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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Social environment is associated with gene regulatory variation in the rhesus macaque immune system

(2012) J. Tung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

B-SOLANA: an approach for the analysis of two-base encoding bisulfite sequencing data

(2011) Benjamin Kreck et al.   BIOINFORMATICS

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Significance analysis and statistical dissection of variably methylated regions

(2011) A. E. Jaffe et al.   BIOSTATISTICS

Directional DNA Methylation Changes and Complex Intermediate States Accompany Lineage Specificity in the Adult Hematopoietic Compartment

(2011) Emily Hodges et al.   MOLECULAR CELL

Hotspots of aberrant epigenomic reprogramming in human induced pluripotent stem cells

(2011) Ryan Lister et al.   NATURE

Spontaneous epigenetic variation in the Arabidopsis thaliana methylome

(2011) Claude Becker et al.   NATURE

Increased methylation variation in epigenetic domains across cancer types

(2011) Kasper Daniel Hansen et al.   NATURE GENETICS

Overcoming bias and systematic errors in next generation sequencing data

(2011) Margaret A Taub et al.   Genome Medicine

Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing

(2010) Cristian Coarfa et al.   BMC BIOINFORMATICS

BS Seeker: precise mapping for bisulfite sequencing

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

Dynamic changes in the human methylome during differentiation

(2010) L. Laurent et al.   GENOME RESEARCH

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

(2010) Yingrui Li et al.   PLOS BIOLOGY

BRAT: bisulfite-treated reads analysis tool

(2009) Elena Y. Harris et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Model-Based Quality Assessment and Base-Calling for Second-Generation Sequencing Data

(2009) Héctor Corrada Bravo et al.   BIOMETRICS

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete

(2009) Michael Zeschnigk et al.   HUMAN MOLECULAR GENETICS

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

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Comprehensive high-throughput arrays for relative methylation (CHARM)

(2008) R. A. Irizarry et al.   GENOME RESEARCH