Published in Bioinformatics on March 25, 2004
Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet (2009) 7.07
Model-based clustering of DNA methylation array data: a recursive-partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics (2008) 3.89
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma. Carcinogenesis (2009) 1.94
A statistical framework for Illumina DNA methylation arrays. Bioinformatics (2010) 1.92
Epigenetic profiles distinguish pleural mesothelioma from normal pleura and predict lung asbestos burden and clinical outcome. Cancer Res (2009) 1.73
Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet (2012) 1.47
Identification of methylated genes associated with aggressive bladder cancer. PLoS One (2010) 1.27
Method to detect differentially methylated loci with case-control designs using Illumina arrays. Genet Epidemiol (2011) 1.07
Including probe-level uncertainty in model-based gene expression clustering. BMC Bioinformatics (2007) 0.98
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies. Bioinformatics (2012) 0.96
Age-adjusted nonparametric detection of differential DNA methylation with case-control designs. BMC Bioinformatics (2013) 0.92
Heritable clustering and pathway discovery in breast cancer integrating epigenetic and phenotypic data. BMC Bioinformatics (2007) 0.90
Integrated profiling reveals a global correlation between epigenetic and genetic alterations in mesothelioma. Cancer Res (2010) 0.89
A latent class model with hidden Markov dependence for array CGH data. Biometrics (2009) 0.86
Recursively partitioned mixture model clustering of DNA methylation data using biologically informed correlation structures. Stat Appl Genet Mol Biol (2013) 0.85
A nonparametric Bayesian approach for clustering bisulfate-based DNA methylation profiles. BMC Genomics (2012) 0.84
Cluster analysis for DNA methylation profiles having a detection threshold. BMC Bioinformatics (2006) 0.80
Comparison of clustering methods for investigation of genome-wide methylation array data. Front Genet (2011) 0.78
Two-part permutation tests for DNA methylation and microarray data. BMC Bioinformatics (2005) 0.78
Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data. Oncotarget (2016) 0.78
Comparison of Methods for Identifying Phenotype Subgroups Using Categorical Features Data With Application to Autism Spectrum Disorder. Comput Stat Data Anal (2012) 0.77
Regularized F-measure maximization for feature selection and classification. J Biomed Biotechnol (2009) 0.76
Bacterially-Associated Transcriptional Remodelling in a Distinct Genomic Subtype of Colorectal Cancer Provides a Plausible Molecular Basis for Disease Development. PLoS One (2016) 0.75
Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. N Engl J Med (2013) 19.87
Identification of a CpG island methylator phenotype that defines a distinct subgroup of glioma. Cancer Cell (2010) 16.12
Integrated genomic characterization of endometrial carcinoma. Nature (2013) 14.29
CpG island methylator phenotype underlies sporadic microsatellite instability and is tightly associated with BRAF mutation in colorectal cancer. Nat Genet (2006) 13.63
The somatic genomic landscape of glioblastoma. Cell (2013) 11.73
Absolute quantification of somatic DNA alterations in human cancer. Nat Biotechnol (2012) 10.87
Epigenetic stem cell signature in cancer. Nat Genet (2006) 9.62
Pan-cancer patterns of somatic copy number alteration. Nat Genet (2013) 7.73
Analysis of repetitive element DNA methylation by MethyLight. Nucleic Acids Res (2005) 6.49
Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Genome Res (2010) 6.03
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina-associated domains. Nat Genet (2011) 5.70
Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res (2011) 4.84
Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis. J Mol Diagn (2006) 4.68
Screening ethnically diverse human embryonic stem cells identifies a chromosome 20 minimal amplicon conferring growth advantage. Nat Biotechnol (2011) 3.97
Survival and development of neonatal rat cardiomyocytes transplanted into adult myocardium. J Mol Cell Cardiol (2002) 3.79
Cooperativity between DNA methyltransferases in the maintenance methylation of repetitive elements. Mol Cell Biol (2002) 3.61
DNA methylation in the human cerebral cortex is dynamically regulated throughout the life span and involves differentiated neurons. PLoS One (2007) 3.30
Association of breast cancer DNA methylation profiles with hormone receptor status and response to tamoxifen. Cancer Res (2004) 3.23
Interplay between the cancer genome and epigenome. Cell (2013) 3.05
Comprehensive Molecular Characterization of Papillary Renal-Cell Carcinoma. N Engl J Med (2015) 3.00
Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun (2013) 2.94
Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns. Hum Mol Genet (2009) 2.85
Cigarette smoking and colorectal cancer risk by molecularly defined subtypes. J Natl Cancer Inst (2010) 2.38
Low-level processing of Illumina Infinium DNA Methylation BeadArrays. Nucleic Acids Res (2013) 2.19
Molecular characterization of MSI-H colorectal cancer by MLHI promoter methylation, immunohistochemistry, and mismatch repair germline mutation screening. Cancer Epidemiol Biomarkers Prev (2008) 2.12
Genome-scale analysis of DNA methylation in lung adenocarcinoma and integration with mRNA expression. Genome Res (2012) 2.10
Long-term epigenetic therapy with oral zebularine has minimal side effects and prevents intestinal tumors in mice. Cancer Prev Res (Phila) (2008) 2.04
DNA methylation as a biomarker for cardiovascular disease risk. PLoS One (2010) 2.04
Bis-SNP: combined DNA methylation and SNP calling for Bisulfite-seq data. Genome Biol (2012) 2.02
Lipopolysaccharide-induced methylation of HuR, an mRNA-stabilizing protein, by CARM1. Coactivator-associated arginine methyltransferase. J Biol Chem (2002) 2.01
Breast cancer DNA methylation profiles in cancer cells and tumor stroma: association with HER-2/neu status in primary breast cancer. Cancer Res (2006) 1.99
Epigenetic analysis of KSHV latent and lytic genomes. PLoS Pathog (2010) 1.94
Analysis of the association between CIMP and BRAF in colorectal cancer by DNA methylation profiling. PLoS One (2009) 1.90
DNA methylation analysis: a powerful new tool for lung cancer diagnosis. Oncogene (2002) 1.89
DNA hypomethylation and ovarian cancer biology. Cancer Res (2004) 1.75
Complete genetic suppression of polyp formation and reduction of CpG-island hypermethylation in Apc(Min/+) Dnmt1-hypomorphic Mice. Cancer Res (2002) 1.73
Epigenetic analysis leads to identification of HNF1B as a subtype-specific susceptibility gene for ovarian cancer. Nat Commun (2013) 1.73
The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell (2013) 1.68
DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PLoS One (2010) 1.65
Sensitive detection of DNA methylation. Ann N Y Acad Sci (2003) 1.65
Hypomethylation and hypermethylation of DNA in Wilms tumors. Oncogene (2002) 1.59
Role of methionine adenosyltransferase 2A and S-adenosylmethionine in mitogen-induced growth of human colon cancer cells. Gastroenterology (2007) 1.56
Widespread epigenetic abnormalities suggest a broad DNA methylation erasure defect in abnormal human sperm. PLoS One (2007) 1.55
DNA methylation-based biomarkers for early detection of non-small cell lung cancer: an update. Mol Cancer (2008) 1.55
Smad3 deficiency promotes tumorigenesis in the distal colon of ApcMin/+ mice. Cancer Res (2006) 1.52
Kinetic studies of RNA-protein interactions using surface plasmon resonance. Methods (2002) 1.52
Vitamin C promotes widespread yet specific DNA demethylation of the epigenome in human embryonic stem cells. Stem Cells (2010) 1.50
Immune response in lung cancer mouse model mimics human anti-Hu reactivity. J Neuroimmunol (2009) 1.47
Unique DNA methylation patterns distinguish noninvasive and invasive urothelial cancers and establish an epigenetic field defect in premalignant tissue. Cancer Res (2010) 1.47
Environmental epigenetics: prospects for studying epigenetic mediation of exposure-response relationships. Hum Genet (2012) 1.47
Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. Nucleic Acids Res (2012) 1.46
MethyLight. Methods Mol Biol (2009) 1.45
Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine. Oncotarget (2013) 1.44
DNA methylation analysis by digital bisulfite genomic sequencing and digital MethyLight. Nucleic Acids Res (2008) 1.42
An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma. J Natl Cancer Inst (2013) 1.42
Distinct methylation profiles of glioma subtypes. Int J Cancer (2003) 1.38
Hierarchical clustering of lung cancer cell lines using DNA methylation markers. Cancer Epidemiol Biomarkers Prev (2002) 1.38
Kaiso contributes to DNA methylation-dependent silencing of tumor suppressor genes in colon cancer cell lines. Cancer Res (2008) 1.36
Sex differential in methylation patterns of selected genes in Singapore Chinese. Hum Genet (2005) 1.35
DNA methylation profiles of gastric carcinoma characterized by quantitative DNA methylation analysis. Lab Invest (2007) 1.34
Rebuilding a damaged heart: long-term survival of transplanted neonatal rat cardiomyocytes after myocardial infarction and effect on cardiac function. Circulation (2002) 1.32
Correlation of pathologic features with CpG island methylator phenotype (CIMP) by quantitative DNA methylation analysis in colorectal carcinoma. Am J Surg Pathol (2006) 1.29
Identification of a panel of sensitive and specific DNA methylation markers for squamous cell lung cancer. Mol Cancer (2008) 1.24
Characterization of the interaction between neuronal RNA-binding protein HuD and AU-rich RNA. J Biol Chem (2003) 1.22
Combined bisulfite restriction analysis (COBRA). Methods Mol Biol (2002) 1.20
Thymidylate synthase: a novel genetic determinant of plasma homocysteine and folate levels. Hum Genet (2002) 1.19
DNA methyltransferase deficiency modifies cancer susceptibility in mice lacking DNA mismatch repair. Mol Cell Biol (2002) 1.18
Dnmt1 deficiency leads to enhanced microsatellite instability in mouse embryonic stem cells. Nucleic Acids Res (2004) 1.17
DNA methylation changes in atypical adenomatous hyperplasia, adenocarcinoma in situ, and lung adenocarcinoma. PLoS One (2011) 1.16
Genome-scale discovery of DNA-methylation biomarkers for blood-based detection of colorectal cancer. PLoS One (2012) 1.14
The methylenetetrahydrofolate reductase C677T mutation induces cell-specific changes in genomic DNA methylation and uracil misincorporation: a possible molecular basis for the site-specific cancer risk modification. Int J Cancer (2009) 1.14
Identification of a panel of sensitive and specific DNA methylation markers for lung adenocarcinoma. Mol Cancer (2007) 1.14
DNA binding by GATA transcription factor suggests mechanisms of DNA looping and long-range gene regulation. Cell Rep (2012) 1.12
The role of positively charged amino acids and electrostatic interactions in the complex of U1A protein and U1 hairpin II RNA. Nucleic Acids Res (2006) 1.12
DNA methylation profile of 28 potential marker loci in malignant mesothelioma. Lung Cancer (2007) 1.11
Small-cell lung cancer-associated autoantibodies: potential applications to cancer diagnosis, early detection, and therapy. Mol Cancer (2011) 1.10
Ovarian cancer early detection claims are biased. Clin Cancer Res (2008) 1.10
Integrated transcriptomic and epigenomic analysis of primary human lung epithelial cell differentiation. PLoS Genet (2013) 1.09
The role of DNA methylation in the development and progression of lung adenocarcinoma. Dis Markers (2007) 1.09
The mutagenic potential of duodenoesophageal reflux. Ann Surg (2005) 1.08
Rapid and quantitative method of allele-specific DNA methylation analysis. Biotechniques (2006) 1.08
Solution structure of the complex formed by the two N-terminal RNA-binding domains of nucleolin and a pre-rRNA target. J Mol Biol (2004) 1.06
Distinct DNA methylation profiles in malignant mesothelioma, lung adenocarcinoma, and non-tumor lung. Lung Cancer (2005) 1.06
HuR/methyl-HuR and AUF1 regulate the MAT expressed during liver proliferation, differentiation, and carcinogenesis. Gastroenterology (2010) 1.04
Mild depletion of dietary folate combined with other B vitamins alters multiple components of the Wnt pathway in mouse colon. J Nutr (2007) 1.04
DNA hypermethylation of ESR1 and PGR in breast cancer: pathologic and epidemiologic associations. Cancer Epidemiol Biomarkers Prev (2009) 1.04
Frequency of deletions of EPCAM (TACSTD1) in MSH2-associated Lynch syndrome cases. J Mol Diagn (2010) 1.04
Associations between intake of folate and related micronutrients with molecularly defined colorectal cancer risks in the Iowa Women's Health Study. Nutr Cancer (2012) 1.03
Kinetic analysis of the role of the tyrosine 13, phenylalanine 56 and glutamine 54 network in the U1A/U1 hairpin II interaction. Nucleic Acids Res (2005) 1.03
The role of RNA structure in the interaction of U1A protein with U1 hairpin II RNA. RNA (2006) 1.02
Complex role of the beta 2-beta 3 loop in the interaction of U1A with U1 hairpin II RNA. J Biol Chem (2002) 1.01
Gene-specific methylation and subsequent risk of colorectal adenomas among participants of the polyp prevention trial. Cancer Epidemiol Biomarkers Prev (2005) 1.01
Analysis of complex methylation data. Methods (2002) 1.00