Published in PLoS Biol on January 25, 2005
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
Detection of nonneutral substitution rates on mammalian phylogenies. Genome Res (2009) 12.58
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Bias of selection on human copy-number variants. PLoS Genet (2006) 4.44
Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet (2009) 3.68
The distribution of fitness effects of new deleterious amino acid mutations in humans. Genetics (2006) 3.63
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
Origins, evolution, and phenotypic impact of new genes. Genome Res (2010) 2.98
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison. Genome Res (2006) 2.64
Evolution in health and medicine Sackler colloquium: Genetic architecture of a complex trait and its implications for fitness and genome-wide association studies. Proc Natl Acad Sci U S A (2010) 2.27
The QTN program and the alleles that matter for evolution: all that's gold does not glitter. Evolution (2011) 2.23
More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc Natl Acad Sci U S A (2007) 2.00
The new mutation theory of phenotypic evolution. Proc Natl Acad Sci U S A (2007) 1.97
Understanding the evolutionary fate of finite populations: the dynamics of mutational effects. PLoS Biol (2007) 1.95
The scale of mutational variation in the murid genome. Genome Res (2005) 1.95
Genomic analysis of estrogen cascade reveals histone variant H2A.Z associated with breast cancer progression. Mol Syst Biol (2008) 1.89
Widespread ectopic expression of olfactory receptor genes. BMC Genomics (2006) 1.80
The complete sequence of the smallest known nuclear genome from the microsporidian Encephalitozoon intestinalis. Nat Commun (2010) 1.75
Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res (2007) 1.75
Heterotachy in mammalian promoter evolution. PLoS Genet (2006) 1.71
The origins and impact of primate segmental duplications. Trends Genet (2009) 1.69
Explaining human uniqueness: genome interactions with environment, behaviour and culture. Nat Rev Genet (2008) 1.67
Impact of mating systems on patterns of sequence polymorphism in flowering plants. Proc Biol Sci (2006) 1.62
Heterogeneous genomic molecular clocks in primates. PLoS Genet (2006) 1.55
Evolutionary turnover of mammalian transcription start sites. Genome Res (2006) 1.51
Evolutionary constraints in conserved nongenic sequences of mammals. Genome Res (2005) 1.50
Genomic selective constraints in murid noncoding DNA. PLoS Genet (2006) 1.46
Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol (2006) 1.46
Adaptations to fluctuating selection in Drosophila. Proc Natl Acad Sci U S A (2007) 1.45
Selective constraint on noncoding regions of hominid genomes. PLoS Comput Biol (2005) 1.32
Chromosomal inversions between human and chimpanzee lineages caused by retrotransposons. PLoS One (2008) 1.32
Duplication and positive selection among hominin-specific PRAME genes. BMC Genomics (2005) 1.29
Darwin in mind: new opportunities for evolutionary psychology. PLoS Biol (2011) 1.29
Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci U S A (2007) 1.28
Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet (2014) 1.25
The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proc Natl Acad Sci U S A (2007) 1.24
Housekeeping genes tend to show reduced upstream sequence conservation. Genome Biol (2007) 1.16
Phylogenomics of primates and their ancestral populations. Genome Res (2009) 1.12
A genome-wide screen for noncoding elements important in primate evolution. BMC Evol Biol (2008) 1.12
Viral ancestors of antiviral systems. Viruses (2011) 1.11
MCALIGN2: faster, accurate global pairwise alignment of non-coding DNA sequences based on explicit models of indel evolution. BMC Bioinformatics (2006) 1.08
No effect of recombination on the efficacy of natural selection in primates. Genome Res (2008) 1.05
Clustering of codons with rare cognate tRNAs in human genes suggests an extra level of expression regulation. PLoS Genet (2009) 1.03
Mutation and the evolution of recombination. Philos Trans R Soc Lond B Biol Sci (2010) 1.02
Can intra-Y gene conversion oppose the degeneration of the human Y chromosome? A simulation study. Genome Biol Evol (2010) 1.01
Genome-wide analysis of natural selection on human cis-elements. PLoS One (2008) 1.00
Correcting for differential transcript coverage reveals a strong relationship between alternative splicing and organism complexity. Mol Biol Evol (2014) 1.00
Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. Genetics (2006) 0.99
Effects of metabolic rate on protein evolution. Biol Lett (2007) 0.98
Long identical multispecies elements in plant and animal genomes. Proc Natl Acad Sci U S A (2012) 0.97
What are the determinants of gene expression levels and breadths in the human genome? Hum Mol Genet (2011) 0.96
Surprising fitness consequences of GC-biased gene conversion: I. Mutation load and inbreeding depression. Genetics (2010) 0.94
Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend. BMC Genomics (2009) 0.94
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
Evolution of primate gene expression: drift and corrective sweeps? Genetics (2008) 0.93
Selective constraints in experimentally defined primate regulatory regions. PLoS Genet (2008) 0.92
Widespread ultraconservation divergence in primates. Mol Biol Evol (2008) 0.90
Reduced selective constraint in endosymbionts: elevation in radical amino acid replacements occurs genome-wide. PLoS One (2011) 0.90
GC-biased evolution near human accelerated regions. PLoS Genet (2010) 0.89
Mutations within lncRNAs are effectively selected against in fruitfly but not in human. Genome Biol (2013) 0.89
Functional analysis of human and chimpanzee promoters. Genome Biol (2005) 0.89
Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics (2011) 0.87
Evidence against the energetic cost hypothesis for the short introns in highly expressed genes. BMC Evol Biol (2008) 0.87
Selection shapes malaria genomes and drives divergence between pathogens infecting hominids versus rodents. BMC Evol Biol (2008) 0.86
DNA sequence and structural properties as predictors of human and mouse promoters. Gene (2007) 0.85
Fast evolution of core promoters in primate genomes. Mol Biol Evol (2008) 0.85
Prediction of functional regulatory SNPs in monogenic and complex disease. Hum Mutat (2011) 0.85
Human and mouse switch-like genes share common transcriptional regulatory mechanisms for bimodality. BMC Genomics (2008) 0.85
Unravelling cis-regulatory elements in the genome of the smallest photosynthetic eukaryote: phylogenetic footprinting in Ostreococcus. J Mol Evol (2009) 0.84
Why Selection Might Be Stronger When Populations Are Small: Intron Size and Density Predict within and between-Species Usage of Exonic Splice Associated cis-Motifs. Mol Biol Evol (2015) 0.84
Reconstructing the phylogenetic history of long-term effective population size and life-history traits using patterns of amino acid replacement in mitochondrial genomes of mammals and birds. Genome Biol Evol (2013) 0.84
Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories. Mol Genet Genomics (2007) 0.83
Substitution patterns are under different influences in primates and rodents. Genome Biol Evol (2011) 0.83
Evolution of candidate transcriptional regulatory motifs since the human-chimpanzee divergence. Genome Biol (2006) 0.83
Identification and characterization of lineage-specific highly conserved noncoding sequences in Mammalian genomes. Genome Biol Evol (2012) 0.82
Association between SNP heterozygosity and quantitative traits in the Framingham Heart Study. Ann Hum Genet (2009) 0.81
A potential role for glucose transporters in the evolution of human brain size. Brain Behav Evol (2011) 0.81
Human variation in short regions predisposed to deep evolutionary conservation. Mol Biol Evol (2010) 0.81
Competition between the sperm of a single male can increase the evolutionary rate of haploid expressed genes. Genetics (2013) 0.80
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome. BMC Evol Biol (2005) 0.80
Natural selection on coding and noncoding DNA sequences is associated with virulence genes in a plant pathogenic fungus. Genome Biol Evol (2014) 0.80
Population genomics of the endangered giant Galápagos tortoise. Genome Biol (2013) 0.80
Primate-specific spliced PMCHL RNAs are non-protein coding in human and macaque tissues. BMC Evol Biol (2008) 0.79
Turnover and lineage-specific broadening of the transcription start site in a testis-specific retrogene. Fly (Austin) (2010) 0.79
The impact of recent population history on the deleterious mutation load in humans and close evolutionary relatives. Curr Opin Genet Dev (2016) 0.78
Cis-regulatory elements and human evolution. Curr Opin Genet Dev (2014) 0.78
Selection on synonymous codons in mammalian rhodopsins: a possible role in optimizing translational processes. BMC Evol Biol (2014) 0.77
Understanding the degradation of hominid gene control. PLoS Comput Biol (2006) 0.76
Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements. Genome Biol Evol (2015) 0.75
Weak Polygenic Selection Drives the Rapid Adaptation of the Chemosensory System: Lessons from the Upstream Regions of the Major Gene Families. Genome Biol Evol (2016) 0.75
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res (1997) 665.31
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Bioconductor: open software development for computational biology and bioinformatics. Genome Biol (2004) 143.19
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
A comparison of normalization methods for high density oligonucleotide array data based on variance and bias. Bioinformatics (2003) 82.89
The hitch-hiking effect of a favourable gene. Genet Res (1974) 34.74
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
Ultraconserved elements in the human genome. Science (2004) 17.14
Slightly deleterious mutant substitutions in evolution. Nature (1973) 13.79
The origins of genome complexity. Science (2003) 12.25
Allelic variation in human gene expression. Science (2002) 11.42
Genomic divergences between humans and other hominoids and the effective population size of the common ancestor of humans and chimpanzees. Am J Hum Genet (2001) 9.35
Intra- and interspecific variation in primate gene expression patterns. Science (2002) 7.92
Positive and negative selection on the human genome. Genetics (2001) 7.25
Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics (1995) 7.19
Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci. Genetics (2003) 7.05
Individuality and variation in gene expression patterns in human blood. Proc Natl Acad Sci U S A (2003) 6.49
High genomic deleterious mutation rates in hominids. Nature (1999) 6.23
Low nucleotide diversity in man. Genetics (1991) 5.83
Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet (2002) 5.80
Adaptive protein evolution in Drosophila. Nature (2002) 5.71
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
A physical map of the mouse genome. Nature (2002) 4.97
Comparative analysis of noncoding regions of 77 orthologous mouse and human gene pairs. Genome Res (1999) 4.50
DNA sequence and comparative analysis of chimpanzee chromosome 22. Nature (2004) 4.12
The high spontaneous mutation rate: is it a health risk? Proc Natl Acad Sci U S A (1997) 3.85
Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science (2003) 3.77
A neutral model of transcriptome evolution. PLoS Biol (2004) 3.44
Evolutionarily conserved sequences on human chromosome 21. Genome Res (2001) 2.95
Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. Mol Biol Evol (1995) 2.68
Quantifying the slightly deleterious mutation model of molecular evolution. Mol Biol Evol (2002) 2.65
The signature of selection mediated by expression on human genes. Genome Res (2003) 2.56
Selection on human genes as revealed by comparisons to chimpanzee cDNA. Genome Res (2003) 2.48
Incongruent expression profiles between human and mouse orthologous genes suggest widespread neutral evolution of transcription control. OMICS (2004) 2.40
Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res (1993) 2.39
Low nucleotide diversity in chimpanzees and bonobos. Genetics (2003) 2.16
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci U S A (2003) 1.98
Genetic and haplotype diversity among wild-derived mouse inbred strains. Genome Res (2004) 1.86
Vanishing GC-rich isochores in mammalian genomes. Genetics (2002) 1.86
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res (2004) 1.78
MCALIGN: stochastic alignment of noncoding DNA sequences based on an evolutionary model of sequence evolution. Genome Res (2004) 1.33
DNA polymorphism in a worldwide sample of human X chromosomes. Mol Biol Evol (2002) 0.96
The evolutionary dynamics of eukaryotic gene order. Nat Rev Genet (2004) 5.79
Adaptive protein evolution in Drosophila. Nature (2002) 5.71
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat Genet (2005) 4.19
An integrated view of protein evolution. Nat Rev Genet (2006) 3.86
Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics (2007) 3.84
Prediction of effective genome size in metagenomic samples. Genome Biol (2007) 3.73
Direct measure of the de novo mutation rate in autism and schizophrenia cohorts. Am J Hum Genet (2010) 3.69
Comparative functional analysis of the Caenorhabditis elegans and Drosophila melanogaster proteomes. PLoS Biol (2009) 3.09
Variation in the mutation rate across mammalian genomes. Nat Rev Genet (2011) 3.09
Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol (2006) 2.81
Gene transfer from bacteria and archaea facilitated evolution of an extremophilic eukaryote. Science (2013) 2.51
Chance and necessity in the evolution of minimal metabolic networks. Nature (2006) 2.48
The genomic rate of adaptive amino acid substitution in Drosophila. Mol Biol Evol (2004) 2.44
Phylogenomic analysis reveals bees and wasps (Hymenoptera) at the base of the radiation of Holometabolous insects. Genome Res (2006) 2.42
Evidence of selection upon genomic GC-content in bacteria. PLoS Genet (2010) 2.42
The McDonald-Kreitman test and slightly deleterious mutations. Mol Biol Evol (2008) 2.02
Human triallelic sites: evidence for a new mutational mechanism? Genetics (2009) 2.01
Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc Natl Acad Sci U S A (2003) 2.01
Human disease genes: patterns and predictions. Gene (2003) 1.99
The rate of adaptive evolution in enteric bacteria. Mol Biol Evol (2006) 1.91
EvolView, an online tool for visualizing, annotating and managing phylogenetic trees. Nucleic Acids Res (2012) 1.90
An mRNA blueprint for C4 photosynthesis derived from comparative transcriptomics of closely related C3 and C4 species. Plant Physiol (2010) 1.87
Estimation of the neutrality index. Mol Biol Evol (2010) 1.84
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res (2004) 1.78
Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol (2010) 1.76
Cryptic variation in the human mutation rate. PLoS Biol (2009) 1.72
X-chromosome-wide profiling of MSL-1 distribution and dosage compensation in Drosophila. Genes Dev (2006) 1.70
The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes. Genome Biol Evol (2012) 1.69
Shotgun proteomics data from multiple organisms reveals remarkable quantitative conservation of the eukaryotic core proteome. Proteomics (2010) 1.64
An integrated approach to characterize genetic interaction networks in yeast metabolism. Nat Genet (2011) 1.62
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution. Bioessays (2013) 1.60
A new perspective on isochore evolution. Gene (2006) 1.57
A broad survey of recombination in animal mitochondria. Mol Biol Evol (2004) 1.56
OGEE: an online gene essentiality database. Nucleic Acids Res (2011) 1.54
Similar gene expression profiles do not imply similar tissue functions. Trends Genet (2006) 1.46
Plant and animal glycolate oxidases have a common eukaryotic ancestor and convergently duplicated to evolve long-chain 2-hydroxy acid oxidases. Mol Biol Evol (2014) 1.44
Evidence for pervasive adaptive protein evolution in wild mice. PLoS Genet (2010) 1.39
The large-scale distribution of somatic mutations in cancer genomes. Hum Mutat (2011) 1.32
The evolution of isochores: evidence from SNP frequency distributions. Genetics (2002) 1.29
The positive correlation between dN/dS and dS in mammals is due to runs of adjacent substitutions. Mol Biol Evol (2010) 1.29
The decline of isochores in mammals: an assessment of the GC content variation along the mammalian phylogeny. J Mol Evol (2004) 1.28
Evidence for variation in the effective population size of animal mitochondrial DNA. PLoS One (2009) 1.28
Hundreds of putatively functional small open reading frames in Drosophila. Genome Biol (2011) 1.26
Predicting C4 photosynthesis evolution: modular, individually adaptive steps on a Mount Fuji fitness landscape. Cell (2013) 1.24
What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Philos Trans R Soc Lond B Biol Sci (2010) 1.24
The other side of the nearly neutral theory, evidence of slightly advantageous back-mutations. Proc Natl Acad Sci U S A (2007) 1.24
The evolution of courtship behaviors through the origination of a new gene in Drosophila. Proc Natl Acad Sci U S A (2008) 1.23
Quantifying the variation in the effective population size within a genome. Genetics (2011) 1.23
Younger genes are less likely to be essential than older genes, and duplicates are less likely to be essential than singletons of the same age. Mol Biol Evol (2012) 1.19
A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics (2011) 1.16
Imprinted chromosomal regions of the human genome have unusually high recombination rates. Genetics (2003) 1.15
A problem with the correlation coefficient as a measure of gene expression divergence. Genetics (2009) 1.13
Transcriptional coupling of neighboring genes and gene expression noise: evidence that gene orientation and noncoding transcripts are modulators of noise. Genome Biol Evol (2011) 1.12
Genome-wide acceleration of protein evolution in flies (Diptera). BMC Evol Biol (2006) 1.10
Gene expression, synteny, and local similarity in human noncoding mutation rates. Mol Biol Evol (2004) 1.09
A resolution of the mutation load paradox in humans. Genetics (2012) 1.07
Co-expression of neighbouring genes in Arabidopsis: separating chromatin effects from direct interactions. BMC Genomics (2010) 1.06
Horizontal gene transfer depends on gene content of the host. Bioinformatics (2005) 1.02
Divergence and polymorphism under the nearly neutral theory of molecular evolution. J Mol Evol (2008) 1.01
An investigation of the variation in the transition bias among various animal mitochondrial DNA. Gene (2005) 1.01
Analysis of the phylogenetic distribution of isochores in vertebrates and a test of the thermal stability hypothesis. J Mol Evol (2002) 1.01
The genomic distribution and local context of coincident SNPs in human and chimpanzee. Genome Biol Evol (2010) 0.98
The effect of transposable element insertions on gene expression evolution in rodents. PLoS One (2009) 0.96
The compositional evolution of the murid genome. J Mol Evol (2002) 0.96
Partitioning the variation in mammalian substitution rates. Mol Biol Evol (2003) 0.94
Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small. J Mol Evol (2012) 0.93
Transposable elements: insertion pattern and impact on gene expression evolution in hominids. Mol Biol Evol (2010) 0.93
Amino acid composition in endothermic vertebrates is biased in the same direction as in thermophilic prokaryotes. BMC Evol Biol (2010) 0.92
Human functional genetic studies are biased against the medically most relevant primate-specific genes. BMC Evol Biol (2010) 0.90
How and why DNA barcodes underestimate the diversity of microbial eukaryotes. PLoS One (2011) 0.90
An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics (2014) 0.89
ColorTree: a batch customization tool for phylogenic trees. BMC Res Notes (2009) 0.88
Regional similarities in polymorphism in the human genome extend over many megabases. Trends Genet (2002) 0.87
The accumulation of gene regulation through time. Genome Biol Evol (2011) 0.87
The effects of network neighbours on protein evolution. PLoS One (2011) 0.83
Why are young and old repetitive elements distributed differently in the human genome? J Mol Evol (2005) 0.83
TreeSnatcher plus: capturing phylogenetic trees from images. BMC Bioinformatics (2012) 0.83
Organellar inheritance in the green lineage: insights from Ostreococcus tauri. Genome Biol Evol (2013) 0.81
Coexpression of linked gene pairs persists long after their separation. Genome Biol Evol (2011) 0.80
Horizontal gene transfers as metagenomic gene duplications. Mol Biosyst (2012) 0.80
Unusual linkage patterns of ligands and their cognate receptors indicate a novel reason for non-random gene order in the human genome. BMC Evol Biol (2005) 0.80
Does negative auto-regulation increase gene duplicability? BMC Evol Biol (2009) 0.79
A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees. PLoS One (2012) 0.79
The excess of small inverted repeats in prokaryotes. J Mol Evol (2008) 0.79
A gene's ability to buffer variation is predicted by its fitness contribution and genetic interactions. PLoS One (2011) 0.77
ODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes. PLoS One (2013) 0.77
A test of whether selection maintains isochores using sites polymorphic for Alu and L1 element insertions. Genetics (2002) 0.77
A dissection of volatility in yeast. Mol Biol Evol (2005) 0.77
Understanding the degradation of hominid gene control. PLoS Comput Biol (2006) 0.76
Assessing the influence of adjacent gene orientation on the evolution of gene upstream regions in Arabidopsis thaliana. Genetics (2010) 0.76
Minimal regulatory spaces in yeast genomes. BMC Genomics (2011) 0.76
Searching for sequence directed mutagenesis in eukaryotes. J Mol Evol (2006) 0.75