Published in Nature on February 03, 2005
Evolution at two levels: on genes and form. PLoS Biol (2005) 5.84
Revealing the architecture of gene regulation: the promise of eQTL studies. Trends Genet (2008) 5.78
Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol (2006) 4.01
Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res (2008) 3.76
The evolution of combinatorial gene regulation in fungi. PLoS Biol (2008) 3.53
Mechanistic approaches to the study of evolution: the functional synthesis. Nat Rev Genet (2007) 3.43
Emerging principles of regulatory evolution. Proc Natl Acad Sci U S A (2007) 3.42
A conserved supergene locus controls colour pattern diversity in Heliconius butterflies. PLoS Biol (2006) 3.15
Transcription factor substitution during the evolution of fungal ribosome regulation. Mol Cell (2008) 3.13
Conservation of core gene expression in vertebrate tissues. J Biol (2009) 2.84
Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science (2009) 2.77
The evolution of hierarchical gene regulatory networks. Nat Rev Genet (2009) 2.62
Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet (2011) 2.60
Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program. PLoS Genet (2005) 2.36
Adaptive variation in beach mice produced by two interacting pigmentation genes. PLoS Biol (2007) 2.33
Stable structural color patterns displayed on transparent insect wings. Proc Natl Acad Sci U S A (2011) 2.32
Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest. Cell (2015) 2.31
The genetic basis of adaptive pigmentation variation in Drosophila melanogaster. Mol Ecol (2007) 2.27
Two or four bristles: functional evolution of an enhancer of scute in Drosophilidae. PLoS Biol (2006) 2.23
Frequent gain and loss of functional transcription factor binding sites. PLoS Comput Biol (2007) 2.04
Rapid evolutionary rewiring of a structurally constrained eye enhancer. Curr Biol (2011) 1.98
Regulatory divergence modifies limb length between mammals. Genes Dev (2008) 1.96
Parallel genetic origins of pelvic reduction in vertebrates. Proc Natl Acad Sci U S A (2006) 1.96
Gene regulation in primates evolves under tissue-specific selection pressures. PLoS Genet (2008) 1.86
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature (2011) 1.83
Evolution of gene regulatory networks controlling body plan development. Cell (2011) 1.80
An atlas of gene expression from seed to seed through barley development. Funct Integr Genomics (2006) 1.79
Evolution of the Yellow/Major Royal Jelly Protein family and the emergence of social behavior in honey bees. Genome Res (2006) 1.79
Rewiring cells: synthetic biology as a tool to interrogate the organizational principles of living systems. Annu Rev Biophys (2010) 1.78
Systematic dissection of regulatory motifs in 2000 predicted human enhancers using a massively parallel reporter assay. Genome Res (2013) 1.78
Genomic hotspots for adaptation: the population genetics of Müllerian mimicry in the Heliconius melpomene clade. PLoS Genet (2010) 1.73
Generation of a novel wing colour pattern by the Wingless morphogen. Nature (2010) 1.69
Evolutionary tinkering with conserved components of a transcriptional regulatory network. PLoS Biol (2010) 1.67
Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins. Cell (2016) 1.59
Global analysis of allele-specific expression in Arabidopsis thaliana. Genetics (2009) 1.58
Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol (2008) 1.53
Canalization of segmentation and its evolution in Drosophila. Proc Natl Acad Sci U S A (2007) 1.47
Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol (2006) 1.46
Development of bat flight: morphologic and molecular evolution of bat wing digits. Proc Natl Acad Sci U S A (2006) 1.45
Evidence for widespread adaptive evolution of gene expression in budding yeast. Proc Natl Acad Sci U S A (2010) 1.44
Comparative Developmental Transcriptomics Reveals Rewiring of a Highly Conserved Gene Regulatory Network during a Major Life History Switch in the Sea Urchin Genus Heliocidaris. PLoS Biol (2016) 1.44
Enhancer Runaway and the Evolution of Diploid Gene Expression. PLoS Genet (2015) 1.39
Quantitative genome-wide enhancer activity maps for five Drosophila species show functional enhancer conservation and turnover during cis-regulatory evolution. Nat Genet (2014) 1.38
Regulatory evolution in proteins by turnover and lineage-specific changes of cyclin-dependent kinase consensus sites. Proc Natl Acad Sci U S A (2007) 1.33
yellow and ebony are the responsible genes for the larval color mutants of the silkworm Bombyx mori. Genetics (2008) 1.28
Speciation genetics: current status and evolving approaches. Philos Trans R Soc Lond B Biol Sci (2010) 1.28
Assessing computational methods of cis-regulatory module prediction. PLoS Comput Biol (2010) 1.27
Many genes in fish have species-specific asymmetric rates of molecular evolution. BMC Genomics (2006) 1.27
Phenotypic plasticity in Drosophila pigmentation caused by temperature sensitivity of a chromatin regulator network. PLoS Genet (2007) 1.25
Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences. Proc Natl Acad Sci U S A (2011) 1.24
Melanin-synthesis enzymes coregulate stage-specific larval cuticular markings in the swallowtail butterfly, Papilio xuthus. Dev Genes Evol (2005) 1.22
The UBX-regulated network in the haltere imaginal disc of D. melanogaster. Dev Biol (2006) 1.21
Protein modularity, cooperative binding, and hybrid regulatory states underlie transcriptional network diversification. Cell (2012) 1.21
New perspectives on pharyngeal dorsoventral patterning in development and evolution of the vertebrate jaw. Dev Biol (2012) 1.20
Using reporter gene assays to identify cis regulatory differences between humans and chimpanzees. Genetics (2007) 1.18
Simpler mode of inheritance of transcriptional variation in male Drosophila melanogaster. Proc Natl Acad Sci U S A (2007) 1.17
The evolution of root hairs and rhizoids. Ann Bot (2012) 1.17
A novel gene family controls species-specific morphological traits in Hydra. PLoS Biol (2008) 1.16
A simplified explanation for the frameshift mutation that created a novel C-terminal motif in the APETALA3 gene lineage. BMC Evol Biol (2006) 1.13
A cis-regulatory sequence within the yellow locus of Drosophila melanogaster required for normal male mating success. Genetics (2005) 1.13
Evolution of transcription networks--lessons from yeasts. Curr Biol (2010) 1.12
De novo genesis of enhancers in vertebrates. PLoS Biol (2011) 1.11
Evolution of sex-specific traits through changes in HOX-dependent doublesex expression. PLoS Biol (2011) 1.10
Not just black and white: pigment pattern development and evolution in vertebrates. Semin Cell Dev Biol (2008) 1.10
Evolutionary history of the recruitment of conserved developmental genes in association to the formation and diversification of a novel trait. BMC Evol Biol (2012) 1.09
Industrial melanism in the peppered moth is not associated with genetic variation in canonical melanisation gene candidates. PLoS One (2010) 1.07
The genetic basis of rapidly evolving male genital morphology in Drosophila. Genetics (2011) 1.07
RNA-seq analysis of allele-specific expression, hybrid effects, and regulatory divergence in hybrids compared with their parents from natural populations. Genome Biol Evol (2013) 1.07
Cross-species RNAi rescue platform in Drosophila melanogaster. Genetics (2009) 1.06
The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks. Curr Biol (2009) 1.06
Blending of animal colour patterns by hybridization. Nat Commun (2010) 1.06
Tempo and mode in evolution of transcriptional regulation. PLoS Genet (2012) 1.05
Systematic detection of polygenic cis-regulatory evolution. PLoS Genet (2011) 1.05
A closer look at the eve stripe 2 enhancers of Drosophila and Themira. PLoS Genet (2008) 1.04
Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature (2014) 1.03
Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genet (2010) 1.02
Eyespot colour pattern determination by serial induction in fish: Mechanistic convergence with butterfly eyespots. Sci Rep (2012) 1.01
Evolution of cis elements in the differential expression of two Hoxa2 coparalogous genes in pufferfish (Takifugu rubripes). Proc Natl Acad Sci U S A (2006) 1.01
Genomic divergence during speciation driven by adaptation to altitude. Mol Biol Evol (2013) 0.99
Dissecting sources of quantitative gene expression pattern divergence between Drosophila species. Mol Syst Biol (2012) 0.99
Cis-regulatory evolution of chalcone-synthase expression in the genus Arabidopsis. Genetics (2006) 0.99
Dissecting the regulatory switches of development: lessons from enhancer evolution in Drosophila. Development (2010) 0.98
Comparative RNAi screens in C. elegans and C. briggsae reveal the impact of developmental system drift on gene function. PLoS Genet (2014) 0.97
A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PLoS Genet (2015) 0.97
Independent recruitments of a translational regulator in the evolution of self-fertile nematodes. Proc Natl Acad Sci U S A (2011) 0.96
Defining and mapping mammalian coat pattern genes: multiple genomic regions implicated in domestic cat stripes and spots. Genetics (2009) 0.96
Gene expression defines natural changes in mammalian lifespan. Aging Cell (2015) 0.96
Diverging functions of Scr between embryonic and post-embryonic development in a hemimetabolous insect, Oncopeltus fasciatus. Dev Biol (2009) 0.95
The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Res (2013) 0.95
Recurrent modification of a conserved cis-regulatory element underlies fruit fly pigmentation diversity. PLoS Genet (2013) 0.95
Identification and analysis of YELLOW protein family genes in the silkworm, Bombyx mori. BMC Genomics (2006) 0.95
Gain of cis-regulatory activities underlies novel domains of wingless gene expression in Drosophila. Proc Natl Acad Sci U S A (2015) 0.95
Convergent, modular expression of ebony and tan in the mimetic wing patterns of Heliconius butterflies. Dev Genes Evol (2011) 0.94
Evolution of transcriptional enhancers and animal diversity. Philos Trans R Soc Lond B Biol Sci (2013) 0.94
Adaptive variation regulates the expression of the human SGK1 gene in response to stress. PLoS Genet (2009) 0.93
The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. Dev Biol (2007) 0.93
Evolutionary plasticity of polycomb/trithorax response elements in Drosophila species. PLoS Biol (2008) 0.92
Polygenic cis-regulatory adaptation in the evolution of yeast pathogenicity. Genome Res (2012) 0.92
The impact of cis-acting polymorphisms on the human phenotype. Hugo J (2011) 0.91
A database of wing diversity in the Hawaiian Drosophila. PLoS One (2007) 0.91
Genome-scale approaches to resolving incongruence in molecular phylogenies. Nature (2003) 10.73
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature (2006) 4.21
Animal evolution and the molecular signature of radiations compressed in time. Science (2005) 3.98
Emerging principles of regulatory evolution. Proc Natl Acad Sci U S A (2007) 3.42
Gene duplication and the adaptive evolution of a classic genetic switch. Nature (2007) 3.41
Molecular architecture of annelid nerve cord supports common origin of nervous system centralization in bilateria. Cell (2007) 3.12
The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell (2008) 3.10
Evolution of key cell signaling and adhesion protein families predates animal origins. Science (2003) 2.85
Evolution of a transcriptional repression domain in an insect Hox protein. Nature (2002) 2.82
Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science (2009) 2.77
Gene co-option in physiological and morphological evolution. Annu Rev Cell Dev Biol (2002) 2.71
Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res (2010) 2.69
Evolution in black and white: genetic control of pigment patterns in Drosophila. Trends Genet (2003) 2.47
Reciprocal functions of the Drosophila yellow and ebony proteins in the development and evolution of pigment patterns. Development (2002) 2.42
Parallel inactivation of multiple GAL pathway genes and ecological diversification in yeasts. Proc Natl Acad Sci U S A (2004) 2.33
The regulation and evolution of a genetic switch controlling sexually dimorphic traits in Drosophila. Cell (2008) 2.27
Evolution of yellow gene regulation and pigmentation in Drosophila. Curr Biol (2002) 2.21
Genetic and molecular insights into the development and evolution of sexual dimorphism. Nat Rev Genet (2009) 2.18
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy. Mol Biol Evol (2005) 2.16
Bushes in the tree of life. PLoS Biol (2006) 2.16
Rapid evolution of sex pheromone-producing enzyme expression in Drosophila. PLoS Biol (2009) 2.09
Genetic mechanisms and constraints governing the evolution of correlated traits in drosophilid flies. Nature (2003) 2.08
Compensatory cis-trans evolution and the dysregulation of gene expression in interspecific hybrids of Drosophila. Genetics (2005) 1.93
Regulation of body pigmentation by the Abdominal-B Hox protein and its gain and loss in Drosophila evolution. Cell (2006) 1.92
Drosophila pigmentation evolution: divergent genotypes underlying convergent phenotypes. Proc Natl Acad Sci U S A (2003) 1.74
Body plan innovation in treehoppers through the evolution of an extra wing-like appendage. Nature (2011) 1.71
Quantitative trait loci responsible for variation in sexually dimorphic traits in Drosophila melanogaster. Genetics (2003) 1.70
Molecular mechanisms of selector gene function and evolution. Curr Opin Genet Dev (2002) 1.70
The regulatory content of intergenic DNA shapes genome architecture. Genome Biol (2004) 1.70
Generation of a novel wing colour pattern by the Wingless morphogen. Nature (2010) 1.69
The causes of repeated genetic evolution. Dev Biol (2009) 1.64
Hox repression of a target gene: extradenticle-independent, additive action through multiple monomer binding sites. Development (2002) 1.64
Frequent and widespread parallel evolution of protein sequences. Mol Biol Evol (2008) 1.47
Sources of bias in measures of allele-specific expression derived from RNA-sequence data aligned to a single reference genome. BMC Genomics (2013) 1.33
Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Mol Ecol (2010) 1.30
Conflicting phylogenetic signals at the base of the metazoan tree. Evol Dev (2003) 1.24
Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis-regulatory elements in Drosophila. Development (2005) 1.24
Evolutionary origin of a novel gene expression pattern through co-option of the latent activities of existing regulatory sequences. Proc Natl Acad Sci U S A (2011) 1.24
The UBX-regulated network in the haltere imaginal disc of D. melanogaster. Dev Biol (2006) 1.21
A gene necessary for normal male courtship, yellow, acts downstream of fruitless in the Drosophila melanogaster larval brain. J Neurobiol (2003) 1.20
Collaboration between Smads and a Hox protein in target gene repression. Development (2007) 1.19
Caudal and even-skipped in the annelid Platynereis dumerilii and the ancestry of posterior growth. Evol Dev (2005) 1.17
Contrasting properties of gene-specific regulatory, coding, and copy number mutations in Saccharomyces cerevisiae: frequency, effects, and dominance. PLoS Genet (2012) 1.07
Tempo and mode of regulatory evolution in Drosophila. Genome Res (2014) 1.05
Emergence and diversification of fly pigmentation through evolution of a gene regulatory module. Science (2013) 1.05
Sexually dimorphic regulation of the Wingless morphogen controls sex-specific segment number in Drosophila. Proc Natl Acad Sci U S A (2011) 1.04
Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genet (2010) 1.02
Genomic imprinting absent in Drosophila melanogaster adult females. Cell Rep (2012) 1.00
Evolution of multiple additive loci caused divergence between Drosophila yakuba and D. santomea in wing rowing during male courtship. PLoS One (2012) 0.97
The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Res (2013) 0.95
A single gene affects both ecological divergence and mate choice in Drosophila. Science (2014) 0.95
Evolution of the tan locus contributed to pigment loss in Drosophila santomea: a response to Matute et al. Cell (2009) 0.94
The evolution of abdominal reduction and the recent origin of distinct Abdominal-B transcript classes in Diptera. Evol Dev (2006) 0.93
The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. Dev Biol (2007) 0.93
Evolution of splicing regulatory networks in Drosophila. Genome Res (2014) 0.90
Pleiotropic functions of a conserved insect-specific Hox peptide motif. Development (2005) 0.89
The ontogeny of color: developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evol Dev (2012) 0.88
Pharmacologic approaches to butterfly wing patterning: sulfated polysaccharides mimic or antagonize cold shock and alter the interpretation of gradients of positional information. Dev Biol (2005) 0.87
Smells like evolution: the role of chemoreceptor evolution in behavioral change. Curr Opin Neurobiol (2012) 0.86
Regulating evolution. Sci Am (2008) 0.85
Effect of genetic variation in a Drosophila model of diabetes-associated misfolded human proinsulin. Genetics (2013) 0.85
Immunohistochemical colocalization of Yellow and male-specific Fruitless in Drosophila melanogaster neuroblasts. Biochem Biophys Res Commun (2002) 0.83
Sex-specific effects of cis-regulatory variants in Drosophila melanogaster. Genetics (2013) 0.81
Evolution of an insect-specific GROUCHO-interaction motif in the ENGRAILED selector protein. Evol Dev (2008) 0.79
Evolutionary biology: Genomic hourglass. Nature (2010) 0.78
Monkey see, monkey do. Nat Genet (2006) 0.76
Behavioural neuroscience: Fruity aphrodisiacs. Nature (2011) 0.75
Annotating ebony on the fly. Mol Ecol (2007) 0.75
Behavioural neurobiology: Chemical love. Nature (2009) 0.75
QnAs with Sean B. Carroll. Proc Natl Acad Sci U S A (2010) 0.75
History: Great myths die hard. Nature (2013) 0.75