Published in Nature on February 19, 2009
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Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet (2011) 3.36
Gene loops enhance transcriptional directionality. Science (2012) 2.50
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Regulation of primary response genes. Mol Cell (2011) 1.56
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In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp. hordei. Mol Cell Proteomics (2009) 0.99
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Systems biology unlimited. Nat Genet (2009) 0.75
RNA maps reveal new RNA classes and a possible function for pervasive transcription. Science (2007) 18.59
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Nascent RNA sequencing reveals widespread pausing and divergent initiation at human promoters. Science (2008) 16.48
Divergent transcription from active promoters. Science (2008) 11.03
Bidirectional promoters generate pervasive transcription in yeast. Nature (2009) 9.29
Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs. Nature (2009) 6.88
RNA exosome depletion reveals transcription upstream of active human promoters. Science (2008) 6.80
5'-terminal cap structure in eucaryotic messenger ribonucleic acids. Microbiol Rev (1980) 6.14
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Antisense RNA stabilization induces transcriptional gene silencing via histone deacetylation in S. cerevisiae. Cell (2007) 5.13
Widespread bidirectional promoters are the major source of cryptic transcripts in yeast. Nature (2009) 4.96
Complex Loci in human and mouse genomes. PLoS Genet (2006) 3.74
Multifaceted mammalian transcriptome. Curr Opin Cell Biol (2008) 1.52
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
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
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The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res (2012) 15.41
Empirical analysis of transcriptional activity in the Arabidopsis genome. Science (2003) 11.62
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
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
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
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Direct generation of functional dopaminergic neurons from mouse and human fibroblasts. Nature (2011) 6.21
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
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
CAGE: cap analysis of gene expression. Nat Methods (2006) 5.04
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
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
Tag-based approaches for transcriptome research and genome annotation. Nat Methods (2005) 3.52
The reality of pervasive transcription. PLoS Biol (2011) 3.41
Hidden layers of human small RNAs. BMC Genomics (2008) 3.31
A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE. Genomics (2008) 3.19
Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat. Nature (2012) 3.08
Small RNAs derived from snoRNAs. RNA (2009) 3.04
Metazoan promoters: emerging characteristics and insights into transcriptional regulation. Nat Rev Genet (2012) 2.92
Methods for analyzing deep sequencing expression data: constructing the human and mouse promoterome with deepCAGE data. Genome Biol (2009) 2.86
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
Chromatin-associated RNA interference components contribute to transcriptional regulation in Drosophila. Nature (2011) 2.70
Genome-wide analysis of cancer/testis gene expression. Proc Natl Acad Sci U S A (2008) 2.66
Understanding transcriptional regulation by integrative analysis of transcription factor binding data. Genome Res (2012) 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
CAGE Basic/Analysis Databases: the CAGE resource for comprehensive promoter analysis. Nucleic Acids Res (2006) 2.54
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
Diversity and dynamics of the Drosophila transcriptome. Nature (2014) 2.47
Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution. Proc Natl Acad Sci U S A (2003) 2.33
Linking promoters to functional transcripts in small samples with nanoCAGE and CAGEscan. Nat Methods (2010) 2.30
Genome-wide analysis of promoter architecture in Drosophila melanogaster. Genome Res (2010) 2.29
Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell (2013) 2.28
Site-specific DICER and DROSHA RNA products control the DNA-damage response. Nature (2012) 2.20
Transcriptome analysis of the aphid bacteriocyte, the symbiotic host cell that harbors an endocellular mutualistic bacterium, Buchnera. Proc Natl Acad Sci U S A (2005) 2.09
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A (2006) 2.02
The abundance of short proteins in the mammalian proteome. PLoS Genet (2006) 1.96
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
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Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 1.91
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol (2006) 1.87
Discrimination of non-protein-coding transcripts from protein-coding mRNA. RNA Biol (2006) 1.82
Unamplified cap analysis of gene expression on a single-molecule sequencer. Genome Res (2011) 1.79
Cross-mapping and the identification of editing sites in mature microRNAs in high-throughput sequencing libraries. Genome Res (2010) 1.73
Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc Natl Acad Sci U S A (2012) 1.72
Transcriptional network dynamics in macrophage activation. Genomics (2006) 1.72
Heterotachy in mammalian promoter evolution. PLoS Genet (2006) 1.71
5' end-centered expression profiling using cap-analysis gene expression and next-generation sequencing. Nat Protoc (2012) 1.70
Antisense transcripts with rice full-length cDNAs. Genome Biol (2003) 1.69
LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res (2006) 1.67
Unexpected expression of alpha- and beta-globin in mesencephalic dopaminergic neurons and glial cells. Proc Natl Acad Sci U S A (2009) 1.64
Development of a DNA barcode tagging method for monitoring dynamic changes in gene expression by using an ultra high-throughput sequencer. Biotechniques (2008) 1.61
The FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Genome Biol (2009) 1.60
A simple physical model predicts small exon length variations. PLoS Genet (2006) 1.59
Gateways to the FANTOM5 promoter level mammalian expression atlas. Genome Biol (2015) 1.58
Evolutionary turnover of mammalian transcription start sites. Genome Res (2006) 1.51
Genetic control of the innate immune response. BMC Immunol (2003) 1.50
CAGE (cap analysis of gene expression): a protocol for the detection of promoter and transcriptional networks. Methods Mol Biol (2012) 1.50
Mice and men: their promoter properties. PLoS Genet (2006) 1.50
Pseudo-messenger RNA: phantoms of the transcriptome. PLoS Genet (2006) 1.46
The genome sequence of the spontaneously hypertensive rat: Analysis and functional significance. Genome Res (2010) 1.45
The complexity of the mammalian transcriptome. J Physiol (2006) 1.43
A novel feature of microsatellites in plants: a distribution gradient along the direction of transcription. FEBS Lett (2003) 1.42
Dynamic usage of transcription start sites within core promoters. Genome Biol (2006) 1.41
High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res (2012) 1.40
Long non-coding RNA modifies chromatin: epigenetic silencing by long non-coding RNAs. Bioessays (2011) 1.39
Gene discovery in genetically labeled single dopaminergic neurons of the retina. Proc Natl Acad Sci U S A (2004) 1.38
Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation. Blood (2014) 1.36
NMDA receptor regulation prevents regression of visual cortical function in the absence of Mecp2. Neuron (2012) 1.35
FANTOM4 EdgeExpressDB: an integrated database of promoters, genes, microRNAs, expression dynamics and regulatory interactions. Genome Biol (2009) 1.32
Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nat Struct Mol Biol (2013) 1.28
Full-length cDNAs from chicken bursal lymphocytes to facilitate gene function analysis. Genome Biol (2004) 1.22
Dynamic regulation of the transcription initiation landscape at single nucleotide resolution during vertebrate embryogenesis. Genome Res (2013) 1.20
NanoCAGE: a high-resolution technique to discover and interrogate cell transcriptomes. Cold Spring Harb Protoc (2011) 1.19
Transcriptional profiling of genes responsive to abscisic acid and gibberellin in rice: phenotyping and comparative analysis between rice and Arabidopsis. Physiol Genomics (2004) 1.18
High-throughput verification of transcriptional starting sites by Deep-RACE. Biotechniques (2009) 1.16
Gene organization in rice revealed by full-length cDNA mapping and gene expression analysis through microarray. PLoS One (2007) 1.16
Solution structure of the RWD domain of the mouse GCN2 protein. Protein Sci (2004) 1.13
Genome-wide review of transcriptional complexity in mouse protein kinases and phosphatases. Genome Biol (2006) 1.13
Differential roles of epigenetic changes and Foxp3 expression in regulatory T cell-specific transcriptional regulation. Proc Natl Acad Sci U S A (2014) 1.12
Differential use of signal peptides and membrane domains is a common occurrence in the protein output of transcriptional units. PLoS Genet (2006) 1.12
Transcription and enhancer profiling in human monocyte subsets. Blood (2014) 1.12
Inferring alternative splicing patterns in mouse from a full-length cDNA library and microarray data. Genome Res (2002) 1.11
Redefinition of the human mast cell transcriptome by deep-CAGE sequencing. Blood (2014) 1.09
Altruistic functions for selfish DNA. Cell Cycle (2009) 1.09
Genomic organization of transcriptomes in mammals: Coregulation and cofunctionality. Genomics (2007) 1.09
Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing. Genome Res (2014) 1.08
Update of the FANTOM web resource: from mammalian transcriptional landscape to its dynamic regulation. Nucleic Acids Res (2010) 1.08