Published in Bioinformatics on September 29, 2010
IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data. Bioinformatics (2012) 2.97
Comprehensive analysis of DNA methylation data with RnBeads. Nat Methods (2014) 2.03
Differential DNA methylation in umbilical cord blood of infants exposed to low levels of arsenic in utero. Environ Health Perspect (2013) 1.66
Replicative senescence of mesenchymal stem cells causes DNA-methylation changes which correlate with repressive histone marks. Aging (Albany NY) (2011) 1.58
Epigenetic-aging-signature to determine age in different tissues. Aging (Albany NY) (2011) 1.55
Specific age-associated DNA methylation changes in human dermal fibroblasts. PLoS One (2011) 1.51
Review of processing and analysis methods for DNA methylation array data. Br J Cancer (2013) 1.33
Statistical approaches for the analysis of DNA methylation microarray data. Hum Genet (2011) 1.31
The interaction of genetic variants and DNA methylation of the interleukin-4 receptor gene increase the risk of asthma at age 18 years. Clin Epigenetics (2013) 1.22
Method to detect differentially methylated loci with case-control designs using Illumina arrays. Genet Epidemiol (2011) 1.07
A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data. Bioinformatics (2012) 1.06
NALP3 inflammasome upregulation and CASP1 cleavage of the glucocorticoid receptor cause glucocorticoid resistance in leukemia cells. Nat Genet (2015) 1.02
The epigenetic landscape of oral squamous cell carcinoma. Br J Cancer (2013) 1.01
Monozygotic twins affected with major depressive disorder have greater variance in methylation than their unaffected co-twin. Transl Psychiatry (2013) 0.98
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
Penalized logistic regression for high-dimensional DNA methylation data with case-control studies. Bioinformatics (2012) 0.96
Placental DNA methylation alterations associated with maternal tobacco smoking at the RUNX3 gene are also associated with gestational age. Epigenomics (2013) 0.95
Detecting differentially methylated loci for Illumina Array methylation data based on human ovarian cancer data. BMC Med Genomics (2013) 0.95
Placental DNA Methylation Related to Both Infant Toenail Mercury and Adverse Neurobehavioral Outcomes. Environ Health Perspect (2015) 0.93
DNA methylation of the filaggrin gene adds to the risk of eczema associated with loss-of-function variants. J Eur Acad Dermatol Venereol (2012) 0.93
Age-adjusted nonparametric detection of differential DNA methylation with case-control designs. BMC Bioinformatics (2013) 0.92
Distinct patterns of DNA methylation in conventional adenomas involving the right and left colon. Mod Pathol (2013) 0.92
Network-based regularization for matched case-control analysis of high-dimensional DNA methylation data. Stat Med (2012) 0.88
Epigenetic alterations and an increased frequency of micronuclei in women with fibromyalgia. Nurs Res Pract (2013) 0.87
Pathway and network approaches for identification of cancer signature markers from omics data. J Cancer (2015) 0.86
Comprehensive analysis of DNA methylation in head and neck squamous cell carcinoma indicates differences by survival and clinicopathologic characteristics. PLoS One (2013) 0.86
Integrative genomic analysis identifies epigenetic marks that mediate genetic risk for epithelial ovarian cancer. BMC Med Genomics (2014) 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
Interaction of prenatal maternal smoking, interleukin 13 genetic variants and DNA methylation influencing airflow and airway reactivity. Clin Epigenetics (2013) 0.83
Effects of phthalate exposure on asthma may be mediated through alterations in DNA methylation. Clin Epigenetics (2015) 0.83
The methylation of the LEPR/LEPROT genotype at the promoter and body regions influence concentrations of leptin in girls and BMI at age 18 years if their mother smoked during pregnancy. Int J Mol Epidemiol Genet (2013) 0.82
DNA methylation changes in the placenta are associated with fetal manganese exposure. Reprod Toxicol (2015) 0.82
Pretreatment dietary intake is associated with tumor suppressor DNA methylation in head and neck squamous cell carcinomas. Epigenetics (2012) 0.82
Adjustment of Cell-Type Composition Minimizes Systematic Bias in Blood DNA Methylation Profiles Derived by DNA Collection Protocols. PLoS One (2016) 0.79
SOCS3 promoter hypermethylation is a favorable prognosticator and a novel indicator for G-CIMP-positive GBM patients. PLoS One (2014) 0.78
Comparison of clustering methods for investigation of genome-wide methylation array data. Front Genet (2011) 0.78
Oral contraceptives modify the effect of GATA3 polymorphisms on the risk of asthma at the age of 18 years via DNA methylation. Clin Epigenetics (2014) 0.78
DNA methylation and genetic polymorphisms of the Leptin gene interact to influence lung function outcomes and asthma at 18 years of age. Int J Mol Epidemiol Genet (2016) 0.77
Penalized Ordinal Regression Methods for Predicting Stage of Cancer in High-Dimensional Covariate Spaces. Cancer Inform (2015) 0.75
Estimating and accounting for tumor purity in the analysis of DNA methylation data from cancer studies. Genome Biol (2017) 0.75
Propensity score method for partially matched omics studies. Cancer Inform (2014) 0.75
Comparisons of non-Gaussian statistical models in DNA methylation analysis. Int J Mol Sci (2014) 0.75
Epigenetic alterations in metastatic cutaneous carcinoma. Head Neck (2014) 0.75
Consistency and Variability of DNA Methylation in Women During Puberty, Young Adulthood, and Pregnancy. Genet Epigenet (2017) 0.75
An epigenome-wide DNA methylation study of PTSD and depression in World Trade Center responders. Transl Psychiatry (2017) 0.75
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis. Nat Biotechnol (2008) 21.72
The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat Genet (2009) 18.90
Principles and challenges of genomewide DNA methylation analysis. Nat Rev Genet (2010) 10.71
Cancer epigenomics: DNA methylomes and histone-modification maps. Nat Rev Genet (2007) 9.88
Comprehensive high-throughput arrays for relative methylation (CHARM). Genome Res (2008) 8.62
High-throughput DNA methylation profiling using universal bead arrays. Genome Res (2006) 8.05
Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. PLoS Genet (2009) 7.07
An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Res (2008) 4.84
Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis. Bioinformatics (2009) 4.21
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
Statistical issues in the analysis of Illumina data. BMC Bioinformatics (2008) 3.66
Genome-wide screen of promoter methylation identifies novel markers in melanoma. Genome Res (2009) 2.13
Variable selection for model-based high-dimensional clustering and its application to microarray data. Biometrics (2007) 2.10
Applications of beta-mixture models in bioinformatics. Bioinformatics (2005) 2.04
Statistical methods of background correction for Illumina BeadArray data. Bioinformatics (2009) 1.99
Interactively optimizing signal-to-noise ratios in expression profiling: project-specific algorithm selection and detection p-value weighting in Affymetrix microarrays. Bioinformatics (2004) 1.98
A comparison of cluster analysis methods using DNA methylation data. Bioinformatics (2004) 1.94
Epigenetic profiling reveals etiologically distinct patterns of DNA methylation in head and neck squamous cell carcinoma. Carcinogenesis (2009) 1.94
Hepatocellular carcinoma displays distinct DNA methylation signatures with potential as clinical predictors. PLoS One (2010) 1.84
DNA methylation profiles of ovarian epithelial carcinoma tumors and cell lines. PLoS One (2010) 1.65
A study of the relationships between oligonucleotide properties and hybridization signal intensities from NimbleGen microarray datasets. Nucleic Acids Res (2008) 1.47
Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Res Notes (2008) 1.28
High-throughput assessment of CpG site methylation for distinguishing between HCV-cirrhosis and HCV-associated hepatocellular carcinoma. Mol Genet Genomics (2010) 1.27
Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms. Stat Methods Med Res (2009) 1.01
On the necessity of different statistical treatment for Illumina BeadChip and Affymetrix GeneChip data and its significance for biological interpretation. Biol Direct (2008) 0.87
An intervention to decrease catheter-related bloodstream infections in the ICU. N Engl J Med (2006) 24.54
The novel zinc finger-containing transcription factor osterix is required for osteoblast differentiation and bone formation. Cell (2002) 15.20
agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res (2010) 10.53
Comparison of sequencing-based methods to profile DNA methylation and identification of monoallelic epigenetic modifications. Nat Biotechnol (2010) 7.00
Parametric survival analysis and taxonomy of hazard functions for the generalized gamma distribution. Stat Med (2007) 3.96
Illustrating bias due to conditioning on a collider. Int J Epidemiol (2009) 3.54
Multiple-imputation for measurement-error correction. Int J Epidemiol (2006) 3.13
The Human Epigenome Browser at Washington University. Nat Methods (2011) 2.62
Estimating efficacy of trivalent, cold-adapted, influenza virus vaccine (CAIV-T) against influenza A (H1N1) and B using surveillance cultures. Am J Epidemiol (2003) 2.50
Bivariate meta-analysis of sensitivity and specificity with sparse data: a generalized linear mixed model approach. J Clin Epidemiol (2006) 2.45
Arabidopsis Argonaute10 specifically sequesters miR166/165 to regulate shoot apical meristem development. Cell (2011) 2.45
Basic concepts and methods for joint models of longitudinal and survival data. J Clin Oncol (2010) 2.41
A prospective, multicenter survey on causes of chronic cough in China. Chest (2013) 2.38
Genome-wide meta-analyses of multiancestry cohorts identify multiple new susceptibility loci for refractive error and myopia. Nat Genet (2013) 2.36
Environmental barcoding: a next-generation sequencing approach for biomonitoring applications using river benthos. PLoS One (2011) 2.32
A dielectric polymer with high electric energy density and fast discharge speed. Science (2006) 2.30
The hippo tumor pathway promotes TAZ degradation by phosphorylating a phosphodegron and recruiting the SCF{beta}-TrCP E3 ligase. J Biol Chem (2010) 2.27
Targeted migration of mesenchymal stem cells modified with CXCR4 gene to infarcted myocardium improves cardiac performance. Mol Ther (2008) 2.25
Top-down quantitative proteomics identified phosphorylation of cardiac troponin I as a candidate biomarker for chronic heart failure. J Proteome Res (2011) 2.17
A heterozygous moth genome provides insights into herbivory and detoxification. Nat Genet (2013) 2.13
Neighborhood poverty and injection cessation in a sample of injection drug users. Am J Epidemiol (2010) 2.07
Missing data in clinical studies: issues and methods. J Clin Oncol (2012) 2.05
High-heeled-related alterations in the static sagittal profile of the spino-pelvic structure in young women. Eur Spine J (2015) 2.04
Levels of prenatal mercury exposure and their relationships to neonatal anthropometry in Wujiang City, China. Environ Pollut (2013) 2.01
PMRD: plant microRNA database. Nucleic Acids Res (2009) 1.94
Adherence of diarrheagenic Escherichia coli strains to epithelial cells. Infect Immun (2005) 1.89
Network meta-analysis of margin threshold for women with ductal carcinoma in situ. J Natl Cancer Inst (2012) 1.87
Inhibition of Wnt signaling by the osteoblast-specific transcription factor Osterix. Proc Natl Acad Sci U S A (2008) 1.86
A 90-day feeding study of glyphosate-tolerant maize with the G2-aroA gene in Sprague-Dawley rats. Food Chem Toxicol (2012) 1.72
Exploring long-range genome interactions using the WashU Epigenome Browser. Nat Methods (2013) 1.71
Granzyme B: Correlates with protection and enhanced CTL response to influenza vaccination in older adults. Vaccine (2009) 1.69
A short Nur77-derived peptide converts Bcl-2 from a protector to a killer. Cancer Cell (2008) 1.66
Mitogenic and oncogenic stimulation of K433 acetylation promotes PKM2 protein kinase activity and nuclear localization. Mol Cell (2013) 1.65
DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat Genet (2013) 1.64
Linear regression with an independent variable subject to a detection limit. Epidemiology (2010) 1.61
Pattern discovery and cancer gene identification in integrated cancer genomic data. Proc Natl Acad Sci U S A (2013) 1.60
Prenatal exposure to mercury and neurobehavioral development of neonates in Zhoushan City, China. Environ Res (2007) 1.58
Bayesian posterior distributions without Markov chains. Am J Epidemiol (2012) 1.54
The unmet need in the elderly: how immunosenescence, CMV infection, co-morbidities and frailty are a challenge for the development of more effective influenza vaccines. Vaccine (2012) 1.54
Development of an unbiased method for the estimation of liver steatosis. Clin Transplant (2004) 1.53
Mobilization of mesenchymal stem cells by granulocyte colony-stimulating factor in rats with acute myocardial infarction. Cardiovasc Drugs Ther (2008) 1.53
Effect of acyclovir on herpetic ocular recurrence using a structural nested model. Contemp Clin Trials (2005) 1.52
Decreased platelet miR-223 expression is associated with high on-clopidogrel platelet reactivity. Thromb Res (2013) 1.52
Spatial separation of photogenerated electrons and holes among {010} and {110} crystal facets of BiVO4. Nat Commun (2013) 1.50
Nak regulates localization of clathrin sites in higher-order dendrites to promote local dendrite growth. Neuron (2011) 1.50
Systematic review and meta-analysis of the effect of various laser wavelengths in the treatment of peri-implantitis. J Periodontol (2014) 1.50
Regulation of bone formation and remodeling by G-protein-coupled receptor 48. Development (2009) 1.50
Confidence intervals for biomarker-based human immunodeficiency virus incidence estimates and differences using prevalent data. Am J Epidemiol (2006) 1.49
Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells. Nucleic Acids Res (2013) 1.48
Coagulation profiles and thromboembolic events of bortezomib plus thalidomide and dexamethasone therapy in newly diagnosed multiple myeloma. Leuk Res (2010) 1.47
Wolbachia and DNA barcoding insects: patterns, potential, and problems. PLoS One (2012) 1.46
Disassociation between left ventricular mechanical and electrical properties in ischemic rat heart after G-CSF treatment. Cardiovasc Drugs Ther (2011) 1.45
PI3K/Akt signaling requires spatial compartmentalization in plasma membrane microdomains. Proc Natl Acad Sci U S A (2011) 1.39
Estimating the odds ratio when exposure has a limit of detection. Int J Epidemiol (2009) 1.39
Genomes of the rice pest brown planthopper and its endosymbionts reveal complex complementary contributions for host adaptation. Genome Biol (2014) 1.34
Annotation and expression profile analysis of 2073 full-length cDNAs from stress-induced maize (Zea mays L.) seedlings. Plant J (2006) 1.31
Comparative genome analysis of lignin biosynthesis gene families across the plant kingdom. BMC Bioinformatics (2009) 1.29
Lysine-5 acetylation negatively regulates lactate dehydrogenase A and is decreased in pancreatic cancer. Cancer Cell (2013) 1.29
Variable selection for multiply-imputed data with application to dioxin exposure study. Stat Med (2013) 1.28
Genetic evidence for the vital function of Osterix in cementogenesis. J Bone Miner Res (2012) 1.26
On estimation of vaccine efficacy using validation samples with selection bias. Biostatistics (2006) 1.25
Hierarchical regression for analyses of multiple outcomes. Am J Epidemiol (2015) 1.22
Phosphoramidate pronucleotides: a comparison of the phosphoramidase substrate specificity of human and Escherichia coli histidine triad nucleotide binding proteins. Mol Pharm (2007) 1.22
Pyrosequencing for mini-barcoding of fresh and old museum specimens. PLoS One (2011) 1.20
Genetic and molecular control of osterix in skeletal formation. J Cell Biochem (2013) 1.19
Increased expression of miR-148b in ovarian carcinoma and its clinical significance. Mol Med Rep (2012) 1.18
Slow hydrogen atom transfer reactions of oxo- and hydroxo-vanadium compounds: the importance of intrinsic barriers. J Am Chem Soc (2009) 1.18
Evaluation of the functional involvement of human immunodeficiency virus type 1 integrase in nuclear import of viral cDNA during acute infection. J Virol (2004) 1.18
Genetic variants on chromosome 1q41 influence ocular axial length and high myopia. PLoS Genet (2012) 1.17
Mycobacterium tuberculosis Rv3586 (DacA) is a diadenylate cyclase that converts ATP or ADP into c-di-AMP. PLoS One (2012) 1.17
Analysis of occupational asbestos exposure and lung cancer mortality using the g formula. Am J Epidemiol (2013) 1.15
PP1 cooperates with ASPP2 to dephosphorylate and activate TAZ. J Biol Chem (2010) 1.15
Death pathways activated in CaCo-2 cells by Clostridium perfringens enterotoxin. Infect Immun (2003) 1.14
Hypoxic preconditioning enhances bone marrow mesenchymal stem cell migration via Kv2.1 channel and FAK activation. Am J Physiol Cell Physiol (2011) 1.13
OsWRKY30 is activated by MAP kinases to confer drought tolerance in rice. Plant Mol Biol (2012) 1.13
Preliminary evidence for a 1000-year-old tsunami in the South China Sea. Sci Rep (2013) 1.12
Prevalence of hepatitis B in the southeast of China: a population-based study with a large sample size. Eur J Gastroenterol Hepatol (2011) 1.12
Algorithms outperform metabolite tests in predicting response of patients with inflammatory bowel disease to thiopurines. Clin Gastroenterol Hepatol (2009) 1.11
Increased frequency and clinical significance of myeloid-derived suppressor cells in human colorectal carcinoma. World J Gastroenterol (2012) 1.10
Large scale international replication and meta-analysis study confirms association of the 15q14 locus with myopia. The CREAM consortium. Hum Genet (2012) 1.09
Determination of dehydroevodiamine in Evodia rutaecarpa (Juss.) Benth by high performance liquid chromatography and classification of the samples by using hierarchical clustering analysis. Fitoterapia (2009) 1.09
Longitudinal increases in waist circumference are associated with HIV-serostatus, independent of antiretroviral therapy. AIDS (2007) 1.09
Effect of sinomenine on cytokine expression of macrophages and synoviocytes in adjuvant arthritis rats. J Ethnopharmacol (2005) 1.08
Rhodium-catalyzed intra- and intermolecular [5 + 2] cycloaddition of 3-acyloxy-1,4-enyne and alkyne with concomitant 1,2-acyloxy migration. J Am Chem Soc (2012) 1.08
microRNA-124 regulates cardiomyocyte differentiation of bone marrow-derived mesenchymal stem cells via targeting STAT3 signaling. Stem Cells (2012) 1.08
DNA-methylation profiling distinguishes malignant melanomas from benign nevi. Pigment Cell Melanoma Res (2011) 1.08
Longitudinal anthropometric changes in HIV-infected and HIV-uninfected men. J Acquir Immune Defic Syndr (2006) 1.07
Vibrio cholerae flagellins induce Toll-like receptor 5-mediated interleukin-8 production through mitogen-activated protein kinase and NF-kappaB activation. Infect Immun (2008) 1.07
Nine loci for ocular axial length identified through genome-wide association studies, including shared loci with refractive error. Am J Hum Genet (2013) 1.06
Variable selection and estimation in generalized linear models with the seamless L0 penalty. Can J Stat (2012) 1.06
Dogmatists cannot learn. Epidemiology (2016) 1.06
A 12-month clinical survey of incidence and outcome of acute respiratory distress syndrome in Shanghai intensive care units. Intensive Care Med (2004) 1.05
Arabidopsis Hormone Database: a comprehensive genetic and phenotypic information database for plant hormone research in Arabidopsis. Nucleic Acids Res (2008) 1.05
DL-3-n-butylphthalide prevents neuronal cell death after focal cerebral ischemia in mice via the JNK pathway. Brain Res (2010) 1.05
Transplantation of embryonic stem cells improves nerve repair and functional recovery after severe sciatic nerve axotomy in rats. Stem Cells (2008) 1.04
Maximum likelihood, profile likelihood, and penalized likelihood: a primer. Am J Epidemiol (2013) 1.04
Sample size and power determination in joint modeling of longitudinal and survival data. Stat Med (2011) 1.04