MethGET: web-based bioinformatics software for correlating genome-wide DNA methylation and gene expression

BS-Seeker3: ultrafast pipeline for bisulfite sequencing

(2018) Kevin Yu Yuan Huang et al.   BMC BIOINFORMATICS

METHimpute: imputation-guided construction of complete methylomes from WGBS data

(2018) Aaron Taudt et al.   BMC GENOMICS

Enduring epigenetic landmarks define the cancer microenvironment

(2018) Ruth Pidsley et al.   GENOME RESEARCH

Deubiquitinating Enzyme OTU5 Contributes to DNA Methylation Patterns and Is Critical for Phosphate Nutrition Signals

(2017) Ming-Ren Yen et al.   PLANT PHYSIOLOGY

Evolutionary Transition of Promoter and Gene Body DNA Methylation across Invertebrate–Vertebrate Boundary

(2015) Thomas E. Keller et al.   MOLECULAR BIOLOGY AND EVOLUTION

Human body epigenome maps reveal noncanonical DNA methylation variation

(2015) Matthew D. Schultz et al.   NATURE

Epigenetic regulation of intragenic transposable elements impacts gene transcription in Arabidopsis thaliana

(2015) Tu N. Le et al.   NUCLEIC ACIDS RESEARCH

On the presence and role of human gene-body DNA methylation

(2015) Daudi Jjingo et al.   Oncotarget

Gene Body Methylation Can Alter Gene Expression and Is a Therapeutic Target in Cancer

(2014) Xiaojing Yang et al.   CANCER CELL

Epigenetic reprogramming in plant sexual reproduction

(2014) Tomokazu Kawashima et al.   NATURE REVIEWS GENETICS

MethHC: a database of DNA methylation and gene expression in human cancer

(2014) Wei-Yun Huang et al.   NUCLEIC ACIDS RESEARCH

Notes on the role of dynamic DNA methylation in mammalian development

(2014) Timothy H. Bestor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2013) Weilong Guo et al.   BMC GENOMICS

RNA-directed DNA methylation regulates parental genomic imprinting at several loci in Arabidopsis

(2013) T. M. Vu et al.   DEVELOPMENT

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

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

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

DNA Methylation and Its Basic Function

(2012) Lisa D Moore et al.   NEUROPSYCHOPHARMACOLOGY

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

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

(2011) Felix Krueger et al.   BIOINFORMATICS

BigWig and BigBed: enabling browsing of large distributed datasets

(2010) W. J. Kent et al.   BIOINFORMATICS

BS Seeker: precise mapping for bisulfite sequencing

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

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Plant genomic DNA methylation in response to stresses: Potential applications and challenges in plant breeding

(2009) Hai Peng et al.   Progress in Natural Science-Materials International

Epigenetics: Definition, Mechanisms and Clinical Perspective

(2009) Cathérine Dupont et al.   SEMINARS IN REPRODUCTIVE MEDICINE