Detection of significantly differentially methylated regions in targeted bisulfite sequencing data

Beta Regression inR

(2015) Francisco Cribari-Neto et al.   Journal of Statistical Software

PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads

(2012) D. Campagna et al.   BIOINFORMATICS

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

(2012) D. Wang et al.   BIOINFORMATICS

SAAP-RRBS: streamlined analysis and annotation pipeline for reduced representation bisulfite sequencing

(2012) Zhifu Sun 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

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

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

DNA methylome analysis using short bisulfite sequencing data

(2012) Felix Krueger et al.   NATURE METHODS

Analysing and interpreting DNA methylation data

(2012) Christoph Bock   NATURE REVIEWS GENETICS

The UCSC Cancer Genomics Browser: update 2013

(2012) Mary Goldman 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

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

(2011) Yuanxin Xi et al.   BIOINFORMATICS

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Dnmt3a is essential for hematopoietic stem cell differentiation

(2011) Grant A Challen et al.   NATURE GENETICS

BiQ Analyzer HT: locus-specific analysis of DNA methylation by high-throughput bisulfite sequencing

(2011) Pavlo Lutsik et al.   NUCLEIC ACIDS RESEARCH

A statistical framework for Illumina DNA methylation arrays

(2010) Pei Fen Kuan et al.   BIOINFORMATICS

SLIM: a sliding linear model for estimating the proportion of true null hypotheses in datasets with dependence structures

(2010) Hong-Qiang Wang et al.   BIOINFORMATICS

BS Seeker: precise mapping for bisulfite sequencing

(2010) Pao-Yang Chen et al.   BMC BIOINFORMATICS

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

(2010) Hongcang Gu et al.   NATURE METHODS

EpiChIP: gene-by-gene quantification of epigenetic modification levels

(2010) Daniel Hebenstreit et al.   NUCLEIC ACIDS RESEARCH

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

(2010) Yingrui Li et al.   PLOS BIOLOGY

Improved estimators for a general class of beta regression models

(2009) Alexandre B. Simas et al.   COMPUTATIONAL STATISTICS & DATA ANALYSIS

The Relationship of DNA Methylation with Age, Gender and Genotype in Twins and Healthy Controls

(2009) Marco P. Boks et al.   PLoS One

DNA methylation in development and human disease

(2008) Suhasni Gopalakrishnan et al.   MUTATION RESEARCH-FUNDAMENTAL AND MOLECULAR MECHANISMS OF MUTAGENESIS