Published in Comp Funct Genomics on March 04, 2012
Epigenome-wide ovarian cancer analysis identifies a methylation profile differentiating clear-cell histology with epigenetic silencing of the HERG K+ channel. Hum Mol Genet (2013) 0.97
Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics (2012) 0.95
Systems biology approach to stage-wise characterization of epigenetic genes in lung adenocarcinoma. BMC Syst Biol (2013) 0.87
On the relationship between an Asian haplotype on chromosome 6 that reduces androstenone levels in boars and the differential expression of SULT2A1 in the testis. BMC Genet (2014) 0.80
Major histocompatibility complex class I core promoter elements are not essential for transcription in vivo. Mol Cell Biol (2013) 0.79
An integrative study identifies KCNC2 as a novel predisposing factor for childhood obesity and the risk of diabetes in the Korean population. Sci Rep (2016) 0.77
Relating gene expression evolution with CpG content changes. BMC Genomics (2014) 0.77
Initial sequencing and analysis of the human genome. Nature (2001) 212.86
A gene atlas of the mouse and human protein-encoding transcriptomes. Proc Natl Acad Sci U S A (2004) 44.81
Human DNA methylomes at base resolution show widespread epigenomic differences. Nature (2009) 34.27
DNA methylation patterns and epigenetic memory. Genes Dev (2002) 33.83
CpG islands in vertebrate genomes. J Mol Biol (1987) 23.16
Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet (2005) 15.37
Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell (2011) 8.21
A novel CpG island set identifies tissue-specific methylation at developmental gene loci. PLoS Biol (2008) 7.95
Cyclical DNA methylation of a transcriptionally active promoter. Nature (2008) 7.62
CpG islands as gene markers in the human genome. Genomics (1992) 7.45
Transient cyclical methylation of promoter DNA. Nature (2008) 5.19
Role for DNA methylation in the control of cell type specific maspin expression. Nat Genet (2002) 4.72
Association of tissue-specific differentially methylated regions (TDMs) with differential gene expression. Proc Natl Acad Sci U S A (2005) 4.59
The methylome: approaches for global DNA methylation profiling. Trends Genet (2008) 3.16
Structure, function and evolution of CpG island promoters. Cell Mol Life Sci (2003) 3.09
CG dinucleotide clustering is a species-specific property of the genome. Nucleic Acids Res (2007) 2.48
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics (2002) 2.22
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics (2004) 2.19
CpGcluster: a distance-based algorithm for CpG-island detection. BMC Bioinformatics (2006) 2.19
The dynamic DNA methylomes of double-stranded DNA viruses associated with human cancer. Genome Res (2009) 1.87
CpG island methylation pattern in different human tissues and its correlation with gene expression. Biochem Biophys Res Commun (2009) 1.58
Gene expression evolves faster in narrowly than in broadly expressed mammalian genes. Mol Biol Evol (2005) 1.44
The necessity of a human epigenome project. Carcinogenesis (2006) 1.40
CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol (2008) 1.30
Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol (2007) 1.23
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
Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics (2011) 1.08
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinformatics (2009) 0.98
Comparative analysis of CpG islands in four fish genomes. Comp Funct Genomics (2008) 0.97
Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics (2009) 0.92
Patient-specific induced pluripotent stem cells as a model for familial dilated cardiomyopathy. Sci Transl Med (2012) 3.53
TSGene: a web resource for tumor suppressor genes. Nucleic Acids Res (2012) 2.90
BRAF(L597) mutations in melanoma are associated with sensitivity to MEK inhibitors. Cancer Discov (2012) 2.48
Abnormal calcium handling properties underlie familial hypertrophic cardiomyopathy pathology in patient-specific induced pluripotent stem cells. Cell Stem Cell (2013) 2.33
dmGWAS: dense module searching for genome-wide association studies in protein-protein interaction networks. Bioinformatics (2010) 2.23
Hdac3 is essential for the maintenance of chromatin structure and genome stability. Cancer Cell (2010) 2.20
AnimalTFDB: a comprehensive animal transcription factor database. Nucleic Acids Res (2011) 2.15
Computational tools for copy number variation (CNV) detection using next-generation sequencing data: features and perspectives. BMC Bioinformatics (2013) 2.07
Dissecting the molecular relationship among various cardiogenic progenitor cells. Circ Res (2013) 2.06
Genome-wide identification of SNPs in microRNA genes and the SNP effects on microRNA target binding and biogenesis. Hum Mutat (2011) 1.98
Common variants conferring risk of schizophrenia: a pathway analysis of GWAS data. Schizophr Res (2010) 1.79
No-boundary thinking in bioinformatics research. BioData Min (2013) 1.76
Gene set analysis of genome-wide association studies: methodological issues and perspectives. Genomics (2011) 1.76
Microfluidic single-cell analysis shows that porcine induced pluripotent stem cell-derived endothelial cells improve myocardial function by paracrine activation. Circ Res (2012) 1.74
Schizophrenia gene networks and pathways and their applications for novel candidate gene selection. PLoS One (2010) 1.67
Mutations in GDF6 are associated with vertebral segmentation defects in Klippel-Feil syndrome. Hum Mutat (2008) 1.62
Construction of a chloroplast protein interaction network and functional mining of photosynthetic proteins in Arabidopsis thaliana. Cell Res (2008) 1.58
DPTF: a database of poplar transcription factors. Bioinformatics (2007) 1.56
Uncovering MicroRNA and Transcription Factor Mediated Regulatory Networks in Glioblastoma. PLoS Comput Biol (2012) 1.54
A multi-dimensional evidence-based candidate gene prioritization approach for complex diseases-schizophrenia as a case. Bioinformatics (2009) 1.50
Epithelial cell organization suppresses Myc function by attenuating Myc expression. Cancer Res (2011) 1.44
Large-scale prediction of adverse drug reactions using chemical, biological, and phenotypic properties of drugs. J Am Med Inform Assoc (2012) 1.43
MicroRNA-302 increases reprogramming efficiency via repression of NR2F2. Stem Cells (2013) 1.41
A novel microRNA and transcription factor mediated regulatory network in schizophrenia. BMC Syst Biol (2010) 1.40
Finding the lost treasures in exome sequencing data. Trends Genet (2013) 1.36
VirusFinder: software for efficient and accurate detection of viruses and their integration sites in host genomes through next generation sequencing data. PLoS One (2013) 1.35
Candidate genes for schizophrenia: a survey of association studies and gene ranking. Am J Med Genet B Neuropsychiatr Genet (2008) 1.31
CpG island density and its correlations with genomic features in mammalian genomes. Genome Biol (2008) 1.30
IL-15 regulates homeostasis and terminal maturation of NKT cells. J Immunol (2011) 1.29
Application of next generation sequencing to human gene fusion detection: computational tools, features and perspectives. Brief Bioinform (2012) 1.23
CADgene: a comprehensive database for coronary artery disease genes. Nucleic Acids Res (2010) 1.23
Network-assisted investigation of combined causal signals from genome-wide association studies in schizophrenia. PLoS Comput Biol (2012) 1.23
A comparative study of cancer proteins in the human protein-protein interaction network. BMC Genomics (2010) 1.23
Features and trend of loss of promoter-associated CpG islands in the human and mouse genomes. Mol Biol Evol (2007) 1.23
The THO complex regulates pluripotency gene mRNA export and controls embryonic stem cell self-renewal and somatic cell reprogramming. Cell Stem Cell (2013) 1.19
Targeted next-generation sequencing of DNA regions proximal to a conserved GXGXXG signaling motif enables systematic discovery of tyrosine kinase fusions in cancer. Nucleic Acids Res (2010) 1.17
MicroRNA and transcription factor co-regulatory network analysis reveals miR-19 inhibits CYLD in T-cell acute lymphoblastic leukemia. Nucleic Acids Res (2012) 1.15
A bias-reducing pathway enrichment analysis of genome-wide association data confirmed association of the MHC region with schizophrenia. J Med Genet (2011) 1.15
Rare variants in RTEL1 are associated with familial interstitial pneumonia. Am J Respir Crit Care Med (2015) 1.15
A comprehensive network and pathway analysis of candidate genes in major depressive disorder. BMC Syst Biol (2011) 1.13
CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun (2009) 1.13
Early stem cell engraftment predicts late cardiac functional recovery: preclinical insights from molecular imaging. Circ Cardiovasc Imaging (2012) 1.13
Interdisciplinary dialogue for education, collaboration, and innovation: intelligent Biology and Medicine in and beyond 2013. BMC Genomics (2013) 1.11
New genomic structure for prostate cancer specific gene PCA3 within BMCC1: implications for prostate cancer detection and progression. PLoS One (2009) 1.11
Mutational spectrum in the recent human genome inferred by single nucleotide polymorphisms. Genomics (2006) 1.09
Conservation and divergence of DNA methylation in eukaryotes: new insights from single base-resolution DNA methylomes. Epigenetics (2011) 1.08
L-arginine supplementation improves responses to injury and inflammation in dextran sulfate sodium colitis. PLoS One (2012) 1.08
The current Salmonella-host interactome. Proteomics Clin Appl (2011) 1.08
Pathway-based analysis of GWAS datasets: effective but caution required. Int J Neuropsychopharmacol (2010) 1.08
GenRev: exploring functional relevance of genes in molecular networks. Genomics (2011) 1.07
The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs. Genomics (2004) 1.07
Deciphering the unique microRNA signature in human esophageal adenocarcinoma. PLoS One (2013) 1.05
The genome of Ganoderma lucidum provides insights into triterpenes biosynthesis and wood degradation [corrected]. PLoS One (2012) 1.05
NGS catalog: A database of next generation sequencing studies in humans. Hum Mutat (2012) 1.05
Discovering disease-specific biomarker genes for cancer diagnosis and prognosis. Technol Cancer Res Treat (2010) 1.04
ERGR: An ethanol-related gene resource. Nucleic Acids Res (2008) 1.04
Preclinical derivation and imaging of autologously transplanted canine induced pluripotent stem cells. J Biol Chem (2011) 1.04
Next-generation sequencing of paired tyrosine kinase inhibitor-sensitive and -resistant EGFR mutant lung cancer cell lines identifies spectrum of DNA changes associated with drug resistance. Genome Res (2013) 1.03
Integrative network analysis identifies key genes and pathways in the progression of hepatitis C virus induced hepatocellular carcinoma. BMC Med Genomics (2011) 1.02
DCGL v2.0: an R package for unveiling differential regulation from differential co-expression. PLoS One (2013) 1.02
Functional complementation between transcriptional methylation regulation and post-transcriptional microRNA regulation in the human genome. BMC Genomics (2011) 1.02
Beyond histology: translating tumor genotypes into clinically effective targeted therapies. Clin Cancer Res (2014) 1.01
An efficient hierarchical generalized linear mixed model for pathway analysis of genome-wide association studies. Bioinformatics (2011) 1.01
Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms? Biochem Biophys Res Commun (2006) 1.01
Advances in systems biology: computational algorithms and applications. BMC Syst Biol (2012) 1.00
Synergetic regulatory networks mediated by oncogene-driven microRNAs and transcription factors in serous ovarian cancer. Mol Biosyst (2013) 0.99
A weighted and integrated drug-target interactome: drug repurposing for schizophrenia as a use case. BMC Syst Biol (2015) 0.99
MLL1, a H3K4 methyltransferase, regulates the TNFα-stimulated activation of genes downstream of NF-κB. J Cell Sci (2012) 0.99
CpG islands or CpG clusters: how to identify functional GC-rich regions in a genome? BMC Bioinformatics (2009) 0.98
Adenoma formation following limited ablation of p120-catenin in the mouse intestine. PLoS One (2011) 0.98
RNA-Seq analysis implicates dysregulation of the immune system in schizophrenia. BMC Genomics (2012) 0.97
Directionality of point mutation and 5-methylcytosine deamination rates in the chimpanzee genome. BMC Genomics (2006) 0.97
Methylation-dependent transition rates are dependent on local sequence lengths and genomic regions. Mol Biol Evol (2006) 0.97
Comparative analysis of CpG islands in four fish genomes. Comp Funct Genomics (2008) 0.97
Dynamic protein interaction modules in human hepatocellular carcinoma progression. BMC Syst Biol (2013) 0.96
Distinct and competitive regulatory patterns of tumor suppressor genes and oncogenes in ovarian cancer. PLoS One (2012) 0.96
Consensus rules in variant detection from next-generation sequencing data. PLoS One (2012) 0.96
The regulation of microRNA expression by DNA methylation in hepatocellular carcinoma. Mol Biosyst (2014) 0.96
The dystrobrevin binding protein 1 (DTNBP1) gene is associated with schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophr Res (2009) 0.95
InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics (2007) 0.95
Investigating the relationship of DNA methylation with mutation rate and allele frequency in the human genome. BMC Genomics (2012) 0.95
Integrative pathway analysis of genome-wide association studies and gene expression data in prostate cancer. BMC Syst Biol (2012) 0.95
Gastric adenocarcinoma has a unique microRNA signature not present in esophageal adenocarcinoma. Cancer (2013) 0.95
The sacred lotus genome provides insights into the evolution of flowering plants. Plant J (2013) 0.94
Network.assisted analysis to prioritize GWAS results: principles, methods and perspectives. Hum Genet (2014) 0.94
Transcription factor and microRNA co-regulatory loops: important regulatory motifs in biological processes and diseases. Brief Bioinform (2013) 0.94
Enriched pathways for major depressive disorder identified from a genome-wide association study. Int J Neuropsychopharmacol (2012) 0.93
CNVannotator: a comprehensive annotation server for copy number variation in the human genome. PLoS One (2013) 0.93
Prioritization and evaluation of depression candidate genes by combining multidimensional data resources. PLoS One (2011) 0.93
Prioritization of epilepsy associated candidate genes by convergent analysis. PLoS One (2011) 0.92
Application of systems biology approach identifies and validates GRB2 as a risk gene for schizophrenia in the Irish Case Control Study of Schizophrenia (ICCSS) sample. Schizophr Res (2010) 0.92
Contrast features of CpG islands in the promoter and other regions in the dog genome. Genomics (2009) 0.92
Role of insulin-like growth factor-1 signaling pathway in cisplatin-resistant lung cancer cells. Int J Radiat Oncol Biol Phys (2011) 0.92
Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes. Brief Bioinform (2015) 0.91
Education, collaboration, and innovation: intelligent biology and medicine in the era of big data. BMC Genomics (2015) 0.90
Safe genetic modification of cardiac stem cells using a site-specific integration technique. Circulation (2012) 0.90