Published in Nucleic Acids Res on April 15, 2008
Reference Maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell (2011) 8.21
Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat Biotechnol (2010) 5.96
Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat Methods (2010) 4.30
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet (2009) 2.85
DNA methylation analysis of chromosome 21 gene promoters at single base pair and single allele resolution. PLoS Genet (2009) 2.37
Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods (2014) 2.03
Prospects for epigenetic epidemiology. Am J Epidemiol (2009) 2.00
EpiGRAPH: user-friendly software for statistical analysis and prediction of (epi)genomic data. Genome Biol (2009) 1.83
Neonatal DNA methylation profile in human twins is specified by a complex interplay between intrauterine environmental and genetic factors, subject to tissue-specific influence. Genome Res (2012) 1.73
Single-cell DNA methylome sequencing and bioinformatic inference of epigenomic cell-state dynamics. Cell Rep (2015) 1.54
Epigenome mapping in normal and disease States. Circ Res (2010) 1.47
Spatial, temporal and interindividual epigenetic variation of functionally important DNA methylation patterns. Nucleic Acids Res (2010) 1.39
QDMR: a quantitative method for identification of differentially methylated regions by entropy. Nucleic Acids Res (2011) 1.37
Genome-wide variation of cytosine modifications between European and African populations and the implications for complex traits. Genetics (2013) 1.31
MBD-seq as a cost-effective approach for methylome-wide association studies: demonstration in 1500 case--control samples. Epigenomics (2012) 1.16
CpG islands: algorithms and applications in methylation studies. Biochem Biophys Res Commun (2009) 1.13
Genetic and non-genetic influences during pregnancy on infant global and site specific DNA methylation: role for folate gene variants and vitamin B12. PLoS One (2012) 1.12
Extensive variation and low heritability of DNA methylation identified in a twin study. Genome Res (2011) 1.07
MethylPCA: a toolkit to control for confounders in methylome-wide association studies. BMC Bioinformatics (2013) 1.06
Epigenetic epidemiology: promises for public health research. Environ Mol Mutagen (2014) 1.06
Quantitation of DNA methylation by melt curve analysis. BMC Cancer (2009) 1.06
Genome-scale analysis of DNA methylation in colorectal cancer using Infinium HumanMethylation450 BeadChips. Epigenetics (2013) 1.02
Interindividual variability and co-regulation of DNA methylation differ among blood cell populations. Epigenetics (2012) 1.00
Methylome-wide comparison of human genomic DNA extracted from whole blood and from EBV-transformed lymphocyte cell lines. Eur J Hum Genet (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
Deep bisulfite sequencing of aberrantly methylated loci in a patient with multiple methylation defects. PLoS One (2013) 0.95
MethMarker: user-friendly design and optimization of gene-specific DNA methylation assays. Genome Biol (2009) 0.94
Profile analysis and prediction of tissue-specific CpG island methylation classes. BMC Bioinformatics (2009) 0.94
Discordance of DNA methylation variance between two accessible human tissues. Sci Rep (2015) 0.91
A statistical method for excluding non-variable CpG sites in high-throughput DNA methylation profiling. BMC Bioinformatics (2010) 0.90
Evaluation of microarray-based DNA methylation measurement using technical replicates: the Atherosclerosis Risk In Communities (ARIC) Study. BMC Bioinformatics (2014) 0.90
MetMap enables genome-scale Methyltyping for determining methylation states in populations. PLoS Comput Biol (2010) 0.89
Space/population and time/age in DNA methylation variability in humans: a study on IGF2/H19 locus in different Italian populations and in mono- and di-zygotic twins of different age. Aging (Albany NY) (2012) 0.88
Features of methylation and gene expression in the promoter-associated CpG islands using human methylome data. Comp Funct Genomics (2012) 0.87
Constitutive promoter methylation of BRCA1 and RAD51C in patients with familial ovarian cancer and early-onset sporadic breast cancer. Hum Mol Genet (2012) 0.86
Characterization of the DNA methylome and its interindividual variation in human peripheral blood monocytes. Epigenomics (2013) 0.86
DNA methylation analysis of phenotype specific stratified Indian population. J Transl Med (2015) 0.85
Computational Epigenetics: the new scientific paradigm. Bioinformation (2010) 0.84
Identification and characterization of putative methylation targets in the MAOA locus using bioinformatic approaches. Epigenetics (2010) 0.83
Gene promoter methylation assayed in exhaled breath, with differences in smokers and lung cancer patients. Respir Res (2009) 0.83
Assessment of DNA methylation at the interferon regulatory factor 5 (IRF5) promoter region in inflammatory bowel diseases. Int J Colorectal Dis (2010) 0.82
Age dependent changes in the LPS induced transcriptome of bovine dermal fibroblasts occurs without major changes in the methylome. BMC Genomics (2015) 0.81
DNA methylation: conducting the orchestra from exposure to phenotype? Clin Epigenetics (2016) 0.81
Genome-scale DNA methylome and transcriptome profiling of human neutrophils. Sci Data (2016) 0.80
The P2 promoter of the IGF1 gene is a major epigenetic locus for GH responsiveness. Pharmacogenomics J (2015) 0.79
Interindividual variation in epigenomic phenomena in humans. Mamm Genome (2009) 0.79
Genome-wide DNA methylation analyses in the brain reveal four differentially methylated regions between humans and non-human primates. BMC Evol Biol (2012) 0.79
Inter-individual methylation variability in differentially methylated regions between maternal whole blood and first trimester CVS. Mol Cytogenet (2014) 0.76
Measurements of DNA methylation at seven loci in various tissues of CD1 mice. PLoS One (2012) 0.76
AgIn: measuring the landscape of CpG methylation of individual repetitive elements. Bioinformatics (2016) 0.75
Genetic predisposition to high anxiety- and depression-like behavior coincides with diminished DNA methylation in the adult rat amygdala. Behav Brain Res (2016) 0.75
Methylation of avpr1a in the cortex of wild prairie voles: effects of CpG position and polymorphism. R Soc Open Sci (2017) 0.75
The IGF1 P2 promoter is an epigenetic QTL for circulating IGF1 and human growth. Clin Epigenetics (2015) 0.75
Differential Analysis of Genetic, Epigenetic, and Cytogenetic Abnormalities in AML. Int J Genomics (2017) 0.75
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
The mammalian epigenome. Cell (2007) 18.13
DNA methylation profiling of human chromosomes 6, 20 and 22. Nat Genet (2006) 18.08
Genome-wide analysis of mammalian promoter architecture and evolution. Nat Genet (2006) 17.19
Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet (2005) 15.37
Genome-wide high-resolution mapping and functional analysis of DNA methylation in arabidopsis. Cell (2006) 15.24
Stability and flexibility of epigenetic gene regulation in mammalian development. Nature (2007) 14.57
Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation and transcription. Nat Genet (2006) 11.88
Phenotypic plasticity and the epigenetics of human disease. Nature (2007) 10.37
Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res (2005) 8.69
Comparative isoschizomer profiling of cytosine methylation: the HELP assay. Genome Res (2006) 5.99
Genome-wide profiling of DNA methylation reveals a class of normally methylated CpG island promoters. PLoS Genet (2007) 5.16
DNA methylation profiling of the human major histocompatibility complex: a pilot study for the human epigenome project. PLoS Biol (2004) 4.96
Large-scale structure of genomic methylation patterns. Genome Res (2005) 4.11
Cancer epigenetics. Hum Mol Genet (2005) 3.63
Genomic patterns of DNA methylation: targets and function of an epigenetic mark. Curr Opin Cell Biol (2007) 3.54
Methylation profiling of CpG islands in human breast cancer cells. Hum Mol Genet (1999) 3.26
Theoretical analysis of epigenetic cell memory by nucleosome modification. Cell (2007) 3.17
CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02
Quantitative DNA methylation analysis based on four-dye trace data from direct sequencing of PCR amplificates. Bioinformatics (2004) 2.79
Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res (2002) 2.71
CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet (2006) 2.66
Phenotypic differences in genetically identical organisms: the epigenetic perspective. Hum Mol Genet (2005) 2.63
Optimization of quantitative MGMT promoter methylation analysis using pyrosequencing and combined bisulfite restriction analysis. J Mol Diagn (2007) 2.35
Tumour class prediction and discovery by microarray-based DNA methylation analysis. Nucleic Acids Res (2002) 2.34
Gene silencing in mammalian cells and the spread of DNA methylation. Oncogene (2002) 2.27
Computational epigenetics. Bioinformatics (2007) 1.92
Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A (2006) 1.83
Pioneer factor interactions and unmethylated CpG dinucleotides mark silent tissue-specific enhancers in embryonic stem cells. Proc Natl Acad Sci U S A (2007) 1.81
Profound flanking sequence preference of Dnmt3a and Dnmt3b mammalian DNA methyltransferases shape the human epigenome. J Mol Biol (2005) 1.65
Predicting methylation status of CpG islands in the human brain. Bioinformatics (2006) 1.38
Epigenetics and phenotypic variation in mammals. Mamm Genome (2006) 1.26
Array-based profiling of reference-independent methylation status (aPRIMES) identifies frequent promoter methylation and consecutive downregulation of ZIC2 in pediatric medulloblastoma. Nucleic Acids Res (2007) 1.19
Dynamics, stability and inheritance of somatic DNA methylation imprints. J Theor Biol (2006) 1.10
Methylation profiles of genes utilizing newly developed CpG island methylation microarray on colorectal cancer patients. Nucleic Acids Res (2005) 0.94
Methylation-specific oligonucleotide microarray. Methods Mol Biol (2004) 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
CpG island mapping by epigenome prediction. PLoS Comput Biol (2007) 3.02
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
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
An integrative approach to gain insights into the cellular function of human ataxin-2. J Mol Biol (2004) 1.26
DNA methylation analysis by bisulfite conversion, cloning, and sequencing of individual clones. Methods Mol Biol (2009) 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
Diversity and functional plasticity of eukaryotic selenoproteins: identification and characterization of the SelJ family. Proc Natl Acad Sci U S A (2005) 1.23
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
Evolution of the Beckwith-Wiedemann syndrome region in vertebrates. Genome Res (2004) 1.06
The potential role of gene duplications in the evolution of imprinting mechanisms. Hum Mol Genet (2003) 1.06