Published in Gan To Kagaku Ryoho on October 01, 2004
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
Landscape of transcription in human cells. Nature (2012) 20.18
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
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
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
A promoter-level mammalian expression atlas. Nature (2014) 6.25
An atlas of combinatorial transcriptional regulation in mouse and man. Cell (2010) 6.24
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
Causal relationship between the loss of RUNX3 expression and gastric cancer. Cell (2002) 5.69
Multipeptide immune response to cancer vaccine IMA901 after single-dose cyclophosphamide associates with longer patient survival. Nat Med (2012) 5.44
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
Tiny RNAs associated with transcription start sites in animals. Nat Genet (2009) 4.19
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
TagDust--a program to eliminate artifacts from next generation sequencing data. Bioinformatics (2009) 3.64
Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia. Genome Res (2003) 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
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
Radixin deficiency causes conjugated hyperbilirubinemia with loss of Mrp2 from bile canalicular membranes. Nat Genet (2002) 3.06
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
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
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
Identification of putative noncoding RNAs among the RIKEN mouse full-length cDNA collection. Genome Res (2003) 2.63
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
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
Deep-sequencing of human Argonaute-associated small RNAs provides insight into miRNA sorting and reveals Argonaute association with RNA fragments of diverse origin. RNA Biol (2011) 2.18
miR-125b inhibits osteoblastic differentiation by down-regulation of cell proliferation. Biochem Biophys Res Commun (2008) 2.16
Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Res (2003) 2.15
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
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
A molecular neuroethological approach for identifying and characterizing a cascade of behaviorally regulated genes. Proc Natl Acad Sci U S A (2006) 2.02
Systematic expression profiling of the mouse transcriptome using RIKEN cDNA microarrays. Genome Res (2003) 1.98
Structure of the oncoprotein gankyrin in complex with S6 ATPase of the 26S proteasome. Structure (2007) 1.97
The abundance of short proteins in the mammalian proteome. PLoS Genet (2006) 1.96
SAMStat: monitoring biases in next generation sequencing data. Bioinformatics (2010) 1.95
Clusters of internally primed transcripts reveal novel long noncoding RNAs. PLoS Genet (2006) 1.95
Asb4, Ata3, and Dcn are novel imprinted genes identified by high-throughput screening using RIKEN cDNA microarray. Biochem Biophys Res Commun (2002) 1.92
FANTOM DB: database of Functional Annotation of RIKEN Mouse cDNA Clones. Nucleic Acids Res (2002) 1.91
Transcribed enhancers lead waves of coordinated transcription in transitioning mammalian cells. Science (2015) 1.91
Constitutively activated ALK2 and increased SMAD1/5 cooperatively induce bone morphogenetic protein signaling in fibrodysplasia ossificans progressiva. J Biol Chem (2008) 1.88
Transcriptional and structural impact of TATA-initiation site spacing in mammalian core promoters. Genome Biol (2006) 1.87
Disclosing hidden transcripts: mouse natural sense-antisense transcripts tend to be poly(A) negative and nuclear localized. Genome Res (2005) 1.85
Discovery of imprinted transcripts in the mouse transcriptome using large-scale expression profiling. Genome Res (2003) 1.82
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
Homozygosity haplotype allows a genomewide search for the autosomal segments shared among patients. Am J Hum Genet (2007) 1.76
A genome-wide and nonredundant mouse transcription factor database. Biochem Biophys Res Commun (2004) 1.75
Metagenomic diagnosis of bacterial infections. Emerg Infect Dis (2008) 1.74
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
Heterotachy in mammalian promoter evolution. PLoS Genet (2006) 1.71
Data-driven normalization strategies for high-throughput quantitative RT-PCR. BMC Bioinformatics (2009) 1.71
CDS annotation in full-length cDNA sequence. Genome Res (2003) 1.70
Antisense transcripts with rice full-length cDNAs. Genome Biol (2003) 1.69
Chromatin conformation signatures of cellular differentiation. Genome Biol (2009) 1.68
LOCATE: a mouse protein subcellular localization database. Nucleic Acids Res (2006) 1.67
RUNX3 suppresses gastric epithelial cell growth by inducing p21(WAF1/Cip1) expression in cooperation with transforming growth factor {beta}-activated SMAD. Mol Cell Biol (2005) 1.64
The mouse secretome: functional classification of the proteins secreted into the extracellular environment. Genome Res (2003) 1.61
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
Exciton Primer-mediated SNP detection in SmartAmp2 reactions. Hum Mutat (2010) 1.59