Sequence-Level Mechanisms of Human Epigenome Evolution

DNA Sequence Explains Seemingly Disordered Methylation Levels in Partially Methylated Domains of Mammalian Genomes

(2014) Dimos Gaidatzis et al.   PLoS Genetics

Charting a dynamic DNA methylation landscape of the human genome

(2013) Michael J. Ziller et al.   NATURE

Extensive Variation in Chromatin States Across Humans

(2013) M. Kasowski et al.   SCIENCE

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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

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

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Repetitive elements and enforced transcriptional repression co-operate to enhance DNA methylation spreading into a promoter CpG-island

(2012) Yan Zhang et al.   NUCLEIC ACIDS RESEARCH

A genome-wide screen in human embryonic stem cells reveals novel sites of allele-specific histone modification associated with known disease loci

(2012) James G D Prendergast et al.   Epigenetics & Chromatin

Extensive Evolutionary Changes in Regulatory Element Activity during Human Origins Are Associated with Altered Gene Expression and Positive Selection

(2012) Yoichiro Shibata et al.   PLoS Genetics

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

(2011) Felix Krueger et al.   BIOINFORMATICS

Chromatin higher-order structures and gene regulation

(2011) Guohong Li et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

Conservation and divergence of DNA methylation in eukaryotes

(2011) Zhixi Su et al.   Epigenetics

Pioneer transcription factors: establishing competence for gene expression

(2011) K. S. Zaret et al.   GENES & DEVELOPMENT

CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing

(2011) Sanjeev Shukla et al.   NATURE

Putting the DNA back into DNA methylation

(2011) Adrian Bird   NATURE GENETICS

Identification of genetic elements that autonomously determine DNA methylation states

(2011) Florian Lienert et al.   NATURE GENETICS

Enhancer function: new insights into the regulation of tissue-specific gene expression

(2011) Chin-Tong Ong et al.   NATURE REVIEWS GENETICS

Spreading of Alu Methylation to the Promoter of the MLH1 Gene in Gastrointestinal Cancer

(2011) Xiyin Wang et al.   PLoS One

Transgenerational Epigenetic Instability Is a Source of Novel Methylation Variants

(2011) R. J. Schmitz et al.   SCIENCE

Genetic Rearrangements Can Modify Chromatin Features at Epialleles

(2011) Andrea M. Foerster et al.   PLoS Genetics

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

GREAT improves functional interpretation of cis-regulatory regions

(2010) Cory Y McLean et al.   NATURE BIOTECHNOLOGY

The NIH Roadmap Epigenomics Mapping Consortium

(2010) Bradley E Bernstein et al.   NATURE BIOTECHNOLOGY

Heritable Individual-Specific and Allele-Specific Chromatin Signatures in Humans

(2010) R. McDaniell et al.   SCIENCE

Abundant Quantitative Trait Loci Exist for DNA Methylation and Gene Expression in Human Brain

(2010) J. Raphael Gibbs et al.   PLoS Genetics

Epigenetic mechanisms in neurological diseases: genes, syndromes, and therapies

(2009) Rocio G Urdinguio et al.   LANCET NEUROLOGY

Human DNA methylomes at base resolution show widespread epigenomic differences

(2009) Ryan Lister et al.   NATURE

Differential methylation of tissue- and cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts

(2009) Akiko Doi et al.   NATURE GENETICS

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

The impact of retrotransposons on human genome evolution

(2009) Richard Cordaux et al.   NATURE REVIEWS GENETICS

Genetics and epigenetics: stability and plasticity during cellular differentiation

(2009) Fabio Mohn et al.   TRENDS IN GENETICS

The origins and impact of primate segmental duplications

(2009) Tomas Marques-Bonet et al.   TRENDS IN GENETICS

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

Genome duplication and gene-family evolution: The case of three OXPHOS gene families

(2008) Anna De Grassi et al.   GENE

Asymmetric histone modifications between the original and derived loci of human segmental duplications

(2008) Deyou Zheng   GENOME BIOLOGY