Genome-wide DNA methylation analysis in precursor B-cells

Functional DNA methylation differences between tissues, cell types, and across individuals discovered using the M&M algorithm

(2013) B. Zhang et al.   GENOME RESEARCH

Chromatin and epigenetic features of long-range gene regulation

(2013) N. Harmston et al.   NUCLEIC ACIDS RESEARCH

DNA methylation of distal regulatory sites characterizes dysregulation of cancer genes

(2013) Dvir Aran et al.   GENOME BIOLOGY

Isolation of Precursor B-cell Subsets from Umbilical Cord Blood

(2013) Md Almamun et al.   Jove-Journal of Visualized Experiments

Combinatorial Assembly of Developmental Stage-Specific Enhancers Controls Gene Expression Programs during Human Erythropoiesis

(2012) Jian Xu et al.   DEVELOPMENTAL CELL

Genome-wide DNA methylation profiles in hematopoietic stem and progenitor cells reveal overrepresentation of ETS transcription factor binding sites

(2012) A. Hogart et al.   GENOME RESEARCH

Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis

(2012) O. Bogdanovic et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

A global DNA methylation and gene expression analysis of early human B-cell development reveals a demethylation signature and transcription factor network

(2012) Seung-Tae Lee et al.   NUCLEIC ACIDS RESEARCH

Functional and Mechanistic Diversity of Distal Transcription Enhancers

(2011) Michael Bulger et al.   CELL

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

(2011) Emily Hodges et al.   MOLECULAR CELL

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Role of Ucp1 enhancer methylation and chromatin remodelling in the control of Ucp1 expression in murine adipose tissue

(2010) A. Shore et al.   DIABETOLOGIA

Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

(2010) L. Chavez et al.   GENOME RESEARCH

Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities

(2010) Sven Heinz et al.   MOLECULAR CELL

Comprehensive methylome map of lineage commitment from haematopoietic progenitors

(2010) Hong Ji et al.   NATURE

Independent filtering increases detection power for high-throughput experiments

(2010) R. Bourgon et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

DNA methylation protects hematopoietic stem cell multipotency from myeloerythroid restriction

(2009) Ann-Marie Bröske et al.   NATURE GENETICS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis

(2008) Thomas A Down et al.   NATURE BIOTECHNOLOGY

Model-based Analysis of ChIP-Seq (MACS)

(2008) Yong Zhang et al.   GENOME BIOLOGY

Epigenetics: The DNA Methylation Profile of Tissue-Dependent and Differentially Methylated Regions in Cells

(2007) J. Ohgane et al.   PLACENTA