Published in Genome Res on June 01, 2003
Identification of mammalian microRNA host genes and transcription units. Genome Res (2004) 14.63
Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs. Genome Res (2007) 7.34
Most "dark matter" transcripts are associated with known genes. PLoS Biol (2010) 6.60
Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol (2004) 4.91
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
Genomic analysis of mouse retinal development. PLoS Biol (2004) 4.66
The complex eukaryotic transcriptome: unexpected pervasive transcription and novel small RNAs. Nat Rev Genet (2009) 4.19
Noncoding RNA in development. Mamm Genome (2008) 3.42
Identification of putative noncoding polyadenylated transcripts in Drosophila melanogaster. Proc Natl Acad Sci U S A (2005) 2.30
The dynamic epitranscriptome: N6-methyladenosine and gene expression control. Nat Rev Mol Cell Biol (2014) 2.19
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
A noncoding RNA is a potential marker of cell fate during mammary gland development. Proc Natl Acad Sci U S A (2006) 1.94
Fast pairwise structural RNA alignments by pruning of the dynamical programming matrix. PLoS Comput Biol (2007) 1.90
Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res (2003) 1.82
CDS annotation in full-length cDNA sequence. Genome Res (2003) 1.70
Long noncoding RNAs in C. elegans. Genome Res (2012) 1.69
Novel long non-protein coding RNAs involved in Arabidopsis differentiation and stress responses. Genome Res (2008) 1.51
A systematic search for new mammalian noncoding RNAs indicates little conserved intergenic transcription. BMC Genomics (2005) 1.47
Complex architecture and regulated expression of the Sox2ot locus during vertebrate development. RNA (2009) 1.44
Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Res (2004) 1.38
Characterization of 43 non-protein-coding mRNA genes in Arabidopsis, including the MIR162a-derived transcripts. Plant Physiol (2006) 1.35
Tsix-mediated epigenetic switch of a CTCF-flanked region of the Xist promoter determines the Xist transcription program. Genes Dev (2006) 1.29
Identification and characterization of wheat long non-protein coding RNAs responsive to powdery mildew infection and heat stress by using microarray analysis and SBS sequencing. BMC Plant Biol (2011) 1.26
Emerging similarities in epigenetic gene silencing by long noncoding RNAs. Mamm Genome (2009) 1.20
Methods for transcriptional profiling in plants. Be fruitful and replicate. Plant Physiol (2004) 1.14
Screening non-coding RNAs in transcriptomes from neglected species using PORTRAIT: case study of the pathogenic fungus Paracoccidioides brasiliensis. BMC Bioinformatics (2009) 1.12
Predicting candidate genomic sequences that correspond to synthetic functional RNA motifs. Nucleic Acids Res (2005) 1.08
Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human. BMC Evol Biol (2007) 1.05
EICO (Expression-based Imprint Candidate Organizer): finding disease-related imprinted genes. Nucleic Acids Res (2004) 1.05
Detection of low-level promoter activity within open reading frame sequences of Escherichia coli. Nucleic Acids Res (2005) 1.01
MicroRNA-encoding long non-coding RNAs. BMC Genomics (2008) 1.01
Genetic dissection of the Canq1 locus governing variation in extent of the collateral circulation. PLoS One (2012) 0.99
Non-polyadenylated transcription in embryonic stem cells reveals novel non-coding RNA related to pluripotency and differentiation. Nucleic Acids Res (2013) 0.94
Abundant novel transcriptional units and unconventional gene pairs on human chromosome 22. Genome Res (2005) 0.94
Non-coding RNAs revealed during identification of genes involved in chicken immune responses. Immunogenetics (2008) 0.91
Systematic identification and evolutionary features of rhesus monkey small nucleolar RNAs. BMC Genomics (2010) 0.91
Organization and transcriptional output of a novel mRNA-like piRNA gene (mpiR) located on mouse chromosome 10. RNA (2008) 0.90
Characterisation of Caenorhabditis elegans sperm transcriptome and proteome. BMC Genomics (2014) 0.89
Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities. BMC Bioinformatics (2008) 0.87
Exploiting Oxytricha trifallax nanochromosomes to screen for non-coding RNA genes. Nucleic Acids Res (2011) 0.86
Systematic identification and characterization of chicken (Gallus gallus) ncRNAs. Nucleic Acids Res (2009) 0.86
Identification and comparative analysis of ncRNAs in human, mouse and zebrafish indicate a conserved role in regulation of genes expressed in brain. PLoS One (2012) 0.86
Comprehensive transcriptome analysis reveals novel genes involved in cardiac glycoside biosynthesis and mlncRNAs associated with secondary metabolism and stress response in Digitalis purpurea. BMC Genomics (2012) 0.86
Long non-coding RNA SOX2OT: expression signature, splicing patterns, and emerging roles in pluripotency and tumorigenesis. Front Genet (2015) 0.85
Paradigm shifts in genomics through the FANTOM projects. Mamm Genome (2015) 0.84
Intrinsic promoter activities of primary DNA sequences in the human genome. DNA Res (2007) 0.84
Long non-coding RNAs and their biological roles in plants. Genomics Proteomics Bioinformatics (2015) 0.82
Comparative transcriptome sequencing of germline and somatic tissues of the Ascaris suum gonad. BMC Genomics (2011) 0.81
Expression of Six3 Opposite Strand (Six3OS) during mouse embryonic development. Gene Expr Patterns (2006) 0.80
No-match ORESTES explored as tumor markers. Nucleic Acids Res (2009) 0.79
Characterization of transcription start sites of putative non-coding RNAs by multifaceted use of massively paralleled sequencer. DNA Res (2010) 0.78
A Review of Computational Methods for Finding Non-Coding RNA Genes. Genes (Basel) (2016) 0.76
Annotating non-coding transcription using functional genomics strategies. Brief Funct Genomic Proteomic (2009) 0.76
Comprehensive expressional analyses of antisense transcripts in colon cancer tissues using artificial antisense probes. BMC Med Genomics (2011) 0.75
Gene expression of protein-coding and non-coding RNAs related to polyembryogenesis in the parasitic wasp, Copidosoma floridanum. PLoS One (2014) 0.75
Estimating the fraction of non-coding RNAs in mammalian transcriptomes. Bioinform Biol Insights (2008) 0.75
Prediction of complete gene structures in human genomic DNA. J Mol Biol (1997) 58.76
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (2001) 44.16
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33
Searching protein sequence libraries: comparison of the sensitivity and selectivity of the Smith-Waterman and FASTA algorithms. Genomics (1991) 9.65
RNA interference--2001. Genes Dev (2001) 7.68
Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev (2001) 7.65
Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol (2001) 7.56
The non-coding Air RNA is required for silencing autosomal imprinted genes. Nature (2002) 7.37
Identification of 86 candidates for small non-messenger RNAs from the archaeon Archaeoglobus fulgidus. Proc Natl Acad Sci U S A (2002) 7.04
An expanding universe of noncoding RNAs. Science (2002) 5.96
Identification and characterization of human BIC, a gene on chromosome 21 that encodes a noncoding RNA. Gene (2001) 5.14
A mammalian gene with introns instead of exons generating stable RNA products. Nature (1996) 4.87
Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol (2001) 4.58
Computational genomics of noncoding RNA genes. Cell (2002) 3.90
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
A maternally methylated CpG island in KvLQT1 is associated with an antisense paternal transcript and loss of imprinting in Beckwith-Wiedemann syndrome. Proc Natl Acad Sci U S A (1999) 3.37
Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5'-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Mol Cell Biol (1998) 3.08
Micro-RNAs: small is plentiful. J Cell Biol (2002) 2.95
Identification of a new imprinted gene, Rian, on mouse chromosome 12 by fluorescent differential display screening. J Biochem (2001) 2.19
Small RNAs in bacteria: diverse regulators of gene expression in response to environmental changes. Cell (2002) 2.00
Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res (2003) 1.98
Identification and analysis of Arabidopsis expressed sequence tags characteristic of non-coding RNAs. Plant Physiol (2001) 1.76
A novel synapse-associated noncoding RNA. Mol Cell Biol (1994) 1.72
The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Genome Res (2003) 1.61
Non-coding, mRNA-like RNAs database Y2K. Nucleic Acids Res (2000) 1.57
Regulatory RNAs. Cell Mol Life Sci (2001) 1.56
The host gene for intronic U17 small nucleolar RNAs in mammals has no protein-coding potential and is a member of the 5'-terminal oligopyrimidine gene family. Mol Cell Biol (1998) 1.56
Characterization of the genomic Xist locus in rodents reveals conservation of overall gene structure and tandem repeats but rapid evolution of unique sequence. Genome Res (2001) 1.54
Human U19 intron-encoded snoRNA is processed from a long primary transcript that possesses little potential for protein coding. RNA (1998) 1.43
A comprehensive transcript map of the mouse Gnas imprinted complex. Genome Res (2003) 1.32
Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between rhabdomyosarcoma subtypes. Oncogene (2002) 1.32
An imprinted mouse transcript homologous to the human imprinted in Prader-Willi syndrome (IPW) gene. Hum Mol Genet (1997) 1.31
Identification of a novel transcript disrupted by a balanced translocation associated with DiGeorge syndrome. Am J Hum Genet (1996) 1.31
Poly(A)-binding protein is associated with neuronal BC1 and BC200 ribonucleoprotein particles. J Mol Biol (2002) 1.26
A new structure for the murine Xist gene and its relationship to chromosome choice/counting during X-chromosome inactivation. Proc Natl Acad Sci U S A (1999) 1.25
Ntab, a novel non-coding RNA abundantly expressed in rat brain. Neuroscience (2001) 1.14
Molecular evolutionary evidence that H19 mRNA is functional. Trends Genet (1999) 1.07
The human NTT gene: identification of a novel 17-kb noncoding nuclear RNA expressed in activated CD4+ T cells. Genomics (1997) 1.06
Identification of a novel osteoblastic gene, inducible by C-type natriuretic peptide, whose transcript might function in mineralization as a noncoding RNA. Calcif Tissue Int (2002) 0.87
Identification and characterization of G90, a novel mouse RNA that lacks an extensive open reading frame. Gene (1999) 0.86
adapt33, a novel oxidant-inducible RNA from hamster HA-1 cells. Arch Biochem Biophys (1996) 0.85
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
Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol (2006) 40.15
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Interferon-gamma: an overview of signals, mechanisms and functions. J Leukoc Biol (2003) 12.34
Complete MHC haplotype sequencing for common disease gene mapping. Genome Res (2004) 12.09
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
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 genome sequence of taurine cattle: a window to ruminant biology and evolution. Science (2009) 8.23
Interferon regulatory factor 6 (IRF6) gene variants and the risk of isolated cleft lip or palate. N Engl J Med (2004) 7.91
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
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
The Drosophila gene collection: identification of putative full-length cDNAs for 70% of D. melanogaster genes. Genome Res (2002) 6.61
HIN-200 proteins regulate caspase activation in response to foreign cytoplasmic DNA. Science (2009) 6.59
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
Fate mapping reveals origins and dynamics of monocytes and tissue macrophages under homeostasis. Immunity (2012) 6.18
Functional annotation of a full-length Arabidopsis cDNA collection. Science (2002) 6.15
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Multiple high-throughput analyses monitor the response of E. coli to perturbations. Science (2007) 5.87
The regulated retrotransposon transcriptome of mammalian cells. Nat Genet (2009) 5.79
Mammalian RNA polymerase II core promoters: insights from genome-wide studies. Nat Rev Genet (2007) 5.75
High-throughput mapping of a dynamic signaling network in mammalian cells. Science (2005) 5.21
CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04
Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Res (2005) 4.86
IFITM3 restricts the morbidity and mortality associated with influenza. Nature (2012) 4.66
Quantitative metabolome analysis using capillary electrophoresis mass spectrometry. J Proteome Res (2003) 4.36
Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res (2006) 4.25
Unravelling mononuclear phagocyte heterogeneity. Nat Rev Immunol (2010) 4.25
Tiny RNAs associated with transcription start sites in animals. Nat Genet (2009) 4.19
Somatic retrotransposition alters the genetic landscape of the human brain. Nature (2011) 4.16
A macrophage colony-stimulating factor receptor-green fluorescent protein transgene is expressed throughout the mononuclear phagocyte system of the mouse. Blood (2002) 4.06
Comprehensive analysis of NAC family genes in Oryza sativa and Arabidopsis thaliana. DNA Res (2003) 4.01
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
Systematic identification of cell cycle-dependent yeast nucleocytoplasmic shuttling proteins by prediction of composite motifs. Proc Natl Acad Sci U S A (2009) 3.64
TagDust--a program to eliminate artifacts from next generation sequencing data. Bioinformatics (2009) 3.64
Expression analysis of G Protein-Coupled Receptors in mouse macrophages. Immunome Res (2008) 3.54
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 3.50
Quantitative metabolome profiling of colon and stomach cancer microenvironment by capillary electrophoresis time-of-flight mass spectrometry. Cancer Res (2009) 3.50
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Antisense transcripts with FANTOM2 clone set and their implications for gene regulation. Genome Res (2003) 3.40
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
Differential metabolomics reveals ophthalmic acid as an oxidative stress biomarker indicating hepatic glutathione consumption. J Biol Chem (2006) 3.23
Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome. Genome Res (2003) 3.21
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
Abnormal skin, limb and craniofacial morphogenesis in mice deficient for interferon regulatory factor 6 (Irf6). Nat Genet (2006) 3.14
CX3CR1+ CD115+ CD135+ common macrophage/DC precursors and the role of CX3CR1 in their response to inflammation. J Exp Med (2009) 3.07
Small RNAs derived from snoRNAs. RNA (2009) 3.04
An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA. Nature (2009) 3.04
Rapid detection of epidermal growth factor receptor mutations in lung cancer by the SMart-Amplification Process. Clin Cancer Res (2007) 3.02
A comprehensive survey of 3' animal miRNA modification events and a possible role for 3' adenylation in modulating miRNA targeting effectiveness. Genome Res (2010) 2.87
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol (2009) 2.86
RNAdb--a comprehensive mammalian noncoding RNA database. Nucleic Acids Res (2005) 2.84
Genetic analysis of completely sequenced disease-associated MHC haplotypes identifies shuffling of segments in recent human history. PLoS Genet (2006) 2.80
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
The macrophage-inducible C-type lectin, mincle, is an essential component of the innate immune response to Candida albicans. J Immunol (2008) 2.71
Connecting sequence and biology in the laboratory mouse. Genome Res (2003) 2.69
Mouse proteome analysis. Genome Res (2003) 2.69
Direct metagenomic detection of viral pathogens in nasal and fecal specimens using an unbiased high-throughput sequencing approach. PLoS One (2009) 2.67
Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A (2008) 2.66
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
Monitoring the expression pattern of around 7,000 Arabidopsis genes under ABA treatments using a full-length cDNA microarray. Funct Integr Genomics (2002) 2.59
Dynamic modeling of genetic networks using genetic algorithm and S-system. Bioinformatics (2003) 2.57
Signal integration between IFNgamma and TLR signalling pathways in macrophages. Immunobiology (2006) 2.55
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res (2006) 2.54
Apoptotic cell removal in development and tissue homeostasis. Trends Immunol (2006) 2.51
Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Mol Syst Biol (2008) 2.49
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48