Published in BMC Bioinformatics on August 03, 2010
Treatment-associated polymorphisms in protease are significantly associated with higher viral load and lower CD4 count in newly diagnosed drug-naive HIV-1 infected patients. Retrovirology (2012) 0.91
The individualized genetic barrier predicts treatment response in a large cohort of HIV-1 infected patients. PLoS Comput Biol (2013) 0.77
Estimating HIV-1 fitness characteristics from cross-sectional genotype data. PLoS Comput Biol (2014) 0.75
An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics (2005) 5.60
The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34
Update of the drug resistance mutations in HIV-1: Fall 2006. Top HIV Med (2006) 3.06
Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol (2003) 2.98
Drug susceptibility in HIV infection after viral rebound in patients receiving indinavir-containing regimens. JAMA (2000) 2.91
Secondary mutations in the protease region of human immunodeficiency virus and virologic failure in drug-naive patients treated with protease inhibitor-based therapy. J Infect Dis (2001) 2.50
HIV-1 genotypic resistance patterns predict response to saquinavir-ritonavir therapy in patients in whom previous protease inhibitor therapy had failed. Ann Intern Med (1999) 2.36
Genotypic changes in human immunodeficiency virus type 1 protease associated with reduced susceptibility and virologic response to the protease inhibitor tipranavir. J Virol (2006) 2.33
Human Immunodeficiency Virus Reverse Transcriptase and Protease Sequence Database: an expanded data model integrating natural language text and sequence analysis programs. Nucleic Acids Res (2001) 2.13
A genotypic drug resistance interpretation algorithm that significantly predicts therapy response in HIV-1-infected patients. Antivir Ther (2002) 1.92
Drug resistance in non-subtype B HIV-1. J Clin Virol (2004) 1.56
Protease mutation M89I/V is linked to therapy failure in patients infected with the HIV-1 non-B subtypes C, F or G. AIDS (2005) 1.41
Risk of failure in patients with 215 HIV-1 revertants starting their first thymidine analog-containing highly active antiretroviral therapy. AIDS (2004) 1.40
Updated European recommendations for the clinical use of HIV drug resistance testing. Antivir Ther (2004) 1.28
The calculated genetic barrier for antiretroviral drug resistance substitutions is largely similar for different HIV-1 subtypes. J Acquir Immune Defic Syndr (2006) 1.27
Analysis of HIV-1 pol sequences using Bayesian Networks: implications for drug resistance. Bioinformatics (2006) 1.24
Novel human immunodeficiency virus type 1 protease mutations potentially involved in resistance to protease inhibitors. Antimicrob Agents Chemother (2005) 1.23
HIV protease and reverse transcriptase variation and therapy outcome in antiretroviral-naive individuals from a large North American cohort. AIDS (2001) 1.10
Estimation of an in vivo fitness landscape experienced by HIV-1 under drug selective pressure useful for prediction of drug resistance evolution during treatment. Bioinformatics (2007) 0.99
Investigation of baseline susceptibility to protease inhibitors in HIV-1 subtypes C, F, G and CRF02_AG. Antivir Ther (2006) 0.97
Variant human immunodeficiency virus type 1 proteases and response to combination therapy including a protease inhibitor. Antimicrob Agents Chemother (2001) 0.90
Changing patterns in the selection of viral mutations among patients receiving nucleoside and nucleotide drug combinations directed against human immunodeficiency virus type 1 reverse transcriptase. Antimicrob Agents Chemother (2005) 0.90
Modelled in vivo HIV fitness under drug selective pressure and estimated genetic barrier towards resistance are predictive for virological response. Antivir Ther (2008) 0.87
Variability in the PR and RT genes of HIV-1 isolated from recently infected subjects. Antivir Chem Chemother (2004) 0.85
Intensive insulin therapy in the medical ICU. N Engl J Med (2006) 22.37
Human immunodeficiency virus reverse transcriptase and protease sequence database. Nucleic Acids Res (2003) 10.50
A human phenome-interactome network of protein complexes implicated in genetic disorders. Nat Biotechnol (2007) 9.90
BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis. Bioinformatics (2005) 9.84
The major genetic determinants of HIV-1 control affect HLA class I peptide presentation. Science (2010) 9.61
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One (2009) 8.37
DECIPHER: Database of Chromosomal Imbalance and Phenotype in Humans Using Ensembl Resources. Am J Hum Genet (2009) 7.61
Gene prioritization through genomic data fusion. Nat Biotechnol (2006) 7.48
PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res (2002) 6.43
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
An automated genotyping system for analysis of HIV-1 and other microbial sequences. Bioinformatics (2005) 5.60
Comparison of sequential three-drug regimens as initial therapy for HIV-1 infection. N Engl J Med (2003) 4.57
The molecular population genetics of HIV-1 group O. Genetics (2004) 4.53
SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics (2011) 4.41
Improving the accuracy of demographic and molecular clock model comparison while accommodating phylogenetic uncertainty. Mol Biol Evol (2012) 4.16
A Gibbs sampling method to detect overrepresented motifs in the upstream regions of coexpressed genes. J Comput Biol (2002) 4.05
HIV-1 protease and reverse transcriptase mutations for drug resistance surveillance. AIDS (2007) 3.94
Chromosome instability is common in human cleavage-stage embryos. Nat Med (2009) 3.85
Human T-lymphotropic virus 1: recent knowledge about an ancient infection. Lancet Infect Dis (2007) 3.80
Genotypic predictors of human immunodeficiency virus type 1 drug resistance. Proc Natl Acad Sci U S A (2006) 3.76
Mapping the origins and expansion of the Indo-European language family. Science (2012) 3.76
Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res (2003) 3.68
Update of the drug resistance mutations in HIV-1: March 2013. Top Antivir Med (2013) 3.58
Prevalence of drug-resistant HIV-1 variants in untreated individuals in Europe: implications for clinical management. J Infect Dis (2005) 3.52
Invasive aspergillosis in critically ill patients without malignancy. Am J Respir Crit Care Med (2004) 3.42
Incomplete reconstitution of T cell subsets on combination antiretroviral therapy in the AIDS Clinical Trials Group protocol 384. Clin Infect Dis (2009) 3.39
Comparison of changes in bone density and turnover with abacavir-lamivudine versus tenofovir-emtricitabine in HIV-infected adults: 48-week results from the ASSERT study. Clin Infect Dis (2010) 3.37
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
Versatile gene-specific sequence tags for Arabidopsis functional genomics: transcript profiling and reverse genetics applications. Genome Res (2004) 3.02
Mutation patterns and structural correlates in human immunodeficiency virus type 1 protease following different protease inhibitor treatments. J Virol (2003) 2.98
Computational detection of cis -regulatory modules. Bioinformatics (2003) 2.89
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
TOUCAN 2: the all-inclusive open source workbench for regulatory sequence analysis. Nucleic Acids Res (2005) 2.68
U.S. Human immunodeficiency virus type 1 epidemic: date of origin, population history, and characterization of early strains. J Virol (2003) 2.64
Transmission of drug-resistant HIV-1 is stabilizing in Europe. J Infect Dis (2009) 2.60
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
Galactomannan in bronchoalveolar lavage fluid: a tool for diagnosing aspergillosis in intensive care unit patients. Am J Respir Crit Care Med (2007) 2.41
Complete genomic sequence of human coronavirus OC43: molecular clock analysis suggests a relatively recent zoonotic coronavirus transmission event. J Virol (2005) 2.35
Invasive aspergillosis in the intensive care unit. Clin Infect Dis (2007) 2.34
Ancient hybridization and an Irish origin for the modern polar bear matriline. Curr Biol (2011) 2.33
ENDEAVOUR update: a web resource for gene prioritization in multiple species. Nucleic Acids Res (2008) 2.31
Tracing the origin and history of the HIV-2 epidemic. Proc Natl Acad Sci U S A (2003) 2.31
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
Genetic history of hepatitis C virus in East Asia. J Virol (2008) 2.20
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
Cytomegalovirus serostatus and outcome in nonimmunocompromised critically ill patients. Crit Care Med (2012) 2.14
Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol (2012) 2.13
INCLUSive: integrated clustering, upstream sequence retrieval and motif sampling. Bioinformatics (2002) 2.13
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
A standardized framework for accurate, high-throughput genotyping of recombinant and non-recombinant viral sequences. Nucleic Acids Res (2009) 2.06
Using ribosomal protein genes as reference: a tale of caution. PLoS One (2008) 2.06
Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol (2012) 2.02
Minority human immunodeficiency virus type 1 variants in antiretroviral-naive persons with reverse transcriptase codon 215 revertant mutations. J Virol (2008) 1.96
Predicting the prognosis of breast cancer by integrating clinical and microarray data with Bayesian networks. Bioinformatics (2006) 1.95
A genotypic drug resistance interpretation algorithm that significantly predicts therapy response in HIV-1-infected patients. Antivir Ther (2002) 1.92
Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog (2010) 1.88
Phylodynamics and human-mediated dispersal of a zoonotic virus. PLoS Pathog (2010) 1.83
Biclustering microarray data by Gibbs sampling. Bioinformatics (2003) 1.82
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
Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. J Acquir Immune Defic Syndr (2005) 1.80
HIV-1 integrase inhibitor resistance and its clinical implications. J Infect Dis (2011) 1.80
The HIV-1 reservoir in eight patients on long-term suppressive antiretroviral therapy is stable with few genetic changes over time. Proc Natl Acad Sci U S A (2013) 1.80
The calibrated population resistance tool: standardized genotypic estimation of transmitted HIV-1 drug resistance. Bioinformatics (2009) 1.80
Integrating influenza antigenic dynamics with molecular evolution. Elife (2014) 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
Single-cell chromosomal imbalances detection by array CGH. Nucleic Acids Res (2006) 1.78
Extended spectrum of HIV-1 reverse transcriptase mutations in patients receiving multiple nucleoside analog inhibitors. AIDS (2003) 1.78
Single-cell paired-end genome sequencing reveals structural variation per cell cycle. Nucleic Acids Res (2013) 1.77
Benchmarking the CATMA microarray. A novel tool for Arabidopsis transcriptome analysis. Plant Physiol (2005) 1.76
Prevalence and correlates of nonadherence to antiretroviral therapy in a population of HIV patients using Medication Event Monitoring System. AIDS Patient Care STDS (2004) 1.75
Ancient papillomavirus-host co-speciation in Felidae. Genome Biol (2007) 1.75
Recombination confounds the early evolutionary history of human immunodeficiency virus type 1: subtype G is a circulating recombinant form. J Virol (2007) 1.74
Three roads diverged? Routes to phylogeographic inference. Trends Ecol Evol (2010) 1.74
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
TXTGate: profiling gene groups with text-based information. Genome Biol (2004) 1.72