Published in Science on September 02, 2005
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
A high-resolution map of transcription in the yeast genome. Proc Natl Acad Sci U S A (2006) 11.81
Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acids Res (2008) 10.10
Long noncoding RNAs: functional surprises from the RNA world. Genes Dev (2009) 9.14
Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA. Nature (2008) 7.64
Specific expression of long noncoding RNAs in the mouse brain. Proc Natl Acad Sci U S A (2008) 7.19
The genetic signatures of noncoding RNAs. PLoS Genet (2009) 6.72
Next-generation tag sequencing for cancer gene expression profiling. Genome Res (2009) 6.50
The functional role of long non-coding RNA in human carcinomas. Mol Cancer (2011) 6.37
The antisense transcriptomes of human cells. Science (2008) 6.29
A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biol (2010) 6.01
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet (2011) 5.62
Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med (2008) 5.62
A large-scale full-length cDNA analysis to explore the budding yeast transcriptome. Proc Natl Acad Sci U S A (2006) 5.24
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol (2013) 4.57
lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res (2010) 4.49
Regulatory roles of natural antisense transcripts. Nat Rev Mol Cell Biol (2009) 4.48
Bidirectional transcription directs both transcriptional gene activation and suppression in human cells. PLoS Genet (2008) 4.45
A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell (2011) 4.42
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
Genome-wide computational prediction of transcriptional regulatory modules reveals new insights into human gene expression. Genome Res (2006) 4.32
Lessons from X-chromosome inactivation: long ncRNA as guides and tethers to the epigenome. Genes Dev (2009) 4.20
Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol (2011) 4.18
Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping. Nat Genet (2008) 4.03
Promoter-associated RNA is required for RNA-directed transcriptional gene silencing in human cells. Proc Natl Acad Sci U S A (2007) 3.99
A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. Genes Dev (2008) 3.85
Pseudogenes in the ENCODE regions: consensus annotation, analysis of transcription, and evolution. Genome Res (2007) 3.82
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
Digital transcriptome profiling using selective hexamer priming for cDNA synthesis. Nat Methods (2009) 3.73
Non-ATG-initiated translation directed by microsatellite expansions. Proc Natl Acad Sci U S A (2010) 3.58
miRNA-dependent gene silencing involving Ago2-mediated cleavage of a circular antisense RNA. EMBO J (2011) 3.55
FRT-seq: amplification-free, strand-specific transcriptome sequencing. Nat Methods (2010) 3.55
Large non-coding RNAs: missing links in cancer? Hum Mol Genet (2010) 3.49
RNA in unexpected places: long non-coding RNA functions in diverse cellular contexts. Nat Rev Mol Cell Biol (2013) 3.47
Comprehensive polyadenylation site maps in yeast and human reveal pervasive alternative polyadenylation. Cell (2010) 3.42
Noncoding RNA in development. Mamm Genome (2008) 3.42
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Two distinct mechanisms generate endogenous siRNAs from bidirectional transcription in Drosophila melanogaster. Nat Struct Mol Biol (2008) 3.40
Systematic analysis of transcribed loci in ENCODE regions using RACE sequencing reveals extensive transcription in the human genome. Genome Biol (2008) 3.34
MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nat Rev Drug Discov (2013) 3.33
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
Editor meets silencer: crosstalk between RNA editing and RNA interference. Nat Rev Mol Cell Biol (2006) 3.31
Long noncoding RNAs: past, present, and future. Genetics (2013) 3.16
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012) 3.08
Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation. Nat Biotechnol (2012) 3.07
Antisense transcripts are targets for activating small RNAs. Nat Struct Mol Biol (2008) 3.02
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
Cold-induced silencing by long antisense transcripts of an Arabidopsis Polycomb target. Nature (2009) 2.97
Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms. EMBO Rep (2006) 2.96
cis-antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev (2011) 2.78
Structured RNAs in the ENCODE selected regions of the human genome. Genome Res (2007) 2.69
Long noncoding RNAs are rarely translated in two human cell lines. Genome Res (2012) 2.64
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol (2010) 2.59
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res (2006) 2.54
Long non-coding RNAs in nervous system function and disease. Brain Res (2010) 2.53
Long noncoding RNA in genome regulation: prospects and mechanisms. RNA Biol (2010) 2.53
Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease. Nat Rev Neurosci (2012) 2.52
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res (2012) 2.47
Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 2.47
RNA gain-of-function in spinocerebellar ataxia type 8. PLoS Genet (2009) 2.45
A single Hox locus in Drosophila produces functional microRNAs from opposite DNA strands. Genes Dev (2008) 2.45
A global view of protein expression in human cells, tissues, and organs. Mol Syst Biol (2009) 2.41
Human cancer long non-coding RNA transcriptomes. PLoS One (2011) 2.38
Toggle involving cis-interfering noncoding RNAs controls variegated gene expression in yeast. Proc Natl Acad Sci U S A (2009) 2.36
RNAdb 2.0--an expanded database of mammalian non-coding RNAs. Nucleic Acids Res (2006) 2.27
Noncoding RNA synthesis and loss of Polycomb group repression accompanies the colinear activation of the human HOXA cluster. RNA (2006) 2.26
Pervasive transcription constitutes a new level of eukaryotic genome regulation. EMBO Rep (2009) 2.22
Genome-wide in silico identification and analysis of cis natural antisense transcripts (cis-NATs) in ten species. Nucleic Acids Res (2006) 2.21
The function of non-coding RNAs in genomic imprinting. Development (2009) 2.21
miRTRAP, a computational method for the systematic identification of miRNAs from high throughput sequencing data. Genome Biol (2010) 2.18
Whole-genome expression profiling of the marine diatom Thalassiosira pseudonana identifies genes involved in silicon bioprocesses. Proc Natl Acad Sci U S A (2008) 2.16
mRNA-seq with agnostic splice site discovery for nervous system transcriptomics tested in chronic pain. Genome Res (2010) 2.12
Evidence for natural antisense transcript-mediated inhibition of microRNA function. Genome Biol (2010) 2.08
A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype. J Appl Physiol (1985) (2010) 2.07
Rapid turnover of long noncoding RNAs and the evolution of gene expression. PLoS Genet (2012) 2.05
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. Mol Syst Biol (2009) 2.02
Pseudogenes: pseudo-functional or key regulators in health and disease? RNA (2011) 2.00
An antisense CAG repeat transcript at JPH3 locus mediates expanded polyglutamine protein toxicity in Huntington's disease-like 2 mice. Neuron (2011) 2.00
A long noncoding RNA protects the heart from pathological hypertrophy. Nature (2014) 1.96
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
PU.1 expression is modulated by the balance of functional sense and antisense RNAs regulated by a shared cis-regulatory element. Genes Dev (2008) 1.90
Gene regulation by antisense transcription. Nat Rev Genet (2013) 1.90
Genome-wide mapping and characterization of Notch-regulated long noncoding RNAs in acute leukemia. Cell (2014) 1.88
Non-coding RNAs in the nervous system. J Physiol (2006) 1.87
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arterioscler Thromb Vasc Biol (2014) 1.87
Transcriptional regulation of Oct4 by a long non-coding RNA antisense to Oct4-pseudogene 5. Transcription (2010) 1.85
Non-coding RNAs as regulators of gene expression and epigenetics. Cardiovasc Res (2011) 1.85
A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes. Genome Res (2013) 1.81
Argonaute proteins couple chromatin silencing to alternative splicing. Nat Struct Mol Biol (2012) 1.80
Transcriptional interferences in cis natural antisense transcripts of humans and mice. Genetics (2007) 1.79
Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta (2013) 1.79
RNA templating the epigenome: long noncoding RNAs as molecular scaffolds. Epigenetics (2011) 1.75
Nuclear RNAi maintains heritable gene silencing in Caenorhabditis elegans. Proc Natl Acad Sci U S A (2011) 1.75
Involvement of argonaute proteins in gene silencing and activation by RNAs complementary to a non-coding transcript at the progesterone receptor promoter. Nucleic Acids Res (2010) 1.74
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
Diagnosis and management of dementia with Lewy bodies: third report of the DLB Consortium. Neurology (2005) 21.67
Mutations in the parkin gene cause autosomal recessive juvenile parkinsonism. Nature (1998) 21.49
Lac repressor-operator interaction. I. Equilibrium studies. J Mol Biol (1970) 13.32
Structural parts involved in activation and inactivation of the sodium channel. Nature (1989) 8.72
Nitric oxide: an endogenous modulator of leukocyte adhesion. Proc Natl Acad Sci U S A (1991) 8.04
Existence of distinct sodium channel messenger RNAs in rat brain. Nature (1986) 7.87
Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase. Nat Genet (2000) 7.83
New topoisomerase essential for chromosome segregation in E. coli. Cell (1990) 7.19
Peroral endoscopic myotomy (POEM) for esophageal achalasia. Endoscopy (2010) 7.10
Glutamine repeats as polar zippers: their possible role in inherited neurodegenerative diseases. Proc Natl Acad Sci U S A (1994) 6.96
On the process of cellular division in Escherichia coli: a series of mutants of E. coli altered in the penicillin-binding proteins. Proc Natl Acad Sci U S A (1978) 6.93
A restriction map of the bacteriophage T4 genome. Mol Gen Genet (1980) 6.37
Delineating developmental and metabolic pathways in vivo by expression profiling using the RIKEN set of 18,816 full-length enriched mouse cDNA arrays. Proc Natl Acad Sci U S A (2001) 6.07
Peptidyl-prolyl cis-trans isomerase is the cyclosporin A-binding protein cyclophilin. Nature (1989) 5.86
Elevated blood pressure and craniofacial abnormalities in mice deficient in endothelin-1. Nature (1994) 5.00
On the process of cellular division in Escherichia coli: a mutant of E. coli lacking a murein-lipoprotein. Proc Natl Acad Sci U S A (1977) 4.58
Hypertension caused by a truncated epithelial sodium channel gamma subunit: genetic heterogeneity of Liddle syndrome. Nat Genet (1995) 4.45
Mutants of Escherichia coli lacking in highly penicillin-sensitive D-alanine carboxypeptidase activity. Proc Natl Acad Sci U S A (1977) 4.44
An unfolded putative transmembrane polypeptide, which can lead to endoplasmic reticulum stress, is a substrate of Parkin. Cell (2001) 4.41
Inactivation of the tumor suppressor PTEN/MMAC1 in advanced human prostate cancer through loss of expression. Proc Natl Acad Sci U S A (1998) 4.40
Aberrant cell cycle checkpoint function and early embryonic death in Chk1(-/-) mice. Genes Dev (2000) 4.38
A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol (2001) 4.29
Clinically mild encephalitis/encephalopathy with a reversible splenial lesion. Neurology (2004) 4.24
Ubiquitination of a new form of alpha-synuclein by parkin from human brain: implications for Parkinson's disease. Science (2001) 4.18
The PILATUS 1M detector. J Synchrotron Radiat (2006) 4.16
In search of America's best hospitals. The promise and reality of quality assessment. JAMA (1997) 3.79
Mutations in the dystrophin-associated protein gamma-sarcoglycan in chromosome 13 muscular dystrophy. Science (1995) 3.66
Acetylcholine releases endothelium-derived hyperpolarizing factor and EDRF from rat blood vessels. Br J Pharmacol (1988) 3.66
A systematic, genome-wide, phenotype-driven mutagenesis programme for gene function studies in the mouse. Nat Genet (2000) 3.63
Cross-contamination potential with dental equipment. Lancet (1992) 3.55
Gene fliA encodes an alternative sigma factor specific for flagellar operons in Salmonella typhimurium. Mol Gen Genet (1990) 3.49
Clinical characteristics of clear cell carcinoma of the ovary: a distinct histologic type with poor prognosis and resistance to platinum-based chemotherapy. Cancer (2000) 3.46
On the process of cellular division in Escherichia coli: nucleotide sequence of the gene for penicillin-binding protein 3. Mol Gen Genet (1983) 3.43
Initiation of Sendai virus multiplication from transfected cDNA or RNA with negative or positive sense. Genes Cells (1996) 3.41
A new form of amyloid protein associated with chronic hemodialysis was identified as beta 2-microglobulin. Biochem Biophys Res Commun (1985) 3.40
A novel transcriptional regulation mechanism in the flagellar regulon of Salmonella typhimurium: an antisigma factor inhibits the activity of the flagellum-specific sigma factor, sigma F. Mol Microbiol (1992) 3.31
Primary structure of the alpha-subunit of transducin and its relationship to ras proteins. Nature (1985) 3.28
CCAAT/enhancer-binding protein alpha (C/EBP alpha) inhibits cell proliferation through the p21 (WAF-1/CIP-1/SDI-1) protein. Genes Dev (1996) 3.27
Characterization of oligonucleotide transport into living cells. Proc Natl Acad Sci U S A (1989) 3.27
Bacterial genomic reorganization upon DNA replication. Science (2001) 3.25
The membrane properties of the smooth muscle cells of the rabbit main pulmonary artery. J Physiol (1977) 3.24
Alymphoplasia is caused by a point mutation in the mouse gene encoding Nf-kappa b-inducing kinase. Nat Genet (1999) 3.17
Apoptosis induction by antisense oligonucleotides against miR-17-5p and miR-20a in lung cancers overexpressing miR-17-92. Oncogene (2007) 3.11
A novel transgenic technique that allows specific marking of the neural crest cell lineage in mice. Dev Biol (1999) 3.11
Development of an MRI-compatible needle insertion manipulator for stereotactic neurosurgery. J Image Guid Surg (1995) 3.07
Excitation-contraction coupling in the smooth muscle cells of the rabbit main pulmonary artery. J Physiol (1977) 3.06
Visualization of neurogenesis in the central nervous system using nestin promoter-GFP transgenic mice. Neuroreport (2000) 3.04
Involvement of interleukin-8, vascular endothelial growth factor, and basic fibroblast growth factor in tumor necrosis factor alpha-dependent angiogenesis. Mol Cell Biol (1997) 3.02
Expression of functional sodium channels from cloned cDNA. Nature (1986) 2.95
Excitation--contraction coupling in smooth muscle cells of the guinea-pig mesenteric artery. J Physiol (1981) 2.92
Immunohistochemical detection of 4-hydroxynonenal protein adducts in Parkinson disease. Proc Natl Acad Sci U S A (1996) 2.88
Murein-lipoprotein of Escherichia coli: a protein involved in the stabilization of bacterial cell envelope. Mol Gen Genet (1978) 2.84
Increased insulin sensitivity and hypoglycaemia in mice lacking the p85 alpha subunit of phosphoinositide 3-kinase. Nat Genet (1999) 2.81
Hepatitis B e antigen and infectivity of hepatitis B virus. J Infect Dis (1977) 2.80
A single point mutation confers tetrodotoxin and saxitoxin insensitivity on the sodium channel II. FEBS Lett (1989) 2.73
Targeted pharmacological depletion of serum amyloid P component for treatment of human amyloidosis. Nature (2002) 2.71
Role for the class A macrophage scavenger receptor in the phagocytosis of apoptotic thymocytes in vitro. Proc Natl Acad Sci U S A (1996) 2.69
Innervation and properties of the smooth muscle of the dog trachea. Jpn J Physiol (1976) 2.65
Factors modifying contraction-relaxation cycle in vascular smooth muscles. Am J Physiol (1982) 2.63
Substance use and sexual transmission risk behavior of HIV-positive men who have sex with men. J Subst Abuse (2001) 2.56
The role of cAMP in flagellation of Salmonella typhimurium. Mol Gen Genet (1976) 2.54
Beta-sarcoglycan (A3b) mutations cause autosomal recessive muscular dystrophy with loss of the sarcoglycan complex. Nat Genet (1995) 2.53
Purification and characterization of DNA topoisomerase IV in Escherichia coli. J Biol Chem (1992) 2.50
A novel mode of DNA recognition by a beta-sheet revealed by the solution structure of the GCC-box binding domain in complex with DNA. EMBO J (1998) 2.48
NAK is an IkappaB kinase-activating kinase. Nature (2000) 2.44
Protein-bound acrolein: potential markers for oxidative stress. Proc Natl Acad Sci U S A (1998) 2.42
Spectrodensitometric determination of trichothecene mycotoxins with 4-(p-nitrobenzyl)pyridine on silica gel thin-layer chromatograms. J Chromatogr (1979) 2.38
Modulation of the Ca2 permeable cation channel TRPV4 by cytochrome P450 epoxygenases in vascular endothelium. Circ Res (2005) 2.38
Pathologic and biochemical studies of juvenile parkinsonism linked to chromosome 6q. Neurology (1998) 2.37
Mutually exclusive expression of odorant receptor transgenes. Nat Neurosci (2000) 2.36
Diverse molecular interactions of the hnRNP K protein. FEBS Lett (1997) 2.35
Truncated CBP protein leads to classical Rubinstein-Taybi syndrome phenotypes in mice: implications for a dominant-negative mechanism. Hum Mol Genet (1999) 2.32
Physiological role of silent receptors of atrial natriuretic factor. Science (1987) 2.31
Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli. J Bacteriol (1988) 2.31
The macrophage scavenger receptor type A is expressed by activated macrophages and protects the host against lethal endotoxic shock. J Exp Med (1997) 2.28
Molecular cloning of engrailed: a gene involved in the development of pattern in Drosophila melanogaster. Cell (1985) 2.26
Differences and similarities in the noradrenaline- and caffeine-induced mechanical responses in the rabbit mesenteric artery. J Physiol (1983) 2.26
Antitumor action of some Basidiomycetes, especially Phllinus linteus. Gan (1968) 2.25
Altered cochlear fibrocytes in a mouse model of DFN3 nonsyndromic deafness. Science (1999) 2.25
Induction of microRNAs, mir-155, mir-222, mir-424 and mir-503, promotes monocytic differentiation through combinatorial regulation. Leukemia (2009) 2.24
'SPKK' motifs prefer to bind to DNA at A/T-rich sites. EMBO J (1989) 2.24
The effects of acetylcholine on the membrane and contractile properties of smooth muscle cells of the rabbit superior mesenteric artery. Br J Pharmacol (1978) 2.23
Synthetic ColE1 plasmids carrying genes for cell division in Escherichia coli. Plasmid (1977) 2.22
A degradation signal located in the C-terminus of p21WAF1/CIP1 is a binding site for the C8 alpha-subunit of the 20S proteasome. EMBO J (2001) 2.22
Biophysical characteristics of HIMAC clinical irradiation system for heavy-ion radiation therapy. Int J Radiat Oncol Biol Phys (1999) 2.19
Protease nexin-II, a potent antichymotrypsin, shows identity to amyloid beta-protein precursor. Nature (1989) 2.17
Effects of endogenous and exogenous noradrenaline on the smooth muscle of guinea-pig mesenteric vein. J Physiol (1981) 2.16
Eukaryotic DNA polymerases: proposal for a revised nomenclature. J Biol Chem (2001) 2.15
Micro-Magnetocardiography System With a Single-Chip SQUID Magnetometer Array for QT Analysis and Diagnosis of Myocardial Injury in Small Animals. IEEE Trans Biomed Circuits Syst (2008) 2.15
Activation of the Keap1/Nrf2 pathway for neuroprotection by electrophilic [correction of electrophillic] phase II inducers. Proc Natl Acad Sci U S A (2006) 2.15
In vitro peptidoglycan polymerization catalysed by penicillin binding protein 1b of Escherichia coli K-12. FEBS Lett (1980) 2.14
Catheter ablation in patients with multiple and unstable ventricular tachycardias after myocardial infarction: short ablation lines guided by reentry circuit isthmuses and sinus rhythm mapping. Circulation (2001) 2.12