Published in Proc Natl Acad Sci U S A on July 01, 2009
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature (2010) 23.55
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Long noncoding RNA as modular scaffold of histone modification complexes. Science (2010) 15.23
Long noncoding RNAs with enhancer-like function in human cells. Cell (2010) 13.00
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
The Polycomb complex PRC2 and its mark in life. Nature (2011) 11.97
Genome regulation by long noncoding RNAs. Annu Rev Biochem (2012) 11.70
Molecular mechanisms of long noncoding RNAs. Mol Cell (2011) 11.44
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes. Cell (2011) 10.56
A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language? Cell (2011) 10.50
Spatial partitioning of the regulatory landscape of the X-inactivation centre. Nature (2012) 9.75
Genetics and pathogenesis of inflammatory bowel disease. Nature (2011) 7.79
Modular regulatory principles of large non-coding RNAs. Nature (2012) 7.42
Epigenetic modifications and human disease. Nat Biotechnol (2010) 7.29
Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell (2010) 6.94
Genome-wide identification of polycomb-associated RNAs by RIP-seq. Mol Cell (2010) 6.88
Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Mol Cell (2011) 6.83
An atlas of active enhancers across human cell types and tissues. Nature (2014) 6.57
lincRNAs: genomics, evolution, and mechanisms. Cell (2013) 6.50
The functional role of long non-coding RNA in human carcinomas. Mol Cancer (2011) 6.37
The emergence of lncRNAs in cancer biology. Cancer Discov (2011) 6.32
Long noncoding RNAs: cellular address codes in development and disease. Cell (2013) 6.01
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Conserved function of lincRNAs in vertebrate embryonic development despite rapid sequence evolution. Cell (2011) 5.65
Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet (2011) 5.62
The hallmarks of cancer: a long non-coding RNA point of view. RNA Biol (2012) 5.60
Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet (2013) 5.48
Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat Genet (2010) 5.37
Whole-genome sequencing of liver cancers identifies etiological influences on mutation patterns and recurrent mutations in chromatin regulators. Nat Genet (2012) 4.84
Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol (2013) 4.57
Polycomb group proteins: navigators of lineage pathways led astray in cancer. Nat Rev Cancer (2009) 4.40
Short RNAs are transcribed from repressed polycomb target genes and interact with polycomb repressive complex-2. Mol Cell (2010) 4.36
starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein-RNA interaction networks from large-scale CLIP-Seq data. Nucleic Acids Res (2013) 4.33
HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer. Oncogene (2012) 4.30
ncRNA- and Pc2 methylation-dependent gene relocation between nuclear structures mediates gene activation programs. Cell (2011) 4.26
Polycomb group proteins: multi-faceted regulators of somatic stem cells and cancer. Cell Stem Cell (2010) 4.18
Targeted RNA sequencing reveals the deep complexity of the human transcriptome. Nat Biotechnol (2011) 4.18
Single-cell RNA-Seq profiling of human preimplantation embryos and embryonic stem cells. Nat Struct Mol Biol (2013) 4.04
Chromatin structure and the inheritance of epigenetic information. Nat Rev Genet (2010) 4.03
The Hox genes and their roles in oncogenesis. Nat Rev Cancer (2010) 3.97
Long non-coding RNAs and cancer: a new frontier of translational research? Oncogene (2012) 3.83
Systematic identification of long noncoding RNAs expressed during zebrafish embryogenesis. Genome Res (2011) 3.81
Principles for the post-GWAS functional characterization of cancer risk loci. Nat Genet (2011) 3.73
Occupying chromatin: Polycomb mechanisms for getting to genomic targets, stopping transcriptional traffic, and staying put. Mol Cell (2013) 3.50
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
The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus. Cell (2013) 3.40
Long intergenic noncoding RNAs: new links in cancer progression. Cancer Res (2011) 3.38
Orphan CpG islands identify numerous conserved promoters in the mammalian genome. PLoS Genet (2010) 3.38
Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet (2011) 3.36
Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell (2013) 3.35
MicroRNAs and other non-coding RNAs as targets for anticancer drug development. Nat Rev Drug Discov (2013) 3.33
Deconstructing repression: evolving models of co-repressor action. Nat Rev Genet (2010) 3.29
A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO J (2010) 3.18
Long noncoding RNAs: past, present, and future. Genetics (2013) 3.16
The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell (2013) 3.14
Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature (2012) 3.08
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
Epigenetic modifications in pluripotent and differentiated cells. Nat Biotechnol (2010) 3.02
Long noncoding RNAs and the genetics of cancer. Br J Cancer (2013) 2.98
Transcriptional regulation by Polycomb group proteins. Nat Struct Mol Biol (2013) 2.96
Peptidomic discovery of short open reading frame-encoded peptides in human cells. Nat Chem Biol (2012) 2.95
The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature (2014) 2.93
Promiscuous RNA binding by Polycomb repressive complex 2. Nat Struct Mol Biol (2013) 2.91
Transcribed dark matter: meaning or myth? Hum Mol Genet (2010) 2.87
Breast cancer risk-associated SNPs modulate the affinity of chromatin for FOXA1 and alter gene expression. Nat Genet (2012) 2.86
Silencing chromatin: comparing modes and mechanisms. Nat Rev Genet (2011) 2.86
Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA (2010) 2.85
A long noncoding RNA mediates both activation and repression of immune response genes. Science (2013) 2.85
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res (2011) 2.82
Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells. Proc Natl Acad Sci U S A (2013) 2.75
A functional genomic approach identifies FAL1 as an oncogenic long noncoding RNA that associates with BMI1 and represses p21 expression in cancer. Cancer Cell (2014) 2.72
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol (2009) 2.70
Lnc RNA HOTAIR functions as a competing endogenous RNA to regulate HER2 expression by sponging miR-331-3p in gastric cancer. Mol Cancer (2014) 2.70
Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife (2013) 2.66
Long noncoding RNAs are rarely translated in two human cell lines. Genome Res (2012) 2.64
Emerging roles for natural microRNA sponges. Curr Biol (2010) 2.62
The majority of total nuclear-encoded non-ribosomal RNA in a human cell is 'dark matter' un-annotated RNA. BMC Biol (2010) 2.59
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
Human long non-coding RNAs promote pluripotency and neuronal differentiation by association with chromatin modifiers and transcription factors. EMBO J (2011) 2.51
RNA traffic control of chromatin complexes. Curr Opin Genet Dev (2010) 2.49
Genome-wide analysis of long noncoding RNA stability. Genome Res (2012) 2.49
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J (2014) 2.47
Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs. Nucleic Acids Res (2012) 2.47
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet (2013) 2.46
The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep (2012) 2.45
Gene silencing in X-chromosome inactivation: advances in understanding facultative heterochromatin formation. Nat Rev Genet (2011) 2.39
LncRNA loc285194 is a p53-regulated tumor suppressor. Nucleic Acids Res (2013) 2.38
Annotating non-coding regions of the genome. Nat Rev Genet (2010) 2.38
Genome-wide characterization of the routes to pluripotency. Nature (2014) 2.34
Intergenic transcription by RNA polymerase II coordinates Pol IV and Pol V in siRNA-directed transcriptional gene silencing in Arabidopsis. Genes Dev (2009) 2.30
Long non-coding RNA: a new player in cancer. J Hematol Oncol (2013) 2.26
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol (2012) 2.22
Structural and functional differences in the long non-coding RNA hotair in mouse and human. PLoS Genet (2011) 2.20
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
High-resolution profiling of histone methylations in the human genome. Cell (2007) 85.74
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature (2007) 75.09
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell (2007) 30.22
Genome-wide mapping of Polycomb target genes unravels their roles in cell fate transitions. Genes Dev (2006) 14.36
Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science (2008) 13.79
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell (2008) 9.76
A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science (2005) 9.25
Chromatin signatures in multipotent human hematopoietic stem cells indicate the fate of bivalent genes during differentiation. Cell Stem Cell (2009) 8.62
The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science (2008) 8.45
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res (2007) 7.34
The genetic signatures of noncoding RNAs. PLoS Genet (2009) 6.72
Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res (2008) 6.43
Mouse polycomb proteins bind differentially to methylated histone H3 and RNA and are enriched in facultative heterochromatin. Mol Cell Biol (2006) 5.99
Small RNAs in transcriptional gene silencing and genome defence. Nature (2009) 5.98
Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat Genet (2002) 5.86
RNA meets chromatin. Genes Dev (2005) 5.66
Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet (2005) 5.07
MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res (2008) 5.06
Non-coding RNAs: the architects of eukaryotic complexity. EMBO Rep (2001) 4.74
CoREST: a functional corepressor required for regulation of neural-specific gene expression. Proc Natl Acad Sci U S A (1999) 4.59
The noncoding RNA taurine upregulated gene 1 is required for differentiation of the murine retina. Curr Biol (2005) 3.15
Performance and scalability of discriminative metrics for comparative gene identification in 12 Drosophila genomes. PLoS Comput Biol (2008) 2.70
Essential dosage-dependent functions of the transcription factor yin yang 1 in late embryonic development and cell cycle progression. Mol Cell Biol (2006) 2.48
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
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
Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature (2007) 65.18
Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol (2011) 53.86
PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes. Nat Genet (2003) 53.59
Model-based analysis of ChIP-Seq (MACS). Genome Biol (2008) 51.63
The structure of haplotype blocks in the human genome. Science (2002) 50.88
A bivalent chromatin structure marks key developmental genes in embryonic stem cells. Cell (2006) 48.80
Integrative genomics viewer. Nat Biotechnol (2011) 42.83
Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc (2012) 35.75
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
The landscape of somatic copy-number alteration across human cancers. Nature (2010) 31.88
Systematic discovery of regulatory motifs in human promoters and 3' UTRs by comparison of several mammals. Nature (2005) 31.60
Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature (2008) 30.29
Somatic mutations affect key pathways in lung adenocarcinoma. Nature (2008) 30.02
Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science (2009) 29.83
Sequencing and comparison of yeast species to identify genes and regulatory elements. Nature (2003) 29.16
In vitro reprogramming of fibroblasts into a pluripotent ES-cell-like state. Nature (2007) 28.24
Transcriptional regulatory code of a eukaryotic genome. Nature (2004) 27.21
Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol (2009) 27.17
The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science (2006) 25.99
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature (2010) 23.55
Genome sequence, comparative analysis and haplotype structure of the domestic dog. Nature (2005) 23.04
High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci U S A (2010) 22.97
ARACHNE: a whole-genome shotgun assembler. Genome Res (2002) 22.72
Detecting recent positive selection in the human genome from haplotype structure. Nature (2002) 22.00
A molecular signature of metastasis in primary solid tumors. Nat Genet (2002) 21.36
ALLPATHS: de novo assembly of whole-genome shotgun microreads. Genome Res (2008) 20.61
International network of cancer genome projects. Nature (2010) 20.35
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A (2007) 18.83
A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell (2006) 18.81
Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nat Biotechnol (2010) 18.44
The mammalian epigenome. Cell (2007) 18.13
Global identification of human transcribed sequences with genome tiling arrays. Science (2004) 17.85
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors. Nat Genet (2008) 17.67
Initial genome sequencing and analysis of multiple myeloma. Nature (2011) 17.28
Genome-wide detection and characterization of positive selection in human populations. Nature (2007) 17.27
Risk alleles for multiple sclerosis identified by a genomewide study. N Engl J Med (2007) 17.06
The mutational landscape of head and neck squamous cell carcinoma. Science (2011) 16.88
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
Meta-analysis of genetic association studies supports a contribution of common variants to susceptibility to common disease. Nat Genet (2003) 16.51
Characterizing the cancer genome in lung adenocarcinoma. Nature (2007) 16.48
Dissecting direct reprogramming through integrative genomic analysis. Nature (2008) 16.47
Assessing the impact of population stratification on genetic association studies. Nat Genet (2004) 16.28
Gene expression correlates of clinical prostate cancer behavior. Cancer Cell (2002) 16.27
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol (2013) 16.13
Active genes are tri-methylated at K4 of histone H3. Nature (2002) 15.68
Prediction of central nervous system embryonal tumour outcome based on gene expression. Nature (2002) 15.36
Genetic mapping in human disease. Science (2008) 15.12
Regulation of noise in the expression of a single gene. Nat Genet (2002) 14.93
Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data. Nat Genet (2003) 14.56
The genomic complexity of primary human prostate cancer. Nature (2011) 14.06
Diffuse large B-cell lymphoma outcome prediction by gene-expression profiling and supervised machine learning. Nat Med (2002) 14.01
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
The NIH Roadmap Epigenomics Mapping Consortium. Nat Biotechnol (2010) 13.99
MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet (2001) 13.79
A landscape of driver mutations in melanoma. Cell (2012) 12.61
High-resolution mapping of copy-number alterations with massively parallel sequencing. Nat Methods (2008) 12.56
Proof and evolutionary analysis of ancient genome duplication in the yeast Saccharomyces cerevisiae. Nature (2004) 12.32
Whole-genome sequence assembly for mammalian genomes: Arachne 2. Genome Res (2003) 12.30
A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell (2010) 12.27
Nature, nurture, or chance: stochastic gene expression and its consequences. Cell (2008) 12.13
Population genomics of domestic and wild yeasts. Nature (2009) 11.79
Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell (2012) 11.69
Systematic RNA interference reveals that oncogenic KRAS-driven cancers require TBK1. Nature (2009) 11.46
The genome sequence of the filamentous fungus Neurospora crassa. Nature (2003) 11.39
lincRNAs act in the circuitry controlling pluripotency and differentiation. Nature (2011) 11.31
The mystery of missing heritability: Genetic interactions create phantom heritability. Proc Natl Acad Sci U S A (2012) 11.23
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
SF3B1 and other novel cancer genes in chronic lymphocytic leukemia. N Engl J Med (2011) 11.07
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03