Published in BMC Evol Biol on March 08, 2011
The continuing value of twin studies in the omics era. Nat Rev Genet (2012) 1.88
Analysis of high-depth sequence data for studying viral diversity: a comparison of next generation sequencing platforms using Segminator II. BMC Bioinformatics (2012) 1.59
The evolution of HIV: inferences using phylogenetics. Mol Phylogenet Evol (2011) 0.94
Towards a liquid self: how time, geography, and life experiences reshape the biological identity. Front Immunol (2014) 0.80
Clinical Determinants of HIV-1B Between-Host Evolution and their Association with Drug Resistance in Pediatric Patients. PLoS One (2016) 0.75
MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics (2003) 130.85
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
MODELTEST: testing the model of DNA substitution. Bioinformatics (1998) 101.19
BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol (2007) 74.13
Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
Relaxed phylogenetics and dating with confidence. PLoS Biol (2006) 37.68
MAFFT version 5: improvement in accuracy of multiple sequence alignment. Nucleic Acids Res (2005) 31.64
Viral dynamics in human immunodeficiency virus type 1 infection. Nature (1995) 28.54
TCS: a computer program to estimate gene genealogies. Mol Ecol (2000) 27.89
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol (2004) 22.36
Bayesian coalescent inference of past population dynamics from molecular sequences. Mol Biol Evol (2005) 18.57
Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc Natl Acad Sci U S A (2008) 16.54
Epigenetic differences arise during the lifetime of monozygotic twins. Proc Natl Acad Sci U S A (2005) 15.46
Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics (1998) 11.25
Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol (2005) 10.21
A cladistic analysis of phenotypic associations with haplotypes inferred from restriction endonuclease mapping and DNA sequence data. III. Cladogram estimation. Genetics (1992) 10.09
Evidence of HIV-1 adaptation to HLA-restricted immune responses at a population level. Science (2002) 9.17
Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics (2005) 8.62
LAMARC 2.0: maximum likelihood and Bayesian estimation of population parameters. Bioinformatics (2006) 6.49
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
HIV and SIV CTL escape: implications for vaccine design. Nat Rev Immunol (2004) 5.18
Potential applications and pitfalls of Bayesian inference of phylogeny. Syst Biol (2002) 4.66
HIV vaccine research: the way forward. Science (2008) 3.86
Antigen load and viral sequence diversification determine the functional profile of HIV-1-specific CD8+ T cells. PLoS Med (2008) 3.48
Genetic diversity and evolution of retroviruses. Curr Top Microbiol Immunol (1992) 2.92
Immunopathogenesis and immunotherapy in AIDS virus infections. Nat Med (2003) 2.79
Analysis of HIV-1 env gene sequences reveals evidence for a low effective number in the viral population. Proc Natl Acad Sci U S A (1997) 2.64
Phenotypic differences in genetically identical organisms: the epigenetic perspective. Hum Mol Genet (2005) 2.63
Recombination in evolutionary genomics. Annu Rev Genet (2002) 2.54
Parallel evolution of drug resistance in HIV: failure of nonsynonymous/synonymous substitution rate ratio to detect selection. Mol Biol Evol (1999) 2.32
Determinant of HIV-1 mutational escape from cytotoxic T lymphocytes. J Exp Med (2003) 2.17
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A (2009) 1.94
Immunopathogenesis of HIV infection. Annu Rev Microbiol (1996) 1.76
Constraints on HIV-1 evolution and immunodominance revealed in monozygotic adult twins infected with the same virus. J Exp Med (2006) 1.72
The epigenetic basis of twin discordance in age-related diseases. Pediatr Res (2007) 1.32
Genetic and stochastic influences on the interaction of human immunodeficiency virus type 1 and cytotoxic T lymphocytes in identical twins. J Virol (2005) 1.22
Mechanisms of pathogenesis and the evolution of parasite virulence. J Evol Biol (2008) 1.18
In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci U S A (2009) 0.96
Random T-cell receptor recruitment in human immunodeficiency virus type 1 (HIV-1)-specific CD8+ T cells from genetically identical twins infected with the same HIV-1 strain. J Virol (2007) 0.91
Disease progression and evolution of the HIV-1 env gene in 24 infected infants. Infect Genet Evol (2007) 0.87
Immunologic response to HIV. AIDS Clin Care (1998) 0.84
Evolutionary control of infectious disease: prospects for vectorborne and waterborne pathogens. Mem Inst Oswaldo Cruz (1999) 0.79
Immune responses and HIV: a little order from the chaos. J Exp Med (2006) 0.79
Evolutionary biology and the concept of disease. Med Health Care Philos (2000) 0.78
DAVID: Database for Annotation, Visualization, and Integrated Discovery. Genome Biol (2003) 84.79
jModelTest: phylogenetic model averaging. Mol Biol Evol (2008) 44.78
Identifying biological themes within lists of genes with EASE. Genome Biol (2003) 31.72
jModelTest 2: more models, new heuristics and parallel computing. Nat Methods (2012) 27.83
ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16
DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res (2007) 17.46
The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol (2007) 16.46
Initiation of Antiretroviral Therapy in Early Asymptomatic HIV Infection. N Engl J Med (2015) 15.06
Inflammatory and coagulation biomarkers and mortality in patients with HIV infection. PLoS Med (2008) 13.72
DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics (2007) 12.76
RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics (2010) 9.49
DAVID gene ID conversion tool. Bioinformation (2008) 9.16
ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics (2011) 8.68
New real-time reverse transcriptase-initiated PCR assay with single-copy sensitivity for human immunodeficiency virus type 1 RNA in plasma. J Clin Microbiol (2003) 8.25
Multiple, linked human immunodeficiency virus type 1 drug resistance mutations in treatment-experienced patients are missed by standard genotype analysis. J Clin Microbiol (2005) 7.91
Automated phylogenetic detection of recombination using a genetic algorithm. Mol Biol Evol (2006) 5.94
Broad and potent neutralization of HIV-1 by a gp41-specific human antibody. Nature (2012) 5.44
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
GARD: a genetic algorithm for recombination detection. Bioinformatics (2006) 4.88
ART suppresses plasma HIV-1 RNA to a stable set point predicted by pretherapy viremia. PLoS Pathog (2007) 4.82
Pharmacogenetic study of statin therapy and cholesterol reduction. JAMA (2004) 4.47
The causes and consequences of HIV evolution. Nat Rev Genet (2004) 4.34
Measuring therapeutic response in chronic graft-versus-host disease: National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease: IV. Response Criteria Working Group report. Biol Blood Marrow Transplant (2006) 4.09
New models for large prospective studies: is there a better way? Am J Epidemiol (2012) 3.85
An exact nonparametric method for inferring mosaic structure in sequence triplets. Genetics (2007) 3.76
Inflammation, coagulation and cardiovascular disease in HIV-infected individuals. PLoS One (2012) 3.68
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified. Proc Natl Acad Sci U S A (2008) 3.56
An evolutionary model-based algorithm for accurate phylogenetic breakpoint mapping and subtype prediction in HIV-1. PLoS Comput Biol (2009) 3.11
The effect of recombination on the accuracy of phylogeny estimation. J Mol Evol (2002) 3.11
The impact of species concept on biodiversity studies. Q Rev Biol (2004) 2.91
Selection and persistence of non-nucleoside reverse transcriptase inhibitor-resistant HIV-1 in patients starting and stopping non-nucleoside therapy. AIDS (2006) 2.71
Recombination in evolutionary genomics. Annu Rev Genet (2002) 2.54
Idiopathic CD4+ lymphocytopenia: natural history and prognostic factors. Blood (2008) 2.27
National Institutes of Health Consensus Development Project on Criteria for Clinical Trials in Chronic Graft-versus-Host Disease: VI. Design of Clinical Trials Working Group report. Biol Blood Marrow Transplant (2006) 2.24
Changes in inflammatory and coagulation biomarkers: a randomized comparison of immediate versus deferred antiretroviral therapy in patients with HIV infection. J Acquir Immune Defic Syndr (2011) 2.21
Accelerated approval of cancer drugs: improved access to therapeutic breakthroughs or early release of unsafe and ineffective drugs? J Clin Oncol (2009) 2.16
DAVID-WS: a stateful web service to facilitate gene/protein list analysis. Bioinformatics (2012) 2.14
A Randomized, Controlled Trial of ZMapp for Ebola Virus Infection. N Engl J Med (2016) 2.09
In vivo expansion of CD4CD45RO-CD25 T cells expressing foxP3 in IL-2-treated HIV-infected patients. J Clin Invest (2005) 1.96
HIV infection-associated immune activation occurs by two distinct pathways that differentially affect CD4 and CD8 T cells. Proc Natl Acad Sci U S A (2008) 1.95
TreeSAAP: selection on amino acid properties using phylogenetic trees. Bioinformatics (2003) 1.91
Subterranean phylogeography of freshwater crayfishes shows extensive gene flow and surprisingly large population sizes. Mol Ecol (2005) 1.90
Tuberculosis risk factors and mortality for HIV-infected persons receiving antiretroviral therapy in South Africa. AIDS (2010) 1.90
Tree scanning: a method for using haplotype trees in phenotype/genotype association studies. Genetics (2004) 1.87
Parallel evolution of the genetic code in arthropod mitochondrial genomes. PLoS Biol (2006) 1.85
Defective human immunodeficiency virus-specific CD8+ T-cell polyfunctionality, proliferation, and cytotoxicity are not restored by antiretroviral therapy. J Virol (2009) 1.84
Incomplete CD4 T cell recovery in HIV-1 infection after 12 months of highly active antiretroviral therapy is associated with ongoing increased CD4 T cell activation and turnover. J Acquir Immune Defic Syndr (2003) 1.82
IL-2-induced CD4+ T-cell expansion in HIV-infected patients is associated with long-term decreases in T-cell proliferation. Blood (2004) 1.82
Induction of prolonged survival of CD4+ T lymphocytes by intermittent IL-2 therapy in HIV-infected patients. J Clin Invest (2005) 1.82
High prevalence of osteonecrosis of the femoral head in HIV-infected adults. Ann Intern Med (2002) 1.74
The evaluation of subcutaneous proleukin (interleukin-2) in a randomized international trial: rationale, design, and methods of ESPRIT. Control Clin Trials (2002) 1.73
Population genetics of microbial pathogens estimated from multilocus sequence typing (MLST) data. Infect Genet Evol (2005) 1.72
When to start therapy for HIV infection: a swinging pendulum in search of data. Ann Intern Med (2003) 1.63
Pathoscope: species identification and strain attribution with unassembled sequencing data. Genome Res (2013) 1.62
Phylogeographic history of the land snail Candidula unifasciata (Helicellinae, Stylommatophora): fragmentation, corridor migration, and secondary contact. Evolution (2002) 1.62
A coalescent model of recombination hotspots. Genetics (2003) 1.60
Phylogenomics and molecular evolution of polyomaviruses. Adv Exp Med Biol (2006) 1.54
Pilot study of the effects of intermittent interleukin-2 on human immunodeficiency virus (HIV)-specific immune responses in patients treated during recently acquired HIV infection. J Infect Dis (2001) 1.54
Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae). Mol Phylogenet Evol (2007) 1.54
Bovine apolipoprotein B-100 is a dominant immunogen in therapeutic cell populations cultured in fetal calf serum in mice and humans. Blood (2007) 1.52
Characteristics and Clinical Management of a Cluster of 3 Patients With Ebola Virus Disease, Including the First Domestically Acquired Cases in the United States. Ann Intern Med (2015) 1.47
Phylogenetic models of molecular evolution: next-generation data, fit, and performance. J Mol Evol (2013) 1.45
Selection pressure on HIV-1 envelope by broadly neutralizing antibodies to the conserved CD4-binding site. J Virol (2012) 1.44
Cutting edge: L-selectin (CD62L) expression distinguishes small resting memory CD4+ T cells that preferentially respond to recall antigen. J Immunol (2003) 1.42
Cutting edge: Ku70 is a novel cytosolic DNA sensor that induces type III rather than type I IFN. J Immunol (2011) 1.41
A comparison of phylogenetic network methods using computer simulation. PLoS One (2008) 1.40
Characterization of the follicular dendritic cell reservoir of human immunodeficiency virus type 1. J Virol (2008) 1.40
Safety (toxicity), pharmacokinetics, immunogenicity, and impact on elements of the normal immune system of recombinant human IL-15 in rhesus macaques. Blood (2011) 1.39
Treatment of intestinal helminths does not reduce plasma concentrations of HIV-1 RNA in coinfected Zambian adults. J Infect Dis (2005) 1.37
A proof-of-concept study of short-cycle intermittent antiretroviral therapy with a once-daily regimen of didanosine, lamivudine, and efavirenz for the treatment of chronic HIV infection. J Infect Dis (2004) 1.37
Evolutionary biology in biodiversity science, conservation, and policy: a call to action. Evolution (2010) 1.36
Human immunodeficiency virus viremia induces plasmacytoid dendritic cell activation in vivo and diminished alpha interferon production in vitro. J Virol (2008) 1.36
IL-27, a novel anti-HIV cytokine, activates multiple interferon-inducible genes in macrophages. AIDS (2008) 1.33
Pre-ART levels of inflammation and coagulation markers are strong predictors of death in a South African cohort with advanced HIV disease. PLoS One (2012) 1.31
Macrophage-tropic simian/human immunodeficiency virus chimeras use CXCR4, not CCR5, for infections of rhesus macaque peripheral blood mononuclear cells and alveolar macrophages. J Virol (2003) 1.29
Detection of KIR3DS1 on the cell surface of peripheral blood NK cells facilitates identification of a novel null allele and assessment of KIR3DS1 expression during HIV-1 infection. J Immunol (2007) 1.29
Unraveling the evolutionary radiation of the thoracican barnacles using molecular and morphological evidence: a comparison of several divergence time estimation approaches. Syst Biol (2004) 1.28
Recodon: coalescent simulation of coding DNA sequences with recombination, migration and demography. BMC Bioinformatics (2007) 1.27
Human immunodeficiency virus type 1 derivative with 7% simian immunodeficiency virus genetic content is able to establish infections in pig-tailed macaques. J Virol (2007) 1.27
Explaining, predicting, and treating HIV-associated CD4 cell loss: after 25 years still a puzzle. JAMA (2006) 1.27
MtArt: a new model of amino acid replacement for Arthropoda. Mol Biol Evol (2006) 1.27
Loss of naïve cells accompanies memory CD4+ T-cell depletion during long-term progression to AIDS in Simian immunodeficiency virus-infected macaques. J Virol (2006) 1.27