Differential methylation analysis for BS-seq data under general experimental design

A novel statistical method for quantitative comparison of multiple ChIP-seq datasets

(2015) Li Chen et al.   BIOINFORMATICS

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

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

(2014) Egor Dolzhenko et al.   BMC BIOINFORMATICS

Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote

(2014) Fan Guo et al.   Cell Stem Cell

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

voom: precision weights unlock linear model analysis tools for RNA-seq read counts

(2014) Charity W Law 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

Genome-wide Profiling of 5-Formylcytosine Reveals Its Roles in Epigenetic Priming

(2013) Chun-Xiao Song et al.   CELL

DNA Methyltransferase Inhibition Reverses Epigenetically Embedded Phenotypes in Lung Cancer Preferentially Affecting Polycomb Target Genes

(2013) A. Hascher et al.   CLINICAL CANCER RESEARCH

TherMos: Estimating protein–DNA binding energies from in vivo binding profiles

(2013) Wenjie Sun et al.   NUCLEIC ACIDS RESEARCH

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

(2012) H. Wu et al.   BIOSTATISTICS

The Dynamics of Genome-wide DNA Methylation Reprogramming in Mouse Primordial Germ Cells

(2012) Stefanie Seisenberger et al.   MOLECULAR CELL

KLC1-ALK: A Novel Fusion in Lung Cancer Identified Using a Formalin-Fixed Paraffin-Embedded Tissue Only

(2012) Yuki Togashi et al.   PLoS One

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

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

Smurf1 ubiquitin ligase targets Kruppel-like factor KLF2 for ubiquitination and degradation in human lung cancer H1299 cells

(2011) Ping Xie et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

5-hmC–mediated epigenetic dynamics during postnatal neurodevelopment and aging

(2011) Keith E Szulwach et al.   NATURE NEUROSCIENCE

Integrating 5-Hydroxymethylcytosine into the Epigenomic Landscape of Human Embryonic Stem Cells

(2011) Keith E. Szulwach et al.   PLoS 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

DNA hypermethylation of tumors from non-small cell lung cancer (NSCLC) patients is associated with gender and histologic type

(2009) Stephen E. Hawes et al.   LUNG CANCER

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Prognostic gene signatures for non-small-cell lung cancer

(2009) Paul C. Boutros et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Nuclear DNA Base 5-Hydroxymethylcytosine Is Present in Purkinje Neurons and the Brain

(2009) S. Kriaucionis et al.   SCIENCE

Variance stabilizing transformations of Poisson, binomial and negative binomial distributions

(2009) Guan Yu   STATISTICS & PROBABILITY LETTERS

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE

Reduced-representation methylation mapping

(2008) Jeffrey A Jeddeloh et al.   GENOME BIOLOGY