Published in PLoS Genet on January 19, 2012
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On the need for mechanistic models in computational genomics and metagenomics. Genome Biol Evol (2013) 0.99
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Drosophila melanogaster Zelda and Single-minded collaborate to regulate an evolutionarily dynamic CNS midline cell enhancer. Dev Biol (2012) 0.80
Gene regulation and speciation in house mice. Genome Res (2016) 0.80
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Evolution of p53 transactivation specificity through the lens of a yeast-based functional assay. PLoS One (2015) 0.76
Histone H3 K27 acetylation marks a potent enhancer element on the adipogenic master regulator gene Pparg2. Cell Cycle (2014) 0.76
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Evolutionarily diverged regulation of X-chromosomal genes as a primal event in mouse reproductive isolation. PLoS Genet (2014) 0.76
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Integrative analysis of the Caenorhabditis elegans genome by the modENCODE project. Science (2010) 9.78
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An insect molecular clock dates the origin of the insects and accords with palaeontological and biogeographic landmarks. Mol Biol Evol (2002) 4.22
Repeated morphological evolution through cis-regulatory changes in a pleiotropic gene. Nature (2006) 4.21
Morphological evolution through multiple cis-regulatory mutations at a single gene. Nature (2007) 4.14
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Phenotypic robustness conferred by apparently redundant transcriptional enhancers. Nature (2010) 3.72
Evolution of alternative transcriptional circuits with identical logic. Nature (2006) 3.58
The evolution of combinatorial gene regulation in fungi. PLoS Biol (2008) 3.53
Caenorhabditis phylogeny predicts convergence of hermaphroditism and extensive intron loss. Proc Natl Acad Sci U S A (2004) 3.47
The evolution of postzygotic isolation: accumulating Dobzhansky-Muller incompatibilities. Evolution (2001) 3.36
A yeast hybrid provides insight into the evolution of gene expression regulation. Science (2009) 3.25
Regulatory changes underlying expression differences within and between Drosophila species. Nat Genet (2008) 3.24
Functional evolution of a cis-regulatory module. PLoS Biol (2005) 3.21
Gene expression divergence recapitulates the developmental hourglass model. Nature (2010) 3.20
Extensive sex-specific nonadditivity of gene expression in Drosophila melanogaster. Genetics (2004) 3.12
The evolution of gene regulation underlies a morphological difference between two Drosophila sister species. Cell (2008) 3.10
Stepwise modification of a modular enhancer underlies adaptation in a Drosophila population. Science (2009) 2.77
Regulatory divergence in Drosophila revealed by mRNA-seq. Genome Res (2010) 2.69
Sepsid even-skipped enhancers are functionally conserved in Drosophila despite lack of sequence conservation. PLoS Genet (2008) 2.67
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Noncanonical compensation of zygotic X transcription in early Drosophila melanogaster development revealed through single-embryo RNA-seq. PLoS Biol (2011) 2.43
Antagonism of LIN-17/Frizzled and LIN-18/Ryk in nematode vulva induction reveals evolutionary alterations in core developmental pathways. PLoS Biol (2011) 2.39
Binding site turnover produces pervasive quantitative changes in transcription factor binding between closely related Drosophila species. PLoS Biol (2010) 2.32
Evolution of yellow gene regulation and pigmentation in Drosophila. Curr Biol (2002) 2.21
Remarkably ancient balanced polymorphisms in a multi-locus gene network. Nature (2010) 2.18
Genetic and molecular insights into the development and evolution of sexual dimorphism. Nat Rev Genet (2009) 2.18
Conserved developmental transcriptomes in evolutionarily divergent species. Genome Biol (2010) 2.16
Rapid evolution of sex pheromone-producing enzyme expression in Drosophila. PLoS Biol (2009) 2.09
Rapid evolutionary rewiring of a structurally constrained eye enhancer. Curr Biol (2011) 1.98
Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet (2010) 1.97
A test of the snowball theory for the rate of evolution of hybrid incompatibilities. Science (2010) 1.97
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
Radical alterations in the roles of homeobox genes during echinoderm evolution. Nature (1997) 1.86
Morphological evolution caused by many subtle-effect substitutions in regulatory DNA. Nature (2011) 1.83
On the origin and spread of an adaptive allele in deer mice. Science (2009) 1.82
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Anomalies in the expression profile of interspecific hybrids of Drosophila melanogaster and Drosophila simulans. Genome Res (2004) 1.72
Generation of a novel wing colour pattern by the Wingless morphogen. Nature (2010) 1.69
Qualifying the relationship between sequence conservation and molecular function. Genome Res (2008) 1.69
Evolutionary innovation of the excretory system in Caenorhabditis elegans. Nat Genet (2004) 1.68
Dominance and the evolutionary accumulation of cis- and trans-effects on gene expression. Proc Natl Acad Sci U S A (2008) 1.67
Natural selection on cis and trans regulation in yeasts. Genome Res (2010) 1.65
Evolutionary plasticity of developmental gene regulatory network architecture. Proc Natl Acad Sci U S A (2007) 1.62
Structural rules and complex regulatory circuitry constrain expression of a Notch- and EGFR-regulated eye enhancer. Dev Cell (2010) 1.61
Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila. Science (2009) 1.56
Conserved regulation of p53 network dosage by microRNA-125b occurs through evolving miRNA-target gene pairs. PLoS Genet (2011) 1.55
Genetic flexibility in the convergent evolution of hermaphroditism in Caenorhabditis nematodes. Dev Cell (2006) 1.53
Evolution acts on enhancer organization to fine-tune gradient threshold readouts. PLoS Biol (2008) 1.53
Regulatory elements controlling chorion gene expression are conserved between flies and moths. Nature (1985) 1.50
Positive and negative selection on noncoding DNA in Drosophila simulans. Mol Biol Evol (2008) 1.47
Interspecies comparison reveals evolution of control regions in the nematode sex-determining gene tra-2. Genetics (1996) 1.47
Functional tests of enhancer conservation between distantly related species. Development (2003) 1.46
Design flexibility in cis-regulatory control of gene expression: synthetic and comparative evidence. Dev Biol (2008) 1.45
Coupled evolution of transcription and mRNA degradation. PLoS Biol (2011) 1.40
Does positive selection drive transcription factor binding site turnover? A test with Drosophila cis-regulatory modules. PLoS Genet (2011) 1.39
Hybrid incompatibility "snowballs" between Solanum species. Science (2010) 1.29
Functional evolution of cis-regulatory modules at a homeotic gene in Drosophila. PLoS Genet (2009) 1.25
Shape and function of the Bicoid morphogen gradient in dipteran species with different sized embryos. Dev Biol (2008) 1.23
Transcription factor binding variation in the evolution of gene regulation. Trends Genet (2010) 1.14
Composite effects of polymorphisms near multiple regulatory elements create a major-effect QTL. PLoS Genet (2011) 1.11
Evolution of the ventral midline in insect embryos. Dev Cell (2006) 1.07
Evolution of the control of sexual identity in nematodes. Semin Cell Dev Biol (2007) 1.06
Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genet (2010) 1.02
Evolutionary conservation of redundancy between a diverged pair of forkhead transcription factor homologues. Development (2000) 1.00
Patterning the ascidian nervous system: structure, expression and transgenic analysis of the CiHox3 gene. Development (1999) 0.97
Tissue-specific regulatory differences for the alcohol dehydrogenase genes of Hawaiian Drosophila are conserved in Drosophila melanogaster transformants. Proc Natl Acad Sci U S A (1988) 0.97
The use of Caenorhabditis elegans in parasitic nematode research. Parasitology (2004) 0.97
Roles of trans and cis variation in yeast intraspecies evolution of gene expression. Mol Biol Evol (2009) 0.96
Conserved function of anopheles gambiae midgut-specific promoters in the fruitfly. EMBO J (1996) 0.95
Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet (2011) 0.91
Roles of cis- and trans-changes in the regulatory evolution of genes in the gluconeogenic pathway in yeast. Mol Biol Evol (2008) 0.90
Changes in selective effects over time facilitate turnover of enhancer sequences. Genetics (2010) 0.88
Bicoid occurrence and Bicoid-dependent hunchback regulation in lower cyclorrhaphan flies. Evol Dev (2008) 0.88
Transgenic animal studies on the evolution of genetic regulatory circuitries. Bioessays (1992) 0.87
Two types of cis-trans compensation in the evolution of transcriptional regulation. Proc Natl Acad Sci U S A (2011) 0.85
Dissection of lin-11 enhancer regions in Caenorhabditis elegans and other nematodes. Dev Biol (2008) 0.82
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The zebrafish van gogh mutation disrupts tbx1, which is involved in the DiGeorge deletion syndrome in humans. Development (2003) 1.43
Detecting heterozygosity in shotgun genome assemblies: Lessons from obligately outcrossing nematodes. Genome Res (2009) 1.27
Conservation of linkage and evolution of developmental function within the Tbx2/3/4/5 subfamily of T-box genes: implications for the origin of vertebrate limbs. Dev Genes Evol (2008) 0.97
Phylogenetic analyses alone are insufficient to determine whether genome duplication(s) occurred during early vertebrate evolution. J Exp Zool B Mol Dev Evol (2003) 0.92
Coevolution within and between regulatory loci can preserve promoter function despite evolutionary rate acceleration. PLoS Genet (2012) 0.92
Distinct functional constraints partition sequence conservation in a cis-regulatory element. PLoS Genet (2011) 0.91
Macro-level modeling of the response of C. elegans reproduction to chronic heat stress. PLoS Comput Biol (2012) 0.88
Evidence that purifying selection acts on promoter sequences. Genetics (2011) 0.79
Family size and turnover rates among several classes of small non-protein-coding RNA genes in Caenorhabditis nematodes. Genome Biol Evol (2012) 0.79
Functional conservation of cis-regulatory elements of heat-shock genes over long evolutionary distances. PLoS One (2011) 0.79
Computational prediction of Caenorhabditis box H/ACA snoRNAs using genomic properties of their host genes. RNA (2009) 0.77