Published in Nat Rev Genet on February 01, 2005
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc Natl Acad Sci U S A (2007) 4.91
Deletion of ultraconserved elements yields viable mice. PLoS Biol (2007) 4.81
Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc Natl Acad Sci U S A (2007) 4.11
Conserved noncoding genomic sequences associated with a flowering-time quantitative trait locus in maize. Proc Natl Acad Sci U S A (2007) 3.63
Forces shaping the fastest evolving regions in the human genome. PLoS Genet (2006) 3.32
Variation in the mutation rate across mammalian genomes. Nat Rev Genet (2011) 3.09
Highly conserved non-coding elements on either side of SOX9 associated with Pierre Robin sequence. Nat Genet (2009) 3.03
Predicting tissue-specific enhancers in the human genome. Genome Res (2007) 2.72
Widely distributed noncoding purifying selection in the human genome. Proc Natl Acad Sci U S A (2007) 2.71
Revisiting Mendelian disorders through exome sequencing. Hum Genet (2011) 2.57
Comprehensive resequence analysis of a 136 kb region of human chromosome 8q24 associated with prostate and colon cancers. Hum Genet (2008) 2.41
Characterization of apparently balanced chromosomal rearrangements from the developmental genome anatomy project. Am J Hum Genet (2008) 2.06
MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons. PLoS One (2011) 2.06
Human triallelic sites: evidence for a new mutational mechanism? Genetics (2009) 2.01
Analysis of sequence conservation at nucleotide resolution. PLoS Comput Biol (2007) 2.01
Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet (2007) 1.92
Finding cis-regulatory elements using comparative genomics: some lessons from ENCODE data. Genome Res (2007) 1.75
Cis-acting noncoding RNAs: friends and foes. Nat Struct Mol Biol (2012) 1.73
Cryptic variation in the human mutation rate. PLoS Biol (2009) 1.72
A family of conserved noncoding elements derived from an ancient transposable element. Proc Natl Acad Sci U S A (2006) 1.68
Genomic approaches towards finding cis-regulatory modules in animals. Nat Rev Genet (2012) 1.65
Fast-evolving noncoding sequences in the human genome. Genome Biol (2007) 1.64
Patterns and rates of intron divergence between humans and chimpanzees. Genome Biol (2007) 1.61
A comprehensive computational characterization of conserved mammalian intronic sequences reveals conserved motifs associated with constitutive and alternative splicing. Genome Res (2007) 1.58
Transcriptional enhancement by GATA1-occupied DNA segments is strongly associated with evolutionary constraint on the binding site motif. Genome Res (2008) 1.58
Intronic RNAs mediate EZH2 regulation of epigenetic targets. Nat Struct Mol Biol (2012) 1.56
The colorectal cancer risk at 18q21 is caused by a novel variant altering SMAD7 expression. Genome Res (2009) 1.52
Evolutionary turnover of mammalian transcription start sites. Genome Res (2006) 1.51
Variable locus length in the human genome leads to ascertainment bias in functional inference for non-coding elements. Bioinformatics (2009) 1.49
The dystrobrevin-binding protein 1 gene: features and networks. Mol Psychiatry (2008) 1.47
Disrupted auto-regulation of the spliceosomal gene SNRPB causes cerebro-costo-mandibular syndrome. Nat Commun (2014) 1.46
Genomic selective constraints in murid noncoding DNA. PLoS Genet (2006) 1.46
Adaptive evolution of conserved noncoding elements in mammals. PLoS Genet (2007) 1.45
Constraints and plasticity in genome and molecular-phenome evolution. Nat Rev Genet (2010) 1.41
Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol (2007) 1.41
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
Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci (2007) 1.29
Mendelian disorders and multifactorial traits: the big divide or one for all? Nat Rev Genet (2010) 1.24
Deletions involving long-range conserved nongenic sequences upstream and downstream of FOXL2 as a novel disease-causing mechanism in blepharophimosis syndrome. Am J Hum Genet (2005) 1.18
Epigenetics and T helper 1 differentiation. Immunology (2008) 1.17
Shuffling of cis-regulatory elements is a pervasive feature of the vertebrate lineage. Genome Biol (2006) 1.16
An autoregulatory loop directs the tissue-specific expression of p63 through a long-range evolutionarily conserved enhancer. Mol Cell Biol (2006) 1.13
Whole-genome phylogeny of mammals: evolutionary information in genic and nongenic regions. Proc Natl Acad Sci U S A (2009) 1.12
Comparative sequence analysis of MONOCULM1-orthologous regions in 14 Oryza genomes. Proc Natl Acad Sci U S A (2009) 1.12
Long non-coding RNA-dependent transcriptional regulation in neuronal development and disease. Front Genet (2014) 1.11
Current concepts of follicle-stimulating hormone receptor gene regulation. Biol Reprod (2010) 1.05
Preferential localization of human origins of DNA replication at the 5'-ends of expressed genes and at evolutionarily conserved DNA sequences. PLoS One (2011) 1.04
Genetic analysis of chromosome 20-related posterior polymorphous corneal dystrophy: genetic heterogeneity and exclusion of three candidate genes. Mol Vis (2008) 1.02
Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol (2011) 1.01
Alu and b1 repeats have been selectively retained in the upstream and intronic regions of genes of specific functional classes. PLoS Comput Biol (2009) 0.99
Functional transcriptomics in the post-ENCODE era. Genome Res (2013) 0.98
Linkage maps of the dwarf and Normal lake whitefish (Coregonus clupeaformis) species complex and their hybrids reveal the genetic architecture of population divergence. Genetics (2006) 0.97
The opossum genome: insights and opportunities from an alternative mammal. Genome Res (2008) 0.94
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
Assaying the regulatory potential of mammalian conserved non-coding sequences in human cells. Genome Biol (2008) 0.92
Investigation of association between the TRAF family genes and RA susceptibility. Ann Rheum Dis (2007) 0.92
Motifs and cis-regulatory modules mediating the expression of genes co-expressed in presynaptic neurons. Genome Biol (2009) 0.90
Significant selective constraint at 4-fold degenerate sites in the avian genome and its consequence for detection of positive selection. Genome Biol Evol (2011) 0.88
The role of MALAT1 correlates with HPV in cervical cancer. Oncol Lett (2014) 0.88
Chromosome conformation capture uncovers potential genome-wide interactions between human conserved non-coding sequences. PLoS One (2011) 0.88
Short sequence motifs, overrepresented in mammalian conserved non-coding sequences. BMC Genomics (2007) 0.87
Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs. Nucleic Acids Res (2008) 0.87
Ranking insertion, deletion and nonsense mutations based on their effect on genetic information. BMC Bioinformatics (2011) 0.87
Transcribed ultraconserved region in human cancers. RNA Biol (2013) 0.87
A p53-Pax2 pathway in kidney development: implications for nephrogenesis. PLoS One (2012) 0.86
Developing a community-based genetic nomenclature for anole lizards. BMC Genomics (2011) 0.86
Genetic mapping of putative Chrna7 and Luzp2 neuronal transcriptional enhancers due to impact of a transgene-insertion and 6.8 Mb deletion in a mouse model of Prader-Willi and Angelman syndromes. BMC Genomics (2005) 0.85
A fish-specific transposable element shapes the repertoire of p53 target genes in zebrafish. PLoS One (2012) 0.83
Context dependent function of APPb enhancer identified using enhancer trap-containing BACs as transgenes in zebrafish. Nucleic Acids Res (2008) 0.83
Prevalence of multinucleotide replacements in evolution of primates and Drosophila. Mol Biol Evol (2013) 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
Gene expression of NMDA receptor subunits in the cerebellum of elderly patients with schizophrenia. Eur Arch Psychiatry Clin Neurosci (2009) 0.82
Balanced translocation in a patient with craniosynostosis disrupts the SOX6 gene and an evolutionarily conserved non-transcribed region. J Med Genet (2005) 0.82
Characterization of mouse Dactylaplasia mutations: a model for human ectrodactyly SHFM3. Mamm Genome (2008) 0.81
CEGA-a catalog of conserved elements from genomic alignments. Nucleic Acids Res (2015) 0.80
Conserved elements within open reading frames of mammalian Hox genes. J Biol (2009) 0.80
Evolution and the complexity of bacteriophages. Virol J (2007) 0.80
Estimation of correlations between copy-number variants in non-coding DNA. Conf Proc IEEE Eng Med Biol Soc (2011) 0.80
Epigenetic Mechanisms Leading to Overexpression of HMGA Proteins in Human Pituitary Adenomas. Front Med (Lausanne) (2015) 0.80
Hypervariable intronic region in NCX1 is enriched in short insertion-deletion polymorphisms and showed association with cardiovascular traits. BMC Med Genet (2010) 0.80
Variable evolutionary signatures at the heart of enhancers. Nat Genet (2010) 0.79
Comparative genomics and evolution of conserved noncoding elements (CNE) in rainbow trout. BMC Genomics (2009) 0.79
Genome desertification in eutherians: can gene deserts explain the uneven distribution of genes in placental mammalian genomes? J Mol Evol (2009) 0.78
LncRNA pathway involved in premature preterm rupture of membrane (PPROM): an epigenomic approach to study the pathogenesis of reproductive disorders. PLoS One (2013) 0.78
Polymorphisms in CTNNBL1 in relation to colorectal cancer with evolutionary implications. Int J Mol Epidemiol Genet (2010) 0.77
Comparative genomics using teleost fish helps to systematically identify target gene bodies of functionally defined human enhancers. BMC Genomics (2013) 0.77
Ultraconserved long non-coding RNA uc.63 in breast cancer. Oncotarget (2016) 0.76
The Evolution of Bony Vertebrate Enhancers at Odds with Their Coding Sequence Landscape. Genome Biol Evol (2015) 0.76
Evolution of conserved secondary structures and their function in transcriptional regulation networks. BMC Genomics (2008) 0.76
Recent computational approaches to understand gene regulation: mining gene regulation in silico. Curr Genomics (2007) 0.76
Organizational heterogeneity of vertebrate genomes. PLoS One (2012) 0.76
Microarray transfection analysis of conserved genomic sequences from three immediate early genes. Genomics (2008) 0.76
Association of new deletion/duplication region at chromosome 1p21 with intellectual disability, severe speech deficit and autism spectrum disorder-like behavior: an all-in approach to solving the DPYD enigma. Transl Neurosci (2015) 0.75
Ways and means of coping with uncertainties of the relationship of the genetic blue print to protein structure and function in the cell. Cell Commun Signal (2010) 0.75
Allele frequencies of variants in ultra conserved elements identify selective pressure on transcription factor binding. PLoS One (2014) 0.75
Local conservation scores without a priori assumptions on neutral substitution rates. BMC Bioinformatics (2008) 0.75
Functional single nucleotide polymorphism-based association studies. Hum Genomics (2006) 0.75
Cis-regulatory elements are harbored in Intron5 of the RUNX1 gene. BMC Genomics (2014) 0.75
Initial sequencing and comparative analysis of the mouse genome. Nature (2002) 96.15
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Landscape of transcription in human cells. Nature (2012) 20.18
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Genome-wide associations of gene expression variation in humans. PLoS Genet (2005) 17.27
A whole-genome association study of major determinants for host control of HIV-1. Science (2007) 15.19
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
Common regulatory variation impacts gene expression in a cell type-dependent manner. Science (2009) 11.28
Recurrent rearrangements of chromosome 1q21.1 and variable pediatric phenotypes. N Engl J Med (2008) 10.88
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
EGASP: the human ENCODE Genome Annotation Assessment Project. Genome Biol (2006) 7.06
Analyses of deep mammalian sequence alignments and constraint predictions for 1% of the human genome. Genome Res (2007) 7.05
Genome scan meta-analysis of schizophrenia and bipolar disorder, part II: Schizophrenia. Am J Hum Genet (2003) 6.63
Numerous potentially functional but non-genic conserved sequences on human chromosome 21. Nature (2002) 5.38
A high-resolution anatomical atlas of the transcriptome in the mouse embryo. PLoS Biol (2011) 4.84
Conserved noncoding sequences are selectively constrained and not mutation cold spots. Nat Genet (2005) 4.79
Human chromosome 21 gene expression atlas in the mouse. Nature (2002) 4.36
Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Genome Res (2007) 4.33
The GENCODE pseudogene resource. Genome Biol (2012) 4.18
Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet (2007) 3.98
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Tandem chimerism as a means to increase protein complexity in the human genome. Genome Res (2005) 3.89
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Evolutionary discrimination of mammalian conserved non-genic sequences (CNGs). Science (2003) 3.77
Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A (2003) 3.73
Common genetic variation and the control of HIV-1 in humans. PLoS Genet (2009) 3.68
Chromosome 21 and down syndrome: from genomics to pathophysiology. Nat Rev Genet (2004) 3.58
Genetic structure of Europeans: a view from the North-East. PLoS One (2009) 3.46
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Submicroscopic deletion in patients with Williams-Beuren syndrome influences expression levels of the nonhemizygous flanking genes. Am J Hum Genet (2006) 3.18
Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma. Nat Genet (2011) 3.10
Emergence of young human genes after a burst of retroposition in primates. PLoS Biol (2005) 3.08
Genome scan meta-analysis of schizophrenia and bipolar disorder, part III: Bipolar disorder. Am J Hum Genet (2003) 3.02
Segmental copy number variation shapes tissue transcriptomes. Nat Genet (2009) 2.95
DNAH5 mutations are a common cause of primary ciliary dyskinesia with outer dynein arm defects. Am J Respir Crit Care Med (2006) 2.92
Multifocal epithelial tumors and field cancerization from loss of mesenchymal CSL signaling. Cell (2012) 2.75
Passive and active DNA methylation and the interplay with genetic variation in gene regulation. Elife (2013) 2.70
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Coordinated effects of sequence variation on DNA binding, chromatin structure, and transcription. Science (2013) 2.66
Copy number variants, diseases and gene expression. Hum Mol Genet (2009) 2.66
Human microRNA-155 on chromosome 21 differentially interacts with its polymorphic target in the AGTR1 3' untranslated region: a mechanism for functional single-nucleotide polymorphisms related to phenotypes. Am J Hum Genet (2007) 2.62
Mirror extreme BMI phenotypes associated with gene dosage at the chromosome 16p11.2 locus. Nature (2011) 2.59
Comparison of human chromosome 21 conserved nongenic sequences (CNGs) with the mouse and dog genomes shows that their selective constraint is independent of their genic environment. Genome Res (2004) 2.58
Meiotic and epigenetic defects in Dnmt3L-knockout mouse spermatogenesis. Proc Natl Acad Sci U S A (2005) 2.56
KCTD13 is a major driver of mirrored neuroanatomical phenotypes of the 16p11.2 copy number variant. Nature (2012) 2.47
Mutations in the DNAH11 (axonemal heavy chain dynein type 11) gene cause one form of situs inversus totalis and most likely primary ciliary dyskinesia. Proc Natl Acad Sci U S A (2002) 2.21
COMT genotype predicts longitudinal cognitive decline and psychosis in 22q11.2 deletion syndrome. Nat Neurosci (2005) 2.21
Gene duplication: a drive for phenotypic diversity and cause of human disease. Annu Rev Genomics Hum Genet (2007) 2.16
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
Primary ciliary dyskinesia associated with normal axoneme ultrastructure is caused by DNAH11 mutations. Hum Mutat (2008) 2.03
Polymorphisms in the low-density lipoprotein receptor-related protein 5 (LRP5) gene are associated with variation in vertebral bone mass, vertebral bone size, and stature in whites. Am J Hum Genet (2004) 1.97
Gene expression variation and expression quantitative trait mapping of human chromosome 21 genes. Hum Mol Genet (2005) 1.96
Early history of mammals is elucidated with the ENCODE multiple species sequencing data. PLoS Genet (2007) 1.92
Genotype-phenotype correlations in Down syndrome identified by array CGH in 30 cases of partial trisomy and partial monosomy chromosome 21. Eur J Hum Genet (2008) 1.90
Natural gene-expression variation in Down syndrome modulates the outcome of gene-dosage imbalance. Am J Hum Genet (2007) 1.86
Nineteen additional unpredicted transcripts from human chromosome 21. Genomics (2002) 1.80
New class of gene-termini-associated human RNAs suggests a novel RNA copying mechanism. Nature (2010) 1.78
Systems medicine and integrated care to combat chronic noncommunicable diseases. Genome Med (2011) 1.78
Gene expression from the aneuploid chromosome in a trisomy mouse model of down syndrome. Genome Res (2004) 1.75
DNA methylation profiles of human active and inactive X chromosomes. Genome Res (2011) 1.68
Identification of cis- and trans-regulatory variation modulating microRNA expression levels in human fibroblasts. Genome Res (2010) 1.67
Efficient targeted transcript discovery via array-based normalization of RACE libraries. Nat Methods (2008) 1.66
Simultaneous identification and prioritization of variants in familial, de novo, and somatic genetic disorders with VariantMaster. Genome Res (2014) 1.63
A 600 kb deletion syndrome at 16p11.2 leads to energy imbalance and neuropsychiatric disorders. J Med Genet (2012) 1.63
Consanguineous marriages, pearls and perils: Geneva International Consanguinity Workshop Report. Genet Med (2011) 1.62
Knobloch syndrome: novel mutations in COL18A1, evidence for genetic heterogeneity, and a functionally impaired polymorphism in endostatin. Hum Mutat (2004) 1.61
Binding of PTEN to specific PDZ domains contributes to PTEN protein stability and phosphorylation by microtubule-associated serine/threonine kinases. J Biol Chem (2005) 1.60
The transmembrane serine protease (TMPRSS3) mutated in deafness DFNB8/10 activates the epithelial sodium channel (ENaC) in vitro. Hum Mol Genet (2002) 1.58
Cell-type, allelic, and genetic signatures in the human pancreatic beta cell transcriptome. Genome Res (2013) 1.58
Synaptojanin 1-linked phosphoinositide dyshomeostasis and cognitive deficits in mouse models of Down's syndrome. Proc Natl Acad Sci U S A (2008) 1.54
DYRK1A-dosage imbalance perturbs NRSF/REST levels, deregulating pluripotency and embryonic stem cell fate in Down syndrome. Am J Hum Genet (2008) 1.45
Phenotypic consequences of copy number variation: insights from Smith-Magenis and Potocki-Lupski syndrome mouse models. PLoS Biol (2010) 1.36
Mutation spectrum of MLL2 in a cohort of Kabuki syndrome patients. Orphanet J Rare Dis (2011) 1.32
Aire-deficient C57BL/6 mice mimicking the common human 13-base pair deletion mutation present with only a mild autoimmune phenotype. J Immunol (2009) 1.32
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
Modelling and rescuing neurodevelopmental defect of Down syndrome using induced pluripotent stem cells from monozygotic twins discordant for trisomy 21. EMBO Mol Med (2013) 1.30
Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements. Proc Natl Acad Sci U S A (2007) 1.28