Published in Bioinformatics on April 01, 2002
A genome-wide analysis of CpG dinucleotides in the human genome distinguishes two distinct classes of promoters. Proc Natl Acad Sci U S A (2006) 10.63
CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02
Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol (2007) 2.86
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
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
Genome-wide assembly and analysis of alternative transcripts in mouse. Genome Res (2005) 1.78
Comprehensive analysis of the base composition around the transcription start site in Metazoa. BMC Genomics (2004) 1.68
PlantPAN: Plant promoter analysis navigator, for identifying combinatorial cis-regulatory elements with distance constraint in plant gene groups. BMC Genomics (2008) 1.68
Towards a molecular dynamics consensus view of B-DNA flexibility. Nucleic Acids Res (2008) 1.56
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
MIR@NT@N: a framework integrating transcription factors, microRNAs and their targets to identify sub-network motifs in a meta-regulation network model. BMC Bioinformatics (2011) 1.33
Toward a gold standard for promoter prediction evaluation. Bioinformatics (2009) 1.17
Dragon gene start finder: an advanced system for finding approximate locations of the start of gene transcriptional units. Genome Res (2003) 1.15
CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun (2009) 1.13
Prediction of CpG-island function: CpG clustering vs. sliding-window methods. BMC Genomics (2010) 1.12
Genetic and epigenetic changes in the common 1p36 deletion in neuroblastoma tumours. Br J Cancer (2007) 1.11
Integrated databanks access and sequence/structure analysis services at the PBIL. Nucleic Acids Res (2003) 1.11
CpG_MI: a novel approach for identifying functional CpG islands in mammalian genomes. Nucleic Acids Res (2009) 0.98
Comparative analysis of CpG islands in four fish genomes. Comp Funct Genomics (2008) 0.97
CpG island structure and trithorax/polycomb chromatin domains in human cells. Genomics (2012) 0.96
CpG_MPs: identification of CpG methylation patterns of genomic regions from high-throughput bisulfite sequencing data. Nucleic Acids Res (2012) 0.96
Particle swarm optimization with reinforcement learning for the prediction of CpG islands in the human genome. PLoS One (2011) 0.95
Dragon Gene Start Finder identifies approximate locations of the 5' ends of genes. Nucleic Acids Res (2003) 0.94
Assessment of clusters of transcription factor binding sites in relationship to human promoter, CpG islands and gene expression. BMC Genomics (2004) 0.90
Maximum-likelihood model averaging to profile clustering of site types across discrete linear sequences. PLoS Comput Biol (2009) 0.90
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. BMC Syst Biol (2013) 0.87
Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data. Comp Funct Genomics (2012) 0.87
CpGIF: an algorithm for the identification of CpG islands. Bioinformation (2008) 0.85
DNA sequence and structural properties as predictors of human and mouse promoters. Gene (2007) 0.85
GPMiner: an integrated system for mining combinatorial cis-regulatory elements in mammalian gene group. BMC Genomics (2012) 0.85
Responsiveness of genes to manipulation of transcription factors in ES cells is associated with histone modifications and tissue specificity. BMC Genomics (2011) 0.84
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. Epigenetics (2010) 0.83
Whole-genome bisulfite sequencing maps from multiple human tissues reveal novel CpG islands associated with tissue-specific regulation. Hum Mol Genet (2015) 0.82
Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis. Front Genet (2014) 0.81
Hepatitis B virus genome asymmetry in hepatocellular carcinoma. Middle East J Dig Dis (2012) 0.79
Analysis of CpG methylation sites and CGI among human papillomavirus DNA genomes. BMC Genomics (2011) 0.79
PCA-HPR: a principle component analysis model for human promoter recognition. Bioinformation (2008) 0.78
Epigenetics and childhood asthma: current evidence and future research directions. Epigenomics (2012) 0.78
Comparison of gene expression and genome-wide DNA methylation profiling between phenotypically normal cloned pigs and conventionally bred controls. PLoS One (2011) 0.78
A hybrid neural network system for prediction and recognition of promoter regions in human genome. J Zhejiang Univ Sci B (2005) 0.78
Evidence for evolutionary and nonevolutionary forces shaping the distribution of human genetic variants near transcription start sites. PLoS One (2014) 0.78
High-resolution genome-wide DNA methylation maps of mouse primary female dermal fibroblasts and keratinocytes. Epigenetics Chromatin (2014) 0.77
High sensitivity TSS prediction: estimates of locations where TSS cannot occur. PLoS One (2010) 0.77
Identification of CpG islands in DNA sequences using statistically optimal null filters. EURASIP J Bioinform Syst Biol (2012) 0.77
Rule-based knowledge acquisition method for promoter prediction in human and Drosophila species. ScientificWorldJournal (2014) 0.76
A Hybrid Approach for CpG Island Detection in the Human Genome. PLoS One (2016) 0.75
Correlating CpG islands, motifs, and sequence variants in human chromosome 21. BMC Genomics (2011) 0.75
CpGPAP: CpG island predictor analysis platform. BMC Genet (2012) 0.75
Modeling the integration of bacterial rRNA fragments into the human cancer genome. BMC Bioinformatics (2016) 0.75
Long-range autocorrelations of CpG islands in the human genome. PLoS One (2012) 0.75
A gradual process of recombination restriction in the evolutionary history of the sex chromosomes in dioecious plants. PLoS Biol (2004) 2.20
Neutral effect of recombination on base composition in Drosophila. Genet Res (2003) 2.11
Vanishing GC-rich isochores in mammalian genomes. Genetics (2002) 1.86
HOPPSIGEN: a database of human and mouse processed pseudogenes. Nucleic Acids Res (2005) 1.38
Relationship between gene expression and GC-content in mammals: statistical significance and biological relevance. Hum Mol Genet (2004) 1.33
Expected relationship between the silent substitution rate and the GC content: implications for the evolution of isochores. J Mol Evol (2002) 1.06
Identitag, a relational database for SAGE tag identification and interspecies comparison of SAGE libraries. BMC Bioinformatics (2004) 0.99
GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance. Mol Biol Evol (2013) 0.95
Unexpected observations after mapping LongSAGE tags to the human genome. BMC Bioinformatics (2007) 0.95
GC content evolution of the human and mouse genomes: insights from the study of processed pseudogenes in regions of different recombination rates. J Mol Evol (2006) 0.93
Meiotic recombination favors the spreading of deleterious mutations in human populations. Hum Mutat (2011) 0.91
In silico whole-genome scanning of cancer-associated nonsynonymous SNPs and molecular characterization of a dynein light chain tumour variant. Oncogene (2005) 0.85
The sex-specific impact of meiotic recombination on nucleotide composition. Genome Biol Evol (2012) 0.82
Bioinformatic screening of human ESTs for differentially expressed genes in normal and tumor tissues. BMC Genomics (2006) 0.81
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions. BMC Genomics (2007) 0.79
DigiPINS: a database for vertebrate exonic single nucleotide polymorphisms and its application to cancer association studies. Biochimie (2007) 0.78
Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules. Am J Physiol Renal Physiol (2006) 0.77