Published in Genome Res on March 01, 2002
miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61
DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet (2006) 18.08
GENCODE: producing a reference annotation for ENCODE. Genome Biol (2006) 15.08
Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res (2003) 12.26
The Ensembl automatic gene annotation system. Genome Res (2004) 12.24
The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res (2005) 7.06
Tandem duplication producing a novel oncogenic BRAF fusion gene defines the majority of pilocytic astrocytomas. Cancer Res (2008) 6.44
Identification and functional analysis of human transcriptional promoters. Genome Res (2003) 6.23
The Ensembl analysis pipeline. Genome Res (2004) 5.90
The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res (2007) 5.67
Computational analysis of core promoters in the Drosophila genome. Genome Biol (2002) 5.60
Genomic analysis of human microRNA transcripts. Proc Natl Acad Sci U S A (2007) 5.20
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. Immunogenetics (2008) 4.25
Toucan: deciphering the cis-regulatory logic of coregulated genes. Nucleic Acids Res (2003) 3.68
Current methods of gene prediction, their strengths and weaknesses. Nucleic Acids Res (2002) 3.12
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
Structure and activity of putative intronic miRNA promoters. RNA (2010) 2.50
Genome sequencing and analysis of the Tasmanian devil and its transmissible cancer. Cell (2012) 2.37
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One (2009) 2.29
Genome-wide analysis of mRNA lengths in Saccharomyces cerevisiae. Genome Biol (2003) 2.25
Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment. Genome Biol (2006) 2.02
ProSOM: core promoter prediction based on unsupervised clustering of DNA physical profiles. Bioinformatics (2008) 1.91
Generic eukaryotic core promoter prediction using structural features of DNA. Genome Res (2007) 1.80
Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol (2013) 1.75
Touring Ensembl: a practical guide to genome browsing. BMC Genomics (2010) 1.70
Statistical analysis of over-represented words in human promoter sequences. Nucleic Acids Res (2004) 1.69
PromoSer: A large-scale mammalian promoter and transcription start site identification service. Nucleic Acids Res (2003) 1.68
Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res (2008) 1.56
The DART classification of unannotated transcription within the ENCODE regions: associating transcription with known and novel loci. Genome Res (2007) 1.56
Understanding genome browsing. Nat Biotechnol (2009) 1.55
Resolving the structural features of genomic islands: a machine learning approach. Genome Res (2007) 1.54
POIMs: positional oligomer importance matrices--understanding support vector machine-based signal detectors. Bioinformatics (2008) 1.51
Computational approaches to identify promoters and cis-regulatory elements in plant genomes. Plant Physiol (2003) 1.50
Determining promoter location based on DNA structure first-principles calculations. Genome Biol (2007) 1.44
BANF1 is downregulated by IRF1-regulated microRNA-203 in cervical cancer. PLoS One (2015) 1.44
Destabilization of B2 RNA by EZH2 Activates the Stress Response. Cell (2016) 1.42
A computational screen for mouse signaling pathways targeted by microRNA clusters. RNA (2008) 1.41
PromH: Promoters identification using orthologous genomic sequences. Nucleic Acids Res (2003) 1.41
Large-scale structural analysis of the core promoter in mammalian and plant genomes. Nucleic Acids Res (2005) 1.39
The common marmoset genome provides insight into primate biology and evolution. Nat Genet (2014) 1.38
The DNA sequence and analysis of human chromosome 13. Nature (2004) 1.33
The Ensembl gene annotation system. Database (Oxford) (2016) 1.31
Plant promoter prediction with confidence estimation. Nucleic Acids Res (2005) 1.27
Signaling between transforming growth factor β (TGF-β) and transcription factor SNAI2 represses expression of microRNA miR-203 to promote epithelial-mesenchymal transition and tumor metastasis. J Biol Chem (2013) 1.25
A transcription factor affinity-based code for mammalian transcription initiation. Genome Res (2009) 1.23
Hypoxia-inducible factor-1-mediated regulation of semaphorin 4D affects tumor growth and vascularity. J Biol Chem (2009) 1.20
SLC6A4 methylation modifies the effect of the number of traumatic events on risk for posttraumatic stress disorder. Depress Anxiety (2011) 1.18
Toward a gold standard for promoter prediction evaluation. Bioinformatics (2009) 1.17
Genome of bovine herpesvirus 5. J Virol (2003) 1.16
Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res (2003) 1.15
Begin at the beginning: predicting genes with 5' UTRs. Genome Res (2005) 1.14
Cis-motifs upstream of the transcription and translation initiation sites are effectively revealed by their positional disequilibrium in eukaryote genomes using frequency distribution curves. BMC Bioinformatics (2006) 1.08
Boosting with stumps for predicting transcription start sites. Genome Biol (2007) 1.08
An integrative genomic approach identifies p73 and p63 as activators of miR-200 microRNA family transcription. Nucleic Acids Res (2011) 1.08
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data. BMC Bioinformatics (2010) 1.05
Identifying regulatory elements in eukaryotic genomes. Brief Funct Genomic Proteomic (2009) 1.02
Small RNAs targeting transcription start site induce heparanase silencing through interference with transcription initiation in human cancer cells. PLoS One (2012) 1.01
Vertebrate gene finding from multiple-species alignments using a two-level strategy. Genome Biol (2006) 0.99
Computational analyses of eukaryotic promoters. BMC Bioinformatics (2007) 0.99
Hormonal regulation of cardiac KCNE2 gene expression. Mol Cell Endocrinol (2008) 0.98
Homozygous deletion of the STK11/LKB1 locus and the generation of novel fusion transcripts in cervical cancer cells. Cancer Genet Cytogenet (2010) 0.97
MicroRNA-148a regulates LDL receptor and ABCA1 expression to control circulating lipoprotein levels. Nat Med (2015) 0.96
Functional annotation of risk loci identified through genome-wide association studies for prostate cancer. Prostate (2010) 0.95
Regulation of p110delta PI 3-kinase gene expression. PLoS One (2009) 0.95
DNA free energy-based promoter prediction and comparative analysis of Arabidopsis and rice genomes. Plant Physiol (2011) 0.95
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. Nucleic Acids Res (2003) 0.94
Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome. BMC Genomics (2009) 0.93
A novel view of the transcriptome revealed from gene trapping in mouse embryonic stem cells. Genome Res (2007) 0.93
A giant novel gene undergoing extensive alternative splicing is severed by a Cornelia de Lange-associated translocation breakpoint at 3q26.3. Hum Genet (2004) 0.92
A composite method based on formal grammar and DNA structural features in detecting human polymerase II promoter region. PLoS One (2013) 0.88
Bioinformatics prediction of overlapping frameshifted translation products in mammalian transcripts. BMC Genomics (2008) 0.87
PromAn: an integrated knowledge-based web server dedicated to promoter analysis. Nucleic Acids Res (2006) 0.87
Machine learning and genome annotation: a match meant to be? Genome Biol (2013) 0.86
Multiple regulatory variants modulate expression of 5-hydroxytryptamine 2A receptors in human cortex. Biol Psychiatry (2012) 0.86
Characterization of the human DYRK1A promoter and its regulation by the transcription factor E2F1. BMC Mol Biol (2008) 0.86
DNA sequence and structural properties as predictors of human and mouse promoters. Gene (2007) 0.85
Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene. BMC Genomics (2005) 0.85
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. BMC Genomics (2012) 0.85
ReLA, a local alignment search tool for the identification of distal and proximal gene regulatory regions and their conserved transcription factor binding sites. Bioinformatics (2012) 0.85
A novel isoform of the B cell tyrosine kinase BTK protects breast cancer cells from apoptosis. Genes Chromosomes Cancer (2013) 0.84
Pol II promoter prediction using characteristic 4-mer motifs: a machine learning approach. BMC Bioinformatics (2008) 0.84
Transcriptional regulation of T-type calcium channel CaV3.2: bi-directionality by early growth response 1 (Egr1) and repressor element 1 (RE-1) protein-silencing transcription factor (REST). J Biol Chem (2012) 0.84
Investigation of G72 (DAOA) expression in the human brain. BMC Psychiatry (2008) 0.83
A comparison study on feature selection of DNA structural properties for promoter prediction. BMC Bioinformatics (2012) 0.83
High DNA melting temperature predicts transcription start site location in human and mouse. Nucleic Acids Res (2009) 0.83
PRESTA: associating promoter sequences with information on gene expression. Genome Biol (2002) 0.82
Gain of function mutant p53 proteins cooperate with E2F4 to transcriptionally downregulate RAD17 and BRCA1 gene expression. Oncotarget (2015) 0.82
Ensemble approach combining multiple methods improves human transcription start site prediction. BMC Genomics (2010) 0.81
NPEST: a nonparametric method and a database for transcription start site prediction. Quant Biol (2013) 0.81
The characteristics of human genes: analysis of human chromosome 22. Comp Funct Genomics (2003) 0.81
Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis. Front Genet (2014) 0.81
Predicting promoter activities of primary human DNA sequences. Nucleic Acids Res (2011) 0.81
Multiple mechanisms contribute to leakiness of a frameshift mutation in canine cone-rod dystrophy. PLoS One (2012) 0.80
Comparative analysis of transcription start sites using mutual information. Genomics Proteomics Bioinformatics (2006) 0.80
What can we learn from noncoding regions of similarity between genomes? BMC Bioinformatics (2004) 0.80
Large-scale modeling of condition-specific gene regulatory networks by information integration and inference. Nucleic Acids Res (2014) 0.80
Computational tools and resources for prediction and analysis of gene regulatory regions in the chick genome. Genesis (2013) 0.79
Regional selection acting on the OFD1 gene family. PLoS One (2011) 0.79
Prediction for human transcription start site using diversity measure with quadratic discriminant. Bioinformation (2008) 0.79
PCA-HPR: a principle component analysis model for human promoter recognition. Bioinformation (2008) 0.78
SSAHA: a fast search method for large DNA databases. Genome Res (2001) 48.64
The DNA sequence of human chromosome 22. Nature (1999) 30.88
Functional annotation of a full-length mouse cDNA collection. Nature (2001) 23.61
Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences. J Mol Biol (1990) 8.75
Meta-MEME: motif-based hidden Markov models of protein families. Comput Appl Biosci (1997) 4.48
The eukaryotic promoter database (EPD). Nucleic Acids Res (2000) 4.21
Eukaryotic promoter recognition. Genome Res (1997) 3.85
Promoter2.0: for the recognition of PolII promoter sequences. Bioinformatics (1999) 2.96
Highly specific localization of promoter regions in large genomic sequences by PromoterInspector: a novel context analysis approach. J Mol Biol (2000) 2.88
First pass annotation of promoters on human chromosome 22. Genome Res (2001) 1.99
Detection of eukaryotic promoters using Markov transition matrices. Comput Chem (1997) 1.55
Identification and functional modelling of DNA sequence elements of transcription. Brief Bioinform (2000) 1.39
The hormone-sensitive lipase gene is transcribed from at least five alternative first exons in mouse adipose tissue. Mamm Genome (2000) 1.28
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
SCOP database in 2002: refinements accommodate structural genomics. Nucleic Acids Res (2002) 18.11
SCOP database in 2004: refinements integrate structure and sequence family data. Nucleic Acids Res (2004) 15.21
Ensembl 2011. Nucleic Acids Res (2010) 14.68
Ensembl 2012. Nucleic Acids Res (2011) 14.55
Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res (2007) 13.44
Ensembl 2014. Nucleic Acids Res (2013) 12.62
Ensembl 2013. Nucleic Acids Res (2012) 11.70
Ensembl's 10th year. Nucleic Acids Res (2009) 10.82
The zebrafish reference genome sequence and its relationship to the human genome. Nature (2013) 8.52
Integrating biological data--the Distributed Annotation System. BMC Bioinformatics (2008) 6.56
Integrating sequence and structural biology with DAS. BMC Bioinformatics (2007) 5.12
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84
MaxBench: evaluation of sequence and structure comparison methods. Bioinformatics (2002) 4.83
Adding some SPICE to DAS. Bioinformatics (2005) 4.62
NestedMICA: sensitive inference of over-represented motifs in nucleic acid sequence. Nucleic Acids Res (2005) 2.58
The Protein Feature Ontology: a tool for the unification of protein feature annotations. Bioinformatics (2008) 2.33
SISYPHUS--structural alignments for proteins with non-trivial relationships. Nucleic Acids Res (2006) 2.18
Dalliance: interactive genome viewing on the web. Bioinformatics (2011) 2.07
Large-scale discovery of promoter motifs in Drosophila melanogaster. PLoS Comput Biol (2006) 1.46
A machine learning strategy to identify candidate binding sites in human protein-coding sequence. BMC Bioinformatics (2006) 1.08
Characterizing genetic variants for clinical action. Am J Med Genet C Semin Med Genet (2014) 1.02
CASP5 target classification. Proteins (2003) 1.01
What can we learn from noncoding regions of similarity between genomes? BMC Bioinformatics (2004) 0.80
iMotifs: an integrated sequence motif visualization and analysis environment. Bioinformatics (2010) 0.79
Corrigendum: Characterisation of mental health conditions in social media using Informed Deep Learning. Sci Rep (2017) 0.75