SMAP: a streamlined methylation analysis pipeline for bisulfite sequencing

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

Methodological aspects of whole-genome bisulfite sequencing analysis

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

Methy-Pipe: An Integrated Bioinformatics Pipeline for Whole Genome Bisulfite Sequencing Data Analysis

(2014) Peiyong Jiang et al.   PLoS One

Comprehensive analyses of imprinted differentially methylated regions reveal epigenetic and genetic characteristics in hepatoblastoma

(2013) Janette Mareska Rumbajan et al.   BMC CANCER

Multilayered molecular profiling supported the monoclonal origin of metastatic renal cell carcinoma

(2013) Yi Huang et al.   INTERNATIONAL JOURNAL OF CANCER

DNA Methylation Signatures for Prediction of Biochemical Recurrence After Radical Prostatectomy of Clinically Localized Prostate Cancer

(2013) Christa Haldrup et al.   JOURNAL OF CLINICAL ONCOLOGY

Elucidating the Landscape of Aberrant DNA Methylation in Hepatocellular Carcinoma

(2013) Min-Ae Song et al.   PLoS One

Global Epigenomic Reconfiguration During Mammalian Brain Development

(2013) R. Lister et al.   SCIENCE

DNA–Methylome Analysis of Mouse Intestinal Adenoma Identifies a Tumour-Specific Signature That Is Partly Conserved in Human Colon Cancer

(2013) Christina Grimm et al.   PLoS Genetics

BRAT-BW: efficient and accurate mapping of bisulfite-treated reads

(2012) Elena Y. Harris et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Comparison of alignment software for genome-wide bisulphite sequence data

(2012) Aniruddha Chatterjee et al.   NUCLEIC ACIDS RESEARCH

Genomic landscape of human allele-specific DNA methylation

(2012) F. Fang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Bis-SNP: Combined DNA methylation and SNP calling for Bisulfite-seq data

(2012) Yaping Liu 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

Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling

(2011) Hongcang Gu et al.   Nature Protocols

Analysis of DNA Methylation in a Three-Generation Family Reveals Widespread Genetic Influence on Epigenetic Regulation

(2011) Jason Gertz et al.   PLoS Genetics

BS Seeker: precise mapping for bisulfite sequencing

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

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

(2010) R. Shoemaker et al.   GENOME RESEARCH

Principles and challenges of genome-wide DNA methylation analysis

(2010) Peter W. Laird   NATURE REVIEWS GENETICS

Targeting DNA methylation for epigenetic therapy

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

SOAP2: an improved ultrafast tool for short read alignment

(2009) R. Li et al.   BIOINFORMATICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Epigenetics in cancer

(2009) S. Sharma et al.   CARCINOGENESIS

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

SOAP: short oligonucleotide alignment program

(2008) R. Li et al.   BIOINFORMATICS

Mapping short DNA sequencing reads and calling variants using mapping quality scores

(2008) H. Li et al.   GENOME RESEARCH

Reduced-representation methylation mapping

(2008) Jeffrey A Jeddeloh et al.   GENOME BIOLOGY