Batch effect correction for genome-wide methylation data with Illumina Infinium platform

Absolute Quantitation of DNA Methylation of 28 Candidate Genes in Prostate Cancer Using Pyrosequencing

(2013) Nataڑa Vasiljeviš et al.   DISEASE MARKERS

DNA methylation in glioblastoma: impact on gene expression and clinical outcome.

(2011) Amandine Etcheverry et al.   BMC GENOMICS

Obesity related methylation changes in DNA of peripheral blood leukocytes

(2011) Xiaoling Wang et al.   BMC Medicine

DNA methylation profiling reveals novel biomarkers and important roles for DNA methyltransferases in prostate cancer

(2011) Y. Kobayashi et al.   GENOME RESEARCH

Removing Batch Effects in Analysis of Expression Microarray Data: An Evaluation of Six Batch Adjustment Methods

(2011) Chao Chen et al.   PLoS One

Preprocessing differential methylation hybridization microarray data

(2011) Shuying Sun et al.   BioData Mining

DNA methylation patterns associate with genetic and gene expression variation in HapMap cell lines

(2011) Jordana T Bell et al.   GENOME BIOLOGY

Supervised normalization of microarrays

(2010) Brigham H. Mecham et al.   BIOINFORMATICS

Aberrant global methylation patterns affect the molecular pathogenesis and prognosis of multiple myeloma

(2010) B. A. Walker et al.   BLOOD

Genome-wide DNA methylation analysis for diabetic nephropathy in type 1 diabetes mellitus

(2010) Christopher G Bell et al.   BMC Medical Genomics

An integrative multi-dimensional genetic and epigenetic strategy to identify aberrant genes and pathways in cancer

(2010) Raj Chari et al.   BMC Systems Biology

Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer

(2010) A. E. Teschendorff et al.   GENOME RESEARCH

Human aging-associated DNA hypermethylation occurs preferentially at bivalent chromatin domains

(2010) V. K. Rakyan et al.   GENOME RESEARCH

Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2

(2010) Myunggon Ko et al.   NATURE

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Genome-wide DNA methylation analysis in cohesin mutant human cell lines

(2010) Jinglan Liu et al.   NUCLEIC ACIDS RESEARCH

A comparison of batch effect removal methods for enhancement of prediction performance using MAQC-II microarray gene expression data

(2010) J Luo et al.   PHARMACOGENOMICS JOURNAL

Altered DNA Methylation in Leukocytes with Trisomy 21

(2010) Kristi Kerkel et al.   PLoS Genetics

Epigenetic profiling of somatic tissues from human autopsy specimens identifies tissue- and individual-specific DNA methylation patterns

(2009) Hyang-Min Byun et al.   HUMAN MOLECULAR GENETICS

Genome-wide DNA methylation profiling using Infinium®assay

(2009) Marina Bibikova et al.   Epigenomics

lumi: a pipeline for processing Illumina microarray

(2008) P. Du et al.   BIOINFORMATICS

Normalization of Illumina Infinium whole-genome SNP data improves copy number estimates and allelic intensity ratios

(2008) Johan Staaf et al.   BMC BIOINFORMATICS

The removal of multiplicative, systematic bias allows integration of breast cancer gene expression datasets – improving meta-analysis and prediction of prognosis

(2008) Andrew H Sims et al.   BMC Medical Genomics