Synonymous-non-synonymous mutation rates between sequences containing ambiguous nucleotides (Syn-SCAN).

PubWeight™: 1.27‹?› | Rank: Top 10%

🔗 View Article (PMC 4388054)

Published in Bioinformatics on June 01, 2002

Authors

Matthew J Gonzales1, Jonathan M Dugan, Robert W Shafer

Author Affiliations

1: Division of Infectious Diseases, Stanford University Medical Center, 300 Pasteur Drive, Room S-156, CA 94305, USA.

Articles citing this

Learning to count: robust estimates for labeled distances between molecular sequences. Mol Biol Evol (2009) 2.75

HIV sequence databases. AIDS Rev (2003) 2.20

Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation. J Infect Dis (2003) 1.42

High frequency of syncytium-inducing and CXCR4-tropic viruses among human immunodeficiency virus type 1 subtype C-infected patients receiving antiretroviral treatment. J Virol (2003) 1.40

Molecular footprint of drug-selective pressure in a human immunodeficiency virus transmission chain. J Virol (2005) 1.36

Laboratory-based surveillance and molecular epidemiology of influenza virus in Taiwan. J Clin Microbiol (2005) 1.26

Genetic diversity of the Leptospiral immunoglobulin-like (Lig) genes in pathogenic Leptospira spp. Infect Genet Evol (2008) 1.21

Sequence quality analysis tool for HIV type 1 protease and reverse transcriptase. AIDS Res Hum Retroviruses (2011) 1.16

Genetic characterization of hepatitis B virus in peripheral blood leukocytes: evidence for selection and compartmentalization of viral variants with the immune escape G145R mutation. J Virol (2009) 1.03

Diversity and evolution of the small multidrug resistance protein family. BMC Evol Biol (2009) 0.95

The distribution and evolutionary history of the PRP8 intein. BMC Evol Biol (2006) 0.91

Cryptic species of Paracoccidioides brasiliensis: impact on paracoccidioidomycosis immunodiagnosis. Mem Inst Oswaldo Cruz (2013) 0.89

Molecular evolution of the mtDNA encoded rps3 gene among filamentous ascomycetes fungi with an emphasis on the Ophiostomatoid fungi. J Mol Evol (2009) 0.88

HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL. J Acquir Immune Defic Syndr (2006) 0.85

Short communication: new HIV infections at Southern New England academic institutions: implications for prevention. AIDS Res Hum Retroviruses (2012) 0.84

GenColors-based comparative genome databases for small eukaryotic genomes. Nucleic Acids Res (2012) 0.83

Differential expression of duplicated opsin genes in two eyetypes of ostracod crustaceans. J Mol Evol (2004) 0.83

Analysis of selection pressure and mutational pattern of HIV type 1 reverse transcriptase region among treated and nontreated patients. AIDS Res Hum Retroviruses (2010) 0.75

Synonymous and nonsynonymous distances help untangle convergent evolution and recombination. Stat Appl Genet Mol Biol (2015) 0.75

Short communication: Nucleotide variation and positively selected sites in HIV type 1 reverse transcriptase among heterosexual transmission pairs. AIDS Res Hum Retroviruses (2010) 0.75

Articles by these authors

(truncated to the top 100)

Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res (2003) 10.50

The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61

Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One (2009) 8.37

Characterization of mutation spectra with ultra-deep pyrosequencing: application to HIV-1 drug resistance. Genome Res (2007) 5.95

Web resources for HIV type 1 genotypic-resistance test interpretation. Clin Infect Dis (2006) 5.90

Viral population estimation using pyrosequencing. PLoS Comput Biol (2008) 5.89

Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection. N Engl J Med (2003) 4.57

Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proc Natl Acad Sci U S A (2006) 3.76

Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med (2013) 3.58

Incomplete reconstitution of T cell subsets on combination antiretroviral therapy in the AIDS Clinical Trials Group protocol 384. Clin Infect Dis (2009) 3.39

Impact of HIV-1 subtype and antiretroviral therapy on protease and reverse transcriptase genotype: results of a global collaboration. PLoS Med (2005) 3.17

A highly prevalent and genetically diversified Picornaviridae genus in South Asian children. Proc Natl Acad Sci U S A (2008) 3.12

Ultra-deep pyrosequencing of hepatitis B virus quasispecies from nucleoside and nucleotide reverse-transcriptase inhibitor (NRTI)-treated patients and NRTI-naive patients. J Infect Dis (2009) 3.08

Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol (2003) 2.98

HIV-1 Protease and reverse-transcriptase mutations: correlations with antiretroviral therapy in subtype B isolates and implications for drug-resistance surveillance. J Infect Dis (2005) 2.86

Effect of baseline- and treatment-related factors on immunologic recovery after initiation of antiretroviral therapy in HIV-1-positive subjects: results from ACTG 384. J Acquir Immune Defic Syndr (2006) 2.56

Pharmacogenetics of long-term responses to antiretroviral regimens containing Efavirenz and/or Nelfinavir: an Adult Aids Clinical Trials Group Study. J Infect Dis (2005) 2.43

World Antimalarial Resistance Network (WARN) III: molecular markers for drug resistant malaria. Malar J (2007) 2.30

A transitional endogenous lentivirus from the genome of a basal primate and implications for lentivirus evolution. Proc Natl Acad Sci U S A (2008) 2.28

HIV sequence databases. AIDS Rev (2003) 2.20

Glucose metabolism, lipid, and body fat changes in antiretroviral-naive subjects randomized to nelfinavir or efavirenz plus dual nucleosides. AIDS (2005) 2.16

Simple PCR assays improve the sensitivity of HIV-1 subtype B drug resistance testing and allow linking of resistance mutations. PLoS One (2007) 2.09

Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. J Virol (2008) 1.96

Distribution of human immunodeficiency virus type 1 protease and reverse transcriptase mutation patterns in 4,183 persons undergoing genotypic resistance testing. Antimicrob Agents Chemother (2004) 1.82

HIV-1 integrase inhibitor resistance and its clinical implications. J Infect Dis (2011) 1.80

Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. J Acquir Immune Defic Syndr (2005) 1.80

The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics (2009) 1.80

Natural variation of HIV-1 group M integrase: implications for a new class of antiretroviral inhibitors. Retrovirology (2008) 1.79

HIV-1 subtype B protease and reverse transcriptase amino acid covariation. PLoS Comput Biol (2007) 1.78

Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. AIDS (2003) 1.78

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. J Acquir Immune Defic Syndr (2009) 1.73

Drug resistance mutations in HIV-1. Top HIV Med (2003) 1.72

HIV-1 antiretroviral resistance: scientific principles and clinical applications. Drugs (2012) 1.70

Comparison of the precision and sensitivity of the Antivirogram and PhenoSense HIV drug susceptibility assays. J Acquir Immune Defic Syndr (2005) 1.68

Prevalence of darunavir resistance-associated mutations: patterns of occurrence and association with past treatment. J Infect Dis (2007) 1.66

Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy. AIDS (2004) 1.65

Biomarker discovery using targeted maximum-likelihood estimation: application to the treatment of antiretroviral-resistant HIV infection. Stat Med (2009) 1.57

Long-term increase in CD4+ T-cell counts during combination antiretroviral therapy for HIV-1 infection. AIDS (2010) 1.54

HIV-1 protease mutations and protease inhibitor cross-resistance. Antimicrob Agents Chemother (2010) 1.53

Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol (2012) 1.48

A uniquely prevalent nonnucleoside reverse transcriptase inhibitor resistance mutation in Russian subtype A HIV-1 viruses. AIDS (2014) 1.47

Nucleic acid template and the risk of a PCR-Induced HIV-1 drug resistance mutation. PLoS One (2010) 1.46

A review of the virological efficacy of the 4 World Health Organization-recommended tenofovir-containing regimens for initial HIV therapy. Clin Infect Dis (2012) 1.46

Lack of detectable human immunodeficiency virus type 1 superinfection during 1072 person-years of observation. J Infect Dis (2003) 1.42

HIV-1 pol mutation frequency by subtype and treatment experience: extension of the HIVseq program to seven non-B subtypes. AIDS (2006) 1.40

Mitochondrial haplogroups and peripheral neuropathy during antiretroviral therapy: an adult AIDS clinical trials group study. AIDS (2005) 1.39

HIV-1 protease and reverse transcriptase mutation patterns responsible for discordances between genotypic drug resistance interpretation algorithms. J Acquir Immune Defic Syndr (2003) 1.38

HIV-1 subtype C reverse transcriptase and protease genotypes in Zimbabwean patients failing antiretroviral therapy. AIDS Res Hum Retroviruses (2002) 1.29

The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology (2012) 1.26

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. AIDS Res Hum Retroviruses (2003) 1.22

Public database for HIV drug resistance in southern Africa. Nature (2010) 1.21

Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. J Infect Dis (2009) 1.20

Evolution of primary protease inhibitor resistance mutations during protease inhibitor salvage therapy. Antimicrob Agents Chemother (2002) 1.20

Panel of prototypical infectious molecular HIV-1 clones containing multiple nucleoside reverse transcriptase inhibitor resistance mutations. AIDS (2005) 1.17

Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther (2007) 1.17

Trends in Genotypic HIV-1 Antiretroviral Resistance between 2006 and 2012 in South African Patients Receiving First- and Second-Line Antiretroviral Treatment Regimens. PLoS One (2013) 1.14

Development of elvitegravir resistance and linkage of integrase inhibitor mutations with protease and reverse transcriptase resistance mutations. PLoS One (2012) 1.11

Constrained patterns of covariation and clustering of HIV-1 non-nucleoside reverse transcriptase inhibitor resistance mutations. J Antimicrob Chemother (2010) 1.09

Sequence editing by Apolipoprotein B RNA-editing catalytic component [corrected] and epidemiological surveillance of transmitted HIV-1 drug resistance. AIDS (2008) 1.09

Rational use of antiretroviral therapy in low-income and middle-income countries: optimizing regimen sequencing and switching. AIDS (2008) 1.08

Whole-genome sequencing of the efficient industrial fuel-ethanol fermentative Saccharomyces cerevisiae strain CAT-1. Mol Genet Genomics (2012) 1.08

Discordances between interpretation algorithms for genotypic resistance to protease and reverse transcriptase inhibitors of human immunodeficiency virus are subtype dependent. Antimicrob Agents Chemother (2006) 1.08

Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis (2009) 1.07

Nucleoside reverse transcriptase inhibitor resistance mutations associated with first-line stavudine-containing antiretroviral therapy: programmatic implications for countries phasing out stavudine. J Infect Dis (2013) 1.06

Nonpolymorphic human immunodeficiency virus type 1 protease and reverse transcriptase treatment-selected mutations. Antimicrob Agents Chemother (2009) 1.04

Colinearity of reverse transcriptase inhibitor resistance mutations detected by population-based sequencing. J Acquir Immune Defic Syndr (2003) 1.04

Hemochromatosis (HFE) gene mutations and peripheral neuropathy during antiretroviral therapy. AIDS (2006) 1.03

Panel of prototypical raltegravir-resistant infectious molecular clones in a novel integrase-deleted cloning vector. Antimicrob Agents Chemother (2009) 1.03

Standardized comparison of the relative impacts of HIV-1 reverse transcriptase (RT) mutations on nucleoside RT inhibitor susceptibility. Antimicrob Agents Chemother (2012) 1.03

Multilocus genetic interactions and response to efavirenz-containing regimens: an adult AIDS clinical trials group study. Pharmacogenet Genomics (2006) 1.03

Non-nucleoside reverse transcriptase inhibitor (NNRTI) cross-resistance: implications for preclinical evaluation of novel NNRTIs and clinical genotypic resistance testing. J Antimicrob Chemother (2013) 1.02

Comparative evaluation of three computerized algorithms for prediction of antiretroviral susceptibility from HIV type 1 genotype. J Antimicrob Chemother (2003) 1.00

Predictive value of HIV-1 genotypic resistance test interpretation algorithms. J Infect Dis (2009) 1.00

Low-level persistence of drug resistance mutations in hepatitis B virus-infected subjects with a past history of Lamivudine treatment. Antimicrob Agents Chemother (2012) 0.99

Hepatitis B virus reverse transcriptase sequence variant database for sequence analysis and mutation discovery. Antiviral Res (2010) 0.99

A combined data mining approach for infrequent events: analyzing HIV mutation changes based on treatment history. Comput Syst Bioinformatics Conf (2006) 0.97

Prediction of HIV mutation changes based on treatment history. AMIA Annu Symp Proc (2006) 0.97

Subtle decreases in stavudine phenotypic susceptibility predict poor virologic response to stavudine monotherapy in zidovudine-experienced patients. J Acquir Immune Defic Syndr (2002) 0.94

Educational attainment and response to HAART during initial therapy for HIV-1 infection. J Psychosom Res (2007) 0.91

Identification of Ugandan HIV type 1 variants with unique patterns of recombination in pol involving subtypes A and D. AIDS Res Hum Retroviruses (2002) 0.91

HIV-1 integrase sequence variability in antiretroviral naïve patients and in triple-class experienced patients subsequently treated with raltegravir. AIDS Res Hum Retroviruses (2010) 0.90

Loss of protease dimerization inhibition activity of darunavir is associated with the acquisition of resistance to darunavir by HIV-1. J Virol (2011) 0.90

A multifaceted analysis of HIV-1 protease multidrug resistance phenotypes. BMC Bioinformatics (2011) 0.89

N88D facilitates the co-occurrence of D30N and L90M and the development of multidrug resistance in HIV type 1 protease following nelfinavir treatment failure. AIDS Res Hum Retroviruses (2006) 0.88

Comparison of the Mechanisms of Drug Resistance among HIV, Hepatitis B, and Hepatitis C. Viruses (2010) 0.87

Association of a novel human immunodeficiency virus type 1 protease substrate cleft mutation, L23I, with protease inhibitor therapy and in vitro drug resistance. Antimicrob Agents Chemother (2004) 0.87

HIV-1 drug resistance genotype results in patients with plasma samples with HIV-1 RNA levels less than 75 copies/mL. J Acquir Immune Defic Syndr (2006) 0.85

Lower prevalence of drug resistance mutations at first-line virological failure to first-line therapy with atripla vs. tenofovir + emtricitabine/lamivudine + efavirenz administered on a multiple tablet therapy. AIDS (2014) 0.85

Advantages of predicted phenotypes and statistical learning models in inferring virological response to antiretroviral therapy from HIV genotype. Antivir Ther (2009) 0.84

The efficacy of an anti-CD4 monoclonal antibody for HIV-1 treatment. Antiviral Res (2011) 0.83

The HIV-1 Non-subtype B Workgroup: an international collaboration for the collection and analysis of HIV-1 non-subtype B data. MedGenMed (2005) 0.83

A classification model for G-to-A hypermutation in hepatitis B virus ultra-deep pyrosequencing reads. Bioinformatics (2010) 0.82

Accuracy, precision, and consistency of expert HIV type 1 genotype interpretation: an international comparison (The GUESS Study). Clin Infect Dis (2005) 0.82

Cooperative effects of drug-resistance mutations in the flap region of HIV-1 protease. ACS Chem Biol (2012) 0.82

Oxidant stress and peripheral neuropathy during antiretroviral therapy: an AIDS clinical trials group study. J Acquir Immune Defic Syndr (2006) 0.82

Nonnucleoside reverse transcriptase inhibitor phenotypic hypersusceptibility can be demonstrated in different assays. J Acquir Immune Defic Syndr (2005) 0.81

Collinearity of protease mutations in HIV-1 samples with high-level protease inhibitor class resistance. J Antimicrob Chemother (2012) 0.81

Virologic efficacy of boosted double versus boosted single protease inhibitor therapy. AIDS (2007) 0.81

Panel of prototypical recombinant infectious molecular clones resistant to nevirapine, efavirenz, etravirine, and rilpivirine. Antimicrob Agents Chemother (2012) 0.81

HIV-1 transmission networks in a small world. J Infect Dis (2013) 0.80