Published in Nat Genet on January 06, 2008
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
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Cleft lip and palate: understanding genetic and environmental influences. Nat Rev Genet (2011) 5.41
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ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32
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Three periods of regulatory innovation during vertebrate evolution. Science (2011) 2.09
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Oct4 switches partnering from Sox2 to Sox17 to reinterpret the enhancer code and specify endoderm. EMBO J (2013) 1.35
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Disease-causing 7.4 kb cis-regulatory deletion disrupting conserved non-coding sequences and their interaction with the FOXL2 promotor: implications for mutation screening. PLoS Genet (2009) 1.32
Transcribed-Ultra Conserved Region expression is associated with outcome in high-risk neuroblastoma. BMC Cancer (2009) 1.29
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Transcriptional control of axonal guidance and sorting in dorsal interneurons by the Lim-HD proteins Lhx9 and Lhx1. Neural Dev (2009) 1.28
A systematic approach to identify functional motifs within vertebrate developmental enhancers. Dev Biol (2009) 1.26
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Integrating diverse datasets improves developmental enhancer prediction. PLoS Comput Biol (2014) 1.16
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The chromatin fingerprint of gene enhancer elements. J Biol Chem (2012) 1.08
Current concepts of follicle-stimulating hormone receptor gene regulation. Biol Reprod (2010) 1.05
Identification of biologically relevant enhancers in human erythroid cells. J Biol Chem (2013) 1.03
Tissue-specific RNA expression marks distant-acting developmental enhancers. PLoS Genet (2014) 1.02
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Genomic landscape of developing male germ cells. Birth Defects Res C Embryo Today (2009) 1.00
Ultradeep sequencing of a human ultraconserved region reveals somatic and constitutional genomic instability. PLoS Biol (2010) 0.99
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In vivo neuronal subtype-specific targets of Atoh1 (Math1) in dorsal spinal cord. J Neurosci (2011) 0.98
Function-based identification of mammalian enhancers using site-specific integration. Nat Methods (2014) 0.98
29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS One (2012) 0.97
Enhancer identification in mouse embryonic stem cells using integrative modeling of chromatin and genomic features. BMC Genomics (2012) 0.96
Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet (2014) 0.95
Promiscuity of enhancer, coding and non-coding transcription functions in ultraconserved elements. BMC Genomics (2010) 0.95
Ultraconserved elements: analyses of dosage sensitivity, motifs and boundaries. Genetics (2008) 0.95
Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos. Nat Commun (2015) 0.95
HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts. Cell Death Differ (2013) 0.94
Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend. BMC Genomics (2009) 0.94
The mystery of extreme non-coding conservation. Philos Trans R Soc Lond B Biol Sci (2013) 0.94
Identification and characterization of new long conserved noncoding sequences in vertebrates. Mamm Genome (2008) 0.93
Increased expression and copy number amplification of LINE-1 and SINE B1 retrotransposable elements in murine mammary carcinoma progression. Oncotarget (2013) 0.93
A mammalian conserved element derived from SINE displays enhancer properties recapitulating Satb2 expression in early-born callosal projection neurons. PLoS One (2011) 0.93
A systematic enhancer screen using lentivector transgenesis identifies conserved and non-conserved functional elements at the Olig1 and Olig2 locus. PLoS One (2010) 0.93
Enhancers of GnRH transcription embedded in an upstream gene use homeodomain proteins to specify hypothalamic expression. Mol Endocrinol (2010) 0.92
Computational identification of active enhancers in model organisms. Genomics Proteomics Bioinformatics (2013) 0.92
Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol (2008) 0.92
Feather development genes and associated regulatory innovation predate the origin of Dinosauria. Mol Biol Evol (2014) 0.91
Reptiles and mammals have differentially retained long conserved noncoding sequences from the amniote ancestor. Genome Biol Evol (2010) 0.91
Widespread ultraconservation divergence in primates. Mol Biol Evol (2008) 0.90
Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res (2011) 0.90
Dispensability of mammalian DNA. Genome Res (2008) 0.90
Computational analysis and characterization of UCE-like elements (ULEs) in plant genomes. Genome Res (2012) 0.89
Primate phylogenomics: developing numerous nuclear non-coding, non-repetitive markers for ecological and phylogenetic applications and analysis of evolutionary rate variation. BMC Genomics (2009) 0.89
Changes in selective effects over time facilitate turnover of enhancer sequences. Genetics (2010) 0.88
Intersectional Cre driver lines generated using split-intein mediated split-Cre reconstitution. Sci Rep (2012) 0.88
Evolutionary conservation of the eumetazoan gene regulatory landscape. Genome Res (2014) 0.88
Investigating the transcriptional control of cardiovascular development. Circ Res (2015) 0.87
Hundreds of conserved non-coding genomic regions are independently lost in mammals. Nucleic Acids Res (2012) 0.86
Simulations of enhancer evolution provide mechanistic insights into gene regulation. Mol Biol Evol (2013) 0.86
Ancestral resurrection of the Drosophila S2E enhancer reveals accessible evolutionary paths through compensatory change. Mol Biol Evol (2014) 0.85
Computational schemes for the prediction and annotation of enhancers from epigenomic assays. Methods (2014) 0.85
A novel virus-inducible enhancer of the interferon-β gene with tightly linked promoter and enhancer activities. Nucleic Acids Res (2014) 0.84
Functional conservation of a forebrain enhancer from the elephant shark (Callorhinchus milii ) in zebrafish and mice. BMC Evol Biol (2010) 0.84
Multiple enhancers associated with ACAN suggest highly redundant transcriptional regulation in cartilage. Matrix Biol (2012) 0.83
Towards an understanding of cell-specific functions of signal-dependent transcription factors. J Mol Endocrinol (2013) 0.83
Transcriptional analysis of Gli3 mutants identifies Wnt target genes in the developing hippocampus. Cereb Cortex (2012) 0.83
Ultraconserved cDNA segments in the human transcriptome exhibit resistance to folding and implicate function in translation and alternative splicing. Nucleic Acids Res (2010) 0.83
Neanderthal genomics and the evolution of modern humans. Genome Res (2010) 0.83
Computational methods to detect conserved non-genic elements in phylogenetically isolated genomes: application to zebrafish. Nucleic Acids Res (2013) 0.83
Deep conservation of cis-regulatory elements in metazoans. Philos Trans R Soc Lond B Biol Sci (2013) 0.82
DNase I hypersensitivity analysis of the mouse brain and retina identifies region-specific regulatory elements. Epigenetics Chromatin (2015) 0.82
Discovery of regulatory elements in human ATP-binding cassette transporters through expression quantitative trait mapping. Pharmacogenomics J (2011) 0.82
Regulatory roles of LINE-1-encoded reverse transcriptase in cancer onset and progression. Oncotarget (2014) 0.82
Identification of polymorphisms in ultraconserved elements associated with clinical outcomes in locally advanced colorectal adenocarcinoma. Cancer (2012) 0.82
Retrotransposon-encoded reverse transcriptase in the genesis, progression and cellular plasticity of human cancer. Cancers (Basel) (2011) 0.81
Comparison of ultra-conserved elements in drosophilids and vertebrates. PLoS One (2013) 0.81
Conserved noncoding elements follow power-law-like distributions in several genomes as a result of genome dynamics. PLoS One (2014) 0.81
The evolution of ultraconserved elements with different phylogenetic origins. BMC Evol Biol (2012) 0.81
Spatiotemporal regulation of an Hcn4 enhancer defines a role for Mef2c and HDACs in cardiac electrical patterning. Dev Biol (2012) 0.80
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
Distribution and intensity of constraint in mammalian genomic sequence. Genome Res (2005) 18.85
Ultraconserved elements in the human genome. Science (2004) 17.14
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Long human-mouse sequence alignments reveal novel regulatory elements: a reason to sequence the mouse genome. Genome Res (1997) 8.49
Deletion of ultraconserved elements yields viable mice. PLoS Biol (2007) 4.81
Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet (2005) 4.79
Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res (2006) 3.92
A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome Res (2005) 2.71
Human genome ultraconserved elements are ultraselected. Science (2007) 2.34
Mammalian ultraconserved elements are strongly depleted among segmental duplications and copy number variants. Nat Genet (2006) 1.92
Distinct cis-regulatory elements from the Dlx1/Dlx2 locus mark different progenitor cell populations in the ganglionic eminences and different subtypes of adult cortical interneurons. J Neurosci (2007) 1.69
In vivo characterization of a vertebrate ultraconserved enhancer. Genomics (2005) 1.49
Ultraconserved non-coding sequence element controls a subset of spatiotemporal GLI3 expression. Dev Growth Differ (2007) 1.16
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Comparative metagenomics of microbial communities. Science (2005) 25.88
Genome sequence of the Brown Norway rat yields insights into mammalian evolution. Nature (2004) 24.40
A common allele on chromosome 9 associated with coronary heart disease. Science (2007) 20.37
Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature (2004) 20.20
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature (2009) 15.06
Population-based resequencing of ANGPTL4 uncovers variations that reduce triglycerides and increase HDL. Nat Genet (2007) 13.78
VISTA: computational tools for comparative genomics. Nucleic Acids Res (2004) 13.52
Most rare missense alleles are deleterious in humans: implications for complex disease and association studies. Am J Hum Genet (2007) 10.92
Genetic variation in PNPLA3 confers susceptibility to nonalcoholic fatty liver disease. Nat Genet (2008) 10.87
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science (2003) 9.93
Scanning human gene deserts for long-range enhancers. Science (2003) 9.75
Dicer, Drosha, and outcomes in patients with ovarian cancer. N Engl J Med (2008) 8.77
Insights into the phylogeny and coding potential of microbial dark matter. Nature (2013) 8.55
Sequencing and analysis of Neanderthal genomic DNA. Science (2006) 8.06
The amphioxus genome and the evolution of the chordate karyotype. Nature (2008) 8.03
Metagenomics: DNA sequencing of environmental samples. Nat Rev Genet (2005) 7.65
Metagenomic and functional analysis of hindgut microbiota of a wood-feeding higher termite. Nature (2007) 7.42
rVista for comparative sequence-based discovery of functional transcription factor binding sites. Genome Res (2002) 7.33
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science (2011) 6.93
Genomic views of distant-acting enhancers. Nature (2009) 6.27
A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature (2006) 5.98
Medical sequencing at the extremes of human body mass. Am J Hum Genet (2007) 5.61
Genome sequencing and analysis of the biomass-degrading fungus Trichoderma reesei (syn. Hypocrea jecorina). Nat Biotechnol (2008) 5.38
Rare loss-of-function mutations in ANGPTL family members contribute to plasma triglyceride levels in humans. J Clin Invest (2008) 5.05
Symbiosis insights through metagenomic analysis of a microbial consortium. Nature (2006) 5.04
Deletion of ultraconserved elements yields viable mice. PLoS Biol (2007) 4.81
Gain-of-function SOS1 mutations cause a distinctive form of Noonan syndrome. Nat Genet (2006) 4.68
Massively parallel functional dissection of mammalian enhancers in vivo. Nat Biotechnol (2012) 4.51
Genome-wide experimental determination of barriers to horizontal gene transfer. Science (2007) 4.37
ChIP-Seq identification of weakly conserved heart enhancers. Nat Genet (2010) 4.32
Integrated analysis of homozygous deletions, focal amplifications, and sequence alterations in breast and colorectal cancers. Proc Natl Acad Sci U S A (2008) 4.13
Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet (2008) 4.04
Close sequence comparisons are sufficient to identify human cis-regulatory elements. Genome Res (2006) 3.92
Accelerated evolution of conserved noncoding sequences in humans. Science (2006) 3.87
Human-specific gain of function in a developmental enhancer. Science (2008) 3.84
Metagenomic analysis of a permafrost microbial community reveals a rapid response to thaw. Nature (2011) 3.80
Targeted deletion of the 9p21 non-coding coronary artery disease risk interval in mice. Nature (2010) 3.77
Comparative genomics at the vertebrate extremes. Nat Rev Genet (2004) 3.50
Gain-of-function RAF1 mutations cause Noonan and LEOPARD syndromes with hypertrophic cardiomyopathy. Nat Genet (2007) 3.47
Genomic sequencing of Pleistocene cave bears. Science (2005) 3.40
Improving the coverage of the cyanobacterial phylum using diversity-driven genome sequencing. Proc Natl Acad Sci U S A (2012) 3.26
The amphioxus genome illuminates vertebrate origins and cephalochordate biology. Genome Res (2008) 3.04
Chromatin stretch enhancer states drive cell-specific gene regulation and harbor human disease risk variants. Proc Natl Acad Sci U S A (2013) 2.93
Two independent apolipoprotein A5 haplotypes influence human plasma triglyceride levels. Hum Mol Genet (2002) 2.71
Large-scale discovery of enhancers from human heart tissue. Nat Genet (2011) 2.70
Megabase deletions of gene deserts result in viable mice. Nature (2004) 2.68
Automated whole-genome multiple alignment of rat, mouse, and human. Genome Res (2004) 2.64