Published in Methods Mol Biol on January 01, 2009
Reemergence of enterovirus 71 in 2008 in taiwan: dynamics of genetic and antigenic evolution from 1998 to 2008. J Clin Microbiol (2009) 2.40
Genome-Wide Comparative Analysis of Chemosensory Gene Families in Five Tsetse Fly Species. PLoS Negl Trop Dis (2016) 1.43
Genetic diversity of human enterovirus 68 strains isolated in Kenya using the hypervariable 3'-end of VP1 gene. PLoS One (2014) 0.93
Genotypic and functional impact of HIV-1 adaptation to its host population during the North American epidemic. PLoS Genet (2014) 0.91
Motif-optimized subtype A HIV envelope-based DNA vaccines rapidly elicit neutralizing antibodies when delivered sequentially. Vaccine (2012) 0.89
Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals. BMC Evol Biol (2011) 0.87
Number of mutations within CTL-defined epitopes of the hepatitis B Virus (HBV) core region is associated with HBV disease progression. J Med Virol (2011) 0.85
Evolution of high mobility group nucleosome-binding proteins and its implications for vertebrate chromatin specialization. Mol Biol Evol (2014) 0.82
A novel mutant 10Ala/Arg together with mutant 144Ser/Arg of hepatitis B virus X protein involved in hepatitis B virus-related hepatocarcinogenesis in HepG2 cell lines. Cancer Lett (2015) 0.78
Not so pseudo: the evolutionary history of protein phosphatase 1 regulatory subunit 2 and related pseudogenes. BMC Evol Biol (2013) 0.78
The comparative study of five sex-determining proteins across insects unveils high rates of evolution at basal components of the sex determination cascade. Dev Genes Evol (2015) 0.77
Bioinformatic analysis of neurotropic HIV envelope sequences identifies polymorphisms in the gp120 bridging sheet that increase macrophage-tropism through enhanced interactions with CCR5. Virology (2015) 0.77
Molecular Epidemiology and Phylogenetic Analysis of Human Adenovirus Caused an Outbreak in Taiwan during 2011. PLoS One (2015) 0.77
The conserved Phe GH5 of importance for hemoglobin intersubunit contact is mutated in gadoid fish. BMC Evol Biol (2014) 0.76
Spatial Temporal Dynamics and Molecular Evolution of Re-Emerging Rabies Virus in Taiwan. Int J Mol Sci (2016) 0.75
Evolutionary Analyses and Natural Selection of Betaine-Homocysteine S-Methyltransferase (BHMT) and BHMT2 Genes. PLoS One (2015) 0.75
Tetrapod V1R-like ora genes in an early-diverging ray-finned fish species: the canonical six ora gene repertoire of teleost fish resulted from gene loss in a larger ancestral repertoire. BMC Genomics (2016) 0.75
Mitogenomics of southern hemisphere blue mussels (Bivalvia: Pteriomorphia): Insights into the evolutionary characteristics of the Mytilus edulis complex. Sci Rep (2016) 0.75
Human Sentinel Surveillance of Influenza and Other Respiratory Viral Pathogens in Border Areas of Western Cambodia. PLoS One (2016) 0.75
Evolution of Hemoglobin Genes in Codfishes Influenced by Ocean Depth. Sci Rep (2017) 0.75
Mechanistic insights into molecular evolution of species-specific differential glycosaminoglycan binding surfaces in growth-related oncogene chemokines. R Soc Open Sci (2017) 0.75
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (2005) 8.62
Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics (2010) 6.14
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
Evaluation of respondent-driven sampling. Epidemiology (2012) 4.75
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
Persistence of transmitted drug resistance among subjects with primary human immunodeficiency virus infection. J Virol (2008) 3.04
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
Characterization of human immunodeficiency virus type 1 (HIV-1) envelope variation and neutralizing antibody responses during transmission of HIV-1 subtype B. J Virol (2005) 2.83
Multiple emergences of genetically diverse amphibian-infecting chytrids include a globalized hypervirulent recombinant lineage. Proc Natl Acad Sci U S A (2011) 2.78
A genetic algorithm approach to detecting lineage-specific variation in selection pressure. Mol Biol Evol (2004) 2.65
Transmission fitness of drug-resistant human immunodeficiency virus and the prevalence of resistance in the antiretroviral-treated population. J Infect Dis (2003) 2.54
Adaptation to different human populations by HIV-1 revealed by codon-based analyses. PLoS Comput Biol (2006) 2.48
Immune-driven recombination and loss of control after HIV superinfection. J Exp Med (2008) 2.34
Phylodynamics of infectious disease epidemics. Genetics (2009) 2.15
Syringe possession arrests are associated with receptive syringe sharing in two Mexico-US border cities. Addiction (2007) 2.14
Lack of neutralizing antibody response to HIV-1 predisposes to superinfection. Virology (2006) 2.07
Coping with viral diversity in HIV vaccine design. PLoS Comput Biol (2007) 2.01
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
An evolutionary-network model reveals stratified interactions in the V3 loop of the HIV-1 envelope. PLoS Comput Biol (2007) 1.82
A public health model for the molecular surveillance of HIV transmission in San Diego, California. AIDS (2009) 1.81
Comparative study of methods for detecting sequence compartmentalization in human immunodeficiency virus type 1. J Virol (2007) 1.71
Long-term persistence of transmitted HIV drug resistance in male genital tract secretions: implications for secondary transmission. J Infect Dis (2007) 1.64
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Genetic attributes of cerebrospinal fluid-derived HIV-1 env. Brain (2006) 1.60
Herpes simplex virus type 2 infection does not influence viral dynamics during early HIV-1 infection. J Infect Dis (2007) 1.59
Simple epidemiological dynamics explain phylogenetic clustering of HIV from patients with recent infection. PLoS Comput Biol (2012) 1.51
A Dirichlet process model for detecting positive selection in protein-coding DNA sequences. Proc Natl Acad Sci U S A (2006) 1.47
A simple hierarchical approach to modeling distributions of substitution rates. Mol Biol Evol (2004) 1.42
Spidermonkey: rapid detection of co-evolving sites using Bayesian graphical models. Bioinformatics (2008) 1.40
Using respondent-driven sampling in a hidden population at risk of HIV infection: who do HIV-positive recruiters recruit? Sex Transm Dis (2009) 1.37
Phylogenetic analysis of population-based and deep sequencing data to identify coevolving sites in the nef gene of HIV-1. Mol Biol Evol (2009) 1.37
Individual and network factors associated with prevalent hepatitis C infection among rural Appalachian injection drug users. Am J Public Health (2012) 1.35
Respondent driven sampling--where we are and where should we be going? Sex Transm Infect (2012) 1.35
Adaptation to human populations is revealed by within-host polymorphisms in HIV-1 and hepatitis C virus. PLoS Pathog (2007) 1.31
Amprenavir-resistant HIV-1 exhibits lopinavir cross-resistance and reduced replication capacity. AIDS (2002) 1.28
Evolutionary interactions between N-linked glycosylation sites in the HIV-1 envelope. PLoS Comput Biol (2006) 1.25
Viral evolution during structured treatment interruptions in chronically human immunodeficiency virus-infected individuals. J Virol (2002) 1.24
Deep molecular characterization of HIV-1 dynamics under suppressive HAART. PLoS Pathog (2011) 1.21
Low-level plasma HIVs in patients on prolonged suppressive highly active antiretroviral therapy are produced mostly by cells other than CD4 T-cells. J Med Virol (2009) 1.19
Evaluation of the role of location and distance in recruitment in respondent-driven sampling. Int J Health Geogr (2011) 1.14
Beyond bushmeat: animal contact, injury, and zoonotic disease risk in Western Uganda. Ecohealth (2014) 1.13
Capture-recapture methods and respondent-driven sampling: their potential and limitations. Sex Transm Infect (2011) 1.13
Selection of drug-resistant HIV-1 mutants in response to repeated structured treatment interruptions. AIDS (2002) 1.12
Evolution of the interferon alpha gene family in eutherian mammals. Gene (2007) 1.12
Clinical, virologic, and immunologic correlates of HIV-1 intraclade B dual infection among men who have sex with men. AIDS (2012) 1.10
Using phylogeography to characterize the origins of the HIV-1 subtype F epidemic in Romania. Infect Genet Evol (2011) 1.07
HIV-1 clade B pol evolution following primary infection. PLoS One (2013) 1.07
Epidemiological bridging by injection drug use drives an early HIV epidemic. Epidemics (2010) 1.07
Phenotypic hypersusceptibility to multiple protease inhibitors and low replicative capacity in patients who are chronically infected with human immunodeficiency virus type 1. J Virol (2005) 1.05
Parsing social network survey data from hidden populations using stochastic context-free grammars. PLoS One (2009) 1.04
Detection in 2009 of the swine origin influenza A (H1N1) virus by a subtyping microarray. J Clin Microbiol (2009) 1.00
Transmitted drug resistance in the CFAR network of integrated clinical systems cohort: prevalence and effects on pre-therapy CD4 and viral load. PLoS One (2011) 0.99
Characteristics of recently HIV-infected men who use the Internet to find male sex partners and sexual practices with those partners. J Acquir Immune Defic Syndr (2006) 0.97
Evolutionary model selection with a genetic algorithm: a case study using stem RNA. Mol Biol Evol (2006) 0.97
Pleocytosis is associated with disruption of HIV compartmentalization between blood and cerebral spinal fluid viral populations. Virology (2008) 0.94
Genetic basis of hypersusceptibility to protease inhibitors and low replicative capacity of human immunodeficiency virus type 1 strains in primary infection. J Virol (2004) 0.93
Mixed adjuvant formulations reveal a new combination that elicit antibody response comparable to Freund's adjuvants. PLoS One (2012) 0.93
Respondent driven sampling: determinants of recruitment and a method to improve point estimation. PLoS One (2013) 0.93
Rapid social network assessment for predicting HIV and STI risk among men attending bars and clubs in San Diego, California. Sex Transm Infect (2010) 0.91
Sampling through time and phylodynamic inference with coalescent and birth-death models. J R Soc Interface (2014) 0.88
Can non-lytic CD8+ T cells drive HIV-1 escape? PLoS Pathog (2013) 0.87
Herpes simplex virus type 2 acquisition during recent HIV infection does not influence plasma HIV levels. J Acquir Immune Defic Syndr (2008) 0.86
Computational analysis and identification of amino acid sites in dengue E proteins relevant to development of diagnostics and vaccines. Virus Genes (2007) 0.86
Mapping protease inhibitor resistance to human immunodeficiency virus type 1 sequence polymorphisms within patients. J Virol (2007) 0.85
Human immunodeficiency virus-1 RNA levels in cerebrospinal fluid exhibit a set point in clinically stable patients not receiving antiretroviral therapy. J Infect Dis (2003) 0.85
Genomic characterization of two novel HIV-1 second-generation recombinant forms among men who have sex with men in Beijing, China. AIDS Res Hum Retroviruses (2015) 0.82
Molecular and contextual markers of hepatitis C virus and drug abuse. Mol Diagn Ther (2009) 0.80
Association of antiretroviral resistance genotypes with response to therapy--comparison of three models. Antivir Ther (2002) 0.80
Viral kinetics and hepatitis C. Hepatology (2003) 0.75
Genetic imprint of vaccination on simian/human immunodeficiency virus type 1 transmitted viral genomes in rhesus macaques. PLoS One (2013) 0.75