Comparative Epigenomic Profiling of the DNA Methylome in Mouse and Zebrafish Uncovers High Interspecies Divergence

Active DNA demethylation at enhancers during the vertebrate phylotypic period

(2016) Ozren Bogdanović et al.   NATURE GENETICS

Protection of CpG islands from DNA methylation is DNA-encoded and evolutionarily conserved

(2016) Hannah K. Long et al.   NUCLEIC ACIDS RESEARCH

Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome

(2016) Junchen Gu et al.   G3-Genes Genomes Genetics

DNA hypomethylation induces a DNA replication-associated cell cycle arrest to block hepatic outgrowth in uhrf1 mutant zebrafish embryos

(2015) V. Jacob et al.   DEVELOPMENT

Zebrafish: An Important Tool for Liver Disease Research

(2015) Wolfram Goessling et al.   GASTROENTEROLOGY

Comparative Analysis of Transposable Elements Highlights Mobilome Diversity and Evolution in Vertebrates

(2015) Domitille Chalopin et al.   Genome Biology and Evolution

Methylomic trajectories across human fetal brain development

(2015) Helen Spiers et al.   GENOME RESEARCH

High-fat diet caused widespread epigenomic differences on hepatic methylome in rat

(2015) Yukun Zhang et al.   PHYSIOLOGICAL GENOMICS

Reply to Wilkinson: Minor role of programmed methylation and demethylation in mammalian development

(2015) Timothy H. Bestor et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Intermediate DNA methylation is a conserved signature of genome regulation

(2015) GiNell Elliott et al.   Nature Communications

Developmental enhancers revealed by extensive DNA methylome maps of zebrafish early embryos

(2015) Hyung Joo Lee et al.   Nature Communications

Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

(2015) Francine E. Garrett-Bakelman et al.   Jove-Journal of Visualized Experiments

methylC Track: visual integration of single-base resolution DNA methylation data on the WashU EpiGenome Browser

(2014) Xin Zhou et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Improved reduced representation bisulfite sequencing for epigenomic profiling of clinical samples

(2014) Yew Lee et al.   BIOLOGICAL PROCEDURES ONLINE

UHRF1 Overexpression Drives DNA Hypomethylation and Hepatocellular Carcinoma

(2014) Raksha Mudbhary et al.   CANCER CELL

The dynamics of DNA methylation fidelity during mouse embryonic stem cell self-renewal and differentiation

(2014) Lei Zhao et al.   GENOME RESEARCH

Dynamic Heterogeneity and DNA Methylation in Embryonic Stem Cells

(2014) Zakary S. Singer et al.   MOLECULAR CELL

Reprogramming the Maternal Zebrafish Genome after Fertilization to Match the Paternal Methylation Pattern

(2013) Magdalena E. Potok et al.   CELL

Mapping the zebrafish brain methylome using reduced representation bisulfite sequencing

(2013) Aniruddha Chatterjee et al.   Epigenetics

Transposable Elements Are Major Contributors to the Origin, Diversification, and Regulation of Vertebrate Long Noncoding RNAs

(2013) Aurélie Kapusta et al.   PLoS Genetics

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

(2013) Hannah K Long et al.   eLife

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Divergent Whole-Genome Methylation Maps of Human and Chimpanzee Brains Reveal Epigenetic Basis of Human Regulatory Evolution

(2012) Jia Zeng et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Diametrically opposite methylome-transcriptome relationships in high- and low-CpG promoter genes in postmitotic neural rat tissue

(2012) Theresa Hartung et al.   Epigenetics

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

(2012) Cole Trapnell et al.   Nature Protocols

Base-Pair Resolution DNA Methylation Sequencing Reveals Profoundly Divergent Epigenetic Landscapes in Acute Myeloid Leukemia

(2012) Altuna Akalin et al.   PLoS Genetics

Comprehensive profiling of zebrafish hepatic proximal promoter CpG island methylation and its modification during chemical carcinogenesis

(2011) Leda Mirbahai et al.   BMC GENOMICS

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

(2011) Hongcang Gu et al.   Nature Protocols

Genomic Distribution and Inter-Sample Variation of Non-CpG Methylation across Human Cell Types

(2011) Michael J. Ziller et al.   PLoS Genetics

Large scale comparison of global gene expression patterns in human and mouse

(2011) Xiangqun Zheng-Bradley et al.   GENOME BIOLOGY

Tissue Distribution of 5-Hydroxymethylcytosine and Search for Active Demethylation Intermediates

(2010) Daniel Globisch et al.   PLoS One

Conservation and divergence in eukaryotic DNA methylation

(2010) T.-f. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Conservation and divergence of methylation patterning in plants and animals

(2010) S. Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-Wide Evolutionary Analysis of Eukaryotic DNA Methylation

(2010) A. Zemach et al.   SCIENCE

BSMAP: whole genome bisulfite sequence MAPping program

(2009) Yuanxin Xi et al.   BMC BIOINFORMATICS

CpG islands - ‘A rough guide’

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

High-throughput bisulfite sequencing in mammalian genomes

(2009) Zachary D. Smith et al.   METHODS

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

Genome-scale DNA methylation maps of pluripotent and differentiated cells

(2008) Alexander Meissner et al.   NATURE