Published in Mol Biol Evol on June 15, 2010
Multidimensional scaling reveals the main evolutionary pathways of class A G-protein-coupled receptors. PLoS One (2011) 0.86
Complex patterns of divergence among green-sensitive (RH2a) African cichlid opsins revealed by Clade model analyses. BMC Evol Biol (2012) 0.79
Interchanging functionality among homologous elongation factors using signatures of heterotachy. J Mol Evol (2013) 0.76
Understanding the functional difference between growth arrest-specific protein 6 and protein S: an evolutionary approach. Open Biol (2014) 0.76
Coevolution of URAT1 and Uricase during Primate Evolution: Implications for Serum Urate Homeostasis and Gout. Mol Biol Evol (2016) 0.76
Tissue-Specificity of Gene Expression Diverges Slowly between Orthologs, and Rapidly between Paralogs. PLoS Comput Biol (2016) 0.75
The evolution of novelty in conserved gene families. Int J Evol Biol (2012) 0.75
Further simulations and analyses demonstrate open problems of phylostratigraphy. Genome Biol Evol (2017) 0.75
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res (2004) 168.89
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol (2003) 102.57
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Statistical significance for genomewide studies. Proc Natl Acad Sci U S A (2003) 88.64
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
Finishing the euchromatic sequence of the human genome. Nature (2004) 41.40
APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics (2004) 39.31
Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol (2000) 35.86
Jalview Version 2--a multiple sequence alignment editor and analysis workbench. Bioinformatics (2009) 31.84
Initial sequence of the chimpanzee genome and comparison with the human genome. Nature (2005) 25.67
Ensembl 2009. Nucleic Acids Res (2008) 25.38
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature (2004) 21.40
Whole-genome shotgun assembly and analysis of the genome of Fugu rubripes. Science (2002) 20.59
The genome sequence of the malaria mosquito Anopheles gambiae. Science (2002) 20.36
Preservation of duplicate genes by complementary, degenerative mutations. Genetics (1999) 18.29
Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics (2009) 16.52
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
Insights into social insects from the genome of the honeybee Apis mellifera. Nature (2006) 13.67
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26
The draft genome of Ciona intestinalis: insights into chordate and vertebrate origins. Science (2002) 11.11
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Genome sequence of Aedes aegypti, a major arbovirus vector. Science (2007) 9.19
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Finishing a whole-genome shotgun: release 3 of the Drosophila melanogaster euchromatic genome sequence. Genome Biol (2002) 8.07
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
Natural history and evolutionary principles of gene duplication in fungi. Nature (2007) 7.26
Turning a hobby into a job: how duplicated genes find new functions. Nat Rev Genet (2008) 6.07
The medaka draft genome and insights into vertebrate genome evolution. Nature (2007) 5.77
The genome of the Western clawed frog Xenopus tropicalis. Science (2010) 4.70
Genome sequence, comparative analysis, and population genetics of the domestic horse. Science (2009) 4.41
Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases. Bioinformatics (2005) 3.62
Protein dynamism and evolvability. Science (2009) 3.57
Statistical methods for testing functional divergence after gene duplication. Mol Biol Evol (1999) 3.06
Consequences of genome duplication. Curr Opin Genet Dev (2007) 2.72
The genomic rate of adaptive evolution. Trends Ecol Evol (2006) 2.61
Heterotachy, an important process of protein evolution. Mol Biol Evol (2002) 2.34
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol (2006) 2.30
How confident can we be that orthologs are similar, but paralogs differ? Trends Genet (2009) 2.21
Databases of homologous gene families for comparative genomics. BMC Bioinformatics (2009) 2.01
Maximum-likelihood approach for gene family evolution under functional divergence. Mol Biol Evol (2001) 1.87
Predicting functional divergence in protein evolution by site-specific rate shifts. Trends Biochem Sci (2002) 1.77
A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol (2004) 1.70
A simple statistical method for estimating type-II (cluster-specific) functional divergence of protein sequences. Mol Biol Evol (2006) 1.63
Melamine deaminase and atrazine chlorohydrolase: 98 percent identical but functionally different. J Bacteriol (2001) 1.61
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
Rate of change of concomitantly variable codons. J Mol Evol (1971) 1.43
Function-structure analysis of proteins using covarion-based evolutionary approaches: Elongation factors. Proc Natl Acad Sci U S A (2001) 1.39
The quest for natural selection in the age of comparative genomics. Heredity (Edinb) (2007) 1.32
Many genes in fish have species-specific asymmetric rates of molecular evolution. BMC Genomics (2006) 1.27
Functional divergence in the caspase gene family and altered functional constraints: statistical analysis and prediction. Genetics (2001) 1.21
Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis. Mol Biol Evol (2008) 1.20
Testing the covarion hypothesis of molecular evolution. Mol Biol Evol (1995) 1.18
A covarion-based method for detecting molecular adaptation: application to the evolution of primate mitochondrial genomes. Proc Biol Sci (2002) 1.12
Asymmetric evolution in two fish-specifically duplicated receptor tyrosine kinase paralogons involved in teleost coloration. Mol Biol Evol (2006) 1.10
Modeling amino acid substitution patterns in orthologous and paralogous genes. Mol Phylogenet Evol (2006) 1.07
Evolutionary modeling of rate shifts reveals specificity determinants in HIV-1 subtypes. PLoS Comput Biol (2008) 1.05
Difficulties in testing for covarion-like properties of sequences under the confounding influence of changing proportions of variable sites. Mol Biol Evol (2008) 1.04
Conceptual bases for quantifying the role of the environment on gene evolution: the participation of positive selection and neutral evolution. Biol Rev Camb Philos Soc (2007) 1.01
The crystal structure of eEF1A refines the functional predictions of an evolutionary analysis of rate changes among elongation factors. Mol Biol Evol (2002) 0.94
Large-scale prediction of function shift in protein families with a focus on enzymatic function. Proteins (2005) 0.92
Heterotachy and functional shift in protein evolution. IUBMB Life (2003) 0.91
BADASP: predicting functional specificity in protein families using ancestral sequences. Bioinformatics (2005) 0.91
A method to predict residues conferring functional differences between related proteins: application to MAP kinase pathways. Protein Sci (2000) 0.90
Functional divergence prediction from evolutionary analysis: a case study of vertebrate hemoglobin. Mol Biol Evol (2003) 0.89
The C. savignyi genetic map and its integration with the reference sequence facilitates insights into chordate genome evolution. Genome Res (2008) 0.89
Evidence for an episodic model of protein sequence evolution. Biochem Soc Trans (2009) 0.84
Use with caution: developmental systems divergence and potential pitfalls of animal models. Yale J Biol Med (2009) 0.81
PROCOV: maximum likelihood estimation of protein phylogeny under covarion models and site-specific covarion pattern analysis. BMC Evol Biol (2009) 0.81
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita. Nat Biotechnol (2008) 5.19
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
Gene loss and evolutionary rates following whole-genome duplication in teleost fishes. Mol Biol Evol (2006) 2.30
How confident can we be that orthologs are similar, but paralogs differ? Trends Genet (2009) 2.21
Resolving the ortholog conjecture: orthologs tend to be weakly, but significantly, more similar in function than paralogs. PLoS Comput Biol (2012) 1.65
Evolutionary genomics of nuclear receptors: from twenty-five ancestral genes to derived endocrine systems. Mol Biol Evol (2004) 1.58
Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res (2008) 1.45
Developmental constraints on vertebrate genome evolution. PLoS Genet (2008) 1.43
Evidence for polygenic adaptation to pathogens in the human genome. Mol Biol Evol (2013) 1.16
Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. Brief Bioinform (2011) 1.15
The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in GC. Mol Biol Evol (2013) 1.14
An ontology to clarify homology-related concepts. Trends Genet (2010) 1.10
Correcting for the bias due to expression specificity improves the estimation of constrained evolution of expression between mouse and human. Bioinformatics (2012) 1.10
NUREBASE: database of nuclear hormone receptors. Nucleic Acids Res (2002) 1.08
When orthologs diverge between human and mouse. Brief Bioinform (2011) 1.07
vHOG, a multispecies vertebrate ontology of homologous organs groups. Bioinformatics (2012) 1.07
Neofunctionalization in vertebrates: the example of retinoic acid receptors. PLoS Genet (2006) 1.05
Age-dependent gain of alternative splice forms and biased duplication explain the relation between splicing and duplication. Genome Res (2010) 1.03
Community-wide plasmid gene mobilization and selection. ISME J (2013) 1.03
Selectome: a database of positive selection. Nucleic Acids Res (2008) 1.02
Molecular signaling in zebrafish development and the vertebrate phylotypic period. Evol Dev (2010) 1.01
Molecular evidence for a functional ecdysone signaling system in Brugia malayi. PLoS Negl Trop Dis (2010) 1.00
The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates. PLoS Genet (2013) 0.97
Homolonto: generating homology relationships by pairwise alignment of ontologies and application to vertebrate anatomy. Bioinformatics (2010) 0.95
A protein interaction atlas for the nuclear receptors: properties and quality of a hub-based dimerisation network. BMC Syst Biol (2007) 0.94
Selectome update: quality control and computational improvements to a database of positive selection. Nucleic Acids Res (2013) 0.93
Interactome mapping of the phosphatidylinositol 3-kinase-mammalian target of rapamycin pathway identifies deformed epidermal autoregulatory factor-1 as a new glycogen synthase kinase-3 interactor. Mol Cell Proteomics (2010) 0.92
Comparative analysis of human and mouse expression data illuminates tissue-specific evolutionary patterns of miRNAs. Nucleic Acids Res (2012) 0.92
Recent advances in biocuration: meeting report from the Fifth International Biocuration Conference. Database (Oxford) (2012) 0.89
Update of NUREBASE: nuclear hormone receptor functional genomics. Nucleic Acids Res (2004) 0.89
Rapid divergence of the ecdysone receptor in Diptera and Lepidoptera suggests coevolution between ECR and USP-RXR. Mol Biol Evol (2003) 0.89
Inventing a sex-specific gene: a conserved role of DMRT1 in teleost fishes plus a recent duplication in the medaka Oryzias latipes resulted in DMY. J Mol Evol (2003) 0.88
Nuclear receptors are markers of animal genome evolution. J Struct Funct Genomics (2003) 0.87
Meta-analysis of estrogen response in MCF-7 distinguishes early target genes involved in signaling and cell proliferation from later target genes involved in cell cycle and DNA repair. BMC Syst Biol (2011) 0.84
How much does the amphioxus genome represent the ancestor of chordates? Brief Funct Genomics (2012) 0.84
Evidence for an episodic model of protein sequence evolution. Biochem Soc Trans (2009) 0.84
Comparative genome analysis of Pseudomonas knackmussii B13, the first bacterium known to degrade chloroaromatic compounds. Environ Microbiol (2014) 0.83
Orthologues of the Drosophila melanogaster E75 molting control gene in the filarial parasites Brugia malayi and Dirofilaria immitis. Mol Biochem Parasitol (2007) 0.82
The challenge of modeling nuclear receptor regulatory networks in mammalian cells. Mol Cell Endocrinol (2010) 0.82
Evolution of the epithelial sodium channel and the sodium pump as limiting factors of aldosterone action on sodium transport. Physiol Genomics (2011) 0.82
gcodeml: a Grid-enabled tool for detecting positive selection in biological evolution. Stud Health Technol Inform (2012) 0.80
Phylogenetic code in the cloud - can it meet the expectations? Stud Health Technol Inform (2010) 0.79
Structural and evolutionary innovation of the heterodimerization interface between USP and the ecdysone receptor ECR in insects. Mol Biol Evol (2009) 0.79
Uncovering hidden duplicated content in public transcriptomics data. Database (Oxford) (2013) 0.79
A benchmark of gene expression tissue-specificity metrics. Brief Bioinform (2017) 0.78
Comparative modular analysis of gene expression in vertebrate organs. BMC Genomics (2012) 0.78
The expansion of amino-acid repeats is not associated to adaptive evolution in mammalian genes. BMC Genomics (2009) 0.78
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics (2016) 0.77
IQRray, a new method for Affymetrix microarray quality control, and the homologous organ conservation score, a new benchmark method for quality control metrics. Bioinformatics (2014) 0.76
DATABASE, The Journal of Biological Databases and Curation, is now the official journal of the International Society for Biocuration. Database (Oxford) (2013) 0.75
Perspective: from molecular endocrinology of mouse to genomic endocrinology of animals. Mol Cell Endocrinol (2008) 0.75