Published in Genome Res on May 01, 2003
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 10.92
Elevated gene expression levels distinguish human from non-human primate brains. Proc Natl Acad Sci U S A (2003) 4.69
Exome sequencing and the genetic basis of complex traits. Nat Genet (2012) 4.11
Regional patterns of gene expression in human and chimpanzee brains. Genome Res (2004) 3.84
Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol (2005) 3.47
Multi-species microarrays reveal the effect of sequence divergence on gene expression profiles. Genome Res (2005) 3.23
Evidence for selection on synonymous mutations affecting stability of mRNA secondary structure in mammals. Genome Biol (2005) 2.94
High guanine and cytosine content increases mRNA levels in mammalian cells. PLoS Biol (2006) 2.74
Synonymous mutations in CFTR exon 12 affect splicing and are not neutral in evolution. Proc Natl Acad Sci U S A (2005) 2.12
Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents. Proc Natl Acad Sci U S A (2003) 1.98
Different evolutionary patterns between young duplicate genes in the human genome. Genome Biol (2003) 1.92
Patterns of evolutionary constraints in intronic and intergenic DNA of Drosophila. Genome Res (2004) 1.78
Comparison of the chicken and turkey genomes reveals a higher rate of nucleotide divergence on microchromosomes than macrochromosomes. Genome Res (2004) 1.73
Evolutionary evidence of the effect of rare variants on disease etiology. Clin Genet (2010) 1.54
A common polymorphism in serotonin receptor 1B mRNA moderates regulation by miR-96 and associates with aggressive human behaviors. Mol Psychiatry (2008) 1.50
Indel-based evolutionary distance and mouse-human divergence. Genome Res (2004) 1.47
Sounds of silence: synonymous nucleotides as a key to biological regulation and complexity. Nucleic Acids Res (2013) 1.44
Transcriptome analysis and comparison reveal divergence between two invasive whitefly cryptic species. BMC Genomics (2011) 1.31
Inferring the mode of speciation from genomic data: a study of the great apes. Genetics (2005) 1.27
Analysis of the Macaca mulatta transcriptome and the sequence divergence between Macaca and human. Genome Biol (2005) 1.20
eShadow: a tool for comparing closely related sequences. Genome Res (2004) 1.18
Positive selection acting on splicing motifs reflects compensatory evolution. Genome Res (2008) 1.18
Widespread positive selection in synonymous sites of mammalian genes. Mol Biol Evol (2007) 1.17
Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol Biol Evol (2006) 1.12
Hypervariable noncoding sequences in Saccharomyces cerevisiae. Genetics (2005) 1.12
No effect of recombination on the efficacy of natural selection in primates. Genome Res (2008) 1.05
Fugu ESTs: new resources for transcription analysis and genome annotation. Genome Res (2003) 1.05
Testing the chromosomal speciation hypothesis for humans and chimpanzees. Genome Res (2004) 1.04
Decoding mechanisms by which silent codon changes influence protein biogenesis and function. Int J Biochem Cell Biol (2015) 1.04
Analysis of a native whitefly transcriptome and its sequence divergence with two invasive whitefly species. BMC Genomics (2012) 1.01
Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals. J Mol Evol (2006) 0.99
Hypermutable non-synonymous sites are under stronger negative selection. PLoS Genet (2008) 0.98
Segmental duplication associated with the human-specific inversion of chromosome 18: a further example of the impact of segmental duplications on karyotype and genome evolution in primates. Hum Genet (2004) 0.98
Regions of extreme synonymous codon selection in mammalian genes. Nucleic Acids Res (2006) 0.97
The characteristics and expression profiles of the mitochondrial genome for the Mediterranean species of the Bemisia tabaci complex. BMC Genomics (2013) 0.93
Primate TNF promoters reveal markers of phylogeny and evolution of innate immunity. PLoS One (2007) 0.92
Developmental stage related patterns of codon usage and genomic GC content: searching for evolutionary fingerprints with models of stem cell differentiation. Genome Biol (2007) 0.89
Effect of the assignment of ancestral CpG state on the estimation of nucleotide substitution rates in mammals. BMC Evol Biol (2008) 0.89
The human progesterone receptor shows evidence of adaptive evolution associated with its ability to act as a transcription factor. Mol Phylogenet Evol (2008) 0.89
Development of the first marmoset-specific DNA microarray (EUMAMA): a new genetic tool for large-scale expression profiling in a non-human primate. BMC Genomics (2007) 0.89
FRAGS: estimation of coding sequence substitution rates from fragmentary data. BMC Bioinformatics (2004) 0.87
Inference of mutation parameters and selective constraint in mammalian coding sequences by approximate Bayesian computation. Genetics (2011) 0.87
Relationship between amino acid composition and gene expression in the mouse genome. BMC Res Notes (2011) 0.85
Evolution and functional diversification of the GLI family of transcription factors in vertebrates. Evol Bioinform Online (2009) 0.84
The functional relevance of somatic synonymous mutations in melanoma and other cancers. Pigment Cell Melanoma Res (2015) 0.84
Accelerated evolution of the pituitary adenylate cyclase-activating polypeptide precursor gene during human origin. Genetics (2005) 0.83
Synonymous site conservation in the HIV-1 genome. BMC Evol Biol (2013) 0.82
Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Mol Biol Evol (2009) 0.81
Evolutionary divergence of exon flanks: a dissection of mutability and selection. Genetics (2006) 0.80
Similarity of synonymous substitution rates across mammalian genomes. J Mol Evol (2007) 0.80
Expression sequence tag library derived from peripheral blood mononuclear cells of the chlorocebus sabaeus. BMC Genomics (2012) 0.78
Analysis of synaptic gene expression in the neocortex of primates reveals evolutionary changes in glutamatergic neurotransmission. Cereb Cortex (2014) 0.77
Comparative transcriptomic analyses revealed divergences of two agriculturally important aphid species. BMC Genomics (2014) 0.77
De novo origin of VCY2 from autosome to Y-transposed amplicon. PLoS One (2015) 0.76
Are Synonymous Sites in Primates and Rodents Functionally Constrained? J Mol Evol (2015) 0.75
Gonadal transcriptomics elucidate patterns of adaptive evolution within marine rockfishes (Sebastes). BMC Genomics (2015) 0.75
Single genome retrieval of context-dependent variability in mutation rates for human germline. BMC Genomics (2017) 0.75
What makes us human? Genome Biol (2004) 0.75
Transcriptome analysis of host-associated differentiation in Bemisia tabaci (Hemiptera: Aleyrodidae). Front Physiol (2014) 0.75
Basic local alignment search tool. J Mol Biol (1990) 659.07
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res (1998) 96.63
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76
A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature (2001) 42.18
Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat Genet (1999) 24.24
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
An SNP map of the human genome generated by reduced representation shotgun sequencing. Nature (2000) 19.19
Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat Genet (1999) 17.09
Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet (2002) 16.29
Estimate of the mutation rate per nucleotide in humans. Genetics (2000) 15.08
Estimate of human gene number provided by genome-wide analysis using Tetraodon nigroviridis DNA sequence. Nat Genet (2000) 14.51
Evolutionary parameters of the transcribed mammalian genome: an analysis of 2,820 orthologous rodent and human sequences. Proc Natl Acad Sci U S A (1998) 11.90
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
The role of DNA methylation in mammalian epigenetics. Science (2001) 9.26
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
Role of very slightly deleterious mutations in molecular evolution and polymorphism. Theor Popul Biol (1976) 6.91
High genomic deleterious mutation rates in hominids. Nature (1999) 6.23
Computational identification of promoters and first exons in the human genome. Nat Genet (2001) 5.88
Genomewide comparison of DNA sequences between humans and chimpanzees. Am J Hum Genet (2002) 5.80
Codon usage in regulatory genes in Escherichia coli does not reflect selection for 'rare' codons. Nucleic Acids Res (1986) 5.68
Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol Biol Evol (2000) 4.70
SNP frequencies in human genes an excess of rare alleles and differing modes of selection. Trends Genet (2000) 3.78
Reduced synonymous substitution rate at the start of enterobacterial genes. Nucleic Acids Res (1993) 2.94
Selective constraint in intergenic regions of human and mouse genomes. Trends Genet (2001) 2.87
Construction and analysis of a human-chimpanzee comparative clone map. Science (2002) 2.83
Synonymous and nonsynonymous substitutions in mammalian genes and the nearly neutral theory. J Mol Evol (1995) 2.65
Strong conservation of non-coding sequences during vertebrates evolution: potential involvement in post-transcriptional regulation of gene expression. Nucleic Acids Res (1993) 2.39
The rate of hydrolytic deamination of 5-methylcytosine in double-stranded DNA. Nucleic Acids Res (1994) 2.37
Codon usage bias covaries with expression breadth and the rate of synonymous evolution in humans, but this is not evidence for selection. Genetics (2001) 1.87
Structural and compositional features of untranslated regions of eukaryotic mRNAs. Gene (1997) 1.69
A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Mol Biol Evol (2002) 1.54
The draft sequences. Comparing species. Nature (2001) 0.88
Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science (2005) 5.68
Fine-scale recombination patterns differ between chimpanzees and humans. Nat Genet (2005) 5.00
Regional patterns of gene expression in human and chimpanzee brains. Genome Res (2004) 3.84
Targeted deletion of AIF decreases mitochondrial oxidative phosphorylation and protects from obesity and diabetes. Cell (2007) 3.82
Multiplex amplification of the mammoth mitochondrial genome and the evolution of Elephantidae. Nature (2005) 3.74
A humanized version of Foxp2 affects cortico-basal ganglia circuits in mice. Cell (2009) 3.63
A neutral explanation for the correlation of diversity with recombination rates in humans. Am J Hum Genet (2003) 3.57
A neutral model of transcriptome evolution. PLoS Biol (2004) 3.44
The derived FOXP2 variant of modern humans was shared with Neandertals. Curr Biol (2007) 3.39
Evolution of primate gene expression. Nat Rev Genet (2006) 3.04
Aspm specifically maintains symmetric proliferative divisions of neuroepithelial cells. Proc Natl Acad Sci U S A (2006) 3.03
Autosomal recessive primary microcephaly (MCPH): a review of clinical, molecular, and evolutionary findings. Am J Hum Genet (2005) 2.86
Genome-wide RNAi screen identifies genes involved in intestinal pathogenic bacterial infection. Science (2009) 2.47
Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments. Proc Natl Acad Sci U S A (2013) 2.45
A phylogenomic approach to resolve the arthropod tree of life. Mol Biol Evol (2010) 2.38
FUNC: a package for detecting significant associations between gene sets and ontological annotations. BMC Bioinformatics (2007) 2.32
Impaired synaptic plasticity and motor learning in mice with a point mutation implicated in human speech deficits. Curr Biol (2008) 2.27
The plant heat stress transcription factor (Hsf) family: structure, function and evolution. Biochim Biophys Acta (2011) 2.18
Inactivation of CMP-N-acetylneuraminic acid hydroxylase occurred prior to brain expansion during human evolution. Proc Natl Acad Sci U S A (2002) 2.00
Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A (2009) 1.78
Mutations in mouse Aspm (abnormal spindle-like microcephaly associated) cause not only microcephaly but also major defects in the germline. Proc Natl Acad Sci U S A (2010) 1.76
Demographic history and genetic differentiation in apes. Curr Biol (2006) 1.69
Structure of the forkhead domain of FOXP2 bound to DNA. Structure (2006) 1.61
Transcriptomes of germinal zones of human and mouse fetal neocortex suggest a role of extracellular matrix in progenitor self-renewal. Proc Natl Acad Sci U S A (2012) 1.36
Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda. Mol Biol Evol (2011) 1.35
Comparative primate genomics. Annu Rev Genomics Hum Genet (2004) 1.33
New phylogenomic data support the monophyly of Lophophorata and an Ectoproct-Phoronid clade and indicate that Polyzoa and Kryptrochozoa are caused by systematic bias. BMC Evol Biol (2013) 1.32
Patterns of coding variation in the complete exomes of three Neandertals. Proc Natl Acad Sci U S A (2014) 1.29
EST sequencing of Onychophora and phylogenomic analysis of Metazoa. Mol Phylogenet Evol (2007) 1.28
Differences in DNA methylation patterns between humans and chimpanzees. Curr Biol (2004) 1.24
Rooted triple consensus and anomalous gene trees. BMC Evol Biol (2008) 1.14
Positive selection on gene expression in the human brain. Curr Biol (2006) 1.14
Decisive data sets in phylogenomics: lessons from studies on the phylogenetic relationships of primarily wingless insects. Mol Biol Evol (2013) 1.10
A recent evolutionary change affects a regulatory element in the human FOXP2 gene. Mol Biol Evol (2012) 1.08
Centrin4 coordinates cell and nuclear division in T. brucei. J Cell Sci (2008) 1.08
Convergent repression of Foxp2 3'UTR by miR-9 and miR-132 in embryonic mouse neocortex: implications for radial migration of neurons. Development (2012) 1.07
Opsins in onychophora (velvet worms) suggest a single origin and subsequent diversification of visual pigments in arthropods. Mol Biol Evol (2012) 1.02
Identification of large-scale human-specific copy number differences by inter-species array comparative genomic hybridization. Hum Genet (2006) 0.99
Structural and functional evolution of the trace amine-associated receptors TAAR3, TAAR4 and TAAR5 in primates. PLoS One (2010) 0.98
Should the draft chimpanzee sequence be finished? Trends Genet (2006) 0.96
Comment on papers by Evans et al. and Mekel-Bobrov et al. on Evidence for Positive Selection of MCPH1 and ASPM. Science (2007) 0.94
Transcription factors are targeted by differentially expressed miRNAs in primates. Genome Biol Evol (2012) 0.93
Linkage disequilibrium extends across putative selected sites in FOXP2. Mol Biol Evol (2009) 0.91
Gene diversity patterns at 10 X-chromosomal loci in humans and chimpanzees. Mol Biol Evol (2003) 0.89
Phylogenomic analyses of malaria parasites and evolution of their exported proteins. BMC Evol Biol (2011) 0.89
Functional analysis of human and chimpanzee promoters. Genome Biol (2005) 0.89
Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data. PLoS One (2012) 0.89
Annotation of primate miRNAs by high throughput sequencing of small RNA libraries. BMC Genomics (2012) 0.88
FACT: functional annotation transfer between proteins with similar feature architectures. BMC Bioinformatics (2010) 0.87
Zygomycetes, microsporidia, and the evolutionary ancestry of sex determination. Genome Biol Evol (2011) 0.86
TbG63, a golgin involved in Golgi architecture in Trypanosoma brucei. J Cell Sci (2008) 0.86
Support for the monophyletic origin of Gnathifera from phylogenomics. Mol Phylogenet Evol (2009) 0.82
Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Mol Phylogenet Evol (2012) 0.78
REvolver: modeling sequence evolution under domain constraints. Mol Biol Evol (2012) 0.76
An annotated draft genome for Radix auricularia (Gastropoda, Mollusca). Genome Biol Evol (2017) 0.75