Epigenome-wide association studies: current knowledge, strategies and recommendations
出版年份 2021 全文链接
标题
Epigenome-wide association studies: current knowledge, strategies and recommendations
作者
关键词
-
出版物
Clinical Epigenetics
Volume 13, Issue 1, Pages -
出版商
Springer Science and Business Media LLC
发表日期
2021-12-05
DOI
10.1186/s13148-021-01200-8
参考文献
相关参考文献
注意:仅列出部分参考文献,下载原文获取全部文献信息。- BDNF Gene's Role in Schizophrenia: From Risk Allele to Methylation Implications
- (2021) Xiaoqian Fu et al. Frontiers in Psychiatry
- DNA methylation and cancer incidence: lymphatic–hematopoietic versus solid cancers in the Strong Heart Study
- (2021) Arce Domingo-Relloso et al. Clinical Epigenetics
- Genomic and phenotypic insights from an atlas of genetic effects on DNA methylation
- (2021) Josine L. Min et al. NATURE GENETICS
- Large-scale cis- and trans-eQTL analyses identify thousands of genetic loci and polygenic scores that regulate blood gene expression
- (2021) Urmo Võsa et al. NATURE GENETICS
- Predicting Complex Traits and Exposures From Polygenic Scores and Blood and Buccal DNA Methylation Profiles
- (2021) Veronika V. Odintsova et al. Frontiers in Psychiatry
- Smoking, DNA Methylation, and Lung Function: a Mendelian Randomization Analysis to Investigate Causal Pathways
- (2020) Emily Jamieson et al. AMERICAN JOURNAL OF HUMAN GENETICS
- Longitudinal DNA methylation differences precede type 1 diabetes
- (2020) Randi K. Johnson et al. Scientific Reports
- Methods for ChIP-seq analysis: A practical workflow and advanced applications
- (2020) Ryuichiro Nakato et al. METHODS
- Epigenome-Wide Association Study Reveals Duration of Breastfeeding Is Associated with Epigenetic Differences in Children
- (2020) William B. Sherwood et al. International Journal of Environmental Research and Public Health
- Epigenomic Assessment of Cardiovascular Disease Risk and Interactions With Traditional Risk Metrics
- (2020) Kenneth Westerman et al. Journal of the American Heart Association
- A decade of epigenetic change in aging twins: Genetic and environmental contributions to longitudinal DNA methylation
- (2020) Chandra A. Reynolds et al. AGING CELL
- Simulating ComBat: how batch correction can lead to the systematic introduction of false positive results in DNA methylation microarray studies
- (2020) Tristan Zindler et al. BMC BIOINFORMATICS
- A panel of DNA methylation signature from peripheral blood may predict colorectal cancer susceptibility
- (2020) Justina Ucheojor Onwuka et al. BMC CANCER
- Genome-Wide DNA Methylation in Peripheral Blood and Long-Term Exposure to Source-Specific Transportation Noise and Air Pollution: The SAPALDIA Study
- (2020) Ikenna C. Eze et al. ENVIRONMENTAL HEALTH PERSPECTIVES
- A comparison of epigenetic mitotic-like clocks for cancer risk prediction
- (2020) Andrew E. Teschendorff Genome Medicine
- Epigenetic Regulation Mediated by Methylation in the Pathogenesis and Precision Medicine of Rheumatoid Arthritis
- (2020) Shicheng Guo et al. Frontiers in Genetics
- Multiple sclerosis risk variants regulate gene expression in innate and adaptive immune cells
- (2020) Melissa M Gresle et al. Life Science Alliance
- DNA methylation clock associated with age-related illnesses is accelerated in PTSD
- (2020) Ruoting Yang et al. NEUROPSYCHOPHARMACOLOGY
- Epigenome-wide association study of Alzheimer’s disease replicates 22 differentially methylated positions and 30 differentially methylated regions
- (2020) Qingqin S. Li et al. Clinical Epigenetics
- DNA methylation GrimAge strongly predicts lifespan and healthspan
- (2019) Ake T. Lu et al. Aging-US
- Longitudinal genome-wide DNA methylation analysis uncovers persistent early-life DNA methylation changes
- (2019) Raúl F. Pérez et al. Journal of Translational Medicine
- DNA methylation changes associated with Parkinson’s disease progression: outcomes from the first longitudinal genome-wide methylation analysis in blood
- (2019) Adrienne Henderson-Smith et al. Epigenetics
- ebGSEA: an improved Gene Set Enrichment Analysis method for Epigenome-Wide-Association Studies
- (2019) Danyue Dong et al. BIOINFORMATICS
- Guidance for DNA methylation studies: statistical insights from the Illumina EPIC array
- (2019) Georgina Mansell et al. BMC GENOMICS
- Methodological challenges in constructing DNA methylation risk scores
- (2019) Anke Hüls et al. Epigenetics
- Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing
- (2019) Li Zhou et al. Scientific Reports
- Improved precision of epigenetic clock estimates across tissues and its implication for biological ageing
- (2019) Qian Zhang et al. Genome Medicine
- EWAS Data Hub: a resource of DNA methylation array data and metadata
- (2019) Zhuang Xiong et al. NUCLEIC ACIDS RESEARCH
- Detecting multiple differentially methylated CpG sites and regions related to dimensional psychopathology in youths
- (2019) Leticia M. Spindola et al. Clinical Epigenetics
- An epigenetic biomarker of aging for lifespan and healthspan
- (2018) Morgan E. Levine et al. Aging-US
- Genome-wide DNA methylation profiling in whole blood reveals epigenetic signatures associated with migraine
- (2018) Zachary F. Gerring et al. BMC GENOMICS
- Statistical harmonization corrects site effects in functional connectivity measurements from multi-site fMRI data
- (2018) Meichen Yu et al. HUMAN BRAIN MAPPING
- Adjusting for Batch Effects in DNA Methylation Microarray Data, a Lesson Learned
- (2018) E. M. Price et al. Frontiers in Genetics
- An evaluation of supervised methods for identifying differentially methylated regions in Illumina methylation arrays
- (2018) Saurav Mallik et al. BRIEFINGS IN BIOINFORMATICS
- Epigenetic influences on aging: a longitudinal genome-wide methylation study in old Swedish twins
- (2018) Yunzhang Wang et al. Epigenetics
- Genome-wide analysis of DNA methylation in buccal cells: a study of monozygotic twins and mQTLs
- (2018) Jenny van Dongen et al. Epigenetics & Chromatin
- Identification of differentially methylated cell types in epigenome-wide association studies
- (2018) Shijie C. Zheng et al. NATURE METHODS
- EWAS Atlas: a curated knowledgebase of epigenome-wide association studies
- (2018) Mengwei Li et al. NUCLEIC ACIDS RESEARCH
- STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets
- (2018) Damian Szklarczyk et al. NUCLEIC ACIDS RESEARCH
- Genome-wide DNA methylation changes in CD19+ B cells from relapsing-remitting multiple sclerosis patients
- (2018) Vicki E. Maltby et al. Scientific Reports
- Association and cis-mQTL analysis of variants in serotonergic genes associated with nicotine dependence in Chinese Han smokers
- (2018) Haijun Han et al. Translational Psychiatry
- Estimation of a significance threshold for epigenome-wide association studies
- (2017) Ayden Saffari et al. GENETIC EPIDEMIOLOGY
- Sorafenib induces variations of the DNA methylome in HA22T/VGH human hepatocellular carcinoma-derived cells
- (2017) Edoardo Abeni et al. INTERNATIONAL JOURNAL OF ONCOLOGY
- Detecting DNA cytosine methylation using nanopore sequencing
- (2017) Jared T Simpson et al. NATURE METHODS
- Harmonization of multi-site diffusion tensor imaging data
- (2017) Jean-Philippe Fortin et al. NEUROIMAGE
- Epigenetic research in multiple sclerosis: progress, challenges, and opportunities
- (2017) Galina Y. Zheleznyakova et al. PHYSIOLOGICAL GENOMICS
- DNA methylation in systemic lupus erythematosus
- (2017) Christian M Hedrich et al. Epigenomics
- Differential methylation at MHC in CD4+ T cells is associated with multiple sclerosis independently of HLA-DRB1
- (2017) Vicki E. Maltby et al. Clinical Epigenetics
- Differential methylation between ethnic sub-groups reflects the effect of genetic ancestry and environmental exposures
- (2017) Joshua M Galanter et al. eLife
- Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans
- (2017) Juan J. Carmona et al. npj Genomic Medicine
- Gene, Environment and Methylation (GEM): a tool suite to efficiently navigate large scale epigenome wide association studies and integrate genotype and interaction between genotype and environment
- (2016) Hong Pan et al. BMC BIOINFORMATICS
- Longitudinal study of DNA methylation during the first 5 years of life
- (2016) Rocio G. Urdinguio et al. Journal of Translational Medicine
- DNA Methylation: a New Player in Multiple Sclerosis
- (2016) Xiang Li et al. MOLECULAR NEUROBIOLOGY
- Validation of a DNA methylation microarray for 850,000 CpG sites of the human genome enriched in enhancer sequences
- (2016) Sebastian Moran et al. Epigenomics
- Epigenome-wide association data implicates DNA methylation-mediated genetic risk in psoriasis
- (2016) Fusheng Zhou et al. Clinical Epigenetics
- Removing Batch Effects from Longitudinal Gene Expression - Quantile Normalization Plus ComBat as Best Approach for Microarray Transcriptome Data
- (2016) Christian Müller et al. PLoS One
- A systematic study of normalization methods for Infinium 450K methylation data using whole-genome bisulfite sequencing data
- (2015) Ting Wang et al. Epigenetics
- Power and sample size estimation for epigenome-wide association scans to detect differential DNA methylation
- (2015) Pei-Chien Tsai et al. INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
- Twin methodology in epigenetic studies
- (2015) Q. Tan et al. JOURNAL OF EXPERIMENTAL BIOLOGY
- Probe Lasso: A novel method to rope in differentially methylated regions with 450K DNA methylation data
- (2015) Lee M. Butcher et al. METHODS
- limma powers differential expression analyses for RNA-sequencing and microarray studies
- (2015) Matthew E. Ritchie et al. NUCLEIC ACIDS RESEARCH
- Variation in cancer risk among tissues can be explained by the number of stem cell divisions
- (2015) C. Tomasetti et al. SCIENCE
- Tissue-Specific Effects of Genetic and Epigenetic Variation on Gene Regulation and Splicing
- (2015) Maria Gutierrez-Arcelus et al. PLoS Genetics
- Age-associated DNA methylation changes in immune genes, histone modifiers and chromatin remodeling factors within 5 years after birth in human blood leukocytes
- (2015) Nathalie Acevedo et al. Clinical Epigenetics
- Genome-wide DNA methylation profiling of CD8+ T cells shows a distinct epigenetic signature to CD4+ T cells in multiple sclerosis patients
- (2015) Vicki E. Maltby et al. Clinical Epigenetics
- Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays
- (2014) Martin J. Aryee et al. BIOINFORMATICS
- A systems-level integrative framework for genome-wide DNA methylation and gene expression data identifies differential gene expression modules under epigenetic control
- (2014) Yinming Jiao et al. BIOINFORMATICS
- Reference-free cell mixture adjustments in analysis of DNA methylation data
- (2014) Eugene Andres Houseman et al. BIOINFORMATICS
- Methylation quantitative trait loci (meQTLs) are consistently detected across ancestry, developmental stage, and tissue type
- (2014) Alicia K Smith et al. BMC GENOMICS
- Molecular Rules Governing De Novo Methylation in Cancer
- (2014) D. Nejman et al. CANCER RESEARCH
- Epigenome-wide association studies without the need for cell-type composition
- (2014) James Zou et al. NATURE METHODS
- ChAMP: 450k Chip Analysis Methylation Pipeline
- (2013) Tiffany J. Morris et al. BIOINFORMATICS
- A comprehensive overview of Infinium HumanMethylation450 data processing
- (2013) S. Dedeurwaerder et al. BRIEFINGS IN BIOINFORMATICS
- Discovery of cross-reactive probes and polymorphic CpGs in the Illumina Infinium HumanMethylation450 microarray
- (2013) Yi-an Chen et al. Epigenetics
- An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform
- (2013) Francesco Marabita et al. Epigenetics
- A systematic assessment of normalization approaches for the Infinium 450K methylation platform
- (2013) Michael C Wu et al. Epigenetics
- Epigenome-wide association data implicate DNA methylation as an intermediary of genetic risk in rheumatoid arthritis
- (2013) Yun Liu et al. NATURE BIOTECHNOLOGY
- Predictors and Consequences of Global DNA Methylation in Cord Blood and at Three Years
- (2013) Julie B. Herbstman et al. PLoS One
- Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia
- (2013) Jessica Nordlund et al. GENOME BIOLOGY
- DNA methylation age of human tissues and cell types
- (2013) Steve Horvath GENOME BIOLOGY
- Epigenetic variation during the adult lifespan: cross-sectional and longitudinal data on monozygotic twin pairs
- (2012) Rudolf P. Talens et al. AGING CELL
- Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values
- (2012) B. S. Pedersen et al. BIOINFORMATICS
- Matrix eQTL: ultra fast eQTL analysis via large matrix operations
- (2012) A. A. Shabalin BIOINFORMATICS
- A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data
- (2012) Andrew E. Teschendorff et al. BIOINFORMATICS
- DNA methylation arrays as surrogate measures of cell mixture distribution
- (2012) Eugene Houseman et al. BMC BIOINFORMATICS
- Individual variation and longitudinal pattern of genome-wide DNA methylation from birth to the first two years of life
- (2012) Deli Wang et al. Epigenetics
- Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies
- (2012) Andrew E Jaffe et al. INTERNATIONAL JOURNAL OF EPIDEMIOLOGY
- Genome-wide Methylation Profiles Reveal Quantitative Views of Human Aging Rates
- (2012) Gregory Hannum et al. MOLECULAR CELL
- SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips
- (2012) Jovana Maksimovic et al. GENOME BIOLOGY
- Evidence for age-related and individual-specific changes in DNA methylation profile of mononuclear cells during early immune development in humans
- (2011) David J. Martino et al. Epigenetics
- High density DNA methylation array with single CpG site resolution
- (2011) Marina Bibikova et al. GENOMICS
- Epigenome-wide association studies for common human diseases
- (2011) Vardhman K. Rakyan et al. NATURE REVIEWS GENETICS
- Evaluation of the Infinium Methylation 450K technology
- (2011) Sarah Dedeurwaerder et al. Epigenomics
- Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis
- (2010) Pan Du et al. BMC BIOINFORMATICS
- Transcript length bias in RNA-seq data confounds systems biology
- (2009) Alicia Oshlack et al. Biology Direct
- Disentangling molecular relationships with a causal inference test
- (2009) Joshua Millstein et al. BMC GENETICS
- ToppGene Suite for gene list enrichment analysis and candidate gene prioritization
- (2009) J. Chen et al. NUCLEIC ACIDS RESEARCH
- Genome-wide DNA methylation profiling using Infinium®assay
- (2009) Marina Bibikova et al. Epigenomics
- Intra-individual Change Over Time in DNA Methylation With Familial Clustering
- (2008) Hans T. Bjornsson JAMA-JOURNAL OF THE AMERICAN MEDICAL ASSOCIATION
- Decline in genomic DNA methylation through aging in a cohort of elderly subjects
- (2008) Valentina Bollati et al. MECHANISMS OF AGEING AND DEVELOPMENT
Become a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get StartedAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started