Published in Genome Res on September 01, 2012
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
GENCODE: the reference human genome annotation for The ENCODE Project. Genome Res (2012) 19.19
Guidelines for investigating causality of sequence variants in human disease. Nature (2014) 7.30
lincRNAs: genomics, evolution, and mechanisms. Cell (2013) 6.50
Long noncoding RNAs: cellular address codes in development and disease. Cell (2013) 6.01
Long non-coding RNAs: new players in cell differentiation and development. Nat Rev Genet (2013) 5.48
Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation. Cell (2014) 5.43
The Norway spruce genome sequence and conifer genome evolution. Nature (2013) 4.74
Structure and function of long noncoding RNAs in epigenetic regulation. Nat Struct Mol Biol (2013) 4.57
The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science (2013) 4.12
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs. Genome Res (2012) 3.83
Ribosome profiling provides evidence that large noncoding RNAs do not encode proteins. Cell (2013) 3.69
The landscape of long noncoding RNAs in the human transcriptome. Nat Genet (2015) 3.58
Sequencing depth and coverage: key considerations in genomic analyses. Nat Rev Genet (2014) 3.52
The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet (2013) 3.39
Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell (2013) 3.35
A comparative encyclopedia of DNA elements in the mouse genome. Nature (2014) 3.22
The rise of regulatory RNA. Nat Rev Genet (2014) 3.02
The evolution of lncRNA repertoires and expression patterns in tetrapods. Nature (2014) 2.93
Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer. Nat Struct Mol Biol (2013) 2.84
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
Topological organization of multichromosomal regions by the long intergenic noncoding RNA Firre. Nat Struct Mol Biol (2014) 2.65
Long noncoding RNAs are rarely translated in two human cell lines. Genome Res (2012) 2.64
The genomic landscape of Neanderthal ancestry in present-day humans. Nature (2014) 2.59
Identification of small ORFs in vertebrates using ribosome footprinting and evolutionary conservation. EMBO J (2014) 2.47
Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 2.47
Pervasive transcription of the human genome produces thousands of previously unidentified long intergenic noncoding RNAs. PLoS Genet (2013) 2.46
Large-scale imputation of epigenomic datasets for systematic annotation of diverse human tissues. Nat Biotechnol (2015) 2.44
Expanded identification and characterization of mammalian circular RNAs. Genome Biol (2014) 2.39
NONCODEv4: exploring the world of long non-coding RNA genes. Nucleic Acids Res (2013) 2.37
Long non-coding RNA: a new player in cancer. J Hematol Oncol (2013) 2.26
A single-molecule long-read survey of the human transcriptome. Nat Biotechnol (2013) 2.24
Transposable elements reveal a stem cell-specific class of long noncoding RNAs. Genome Biol (2012) 2.22
Transdifferentiation of human fibroblasts to endothelial cells: role of innate immunity. Circulation (2014) 2.19
A long noncoding RNA associated with susceptibility to celiac disease. Science (2016) 2.19
The landscape of viral expression and host gene fusion and adaptation in human cancer. Nat Commun (2013) 2.17
RNA-RNA interactions enable specific targeting of noncoding RNAs to nascent Pre-mRNAs and chromatin sites. Cell (2014) 2.13
Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res (2012) 2.13
Global discovery of erythroid long noncoding RNAs reveals novel regulators of red cell maturation. Blood (2013) 2.12
P53-regulated long non-coding RNA TUG1 affects cell proliferation in human non-small cell lung cancer, partly through epigenetically regulating HOXB7 expression. Cell Death Dis (2014) 2.09
Transposable elements are major contributors to the origin, diversification, and regulation of vertebrate long noncoding RNAs. PLoS Genet (2013) 2.07
Single-cell RNA-seq: advances and future challenges. Nucleic Acids Res (2014) 2.06
Gene regulation by the act of long non-coding RNA transcription. BMC Biol (2013) 1.97
The selection and function of cell type-specific enhancers. Nat Rev Mol Cell Biol (2015) 1.93
Long noncoding RNA ANRIL indicates a poor prognosis of gastric cancer and promotes tumor growth by epigenetically silencing of miR-99a/miR-449a. Oncotarget (2014) 1.90
Gene regulation by antisense transcription. Nat Rev Genet (2013) 1.90
Origins and functional evolution of Y chromosomes across mammals. Nature (2014) 1.89
Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep (2013) 1.89
Identification and initial functional characterization of a human vascular cell-enriched long noncoding RNA. Arterioscler Thromb Vasc Biol (2014) 1.87
The long intergenic noncoding RNA landscape of human lymphocytes highlights the regulation of T cell differentiation by linc-MAF-4. Nat Immunol (2015) 1.82
Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov (2013) 1.82
Unique features of long non-coding RNA biogenesis and function. Nat Rev Genet (2015) 1.81
Evolutionary conservation of long non-coding RNAs; sequence, structure, function. Biochim Biophys Acta (2013) 1.79
Fine-scale chromatin interaction maps reveal the cis-regulatory landscape of human lincRNA genes. Nat Methods (2014) 1.76
Deep RNA sequencing reveals dynamic regulation of myocardial noncoding RNAs in failing human heart and remodeling with mechanical circulatory support. Circulation (2014) 1.76
Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation. Nat Immunol (2013) 1.71
Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals. Genome Res (2014) 1.69
lncRNAdb v2.0: expanding the reference database for functional long noncoding RNAs. Nucleic Acids Res (2014) 1.69
The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. Mol Cell (2014) 1.68
Extensive localization of long noncoding RNAs to the cytosol and mono- and polyribosomal complexes. Genome Biol (2014) 1.66
Utilizing sequence intrinsic composition to classify protein-coding and long non-coding transcripts. Nucleic Acids Res (2013) 1.64
Long Noncoding RNAs in Cancer Pathways. Cancer Cell (2016) 1.63
Analysis of intronic and exonic reads in RNA-seq data characterizes transcriptional and post-transcriptional regulation. Nat Biotechnol (2015) 1.62
Long non-coding RNA MEG3 inhibits NSCLC cells proliferation and induces apoptosis by affecting p53 expression. BMC Cancer (2013) 1.62
Long noncoding RNA LINP1 regulates repair of DNA double-strand breaks in triple-negative breast cancer. Nat Struct Mol Biol (2016) 1.61
Comparison of the transcriptional landscapes between human and mouse tissues. Proc Natl Acad Sci U S A (2014) 1.60
Microprocessor mediates transcriptional termination of long noncoding RNA transcripts hosting microRNAs. Nat Struct Mol Biol (2015) 1.60
Identification of novel long noncoding RNAs underlying vertebrate cardiovascular development. Circulation (2015) 1.60
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages. Nat Commun (2014) 1.60
Choice of transcripts and software has a large effect on variant annotation. Genome Med (2014) 1.58
Localization and abundance analysis of human lncRNAs at single-cell and single-molecule resolution. Genome Biol (2015) 1.56
Long non-coding RNAs as a source of new peptides. Elife (2014) 1.56
Long noncoding RNAs: fresh perspectives into the RNA world. Trends Biochem Sci (2013) 1.55
An evolutionarily conserved long noncoding RNA TUNA controls pluripotency and neural lineage commitment. Mol Cell (2014) 1.55
The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat Struct Mol Biol (2014) 1.55
Proteogenomics: concepts, applications and computational strategies. Nat Methods (2014) 1.54
Ribosome profiling reveals resemblance between long non-coding RNAs and 5' leaders of coding RNAs. Development (2013) 1.54
On the classification of long non-coding RNAs. RNA Biol (2013) 1.53
MelanomaDB: A Web Tool for Integrative Analysis of Melanoma Genomic Information to Identify Disease-Associated Molecular Pathways. Front Oncol (2013) 1.53
Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR. Nat Protoc (2015) 1.51
UV Irradiation Induces a Non-coding RNA that Functionally Opposes the Protein Encoded by the Same Gene. Cell (2017) 1.50
Interactive visualization and analysis of large-scale sequencing datasets using ZENBU. Nat Biotechnol (2014) 1.48
Characterization of the human ESC transcriptome by hybrid sequencing. Proc Natl Acad Sci U S A (2013) 1.48
Modulation of long noncoding RNAs by risk SNPs underlying genetic predispositions to prostate cancer. Nat Genet (2016) 1.48
What does our genome encode? Genome Res (2012) 1.47
Long noncoding RNAs in cell-fate programming and reprogramming. Cell Stem Cell (2014) 1.47
The Landscape of long noncoding RNA classification. Trends Genet (2015) 1.47
mTORC1 and muscle regeneration are regulated by the LINC00961-encoded SPAR polypeptide. Nature (2016) 1.46
Transcriptome analyses of the human retina identify unprecedented transcript diversity and 3.5 Mb of novel transcribed sequence via significant alternative splicing and novel genes. BMC Genomics (2013) 1.46
Distinctive Patterns of Transcription and RNA Processing for Human lincRNAs. Mol Cell (2016) 1.46
CRNDE: A Long Non-Coding RNA Involved in CanceR, Neurobiology, and DEvelopment. Front Genet (2012) 1.45
DECKO: Single-oligo, dual-CRISPR deletion of genomic elements including long non-coding RNAs. BMC Genomics (2015) 1.45
Genome-wide discovery and characterization of maize long non-coding RNAs. Genome Biol (2014) 1.45
The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry (2013) 1.44
Transcriptional dynamics reveal critical roles for non-coding RNAs in the immediate-early response. PLoS Comput Biol (2015) 1.44
Comprehensive Genomic Characterization of Long Non-coding RNAs across Human Cancers. Cancer Cell (2015) 1.43
Regulation of transcription by long noncoding RNAs. Annu Rev Genet (2014) 1.43
Chromatin signatures at transcriptional start sites separate two equally populated yet distinct classes of intergenic long noncoding RNAs. Genome Biol (2013) 1.41
Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq. Elife (2014) 1.40
Basic local alignment search tool. J Mol Biol (1990) 659.07
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc (2009) 137.99
Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods (2008) 126.81
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
An integrated encyclopedia of DNA elements in the human genome. Nature (2012) 64.73
RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet (2009) 58.77
BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics (2010) 53.23
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes. Genome Res (2005) 44.08
The transcriptional landscape of the mammalian genome. Science (2005) 37.63
Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature (2009) 35.48
Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics (2005) 24.54
Mapping and analysis of chromatin state dynamics in nine human cell types. Nature (2011) 24.37
Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A (2009) 20.66
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
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Evolution and functions of long noncoding RNAs. Cell (2009) 17.54
Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev (2011) 16.77
Widespread transcription at neuronal activity-regulated enhancers. Nature (2010) 16.52
Transcriptome genetics using second generation sequencing in a Caucasian population. Nature (2010) 14.85
Long noncoding RNAs with enhancer-like function in human cells. Cell (2010) 13.00
A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science (2005) 9.25
The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science (2008) 8.45
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
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
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
The product of the mouse Xist gene is a 15 kb inactive X-specific transcript containing no conserved ORF and located in the nucleus. Cell (1992) 6.26
The product of the H19 gene may function as an RNA. Mol Cell Biol (1990) 5.61
lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature (2011) 5.42
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
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Sci Signal (2010) 4.77
3' end processing of a long nuclear-retained noncoding RNA yields a tRNA-like cytoplasmic RNA. Cell (2008) 4.54
lncRNAdb: a reference database for long noncoding RNAs. Nucleic Acids Res (2010) 4.49
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
Estimating accuracy of RNA-Seq and microarrays with proteomics. BMC Genomics (2009) 3.87
Differentiating protein-coding and noncoding RNA: challenges and ambiguities. PLoS Comput Biol (2008) 3.66
Small peptides switch the transcriptional activity of Shavenbaby during Drosophila embryogenesis. Science (2010) 3.62
Activation of p53 by MEG3 non-coding RNA. J Biol Chem (2007) 3.07
Genome-wide computational identification and manual annotation of human long noncoding RNA genes. RNA (2010) 2.85
ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J (2010) 2.73
Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness. Genome Biol (2009) 2.70
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
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet (2006) 2.41
Origin of phenotypes: genes and transcripts. Genome Res (2007) 2.30
NRED: a database of long noncoding RNA expression. Nucleic Acids Res (2008) 2.21
U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res (2006) 2.09
Using geneid to identify genes. Curr Protoc Bioinformatics (2007) 2.04
SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer. RNA (2011) 2.03
Characterization of the RNA content of chromatin. Genome Res (2010) 1.99
The steroid receptor RNA activator is the first functional RNA encoding a protein. FEBS Lett (2004) 1.92
The evolution of RNAs with multiple functions. Biochimie (2011) 1.39
A novel family of plasmid-transferred anti-sense ncRNAs. RNA Biol (2010) 1.18
A thymus-specific noncoding RNA, Thy-ncR1, is a cytoplasmic riboregulator of MFAP4 mRNA in immature T-cell lines. BMC Mol Biol (2010) 1.04
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
Pfam: clans, web tools and services. Nucleic Acids Res (2006) 34.83
Paired-end mapping reveals extensive structural variation in the human genome. Science (2007) 30.46
Integration of external signaling pathways with the core transcriptional network in embryonic stem cells. Cell (2008) 28.29
STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2012) 25.21
The Oct4 and Nanog transcription network regulates pluripotency in mouse embryonic stem cells. Nat Genet (2006) 20.76
A global map of p53 transcription-factor binding sites in the human genome. Cell (2006) 20.65
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proc Natl Acad Sci U S A (2002) 20.48
International network of cancer genome projects. Nature (2010) 20.35
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
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Genome-wide analysis of estrogen receptor binding sites. Nat Genet (2006) 18.63
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
The Microprocessor complex mediates the genesis of microRNAs. Nature (2004) 17.70
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes. Genome Res (2009) 14.90
Ensembl 2012. Nucleic Acids Res (2011) 14.55
CD127 expression inversely correlates with FoxP3 and suppressive function of human CD4+ T reg cells. J Exp Med (2006) 14.33
Large-scale transcriptional activity in chromosomes 21 and 22. Science (2002) 14.01
TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature (2005) 13.44
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature (2011) 13.18
Long noncoding RNAs with enhancer-like function in human cells. Cell (2010) 13.00
Ensembl 2014. Nucleic Acids Res (2013) 12.62
Identification of functional elements and regulatory circuits by Drosophila modENCODE. Science (2010) 12.39
A systematic survey of loss-of-function variants in human protein-coding genes. Science (2012) 12.25
An oestrogen-receptor-alpha-bound human chromatin interactome. Nature (2009) 12.16
The developmental transcriptome of Drosophila melanogaster. Nature (2010) 11.85
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype. Nature (2004) 11.03
Functional metagenomic profiling of nine biomes. Nature (2008) 11.00
A conditional knockout resource for the genome-wide study of mouse gene function. Nature (2011) 9.93
Genome-wide transcription and the implications for genomic organization. Nat Rev Genet (2007) 9.45
Human RISC couples microRNA biogenesis and posttranscriptional gene silencing. Cell (2005) 9.27
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Res (2012) 9.13
Characterization of mammalian selenoproteomes. Science (2003) 9.07
Transcriptome and genome sequencing uncovers functional variation in humans. Nature (2013) 8.89
Cap analysis gene expression for high-throughput analysis of transcriptional starting point and identification of promoter usage. Proc Natl Acad Sci U S A (2003) 8.73
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Extensive promoter-centered chromatin interactions provide a topological basis for transcription regulation. Cell (2012) 8.41
Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22. Genome Res (2004) 8.35
The genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Gene identification signature (GIS) analysis for transcriptome characterization and genome annotation. Nat Methods (2005) 7.87
Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. Plant J (2002) 7.70
Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol (2005) 7.49
Demethylation of H3K27 regulates polycomb recruitment and H2A ubiquitination. Science (2007) 7.41
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
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
Whole-genome mapping of histone H3 Lys4 and 27 trimethylations reveals distinct genomic compartments in human embryonic stem cells. Cell Stem Cell (2007) 7.05