Published in BMC Bioinformatics on May 08, 2012
Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis. Nat Biotechnol (2013) 5.89
Accounting for cellular heterogeneity is critical in epigenome-wide association studies. Genome Biol (2014) 3.89
Analysing and interpreting DNA methylation data. Nat Rev Genet (2012) 3.77
Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics (2014) 2.61
DNA methylation age of blood predicts all-cause mortality in later life. Genome Biol (2015) 2.51
Epigenome-wide association of DNA methylation markers in peripheral blood from Indian Asians and Europeans with incident type 2 diabetes: a nested case-control study. Lancet Diabetes Endocrinol (2015) 2.46
Functional normalization of 450k methylation array data improves replication in large cancer studies. Genome Biol (2014) 2.37
Mapping DNA methylation across development, genotype and schizophrenia in the human frontal cortex. Nat Neurosci (2015) 2.31
Molecular signatures of major depression. Curr Biol (2015) 2.28
Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods (2013) 2.19
Methylome-wide association study of schizophrenia: identifying blood biomarker signatures of environmental insults. JAMA Psychiatry (2014) 2.11
Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods (2014) 2.03
A cell epigenotype specific model for the correction of brain cellular heterogeneity bias and its application to age, brain region and major depression. Epigenetics (2013) 1.97
Heterogeneity in white blood cells has potential to confound DNA methylation measurements. PLoS One (2012) 1.91
The epigenetic clock is correlated with physical and cognitive fitness in the Lothian Birth Cohort 1936. Int J Epidemiol (2015) 1.88
From promises to practical strategies in epigenetic epidemiology. Nat Rev Genet (2013) 1.82
Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis. Epigenetics (2013) 1.79
Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers. Cancer Epidemiol Biomarkers Prev (2012) 1.76
Age-associated epigenetic drift: implications, and a case of epigenetic thrift? Hum Mol Genet (2013) 1.76
A coherent approach for analysis of the Illumina HumanMethylation450 BeadChip improves data quality and performance in epigenome-wide association studies. Genome Biol (2015) 1.71
HIV-1 Infection Accelerates Age According to the Epigenetic Clock. J Infect Dis (2015) 1.70
Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in utero. Environ Health Perspect (2013) 1.66
Aging and epigenetic drift: a vicious cycle. J Clin Invest (2014) 1.63
Epigenome-wide association study of body mass index, and the adverse outcomes of adiposity. Nature (2016) 1.59
The effect of smoking on DNA methylation of peripheral blood mononuclear cells from African American women. BMC Genomics (2014) 1.57
Mouse-human experimental epigenetic analysis unmasks dietary targets and genetic liability for diabetic phenotypes. Cell Metab (2015) 1.52
A comprehensive overview of Infinium HumanMethylation450 data processing. Brief Bioinform (2013) 1.49
Epigenome-wide association study (EWAS) of BMI, BMI change and waist circumference in African American adults identifies multiple replicated loci. Hum Mol Genet (2015) 1.45
Whole-Genome Saliva and Blood DNA Methylation Profiling in Individuals with a Respiratory Allergy. PLoS One (2016) 1.44
Epigenomic association analysis identifies smoking-related DNA methylation sites in African Americans. Hum Genet (2013) 1.43
Computational deconvolution: extracting cell type-specific information from heterogeneous samples. Curr Opin Immunol (2013) 1.40
An epigenome-wide association study of total serum immunoglobulin E concentration. Nature (2015) 1.37
Epigenome-wide association study of breast cancer using prospectively collected sister study samples. J Natl Cancer Inst (2013) 1.35
Identification of DNA methylation changes in newborns related to maternal smoking during pregnancy. Environ Health Perspect (2014) 1.35
Differences in smoking associated DNA methylation patterns in South Asians and Europeans. Clin Epigenetics (2014) 1.33
Review of processing and analysis methods for DNA methylation array data. Br J Cancer (2013) 1.33
DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis. Am J Hum Genet (2016) 1.32
Quantitative reconstruction of leukocyte subsets using DNA methylation. Genome Biol (2014) 1.32
Developmental regulation of human cortex transcription and its clinical relevance at single base resolution. Nat Neurosci (2014) 1.31
Trans-ancestry genome-wide association study identifies 12 genetic loci influencing blood pressure and implicates a role for DNA methylation. Nat Genet (2015) 1.28
Cadmium exposure and the epigenome: Exposure-associated patterns of DNA methylation in leukocytes from mother-baby pairs. Epigenetics (2013) 1.27
DNA methylation age is associated with mortality in a longitudinal Danish twin study. Aging Cell (2015) 1.25
Accounting for population stratification in DNA methylation studies. Genet Epidemiol (2014) 1.25
Dynamics of smoking-induced genome-wide methylation changes with time since smoking cessation. Hum Mol Genet (2015) 1.25
A methylome-wide study of aging using massively parallel sequencing of the methyl-CpG-enriched genomic fraction from blood in over 700 subjects. Hum Mol Genet (2013) 1.24
DNA methylation changes of whole blood cells in response to active smoking exposure in adults: a systematic review of DNA methylation studies. Clin Epigenetics (2015) 1.24
Effect of prenatal arsenic exposure on DNA methylation and leukocyte subpopulations in cord blood. Epigenetics (2014) 1.22
Contribution of genetic variation to transgenerational inheritance of DNA methylation. Genome Biol (2014) 1.20
Differential methylation of the TRPA1 promoter in pain sensitivity. Nat Commun (2014) 1.19
An analysis of DNA methylation in human adipose tissue reveals differential modification of obesity genes before and after gastric bypass and weight loss. Genome Biol (2015) 1.19
Measuring cell-type specific differential methylation in human brain tissue. Genome Biol (2013) 1.19
Long-range epigenetic regulation is conferred by genetic variation located at thousands of independent loci. Nat Commun (2015) 1.18
Prenatal exposure to maternal cigarette smoking and DNA methylation: epigenome-wide association in a discovery sample of adolescents and replication in an independent cohort at birth through 17 years of age. Environ Health Perspect (2014) 1.17
Batch effects and pathway analysis: two potential perils in cancer studies involving DNA methylation array analysis. Cancer Epidemiol Biomarkers Prev (2013) 1.16
Antenatal prediction of postpartum depression with blood DNA methylation biomarkers. Mol Psychiatry (2013) 1.16
Decreased epigenetic age of PBMCs from Italian semi-supercentenarians and their offspring. Aging (Albany NY) (2015) 1.15
Increased epigenetic age and granulocyte counts in the blood of Parkinson's disease patients. Aging (Albany NY) (2015) 1.15
GeMes, clusters of DNA methylation under genetic control, can inform genetic and epigenetic analysis of disease. Am J Hum Genet (2014) 1.15
A-clustering: a novel method for the detection of co-regulated methylation regions, and regions associated with exposure. Bioinformatics (2013) 1.14
Genetic and environmental exposures constrain epigenetic drift over the human life course. Genome Res (2014) 1.13
An integrative multi-scale analysis of the dynamic DNA methylation landscape in aging. PLoS Genet (2015) 1.13
Maternal smoking and DNA methylation in newborns: in utero effect or epigenetic inheritance? Cancer Epidemiol Biomarkers Prev (2014) 1.12
DNA methylation of lipid-related genes affects blood lipid levels. Circ Cardiovasc Genet (2015) 1.12
Genome-wide age-related changes in DNA methylation and gene expression in human PBMCs. Age (Dordr) (2014) 1.12
Neonatal genome-wide methylation patterns in relation to birth weight in the Norwegian Mother and Child Cohort. Am J Epidemiol (2014) 1.11
DNA methylation biomarkers: cancer and beyond. Genes (Basel) (2014) 1.11
Plasma DNA tissue mapping by genome-wide methylation sequencing for noninvasive prenatal, cancer, and transplantation assessments. Proc Natl Acad Sci U S A (2015) 1.10
Genome-wide age-related DNA methylation changes in blood and other tissues relate to histone modification, expression and cancer. Carcinogenesis (2013) 1.08
Sex-specific effects of early life cadmium exposure on DNA methylation and implications for birth weight. Epigenetics (2013) 1.08
DNA methylation mediates the effect of maternal smoking during pregnancy on birthweight of the offspring. Int J Epidemiol (2015) 1.08
DNA methylation-based measures of biological age: meta-analysis predicting time to death. Aging (Albany NY) (2016) 1.08
Maternal pre-pregnancy BMI and gestational weight gain, offspring DNA methylation and later offspring adiposity: findings from the Avon Longitudinal Study of Parents and Children. Int J Epidemiol (2015) 1.07
DNA extracted from saliva for methylation studies of psychiatric traits: evidence tissue specificity and relatedness to brain. Am J Med Genet B Neuropsychiatr Genet (2014) 1.07
DNA methylation and childhood asthma in the inner city. J Allergy Clin Immunol (2015) 1.07
Epigenetic epidemiology: promises for public health research. Environ Mol Mutagen (2014) 1.06
Improving cell mixture deconvolution by identifying optimal DNA methylation libraries (IDOL). BMC Bioinformatics (2016) 1.06
Statistical methods for detecting differentially methylated loci and regions. Front Genet (2014) 1.06
Analysis of epigenetic changes in survivors of preterm birth reveals the effect of gestational age and evidence for a long term legacy. Genome Med (2013) 1.06
Epigenome-wide Association Studies and the Interpretation of Disease -Omics. PLoS Genet (2016) 1.05
Environmental epigenetics: from novelty to scientific discipline. J Appl Toxicol (2013) 1.04
Analysis pipelines and packages for Infinium HumanMethylation450 BeadChip (450k) data. Methods (2014) 1.03
Methylome-wide Analysis of Chronic HIV Infection Reveals Five-Year Increase in Biological Age and Epigenetic Targeting of HLA. Mol Cell (2016) 1.03
An integrated genetic-epigenetic analysis of schizophrenia: evidence for co-localization of genetic associations and differential DNA methylation. Genome Biol (2016) 1.02
DNA methylation of cord blood cell types: Applications for mixed cell birth studies. Epigenetics (2016) 1.02
Concordant and discordant DNA methylation signatures of aging in human blood and brain. Epigenetics Chromatin (2015) 1.01
Genome-wide association study identifies peanut allergy-specific loci and evidence of epigenetic mediation in US children. Nat Commun (2015) 1.01
Sparse PCA corrects for cell type heterogeneity in epigenome-wide association studies. Nat Methods (2016) 1.00
Advances in epigenome-wide association studies for common diseases. Trends Mol Med (2014) 1.00
Systematic identification of genetic influences on methylation across the human life course. Genome Biol (2016) 1.00
Prenatal tobacco smoke exposure is associated with childhood DNA CpG methylation. PLoS One (2014) 0.99
Epigenetics and life-long consequences of an adverse nutritional and diabetic intrauterine environment. Reproduction (2014) 0.99
Multigenerational epigenetic inheritance in humans: DNA methylation changes associated with maternal exposure to lead can be transmitted to the grandchildren. Sci Rep (2015) 0.99
Mosaic epigenetic dysregulation of ectodermal cells in autism spectrum disorder. PLoS Genet (2014) 0.98
Gene-specific differential DNA methylation and chronic arsenic exposure in an epigenome-wide association study of adults in Bangladesh. Environ Health Perspect (2014) 0.98
ENmix: a novel background correction method for Illumina HumanMethylation450 BeadChip. Nucleic Acids Res (2015) 0.98
Environmental chemicals and DNA methylation in adults: a systematic review of the epidemiologic evidence. Clin Epigenetics (2015) 0.98
Grasping nettles: cellular heterogeneity and other confounders in epigenome-wide association studies. Hum Mol Genet (2014) 0.97
An epigenetic clock analysis of race/ethnicity, sex, and coronary heart disease. Genome Biol (2016) 0.97
An epigenetic clock for gestational age at birth based on blood methylation data. Genome Biol (2016) 0.97
Accelerated DNA methylation age: Associations with PTSD and neural integrity. Psychoneuroendocrinology (2015) 0.97
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A (2005) 167.46
Hallmarks of cancer: the next generation. Cell (2011) 140.01
Linear models and empirical bayes methods for assessing differential expression in microarray experiments. Stat Appl Genet Mol Biol (2004) 101.91
Capturing heterogeneity in gene expression studies by surrogate variable analysis. PLoS Genet (2007) 12.08
Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts. Nat Genet (2009) 10.54
Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics (2007) 9.87
Comprehensive methylome map of lineage commitment from haematopoietic progenitors. Nature (2010) 6.06
Cell type-specific gene expression differences in complex tissues. Nat Methods (2010) 4.75
Fetal and adult hematopoietic stem cells give rise to distinct T cell lineages in humans. Science (2010) 4.22
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
A HaemAtlas: characterizing gene expression in differentiated human blood cells. Blood (2009) 3.63
Epigenetic predictor of age. PLoS One (2011) 3.46
An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One (2009) 3.33
Pre-treatment neutrophil to lymphocyte ratio is elevated in epithelial ovarian cancer and predicts survival after treatment. Cancer Immunol Immunother (2008) 3.32
Independent surrogate variable analysis to deconvolve confounding factors in large-scale microarray profiling studies. Bioinformatics (2011) 2.91
Neutrophil/lymphocyte ratio predicts chemotherapy outcomes in patients with advanced colorectal cancer. Br J Cancer (2011) 2.88
Quantitative DNA methylation analysis of FOXP3 as a new method for counting regulatory T cells in peripheral blood and solid tissue. Cancer Res (2009) 2.75
Immune surveillance: a balance between protumor and antitumor immunity. Curr Opin Genet Dev (2008) 2.62
Obesity related methylation changes in DNA of peripheral blood leukocytes. BMC Med (2010) 2.24
Maintaining cell identity through global control of genomic organization. Immunity (2010) 2.03
DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J Clin Oncol (2011) 1.92
Gene expression profiles in peripheral blood mononuclear cells can distinguish patients with non-small cell lung cancer from patients with nonmalignant lung disease. Cancer Res (2009) 1.86
Decreased absolute counts of T lymphocyte subsets and their relation to disease in squamous cell carcinoma of the head and neck. Clin Cancer Res (2004) 1.85
The ADH1C polymorphism modifies the risk of squamous cell carcinoma of the head and neck associated with alcohol and tobacco use. Cancer Epidemiol Biomarkers Prev (2005) 1.64
Semi-supervised recursively partitioned mixture models for identifying cancer subtypes. Bioinformatics (2010) 1.63
Optimal deconvolution of transcriptional profiling data using quadratic programming with application to complex clinical blood samples. PLoS One (2011) 1.62
Infections and immunodeficiency in Down syndrome. Clin Exp Immunol (2011) 1.61
Adipose tissue recruitment of leukocytes. Curr Opin Lipidol (2010) 1.60
DNA methylation analysis as a tool for cell typing. Epigenetics (2006) 1.58
Epigenetic quantification of tumor-infiltrating T-lymphocytes. Epigenetics (2011) 1.57
Polymorphonuclear granulocytes in human head and neck cancer: enhanced inflammatory activity, modulation by cancer cells and expansion in advanced disease. Int J Cancer (2011) 1.55
Leukocyte DNA methylation signature differentiates pancreatic cancer patients from healthy controls. PLoS One (2011) 1.55
Are natural killer cells protecting the metabolically healthy obese patient? Obesity (Silver Spring) (2008) 1.50
Altered DNA methylation in leukocytes with trisomy 21. PLoS Genet (2010) 1.44
DNA methylation and epigenetic control of cellular differentiation. Cell Cycle (2010) 1.44
Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: a case study. Infect Genet Evol (2011) 1.33
Pre-treatment white blood cell subtypes as prognostic indicators in ovarian cancer. Eur J Obstet Gynecol Reprod Biol (2007) 1.29
Resection of non-small cell lung cancers reverses tumor-induced gene expression changes in the peripheral immune system. Clin Cancer Res (2011) 1.24
Inferring relative numbers of human leucocyte genome replications. Br J Haematol (2008) 1.22
Imbalance in absolute counts of T lymphocyte subsets in patients with head and neck cancer and its relation to disease. Adv Otorhinolaryngol (2005) 1.21
T-lymphocyte subsets in smoking and lung cancer: Analysis of monoclonal antibodies and flow cytometry. Am Rev Respir Dis (1982) 1.17
Measurement error, biases, and the validation of complex models for blood lead levels in children. Environ Health Perspect (1998) 1.12
Down syndrome B-lymphocyte subpopulations, intrinsic defect or decreased T-lymphocyte help. Pediatr Res (2010) 1.05
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Lymphocyte subpopulations anomalies in lung cancer patients and relationship to the stage of disease. In Vivo (1999) 0.94
Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet (2009) 7.07
Variants in the CDKN2B and RTEL1 regions are associated with high-grade glioma susceptibility. Nat Genet (2009) 5.13
Glioma Groups Based on 1p/19q, IDH, and TERT Promoter Mutations in Tumors. N Engl J Med (2015) 5.03
New common variants affecting susceptibility to basal cell carcinoma. Nat Genet (2009) 4.15
Global DNA methylation level in whole blood as a biomarker in head and neck squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev (2007) 4.01
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
Detectable clonal mosaicism and its relationship to aging and cancer. Nat Genet (2012) 3.69
Replication of lung cancer susceptibility loci at chromosomes 15q25, 5p15, and 6p21: a pooled analysis from the International Lung Cancer Consortium. J Natl Cancer Inst (2010) 3.18
MicroRNA responses to cellular stress. Cancer Res (2006) 3.13
The landscape of recombination in African Americans. Nature (2011) 3.06
Fundamental differences in cell cycle deregulation in human papillomavirus-positive and human papillomavirus-negative head/neck and cervical cancers. Cancer Res (2007) 2.93
DNA methylation, isocitrate dehydrogenase mutation, and survival in glioma. J Natl Cancer Inst (2010) 2.87
Lack of association of alcohol and tobacco with HPV16-associated head and neck cancer. J Natl Cancer Inst (2007) 2.68
Reference-free cell mixture adjustments in analysis of DNA methylation data. Bioinformatics (2014) 2.61
Population- and community-based recruitment of African Americans and Latinos: the San Francisco Bay Area Lung Cancer Study. Am J Epidemiol (2003) 2.52
Human papillomavirus infection and incidence of squamous cell and basal cell carcinomas of the skin. J Natl Cancer Inst (2006) 2.40
A case-control study of smoking and bladder cancer risk: emergent patterns over time. J Natl Cancer Inst (2009) 2.40
Extensive somatic L1 retrotransposition in colorectal tumors. Genome Res (2012) 2.29
A let-7 microRNA-binding site polymorphism in the KRAS 3' UTR is associated with reduced survival in oral cancers. Carcinogenesis (2009) 2.28
Human papillomavirus type 16 and squamous cell carcinoma of the head and neck. Clin Cancer Res (2002) 2.20
Recommendations for the design and analysis of epigenome-wide association studies. Nat Methods (2013) 2.19
MicroRNA expression ratio is predictive of head and neck squamous cell carcinoma. Clin Cancer Res (2009) 2.13
Implications of LINE1 methylation for bladder cancer risk in women. Clin Cancer Res (2010) 2.10
Concordance of multiple analytical approaches demonstrates a complex relationship between DNA repair gene SNPs, smoking and bladder cancer susceptibility. Carcinogenesis (2005) 2.08
Nightshift work and genome-wide DNA methylation. Chronobiol Int (2014) 2.01
Genome-wide association study of glioma and meta-analysis. Hum Genet (2012) 1.96
Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma. Carcinogenesis (2009) 1.94
DNA methylation array analysis identifies profiles of blood-derived DNA methylation associated with bladder cancer. J Clin Oncol (2011) 1.92
A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry. Nat Genet (2013) 1.82
Inactivation of the Fanconi anemia/BRCA pathway in lung and oral cancers: implications for treatment and survival. Oncogene (2004) 1.82
Toxicity testing in the 21st century: a vision and a strategy. J Toxicol Environ Health B Crit Rev (2010) 1.81
Blood-based profiles of DNA methylation predict the underlying distribution of cell types: a validation analysis. Epigenetics (2013) 1.79
Human papillomavirus 16 and head and neck squamous cell carcinoma. Int J Cancer (2007) 1.78
History of allergies among adults with glioma and controls. Int J Cancer (2002) 1.78
Distinct germ line polymorphisms underlie glioma morphologic heterogeneity. Cancer Genet (2011) 1.77
Epigenetics in the placenta. Am J Reprod Immunol (2009) 1.77
Peripheral blood immune cell methylation profiles are associated with nonhematopoietic cancers. Cancer Epidemiol Biomarkers Prev (2012) 1.76
Biomarkers of HPV in head and neck squamous cell carcinoma. Cancer Res (2012) 1.76
Breast cancer DNA methylation profiles are associated with tumor size and alcohol and folate intake. PLoS Genet (2010) 1.74
Epigenetic profiles distinguish pleural mesothelioma from normal pleura and predict lung asbestos burden and clinical outcome. Cancer Res (2009) 1.73
A low-frequency variant at 8q24.21 is strongly associated with risk of oligodendroglial tumors and astrocytomas with IDH1 or IDH2 mutation. Nat Genet (2012) 1.73
Sexual behaviours and the risk of head and neck cancers: a pooled analysis in the International Head and Neck Cancer Epidemiology (INHANCE) consortium. Int J Epidemiol (2009) 1.70
The Pathways Study: a prospective study of breast cancer survivorship within Kaiser Permanente Northern California. Cancer Causes Control (2008) 1.70
A genome-wide association study of upper aerodigestive tract cancers conducted within the INHANCE consortium. PLoS Genet (2011) 1.68
PTEN expression in non-small-cell lung cancer: evaluating its relation to tumor characteristics, allelic loss, and epigenetic alteration. Hum Pathol (2005) 1.67
Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in utero. Environ Health Perspect (2013) 1.66
The ADH1C polymorphism modifies the risk of squamous cell carcinoma of the head and neck associated with alcohol and tobacco use. Cancer Epidemiol Biomarkers Prev (2005) 1.64
Semi-supervised recursively partitioned mixture models for identifying cancer subtypes. Bioinformatics (2010) 1.63
A computationally efficient hypothesis testing method for epistasis analysis using multifactor dimensionality reduction. Genet Epidemiol (2009) 1.61
Pathway analysis of single-nucleotide polymorphisms potentially associated with glioblastoma multiforme susceptibility using random forests. Cancer Epidemiol Biomarkers Prev (2008) 1.56