Published in Syst Biol on March 10, 2010
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Non-negative matrix factorization for learning alignment-specific models of protein evolution. PLoS One (2011) 0.86
Markovian and non-Markovian protein sequence evolution: aggregated Markov process models. J Mol Biol (2011) 0.84
Toward more accurate ancestral protein genotype-phenotype reconstructions with the use of species tree-aware gene trees. Mol Biol Evol (2014) 0.81
Evolutionary patchwork of an insecticidal toxin shared between plant-associated pseudomonads and the insect pathogens Photorhabdus and Xenorhabdus. BMC Genomics (2015) 0.79
Evidence of Statistical Inconsistency of Phylogenetic Methods in the Presence of Multiple Sequence Alignment Uncertainty. Genome Biol Evol (2015) 0.76
The phycocyanobilin chromophore of streptophyte algal phytochromes is synthesized by HY2. New Phytol (2017) 0.76
Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula. BMC Plant Biol (2016) 0.75
Ferredoxin-dependent bilin reductases in eukaryotic algae: Ubiquity and diversity. J Plant Physiol (2017) 0.75
Molecular evolution of type II MAGE genes from ancestral MAGED2 gene and their phylogenetic resolution of basal mammalian clades. Mamm Genome (2017) 0.75
Improved mitochondrial amino acid substitution models for metazoan evolutionary studies. BMC Evol Biol (2017) 0.75
A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol (2010) 53.37
SeaView version 4: A multiplatform graphical user interface for sequence alignment and phylogenetic tree building. Mol Biol Evol (2009) 21.24
Approximate likelihood-ratio test for branches: A fast, accurate, and powerful alternative. Syst Biol (2006) 12.96
An improved general amino acid replacement matrix. Mol Biol Evol (2008) 9.36
PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res (2005) 8.20
Fast and accurate phylogeny reconstruction algorithms based on the minimum-evolution principle. J Comput Biol (2002) 5.50
Estimating maximum likelihood phylogenies with PhyML. Methods Mol Biol (2009) 5.12
Modeling protein evolution with several amino acid replacement matrices depending on site rates. Mol Biol Evol (2012) 3.35
Theoretical foundation of the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting. Mol Biol Evol (2003) 3.26
Improving the efficiency of SPR moves in phylogenetic tree search methods based on maximum likelihood. Bioinformatics (2005) 2.70
Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Syst Biol (2011) 2.66
Genomics, biogeography, and the diversification of placental mammals. Proc Natl Acad Sci U S A (2007) 1.86
Consistency of topological moves based on the balanced minimum evolution principle of phylogenetic inference. IEEE/ACM Trans Comput Biol Bioinform (2009) 1.58
Identification of novel peptide hormones in the human proteome by hidden Markov model screening. Genome Res (2007) 1.50
Phylogenetic mixture models for proteins. Philos Trans R Soc Lond B Biol Sci (2008) 1.45
Empirical profile mixture models for phylogenetic reconstruction. Bioinformatics (2008) 1.43
SDM: a fast distance-based approach for (super) tree building in phylogenomics. Syst Biol (2006) 1.36
Duplication and inversion history of a tandemly repeated genes family. J Comput Biol (2007) 1.22
Efficient biased estimation of evolutionary distances when substitution rates vary across sites. Mol Biol Evol (2002) 1.14
Reconstructing the duplication history of tandemly repeated genes. Mol Biol Evol (2002) 1.08
Branch lengths on birth-death trees and the expected loss of phylogenetic diversity. Syst Biol (2011) 0.97
Improvement of distance-based phylogenetic methods by a local maximum likelihood approach using triplets. Mol Biol Evol (2002) 0.96
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data. BMC Bioinformatics (2008) 0.93
A fast and specific alignment method for minisatellite maps. Evol Bioinform Online (2007) 0.92
Getting a tree fast: Neighbor Joining, FastME, and distance-based methods. Curr Protoc Bioinformatics (2006) 0.91
FLU, an amino acid substitution model for influenza proteins. BMC Evol Biol (2010) 0.91
Detection of new protein domains using co-occurrence: application to Plasmodium falciparum. Bioinformatics (2009) 0.91
Deep conservation of human protein tandem repeats within the eukaryotes. Mol Biol Evol (2014) 0.91
Fast NJ-like algorithms to deal with incomplete distance matrices. BMC Bioinformatics (2008) 0.90
Discrimination of yeast genes involved in methionine and phosphate metabolism on the basis of upstream motifs. Bioinformatics (2005) 0.90
The origin and evolutionary history of HIV-1 subtype C in Senegal. PLoS One (2012) 0.89
Searching for virus phylotypes. Bioinformatics (2013) 0.89
A phylotype-based analysis highlights the role of drug-naive HIV-positive individuals in the transmission of antiretroviral resistance in the UK. AIDS (2015) 0.87
An efficient and accurate distance based algorithm to reconstruct tandem duplication trees. Bioinformatics (2002) 0.87
Sexually-transmitted/founder HIV-1 cannot be directly predicted from plasma or PBMC-derived viral quasispecies in the transmitting partner. PLoS One (2013) 0.83
A simple method to predict protein-binding from aligned sequences--application to MHC superfamily and beta2-microglobulin. Bioinformatics (2005) 0.83
Combinatorics of distance-based tree inference. Proc Natl Acad Sci U S A (2012) 0.83
Assessing functional annotation transfers with inter-species conserved coexpression: application to Plasmodium falciparum. BMC Genomics (2010) 0.82
The behavior of admixed populations in neighbor-joining inference of population trees. Pac Symp Biocomput (2013) 0.81
ReplacementMatrix: a web server for maximum-likelihood estimation of amino acid replacement rate matrices. Bioinformatics (2011) 0.81
EuPathDomains: the divergent domain database for eukaryotic pathogens. Infect Genet Evol (2010) 0.80
Using repeated measurements to validate hierarchical gene clusters. Bioinformatics (2008) 0.79
A Plasmodium falciparum FcB1-schizont-EST collection providing clues to schizont specific gene structure and polymorphism. BMC Genomics (2009) 0.79
Topological rearrangements and local search method for tandem duplication trees. IEEE/ACM Trans Comput Biol Bioinform (2006) 0.78
Robustness of phylogenetic inference based on minimum evolution. Bull Math Biol (2010) 0.78
Bamako 2009 conference on the bioinformatics of infectious diseases. Infect Genet Evol (2011) 0.77
Fitting hidden Markov models of protein domains to a target species: application to Plasmodium falciparum. BMC Bioinformatics (2012) 0.77
Computational discovery of regulatory elements in a continuous expression space. Genome Biol (2012) 0.77
In-depth analysis of HIV-1 drug resistance mutations in HIV-infected individuals failing first-line regimens in West and Central Africa. AIDS (2016) 0.77
Mitochondrial genes support a common origin of rodent malaria parasites and Plasmodium falciparum's relatives infecting great apes. BMC Evol Biol (2011) 0.76
FastMG: a simple, fast, and accurate maximum likelihood procedure to estimate amino acid replacement rate matrices from large data sets. BMC Bioinformatics (2014) 0.75
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Bioinformatics of African Pathogens and Vectors conference. Editorial. Infect Genet Evol (2008) 0.75