Published in Genome Biol Evol on September 16, 2011
Reference-free population genomics from next-generation transcriptome data and the vertebrate-invertebrate gap. PLoS Genet (2013) 1.91
Genomic signatures of selection at linked sites: unifying the disparity among species. Nat Rev Genet (2013) 1.85
Recombination modulates how selection affects linked sites in Drosophila. PLoS Biol (2012) 1.77
Evolutionary change during experimental ocean acidification. Proc Natl Acad Sci U S A (2013) 1.51
The relationship of recombination rate, genome structure, and patterns of molecular evolution across angiosperms. BMC Evol Biol (2015) 1.41
Evidence for widespread positive and negative selection in coding and conserved noncoding regions of Capsella grandiflora. PLoS Genet (2014) 0.97
Rapid speciation with gene flow following the formation of Mt. Etna. Genome Biol Evol (2013) 0.92
Keeping it local: evidence for positive selection in Swedish Arabidopsis thaliana. Mol Biol Evol (2014) 0.91
Evolution of flux control in the glucosinolate pathway in Arabidopsis thaliana. Mol Biol Evol (2012) 0.91
Sequencing of the needle transcriptome from Norway spruce (Picea abies Karst L.) reveals lower substitution rates, but similar selective constraints in gymnosperms and angiosperms. BMC Genomics (2012) 0.91
The Population Genomics of Sunflowers and Genomic Determinants of Protein Evolution Revealed by RNAseq. Biology (Basel) (2012) 0.89
Efficient purging of deleterious mutations in plants with haploid selfing. Genome Biol Evol (2014) 0.88
Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol (2015) 0.86
The impact of linked selection on plant genomic variation. Brief Funct Genomics (2014) 0.85
Evolutionary rate and duplicability in the Arabidopsis thaliana protein-protein interaction network. Genome Biol Evol (2012) 0.85
Hitchhiking of deleterious alleles and the cost of adaptation in partially selfing species. Genetics (2013) 0.84
Genome-wide analysis in chicken reveals that local levels of genetic diversity are mainly governed by the rate of recombination. BMC Genomics (2013) 0.84
Highly variable recombinational landscape modulates efficacy of natural selection in birds. Genome Biol Evol (2014) 0.82
The landscape of nucleotide polymorphism among 13,500 genes of the conifer picea glauca, relationships with functions, and comparison with medicago truncatula. Genome Biol Evol (2013) 0.82
A neutrality test for detecting selection on DNA methylation using single methylation polymorphism frequency spectrum. Genome Biol Evol (2014) 0.81
Flagellated algae protein evolution suggests the prevalence of lineage-specific rules governing evolutionary rates of eukaryotic proteins. Genome Biol Evol (2013) 0.81
Domestication and the storage starch biosynthesis pathway: signatures of selection from a whole sorghum genome sequencing strategy. Plant Biotechnol J (2016) 0.80
Mining transcriptomic data to study the origins and evolution of a plant allopolyploid complex. PeerJ (2014) 0.77
Genome-wide identification, phylogenetic analysis, expression profiling, and protein-protein interaction properties of TOPLESS gene family members in tomato. J Exp Bot (2014) 0.77
Determinants of exon-level evolutionary rates in Arabidopsis species. Evol Bioinform Online (2012) 0.77
Genomic analysis reveals major determinants of cis-regulatory variation in Capsella grandiflora. Proc Natl Acad Sci U S A (2017) 0.77
Lineage-specific sequence evolution and exon edge conservation partially explain the relationship between evolutionary rate and expression level in A. thaliana. Mol Ecol (2015) 0.75
Transcriptomes of Plant Gametophytes Have a Higher Proportion of Rapidly Evolving and Young Genes than Sporophytes. Mol Biol Evol (2016) 0.75
Evolutionary Rate Heterogeneity of Primary and Secondary Metabolic Pathway Genes in Arabidopsis thaliana. Genome Biol Evol (2015) 0.75
Limits to Adaptation in Partially Selfing Species. Genetics (2016) 0.75
Selfing in haploid plants and efficacy of selection: codon usage bias in the model moss Physcomitrella patens. Genome Biol Evol (2017) 0.75
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol (2007) 45.68
Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol (1986) 36.06
A codon-based model of nucleotide substitution for protein-coding DNA sequences. Mol Biol Evol (1994) 19.91
A gene expression map of Arabidopsis thaliana development. Nat Genet (2005) 17.39
Common sequence polymorphisms shaping genetic diversity in Arabidopsis thaliana. Science (2007) 9.85
Sequencing of natural strains of Arabidopsis thaliana with short reads. Genome Res (2008) 8.44
Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell (2008) 6.91
Adaptive evolution of non-coding DNA in Drosophila. Nature (2005) 6.68
Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol (2007) 6.18
Adaptive protein evolution in Drosophila. Nature (2002) 5.71
Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics (2004) 4.88
The Arabidopsis lyrata genome sequence and the basis of rapid genome size change. Nat Genet (2011) 4.65
The cost of inbreeding in Arabidopsis. Nature (2002) 3.80
transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences. BMC Bioinformatics (2005) 3.41
Pervasive natural selection in the Drosophila genome? PLoS Genet (2009) 3.27
Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol (2009) 2.86
Synonymous codon usage in Escherichia coli: selection for translational accuracy. Mol Biol Evol (2006) 2.81
Association mapping of local climate-sensitive quantitative trait loci in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 2.51
The genomic rate of adaptive amino acid substitution in Drosophila. Mol Biol Evol (2004) 2.44
Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J Mol Evol (2003) 2.39
Evolution of protein-coding genes in Drosophila. Trends Genet (2008) 2.36
Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome. Genome Res (2007) 2.17
Genomewide spatial correspondence between nonsynonymous divergence and neutral polymorphism reveals extensive adaptation in Drosophila. Genetics (2007) 1.89
Estimating the genomewide rate of adaptive protein evolution in Drosophila. Genetics (2006) 1.76
Genome wide analyses reveal little evidence for adaptive evolution in many plant species. Mol Biol Evol (2010) 1.76
Quantifying adaptive evolution in the Drosophila immune system. PLoS Genet (2009) 1.74
Contrasting patterns of nonneutral evolution in proteins encoded in nuclear and mitochondrial genomes. Genetics (2000) 1.52
Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol (2008) 1.47
Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Mol Biol Evol (2010) 1.47
Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol (2004) 1.46
Gene expression and protein length influence codon usage and rates of sequence evolution in Populus tremula. Mol Biol Evol (2007) 1.38
The quest for the universals of protein evolution. Trends Genet (2006) 1.35
Factors that contribute to variation in evolutionary rate among Arabidopsis genes. Mol Biol Evol (2011) 1.31
Detecting positive selection within genomes: the problem of biased gene conversion. Philos Trans R Soc Lond B Biol Sci (2010) 1.25
Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol (2008) 1.23
Effective population size is positively correlated with levels of adaptive divergence among annual sunflowers. Mol Biol Evol (2010) 1.16
Recombination and base composition: the case of the highly self-fertilizing plant Arabidopsis thaliana. Genome Biol (2004) 1.11
Natural selection on synonymous and nonsynonymous mutations shapes patterns of polymorphism in Populus tremula. Mol Biol Evol (2009) 1.10
No effect of recombination on the efficacy of natural selection in primates. Genome Res (2008) 1.05
Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice. Mol Biol Evol (2010) 0.98
The effects of network neighbours on protein evolution. PLoS One (2011) 0.83
RNA exosome depletion reveals transcription upstream of active human promoters. Science (2008) 6.80
Insights into hominid evolution from the gorilla genome sequence. Nature (2012) 4.12
Comparative and demographic analysis of orang-utan genomes. Nature (2011) 3.83
Genomic relationships and speciation times of human, chimpanzee, and gorilla inferred from a coalescent hidden Markov model. PLoS Genet (2006) 3.53
Great ape genetic diversity and population history. Nature (2013) 2.95
Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nat Genet (2006) 2.59
The bonobo genome compared with the chimpanzee and human genomes. Nature (2012) 2.49
Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing. BMC Genomics (2005) 2.34
CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics (2005) 1.96
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection. Genome Res (2011) 1.88
Nested core collections maximizing genetic diversity in Arabidopsis thaliana. Plant J (2004) 1.88
Recombination: an underappreciated factor in the evolution of plant genomes. Nat Rev Genet (2007) 1.84
Recent speciation associated with the evolution of selfing in Capsella. Proc Natl Acad Sci U S A (2009) 1.83
Evidence for a large-scale population structure among accessions of Arabidopsis thaliana: possible causes and consequences for the distribution of linkage disequilibrium. Mol Ecol (2006) 1.73
The Capsella rubella genome and the genomic consequences of rapid mating system evolution. Nat Genet (2013) 1.69
An atlas of over 90,000 conserved noncoding sequences provides insight into crucifer regulatory regions. Nat Genet (2013) 1.68
Whole genome association mapping by incompatibilities and local perfect phylogenies. BMC Bioinformatics (2006) 1.68
Patterns of polymorphism and demographic history in natural populations of Arabidopsis lyrata. PLoS One (2008) 1.63
SOAPindel: efficient identification of indels from short paired reads. Genome Res (2012) 1.59
Recent speciation of Capsella rubella from Capsella grandiflora, associated with loss of self-incompatibility and an extreme bottleneck. Proc Natl Acad Sci U S A (2009) 1.57
The transition to self-compatibility in Arabidopsis thaliana and evolution within S-haplotypes over 10 Myr. Mol Biol Evol (2006) 1.57
Ancestral population genomics: the coalescent hidden Markov model approach. Genetics (2009) 1.54
The making of a new pathogen: insights from comparative population genomics of the domesticated wheat pathogen Mycosphaerella graminicola and its wild sister species. Genome Res (2011) 1.53
Genome-wide evidence for efficient positive and purifying selection in Capsella grandiflora, a plant species with a large effective population size. Mol Biol Evol (2010) 1.47
Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula. Proc Natl Acad Sci U S A (2011) 1.46
Direct estimation of mutation rate for 10 microsatellite loci in durum wheat, Triticum turgidum (L.) Thell. ssp durum desf. Mol Biol Evol (2002) 1.40
The properties of adaptive walks in evolving populations of fungus. PLoS Biol (2009) 1.38
Estimating divergence time and ancestral effective population size of Bornean and Sumatran orangutan subspecies using a coalescent hidden Markov model. PLoS Genet (2011) 1.37
Microsatellite diversity and broad scale geographic structure in a model legume: building a set of nested core collection for studying naturally occurring variation in Medicago truncatula. BMC Plant Biol (2006) 1.33
A comparative view of the evolution of grasses under domestication. New Phytol (2009) 1.31
Repeated adaptive introgression at a gene under multiallelic balancing selection. PLoS Genet (2008) 1.29
Haplotype structure of the stigmatic self-incompatibility gene in natural populations of Arabidopsis lyrata. Mol Biol Evol (2003) 1.25
Whole-genome and chromosome evolution associated with host adaptation and speciation of the wheat pathogen Mycosphaerella graminicola. PLoS Genet (2010) 1.24
Extensive X-linked adaptive evolution in central chimpanzees. Proc Natl Acad Sci U S A (2012) 1.23
Selection on amino acid substitutions in Arabidopsis. Mol Biol Evol (2008) 1.23
A new isolation with migration model along complete genomes infers very different divergence processes among closely related great ape species. PLoS Genet (2012) 1.23
Patterns of inbreeding depression and architecture of the load in subdivided populations. Genetics (2003) 1.19
Diversity and linkage of genes in the self-incompatibility gene family in Arabidopsis lyrata. Genetics (2003) 1.14
Relative roles of mutation and recombination in generating allelic polymorphism at an MHC class II locus in Peromyscus maniculatus. Genet Res (2003) 1.13
Long-term stability and effective population size in North Sea and Baltic Sea cod (Gadus morhua). Mol Ecol (2006) 1.10
The Icelandic Cancer Project--a population-wide approach to studying cancer. Nat Rev Cancer (2004) 1.09
Genomic screening for artificial selection during domestication and improvement in maize. Ann Bot (2007) 1.09
Mating-system variation, demographic history and patterns of nucleotide diversity in the Tristylous plant Eichhornia paniculata. Genetics (2009) 1.08
High DNA sequence diversity in pericentromeric genes of the plant Arabidopsis lyrata. Genetics (2008) 1.07
Local phylogeny mapping of quantitative traits: higher accuracy and better ranking than single-marker association in genomewide scans. Genetics (2008) 1.07
The population genomics of plant adaptation. New Phytol (2010) 1.06
Molecular footprints of local adaptation in two Mediterranean conifers. Mol Biol Evol (2010) 1.05
'Inconstant males' and the maintenance of labile sex expression in subdioecious plants. New Phytol (2007) 1.03
Expression of distinct self-incompatibility specificities in Arabidopsis thaliana. Genetics (2009) 1.02
The ARC1 E3 ligase gene is frequently deleted in self-compatible Brassicaceae species and has a conserved role in Arabidopsis lyrata self-pollen rejection. Plant Cell (2012) 1.02
Co-evolution between transposable elements and their hosts: a major factor in genome size evolution? Chromosome Res (2011) 1.01
On the distribution of temporal variations in allele frequency: consequences for the estimation of effective population size and the detection of loci undergoing selection. Genetics (2004) 0.98
Does speciation between Arabidopsis halleri and Arabidopsis lyrata coincide with major changes in a molecular target of adaptation? PLoS One (2011) 0.97
Reconstructing origins of loss of self-incompatibility and selfing in North American Arabidopsis lyrata: a population genetic context. Evolution (2010) 0.97
Genomic identification of founding haplotypes reveals the history of the selfing species Capsella rubella. PLoS Genet (2013) 0.96
Genetic architecture and adaptive significance of the selfing syndrome in Capsella. Evolution (2012) 0.96
Molecular evolution and positive selection of the symbiotic gene NORK in Medicago truncatula. J Mol Evol (2006) 0.92
Insertion and deletion processes in recent human history. PLoS One (2010) 0.91
Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus. BMC Genomics (2012) 0.91
An effort to use human-based exome capture methods to analyze chimpanzee and macaque exomes. PLoS One (2012) 0.88
Selective constraints on codon usage of nuclear genes from Arabidopsis thaliana. Mol Biol Evol (2006) 0.88
Properties of selected mutations and genotypic landscapes under Fisher's geometric model. Evolution (2014) 0.88
Pollen-specific, but not sperm-specific, genes show stronger purifying selection and higher rates of positive selection than sporophytic genes in Capsella grandiflora. Mol Biol Evol (2013) 0.87
The effective size of the Icelandic population and the prospects for LD mapping: inference from unphased microsatellite markers. Eur J Hum Genet (2006) 0.87
Selection, genome-wide fitness effects and evolutionary rates in the model legume Medicago truncatula. Mol Ecol (2013) 0.87
RNA polymerase plays both sides: vivid and bidirectional transcription around and upstream of active promoters. Cell Cycle (2009) 0.87
Signature of diversifying selection on members of the pentatricopeptide repeat protein family in Arabidopsis lyrata. Genetics (2009) 0.87
Purifying selection and molecular adaptation in the genome of Verminephrobacter, the heritable symbiotic bacteria of earthworms. Genome Biol Evol (2012) 0.86
Investigation of the demographic and selective forces shaping the nucleotide diversity of genes involved in nod factor signaling in Medicago truncatula. Genetics (2007) 0.86
A population genomics perspective on the emergence and adaptation of new plant pathogens in agro-ecosystems. PLoS Pathog (2012) 0.85
Conditional neutrality at two adjacent NBS-LRR disease resistance loci in natural populations of Arabidopsis lyrata. Mol Ecol (2008) 0.85
Coalescent-based analysis distinguishes between allo- and autopolyploid origin in Shepherd's Purse (Capsella bursa-pastoris). Mol Biol Evol (2012) 0.85
Claudin-3 tight junction proteins in Tetraodon nigroviridis: cloning, tissue-specific expression, and a role in hydromineral balance. Am J Physiol Regul Integr Comp Physiol (2008) 0.85
Sex-linked inheritance in macaque monkeys: implications for effective population size and dispersal to Sulawesi. Genetics (2010) 0.84
Signatures of balancing selection are maintained at disease resistance loci following mating system evolution and a population bottleneck in the genus Capsella. BMC Evol Biol (2012) 0.84
Mating system shifts and transposable element evolution in the plant genus Capsella. BMC Genomics (2014) 0.83
Molecular adaptation in flowering and symbiotic recognition pathways: insights from patterns of polymorphism in the legume Medicago truncatula. BMC Evol Biol (2011) 0.83
Neutral evolution of synonymous base composition in the Brassicaceae. J Mol Evol (2006) 0.83
No evidence that sex and transposable elements drive genome size variation in evening primroses. Evolution (2015) 0.83
Sex inheritance in gynodioecious species: a polygenic view. Proc Biol Sci (2005) 0.83
GeneRecon--a coalescent based tool for fine-scale association mapping. Bioinformatics (2006) 0.82
Claudin-8 and -27 tight junction proteins in puffer fish Tetraodon nigroviridis acclimated to freshwater and seawater. J Comp Physiol B (2008) 0.81
Contrasting patterns of transposable-element insertion polymorphism and nucleotide diversity in autotetraploid and allotetraploid Arabidopsis species. Genetics (2008) 0.81
Analysis of site frequency spectra from Arabidopsis with context-dependent corrections for ancestral misinference. Plant Physiol (2008) 0.81
Sequence analysis of measles virus strains collected during the pre- and early-vaccination era in Denmark reveals a considerable diversity of ancient strains. APMIS (2002) 0.81
When gametophytic self-incompatibility meets gynodioecy. Genet Res (Camb) (2008) 0.80
Increased rate of human mutations where DNA and RNA polymerases collide. Trends Genet (2009) 0.79
Adaptive evolution of the symbiotic gene NORK is not correlated with shifts of rhizobial specificity in the genus Medicago. BMC Evol Biol (2007) 0.78
"Ménage à trois": the presence/absence of thyme shapes the mutualistic interaction between the host plant Medicago truncatula (Fabaceae) and its symbiotic bacterium Sinorhizobium meliloti. Ecol Evol (2012) 0.77
Contrasted patterns of selective pressure in three recent paralogous gene pairs in the Medicago genus (L.). BMC Evol Biol (2012) 0.76
Association mapping and disease: evolutionary perspectives. Methods Mol Biol (2012) 0.76
Unraveling recombination rate evolution using ancestral recombination maps. Bioessays (2014) 0.75