Published in BMC Genomics on April 02, 2013
Functional and topological characteristics of mammalian regulatory domains. Genome Res (2014) 1.43
Hoxa2 selectively enhances Meis binding to change a branchial arch ground state. Dev Cell (2015) 1.19
A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes. PLoS Genet (2015) 0.97
Investigating the transcriptional control of cardiovascular development. Circ Res (2015) 0.87
PhenoImageShare: an image annotation and query infrastructure. J Biomed Semantics (2016) 0.84
eMouseAtlas: An atlas-based resource for understanding mammalian embryogenesis. Dev Biol (2017) 0.75
BLAT--the BLAST-like alignment tool. Genome Res (2002) 126.78
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
Histone modifications at human enhancers reflect global cell-type-specific gene expression. Nature (2009) 24.41
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
ChIP-seq accurately predicts tissue-specific activity of enhancers. Nature (2009) 18.38
Topological domains in mammalian genomes identified by analysis of chromatin interactions. Nature (2012) 18.23
The UCSC Genome Browser database: update 2011. Nucleic Acids Res (2010) 16.24
Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc Natl Acad Sci U S A (2010) 15.13
Ensembl 2012. Nucleic Acids Res (2011) 14.55
A unique chromatin signature uncovers early developmental enhancers in humans. Nature (2010) 14.02
In vivo enhancer analysis of human conserved non-coding sequences. Nature (2006) 10.60
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Scanning human gene deserts for long-range enhancers. Science (2003) 9.75
Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet (2004) 8.85
A map of the cis-regulatory sequences in the mouse genome. Nature (2012) 8.74
Molecular reconstruction of Sleeping Beauty, a Tc1-like transposon from fish, and its transposition in human cells. Cell (1997) 8.68
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
A 5' element of the chicken beta-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell (1993) 8.05
Efficient transposition of the piggyBac (PB) transposon in mammalian cells and mice. Cell (2005) 7.29
VISTA Enhancer Browser--a database of tissue-specific human enhancers. Nucleic Acids Res (2006) 7.04
A long-range Shh enhancer regulates expression in the developing limb and fin and is associated with preaxial polydactyly. Hum Mol Genet (2003) 6.82
Genomic views of distant-acting enhancers. Nature (2009) 6.27
9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response. Nature (2011) 6.25
The common colorectal cancer predisposition SNP rs6983267 at chromosome 8q24 confers potential to enhanced Wnt signaling. Nat Genet (2009) 5.65
GenePaint.org: an atlas of gene expression patterns in the mouse embryo. Nucleic Acids Res (2004) 5.45
Disruption of a long-range cis-acting regulator for Shh causes preaxial polydactyly. Proc Natl Acad Sci U S A (2002) 5.18
A global control region defines a chromosomal regulatory landscape containing the HoxD cluster. Cell (2003) 4.85
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
Gene expression nervous system atlas (GENSAT). Nat Neurosci (2004) 4.74
Mouse embryonic stem cells and reporter constructs to detect developmentally regulated genes. Science (1989) 4.43
Disruption of an AP-2alpha binding site in an IRF6 enhancer is associated with cleft lip. Nat Genet (2008) 4.04
Gene targeting by homologous recombination in mouse zygotes mediated by zinc-finger nucleases. Proc Natl Acad Sci U S A (2010) 3.90
Molecular evolution of a novel hyperactive Sleeping Beauty transposase enables robust stable gene transfer in vertebrates. Nat Genet (2009) 3.86
Genomic regulatory blocks encompass multiple neighboring genes and maintain conserved synteny in vertebrates. Genome Res (2007) 3.11
Precision genome engineering with programmable DNA-nicking enzymes. Genome Res (2012) 3.05
Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet (2009) 3.03
A functional screen for sonic hedgehog regulatory elements across a 1 Mb interval identifies long-range ventral forebrain enhancers. Development (2006) 2.90
MiMIC: a highly versatile transposon insertion resource for engineering Drosophila melanogaster genes. Nat Methods (2011) 2.76
A regulatory archipelago controls Hox genes transcription in digits. Cell (2011) 2.74
Region-specific saturation germline mutagenesis in mice using the Sleeping Beauty transposon system. Nat Methods (2005) 2.70
KRAB-zinc finger proteins and KAP1 can mediate long-range transcriptional repression through heterochromatin spreading. PLoS Genet (2010) 2.44
Functional analysis of chicken Sox2 enhancers highlights an array of diverse regulatory elements that are conserved in mammals. Dev Cell (2003) 2.43
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Double-strand breaks at the target locus stimulate gene targeting in embryonic stem cells. Nucleic Acids Res (1995) 2.36
An 8q24 gene desert variant associated with prostate cancer risk confers differential in vivo activity to a MYC enhancer. Genome Res (2010) 2.24
Transgenes as probes for active chromosomal domains in mouse development. Nature (1988) 2.16
EMAGE mouse embryo spatial gene expression database: 2010 update. Nucleic Acids Res (2009) 2.16
Characterization of Sleeping Beauty transposition and its application to genetic screening in mice. Mol Cell Biol (2003) 2.13
Duplications involving a conserved regulatory element downstream of BMP2 are associated with brachydactyly type A2. Am J Hum Genet (2009) 2.09
The mouse Gene Expression Database (GXD): 2011 update. Nucleic Acids Res (2010) 2.07
Targeted gene addition to a predetermined site in the human genome using a ZFN-based nicking enzyme. Genome Res (2012) 2.02
Engineering chromosomes in mice through targeted meiotic recombination (TAMERE). Nat Genet (1998) 1.97
HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter. Genome Res (2012) 1.96
Large-scale enhancer detection in the zebrafish genome. Development (2005) 1.88
Toward simpler and faster genome-wide mutagenesis in mice. Nat Genet (2007) 1.77
Duplications of noncoding elements 5' of SOX9 are associated with brachydactyly-anonychia. Nat Genet (2009) 1.75
Enhancer trapping in zebrafish using the Sleeping Beauty transposon. BMC Genomics (2004) 1.73
Long-range downstream enhancers are essential for Pax6 expression. Dev Biol (2006) 1.62
Ten years of enhancer detection: lessons from the fly. Plant Cell (1999) 1.61
Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev (2004) 1.60
Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet (2011) 1.59
Inversion-induced disruption of the Hoxd cluster leads to the partition of regulatory landscapes. Nat Genet (2005) 1.59
A systems approach reveals that the myogenesis genome network is regulated by the transcriptional repressor RP58. Dev Cell (2009) 1.53
A microduplication of the long range SHH limb regulator (ZRS) is associated with triphalangeal thumb-polysyndactyly syndrome. J Med Genet (2008) 1.49
Large-scale screen for genes controlling mammalian embryogenesis, using high-throughput gene expression analysis in mouse embryos. Mech Dev (2000) 1.47
Ancora: a web resource for exploring highly conserved noncoding elements and their association with developmental regulatory genes. Genome Biol (2008) 1.46
Regulation of a remote Shh forebrain enhancer by the Six3 homeoprotein. Nat Genet (2008) 1.45
Zebrafish transgenic Enhancer TRAP line database (ZETRAP). BMC Dev Biol (2006) 1.35
Triphalangeal thumb-polysyndactyly syndrome and syndactyly type IV are caused by genomic duplications involving the long range, limb-specific SHH enhancer. J Med Genet (2008) 1.33
zTrap: zebrafish gene trap and enhancer trap database. BMC Dev Biol (2010) 1.21
Distal limb deficiencies, micrognathia syndrome, and syndromic forms of split hand foot malformation (SHFM) are caused by chromosome 10q genomic rearrangements. J Med Genet (2009) 0.89
Genetic labeling of neuronal subsets through enhancer trapping in mice. PLoS One (2012) 0.81
EnsMart: a generic system for fast and flexible access to biological data. Genome Res (2004) 17.64
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
An overview of Ensembl. Genome Res (2004) 10.35
BioMart Central Portal--unified access to biological data. Nucleic Acids Res (2009) 9.06
The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data. Nucleic Acids Res (2013) 5.66
eVOC: a controlled vocabulary for unifying gene expression data. Genome Res (2003) 5.41
KAP1 controls endogenous retroviruses in embryonic stem cells. Nature (2010) 4.02
An aneuploid mouse strain carrying human chromosome 21 with Down syndrome phenotypes. Science (2005) 3.61
The IKMC web portal: a central point of entry to data and resources from the International Knockout Mouse Consortium. Nucleic Acids Res (2010) 3.23
Ensembl variation resources. BMC Genomics (2010) 3.17
BioMart Central Portal: an open database network for the biological community. Database (Oxford) (2011) 3.03
A switch between topological domains underlies HoxD genes collinearity in mouse limbs. Science (2013) 2.86
A regulatory archipelago controls Hox genes transcription in digits. Cell (2011) 2.74
The mammalian gene function resource: the International Knockout Mouse Consortium. Mamm Genome (2012) 2.65
Critical roles for Rac1 and Rac2 GTPases in B cell development and signaling. Science (2003) 2.46
Improved exome prioritization of disease genes through cross-species phenotype comparison. Genome Res (2013) 2.24
Requirement of Rac1 and Rac2 expression by mature dendritic cells for T cell priming. Science (2004) 2.20
The International Mouse Phenotyping Consortium Web Portal, a unified point of access for knockout mice and related phenotyping data. Nucleic Acids Res (2013) 2.20
Rac1 is essential for platelet lamellipodia formation and aggregate stability under flow. J Biol Chem (2005) 2.07
Phenotypic impact of genomic structural variation: insights from and for human disease. Nat Rev Genet (2013) 1.98
Towards BioDBcore: a community-defined information specification for biological databases. Nucleic Acids Res (2010) 1.97
EMMA--mouse mutant resources for the international scientific community. Nucleic Acids Res (2009) 1.75
Models for financial sustainability of biological databases and resources. Database (Oxford) (2009) 1.64
Mouse limb deformity mutations disrupt a global control region within the large regulatory landscape required for Gremlin expression. Genes Dev (2004) 1.60
Large-scale analysis of the regulatory architecture of the mouse genome with a transposon-associated sensor. Nat Genet (2011) 1.59
DYRK1A-dosage imbalance perturbs NRSF/REST levels, deregulating pluripotency and embryonic stem cell fate in Down syndrome. Am J Hum Genet (2008) 1.45
Functional and topological characteristics of mammalian regulatory domains. Genome Res (2014) 1.43
MouseFinder: Candidate disease genes from mouse phenotype data. Hum Mutat (2012) 1.41
Phenotypic overlap in the contribution of individual genes to CNV pathogenicity revealed by cross-species computational analysis of single-gene mutations in humans, mice and zebrafish. Dis Model Mech (2012) 1.39
Six1 and Eya1 expression can reprogram adult muscle from the slow-twitch phenotype into the fast-twitch phenotype. Mol Cell Biol (2004) 1.39
An integrated holo-enhancer unit defines tissue and gene specificity of the Fgf8 regulatory landscape. Dev Cell (2013) 1.33
Towards BioDBcore: a community-defined information specification for biological databases. Database (Oxford) (2011) 1.24
Transgenic analysis of Hoxd gene regulation during digit development. Dev Biol (2007) 1.22
Research funding. Sustaining the data and bioresource commons. Science (2010) 1.21
Rac GTPases play critical roles in early T-cell development. Blood (2008) 1.13
Uncoupling time and space in the collinear regulation of Hox genes. PLoS Genet (2009) 1.12
New methods for finding disease-susceptibility genes: impact and potential. Genome Biol (2003) 1.11
XGAP: a uniform and extensible data model and software platform for genotype and phenotype experiments. Genome Biol (2010) 1.07
Deletions of chromosomal regulatory boundaries are associated with congenital disease. Genome Biol (2014) 1.07
Microarray-based genomic profiling reveals novel genomic aberrations in follicular lymphoma which associate with patient survival and gene expression status. Genes Chromosomes Cancer (2009) 1.06
Beyond knockouts: cre resources for conditional mutagenesis. Mamm Genome (2012) 1.04
Clustering of disease-causing mutations on the domain-domain interfaces of ABCC6. Biochem Biophys Res Commun (2009) 1.03
BioMart as an integration solution for the International Knockout Mouse Consortium. Database (Oxford) (2011) 0.96
Genotypic features of lentivirus transgenic mice. J Virol (2008) 0.94
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
Association and haplotype analysis of the insulin-degrading enzyme (IDE) gene, a strong positional and biological candidate for type 2 diabetes susceptibility. Diabetes (2003) 0.91
Jannovar: a java library for exome annotation. Hum Mutat (2014) 0.90
Lineage-specific requirement for the PH domain of Vav1 in the activation of CD4+ but not CD8+ T cells. Immunity (2005) 0.89
Rescue from oculocutaneous albinism type 4 using medaka slc45a2 cDNA driven by its own promoter. Genetics (2008) 0.87
Bipolar cell-photoreceptor connectivity in the zebrafish (Danio rerio) retina. J Comp Neurol (2012) 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
Towards the integration of mouse databases - definition and implementation of solutions to two use-cases in mouse functional genomics. BMC Res Notes (2010) 0.85
An additional human chromosome 21 causes suppression of neural fate of pluripotent mouse embryonic stem cells in a teratoma model. BMC Dev Biol (2007) 0.85
Mouse Resource Browser--a database of mouse databases. Database (Oxford) (2010) 0.83
Application of eVOC: controlled vocabularies for unifying gene expression data. C R Biol (2004) 0.82
Getting ready for the Human Phenome Project: the 2012 forum of the Human Variome Project. Hum Mutat (2013) 0.82
Linking tissues to phenotypes using gene expression profiles. Database (Oxford) (2014) 0.82
Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3. Mamm Genome (2008) 0.81
CreZOO--the European virtual repository of Cre and other targeted conditional driver strains. Database (Oxford) (2012) 0.78
Characterization of transgenic zebrafish lines that express GFP in the retina, pineal gland, olfactory bulb, hatching gland, and optic tectum. Gene Expr Patterns (2013) 0.77
Developmental biology: reproduction in clusters. Nature (2005) 0.77
Analysis of mammalian gene batteries reveals both stable ancestral cores and highly dynamic regulatory sequences. Genome Biol (2008) 0.77
Erratum: Cis-regulatory architecture of a brain signaling center predates the origin of chordates. Nat Genet (2016) 0.76
Evolutionarily conserved and divergent regulatory sequences in the fish rod opsin promoter. Comp Biochem Physiol B Biochem Mol Biol (2005) 0.76
GANESH: software for customized annotation of genome regions. Genome Res (2003) 0.75
Predictable difficulty or difficulty to predict. Protein Sci (2011) 0.75
[Genes without borders: global control of transcription activity at the level of several genes]. Med Sci (Paris) (2004) 0.75
Variation at the IRF2 gene and susceptibility to psoriasis in chromosome 4q-linked families. J Invest Dermatol (2004) 0.75