Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays

A data-driven approach to preprocessing Illumina 450K methylation array data

(2013) Ruth Pidsley et al.   BMC GENOMICS

Considerations for normalization of DNA methylation data by Illumina 450K BeadChip assay in population studies

(2013) Paul Yousefi et al.   Epigenetics

SNPs located at CpG sites modulate genome-epigenome interaction

(2013) Degui Zhi et al.   Epigenetics

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform

(2013) Francesco Marabita et al.   Epigenetics

Low-level processing of Illumina Infinium DNA Methylation BeadArrays

(2013) Timothy J. Triche et al.   NUCLEIC ACIDS RESEARCH

Additional annotation enhances potential for biologically-relevant analysis of the Illumina Infinium HumanMethylation450 BeadChip array

(2013) Magda E Price et al.   Epigenetics & Chromatin

IMA: an R package for high-throughput analysis of Illumina's 450K Infinium methylation data

(2012) D. Wang et al.   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

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

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

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Complete pipeline for Infinium® Human Methylation 450K BeadChip data processing using subset quantile normalization for accurate DNA methylation estimation

(2012) Nizar Touleimat et al.   Epigenomics

SWAN: Subset-quantile Within Array Normalization for Illumina Infinium HumanMethylation450 BeadChips

(2012) Jovana Maksimovic et al.   GENOME BIOLOGY

Identification of DNA methylation biomarkers from Infinium arrays

(2012) Frank Wessely et al.   Frontiers in Genetics

Assessing affymetrix GeneChip microarray quality

(2011) Matthew N McCall et al.   BMC BIOINFORMATICS

Identification of Genes Upregulated in ALK-Positive and EGFR/KRAS/ALK-Negative Lung Adenocarcinomas

(2011) H. Okayama et al.   CANCER RESEARCH

High density DNA methylation array with single CpG site resolution

(2011) Marina Bibikova et al.   GENOMICS

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Regions of focal DNA hypermethylation and long-range hypomethylation in colorectal cancer coincide with nuclear lamina–associated domains

(2011) Benjamin P Berman et al.   NATURE GENETICS

Epigenome-wide association studies for common human diseases

(2011) Vardhman K. Rakyan et al.   NATURE REVIEWS GENETICS

Accurate genome-scale percentage DNA methylation estimates from microarray data

(2010) M. J. Aryee et al.   BIOSTATISTICS

Frozen robust multiarray analysis (fRMA)

(2010) M. N. McCall et al.   BIOSTATISTICS

Subset Quantile Normalization Using Negative Control Features

(2010) Zhijin Wu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability

(2010) Magdalena Skrzypczak et al.   PLoS One

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH