An evaluation of methods to test predefined genomic regions for differential methylation in bisulfite sequencing data

A meta-analysis on age-associated changes in blood DNA methylation: results from an original analysis pipeline for Infinium 450k data

(2015) Maria Giulia Bacalini et al.   Aging-US

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

DMAP: differential methylation analysis package for RRBS and WGBS data

(2014) Peter A. Stockwell et al.   BIOINFORMATICS

Using beta-binomial regression for high-precision differential methylation analysis in multifactor whole-genome bisulfite sequencing experiments

(2014) Egor Dolzhenko et al.   BMC BIOINFORMATICS

Methodological aspects of whole-genome bisulfite sequencing analysis

(2014) S. Adusumalli et al.   BRIEFINGS IN BIOINFORMATICS

Decoding the regulatory landscape of medulloblastoma using DNA methylation sequencing

(2014) Volker Hovestadt et al.   NATURE

Coverage recommendations for methylation analysis by whole-genome bisulfite sequencing

(2014) Michael J Ziller et al.   NATURE METHODS

Comprehensive analysis of DNA methylation data with RnBeads

(2014) Yassen Assenov et al.   NATURE METHODS

A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data

(2014) Hao Feng et al.   NUCLEIC ACIDS RESEARCH

Bisulfighter: accurate detection of methylated cytosines and differentially methylated regions

(2014) Yutaka Saito et al.   NUCLEIC ACIDS RESEARCH

DNA methylation signatures link prenatal famine exposure to growth and metabolism

(2014) Elmar W. Tobi et al.   Nature Communications

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

Statistical methods for detecting differentially methylated loci and regions

(2014) Mark D. Robinson et al.   Frontiers in Genetics

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

An optimized algorithm for detecting and annotating regional differential methylation

(2013) Sheng Li et al.   BMC BIOINFORMATICS

BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data

(2013) Weilong Guo et al.   BMC GENOMICS

Large-scale hypomethylated blocks associated with Epstein-Barr virus-induced B-cell immortalization

(2013) K. D. Hansen et al.   GENOME RESEARCH

RRBS-Analyser: A Comprehensive Web Server for Reduced Representation Bisulfite Sequencing Data Analysis

(2013) Tao Wang et al.   HUMAN MUTATION

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

DNA methylation regulates associative reward learning

(2013) Jeremy J Day et al.   NATURE NEUROSCIENCE

DNA methylation: roles in mammalian development

(2013) Zachary D. Smith et al.   NATURE REVIEWS GENETICS

COHCAP: an integrative genomic pipeline for single-nucleotide resolution DNA methylation analysis

(2013) Charles D. Warden et al.   NUCLEIC ACIDS RESEARCH

Differential DNA Methylation Regions in Cytokine and Transcription Factor Genomic Loci Associate with Childhood Physical Aggression

(2013) Nadine Provençal et al.   PLoS One

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

(2012) D. Wang et al.   BIOINFORMATICS

Comb-p: software for combining, analyzing, grouping and correcting spatially correlated P-values

(2012) B. S. Pedersen et al.   BIOINFORMATICS

DNA methylation changes are a late event in acute promyelocytic leukemia and coincide with loss of transcription factor binding

(2012) T. Schoofs et al.   BLOOD

Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia

(2012) Lirong Pei et al.   Epigenetics

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

(2012) Andrew E Jaffe et al.   INTERNATIONAL JOURNAL OF EPIDEMIOLOGY

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

A mostly traditional approach improves alignment of bisulfite-converted DNA

(2012) Martin C. Frith et al.   NUCLEIC ACIDS RESEARCH

BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

methylKit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles

(2012) Altuna Akalin et al.   GENOME BIOLOGY

Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications

(2011) Felix Krueger et al.   BIOINFORMATICS

DNA-binding factors shape the mouse methylome at distal regulatory regions

(2011) Michael B. Stadler et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

DNA methylation-associated silencing of tumor-suppressor microRNAs in cancer

(2011) P Lopez-Serra et al.   ONCOGENE

Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution

(2010) Hongcang Gu et al.   NATURE METHODS

Targeting DNA methylation for epigenetic therapy

(2010) Xiaojing Yang et al.   TRENDS IN PHARMACOLOGICAL SCIENCES

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores

(2009) Rafael A Irizarry et al.   NATURE GENETICS

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE