Published in Mol Biol Evol on May 04, 2007
Estimating divergence times in large molecular phylogenies. Proc Natl Acad Sci U S A (2012) 13.49
EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates. Genome Res (2008) 12.72
High-resolution mapping of expression-QTLs yields insight into human gene regulation. PLoS Genet (2008) 9.68
A complete Neandertal mitochondrial genome sequence determined by high-throughput sequencing. Cell (2008) 6.98
Fast and slow implementations of relaxed-clock methods show similar patterns of accuracy in estimating divergence times. Mol Biol Evol (2011) 6.93
Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biol (2010) 5.39
ALTER: program-oriented conversion of DNA and protein alignments. Nucleic Acids Res (2010) 5.32
Performance of relaxed-clock methods in estimating evolutionary divergence times and their credibility intervals. Mol Biol Evol (2010) 5.13
Human T cell epitopes of Mycobacterium tuberculosis are evolutionarily hyperconserved. Nat Genet (2010) 4.94
PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions. Bioinformatics (2011) 4.50
The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan. Nat Genet (2013) 4.40
Species-specific activity of HIV-1 Vpu and positive selection of tetherin transmembrane domain variants. PLoS Pathog (2009) 4.18
The population genetics of dN/dS. PLoS Genet (2008) 3.88
Accelerated evolution of the Prdm9 speciation gene across diverse metazoan taxa. PLoS Genet (2009) 3.60
The banana (Musa acuminata) genome and the evolution of monocotyledonous plants. Nature (2012) 3.53
Bayesian random local clocks, or one rate to rule them all. BMC Biol (2010) 3.44
Epistasis as the primary factor in molecular evolution. Nature (2012) 3.34
A "Copernican" reassessment of the human mitochondrial DNA tree from its root. Am J Hum Genet (2012) 3.31
Genome-scale phylogenetic analyses of chikungunya virus reveal independent emergences of recent epidemics and various evolutionary rates. J Virol (2010) 3.18
The draft genome of a diploid cotton Gossypium raimondii. Nat Genet (2012) 3.18
Evolutionary dynamics of Clostridium difficile over short and long time scales. Proc Natl Acad Sci U S A (2010) 3.18
Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell (2011) 3.03
Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs. PLoS Biol (2010) 2.90
An uncorrelated relaxed-clock analysis suggests an earlier origin for flowering plants. Proc Natl Acad Sci U S A (2010) 2.83
Learning to count: robust estimates for labeled distances between molecular sequences. Mol Biol Evol (2009) 2.75
Genomic epidemiology of a dengue virus epidemic in urban Singapore. J Virol (2009) 2.74
Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny. Proc Biol Sci (2012) 2.68
Evolutionary and functional analyses of the interaction between the myeloid restriction factor SAMHD1 and the lentiviral Vpx protein. Cell Host Microbe (2012) 2.66
Null mutations in human and mouse orthologs frequently result in different phenotypes. Proc Natl Acad Sci U S A (2008) 2.60
On the diversity of malaria parasites in African apes and the origin of Plasmodium falciparum from Bonobos. PLoS Pathog (2010) 2.60
Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease. PLoS Pathog (2013) 2.58
The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res (2012) 2.55
The universal distribution of evolutionary rates of genes and distinct characteristics of eukaryotic genes of different apparent ages. Proc Natl Acad Sci U S A (2009) 2.50
Convergent evolution of metabolic roles in bacterial co-symbionts of insects. Proc Natl Acad Sci U S A (2009) 2.48
Exceptional diversity, non-random distribution, and rapid evolution of retroelements in the B73 maize genome. PLoS Genet (2009) 2.45
Evolution of human-specific neural SRGAP2 genes by incomplete segmental duplication. Cell (2012) 2.43
The malaria parasite Plasmodium vivax exhibits greater genetic diversity than Plasmodium falciparum. Nat Genet (2012) 2.43
PHAST and RPHAST: phylogenetic analysis with space/time models. Brief Bioinform (2010) 2.36
The rainbow trout genome provides novel insights into evolution after whole-genome duplication in vertebrates. Nat Commun (2014) 2.36
Analysis of Drosophila TRPA1 reveals an ancient origin for human chemical nociception. Nature (2010) 2.35
Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre. Appl Environ Microbiol (2009) 2.35
Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates. Proc Natl Acad Sci U S A (2008) 2.34
The yak genome and adaptation to life at high altitude. Nat Genet (2012) 2.34
Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana. Nature (2010) 2.34
Genomic variation in natural populations of Drosophila melanogaster. Genetics (2012) 2.33
Dynamics of dengue disease severity determined by the interplay between viral genetics and serotype-specific immunity. Sci Transl Med (2011) 2.29
Evolution and transmission of drug-resistant tuberculosis in a Russian population. Nat Genet (2014) 2.29
Large-scale reconstruction and phylogenetic analysis of metabolic environments. Proc Natl Acad Sci U S A (2008) 2.23
The origin and phylogeography of dog rabies virus. J Gen Virol (2008) 2.23
Gene discovery using massively parallel pyrosequencing to develop ESTs for the flesh fly Sarcophaga crassipalpis. BMC Genomics (2009) 2.21
Whole genome sequencing of multiple Leishmania donovani clinical isolates provides insights into population structure and mechanisms of drug resistance. Genome Res (2011) 2.21
Mosquito genomics. Highly evolvable malaria vectors: the genomes of 16 Anopheles mosquitoes. Science (2014) 2.21
Genetic variability of human respiratory syncytial virus A strains circulating in Ontario: a novel genotype with a 72 nucleotide G gene duplication. PLoS One (2012) 2.21
Long noncoding RNA genes: conservation of sequence and brain expression among diverse amniotes. Genome Biol (2010) 2.20
De novo analysis of transcriptome dynamics in the migratory locust during the development of phase traits. PLoS One (2010) 2.19
Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature (2010) 2.18
Genome-wide comparative analysis of the Brassica rapa gene space reveals genome shrinkage and differential loss of duplicated genes after whole genome triplication. Genome Biol (2009) 2.17
AIR: A batch-oriented web program package for construction of supermatrices ready for phylogenomic analyses. BMC Bioinformatics (2009) 2.17
Identification of evolutionarily conserved non-AUG-initiated N-terminal extensions in human coding sequences. Nucleic Acids Res (2011) 2.16
Gourds afloat: a dated phylogeny reveals an Asian origin of the gourd family (Cucurbitaceae) and numerous oversea dispersal events. Proc Biol Sci (2009) 2.16
Comparative genomics yields insights into niche adaptation of plant vascular wilt pathogens. PLoS Pathog (2011) 2.13
Protein kinase R reveals an evolutionary model for defeating viral mimicry. Nature (2008) 2.13
A heterozygous moth genome provides insights into herbivory and detoxification. Nat Genet (2013) 2.13
Formyl peptide receptors are candidate chemosensory receptors in the vomeronasal organ. Proc Natl Acad Sci U S A (2009) 2.11
Thermodynamic system drift in protein evolution. PLoS Biol (2014) 2.10
The duck genome and transcriptome provide insight into an avian influenza virus reservoir species. Nat Genet (2013) 2.10
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria). BMC Biol (2012) 2.08
Molecular phylogenetics: principles and practice. Nat Rev Genet (2012) 2.08
The consequences of genetic drift for bacterial genome complexity. Genome Res (2009) 2.06
Mutations in centrosomal protein CEP152 in primary microcephaly families linked to MCPH4. Am J Hum Genet (2010) 2.05
Virulence differences in Toxoplasma mediated by amplification of a family of polymorphic pseudokinases. Proc Natl Acad Sci U S A (2011) 2.02
Comparative analysis between homoeologous genome segments of Brassica napus and its progenitor species reveals extensive sequence-level divergence. Plant Cell (2009) 2.01
webPRANK: a phylogeny-aware multiple sequence aligner with interactive alignment browser. BMC Bioinformatics (2010) 1.99
Chromosomal redistribution of male-biased genes in mammalian evolution with two bursts of gene gain on the X chromosome. PLoS Biol (2010) 1.98
Angiosperm genome comparisons reveal early polyploidy in the monocot lineage. Proc Natl Acad Sci U S A (2009) 1.94
Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics. Science (2014) 1.94
The life cycle of Drosophila orphan genes. Elife (2014) 1.94
Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci U S A (2009) 1.94
Transcriptional diversity during lineage commitment of human blood progenitors. Science (2014) 1.93
Complete genome sequence and comparative metabolic profiling of the prototypical enteroaggregative Escherichia coli strain 042. PLoS One (2010) 1.90
PGDD: a database of gene and genome duplication in plants. Nucleic Acids Res (2012) 1.90
Hotspots of biased nucleotide substitutions in human genes. PLoS Biol (2009) 1.89
Massive turnover of functional sequence in human and other mammalian genomes. Genome Res (2010) 1.89
Molecular evolutionary consequences of niche restriction in Francisella tularensis, a facultative intracellular pathogen. PLoS Pathog (2009) 1.88
The western painted turtle genome, a model for the evolution of extreme physiological adaptations in a slowly evolving lineage. Genome Biol (2013) 1.87
The Awesome Power of Yeast Evolutionary Genetics: New Genome Sequences and Strain Resources for the Saccharomyces sensu stricto Genus. G3 (Bethesda) (2011) 1.86
The African Turquoise Killifish Genome Provides Insights into Evolution and Genetic Architecture of Lifespan. Cell (2015) 1.86
Isolation and characterization of adenoviruses persistently shed from the gastrointestinal tract of non-human primates. PLoS Pathog (2009) 1.85
KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genomics Proteomics Bioinformatics (2010) 1.85
Dating primate divergences through an integrated analysis of palaeontological and molecular data. Syst Biol (2010) 1.85
The evolutionary dynamics of human influenza B virus. J Mol Evol (2008) 1.84
The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine. Elife (2013) 1.84
Adaptive evolution of young gene duplicates in mammals. Genome Res (2009) 1.82
Major taste loss in carnivorous mammals. Proc Natl Acad Sci U S A (2012) 1.81
The genome of Prunus mume. Nat Commun (2012) 1.80
Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLoS Biol (2008) 1.80
A Phylogenetic Analysis of 34 Chloroplast Genomes Elucidates the Relationships between Wild and Domestic Species within the Genus Citrus. Mol Biol Evol (2015) 1.79
Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes. J Bacteriol (2008) 1.79
Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics (2010) 1.78
The bovine lactation genome: insights into the evolution of mammalian milk. Genome Biol (2009) 1.77
Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics. Mol Biol Evol (2007) 1.01