Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates

Function and information content of DNA methylation

(2015) Dirk Schübeler   NATURE

Epigenetic remodeling in B-cell acute lymphoblastic leukemia occurs in two tracks and employs embryonic stem cell-like signatures

(2015) Seung-Tae Lee et al.   NUCLEIC ACIDS RESEARCH

Base-resolution methylation patterns accurately predict transcription factor bindings in vivo

(2015) Tianlei Xu et al.   NUCLEIC ACIDS RESEARCH

MethylSig: a whole genome DNA methylation analysis pipeline

(2014) Yongseok Park et al.   BIOINFORMATICS

DMAP: differential methylation analysis package for RRBS and WGBS data

(2014) Peter A. Stockwell et al.   BIOINFORMATICS

Role of Tet proteins in enhancer activity and telomere elongation

(2014) Falong Lu et al.   GENES & DEVELOPMENT

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

(2014) Lei Zhao et al.   GENOME RESEARCH

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

MOABS: model based analysis of bisulfite sequencing data

(2014) Deqiang Sun et al.   GENOME BIOLOGY

Accounting for cellular heterogeneity is critical in epigenome-wide association studies

(2014) Andrew E Jaffe et al.   GENOME BIOLOGY

Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

(2013) Katja Hebestreit et al.   BIOINFORMATICS

A new shrinkage estimator for dispersion improves differential expression detection in RNA-seq data

(2012) H. Wu et al.   BIOSTATISTICS

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Base-Resolution Analyses of Sequence and Parent-of-Origin Dependent DNA Methylation in the Mouse Genome

(2012) Wei Xie et al.   CELL

ENCODE: The human encyclopaedia

(2012) Brendan Maher   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Absolute quantification of somatic DNA alterations in human cancer

(2012) Scott L Carter et al.   NATURE BIOTECHNOLOGY

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

GBSA: a comprehensive software for analysing whole genome bisulfite sequencing data

(2012) Touati Benoukraf et al.   NUCLEIC ACIDS RESEARCH

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

(2012) Kasper D Hansen et al.   GENOME BIOLOGY

MAnorm: a robust model for quantitative comparison of ChIP-Seq data sets

(2012) Zhen Shao 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

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

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

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

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