Published in PLoS One on December 22, 2011
Gene-wide identification of episodic selection. Mol Biol Evol (2015) 1.00
Online multi-modal robust non-negative dictionary learning for visual tracking. PLoS One (2015) 0.79
Discriminant projective non-negative matrix factorization. PLoS One (2013) 0.78
Superiority of a mechanistic codon substitution model even for protein sequences in phylogenetic analysis. BMC Evol Biol (2013) 0.76
MODELTEST: testing the model of DNA substitution. Bioinformatics (1998) 101.19
Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol (1981) 67.56
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci (1992) 44.38
Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst Biol (2004) 22.36
Learning the parts of objects by non-negative matrix factorization. Nature (1999) 21.77
ProtTest: selection of best-fit models of protein evolution. Bioinformatics (2005) 19.16
HyPhy: hypothesis testing using phylogenies. Bioinformatics (2004) 17.33
A tool for multiple sequence alignment. Proc Natl Acad Sci U S A (1989) 17.09
A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Mol Biol Evol (2001) 16.83
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Mol Biol Evol (2004) 7.34
Model of amino acid substitution in proteins encoded by mitochondrial DNA. J Mol Evol (1996) 3.53
Models of amino acid substitution and applications to mitochondrial protein evolution. Mol Biol Evol (1998) 3.03
Nonnegative matrix factorization: an analytical and interpretive tool in computational biology. PLoS Comput Biol (2008) 2.27
Different versions of the Dayhoff rate matrix. Mol Biol Evol (2004) 2.23
rtREV: an amino acid substitution matrix for inference of retrovirus and reverse transcriptase phylogeny. J Mol Evol (2002) 2.06
Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics (1998) 2.05
A maximum likelihood method for detecting directional evolution in protein sequences and its application to influenza A virus. Mol Biol Evol (2008) 1.96
A new approach to clustering the amino acids. J Theor Biol (1996) 1.62
HIV-specific probabilistic models of protein evolution. PLoS One (2007) 1.61
PANDIT: an evolution-centric database of protein and associated nucleotide domains with inferred trees. Nucleic Acids Res (2006) 1.58
CodonTest: modeling amino acid substitution preferences in coding sequences. PLoS Comput Biol (2010) 1.56
Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci (2008) 1.45
The complete mitochondrial DNA sequence of the shark Mustelus manazo: evaluating rooting contradictions to living bony vertebrates. Mol Biol Evol (1998) 1.28
Accounting for solvent accessibility and secondary structure in protein phylogenetics is clearly beneficial. Syst Biol (2010) 0.96
A new semiempirical codon substitution model based on principal component analysis of mammalian sequences. Mol Biol Evol (2011) 0.79
Detecting individual sites subject to episodic diversifying selection. PLoS Genet (2012) 3.77
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
Evolutionary fingerprinting of genes. Mol Biol Evol (2009) 1.64
Models of coding sequence evolution. Brief Bioinform (2008) 1.64
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
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
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
Genome-wide survey of allele-specific splicing in humans. BMC Genomics (2008) 0.97
Extensive purifying selection acting on synonymous sites in HIV-1 Group M sequences. Virol J (2008) 0.94
Maximum likelihood inference of imprinting and allele-specific expression from EST data. Bioinformatics (2006) 0.90
Epitope discovery with phylogenetic hidden Markov models. Mol Biol Evol (2010) 0.89
Benchmarking multi-rate codon models. PLoS One (2010) 0.84
Evidence of HIV-1 adaptation to host HLA alleles following chimp-to-human transmission. Virol J (2009) 0.81
Standard vaccines increase HIV-1 transcription during antiretroviral therapy. AIDS (2016) 0.77