Published in Nucleic Acids Res on January 01, 2006
Hypoxia-inducible factor-dependent induction of netrin-1 dampens inflammation caused by hypoxia. Nat Immunol (2009) 3.24
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol (2007) 2.86
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
TRED: a transcriptional regulatory element database, new entries and other development. Nucleic Acids Res (2007) 2.67
Transcription factor binding and modified histones in human bidirectional promoters. Genome Res (2007) 2.40
CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinformatics (2006) 2.19
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
Comparative genomics of Drosophila and human core promoters. Genome Biol (2006) 1.99
Identification of plant promoter constituents by analysis of local distribution of short sequences. BMC Genomics (2007) 1.77
Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes. PLoS Comput Biol (2007) 1.69
Beyond microarrays: find key transcription factors controlling signal transduction pathways. BMC Bioinformatics (2006) 1.46
Distinct class of putative "non-conserved" promoters in humans: comparative studies of alternative promoters of human and mouse genes. Genome Res (2007) 1.37
Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs. Nucleic Acids Res (2006) 1.31
Differentiation of core promoter architecture between plants and mammals revealed by LDSS analysis. Nucleic Acids Res (2007) 1.19
Prediction of CpG-island function: CpG clustering vs. sliding-window methods. BMC Genomics (2010) 1.12
Finding sequence motifs with Bayesian models incorporating positional information: an application to transcription factor binding sites. BMC Bioinformatics (2008) 1.08
Identification of vasodilator-stimulated phosphoprotein (VASP) as an HIF-regulated tissue permeability factor during hypoxia. FASEB J (2007) 1.08
Search for basonuclin target genes. Biochem Biophys Res Commun (2006) 1.07
c-myc Repression of TSC2 contributes to control of translation initiation and Myc-induced transformation. Cancer Res (2007) 1.07
Prediction of synergistic transcription factors by function conservation. Genome Biol (2007) 1.01
Retrotransposition as a source of new promoters. Mol Biol Evol (2008) 1.00
Identification of N-acetyltransferase 2 (NAT2) transcription start sites and quantitation of NAT2-specific mRNA in human tissues. Drug Metab Dispos (2007) 1.00
Comprehensive detection of human terminal oligo-pyrimidine (TOP) genes and analysis of their characteristics. Nucleic Acids Res (2008) 0.99
Organismal complexity, cell differentiation and gene expression: human over mouse. Nucleic Acids Res (2007) 0.96
Inflammation-associated repression of vasodilator-stimulated phosphoprotein (VASP) reduces alveolar-capillary barrier function during acute lung injury. FASEB J (2009) 0.96
Transcription of the human cell cycle regulated BUB1B gene requires hStaf/ZNF143. Nucleic Acids Res (2007) 0.96
Cross-species comparison of genomewide gene expression profiles reveals induction of hypoxia-inducible factor-responsive genes in iron-deprived intestinal epithelial cells. Am J Physiol Cell Physiol (2010) 0.95
MetaProm: a neural network based meta-predictor for alternative human promoter prediction. BMC Genomics (2007) 0.94
PU.1 can recruit BCL6 to DNA to repress gene expression in germinal center B cells. Mol Cell Biol (2009) 0.94
Core promoters are predicted by their distinct physicochemical properties in the genome of Plasmodium falciparum. Genome Biol (2008) 0.93
Growth controls connect: interactions between c-myc and the tuberous sclerosis complex-mTOR pathway. Cell Cycle (2009) 0.92
Profiling the thermodynamic softness of adenoviral promoters. Biophys J (2008) 0.92
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res (2010) 0.90
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Nucleic Acids Res (2006) 0.87
IFN-γ attenuates hypoxia-inducible factor (HIF) activity in intestinal epithelial cells through transcriptional repression of HIF-1β. J Immunol (2011) 0.86
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. BMC Genomics (2012) 0.85
DNA sequence and structural properties as predictors of human and mouse promoters. Gene (2007) 0.85
Intrinsic promoter activities of primary DNA sequences in the human genome. DNA Res (2007) 0.84
A data integration approach for cell cycle analysis oriented to model simulation in systems biology. BMC Syst Biol (2007) 0.84
A comparison study on feature selection of DNA structural properties for promoter prediction. BMC Bioinformatics (2012) 0.83
Weak correlation between sequence conservation in promoter regions and in protein-coding regions of human-mouse orthologous gene pairs. BMC Genomics (2008) 0.82
Cap-proximal nucleotides via differential eIF4E binding and alternative promoter usage mediate translational response to energy stress. Elife (2017) 0.81
Vasodilator phosphostimulated protein (VASP) protects endothelial barrier function during hypoxia. Inflammation (2012) 0.79
Prediction for human transcription start site using diversity measure with quadratic discriminant. Bioinformation (2008) 0.79
Profiling ascidian promoters as the primordial type of vertebrate promoter. BMC Genomics (2011) 0.79
Identifying genes progressively silenced in preneoplastic and neoplastic liver tissues. Int J Comput Biol Drug Des (2010) 0.79
HIF-dependent regulation of AKAP12 (gravin) in the control of human vascular endothelial function. FASEB J (2013) 0.78
Fine expression profiling of full-length transcripts using a size-unbiased cDNA library prepared with the vector-capping method. DNA Res (2008) 0.78
RBF-TSS: identification of transcription start site in human using radial basis functions network and oligonucleotide positional frequencies. PLoS One (2009) 0.75
IN-MACA-MCC: Integrated Multiple Attractor Cellular Automata with Modified Clonal Classifier for Human Protein Coding and Promoter Prediction. Adv Bioinformatics (2014) 0.75
Genome-wide analysis of promoters: clustering by alignment and analysis of regular patterns. PLoS One (2014) 0.75
Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature (2002) 28.79
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98
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Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature (2004) 5.08
High-efficiency full-length cDNA cloning by biotinylated CAP trapper. Genomics (1996) 4.41
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
Construction and characterization of a full length-enriched and a 5'-end-enriched cDNA library. Gene (1997) 4.02
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res (2004) 3.73
Complex controls: the role of alternative promoters in mammalian genomes. Trends Genet (2003) 3.11
The Eukaryotic Promoter Database, EPD: new entry types and links to gene expression data. Nucleic Acids Res (2002) 2.30
High efficiency selection of full-length cDNA by improved biotinylated cap trapper. DNA Res (1997) 2.11
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
Full-malaria 2004: an enlarged database for comparative studies of full-length cDNAs of malaria parasites, Plasmodium species. Nucleic Acids Res (2004) 1.20
Parallelization of a local similarity algorithm. Comput Appl Biosci (1992) 1.03
Conservation of the PRM1 --> PRM2 --> TNP2 domain. DNA Seq (2003) 0.97
Genomic sequences of human protamines whose genes, PRM1 and PRM2, are clustered. Genomics (1990) 0.97
Frequent pathway mutations of splicing machinery in myelodysplasia. Nature (2011) 11.44
WoLF PSORT: protein localization predictor. Nucleic Acids Res (2007) 10.14
The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). Genome Res (2004) 9.18
Collection, mapping, and annotation of over 28,000 cDNA clones from japonica rice. Science (2003) 8.65
The Physcomitrella genome reveals evolutionary insights into the conquest of land by plants. Science (2007) 8.12
Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat Genet (2003) 7.98
Mapping human genetic diversity in Asia. Science (2009) 7.40
Integrative annotation of 21,037 human genes validated by full-length cDNA clones. PLoS Biol (2004) 7.17
A transcription factor response element for gene expression during circadian night. Nature (2002) 6.55
The medaka draft genome and insights into vertebrate genome evolution. Nature (2007) 5.77
Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res (2005) 5.22
Extensive feature detection of N-terminal protein sorting signals. Bioinformatics (2002) 5.16
Genome sequence of the ultrasmall unicellular red alga Cyanidioschyzon merolae 10D. Nature (2004) 5.08
Curved EFC/F-BAR-domain dimers are joined end to end into a filament for membrane invagination in endocytosis. Cell (2007) 4.73
The Jmjd3-Irf4 axis regulates M2 macrophage polarization and host responses against helminth infection. Nat Immunol (2010) 4.66
Integrated molecular analysis of clear-cell renal cell carcinoma. Nat Genet (2013) 4.61
DBTSS: DataBase of human Transcriptional Start Sites and full-length cDNAs. Nucleic Acids Res (2002) 4.29
PSORT-B: Improving protein subcellular localization prediction for Gram-negative bacteria. Nucleic Acids Res (2003) 4.25
Human Proteinpedia enables sharing of human protein data. Nat Biotechnol (2008) 4.21
Phosphate-activated glutaminase (GLS2), a p53-inducible regulator of glutamine metabolism and reactive oxygen species. Proc Natl Acad Sci U S A (2010) 4.18
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res (2007) 3.80
ATTED-II: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res (2006) 3.74
DBTSS, DataBase of Transcriptional Start Sites: progress report 2004. Nucleic Acids Res (2004) 3.73
Large-scale identification and characterization of human genes that activate NF-kappaB and MAPK signaling pathways. Oncogene (2003) 3.53
A vertebrate RNA-binding protein Fox-1 regulates tissue-specific splicing via the pentanucleotide GCAUG. EMBO J (2003) 3.44
The landscape of C. elegans 3'UTRs. Science (2010) 3.32
DBTSS: database of transcription start sites, progress report 2008. Nucleic Acids Res (2007) 3.11
Chromatin-associated periodicity in genetic variation downstream of transcriptional start sites. Science (2008) 3.10
HDAC8 mutations in Cornelia de Lange syndrome affect the cohesin acetylation cycle. Nature (2012) 3.08
Contribution of intragenic DNA methylation in mouse gametic DNA methylomes to establish oocyte-specific heritable marks. PLoS Genet (2012) 2.89
T cell receptor stimulation-induced epigenetic changes and Foxp3 expression are independent and complementary events required for Treg cell development. Immunity (2012) 2.78
DKK1, a negative regulator of Wnt signaling, is a target of the beta-catenin/TCF pathway. Oncogene (2004) 2.73
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res (2004) 2.61
Thyrotrophin in the pars tuberalis triggers photoperiodic response. Nature (2008) 2.60
Prophylactic clip application does not decrease delayed bleeding after colonoscopic polypectomy. Gastrointest Endosc (2003) 2.55
Prediction of transcriptional terminators in Bacillus subtilis and related species. PLoS Comput Biol (2005) 2.54
The functional consequences of alternative promoter use in mammalian genomes. Trends Genet (2008) 2.47
Construction of a full-length enriched and a 5'-end enriched cDNA library using the oligo-capping method. Methods Mol Biol (2003) 2.45
5'-end SAGE for the analysis of transcriptional start sites. Nat Biotechnol (2004) 2.34
Genome sequence of an Australian kangaroo, Macropus eugenii, provides insight into the evolution of mammalian reproduction and development. Genome Biol (2011) 2.18
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Res (2007) 2.07
PrognoScan: a new database for meta-analysis of the prognostic value of genes. BMC Med Genomics (2009) 2.07
Recount: expectation maximization based error correction tool for next generation sequencing data. Genome Inform (2009) 1.95
Rate of evolution in brain-expressed genes in humans and other primates. PLoS Biol (2007) 1.87
Inhibition of angiogenesis and vascular leakiness by angiopoietin-related protein 4. Cancer Res (2003) 1.78
Genome-wide determination of RNA stability reveals hundreds of short-lived noncoding transcripts in mammals. Genome Res (2012) 1.76
High-resolution DNA methylome analysis of primordial germ cells identifies gender-specific reprogramming in mice. Genome Res (2013) 1.75
Draft assembly of the Symbiodinium minutum nuclear genome reveals dinoflagellate gene structure. Curr Biol (2013) 1.69
Functional gene screening system identified TRPV4 as a regulator of chondrogenic differentiation. J Biol Chem (2007) 1.66
Pathway for differentiation of human embryonic stem cells to vascular cell components and their potential for vascular regeneration. Arterioscler Thromb Vasc Biol (2007) 1.63
Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs. Genome Res (2004) 1.63
Deletion of angiotensin-converting enzyme 2 accelerates pressure overload-induced cardiac dysfunction by increasing local angiotensin II. Hypertension (2006) 1.61
Massive transcriptional start site analysis of human genes in hypoxia cells. Nucleic Acids Res (2009) 1.60
Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium. C R Biol (2004) 1.58
Genome-wide analysis reveals strong correlation between CpG islands with nearby transcription start sites of genes and their tissue specificity. Gene (2005) 1.57
Genome-wide characterization of transcriptional start sites in humans by integrative transcriptome analysis. Genome Res (2011) 1.57
Ezh2 augments leukemogenicity by reinforcing differentiation blockage in acute myeloid leukemia. Blood (2012) 1.56