Human-specific loss of regulatory DNA and the evolution of human-specific traits.

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Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nat Rev Genet (2011) 2.60

Differential relationship of DNA replication timing to different forms of human mutation and variation. Am J Hum Genet (2012) 2.33

Enhancer Divergence and cis-Regulatory Evolution in the Human and Chimp Neural Crest. Cell (2015) 2.31

Inhibition of SRGAP2 function by its human-specific paralogs induces neoteny during spine maturation. Cell (2012) 2.02

Regulation of eukaryotic gene expression by the untranslated gene regions and other non-coding elements. Cell Mol Life Sci (2012) 1.96

Comparative studies of gene expression and the evolution of gene regulation. Nat Rev Genet (2012) 1.79

Progressive Loss of Function in a Limb Enhancer during Snake Evolution. Cell (2016) 1.76

Evolving New Skeletal Traits by cis-Regulatory Changes in Bone Morphogenetic Proteins. Cell (2016) 1.59

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The evolution of lineage-specific regulatory activities in the human embryonic limb. Cell (2013) 1.51

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Enhancer evolution across 20 mammalian species. Cell (2015) 1.48

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior. Cell (2016) 1.46

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Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. PLoS Genet (2012) 1.22

The ensembl regulatory build. Genome Biol (2015) 1.21

Human cerebral organoids recapitulate gene expression programs of fetal neocortex development. Proc Natl Acad Sci U S A (2015) 1.20

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Radial glia require PDGFD-PDGFRβ signalling in human but not mouse neocortex. Nature (2014) 1.14

Exploring the role of copy number variants in human adaptation. Trends Genet (2012) 1.14

A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep (2012) 1.10

Human-specific histone methylation signatures at transcription start sites in prefrontal neurons. PLoS Biol (2012) 1.08

8.2% of the Human genome is constrained: variation in rates of turnover across functional element classes in the human lineage. PLoS Genet (2014) 1.08

Human-specific CpG "beacons" identify loci associated with human-specific traits and disease. Epigenetics (2012) 1.07

Genomic perspectives of transcriptional regulation in forebrain development. Neuron (2015) 0.97

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Analytical tools and current challenges in the modern era of neuroepigenomics. Nat Neurosci (2014) 0.94

Globularity and language-readiness: generating new predictions by expanding the set of genes of interest. Front Psychol (2014) 0.94

Evolution of transcriptional enhancers and animal diversity. Philos Trans R Soc Lond B Biol Sci (2013) 0.94

The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci (2013) 0.94

Selection on a variant associated with improved viral clearance drives local, adaptive pseudogenization of interferon lambda 4 (IFNL4). PLoS Genet (2014) 0.92

Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol (2014) 0.91

Disruption of long-range gene regulation in human genetic disease: a kaleidoscope of general principles, diverse mechanisms and unique phenotypic consequences. Hum Genet (2014) 0.91

Genetic changes shaping the human brain. Dev Cell (2015) 0.89

A Grand Challenge in Evolutionary and Population Genetics: New Paradigms for Exploring the Past and Charting the Future in the Post-Genomic era. Front Genet (2011) 0.89

A panel of induced pluripotent stem cells from chimpanzees: a resource for comparative functional genomics. Elife (2015) 0.88

Creation of targeted genomic deletions using TALEN or CRISPR/Cas nuclease pairs in one-cell mouse embryos. FEBS Open Bio (2014) 0.87

Widespread recurrent evolution of genomic features. Genome Biol Evol (2012) 0.87

Simian immunodeficiency virus and human immunodeficiency virus type 1 matrix proteins specify different capabilities to modulate B cell growth. J Virol (2014) 0.86

Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res (2012) 0.86

New type of Sendai virus vector provides transgene-free iPS cells derived from chimpanzee blood. PLoS One (2014) 0.86

From remote enhancers to gene regulation: charting the genome's regulatory landscapes. Philos Trans R Soc Lond B Biol Sci (2013) 0.86

Mechanisms governing the reactivation-dependent destabilization of memories and their role in extinction. Front Behav Neurosci (2013) 0.85

Analysis of the canine brain transcriptome with an emphasis on the hypothalamus and cerebral cortex. Mamm Genome (2013) 0.85

The evolution and functional impact of human deletion variants shared with archaic hominin genomes. Mol Biol Evol (2015) 0.85

Potential role of human-specific genes, human-specific microRNAs and human-specific non-coding regulatory RNAs in the pathogenesis of systemic sclerosis and Sjögren's syndrome. Autoimmun Rev (2013) 0.84

Large-scale gene expression study in the ophiuroid Amphiura filiformis provides insights into evolution of gene regulatory networks. Evodevo (2016) 0.84

Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. Genome Med (2014) 0.83

Seq2pathway: an R/Bioconductor package for pathway analysis of next-generation sequencing data. Bioinformatics (2015) 0.83

ComPlEx: conservation and divergence of co-expression networks in A. thaliana, Populus and O. sativa. BMC Genomics (2014) 0.83

Insights on the functional interactions between miRNAs and copy number variations in the aging brain. Front Mol Neurosci (2013) 0.83

Rational design of an artificial genetic switch: Co-option of the H-NS-repressed proU operon by the VirB virulence master regulator. J Bacteriol (2011) 0.83

Ensembl regulation resources. Database (Oxford) (2016) 0.82

From trans to cis: transcriptional regulatory networks in neocortical development. Trends Genet (2015) 0.81

Regulatory element copy number differences shape primate expression profiles. Proc Natl Acad Sci U S A (2012) 0.81

Changes in Cis-regulatory Elements during Morphological Evolution. Biology (Basel) (2012) 0.80

Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework. PLoS Comput Biol (2014) 0.80

Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site. Elife (2015) 0.80

Dynamics of genome size evolution in birds and mammals. Proc Natl Acad Sci U S A (2017) 0.80

A Primate lncRNA Mediates Notch Signaling during Neuronal Development by Sequestering miRNA. Neuron (2016) 0.79

Divergence in sex steroid hormone signaling between sympatric species of Japanese threespine stickleback. PLoS One (2011) 0.79

Comprehensive human transcription factor binding site map for combinatory binding motifs discovery. PLoS One (2012) 0.79

Abnormal levels of Gadd45alpha in developing neocortex impair neurite outgrowth. PLoS One (2012) 0.79

Gadd45g is essential for primary sex determination, male fertility and testis development. PLoS One (2013) 0.78

The existence of species rests on a metastable equilibrium between inbreeding and outbreeding. An essay on the close relationship between speciation, inbreeding and recessive mutations. Biol Direct (2011) 0.78

Noncoding origins of anthropoid traits and a new null model of transposon functionalization. Genome Res (2014) 0.78

Genomic divergence and brain evolution: How regulatory DNA influences development of the cerebral cortex. Bioessays (2015) 0.78

"Reverse Genomics" Predicts Function of Human Conserved Noncoding Elements. Mol Biol Evol (2016) 0.78

What's Wrong with Human/Nonhuman Chimera Research? PLoS Biol (2016) 0.77

Variation in vertebrate cis-regulatory elements in evolution and disease. Transcription (2014) 0.77

Adaptive Evolution as a Predictor of Species-Specific Innate Immune Response. Mol Biol Evol (2015) 0.77

Role of maternal thyroid hormones in the developing neocortex and during human evolution. Front Neuroanat (2013) 0.77

Species-specific exon loss in human transcriptomes. Mol Biol Evol (2014) 0.76

The role of DNA insertions in phenotypic differentiation between humans and other primates. Genome Biol Evol (2015) 0.76

Inferring Selective Constraint from Population Genomic Data Suggests Recent Regulatory Turnover in the Human Brain. Genome Biol Evol (2015) 0.76

A penile spine/vibrissa enhancer sequence is missing in modern and extinct humans but is retained in multiple primates with penile spines and sensory vibrissae. PLoS One (2013) 0.76

The evolution of the human genome. Curr Opin Genet Dev (2015) 0.76

Ancient DNA reveals secrets of human history. Nature (2011) 0.76

The evolution and population diversity of human-specific segmental duplications. Nat Ecol Evol (2017) 0.76

Lineage-specific genomics: Frequent birth and death in the human genome: The human genome contains many lineage-specific elements created by both sequence and functional turnover. Bioessays (2016) 0.75

Identification of Multiple Forms of RNA Transcripts Associated with Human-Specific Retrotransposed Gene Copies. Genome Biol Evol (2016) 0.75

Indel reliability in indel-based phylogenetic inference. Genome Biol Evol (2014) 0.75

Brain evolution and development: adaptation, allometry and constraint. Proc Biol Sci (2016) 0.75

Decay of Sexual Trait Genes in an Asexual Parasitoid Wasp. Genome Biol Evol (2016) 0.75

Loss of gene function and evolution of human phenotypes. BMB Rep (2015) 0.75

Decoding transcriptional enhancers: Evolving from annotation to functional interpretation. Semin Cell Dev Biol (2016) 0.75

A compendium of developmental gene expression in Lake Malawi cichlid fishes. BMC Dev Biol (2017) 0.75

Words of wisdom. Re: Human-specific loss of regulatory DNA and the evolution of human-specific traits. Eur Urol (2011) 0.75

Populational landscape of INDELs affecting transcription factor-binding sites in humans. BMC Genomics (2015) 0.75

Controlling for Phylogenetic Relatedness and Evolutionary Rates Improves the Discovery of Associations Between Species' Phenotypic and Genomic Differences. Mol Biol Evol (2016) 0.75

Evolutionary acquisition of promoter-associated non-coding RNA (pancRNA) repertoires diversifies species-dependent gene activation mechanisms in mammals. BMC Genomics (2017) 0.75

Elevated rate of fixation of endogenous retroviral elements in Haplorhini TRIM5 and TRIM22 genomic sequences: impact on transcriptional regulation. PLoS One (2013) 0.75

Evolution of Shh endoderm enhancers during morphological transition from ventral lungs to dorsal gas bladder. Nat Commun (2017) 0.75

Initial sequence of the chimpanzee genome and comparison with the human genome. Nature (2005) 25.67

Evolution at two levels in humans and chimpanzees. Science (1975) 21.07

A draft sequence of the Neandertal genome. Science (2010) 19.55

ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38

GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72

Natural selection on protein-coding genes in the human genome. Nature (2005) 10.84

Evo-devo and an expanding evolutionary synthesis: a genetic theory of morphological evolution. Cell (2008) 9.47

An RNA gene expressed during cortical development evolved rapidly in humans. Nature (2006) 7.23

Parallel patterns of evolution in the genomes and transcriptomes of humans and chimpanzees. Science (2005) 5.68

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science (2009) 5.64

When less is more: gene loss as an engine of evolutionary change. Am J Hum Genet (1999) 5.32

Patterns of neural stem and progenitor cell division may underlie evolutionary cortical expansion. Nat Rev Neurosci (2006) 5.02

Biased gene conversion and the evolution of mammalian genomic landscapes. Annu Rev Genomics Hum Genet (2009) 4.12

Human-specific gain of function in a developmental enhancer. Science (2008) 3.84

A mutation in human CMP-sialic acid hydroxylase occurred after the Homo-Pan divergence. Proc Natl Acad Sci U S A (1998) 3.26

Reexamining human origins in light of Ardipithecus ramidus. Science (2009) 1.99

Comparing the human and chimpanzee genomes: searching for needles in a haystack. Genome Res (2005) 1.95

The embryonic preoptic area is a novel source of cortical GABAergic interneurons. J Neurosci (2009) 1.81

NF-kappa B-mediated repression of growth arrest- and DNA-damage-inducible proteins 45alpha and gamma is essential for cancer cell survival. Proc Natl Acad Sci U S A (2004) 1.66

Characterization of the proneural gene regulatory network during mouse telencephalon development. BMC Biol (2008) 1.59

Characterization of progenitor domains in the developing mouse thalamus. J Comp Neurol (2007) 1.55

GABAergic neurons in mammalian thalamus: a marker of thalamic complexity? Brain Res Bull (1997) 1.44

A histological study of the development of the penis of wild-type and androgen-insensitive mice. J Anat (1987) 1.35

Loss of expression of GADD45 gamma, a growth inhibitory gene, in human pituitary adenomas: implications for tumorigenesis. J Clin Endocrinol Metab (2002) 1.29

A comparative analysis of vibrissa count and infraorbital foramen area in primates and other mammals. J Hum Evol (2010) 1.08

Expression of androgen receptor mRNA during mouse embryogenesis. Mech Dev (1998) 1.05

Effects of testosterone on the sternal cutaneous glands and genitalia of the male greater galago (Galago crassicaudatus crassicaudatus). Folia Primatol (Basel) (1976) 0.91

Effect of castration and testosterone propionate on mouse vibrissae. Br J Dermatol (1983) 0.89

Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08

GREAT improves functional interpretation of cis-regulatory regions. Nat Biotechnol (2010) 16.72

Widespread parallel evolution in sticklebacks by repeated fixation of Ectodysplasin alleles. Science (2005) 10.46

Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature (2004) 7.62

Identification and classification of conserved RNA secondary structures in the human genome. PLoS Comput Biol (2006) 6.73

Adaptive evolution of pelvic reduction in sticklebacks by recurrent deletion of a Pitx1 enhancer. Science (2009) 5.64

The genomic basis of adaptive evolution in threespine sticklebacks. Nature (2012) 5.20

In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nat Genet (2006) 5.14

Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11

Retinoic acid regulates sex-specific timing of meiotic initiation in mice. Proc Natl Acad Sci U S A (2006) 3.94

cis-Regulatory changes in Kit ligand expression and parallel evolution of pigmentation in sticklebacks and humans. Cell (2007) 3.72

The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS Biol (2004) 3.46

Forces shaping the fastest evolving regions in the human genome. PLoS Genet (2006) 3.32

E2F mediates cell cycle-dependent transcriptional repression in vivo by recruitment of an HDAC1/mSin3B corepressor complex. Genes Dev (2002) 3.12

The master sex-determination locus in threespine sticklebacks is on a nascent Y chromosome. Curr Biol (2004) 2.90

Evidence for ecology's role in speciation. Nature (2004) 2.78

CP110, a cell cycle-dependent CDK substrate, regulates centrosome duplication in human cells. Dev Cell (2002) 2.74

Human genome ultraconserved elements are ultraselected. Science (2007) 2.34

Human neural stem cells enhance structural plasticity and axonal transport in the ischaemic brain. Brain (2011) 2.27

Multiple joint and skeletal patterning defects caused by single and double mutations in the mouse Gdf6 and Gdf5 genes. Dev Biol (2003) 2.17

The genetics of adaptive shape shift in stickleback: pleiotropy and effect size. Evolution (2007) 2.15

Muscle contraction is necessary to maintain joint progenitor cell fate. Dev Cell (2009) 2.09

Three periods of regulatory innovation during vertebrate evolution. Science (2011) 2.09

A distinct cohort of progenitor cells participates in synovial joint and articular cartilage formation during mouse limb skeletogenesis. Dev Biol (2008) 2.09

A role for a neo-sex chromosome in stickleback speciation. Nature (2009) 2.06

BMP receptor signaling is required for postnatal maintenance of articular cartilage. PLoS Biol (2004) 2.05

Ultraconserved elements in insect genomes: a highly conserved intronic sequence implicated in the control of homothorax mRNA splicing. Genome Res (2005) 2.02

Follistatin operates downstream of Wnt4 in mammalian ovary organogenesis. Dev Dyn (2004) 1.96

Parallel genetic origins of pelvic reduction in vertebrates. Proc Natl Acad Sci U S A (2006) 1.96

Coding exons function as tissue-specific enhancers of nearby genes. Genome Res (2012) 1.64

Mutations in ANKH cause chondrocalcinosis. Am J Hum Genet (2002) 1.63

Biochemical and genetic analysis of ANK in arthritis and bone disease. Am J Hum Genet (2006) 1.56

A genome-wide SNP genotyping array reveals patterns of global and repeated species-pair divergence in sticklebacks. Curr Biol (2011) 1.50

A general approach for identifying distant regulatory elements applied to the Gdf6 gene. Genome Res (2003) 1.49

Enhancers: five essential questions. Nat Rev Genet (2013) 1.46

Inflammatory factor profiles one hour following vocal fold injury. Ann Otol Rhinol Laryngol (2008) 1.33

CP110 cooperates with two calcium-binding proteins to regulate cytokinesis and genome stability. Mol Biol Cell (2006) 1.27

Population genomics of parallel phenotypic evolution in stickleback across stream-lake ecological transitions. Proc Biol Sci (2011) 1.21

Mineral formation in joints caused by complete or joint-specific loss of ANK function. J Bone Miner Res (2006) 1.20

Dual hindlimb control elements in the Tbx4 gene and region-specific control of bone size in vertebrate limbs. Development (2008) 1.19

Cell production in injured vocal folds: a rat study. Ann Otol Rhinol Laryngol (2006) 1.15

A "forward genomics" approach links genotype to phenotype using independent phenotypic losses among related species. Cell Rep (2012) 1.10

Modular skeletal evolution in sticklebacks is controlled by additive and clustered quantitative trait Loci. Genetics (2014) 1.09

Genetic architecture of variation in the lateral line sensory system of threespine sticklebacks. G3 (Bethesda) (2012) 1.09

Synovial joint morphogenesis requires the chondrogenic action of Sox5 and Sox6 in growth plate and articular cartilage. Dev Biol (2010) 1.08

Human developmental enhancers conserved between deuterostomes and protostomes. PLoS Genet (2012) 1.07

Shaping skeletal growth by modular regulatory elements in the Bmp5 gene. PLoS Genet (2008) 1.07

The genetic architecture of skeletal convergence and sex determination in ninespine sticklebacks. Curr Biol (2009) 1.06

Genetic signature of adaptive peak shift in threespine stickleback. Evolution (2012) 1.06

Spatio-temporal expression of Pbx3 during mouse organogenesis. Gene Expr Patterns (2006) 1.05

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Synovial joint formation during mouse limb skeletogenesis: roles of Indian hedgehog signaling. Ann N Y Acad Sci (2007) 1.01

Heparan sulfate mediates the proliferation and differentiation of rat mesenchymal stem cells. Stem Cells Dev (2009) 0.99

Comparative genomic analysis using the UCSC genome browser. Methods Mol Biol (2007) 0.98

Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. Dev Biol (2012) 0.97

The pisiform growth plate is lost in humans and supports a role for Hox in growth plate formation. J Anat (2014) 0.96

Endangered species hold clues to human evolution. J Hered (2010) 0.96

Spatial-temporal targeting of lung-specific mesenchyme by a Tbx4 enhancer. BMC Biol (2013) 0.95

PRISM offers a comprehensive genomic approach to transcription factor function prediction. Genome Res (2013) 0.94

Congenital asplenia in mice and humans with mutations in a Pbx/Nkx2-5/p15 module. Dev Cell (2012) 0.94

Investigation of anti-hyaluronidase treatment on vocal fold wound healing. J Voice (2005) 0.93

The enhancer landscape during early neocortical development reveals patterns of dense regulation and co-option. PLoS Genet (2013) 0.91

Lung mesenchymal expression of Sox9 plays a critical role in tracheal development. BMC Biol (2013) 0.91

A novel 13 base pair insertion in the sonic hedgehog ZRS limb enhancer (ZRS/LMBR1) causes preaxial polydactyly with triphalangeal thumb. Hum Mutat (2012) 0.90

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The case is unchanged and remains robust: Australopithecus afarensis exhibits only moderate skeletal dimorphism. A reply to Plavcan et al. (2005). J Hum Evol (2005) 0.90

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C. elegans HAM-1 positions the cleavage plane and regulates apoptosis in asymmetric neuroblast divisions. Dev Biol (2005) 0.89

Over-expression of BMP4 and BMP5 in a child with axial skeletal malformations and heterotopic ossification: a new syndrome. Am J Med Genet A (2007) 0.88

Structure-aided prediction of mammalian transcription factor complexes in conserved non-coding elements. Philos Trans R Soc Lond B Biol Sci (2013) 0.87

Dominant negative Bmp5 mutation reveals key role of BMPs in skeletal response to mechanical stimulation. BMC Dev Biol (2008) 0.86

Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res (2012) 0.86

Detection of potential GDF6 regulatory elements by multispecies sequence comparisons and identification of a skeletal joint enhancer. Genomics (2005) 0.86

Developing a community-based genetic nomenclature for anole lizards. BMC Genomics (2011) 0.86

Cooperation between p27 and p107 during endochondral ossification suggests a genetic pathway controlled by p27 and p130. Mol Cell Biol (2007) 0.84

Wt1 functions in the development of germ cells in addition to somatic cell lineages of the testis. Dev Biol (2004) 0.84

Noninvasive monitoring of placenta-specific transgene expression by bioluminescence imaging. PLoS One (2011) 0.83