Published in Mol Biol Evol on January 20, 2010
Correcting the bias of empirical frequency parameter estimators in codon models. PLoS One (2010) 1.30
Modeling HIV-1 drug resistance as episodic directional selection. PLoS Comput Biol (2012) 1.05
Detecting patches of protein sites of influenza A viruses under positive selection. Mol Biol Evol (2012) 0.95
Identification of broadly neutralizing antibody epitopes in the HIV-1 envelope glycoprotein using evolutionary models. Virol J (2013) 0.82
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
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Founder effects in the assessment of HIV polymorphisms and HLA allele associations. Science (2007) 4.60
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Transmission and accumulation of CTL escape variants drive negative associations between HIV polymorphisms and HLA. J Exp Med (2005) 3.68
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Site-to-site variation of synonymous substitution rates. Mol Biol Evol (2005) 2.74
Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog (2008) 2.59
Evolution of HLA-B*5703 HIV-1 escape mutations in HLA-B*5703-positive individuals and their transmission recipients. J Exp Med (2009) 2.39
An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol (2005) 2.19
HLA class I-driven evolution of human immunodeficiency virus type 1 subtype c proteome: immune escape and viral load. J Virol (2008) 2.14
Leveraging information across HLA alleles/supertypes improves epitope prediction. J Comput Biol (2007) 2.03
Viral replication capacity as a correlate of HLA B57/B5801-associated nonprogressive HIV-1 infection. J Immunol (2007) 1.89
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Structures of three HIV-1 HLA-B*5703-peptide complexes and identification of related HLAs potentially associated with long-term nonprogression. J Immunol (2005) 1.60
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An integrative bioinformatic approach for studying escape mutations in human immunodeficiency virus type 1 gag in the Pumwani Sex Worker Cohort. J Virol (2007) 1.10
Application of support vector machines for T-cell epitopes prediction. Bioinformatics (2003) 1.05
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Molecular evolution of human immunodeficiency virus type 1 upon transmission between human leukocyte antigen disparate donor-recipient pairs. PLoS One (2008) 0.96
Immunodominance and cross-reactivity of B5703-restricted CD8 T lymphocytes from HIV type 1 subtype C-infected Ethiopians. AIDS Res Hum Retroviruses (2005) 0.87
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
Detecting individual sites subject to episodic diversifying selection. PLoS Genet (2012) 3.77
A flexible R package for nonnegative matrix factorization. BMC Bioinformatics (2010) 3.28
Immune and Genetic Correlates of Vaccine Protection Against Mucosal Infection by SIV in Monkeys. Sci Transl Med (2011) 3.08
A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol (2011) 2.88
FUBAR: a fast, unconstrained bayesian approximation for inferring selection. Mol Biol Evol (2013) 2.73
Transmission of HIV-1 CTL escape variants provides HLA-mismatched recipients with a survival advantage. PLoS Pathog (2008) 2.59
Robust inference of positive selection from recombining coding sequences. Bioinformatics (2006) 2.43
Allele-specific transcript isoforms in human. FEBS Lett (2004) 2.38
Incidence of HIV-1 dual infection and its association with increased viral load set point in a cohort of HIV-1 subtype C-infected female sex workers. J Infect Dis (2004) 2.29
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HIV evolution in early infection: selection pressures, patterns of insertion and deletion, and the impact of APOBEC. PLoS Pathog (2009) 2.15
Rapid, complex adaptation of transmitted HIV-1 full-length genomes in subtype C-infected individuals with differing disease progression. AIDS (2013) 2.04
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Models of coding sequence evolution. Brief Bioinform (2008) 1.64
Genome-wide analysis of the structure of the South African Coloured Population in the Western Cape. Hum Genet (2010) 1.61
CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol (2010) 1.56
Frequent toggling between alternative amino acids is driven by selection in HIV-1. PLoS Pathog (2008) 1.49
A genomic portrait of haplotype diversity and signatures of selection in indigenous southern African populations. PLoS Genet (2015) 1.43
CellMix: a comprehensive toolbox for gene expression deconvolution. Bioinformatics (2013) 1.40
Impact of the presence of paralogs on sequence divergence in a set of mouse-human orthologs. Genome Res (2002) 1.38
Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study. Infect Genet Evol (2011) 1.33
Correcting the bias of empirical frequency parameter estimators in codon models. PLoS One (2010) 1.30
A model of directional selection applied to the evolution of drug resistance in HIV-1. Mol Biol Evol (2007) 1.27
Deep sequencing reveals minor protease resistance mutations in patients failing a protease inhibitor regimen. J Virol (2012) 1.15
Induced stem cell neoplasia in a cnidarian by ectopic expression of a POU domain transcription factor. Development (2011) 1.09
Phylogenetic relatedness of HIV-1 donor and recipient populations. J Infect Dis (2013) 1.05
Modeling HIV-1 drug resistance as episodic directional selection. PLoS Comput Biol (2012) 1.05
A plant natriuretic peptide-like gene in the bacterial pathogen Xanthomonas axonopodis may induce hyper-hydration in the plant host: a hypothesis of molecular mimicry. BMC Evol Biol (2004) 1.04
The shared genomic architecture of human nucleolar organizer regions. Genome Res (2013) 1.03
Genome-wide survey of allele-specific splicing in humans. BMC Genomics (2008) 0.97
Gene-set analysis is severely biased when applied to genome-wide methylation data. Bioinformatics (2013) 0.94
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. Virol J (2008) 0.94
Comparative evolutionary analysis of the FoxG1 transcription factor from diverse vertebrates identifies conserved recognition sites for microRNA regulation. Dev Genes Evol (2007) 0.92
Protein kinase C delta is essential for optimal macrophage-mediated phagosomal containment of Listeria monocytogenes. Proc Natl Acad Sci U S A (2007) 0.91
Maximum likelihood inference of imprinting and allele-specific expression from EST data. Bioinformatics (2006) 0.90
FRAGS: estimation of coding sequence substitution rates from fragmentary data. BMC Bioinformatics (2004) 0.87
The hidden geometries of the Arabidopsis thaliana epidermis. PLoS One (2012) 0.87
Plant nucleotide cyclases: an increasingly complex and growing family. Plant Signal Behav (2007) 0.86
Non-negative matrix factorization for learning alignment-specific models of protein evolution. PLoS One (2011) 0.86
Benchmarking multi-rate codon models. PLoS One (2010) 0.84
The miRNAome of the postpartum dairy cow liver in negative energy balance. BMC Genomics (2014) 0.84
CTL response to HIV type 1 subtype C is poorly predicted by known epitope motifs. AIDS Res Hum Retroviruses (2007) 0.82
Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission. Virol J (2009) 0.81
Inhibition of human BK polyomavirus replication by small noncoding RNAs. J Virol (2011) 0.80
The regulatory effect of miRNAs is a heritable genetic trait in humans. BMC Genomics (2012) 0.79
Inference of allele-specific expression from RNA-seq data. Methods Mol Biol (2014) 0.78
Standard vaccines increase HIV-1 transcription during antiretroviral therapy. AIDS (2016) 0.77
Alterations in hepatic miRNA expression during negative energy balance in postpartum dairy cattle. BMC Genomics (2014) 0.77
Duplication of the Asymmetric Leaves1/Rough Sheath 2/Phantastica (ARP) gene precedes the explosive radiation of the Ruschioideae. Dev Genes Evol (2009) 0.76
Integrative analysis of mRNA expression and half-life data reveals trans-acting genetic variants associated with increased expression of stable transcripts. PLoS One (2013) 0.75
Investigating the effect of paralogs on microarray gene-set analysis. BMC Bioinformatics (2011) 0.75
Intron Length Coevolution across Mammalian Genomes. Mol Biol Evol (2016) 0.75
Co-acting gene networks predict TRAIL responsiveness of tumour cells with high accuracy. BMC Genomics (2014) 0.75
Association between the 4 bp proinsulin gene insertion polymorphism (IVS-69) and body composition in black South African women. Obesity (Silver Spring) (2009) 0.75
Correction: A Database of Human Immune Receptor Alleles Recovered from Population Sequencing Data. J Immunol (2017) 0.75