Published in Mol Biol Evol on October 10, 2013
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Gene pleiotropy constrains gene expression changes in fish adapted to different thermal conditions. Nat Commun (2014) 0.82
Positive Selection Underlies Faster-Z Evolution of Gene Expression in Birds. Mol Biol Evol (2015) 0.81
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Neutral and adaptive explanations for an association between caste-biased gene expression and rate of sequence evolution. Front Genet (2014) 0.78
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Phylogenetic ANOVA: The Expression Variance and Evolution Model for Quantitative Trait Evolution. Syst Biol (2015) 0.77
Identification of Lineage-Specific Cis-Regulatory Modules Associated with Variation in Transcription Factor Binding and Chromatin Activity Using Ornstein-Uhlenbeck Models. Mol Biol Evol (2015) 0.76
Widespread adaptive evolution during repeated evolutionary radiations in New World lupins. Nat Commun (2016) 0.75
Age-related association of venom gene expression and diet of predatory gastropods. BMC Evol Biol (2016) 0.75
Population perspectives on functional genomic variation in yeast. Brief Funct Genomics (2015) 0.75
Accelerated Evolution of Developmentally Biased Genes in the Tetraphenic Ant Cardiocondyla obscurior. Mol Biol Evol (2017) 0.75
Phase transition on the convergence rate of parameter estimation under an Ornstein-Uhlenbeck diffusion on a tree. J Math Biol (2016) 0.75
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Understanding mechanisms underlying human gene expression variation with RNA sequencing. Nature (2010) 16.86
Epigenetics in human disease and prospects for epigenetic therapy. Nature (2004) 11.46
Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet (2007) 9.88
Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet (2004) 8.85
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The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Evolution of gene expression in the Drosophila melanogaster subgroup. Nat Genet (2003) 6.60
Expression profiling in primates reveals a rapid evolution of human transcription factors. Nature (2006) 4.26
Regional patterns of gene expression in human and chimpanzee brains. Genome Res (2004) 3.84
Sex-specific and lineage-specific alternative splicing in primates. Genome Res (2009) 3.61
A neutral model of transcriptome evolution. PLoS Biol (2004) 3.44
Variation within and among species in gene expression: raw material for evolution. Mol Ecol (2006) 3.36
Gene expression divergence recapitulates the developmental hourglass model. Nature (2010) 3.20
Evolution of primate gene expression. Nat Rev Genet (2006) 3.04
Common pattern of evolution of gene expression level and protein sequence in Drosophila. Mol Biol Evol (2004) 2.66
Single-tissue and cross-tissue heritability of gene expression via identity-by-descent in related or unrelated individuals. PLoS Genet (2011) 2.53
Mixed-model reanalysis of primate data suggests tissue and species biases in oligonucleotide-based gene expression profiles. Genetics (2003) 2.50
Geographical genomics of human leukocyte gene expression variation in southern Morocco. Nat Genet (2009) 2.38
Statistical framework for phylogenomic analysis of gene family expression profiles. Genetics (2004) 2.01
Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories. Evolution (2005) 1.93
Natural selection on gene expression. Trends Genet (2006) 1.90
Comparative methods for the analysis of gene-expression evolution: an example using yeast functional genomic data. Mol Biol Evol (2004) 1.88
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
Within-species variation and measurement error in phylogenetic comparative methods. Syst Biol (2007) 1.81
Transcriptional neoteny in the human brain. Proc Natl Acad Sci U S A (2009) 1.78
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci U S A (2012) 1.72
Comparative methods with sampling error and within-species variation: contrasts revisited and revised. Am Nat (2008) 1.65
A comparative method for studying adaptation to a randomly evolving environment. Evolution (2008) 1.64
Optimization of gene expression by natural selection. Proc Natl Acad Sci U S A (2009) 1.50
Toward a neutral evolutionary model of gene expression. Genetics (2005) 1.38
Comparative RNA sequencing reveals substantial genetic variation in endangered primates. Genome Res (2011) 1.36
Stress and the epigenetic landscape: a link to the pathobiology of human diseases? Nat Rev Genet (2010) 1.13
Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance. PLoS Genet (2012) 1.07
Interpreting the evolutionary regression: the interplay between observational and biological errors in phylogenetic comparative studies. Syst Biol (2012) 1.06
A comparison of brain gene expression levels in domesticated and wild animals. PLoS Genet (2012) 1.04
Evolution of primate gene expression: drift and corrective sweeps? Genetics (2008) 0.93
A test of the neutral model of expression change in natural populations of house mouse subspecies. Evolution (2009) 0.86
A selection index for gene expression evolution and its application to the divergence between humans and chimpanzees. PLoS One (2012) 0.79
The diploid genome sequence of an Asian individual. Nature (2008) 46.29
Evolution of genes and genomes on the Drosophila phylogeny. Nature (2007) 18.01
Evolutionary and biomedical insights from the rhesus macaque genome. Science (2007) 16.21
The sequence and de novo assembly of the giant panda genome. Nature (2009) 15.76
A metagenome-wide association study of gut microbiota in type 2 diabetes. Nature (2012) 11.68
Sequencing of 50 human exomes reveals adaptation to high altitude. Science (2010) 11.27
Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol (2005) 11.26
Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84
Inferring nonneutral evolution from human-chimp-mouse orthologous gene trios. Science (2003) 9.20
The use of coded PCR primers enables high-throughput sequencing of multiple homolog amplification products by 454 parallel sequencing. PLoS One (2007) 9.17
Assessing the evolutionary impact of amino acid mutations in the human genome. PLoS Genet (2008) 8.92
Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol (2005) 8.74
Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution. Genome Res (2005) 8.38
Multilocus methods for estimating population sizes, migration rates and divergence time, with applications to the divergence of Drosophila pseudoobscura and D. persimilis. Genetics (2004) 7.79
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol (2002) 7.21
The evolution of gene expression levels in mammalian organs. Nature (2011) 7.16
Ascertainment bias in studies of human genome-wide polymorphism. Genome Res (2005) 6.63
Proportionally more deleterious genetic variation in European than in African populations. Nature (2008) 6.61
Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc Natl Acad Sci U S A (2005) 5.94
Integration within the Felsenstein equation for improved Markov chain Monte Carlo methods in population genetics. Proc Natl Acad Sci U S A (2007) 5.64
Resequencing of 200 human exomes identifies an excess of low-frequency non-synonymous coding variants. Nat Genet (2010) 5.44
Localizing recent adaptive evolution in the human genome. PLoS Genet (2007) 5.11
Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes. Nat Biotechnol (2011) 4.84
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Patterns of positive selection in six Mammalian genomes. PLoS Genet (2008) 4.69
Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics (2004) 4.22
Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites. Genetics (2003) 3.89
Genome-wide patterns of nucleotide polymorphism in domesticated rice. PLoS Genet (2007) 3.83
The cost of inbreeding in Arabidopsis. Nature (2002) 3.80
Ancient biomolecules from deep ice cores reveal a forested southern Greenland. Science (2007) 3.79
Linkage disequilibrium as a signature of selective sweeps. Genetics (2004) 3.52
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol (2003) 3.42
Stochastic mapping of morphological characters. Syst Biol (2003) 3.08
Complete resequencing of 40 genomes reveals domestication events and genes in silkworm (Bombyx). Science (2009) 2.68
Demographic histories and patterns of linkage disequilibrium in Chinese and Indian rhesus macaques. Science (2007) 2.62
Species-specific responses of Late Quaternary megafauna to climate and humans. Nature (2011) 2.60
Adaptive genic evolution in the Drosophila genomes. Proc Natl Acad Sci U S A (2007) 2.56
Ascertainment biases in SNP chips affect measures of population divergence. Mol Biol Evol (2010) 2.56
Inference of historical changes in migration rate from the lengths of migrant tracts. Genetics (2008) 2.53
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46
Signatures of environmental genetic adaptation pinpoint pathogens as the main selective pressure through human evolution. PLoS Genet (2011) 2.44
Genome sequencing and comparison of two nonhuman primate animal models, the cynomolgus and Chinese rhesus macaques. Nat Biotechnol (2011) 2.37
Radiation of extant cetaceans driven by restructuring of the oceans. Syst Biol (2009) 2.33
Population genetic inference from genomic sequence variation. Genome Res (2010) 2.29
Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol Biol Evol (2008) 2.25
Balancing selection maintains a form of ERAP2 that undergoes nonsense-mediated decay and affects antigen presentation. PLoS Genet (2010) 2.14
Statistical assignment of DNA sequences using Bayesian phylogenetics. Syst Biol (2008) 2.13
Estimation of 2Nes from temporal allele frequency data. Genetics (2008) 2.12
Ancient DNA reveals late survival of mammoth and horse in interior Alaska. Proc Natl Acad Sci U S A (2009) 2.10
Design of association studies with pooled or un-pooled next-generation sequencing data. Genet Epidemiol (2010) 2.06
Relatedness mapping and tracts of relatedness for genome-wide data in the presence of linkage disequilibrium. Genet Epidemiol (2009) 2.02
Using nuclear haplotypes with microsatellites to study gene flow between recently separated Cichlid species. Mol Ecol (2004) 1.99
Population size changes reshape genomic patterns of diversity. Evolution (2007) 1.95
Estimation of allele frequency and association mapping using next-generation sequencing data. BMC Bioinformatics (2011) 1.93
A likelihood ratio test for species membership based on DNA sequence data. Philos Trans R Soc Lond B Biol Sci (2005) 1.85
Ancient bacteria show evidence of DNA repair. Proc Natl Acad Sci U S A (2007) 1.81
Unlocking the vault: next-generation museum population genomics. Mol Ecol (2013) 1.77
Inferring demographic history from a spectrum of shared haplotype lengths. PLoS Genet (2013) 1.77
Genes under positive selection in Escherichia coli. Genome Res (2007) 1.70
Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor Popul Biol (2003) 1.69
Targets of balancing selection in the human genome. Mol Biol Evol (2009) 1.69
Human genomics: disclosure of variation. Nature (2005) 1.67
Linkage disequilibrium and inference of ancestral recombination in 538 single-nucleotide polymorphism clusters across the human genome. Am J Hum Genet (2003) 1.58
Adaptive evolution of cytochrome c oxidase: Infrastructure for a carnivorous plant radiation. Proc Natl Acad Sci U S A (2004) 1.56
A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Mol Biol Evol (2002) 1.54
Natural selection affects multiple aspects of genetic variation at putatively neutral sites across the human genome. PLoS Genet (2011) 1.54
Natural selection and the distribution of identity-by-descent in the human genome. Genetics (2010) 1.52
Rational design of DNA sequence-based strategies for subtyping Listeria monocytogenes. J Clin Microbiol (2002) 1.51
Detecting selection in noncoding regions of nucleotide sequences. Genetics (2004) 1.50
Evolution of the integral membrane desaturase gene family in moths and flies. Genetics (2002) 1.47
Molecular footprints of domestication and improvement in soybean revealed by whole genome re-sequencing. BMC Genomics (2013) 1.46
Correcting estimators of theta and Tajima's D for ascertainment biases caused by the single-nucleotide polymorphism discovery process. Genetics (2008) 1.44
Ancient DNA chronology within sediment deposits: are paleobiological reconstructions possible and is DNA leaching a factor? Mol Biol Evol (2007) 1.44
Whole-exome sequencing of 2,000 Danish individuals and the role of rare coding variants in type 2 diabetes. Am J Hum Genet (2013) 1.43
A method for detecting IBD regions simultaneously in multiple individuals--with applications to disease genetics. Genome Res (2011) 1.41
Quantifying population genetic differentiation from next-generation sequencing data. Genetics (2013) 1.41
Microsatellite mutation models: insights from a comparison of humans and chimpanzees. Genetics (2004) 1.38
Discerning between recurrent gene flow and recent divergence under a finite-site mutation model applied to North Atlantic and Mediterranean Sea fin whale (Balaenoptera physalus) populations. Evolution (2004) 1.35
Genetic signatures reveal high-altitude adaptation in a set of ethiopian populations. Mol Biol Evol (2013) 1.33
Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet (2012) 1.31
Fast phylogenetic DNA barcoding. Philos Trans R Soc Lond B Biol Sci (2008) 1.27
On detecting incomplete soft or hard selective sweeps using haplotype structure. Mol Biol Evol (2014) 1.25
Genomics: In search of rare human variants. Nature (2010) 1.20
Bayesian estimation of genomic distance. Genetics (2004) 1.19
Detecting site-specific physicochemical selective pressures: applications to the Class I HLA of the human major histocompatibility complex and the SRK of the plant sporophytic self-incompatibility system. J Mol Evol (2005) 1.19
Radiation and speciation of pelagic organisms during periods of global warming: the case of the common minke whale, Balaenoptera acutorostrata. Mol Ecol (2007) 1.16
Bacterial natural transformation by highly fragmented and damaged DNA. Proc Natl Acad Sci U S A (2013) 1.15
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation. Genome Res (2013) 1.12
Detecting coevolving amino acid sites using Bayesian mutational mapping. Bioinformatics (2005) 1.11
An investigation of the statistical power of neutrality tests based on comparative and population genetic data. Mol Biol Evol (2008) 1.11
Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data. BMC Bioinformatics (2013) 1.10
The impact of founder events on chromosomal variability in multiply mating species. Mol Biol Evol (2008) 1.05
Bayesian estimation of the number of inversions in the history of two chromosomes. J Comput Biol (2002) 1.04
Genetic architecture of vitamin B12 and folate levels uncovered applying deeply sequenced large datasets. PLoS Genet (2013) 1.04
Patterns of mutation and selection at synonymous sites in Drosophila. Mol Biol Evol (2007) 1.03
Evidence for positive selection on a number of MicroRNA regulatory interactions during recent human evolution. PLoS Genet (2012) 1.03