Published in PLoS Comput Biol on May 02, 2007
Abundant quantitative trait loci exist for DNA methylation and gene expression in human brain. PLoS Genet (2010) 8.74
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Distinct DNA methylomes of newborns and centenarians. Proc Natl Acad Sci U S A (2012) 4.26
Integrated genetic and epigenetic analysis identifies three different subclasses of colon cancer. Proc Natl Acad Sci U S A (2007) 4.16
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DNA methylation profiling identifies epigenetic dysregulation in pancreatic islets from type 2 diabetic patients. EMBO J (2012) 2.21
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DNA methylation profiling reveals a predominant immune component in breast cancers. EMBO Mol Med (2011) 1.81
GC skew at the 5' and 3' ends of human genes links R-loop formation to epigenetic regulation and transcription termination. Genome Res (2013) 1.71
Patterns of regulatory activity across diverse human cell types predict tissue identity, transcription factor binding, and long-range interactions. Genome Res (2013) 1.69
DNA methylation profiles of human active and inactive X chromosomes. Genome Res (2011) 1.68
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The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle. J Biol Chem (2011) 1.36
DNA methylation signatures link prenatal famine exposure to growth and metabolism. Nat Commun (2014) 1.28
Expression analysis and in silico characterization of intronic long noncoding RNAs in renal cell carcinoma: emerging functional associations. Mol Cancer (2013) 1.18
Systematic CpG islands methylation profiling of genes in the wnt pathway in epithelial ovarian cancer identifies biomarkers of progression-free survival. Clin Cancer Res (2011) 1.15
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DNA methylation is associated with downregulation of the organic cation transporter OCT1 (SLC22A1) in human hepatocellular carcinoma. Genome Med (2011) 1.05
High-throughput engineering of a mammalian genome reveals building principles of methylation states at CG rich regions. Elife (2014) 1.03
Substitution rate variation at human CpG sites correlates with non-CpG divergence, methylation level and GC content. Genome Biol (2011) 1.01
The DNA methylation-regulated miR-193a-3p dictates the multi-chemoresistance of bladder cancer via repression of SRSF2/PLAU/HIC2 expression. Cell Death Dis (2014) 0.98
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Methylation profiling in individuals with uniparental disomy identifies novel differentially methylated regions on chromosome 15. Genome Res (2010) 0.97
Expanded methyl-sensitive cut counting reveals hypomethylation as an epigenetic state that highlights functional sequences of the genome. Proc Natl Acad Sci U S A (2011) 0.96
Genome-wide DNA methylation analysis in cohesin mutant human cell lines. Nucleic Acids Res (2010) 0.95
Profile analysis and prediction of tissue-specific CpG island methylation classes. BMC Bioinformatics (2009) 0.94
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CG dinucleotide periodicities recognized by the Dnmt3a-Dnmt3L complex are distinctive at retroelements and imprinted domains. Mamm Genome (2009) 0.93
Histone methylation marks play important roles in predicting the methylation status of CpG islands. Biochem Biophys Res Commun (2008) 0.93
A minimal set of tissue-specific hypomethylated CpGs constitute epigenetic signatures of developmental programming. PLoS One (2013) 0.93
Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters. Nucleic Acids Res (2010) 0.90
Tight associations between transcription promoter type and epigenetic variation in histone positioning and modification. BMC Genomics (2011) 0.89
MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol (2010) 0.89
Vitamin D receptor gene methylation is associated with ethnicity, tuberculosis, and TaqI polymorphism. Hum Immunol (2010) 0.89
DNA sequence explains seemingly disordered methylation levels in partially methylated domains of Mammalian genomes. PLoS Genet (2014) 0.87
Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands. PLoS One (2012) 0.85
CpGIF: an algorithm for the identification of CpG islands. Bioinformation (2008) 0.85
Enriched transcription factor binding sites in hypermethylated gene promoters in drug resistant cancer cells. Bioinformatics (2008) 0.84
Computational Epigenetics: the new scientific paradigm. Bioinformation (2010) 0.84
Human-specific epigenetic variation in the immunological Leukotriene B4 Receptor (LTB4R/BLT1) implicated in common inflammatory diseases. Genome Med (2014) 0.83
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. Epigenetics (2010) 0.83
Characterizing the Retinoblastoma 1 locus: putative elements for Rb1 regulation by in silico analysis. Front Genet (2014) 0.81
Global analysis of biogenesis, stability and sub-cellular localization of lncRNAs mapping to intragenic regions of the human genome. RNA Biol (2015) 0.79
Predicting DNA-binding specificities of eukaryotic transcription factors. PLoS One (2010) 0.79
Racial differences in genome-wide methylation profiling and gene expression in breast tissues from healthy women. Epigenetics (2015) 0.78
ContDist: a tool for the analysis of quantitative gene and promoter properties. BMC Bioinformatics (2009) 0.78
Genesis and regulatory wiring of retroelement-derived domesticated genes: a phylogenomic perspective. Mol Biol Evol (2013) 0.78
Methylation of class II transactivator gene promoter IV is not associated with susceptibility to multiple sclerosis. BMC Med Genet (2008) 0.77
Identification of CpG islands in DNA sequences using statistically optimal null filters. EURASIP J Bioinform Syst Biol (2012) 0.77
A computational model for histone mark propagation reproduces the distribution of heterochromatin in different human cell types. PLoS One (2013) 0.77
Association and CpG SNP analysis of HTR4 polymorphisms with suicidal behavior in subjects with schizophrenia. J Neural Transm (Vienna) (2012) 0.76
AT1 receptor induced alterations in histone H2A reveal novel insights into GPCR control of chromatin remodeling. PLoS One (2010) 0.75
ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining. BMC Bioinformatics (2016) 0.75
CpGPAP: CpG island predictor analysis platform. BMC Genet (2012) 0.75
Empirical bayes model comparisons for differential methylation analysis. Comp Funct Genomics (2012) 0.75
Molecular mechanisms underlying noncoding risk variations in psychiatric genetic studies. Mol Psychiatry (2017) 0.75
No Evidence for a Parent-of-Origin Specific Differentially Methylated Region Linked to RASGRF1. Front Genet (2012) 0.75
Prediction of genome-wide DNA methylation in repetitive elements. Nucleic Acids Res (2017) 0.75
Comprehensive strategy for the design of precision drugs and identification of genetic signature behind proneness of the disease-a pharmacogenomic approach. Funct Integr Genomics (2017) 0.75
DNA methylation patterns and epigenetic memory. Genes Dev (2002) 33.83
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CpG-rich islands and the function of DNA methylation. Nature (1986) 24.90
A high-resolution map of active promoters in the human genome. Nature (2005) 24.35
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Distribution, silencing potential and evolutionary impact of promoter DNA methylation in the human genome. Nat Genet (2007) 20.22
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
Genomic maps and comparative analysis of histone modifications in human and mouse. Cell (2005) 18.96
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell (2004) 16.15
Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proc Natl Acad Sci U S A (2002) 12.33
Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics (2000) 11.75
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 islands as gene markers in the human genome. Genomics (1992) 7.45
Active chromatin domains are defined by acetylation islands revealed by genome-wide mapping. Genes Dev (2005) 7.21
Genome-wide mapping of DNase hypersensitive sites using massively parallel signature sequencing (MPSS). Genome Res (2005) 5.71
TileMap: create chromosomal map of tiling array hybridizations. Bioinformatics (2005) 5.68
A standard reference frame for the description of nucleic acid base-pair geometry. J Mol Biol (2001) 4.29
Large-scale structure of genomic methylation patterns. Genome Res (2005) 4.11
Cancer epigenetics. Hum Mol Genet (2005) 3.63
Detection and interpretation of altered methylation patterns in cancer cells. Nat Rev Cancer (2005) 3.27
Structure, function and evolution of CpG island promoters. Cell Mol Life Sci (2003) 3.09
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
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A comprehensive analysis of allelic methylation status of CpG islands on human chromosome 21q. Genome Res (2004) 2.56
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences. Bioinformatics (2002) 2.22
An evaluation of new criteria for CpG islands in the human genome as gene markers. Bioinformatics (2004) 2.19
Promoter prediction analysis on the whole human genome. Nat Biotechnol (2004) 2.08
Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83
Mice and men: their promoter properties. PLoS Genet (2006) 1.50
DNA methylation and chromatin structure: the puzzling CpG islands. J Cell Biochem (2005) 1.45
Predicting methylation status of CpG islands in the human brain. Bioinformatics (2006) 1.38
Sequence-dependent DNA structure: a database of octamer structural parameters. J Mol Biol (2003) 1.33
Applications of recursive segmentation to the analysis of DNA sequences. Comput Chem (2002) 1.25
Compositional searching of CpG islands in the human genome. Phys Rev E Stat Nonlin Soft Matter Phys (2005) 1.00
German human methylome project started. Cancer Res (2006) 0.83
ROCR: visualizing classifier performance in R. Bioinformatics (2005) 19.60
A genome-wide association scan of nonsynonymous SNPs identifies a susceptibility variant for Crohn disease in ATG16L1. Nat Genet (2006) 15.14
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure. Bioinformatics (2006) 11.33
Epigenetic reprogramming in mouse primordial germ cells. Mech Dev (2002) 6.67
BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics (2005) 5.95
5-Hydroxymethylcytosine in the mammalian zygote is linked with epigenetic reprogramming. Nat Commun (2011) 5.66
Computing topological parameters of biological networks. Bioinformatics (2007) 5.36
Resistance of IAPs to methylation reprogramming may provide a mechanism for epigenetic inheritance in the mouse. Genesis (2003) 5.19
A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics (2006) 4.82
Imprinted microRNA genes transcribed antisense to a reciprocally imprinted retrotransposon-like gene. Nat Genet (2003) 4.68
The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol Cell (2012) 4.32
Asymmetric regulation of imprinting on the maternal and paternal chromosomes at the Dlk1-Gtl2 imprinted cluster on mouse chromosome 12. Nat Genet (2003) 4.25
Sarcoidosis is associated with a truncating splice site mutation in BTNL2. Nat Genet (2005) 4.23
Dynamic readers for 5-(hydroxy)methylcytosine and its oxidized derivatives. Cell (2013) 4.16
Promiscuous gene expression in thymic epithelial cells is regulated at multiple levels. J Exp Med (2005) 4.06
The implications of alternative splicing in the ENCODE protein complement. Proc Natl Acad Sci U S A (2007) 3.93
Diversity and complexity of HIV-1 drug resistance: a bioinformatics approach to predicting phenotype from genotype. Proc Natl Acad Sci U S A (2002) 3.46
BLUEPRINT to decode the epigenetic signature written in blood. Nat Biotechnol (2012) 3.24
Genetic variation in DLG5 is associated with inflammatory bowel disease. Nat Genet (2004) 3.19
Recruitment and activation of a lipid kinase by hepatitis C virus NS5A is essential for integrity of the membranous replication compartment. Cell Host Microbe (2011) 3.05
Genomic distribution and inter-sample variation of non-CpG methylation across human cell types. PLoS Genet (2011) 2.98
FGF signaling inhibition in ESCs drives rapid genome-wide demethylation to the epigenetic ground state of pluripotency. Cell Stem Cell (2013) 2.79
In vivo control of CpG and non-CpG DNA methylation by DNA methyltransferases. PLoS Genet (2012) 2.70
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
Identification of tandemly-repeated C/D snoRNA genes at the imprinted human 14q32 domain reminiscent of those at the Prader-Willi/Angelman syndrome region. Hum Mol Genet (2002) 2.55
Predicting HIV coreceptor usage on the basis of genetic and clinical covariates. Antivir Ther (2007) 2.49
Calculating the statistical significance of changes in pathway activity from gene expression data. Stat Appl Genet Mol Biol (2004) 2.48
AltAnalyze and DomainGraph: analyzing and visualizing exon expression data. Nucleic Acids Res (2010) 2.41
Geno2pheno: Estimating phenotypic drug resistance from HIV-1 genotypes. Nucleic Acids Res (2003) 2.37
DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet (2009) 2.37
Epigenetic analysis of the Dlk1-Gtl2 imprinted domain on mouse chromosome 12: implications for imprinting control from comparison with Igf2-H19. Hum Mol Genet (2002) 2.33
Whole-genome bisulfite sequencing of two distinct interconvertible DNA methylomes of mouse embryonic stem cells. Cell Stem Cell (2013) 2.32
Dynamic link of DNA demethylation, DNA strand breaks and repair in mouse zygotes. EMBO J (2010) 2.30
The HIN domain of IFI-200 proteins consists of two OB folds. Biochem Biophys Res Commun (2005) 2.25
Dnmt1 overexpression causes genomic hypermethylation, loss of imprinting, and embryonic lethality. Mol Cell Biol (2002) 2.24
Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping. Nucleic Acids Res (2008) 2.19
A DNA methylation fingerprint of 1628 human samples. Genome Res (2011) 2.16
Co-clustering of biological networks and gene expression data. Bioinformatics (2002) 2.12
Computational epigenetics. Bioinformatics (2007) 1.92
DNA-methylation analysis by the bisulfite-assisted genomic sequencing method. Methods Mol Biol (2002) 1.91
BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing. Nucleic Acids Res (2011) 1.90
Dissection of the inflammatory bowel disease transcriptome using genome-wide cDNA microarrays. PLoS Med (2005) 1.88
NOXclass: prediction of protein-protein interaction types. BMC Bioinformatics (2006) 1.85
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83
Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation. Plant Physiol (2006) 1.75
Learning multiple evolutionary pathways from cross-sectional data. J Comput Biol (2005) 1.74
Epigenetic modifications in an imprinting cluster are controlled by a hierarchy of DMRs suggesting long-range chromatin interactions. Hum Mol Genet (2003) 1.73
Recco: recombination analysis using cost optimization. Bioinformatics (2006) 1.68
Functional evaluation of domain-domain interactions and human protein interaction networks. Bioinformatics (2007) 1.65
DASMI: exchanging, annotating and assessing molecular interaction data. Bioinformatics (2009) 1.64
High-resolution map and imprinting analysis of the Gtl2-Dnchc1 domain on mouse chromosome 12. Genomics (2005) 1.60
Computational analysis of human protein interaction networks. Proteomics (2007) 1.53
Active demethylation of the Foxp3 locus leads to the generation of stable regulatory T cells within the thymus. J Immunol (2013) 1.45
A critical control element for interleukin-4 memory expression in T helper lymphocytes. J Biol Chem (2005) 1.44
Mtreemix: a software package for learning and using mixture models of mutagenetic trees. Bioinformatics (2005) 1.41
EpiExplorer: live exploration and global analysis of large epigenomic datasets. Genome Biol (2012) 1.40
Structural descriptors of gp120 V3 loop for the prediction of HIV-1 coreceptor usage. PLoS Comput Biol (2007) 1.39
Novel Sm-like proteins with long C-terminal tails and associated methyltransferases. FEBS Lett (2004) 1.38
Improving disease gene prioritization using the semantic similarity of Gene Ontology terms. Bioinformatics (2010) 1.37
Permutation importance: a corrected feature importance measure. Bioinformatics (2010) 1.32
Tandem repeats in the CpG islands of imprinted genes. Genomics (2006) 1.31
Differential dynamics of histone H3 methylation at positions K4 and K9 in the mouse zygote. BMC Dev Biol (2004) 1.30
Involvement of novel human immunodeficiency virus type 1 reverse transcriptase mutations in the regulation of resistance to nucleoside inhibitors. J Virol (2006) 1.28
Computational methods for the design of effective therapies against drug resistant HIV strains. Bioinformatics (2005) 1.27
DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones. Methods Mol Biol (2009) 1.26
An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol (2004) 1.26
Survey on the PABC recognition motif PAM2. Biochem Biophys Res Commun (2004) 1.26
Imprinting and disease. Semin Cell Dev Biol (2003) 1.24
Structural and functional analysis of ataxin-2 and ataxin-3. Eur J Biochem (2004) 1.24
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Confirmation of human protein interaction data by human expression data. BMC Bioinformatics (2005) 1.23
Decomposing protein networks into domain-domain interactions. Bioinformatics (2005) 1.22
Ataxin-2 and huntingtin interact with endophilin-A complexes to function in plastin-associated pathways. Hum Mol Genet (2005) 1.21
Identification of PatL1, a human homolog to yeast P body component Pat1. Biochim Biophys Acta (2007) 1.21
Estimating HIV evolutionary pathways and the genetic barrier to drug resistance. J Infect Dis (2005) 1.19
A rapid, quantitative, non-radioactive bisulfite-SNuPE- IP RP HPLC assay for methylation analysis at specific CpG sites. Nucleic Acids Res (2002) 1.19
Microarrays: how many do you need? J Comput Biol (2003) 1.19
Managing drug resistance in cancer: lessons from HIV therapy. Nat Rev Cancer (2012) 1.19
DynaPred: a structure and sequence based method for the prediction of MHC class I binding peptide sequences and conformations. Bioinformatics (2006) 1.18
Estimating cancer survival and clinical outcome based on genetic tumor progression scores. Bioinformatics (2005) 1.18
Improved prediction of response to antiretroviral combination therapy using the genetic barrier to drug resistance. Antivir Ther (2007) 1.17
Arby: automatic protein structure prediction using profile-profile alignment and confidence measures. Bioinformatics (2004) 1.16
Structural conservation versus functional divergence of maternally expressed microRNAs in the Dlk1/Gtl2 imprinting region. BMC Genomics (2008) 1.16
DNA-methylome analysis of mouse intestinal adenoma identifies a tumour-specific signature that is partly conserved in human colon cancer. PLoS Genet (2013) 1.13
Tenofovir resistance and resensitization. Antimicrob Agents Chemother (2003) 1.10
Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues. Epigenetics (2012) 1.08
Predicting the response to combination antiretroviral therapy: retrospective validation of geno2pheno-THEO on a large clinical database. J Infect Dis (2009) 1.07
Comparison of classifier fusion methods for predicting response to anti HIV-1 therapy. PLoS One (2008) 1.07