 Subtype B in Untreated Individuals and Patients Treated With Antiretroviral Drugs
, 2005
"... The nucleotide transition G�A is known as a hypermutation due to its high prevalence in HIV-1 and other pathogens. However, the contribution of the G�A transition in the generation of drug resistance mutations is unknown. Our objective was to ascertain the rate of nucleotide substitutions in proteas ..."
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Cited by 2 (1 self)
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in protease (PR) and reverse transcriptase (RT) in both untreated and treated HIV-1 patients. Genotypic analysis was performed on viruses from both treated and untreated patients with subtype B infections. Nucleotide genomic diversity was compared with a consensus subtype B reference virus. Then
Transcriptase and Protease Inhibitors
, 2000
"... Porcine xenografts may offer a solution to the shortage of human donor allografts. However, all pigs contain the porcine endogenous retrovirus (PERV), raising concerns regarding the transmission of PERV and the possible development of disease in xenotransplant recipients. We evaluated 11 antiretrovi ..."
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antiretroviral drugs licensed for human immunodeficiency virus type 1 (HIV-1) therapy for their activities against PERV to assess their po-tential for clinical use. Fifty and 90 % inhibitory concentrations (IC50s and IC90s, respectively) of five nucleoside reverse transcriptase inhibitors (RTIs) were determined
an 8-Amino-Acid Insert in the Reverse Transcriptase
, 2004
"... Updated information and services can be found at: ..."
Large-scale simultaneous hypothesis testing: the choice of a null hypothesis
- JASA
, 2004
"... Current scientific techniques in genomics and image processing routinely produce hypothesis testing problems with hundreds or thousands of cases to consider simultaneously. This poses new difficulties for the statistician, but also opens new opportunities. In particular it allows empirical estimatio ..."
Abstract
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Cited by 300 (15 self)
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discovery rate to examine the inference issues. Two genomics problems are used as examples to show the importance of correctly choosing the null hypothesis. Key Words: local false discovery rate, empirical Bayes, microarray analysis, empirical null hypothesis, unobserved covariates
and Positive Fitness Mutations in HIV Protease and Reverse Transcriptase
, 2003
"... Updated information and services can be found at: ..."
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