Differential DNA methylation patterns of homeobox genes in proximal and distal colon epithelial cells

Integrative analysis of 111 reference human epigenomes

(2015) Anshul Kundaje et al.   NATURE

Differences in DNA Methylation Signatures Reveal Multiple Pathways of Progression From Adenoma to Colorectal Cancer

(2014) Yanxin Luo et al.   GASTROENTEROLOGY

Reprogramming of the human intestinal epigenome by surgical tissue transposition

(2014) F. D. Lay et al.   GENOME RESEARCH

An atlas of active enhancers across human cell types and tissues

(2014) Robin Andersson et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

The meta-epigenomic structure of purified human stem cell populations is defined at cis-regulatory sequences

(2014) N. Ari Wijetunga et al.   Nature Communications

CellMix: a comprehensive toolbox for gene expression deconvolution

(2013) R. Gaujoux et al.   BIOINFORMATICS

Gene-set analysis is severely biased when applied to genome-wide methylation data

(2013) Paul Geeleher et al.   BIOINFORMATICS

Computational deconvolution: extracting cell type-specific information from heterogeneous samples

(2013) Shai S Shen-Orr et al.   CURRENT OPINION IN IMMUNOLOGY

Dynamic DNA methylation across diverse human cell lines and tissues

(2013) K. E. Varley et al.   GENOME RESEARCH

DNA Methylation Analysis in the Intestinal Epithelium—Effect of Cell Separation on Gene Expression and Methylation Profile

(2013) Andreas C. Jenke et al.   PLoS One

Measuring cell-type specific differential methylation in human brain tissue

(2013) Carolina M Montaño et al.   GENOME BIOLOGY

DNA methylation arrays as surrogate measures of cell mixture distribution

(2012) Eugene Houseman et al.   BMC BIOINFORMATICS

Comparative genome-wide DNA methylation analysis of colorectal tumor and matched normal tissues

(2012) Femke Simmer et al.   Epigenetics

Bump hunting to identify differentially methylated regions in epigenetic epidemiology studies

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

ChromHMM: automating chromatin-state discovery and characterization

(2012) Jason Ernst et al.   NATURE METHODS

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Evidence for widespread changes in promoter methylation profile in human placenta in response to increasing gestational age and environmental/stochastic factors

(2011) Boris Novakovic et al.   BMC GENOMICS

DNA methylation profiling in Barrett’s esophagus and esophageal adenocarcinoma reveals unique methylation signatures and molecular subclasses

(2011) Andrew M. Kaz et al.   Epigenetics

Semi-supervised Nonnegative Matrix Factorization for gene expression deconvolution: A case study

(2011) Renaud Gaujoux et al.   INFECTION GENETICS AND EVOLUTION

DNA methylation of colon mucosa in ulcerative colitis patients: Correlation with inflammatory status

(2011) Shunsuke Saito et al.   INFLAMMATORY BOWEL DISEASES

Clinical and pathological analysis of colonic Crohn's disease, including a subgroup with ulcerative colitis-like features

(2011) Genevieve Soucy et al.   MODERN PATHOLOGY

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

(2011) Emily Hodges et al.   MOLECULAR CELL

Epigenetics and colorectal cancer

(2011) Victoria Valinluck Lao et al.   Nature Reviews Gastroenterology & Hepatology

Methylation Status of Genes in Non-Neoplastic Mucosa From Patients With Ulcerative Colitis-Associated Colorectal Cancer

(2010) Megan M Garrity-Park et al.   AMERICAN JOURNAL OF GASTROENTEROLOGY

DNA methylation analysis of multiple tissues from newborn twins reveals both genetic and intrauterine components to variation in the human neonatal epigenome

(2010) Miina Ollikainen et al.   HUMAN MOLECULAR GENETICS

Optimized design and data analysis of tag-based cytosine methylation assays

(2010) Masako Suzuki et al.   GENOME BIOLOGY

CpG islands - ‘A rough guide’

(2009) Robert S. Illingworth et al.   FEBS LETTERS

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

Genetics and epigenetics: stability and plasticity during cellular differentiation

(2009) Fabio Mohn et al.   TRENDS IN GENETICS

Map of differential transcript expression in the normal human large intestine

(2007) Lawrence C. LaPointe et al.   PHYSIOLOGICAL GENOMICS